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

• Published in: Molecular breeding Vol. 40; no. 7
• Main Authors: Tang, Bin, Li, Yongxiang, Mu, Zhisheng, Chen, Lin, Guo, Huanle, Chen, Zhihui, Li, Chunhui, Liu, Xuyang, Zhang, Dengfeng, Shi, Yunsu, Li, Yu, Wang, Tianyu
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01-07-2020; Springer Nature B.V
• Subjects: Biomedical and Life Sciences; Biotechnology; Collinearity; Corn; Domestication; Gene mapping; Genetic effects; Genomes; Germplasm; Homeobox; Inversions; Kernels; Life Sciences; Mapping; Marker-assisted selection; Markers; Molecular biology; Plant biology; Plant Genetics and Genomics; Plant Pathology; Plant Physiology; Plant Sciences; Population studies; Quantitative trait loci; Zinc finger proteins; Kernel width; Quantitative trait loci; Fine mapping; Maize; L; Near isogenic line
• ISSN: 1380-3743; 1572-9788
• DOI: 10.1007/s11032-020-01146-4

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.