Genome-wide association and co-expression uncovered ZmMYB71 controls kernel starch content in maize

Abstract

Starch plays a crucial role as a storage component, greatly affecting the grain yield and quality of maize ( L.). To meet future demands, it is essential to understand the genetic basis of the natural variation in kernel starch content (SC) for maize breeding. Through a genome-wide association study (GWAS), we identified 84 and 96 loci associated with kernel SC within two years that overlapped with 185 candidate genes. The candidate gene , which encodes a myeloblastosis (MYB)-related transcription factor, exhibited the highest co-expression frequency with starch synthesis genes. We demonstrated that ZmMYB71 functions as a nuclear located transcription repressor, and the kernel SC of mutants increased by over 2.32%, with a minor effect on amylose content or 100-grain weight. , , and showed up-regulation in mutants by 1.56-, 1.45- and 1.32-fold, respectively, consistently with the RNA sequencing result; their promoter activities may be directly repressed by ZmMYB71 through the GATATC and TTAGGG motifs. Furthermore, the elite haplotype Hap1 was present in over 55% of the high-starch maize sub-populations BSSS and PB but only in 7.14% of the low-starch sub-population PA. Comparing the Hap1 haplotype frequencies in different breeding stages found that its frequency in the inbred group released after 2010 is significantly higher at 40.28%, in contrast to 28.57% and 27.94% in the years 1980 and 1990, and 2000, respectively. The finding provides valuable information on the natural variation in SC of the maize kernel and suggests that ZmMYB71 serves as a negative regulator with the potential to be used to improve SC in the kernels.