Genetic Mapping by Integration of 55K SNP Array and KASP Markers Reveals Candidate Genes for Important Agronomic Traits in Hexaploid Wheat.

Hongchun Xiong,Jiayu Gu,Linshu Zhao,Yongdun Xie,Yuting Li,Shirong Zhao,Yuping Ding,Huijun Guo,Luxiang Liu

doi:10.3389/fpls.2021.628478

Abstract

Agronomic traits such as heading date (HD), plant height (PH), thousand grain weight (TGW), and spike length (SL) are important factors affecting wheat yield. In this study, we constructed a high-density genetic linkage map using the Wheat55K SNP Array to map quantitative trait loci (QTLs) for these traits in 207 recombinant inbred lines (RILs). A total of 37 QTLs were identified, including 9 QTLs for HD, 7 QTLs for PH, 12 QTLs for TGW, and 9 QTLs for SL, which explained 3.0–48.8% of the phenotypic variation. Kompetitive Allele Specific PCR (KASP) markers were developed based on sequencing data and used for validation of the stably detected QTLs on chromosomes 3A, 4B and 6A using 400 RILs. A QTL cluster on chromosome 4B for PH and TGW was delimited to a 0.8 Mb physical interval explaining 12.2–22.8% of the phenotypic variation. Gene annotations and analyses of SNP effects suggested that a gene encoding protein Photosynthesis Affected Mutant 68, which is essential for photosystem II assembly, is a candidate gene affecting PH and TGW. In addition, the QTL for HD on chromosome 3A was narrowed down to a 2.5 Mb interval, and a gene encoding an R3H domain-containing protein was speculated to be the causal gene influencing HD. The linked KASP markers developed in this study will be useful for marker-assisted selection in wheat breeding, and the candidate genes provide new insight into genetic study for those traits in wheat.

Highlights

Wheat (Triticum aestivum L.) is one of the most important cereal crops worldwide, providing a food source for 30% of the human population (Mayer et al, 2014)
In addition to heading date (HD), we found that plant height (PH), thousand grain weight (TGW), and spike length (SL) differed between eh1 and LX987; the values of these traits were significantly lower in eh1 than in LX987 from 2016–2018 (Table 1)
In the recombinant inbred lines (RILs) population, the percent variation in PH, TGW, and SL ranged from 9.1% to 14.4% from 2016–2018, and all three traits showed moderate h2 values ranging from 0.77 to 0.82 (Table 1)

Summary

Introduction

Wheat (Triticum aestivum L.) is one of the most important cereal crops worldwide, providing a food source for 30% of the human population (Mayer et al, 2014). Improving the yield potential of wheat is of great significance for meeting the food demand from an increasing population (Tshikunde et al, 2019). Agronomic traits such as heading date (HD), plant height (PH), thousand grain weight (TGW), and spike length (SL) are important factors affecting yield and always targeted by wheat breeders (Tshikunde et al, 2019). The Ppd genes for photoperiod responses in wheat are mainly located on chromosomes 2A, 2B, and 2D (Beales et al, 2007). The Eps genes were identified on chromosome 1Am in Triticum monococcum (Alvarez et al, 2016) and on long arm of chromosome 1D in hexaploid wheat (Zikhali et al, 2014)

Methods

Results

Discussion

Conclusion