Integrating a genome-wide association study with transcriptomic analysis to detect genes controlling grain drying rate in maize (Zea may, L.)

Abstract

Candidate genes on grain drying rate (GDR) were identified, and drying molecular mechanism of grain was explored by integrating genome-wide association with transcriptomic analysis in maize. Grain drying rate (GDR) is a key determinant of grain moisture at harvest. Here, a genome-wide association study (GWAS) of 309 inbred maize lines was used to identify single-nucleotide polymorphisms (SNPs) associated with drying rates of grain, cob and bract. Out of 217,933 SNPs, seven significant SNPs were repeatedly identified in four environments (P < 10^-4). Based on genomic position of significant SNPs, six candidate genes were identified, one of which (Zm00001d047468) was verified by transcriptomic data between inbred lines with high and low GDR, indicating stable and reliable correlation with GDR. To further detect more genes correlated with GDR and explore drying molecular mechanism of grain, expression profile of all GWAS-identified genes (4941) detected from different environments, tissues and developmental stage was evaluated by transcriptomic data of six inbred lines with high or low GDR. Results revealed 162 genes exhibit up-regulated expression and another 123 down-regulated in three higher-GDR inbred lines. Based on GO enrichment, 162 up-regulated genes were significantly enriched into grain primary metabolic process, nitrogen compound metabolic process and macromolecule metabolic process (P < 0.05), which indicated grain filling imposes notable influence on GDR before and after physiological maturity. Our results lay foundation in accelerating development of higher-GDR maize germplasm through marker-assisted selection and clarifying genetic mechanism of GDR in maize.