Meta-analysis of the quantitative trait loci associated with agronomic traits, fertility restoration, disease resistance, and seed quality traits in pigeonpea (Cajanus cajan L.)

Abstract A meta-analysis of quantitative trait loci (QTLs) associated with agronomic traits, fertility restoration, disease resistance, and seed quality traits, was conducted for the first time in pigeonpea. Data on 498 QTLs was collected from 9 linkage mapping studies (involving 21 bi-parental populations). Of these 498, 203 QTLs were projected onto "PigeonPea_ConsensusMap_2022," saturated with 10,522 markers, which resulted in the prediction of 34 meta-QTLs (MQTLs). The average confidence interval (CI) of these MQTLs (2.54 cM) was 3.37-times lower than the CI of the initial QTLs (8.56 cM). Of the 34 MQTLs, 12 high-confidence MQTLs with smaller CI (≤ 5 cM) and a greater number of initial QTLs (≥ 5) were utilized to extract 2,255 gene models, of which 105 were believed to be associated with different traits. The comparison of physical coordinates of MQTLs and marker trait associations reported from genome-wide association studies enabled the validation of eight MQTLs. Furthermore, synteny and ortho-MQTL analysis among pigeonpea and four related legumes crops such as chickpea, pea, cowpea, and french bean led to the identification 117 orthologous genes from 20 MQTL regions. Flanking markers of identified MQTLs can be employed for MQTL-assisted breeding as well as to improve the prediction accuracy of genomic selection in pigeonpea. Furthermore, genes identified in this study could be potential targets for positional cloning and functional analysis to unveil the molecular mechanisms underlying the target traits.