Genome-wide association study of quality traits and starch pasting properties of maize kernels

BACKGROUND: Starch are the main nutritional components of maize (Zea mays L.), and starch pasting properties are widely used as essential indicators for quality estimation. Based on the previous studies, various genes related to pasting properties have been identified in maize. However, the loci underlying variations in starch pasting properties in maize inbred lines remain to be identified. RESULTS: To investigate the genetic architecture of these traits, the starch pasting properties were examined based on 292 maize inbred lines, which were genotyped with the MaizeSNP50 BeadChip composed of 55,126 evenly spaced, random SNPs. A genome-wide association study (GWAS) implemented in the software package FarmCPU was employed to identify genomic loci for the starch pasting properties. 48 SNPs were found to be associated with pasting properties. Moreover, 37 candidate genes were correlated with pasting properties. Among the candidate genes, GRMZM2G143646 and GRMZM2G166407 were associated with breakdown and final viscosity significantly, and both genes encode PPR (Pentatricopeptide repeat) protein. We used GWAS to explore candidate genes of maize starch pasting properties in this study. The identified candidate genes will be useful for further understanding of the genetic architecture of starch pasting properties in maize. CONCLUSION: This study showed a complex regulation network about maize quality trait and starch pasting properties. It may provide some useful markers for marker assisted selection and a basis for cloning the genes behind these SNPs.