GWAS and QTL Analysis of Anthocyanin Pigmentation in Sorghum

Many plants respond to stresses, such as low temperature, disease, and strong light by producing anthocyanin. In sorghum (Sorghum bicolor), anthocyanin pigmentation is observed on the leaf sheath or lemma, but the underlying genes have not been identified. Here, we tried to search quickly and correctly for the candidate locus related to anthocyanin pigmentation by GWAS and QTL analysis.

We used genome-wide SNPs markers derived from RAD-seq and sorghum inbred lines from ICRISAT, NARO, and USDA for GWAS, and recombinant inbred lines derived from the reference line, BTx623 and Japanese landrace, NOG for QTL analysis. We detected the most significant peak for anthocyanin pigmentation on chromosome 6 by GWAS and two significant QTLs on chromosome 4 (qChr4) and 6 (qChr6) by QTL analysis. We found qChr4 was located physically near Tannin1, a WD40 regulator (~0.5 Mb region). The detected peaks on chromosome 6 by GWAS and QTL analysis are almost the same region, suggesting that we detect the same locus. The most significant SNP on chromosome 6 detected by GWAS was found in the ~10kb upstream of a putative basic helix-loop-helix (bHLH) transcription factor, and a sorghum co-ortholog of rice OSB1 and OSB2 which have been reported as factors related to anthocyanin biosynthesis pathway. This result suggests that qChr6 is likely to be related to anthocyanin pigmentation in sorghum.

Future study about qChr6 may shed light on the molecular mechanism underlying anthocyanin pigmentation in sorghum.