QTL mapping using Arabidopsis thaliana MAGIC Lines identifies candidate genes controlling adventitious root development

QTL mapping using Arabidopsis thaliana MAGIC Lines identifies candidate genes controlling adventitious root development | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article QTL mapping using Arabidopsis thaliana MAGIC Lines identifies candidate genes controlling adventitious root development Brenda Anabel López-Ruiz, Joshua Banta, Perla Salazar-Hernández, and 3 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-4432917/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Background The Multi-Parent Advanced Generation Inter-Cross (MAGIC) population is a powerful tool for dissecting the genetic architecture controlling natural variation in complex traits. In this work, the natural variation available in Arabidopsis thaliana MAGIC lines was evaluated by mapping quantitative trait loci (QTLs) for primary root length (PRL), lateral root number (LRN), lateral root length (LRL), adventitious root number (ARN) and adventitious root length (ARL). Methods and Results We analyzed the differences in the root structure of 139 MAGIC lines by measuring PRL, LRN, LRL, ARN and ARL. Through QTL mapping, we identified new potential genes that may be responsible for these traits. Furthermore, we detected single nucleotide polymorphisms (SNPs) in the coding regions of candidate genes in the founder accessions. We obtained a significant region on chromosome 1 associated with ARN. This region spans 316 genes, some of which are related to auxin and gibberellin signaling and homeostasis. We identified SNPs in the coding regions of these candidate genes in the founder accessions that could contribute to natural variation in the AR of the recombinant inbred lines. Additionally, we found a novel gene encoding a Hydroxyproline-rich glycoprotein family protein that displays differential SNPs in accessions with contrasting AR formation. Conclusions The study found that natural variation in AR number could be explained by a significant QTL on chromosome 1 associated with genes related to auxin and gibberellin signaling and homeostasis. Some founder accessions showed missense and in-frame deletions in these genes, which could explain the observed differences in AR development. MAGIC lines Arabidopsis thaliana QTL mapping adventitious roots natural variation root architecture Figures Figure 1 Figure 2 Figure 3 Figure 4 Introduction The root system anchors the plant and absorbs water and nutrients; studying root architecture and growth is essential in the field of plant organ development [1]. Arabidopsis thalian a (hereafter Arabidopsis ) has a simple root system, which makes it useful for studying root architecture and identifying new genes that control these characteristics. Moreover, it is relatively easy to visualize the root system of Arabidopsis on vertical agar plates in vitro [2]. The Arabidopsis root system consists of three main types of roots: the primary root (PR), the lateral roots (LRs), and the adventitious roots (ARs) [3, 4]. The PR originates from the embryonic meristem and is the first organ to develop during germination [5]. Its principal function is to anchor the plant into the soil by growing downwards [3]. The LRs develop from founder cells in the pericycle adjacent to the protoxylem poles of the vascular cylinder, and they explore the soil in response to environmental clues [6]. The ARs, on the other hand, develop from non-root organs such as hypocotyl, stems or leaves. They are observed when Arabidopsis is grown vertically on a synthetic medium or in response to wounding or environmental signals [4, 7]. Several genes have been identified to play a vital role in developing PR, LR, and AR [8–11]. These genes include transcription factors such as WUSCHEL RELATED HOMEOBOX (WOX), PLETHORA (PLT), AUXIN RESPONSE FACTORS (ARFs), SHORT ROOT (SHR) , and SCARECROW (SCR) , as well as cell cycle genes like CYCLIN-DEPENDENT KINASES and CYCLINS . Additionally, plant hormones are crucial regulators of cell division, elongation, and differentiation [8–10]. In Arabidopsis , the Multi-Parent Advanced Generation Inter-Cross (MAGIC) population is a large set of recombinant inbred lines (RILs) that are used to map a vast amount of phenotypic diversity, combining the benefits of association mapping and linkage analysis; these lines offer great power for detecting quantitative trait loci (QTL) [12]. The MAGIC lines were developed by crossing 19 natural accessions of A. thaliana over multiple generations [13]. This breeding strategy not only introduced additional recombination events, but also increased the number of segregating alleles within the lines. Consequently, QTL can be pinpointed to much smaller genomic regions than usual, often less than 1 Mb in size [13]. Moreover, they contain 3.3 million segregating SNPs, which is 68% of SNPs with a frequency above 0.05 identified by the 1001 genome project, thus capturing a substantial portion of the common molecular variation present in the species [13]. MAGIC populations increase genetic recombination and genetic variation and reduce the limitations of bi-parental populations for QTL mapping (lack of mapping precision and low genetic diversity) [14]. Potentially, each MAGIC line can inherit alleles from all the progenitors, and the MAGIC chromosomes are random mosaics of the parental haplotypes [14]. The MAGIC population is well-suited for breeding improvement, and analysis of the relationship between genotypes and phenotypes allows the identification of QTLs, which can then be confirmed using functional genomics [15, 16]. The Arabidopsis MAGIC population has been used to map several traits involved in germination and bolting time [17] and to examine the natural genetic basis of variation in seed size and number [18]. However, the genetic basis of root phenotypic variation in MAGIC lines has not yet been addressed. This study aimed to evaluate the variation in root architecture in 139 recombinant inbred lines. Additionally, QTL mapping was performed to detect new candidate genes contributing to these traits. Material and Methods Growth Conditions and Phenotyping. The MAGIC population used in this study was created with 19 Arabidopsis founder accessions (Bur-0, Can-0, Col-0, Ct-1, Edi-0, Hi-0, Kn-0, Ler-0, Mt-0, No-0, Oy-0, Po-0, Rsch-4, Sf-2, Tsu-0, Wil-2, Ws-0, Wu-0, and Zu-0) [17]. A total of 139 lines, each consisting of approximately ten individuals, were used to record the root traits for the study. Seeds were disinfected with a solution of 70% ethanol, 50% bleach and three rinses of sterilized water. Seeds were sown on square Petri dishes with 50% MS salts (Caisson, MSP09), 0.05% MES and 1% agar (Bacto Agar BD) at pH 5.6. The plates with the seeds were stratified for three days at 4°C in darkness and then placed vertically in a growth chamber under 22°C, long-day 16h/8h at 200 µmol/m²/s light intensity (Percival Scientific). 18 days after sowing (das), plates were digitized at 600 dpi and five root traits were measured using the Image J version Fiji software (NIH, USA) using a ruler as a scale: primary root length, lateral root number, lateral root length, adventitious root number, and adventitious root length. QTL Mapping QTL mapping was performed using the ‘scan1’ function of the R/qtl2 package R, in combination with a custom R data package containing the genotype data in a suitable format for analysis (available at https://github.com/tavareshugo/atMAGIC ). Genome-wide significance was determined empirically for each trait, using 1000 permutations of the data with the ‘scan1perm’ function of the R/qtl2 package, corresponding to a genome-wide false positive rate of 5%. A total of 139 MAGIC lines for five root traits were used. Candidate genes within the QTL interval were determined in TAIR10. Polymorphism patterns Sequence data from the 1001 genome project [19] ( http://signal.salk.edu/atg1001/3.0/gebrowser.php (accessed on December 2023) was used to analyze single nucleotide polymorphism (SNPs) of candidate genes among founder accessions (Bur-0, Can-0, Col-0, Ct-1, Edi-0, Hi-0, Kn-0, Ler-0, Mt-0, No-0, Oy-0, Po-0, Rsch-4, Sf-2, Tsu-0, Wil-2, Ws-0, Wu-0, and Zu-0). To determine the effects of these variations and their exact positions, Variant Effect Predictor (VEP; [20]) was executed on the coding sequence, with default parameters ( https://plants.ensembl.org/Arabidopsis_thaliana/Tools/VEP (accessed on December 2023). We searched the AraPheno ( https://arapheno.1001genomes.org ) and AraGWAS Catalog ( https://aragwas.1001genomes.org ) data repositories for publicly available phenotypic data and distinct loci related to adventitious root formation. Protein domains were retrieved from InterPro, visualized using Unipro UGENE, and edited with Adobe Illustrator. Results Root variation in Arabidopsis MAGIC lines We analyzed five root characteristics in 139 Arabidopsis recombinant inbred lines derived by intermating 19 natural accessions [17]. We recorded the length of the primary root (PRL), the number of lateral roots (LRN), the length of lateral roots (LRL), the number of adventitious roots (ARN), and the length of adventitious roots (ARL) for 18 DAS by marking their positions in the Petri dish. The variability in root architecture can be observed in Fig. 1 A-E. Table S1 presents the mean and standard deviation (SD) of the 139 MAGIC lines; the range of PR varies from 0.22 cm ± 0.28 to 3.38 cm ± 2.9 cm. The LR number goes from 0 to 