Fine mapping and candidate gene analysis of qKW7b , a major QTL for kernel width in maize

Kernel width (KW) is a key determinant of kernel weight and an important selection trait during the maize domestication and improvement. KW is a complex quantitative trait that is controlled by many quantitative trait loci (QTL) with minor effects, but the underlying genes for KW using natural variation remain rarely reported in maize. In this study, using advanced backcross populations from the cross of Huangzaosi (HZS, recurrent parent) × YE478 (donor parent), a major QTL responsible for KW previously reported, qKW7 , were divided into two tightly linked loci with opposite genetic effects, qKW7a and qKW7b . Further, a near isogenic line (NIL) of qKW7b YE478 with the HZS background was developed by molecular marker-assisted selection (MAS). Using a large segregation population developed from the NIL and its recurrent parent, qKW7b was fine mapped to a physical interval of 59 kb. By the assembled genome collinearity analysis in the qKW7b region, redundant genomic structural variations which included insertions, deletions, and inversions were determined. A putative zinc finger homeodomain transcription factor gene, Zm00001d020460 , was supposed to be the candidate gene responsible for qKW7b . Quantitative real-time PCR showed that Zm00001d020460 was differently expressed during early kernel development between the qKW7b NILs, indicating that this gene might be a causal gene of qKW7b. This result enriches our knowledge of the genetic basis for KW and paves a new way to efficiently improve KW through functional marker in maize germplasm.