Genome-Wide Association Study and Candidate Gene Mining of Husk Number Trait in Maize

Husk number (HN) trait is an important factor affecting maize kernel dehydration rate after the physiological maturity stage. In general, a reasonable reduction in HN is a key target sought for breeding maize varieties that are suitable for mechanized harvesting. In this study, the HN of a maize natural population panel containing 232 inbred lines was analyzed, and the results showed a broad-sense heritability of 0.89, along with a wide range of phenotypic variation. With the best linear unbiased prediction (BLUP) values across the three environments, a genome-wide association study (GWAS) was conducted using 995,106 single-nucleotide polymorphism (SNP) markers. A total of 16 SNPs significantly associated with HN were identified by the mixed linear model and general linear model using the TASSEL 5.0 software program. A local linkage disequilibrium (LD) study was performed to infer the candidate interval around the lead SNPs. A total of 19 functionally annotated genes were identified. The candidate genes were divided into multiple functional types, including transcriptional regulation, signal transduction, and metabolic and cellular transport. These results provide hints for the understanding of the genetic basis of the HN trait and for the breeding of maize varieties with fewer HN and faster dehydration rate.