12.46 ± 15.10, and the LR length fluctuates from 0.006 ± 0.01 to 3.12 cm. Concerning ARN, some MAGIC lines lack ARs, and the highest value is 3.5 ± 3.53. Regarding ARL, the minimum mean length is 0.019 ± 0.03 cm, whereas the maximum is 8.01 ± 11.2 cm. This considerable SD has been observed previously in other studies that have used the Arabidopsis recombinant inbred lines [21]. We conducted multiple correlations to study the association between the five traits (Fig. 2 ). The results showed the highest positive correlation (0.882) between the PR length and the LR number. We also found strong associations between the number of LR and the length of AR and LR (0.781 and 0.747, respectively). However, the correlation between the number of AR and the length of LR was the weakest (0.457) among all (Fig. 2 ). QTLs accounted for adventitious root number and candidate genes. We conducted QTL mapping through association analysis of the five root traits. With a LOD score of > 11, we identified a peak on chromosome 1 in the trait for adventitious root number (ARN). The physical intervals of the QTL covered 316 genes, most of which were protein-coding genes (Table S2 ). After researching the literature, we identified which genes in our candidate gene list were previously recognized as regulators of AR formation. We found that TARGET OF RAPAMYCIN (TOR) and INDOLE-3-ACETIC ACID INDUCIBLE28 (IAA28) affected AR initiation [22–24]. Furthermore, GA biosynthesis, signaling, and auxin homeostasis are involved in AR formation [25]; therefore, we selected two additional hormone-related genes: PLETORA (PLT2) and ARABIDOPSIS THALIANA GIBBERELLIN 2-OXIDASE 7 (GA2ox7) . PLT2 has been suggested to participate in AR primordium formation since plt1 plt2 plt3 triple homozygotes arrest its AR growth development [26]. Furthermore, it has been observed that GA hinders the growth of adventitious roots by interrupting auxin transport [27]. While GA2ox7 has not been recognized as a regulator of AR, it could facilitate AR development by reducing GA levels through hydroxylation and deactivation of GA precursors [28]. Besides, it has been reported that specific accessions exhibit differential AR formation when exposed to auxin [29], and these accessions are shared with the Arabidopsis founder accession used in this study. Because of this, we selected a gene that encodes for a Hydroxyproline-rich glycoprotein family protein that, although it has not yet been characterized, is of interest due to the presence of differential SNPs in these accessions with contrasting AR phenotypes after auxin treatment (medium-high rooting: Bur-0, Edi-0, Ler-0, low rooting: Mt-0, Wil-2, Oy-0, Ct-1 (Supplemental Fig. 1. Table 1 ). Allelic variants in five candidate genes of the founder accessions. We searched for allelic variants in the five candidate genes ( TOR, GA2ox7, PLT2, IAA18 and Hydroxyproline-rich glycoprotein family protein) of the founder accessions to identify nucleotide changes that may contribute to natural phenotypic variation in ARs observed in the recombinant inbred lines. Our search was limited to the coding region, and we only selected significant changes such as missense variants or inframe deletions (Table 1 ). Upon analyzing TOR , we found that although there were numerous changes in its 56 exons, they were mainly synonymous variants that did not affect the translated amino acid. The main change was a 3-nucleotide inframe deletion in the Rsch-4 accession localized in the kinase domain (protein position: 2368–2369 aminoacid; Fig. 3 ). PLT2 has two deleterious variations in No-0 and Ct-1 that do not localize in the AP2/ERF domains, whereas Sf-0 and Ct-1 share an in-frame deletion that could shift the gene open reading frame. Besides, IAA18 has several tolerated missense variants in the AUX/IAA domain and only one deleterious variant in Zu-0 that changes the amino acid from Glycine to Valine in the same domain (Fig. 3 ). On the other hand, GA2ox7 has six missense variants, two of which are deleterious in Oy-0 and Hi-0, and whose position is in the Diox-N domain, a highly conserved N-terminal region with 2-oxoglutarate/Fe (II)-dependent dioxygenase activity (Table 1 ; Fig. 3 ). The SNP 1:18250388 mapped in the gene that encodes a Hydroxyproline-rich glycoprotein family protein; this variation results in a change from proline to serine in a coding region that has not been characterized (Fig. 3 ). This SNP is present in accessions like Bur-0, Edi-0, Ler-0, and En-2, which have a high capability of forming AR [29] (Figure S1 ). However, accessions like Mt-o, Wil-2, An-1, Oy-0, and Ct-1, with low competence of AR formation, do not have this variant (Figure S1 . Table 1 ). In addition, we detected that Can-0, Tsu-0, and Zu-0 accessions contain a harmful genetic variation, whereas Po-0 displays two deleterious SNPs (Table 1 ) Table 1 Candidate genes associated with adventitious root numbers were identified via QTL mapping. The position and impact of the allelic variants of these genes in the coding regions of the Arabidopsis founder accessions are indicated. Gene Founder accessions Chr: bp Alleles Class Conseq. Type AA At1G50030 TOR Rsch-4 1:18523147–18523149 TCT/- Deletion Inframe deletion - ED/D Kn-0 1:18539595 C/T SNP Missense variant Tolerated V/M No-0 1:18539612 G/T SNP Missense variant Tolerated T/N At1g50960 GA2ox7 Can-0, Hi-0, Kn-0, No-0, Rsch4, Sf-2 1:18889623 G/T SNP Missense variant Tolerated E/D Can-0, Sf-2 1:18889660 A/T SNP Missense variant Tolerated I/L Hi-0 1:18889744 G/A SNP Missense variant Deleterious A/T Oy-0 1:18889756 T/A SNP Missense variant Deleterious W/R Oy-0 1:18889890 T/A SNP Missense variant Tolerated N/K Mt-0 1:18889922 C/G SNP Missense variant Tolerated S/C At1G51190 PLT2 Bur-0, Can-0, Ct-1, Edi-0, Hi-0, Kn-0, Mt-0, Oy-0, Po-0, Rsch-4, Sf-2, Tsu-0, Wil-2, Ws-0, Wu-0, and Zu-0 1:18978006 A/C/T SNP Missense variant Tolerated E/P Kn-0 1:18978071 A/T SNP Missense variant Tolerated Q/H Can-0, Sf-0 1:18978257–18978259 CAC/- Deletion Inframe deletion - ST/S Kn-0 1:18979010 G/C SNP Missense variant Tolerated E/D Ct-1 1:18980072 C/T/A SNP Missense variant Deleterious L/I No-0 1:18980238 G/T SNP Missense variant Deleterious G/V At1G51950 IAA18 Kn-0 1:19305779 C/A SNP Missense variant Tolerated T/K Mt-0 1:19305855 G/A SNP Missense variant Tolerated M/I Mt-0 1:19305901 T/C SNP Missense variant Tolerated Y/H Zu-0 1:19306234 G/C SNP Missense variant Deleterious G/V Can-0, Hi-0, Kn-0, Ler-0, Mt-0, No-0, Wil-2, Ws-0Zu-0 1:19306355 C/A SNP Missense variant Tolerated A/D AT1G49330 Hydroxyproline- rich glycoprotein family protein Can-0, Po-0, Tsu-0, Zu-0 1:18250209 C/A SNP Missense variant Deleterious S/Y Po-0 1:18250260 A/C SNP Missense variant Deleterious E/A No.0 1:18250338 C/G/T SNP Missense variant Tolerated P/R Bur-0, Ler-0, Edi-0 1:18250388 C/T SNP Missense variant Tolerated P/S No-0 1:18250417 C/A SNP Missense variant Tolerated F/L Edi-0, Oy-0 1:18250605 A/C SNP Missense variant Tolerated E/A Discussion There has been a longstanding interest in understanding the link between genetic and phenotypic variation in natural populations. This insight is crucial for identifying the genetic basis of adaptation and discovering naturally occurring alleles that influence various traits. The root system is vital to plant growth and productivity. Therefore, it is necessary to comprehend the genetic basis of natural variation in this particular trait [30]. One approach to identify genes responsible for natural variations in complex traits, such as root architecture, is to link genetic and phenotypic differences using recombinant inbred lines. In the case of MAGIC lines, there are several parental accessions and additional recombination generations [17]. Although only 19 accessions were used to establish the MAGIC recombinant inbred lines, they still capture a significant portion of the common genetic variation present in Arabidopsis [17]. In this work, we evaluated five root traits: PR length, LR and AR length and number; we observed a wide range of variations in phenotype among the MAGIC lines for all the measured traits and a positive correlation between the length of PR and the number of LR was detected. It has previously been reported that there is no correlation between the length of the primary root (PR) and the number of lateral roots in Arabidopsis natural accessions [31]. However, we have observed the opposite trend and believe as the lateral roots emerge from the PR, longer PRs may indicate more physical space for lateral root initiation. QTL mapping revealed a significant region on chromosome 1 associated with ARN. ARs originate post-embryonically from aerial parts such as stems or hypocotyls, and they are induced by many environmental and physiological stresses to expand absorbing areas or enhance resistance to adversity [32, 33]. ARs are used in asexual propagation, which results in difficulty in achieving in many crops. Understanding its molecular mechanisms is essential for such species [34, 35]. AR development is a complex process controlled by diverse factors such as phytohormones, particularly auxin. The critical step in ARs formation is the development of AR primordia, which begins with the auxin synthesis and accumulation [36]. According to the repositories AraPheno and AraGWAS, no data exists about the genetic associations between distinct loci and AR development. In this work, we detected 316 genes associated with ARN, some associated with auxin and GA synthesis, signaling and transport. It has been discovered