GWAS determined genetic loci associated with callus induction in oil palm tissue culture

Abstract Efficient callus induction is vital for successful oil palm tissue culture, yet identifying genomic loci and markers for early detection of genotypes with high potential of callus induction remains unclear. In this study, immature male inflorescences from 198 oil palm accessions (dura, tenera and pisifera) were used as explants for tissue culture. Callus induction rates were collected at one-, two- and three-months after inoculation (C1, C2 and C3) as phenotypes. Resequencing generated 11,475,258 high quality single nucleotide polymorphisms (SNPs) as genotypes. GWAS was then performed and correlation analysis revealed a positive association of C1 with both C2 (R=0.81) and C3 (R=0.50), indicating that C1 could be used as the major phenotype for callus induction rate. Therefore, only significant SNPs in C1 (including samples with and without callus) were identified to develop markers for screeningindividuals with high potential of callus induction. Among 21 significant SNPs (P ≤ 0.05) in C1, LD block analysis revealed 6 SNPs on chromosome 12 (Chr12) potentially linked to callus formation. Subsequently, 13 SNP markers were identified from these loci and electrophoresis results showed that marker C-12 at locus Chr12_12704856 can be used effectively to distinguish the GG allele, which showed the highest probability (69%) of callus induction. Furthermore, a rapid SNP variant detection method without electrophoresis was established via qPCR-based melting curve analysis. Our findings facilitated marker-assisted selection for specific palms with high potential of callus induction using immature male inflorescence as explant, aiding ortet palm selection in oil palm tissue culture.