Insights into callus induction by GWAS and development of SNP marker for donor plants selection in oil palm tissue culture

Abstract

Abstract Efficient callus induction is vital for successful tissue culture of oil palm, yet identifying genomic loci and markers for early identification of specific individuals with high potential of callus induction is still unclear. In this study, callus induction rate at 1-, 2-, and 3-months after inoculation (C1, C2 and C3) of 198 oil palm individuals were investigated as phenotypes, and totally 11,475,258 high quality single nucleotide polymorphisms (SNPs) were generated by resequencing as genotypes. Genome-wide association study (GWAS) was performed accordingly using these phenotypes and genotypes. Correlation analysis revealed a positive association of C1 with both C2 (R = 0.81) and C3 (R = 0.50). Therefore, only SNPs in C1 were identified to develop markers for screening individuals capable of callus induction at early stage. A total of 21 significant SNPs were observed in C1, in which six of them on chromosome 12 (Chr12) potentially linked to callus induction were further revealed by the linkage disequilibrium (LD) block analysis. Totally 13 SNP markers from these six loci were tested accordingly and only the marker C-12 at locus Chr12_12704856 effectively distinguishing the GG allele, which showed the highest probability (69%) of callus induction. Moreover, the method for rapid SNP variant detection without electrophoresis was established via qPCR analysis. Notably, individuals S30 and S46, carrying the GG allele, consistently showed high callus induction rates (> 50%) from C1 to C3. Our findings facilitated marker-assisted selection for specific individuals with high potential of callus induction, thereby providing valuable assistance for donor plants selection in oil palm tissue culture.