that genes encoding proteins associated with gibberellin biosynthesis and signaling and auxin homeostasis are involved in forming AR [37]. Auxin and TOR work together to regulate ARs formation. TOR is a protein kinase and a master regulator that integrates energy, nutrients, stress, and hormone signaling to promote cell growth and proliferation [38]. When Arabidopsis roots are treated with TOR inhibitors, the formation of ARs is significantly slower. However, the overexpression of the auxin receptor TIR1 can partially restore the formation of ARs that were inhibited by TOR inhibitors. This suggests that there may be a connection between the TOR and auxin signaling mechanisms during the ARs formation process [22]. Besides, we identified a nucleotide in-frame deletion in the kinase domain of TOR from the parental accession Rsch-4. This deletion might contribute to natural variation in AR. Moreover, the gain-of-function mutants crane-2 , which harbor mutations in domain II of IAA18 that confer resistance to degradation by the proteasome, was also shown to be affected in AR initiation [24]. We observed that IAA18 has several missense variants in the AUX/IAA domain and only one deleterious variant in Zu-0 that leads to an amino acid change. On the other hand, PLT2 is a crucial gene that plays a significant role in maintaining the identity of the quiescent center (QC), root apical meristem (RAM) maintenance, and activating the gene expression of polar auxin transports, biosynthesis, and response genes [39, 40]. It has also been associated with AR initiation [26]. We detected that some parental accessions of MAGIC lines have an in-frame deletion that could shift the gene open reading frame of PLT2 . Additionally, for the polymorphism analysis, we selected a gene that encodes for a Hydroxyproline-rich glycoprotein family protein that displays differential SNPs in accessions with contrasting AR phenotypes. These accessions come from a study where the variation in the number of ARs formed on seedling hypocotyls in response to auxin was evaluated in 18 ecotypes [29]. Mt-0, Wil-2, and An-1 are accessions with low ARs formed, whereas Bur-0, En-2, Ler-0 and Edi-0 are accessions that display a high number of ARs formation after auxin treatment. We noticed that an SNP changes from proline to serine in a coding region in these accessions with high AR formation. The cross between Mt-o with Ha-S (accession with high capability of AR formation) shows a low proportion of high rooting segregants in the F2, suggesting a multigene control in AR formation [29]. Regarding GA regulation in AR formation, we noticed that GA2ox7 has six missense variants, two of which are deleterious in Oy-0 and Hi-0. Whose position is in the Diox-N domain, a highly conserved N-terminal region with 2-oxoglutarate/Fe (II)-dependent dioxygenase activity. It has been described that loss-of-function mutations of GA REQUIRING 1 (GA1) and GA5 , which encode for the enzymes ENT-COPALYL DIPHOSPHATE SYNTHETASE 1 and GA 20-OXIDASE respectively, lead to a significant reduction in the number of ARs in both hypocotyl explants and excised leaves [37]. Likewise, it has been reported that treating WT plants with GA4 (1 µm) significantly inhibited adventitious rooting [27]. Similarly, transgenic plants with higher GA biosynthesis via overexpressing of GA20ox1 have significantly fewer ARs in stem cuttings due to the perturbation of polar auxin transport [27]. Conclusions In summary, in this study, we assessed various physical traits in the root structure of MAGIC lines and discovered a significant QTL on chromosome 1 that affects the number of AR. This QTL was found to map several genes related to phytohormones, including those involved in auxin and gibberellin signalling and homeostasis. We observed that some founder accessions displayed missense and in-frame deletions in these genes, which could lead to natural variation in AR development. Further research is required to fully understand the complex interaction between GA and auxin signalling and its role in the natural variation of AR development. Declarations Funding. This study was funded by the grant UNAM PAPIIT DGAPA IN214422 to UR. This work was supported by UNAM Posdoctoral Program (POSDOC) to BALR. Author Contributions Ulises Rosas, Joshua Banta and Brenda Anabel López-Ruiz.contributed to the study's conception and design. Material preparation, data collection and analysis were performed by Ulises Rosas, Joshua Banta, Perla Salazar-Hernández, Daniela Espinoza-Gutiérrez, Andrea Alfaro and Brenda Anabel López-Ruiz. The first draft of the manuscript was written by Brenda Anabel López-Ruiz. Ulises Rosas and Joshua Banta commented on previous versions of the manuscript. All authors read and approved the final manuscript. Conflicts of interest/Competing interests: The authors declare no conflict of interest. Ethics approval: NA Consent to participate: NA Consent for publication : All authors have approved the manuscript and agree with its submission to Molecular Biology Reports. Availability of data and material All data generated or analyzed during this study are included in this published article and its supplementary information. References Petricka JJ, Winter CM, Benfey PN (2012) Control of Arabidopsis Root Development. Annu Rev Plant Biol 63:563–590. https://doi.org/10.1146/annurev-arplant-042811-105501 Benfey PN, Schiefelbein JW (1994) Getting to the root of plant development: the genetics of Arabidopsis root formation. Trends in Genetics 10:84–88. https://doi.org/10.1016/0168-9525(94)90230-5 Waidmann S, Sarkel E, Kleine-Vehn J (2020) Same same, but different: growth responses of primary and lateral roots. 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Journal of Heredity 89:481–487. https://doi.org/10.1093/jhered/89.6.481 Deja-Muylle A, Parizot B, Motte H, Beeckman T (2020) Exploiting natural variation in root system architecture via genome-wide association studies. Journal of Experimental Botany 71:2379–2389. https://doi.org/10.1093/jxb/eraa029 Wintermans PCA, Bakker PAHM, Pieterse CMJ (2016) Natural genetic variation in Arabidopsis for responsiveness to plant growth-promoting rhizobacteria. Plant Mol Biol 90:623–634. https://doi.org/10.1007/s11103-016-0442-2 Esau K (1977) Anatomy of seed plants, 2. ed. Wiley, New York Falasca G, Altamura MM (2003) Histological analysis of adventitious rooting in Arabidopsis thaliana (L.) Heynh seedlings. Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology 137:265–273. https://doi.org/10.1080/11263500312331351511 Bellini C, Pacurar DI, Perrone I (2014) Adventitious Roots and Lateral Roots: Similarities and Differences. Annu Rev Plant Biol 65:639–666. https://doi.org/10.1146/annurev-arplant-050213-035645 Welander M, Geier T, Smolka A, et al (2014) Origin, timing, and gene expression profile of adventitious rooting in Arabidopsis hypocotyls and stems. American J of Botany 101:255–266. https://doi.org/10.3732/ajb.1300258 Della Rovere F, Fattorini L, Ronzan M, et al (2016) The quiescent center and the stem cell niche in the adventitious roots of Arabidopsis thaliana. Plant Signaling & Behavior 11:e1176660. https://doi.org/10.1080/15592324.2016.1176660 Ibáñez S, Ruiz-Cano H, Fernández MÁ, et al (2019) A Network-Guided Genetic Approach to Identify Novel Regulators of Adventitious Root Formation in Arabidopsis thaliana. Front Plant Sci 10:461. https://doi.org/10.3389/fpls.2019.00461 Xiong Y, Sheen J (2014) The Role of Target of Rapamycin Signaling Networks in Plant Growth and Metabolism. Plant Physiol 164:499–512. https://doi.org/10.1104/pp.113.229948 Aida M, Beis D, Heidstra R, et al (2004) The PLETHORA genes mediate patterning of the Arabidopsis root stem cell niche. Cell 119:109–120. https://doi.org/10.1016/j.cell.2004.09.018 Santuari L, Sanchez-Perez GF, Luijten M, et al (2016) The PLETHORA gene regulatory network guides growth and cell differentiation in Arabidopsis roots. Plant Cell 28:2937–2951. https://doi.org/10.1105/tpc.16.00656 Additional Declarations No competing interests reported. Supplementary Files FigureS1.pdf Supplementary information. Figure S1. SNPs found in the gene that encodes for a Hydroxyproline-rich glycoprotein family protein in accessions described with variation in the number of AR formed after auxin treatment. TableS1.xlsx Table S1. Mean and standard deviation of the five traits measured in the 139 MAGIC Lines. TableS2.xlsx Table S2. Genes associated with the significant QTL for adventitious root number. