QTL Mapping of Kernel Traits and Validation of a Major QTL for Kernel Length-Width Ratio Using SNP and Bulked Segregant Analysis in Wheat

Abstract

One RIL population derived from the cross between Dalibao and BYL8 was used to examine the phenotypes of kernel-related traits in four different environments. Six important kernel traits, kernel length (KL), kernel width (KW), kernel perimeter (KP), kernel area (KA), kernel length/width ratio (KLW), and thousand-kernel weight (TKW) were evaluated in Yangling, Shaanxi Province, China (2016 and 2017), Nanyang, Henan Province, China (2017) and Suqian, Jiangsu Province, China (2017). A genetic linkage map was constructed using 205 SSR markers, and a total of 21 significant QTLs for KL, KW, KP, KA, KLW and TKW were located on 10 of the 21 wheat chromosomes, including 1A, 1B, 2A, 2B, 2D, 3D, 4D, 5A, 5B, and 7D, with a single QTL in different environments explaining 3.495-30.130% of the phenotypic variation. There were four loci for KLW, five for KA, five for KL, three for KP, two for KW, and two for TKW among the detected QTLs. We used BSA + 660 K gene chip technology to reveal the positions of major novel QTLs for KLW. A total of 670 out of 5285 polymorphic SNPs were detected on chromosome 2A. The SNPs in 2A are most likely related to the major QTL, and there may be minor QTLs on 5B, 7A, 3A and 4B. SSR markers were developed to verify the chromosome region associated with KLW. A linkage map was constructed with 7 SSR markers, and a major effect QTL was identified within a 21.55 cM interval, corresponding to a physical interval of 10.8 Mb in the Chinese Spring RefSeq v1.0 sequence. This study can provide useful information for subsequent construction of fine mapping and marker-assisted selection breeding.

Figure 1

Histograms of distributions for wheat kernel related traits in Dalibao/BYL8 RIL population. TKW thousand kernel weight (a), KA kernel area (b), KP kernel perimeter (c), KLW kernel length/width ratio (d), KL kernel length (e), KW kernel width (f) E1 Yangling 2016–2017, E2 Yangling 2017–2018, E3 Nanyang 2017–2018, E4 Suqian 2017–2018.

Figure 2

Locations of QTLs for kernel related trait.

Figure 3

A Distribution of polymorphic SNPs in each chromosome identified by the 660 K SNP array and corresponding percentages. B Positions of SNPs in chromosome 2A based on the 660 K SNP. C LOD Score and genetic linkage map.