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-4432917","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":306815857,"identity":"30897281-2659-4ca3-8264-ea92fa40fb0f","order_by":0,"name":"Brenda Anabel López-Ruiz","email":"","orcid":"","institution":"Universidad Nacional Autónoma de México","correspondingAuthor":false,"prefix":"","firstName":"Brenda","middleName":"Anabel","lastName":"López-Ruiz","suffix":""},{"id":306815858,"identity":"3eda07f9-ff51-4ade-b958-58f5e7f88c7b","order_by":1,"name":"Joshua Banta","email":"","orcid":"","institution":"The University of Texas at Tyler","correspondingAuthor":false,"prefix":"","firstName":"Joshua","middleName":"","lastName":"Banta","suffix":""},{"id":306815859,"identity":"0b5faabd-8f0c-47c9-b5e7-c34055213c90","order_by":2,"name":"Perla Salazar-Hernández","email":"","orcid":"","institution":"Universidad Nacional Autónoma de México","correspondingAuthor":false,"prefix":"","firstName":"Perla","middleName":"","lastName":"Salazar-Hernández","suffix":""},{"id":306815860,"identity":"e7354adc-e99e-4d21-a547-284b1796920a","order_by":3,"name":"Daniela Espinoza-Gutiérrez","email":"","orcid":"","institution":"Universidad Nacional Autónoma de México","correspondingAuthor":false,"prefix":"","firstName":"Daniela","middleName":"","lastName":"Espinoza-Gutiérrez","suffix":""},{"id":306815861,"identity":"3ca56016-4c5d-47ff-8517-12f57f9111a9","order_by":4,"name":"Andrea Alfaro-Mendoza","email":"","orcid":"","institution":"Universidad Nacional Autónoma de México","correspondingAuthor":false,"prefix":"","firstName":"Andrea","middleName":"","lastName":"Alfaro-Mendoza","suffix":""},{"id":306815862,"identity":"f522552a-1f78-4831-9405-cf4b5f3824cb","order_by":5,"name":"Ulises Rosas","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAtklEQVRIiWNgGAWjYPACGx4DUrWkka7lMAPxWgxuHz784cef8zLmDDxmD37mMEQbHCCk5VxammRv220eywYec8PebQy5MxsIaTnDY8bA23Cbx+AAj5kEL1BLP0GHneEx/vjnzzmwFsm/QC1tRGgxkOZhOwDWIk2ULZJn2NKkZduSeSyb2cqkZbdJEPYL3xnmwx/f/LGzN2dv3ib5dptN7oYDhKyBA2YwKUG0+lEwCkbBKBgFeAAAJsg40K5KisoAAAAASUVORK5CYII=","orcid":"","institution":"Universidad Nacional Autónoma de México","correspondingAuthor":true,"prefix":"","firstName":"Ulises","middleName":"","lastName":"Rosas","suffix":""}],"badges":[],"createdAt":"2024-05-16 19:23:25","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-4432917/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-4432917/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":57445902,"identity":"eb346cc1-cac7-4c0e-91c8-ee80b45a0c4b","added_by":"auto","created_at":"2024-05-30 19:26:14","extension":"jpg","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":5033356,"visible":true,"origin":"","legend":"\u003cp\u003eA. Five root traits were quantified in the \u003cem\u003eArabidopsis\u003c/em\u003eMAGIC lines: PRL, LRN, LRL, ARN and ARL. The box plot displays the first and third quartiles, median, and whiskers extending to the maximum or minimum value.\u003c/p\u003e","description":"","filename":"Figure1.jpg","url":"https://assets-eu.researchsquare.com/files/rs-4432917/v1/e73f2730071db94a3a4da5df.jpg"},{"id":57445903,"identity":"54cd4aa7-287a-460a-b5d0-eaf277e973b5","added_by":"auto","created_at":"2024-05-30 19:26:14","extension":"jpg","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":1381832,"visible":true,"origin":"","legend":"\u003cp\u003ePair plots indicate the correlation between the five root traits analyzed in this study. The upper panel of the plots exhibits the correlation between the traits, while the lower panel displays the scatter plots of the traits. The histograms are displayed on the diagonal. The significant value is indicated with (***) p \u0026lt; 0.001. Primary Root (PR), Lateral Root (LR) and Adventitious Roots (AR).\u003c/p\u003e","description":"","filename":"Figure2.jpg","url":"https://assets-eu.researchsquare.com/files/rs-4432917/v1/11b9c1bc2c63aebedb8a16b9.jpg"},{"id":57445906,"identity":"b5c60786-9dbc-4e9f-b8dc-2e3f3383c7b3","added_by":"auto","created_at":"2024-05-30 19:26:15","extension":"jpg","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":158862,"visible":true,"origin":"","legend":"\u003cp\u003eChromosomal location of significant QTLs for the Adventitious root number (ARN).\u003c/p\u003e","description":"","filename":"Figure3.jpg","url":"https://assets-eu.researchsquare.com/files/rs-4432917/v1/e3c196bb091c448b2c2e1c50.jpg"},{"id":57445905,"identity":"11a2303e-097e-48e3-85b9-aaf55e7aa9f0","added_by":"auto","created_at":"2024-05-30 19:26:15","extension":"jpg","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":1278048,"visible":true,"origin":"","legend":"\u003cp\u003eProteins obtained via QTL mapping and their changes in founder accessions. Each protein domain is represented in different colors. Amino acid changes are displayed with arrowheads. Aminoacid deletions are represented in red, deleterious missense variants are in blue, and tolerated changes are in black. HEAT (huntingtin, elongation factor 3 (EF3)), FAT (FRAP, ATM, and TRAP), FRB (FKB12-rapamycin binding), DIOX-N (N-terminal region of proteins with 2-oxoglutarate/Fe (II)-dependent dioxygenase activity), FE2OG_OXY \u0026nbsp;(Fe(2+) 2-oxoglutarate dioxygenase domain profile), AP2/ERF (APETALA 2/ Ethylene-Responsive Element binding factors), AUX/IAA ( AUXIN/INDOLE-3-ACETIC ACID), PB1 (Phox and Bem1 domain).\u003c/p\u003e","description":"","filename":"Figure4.jpg","url":"https://assets-eu.researchsquare.com/files/rs-4432917/v1/7fd625f3daf7b7056a21dc23.jpg"},{"id":68898566,"identity":"0b46fb05-463c-463b-8775-68cc91d0c7f3","added_by":"auto","created_at":"2024-11-13 09:18:00","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":8382257,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-4432917/v1/c4bddb9c-d5d9-48f3-afdf-9f9df892289f.pdf"},{"id":57446727,"identity":"8d27ac4b-a6ae-436c-b500-c10d469e8e72","added_by":"auto","created_at":"2024-05-30 19:34:14","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":62342,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eSupplementary information.\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eFigure S1. SNPs found in the gene that encodes for a Hydroxyproline-rich glycoprotein family protein in accessions described with variation in the number of AR formed after auxin treatment.\u003c/p\u003e","description":"","filename":"FigureS1.pdf","url":"https://assets-eu.researchsquare.com/files/rs-4432917/v1/a0cf1d0853d369532f616d05.pdf"},{"id":57445900,"identity":"36cd73c1-1ce1-4bbb-9d2a-3bb19648565d","added_by":"auto","created_at":"2024-05-30 19:26:14","extension":"xlsx","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":25887,"visible":true,"origin":"","legend":"\u003cp\u003eTable S1. Mean and standard deviation of the five traits measured in the 139 MAGIC Lines.\u003c/p\u003e","description":"","filename":"TableS1.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-4432917/v1/0a8cc774756d36df4926bc00.xlsx"},{"id":57445907,"identity":"f8b13ea9-ce65-4fa1-bc4a-719408a7984d","added_by":"auto","created_at":"2024-05-30 19:26:15","extension":"xlsx","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":39215,"visible":true,"origin":"","legend":"\u003cp\u003eTable S2. Genes associated with the significant QTL for adventitious root number.\u003c/p\u003e","description":"","filename":"TableS2.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-4432917/v1/4331565e34e477e36777f602.xlsx"}],"financialInterests":"No competing interests reported.","formattedTitle":"QTL mapping using Arabidopsis thaliana MAGIC Lines identifies candidate genes controlling adventitious root development","fulltext":[{"header":"Introduction","content":"\u003cp\u003eThe root system anchors the plant and absorbs water and nutrients; studying root architecture and growth is essential in the field of plant organ development [1]. \u003cem\u003eArabidopsis thalian\u003c/em\u003ea (hereafter \u003cem\u003eArabidopsis\u003c/em\u003e) has a simple root system, which makes it useful for studying root architecture and identifying new genes that control these characteristics. Moreover, it is relatively easy to visualize the root system of \u003cem\u003eArabidopsis\u003c/em\u003e on vertical agar plates \u003cem\u003ein vitro\u003c/em\u003e [2].\u003c/p\u003e \u003cp\u003eThe \u003cem\u003eArabidopsis\u003c/em\u003e root system consists of three main types of roots: the primary root (PR), the lateral roots (LRs), and the adventitious roots (ARs) [3, 4]. The PR originates from the embryonic meristem and is the first organ to develop during germination [5]. Its principal function is to anchor the plant into the soil by growing downwards [3]. The LRs develop from founder cells in the pericycle adjacent to the protoxylem poles of the vascular cylinder, and they explore the soil in response to environmental clues [6]. The ARs, on the other hand, develop from non-root organs such as hypocotyl, stems or leaves. They are observed when \u003cem\u003eArabidopsis\u003c/em\u003e is grown vertically on a synthetic medium or in response to wounding or environmental signals [4, 7]. Several genes have been identified to play a vital role in developing PR, LR, and AR [8\u0026ndash;11]. These genes include transcription factors such as \u003cem\u003eWUSCHEL RELATED HOMEOBOX (WOX), PLETHORA (PLT), AUXIN RESPONSE FACTORS (ARFs), SHORT ROOT (SHR)\u003c/em\u003e, and \u003cem\u003eSCARECROW (SCR)\u003c/em\u003e, as well as cell cycle genes like \u003cem\u003eCYCLIN-DEPENDENT KINASES\u003c/em\u003e and \u003cem\u003eCYCLINS\u003c/em\u003e. Additionally, plant hormones are crucial regulators of cell division, elongation, and differentiation [8\u0026ndash;10].\u003c/p\u003e \u003cp\u003eIn \u003cem\u003eArabidopsis\u003c/em\u003e, the Multi-Parent Advanced Generation Inter-Cross (MAGIC) population is a large set of recombinant inbred lines (RILs) that are used to map a vast amount of phenotypic diversity, combining the benefits of association mapping and linkage analysis; these lines offer great power for detecting quantitative trait loci (QTL) [12]. The MAGIC lines were developed by crossing 19 natural accessions of \u003cem\u003eA. thaliana\u003c/em\u003e over multiple generations [13]. This breeding strategy not only introduced additional recombination events, but also increased the number of segregating alleles within the lines. Consequently, QTL can be pinpointed to much smaller genomic regions than usual, often less than 1 Mb in size [13]. Moreover, they contain 3.3\u0026nbsp;million segregating SNPs, which is 68% of SNPs with a frequency above 0.05 identified by the 1001 genome project, thus capturing a substantial portion of the common molecular variation present in the species [13]. MAGIC populations increase genetic recombination and genetic variation and reduce the limitations of bi-parental populations for QTL mapping (lack of mapping precision and low genetic diversity) [14]. Potentially, each MAGIC line can inherit alleles from all the progenitors, and the MAGIC chromosomes are random mosaics of the parental haplotypes [14]. The MAGIC population is well-suited for breeding improvement, and analysis of the relationship between genotypes and phenotypes allows the identification of QTLs, which can then be confirmed using functional genomics [15, 16].\u003c/p\u003e \u003cp\u003eThe \u003cem\u003eArabidopsis\u003c/em\u003e MAGIC population has been used to map several traits involved in germination and bolting time [17] and to examine the natural genetic basis of variation in seed size and number [18]. However, the genetic basis of root phenotypic variation in MAGIC lines has not yet been addressed. This study aimed to evaluate the variation in root architecture in 139 recombinant inbred lines. Additionally, QTL mapping was performed to detect new candidate genes contributing to these traits.\u003c/p\u003e"},{"header":"Material and Methods","content":"\u003cp\u003e \u003cem\u003eGrowth Conditions and Phenotyping.\u003c/em\u003e \u003c/p\u003e \u003cp\u003eThe MAGIC population used in this study was created with 19 \u003cem\u003eArabidopsis\u003c/em\u003e founder accessions (Bur-0, Can-0, Col-0, Ct-1, Edi-0, Hi-0, Kn-0, Ler-0, Mt-0, No-0, Oy-0, Po-0, Rsch-4, Sf-2, Tsu-0, Wil-2, Ws-0, Wu-0, and Zu-0) [17]. A total of 139 lines, each consisting of approximately ten individuals, were used to record the root traits for the study.\u003c/p\u003e \u003cp\u003eSeeds were disinfected with a solution of 70% ethanol, 50% bleach and three rinses of sterilized water. Seeds were sown on square Petri dishes with 50% MS salts (Caisson, MSP09), 0.05% MES and 1% agar (Bacto Agar BD) at pH 5.6. The plates with the seeds were stratified for three days at 4\u0026deg;C in darkness and then placed vertically in a growth chamber under 22\u0026deg;C, long-day 16h/8h at 200 \u0026micro;mol/m\u0026sup2;/s light intensity (Percival Scientific).\u003c/p\u003e \u003cp\u003e18 days after sowing (das), plates were digitized at 600 dpi and five root traits were measured using the Image J version Fiji software (NIH, USA) using a ruler as a scale: primary root length, lateral root number, lateral root length, adventitious root number, and adventitious root length.\u003c/p\u003e \u003cdiv id=\"Sec3\" class=\"Section2\"\u003e \u003ch2\u003eQTL Mapping\u003c/h2\u003e \u003cp\u003eQTL mapping was performed using the \u0026lsquo;scan1\u0026rsquo; function of the R/qtl2 package R, in combination with a custom R data package containing the genotype data in a suitable format for analysis (available at \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://github.com/tavareshugo/atMAGIC\u003c/span\u003e\u003cspan address=\"https://github.com/tavareshugo/atMAGIC\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003e).\u003c/span\u003e Genome-wide significance was determined empirically for each trait, using 1000 permutations of the data with the \u0026lsquo;scan1perm\u0026rsquo; function of the R/qtl2 package, corresponding to a genome-wide false positive rate of 5%. A total of 139 MAGIC lines for five root traits were used. Candidate genes within the QTL interval were determined in TAIR10.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec4\" class=\"Section2\"\u003e \u003ch2\u003ePolymorphism patterns\u003c/h2\u003e \u003cp\u003eSequence data from the 1001 genome project [19] (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttp://signal.salk.edu/atg1001/3.0/gebrowser.php\u003c/span\u003e\u003cspan address=\"http://signal.salk.edu/atg1001/3.0/gebrowser.php\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e (accessed on December 2023) was used to analyze single nucleotide polymorphism (SNPs) of candidate genes among founder accessions (Bur-0, Can-0, Col-0, Ct-1, Edi-0, Hi-0, Kn-0, Ler-0, Mt-0, No-0, Oy-0, Po-0, Rsch-4, Sf-2, Tsu-0, Wil-2, Ws-0, Wu-0, and Zu-0). To determine the effects of these variations and their exact positions, Variant Effect Predictor (VEP; [20]) was executed on the coding sequence, with default parameters (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://plants.ensembl.org/Arabidopsis_thaliana/Tools/VEP\u003c/span\u003e\u003cspan address=\"https://plants.ensembl.org/Arabidopsis_thaliana/Tools/VEP\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e (accessed on December 2023). We searched the AraPheno (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://arapheno.1001genomes.org\u003c/span\u003e\u003cspan address=\"https://arapheno.1001genomes.org\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e) and AraGWAS Catalog (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://aragwas.1001genomes.org\u003c/span\u003e\u003cspan address=\"https://aragwas.1001genomes.org\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e) data repositories for publicly available phenotypic data and distinct loci related to adventitious root formation. Protein domains were retrieved from InterPro, visualized using Unipro UGENE, and edited with Adobe Illustrator.\u003c/p\u003e \u003c/div\u003e"},{"header":"Results","content":"\u003cdiv id=\"Sec6\" class=\"Section2\"\u003e \u003ch2\u003eRoot variation in Arabidopsis MAGIC lines\u003c/h2\u003e \u003cp\u003eWe analyzed five root characteristics in 139 \u003cem\u003eArabidopsis\u003c/em\u003e recombinant inbred lines derived by intermating 19 natural accessions [17]. We recorded the length of the primary root (PRL), the number of lateral roots (LRN), the length of lateral roots (LRL), the number of adventitious roots (ARN), and the length of adventitious roots (ARL) for 18 DAS by marking their positions in the Petri dish. The variability in root architecture can be observed in Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eA-E.\u003c/p\u003e \u003cp\u003eTable \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e presents the mean and standard deviation (SD) of the 139 MAGIC lines; the range of PR varies from 0.22 cm\u0026thinsp;\u0026plusmn;\u0026thinsp;0.28 to 3.38 cm\u0026thinsp;\u0026plusmn;\u0026thinsp;2.9 cm. The LR number goes from 0 to 12.46\u0026thinsp;\u0026plusmn;\u0026thinsp;15.10, and the LR length fluctuates from 0.006\u0026thinsp;\u0026plusmn;\u0026thinsp;0.01 to 3.12 cm. Concerning ARN, some MAGIC lines lack ARs, and the highest value is 3.5\u0026thinsp;\u0026plusmn;\u0026thinsp;3.53. Regarding ARL, the minimum mean length is 0.019\u0026thinsp;\u0026plusmn;\u0026thinsp;0.03 cm, whereas the maximum is 8.01\u0026thinsp;\u0026plusmn;\u0026thinsp;11.2 cm. This considerable SD has been observed previously in other studies that have used the \u003cem\u003eArabidopsis\u003c/em\u003e recombinant inbred lines [21].\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eWe conducted multiple correlations to study the association between the five traits (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e). The results showed the highest positive correlation (0.882) between the PR length and the LR number. We also found strong associations between the number of LR and the length of AR and LR (0.781 and 0.747, respectively). However, the correlation between the number of AR and the length of LR was the weakest (0.457) among all (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003e \u003cem\u003eQTLs accounted for adventitious root number and candidate genes.\u003c/em\u003e \u003c/p\u003e \u003cp\u003eWe conducted QTL mapping through association analysis of the five root traits. With a LOD score of \u0026gt;\u0026thinsp;11, we identified a peak on chromosome 1 in the trait for adventitious root number (ARN). The physical intervals of the QTL covered 316 genes, most of which were protein-coding genes (Table \u003cspan refid=\"MOESM2\" class=\"InternalRef\"\u003eS2\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eAfter researching the literature, we identified which genes in our candidate gene list were previously recognized as regulators of AR formation. We found that \u003cem\u003eTARGET OF RAPAMYCIN (TOR)\u003c/em\u003e and \u003cem\u003eINDOLE-3-ACETIC ACID INDUCIBLE28 (IAA28)\u003c/em\u003e affected AR initiation [22\u0026ndash;24]. Furthermore, GA biosynthesis, signaling, and auxin homeostasis are involved in AR formation [25]; therefore, we selected two additional hormone-related genes: \u003cem\u003ePLETORA (PLT2)\u003c/em\u003e and \u003cem\u003eARABIDOPSIS THALIANA GIBBERELLIN 2-OXIDASE 7 (GA2ox7)\u003c/em\u003e. \u003cem\u003ePLT2\u003c/em\u003e has been suggested to participate in AR primordium formation since \u003cem\u003eplt1 plt2 plt3\u003c/em\u003e triple homozygotes arrest its AR growth development [26]. Furthermore, it has been observed that GA hinders the growth of adventitious roots by interrupting auxin transport [27]. While GA2ox7 has not been recognized as a regulator of AR, it could facilitate AR development by reducing GA levels through hydroxylation and deactivation of GA precursors [28]. Besides, it has been reported that specific accessions exhibit differential AR formation when exposed to auxin [29], and these accessions are shared with the \u003cem\u003eArabidopsis\u003c/em\u003e founder accession used in this study. Because of this, we selected a gene that encodes for a Hydroxyproline-rich glycoprotein family protein that, although it has not yet been characterized, is of interest due to the presence of differential SNPs in these accessions with contrasting AR phenotypes after auxin treatment (medium-high rooting: Bur-0, Edi-0, Ler-0, low rooting: Mt-0, Wil-2, Oy-0, Ct-1 (Supplemental Fig.\u0026nbsp;1. Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003cem\u003eAllelic variants in five candidate genes of the founder accessions.\u003c/em\u003e \u003c/p\u003e \u003cp\u003eWe searched for allelic variants in the five candidate genes (\u003cem\u003eTOR, GA2ox7, PLT2, IAA18\u003c/em\u003e and Hydroxyproline-rich glycoprotein family protein) of the founder accessions to identify nucleotide changes that may contribute to natural phenotypic variation in ARs observed in the recombinant inbred lines. Our search was limited to the coding region, and we only selected significant changes such as missense variants or inframe deletions (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). Upon analyzing \u003cem\u003eTOR\u003c/em\u003e, we found that although there were numerous changes in its 56 exons, they were mainly synonymous variants that did not affect the translated amino acid. The main change was a 3-nucleotide inframe deletion in the Rsch-4 accession localized in the kinase domain (protein position: 2368\u0026ndash;2369 aminoacid; Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e). \u003cem\u003ePLT2\u003c/em\u003e has two deleterious variations in No-0 and Ct-1 that do not localize in the AP2/ERF domains, whereas Sf-0 and Ct-1 share an in-frame deletion that could shift the gene open reading frame. Besides, \u003cem\u003eIAA18\u003c/em\u003e has several tolerated missense variants in the AUX/IAA domain and only one deleterious variant in Zu-0 that changes the amino acid from Glycine to Valine in the same domain (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eOn the other hand, \u003cem\u003eGA2ox7\u003c/em\u003e has six missense variants, two of which are deleterious in Oy-0 and Hi-0, and whose position is in the Diox-N domain, a highly conserved N-terminal region with 2-oxoglutarate/Fe (II)-dependent dioxygenase activity (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e; Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eThe SNP 1:18250388 mapped in the gene that encodes a Hydroxyproline-rich glycoprotein family protein; this variation results in a change from proline to serine in a coding region that has not been characterized (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e). This SNP is present in accessions like Bur-0, Edi-0, Ler-0, and En-2, which have a high capability of forming AR [29] (Figure \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e). However, accessions like Mt-o, Wil-2, An-1, Oy-0, and Ct-1, with low competence of AR formation, do not have this variant (Figure \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e. Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). In addition, we detected that Can-0, Tsu-0, and Zu-0 accessions contain a harmful genetic variation, whereas Po-0 displays two deleterious SNPs (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e)\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eCandidate genes associated with adventitious root numbers were identified via QTL mapping. The position and impact of the allelic variants of these genes in the coding regions of the Arabidopsis founder accessions are indicated.\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"8\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c8\" colnum=\"8\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eGene\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eFounder accessions\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eChr: bp\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eAlleles\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003eClass\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colspan=\"2\" nameend=\"c7\" namest=\"c6\"\u003e \u003cp\u003eConseq.\u0026nbsp;Type\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c8\"\u003e \u003cp\u003eAA\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"2\" rowspan=\"3\"\u003e \u003cp\u003eAt1G50030\u003c/p\u003e \u003cp\u003eTOR\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eRsch-4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1:18523147\u0026ndash;18523149\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eTCT/-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eDeletion\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eInframe deletion\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eED/D\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eKn-0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1:18539595\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eC/T\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSNP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMissense variant\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eTolerated\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eV/M\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eNo-0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1:18539612\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eG/T\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSNP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMissense variant\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eTolerated\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eT/N\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"5\" rowspan=\"6\"\u003e \u003cp\u003eAt1g50960\u003c/p\u003e \u003cp\u003eGA2ox7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eCan-0, Hi-0, Kn-0, No-0, Rsch4, Sf-2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1:18889623\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eG/T\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSNP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMissense variant\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eTolerated\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eE/D\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eCan-0, Sf-2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1:18889660\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eA/T\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSNP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMissense variant\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eTolerated\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eI/L\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHi-0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1:18889744\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eG/A\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSNP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMissense variant\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eDeleterious\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eA/T\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eOy-0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1:18889756\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eT/A\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSNP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMissense variant\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eDeleterious\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eW/R\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eOy-0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1:18889890\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eT/A\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSNP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMissense variant\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eTolerated\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eN/K\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMt-0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1:18889922\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eC/G\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSNP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMissense variant\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eTolerated\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eS/C\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"5\" rowspan=\"6\"\u003e \u003cp\u003eAt1G51190\u003c/p\u003e \u003cp\u003ePLT2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eBur-0, Can-0, Ct-1, Edi-0, Hi-0, Kn-0, Mt-0, Oy-0, Po-0, Rsch-4, Sf-2, Tsu-0, Wil-2, Ws-0, Wu-0, and Zu-0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1:18978006\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eA/C/T\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSNP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMissense variant\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eTolerated\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eE/P\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eKn-0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1:18978071\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eA/T\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSNP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMissense variant\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eTolerated\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eQ/H\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eCan-0, Sf-0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1:18978257\u0026ndash;18978259\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eCAC/-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eDeletion\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eInframe deletion\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e-\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eST/S\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eKn-0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1:18979010\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eG/C\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSNP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMissense variant\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eTolerated\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eE/D\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eCt-1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1:18980072\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eC/T/A\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSNP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMissense variant\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eDeleterious\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eL/I\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eNo-0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1:18980238\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eG/T\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSNP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMissense variant\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eDeleterious\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eG/V\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"4\" rowspan=\"5\"\u003e \u003cp\u003eAt1G51950\u003c/p\u003e \u003cp\u003eIAA18\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eKn-0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1:19305779\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eC/A\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSNP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMissense variant\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eTolerated\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eT/K\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMt-0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1:19305855\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eG/A\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSNP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMissense variant\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eTolerated\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eM/I\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMt-0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1:19305901\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eT/C\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSNP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMissense variant\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eTolerated\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eY/H\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eZu-0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1:19306234\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eG/C\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSNP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMissense variant\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eDeleterious\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eG/V\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eCan-0, Hi-0, Kn-0, Ler-0, Mt-0, No-0, Wil-2, Ws-0Zu-0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1:19306355\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eC/A\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSNP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMissense variant\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eTolerated\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eA/D\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"5\" rowspan=\"6\"\u003e \u003cp\u003eAT1G49330\u003c/p\u003e \u003cp\u003eHydroxyproline- rich glycoprotein family protein\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eCan-0, Po-0, Tsu-0, Zu-0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1:18250209\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eC/A\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSNP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMissense variant\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eDeleterious\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eS/Y\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ePo-0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1:18250260\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eA/C\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSNP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMissense variant\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eDeleterious\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eE/A\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eNo.0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1:18250338\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eC/G/T\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSNP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMissense variant\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eTolerated\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eP/R\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eBur-0, Ler-0, Edi-0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1:18250388\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eC/T\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSNP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMissense variant\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eTolerated\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eP/S\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eNo-0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1:18250417\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eC/A\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSNP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMissense variant\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eTolerated\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eF/L\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eEdi-0, Oy-0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e1:18250605\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eA/C\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSNP\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMissense variant\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eTolerated\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003eE/A\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003c/div\u003e"},{"header":"Discussion","content":"\u003cp\u003eThere has been a longstanding interest in understanding the link between genetic and phenotypic variation in natural populations. This insight is crucial for identifying the genetic basis of adaptation and discovering naturally occurring alleles that influence various traits. The root system is vital to plant growth and productivity. Therefore, it is necessary to comprehend the genetic basis of natural variation in this particular trait [30].\u003c/p\u003e \u003cp\u003eOne approach to identify genes responsible for natural variations in complex traits, such as root architecture, is to link genetic and phenotypic differences using recombinant inbred lines. In the case of MAGIC lines, there are several parental accessions and additional recombination generations [17]. Although only 19 accessions were used to establish the MAGIC recombinant inbred lines, they still capture a significant portion of the common genetic variation present in Arabidopsis [17]. In this work, we evaluated five root traits: PR length, LR and AR length and number; we observed a wide range of variations in phenotype among the MAGIC lines for all the measured traits and a positive correlation between the length of PR and the number of LR was detected. It has previously been reported that there is no correlation between the length of the primary root (PR) and the number of lateral roots in \u003cem\u003eArabidopsis\u003c/em\u003e natural accessions [31]. However, we have observed the opposite trend and believe as the lateral roots emerge from the PR, longer PRs may indicate more physical space for lateral root initiation.\u003c/p\u003e \u003cp\u003eQTL mapping revealed a significant region on chromosome 1 associated with ARN. ARs originate post-embryonically from aerial parts such as stems or hypocotyls, and they are induced by many environmental and physiological stresses to expand absorbing areas or enhance resistance to adversity [32, 33]. ARs are used in asexual propagation, which results in difficulty in achieving in many crops. Understanding its molecular mechanisms is essential for such species [34, 35]. AR development is a complex process controlled by diverse factors such as phytohormones, particularly auxin. The critical step in ARs formation is the development of AR primordia, which begins with the auxin synthesis and accumulation [36]. According to the repositories AraPheno and AraGWAS, no data exists about the genetic associations between distinct loci and AR development. In this work, we detected 316 genes associated with ARN, some associated with auxin and GA synthesis, signaling and transport. It has been discovered that genes encoding proteins associated with gibberellin biosynthesis and signaling and auxin homeostasis are involved in forming AR [37].\u003c/p\u003e \u003cp\u003eAuxin and TOR work together to regulate ARs formation. TOR is a protein kinase and a master regulator that integrates energy, nutrients, stress, and hormone signaling to promote cell growth and proliferation [38]. When \u003cem\u003eArabidopsis\u003c/em\u003e roots are treated with TOR inhibitors, the formation of ARs is significantly slower. However, the overexpression of the auxin receptor TIR1 can partially restore the formation of ARs that were inhibited by TOR inhibitors. This suggests that there may be a connection between the TOR and auxin signaling mechanisms during the ARs formation process [22].\u003c/p\u003e \u003cp\u003eBesides, we identified a nucleotide in-frame deletion in the kinase domain of TOR from the parental accession Rsch-4. This deletion might contribute to natural variation in AR.\u003c/p\u003e \u003cp\u003eMoreover, the gain-of-function mutants \u003cem\u003ecrane-2\u003c/em\u003e, which harbor mutations in domain II of IAA18 that confer resistance to degradation by the proteasome, was also shown to be affected in AR initiation [24]. We observed that IAA18 has several missense variants in the AUX/IAA domain and only one deleterious variant in Zu-0 that leads to an amino acid change. On the other hand, \u003cem\u003ePLT2\u003c/em\u003e is a crucial gene that plays a significant role in maintaining the identity of the quiescent center (QC), root apical meristem (RAM) maintenance, and activating the gene expression of polar auxin transports, biosynthesis, and response genes [39, 40]. It has also been associated with AR initiation [26]. We detected that some parental accessions of MAGIC lines have an in-frame deletion that could shift the gene open reading frame of \u003cem\u003ePLT2\u003c/em\u003e.\u003c/p\u003e \u003cp\u003eAdditionally, for the polymorphism analysis, we selected a gene that encodes for a Hydroxyproline-rich glycoprotein family protein that displays differential SNPs in accessions with contrasting AR phenotypes. These accessions come from a study where the variation in the number of ARs formed on seedling hypocotyls in response to auxin was evaluated in 18 ecotypes [29]. Mt-0, Wil-2, and An-1 are accessions with low ARs formed, whereas Bur-0, En-2, Ler-0 and Edi-0 are accessions that display a high number of ARs formation after auxin treatment. We noticed that an SNP changes from proline to serine in a coding region in these accessions with high AR formation. The cross between Mt-o with Ha-S (accession with high capability of AR formation) shows a low proportion of high rooting segregants in the F2, suggesting a multigene control in AR formation [29].\u003c/p\u003e \u003cp\u003eRegarding GA regulation in AR formation, we noticed that GA2ox7 has six missense variants, two of which are deleterious in Oy-0 and Hi-0. Whose position is in the Diox-N domain, a highly conserved N-terminal region with 2-oxoglutarate/Fe (II)-dependent dioxygenase activity. It has been described that loss-of-function mutations of \u003cem\u003eGA REQUIRING 1 (GA1)\u003c/em\u003e and \u003cem\u003eGA5\u003c/em\u003e, which encode for the enzymes ENT-COPALYL DIPHOSPHATE SYNTHETASE 1 and GA 20-OXIDASE respectively, lead to a significant reduction in the number of ARs in both hypocotyl explants and excised leaves [37]. Likewise, it has been reported that treating WT plants with GA4 (1 \u0026micro;m) significantly inhibited adventitious rooting [27]. Similarly, transgenic plants with higher GA biosynthesis via overexpressing of GA20ox1 have significantly fewer ARs in stem cuttings due to the perturbation of polar auxin transport [27].\u003c/p\u003e"},{"header":"Conclusions","content":"\u003cp\u003eIn summary, in this study, we assessed various physical traits in the root structure of MAGIC lines and discovered a significant QTL on chromosome 1 that affects the number of AR. This QTL was found to map several genes related to phytohormones, including those involved in auxin and gibberellin signalling and homeostasis. We observed that some founder accessions displayed missense and in-frame deletions in these genes, which could lead to natural variation in AR development. Further research is required to fully understand the complex interaction between GA and auxin signalling and its role in the natural variation of AR development.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eFunding.\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis study was funded by the grant UNAM PAPIIT DGAPA IN214422 to UR. \u0026nbsp;This work was supported by UNAM Posdoctoral Program (POSDOC) to BALR.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthor Contributions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eUlises Rosas, Joshua Banta and Brenda Anabel L\u0026oacute;pez-Ruiz.contributed to the study\u0026apos;s conception and design. Material preparation, data collection and analysis were performed by Ulises Rosas, Joshua Banta, Perla Salazar-Hern\u0026aacute;ndez, Daniela Espinoza-Guti\u0026eacute;rrez, Andrea Alfaro and Brenda Anabel L\u0026oacute;pez-Ruiz.\u003c/p\u003e\n\u003cp\u003eThe first draft of the manuscript was written by Brenda Anabel L\u0026oacute;pez-Ruiz. Ulises Rosas and Joshua Banta commented on previous versions of the manuscript. All authors read and approved the final manuscript.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConflicts of interest/Competing interests:\u003c/strong\u003e The authors declare no conflict of interest.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eEthics approval:\u003c/strong\u003e NA\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConsent to participate:\u0026nbsp;\u003c/strong\u003eNA\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConsent for publication\u003c/strong\u003e: All authors have approved the manuscript and agree with its submission to Molecular Biology Reports.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAvailability of data and material\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eAll data generated or analyzed during this study are included in this published article and its supplementary information.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003ePetricka JJ, Winter CM, Benfey PN (2012) Control of \u003cem\u003eArabidopsis\u003c/em\u003e Root Development. 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Plant Cell 28:2937\u0026ndash;2951. https://doi.org/10.1105/tpc.16.00656\u003c/li\u003e\n\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"MAGIC lines, Arabidopsis thaliana, QTL mapping, adventitious roots, natural variation, root architecture","lastPublishedDoi":"10.21203/rs.3.rs-4432917/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-4432917/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eBackground\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe Multi-Parent Advanced Generation Inter-Cross (MAGIC) population is a powerful tool for dissecting the genetic architecture controlling natural variation in complex traits. In this work, the natural variation available in \u003cem\u003eArabidopsis thaliana \u003c/em\u003eMAGIC lines was evaluated by mapping quantitative trait loci (QTLs) for primary root length (PRL), lateral root number (LRN), lateral root length (LRL), adventitious root number (ARN) and adventitious root length (ARL).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eMethods and Results\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eWe analyzed the differences in the root structure of 139 MAGIC lines by measuring PRL, LRN, LRL, ARN and ARL. Through QTL mapping, we identified new potential genes that may be responsible for these traits. Furthermore, we detected single nucleotide polymorphisms (SNPs) in the coding regions of candidate genes in the founder accessions. We obtained a significant region on chromosome 1 associated with ARN. This region spans 316 genes, some of which are related to auxin and gibberellin signaling and homeostasis. We identified SNPs in the coding regions of these candidate genes in the founder accessions that could contribute to natural variation in the AR of the recombinant inbred lines. Additionally, we found a novel gene encoding a Hydroxyproline-rich glycoprotein family protein that displays differential SNPs in accessions with contrasting AR formation.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConclusions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe study found that natural variation in AR number could be explained by a significant QTL on chromosome 1 associated with genes related to auxin and gibberellin signaling and homeostasis. Some founder accessions showed missense and in-frame deletions in these genes, which could explain the observed differences in AR development.\u003c/p\u003e","manuscriptTitle":"QTL mapping using Arabidopsis thaliana MAGIC Lines identifies candidate genes controlling adventitious root development","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-05-30 19:26:10","doi":"10.21203/rs.3.rs-4432917/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"b0755a45-8714-424b-9c3b-a29136094f73","owner":[],"postedDate":"May 30th, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2024-11-13T09:09:32+00:00","versionOfRecord":[],"versionCreatedAt":"2024-05-30 19:26:10","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-4432917","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-4432917","identity":"rs-4432917","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}