A major quantitative trait locus for wheat total root length associated with precipitation distribution

Huangxin Chen; Jiatai Wei; Rong Tian; Zhaoyong Zeng; Huaping Tang; Yanlin Liu; Qiang Xu; Mei Deng; Qiantao Jiang; Guoyue Chen; Yaxi Liu; Wei Li; Pengfei Qi; Yunfeng Jiang; Yun Jiang; Liwei Tang; Yuming Wei; Youliang Zheng; Xiujin Lan; Jian Ma

doi:10.3389/fpls.2022.995183

A major quantitative trait locus for wheat total root length associated with precipitation distribution

Front Plant Sci. 2022 Aug 24:13:995183. doi: 10.3389/fpls.2022.995183. eCollection 2022.

Authors

Huangxin Chen^{1

2}, Jiatai Wei², Rong Tian², Zhaoyong Zeng², Huaping Tang², Yanlin Liu², Qiang Xu², Mei Deng², Qiantao Jiang^{1

2}, Guoyue Chen^{1

2}, Yaxi Liu^{1

2}, Wei Li³, Pengfei Qi^{1

2}, Yunfeng Jiang^{1

2}, Yun Jiang⁴, Liwei Tang⁵, Yuming Wei^{1

2}, Youliang Zheng², Xiujin Lan^{1

2}, Jian Ma^{1

2}

Affiliations

¹ State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
² Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
³ College of Agronomy, Sichuan Agricultural University, Chengdu, China.
⁴ Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu, China.
⁵ Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China.

Abstract

Optimizing root system architecture (RSA) allows crops to better capture water and nutrients and adapt to harsh environment. Parental reproductive environment (PRE) has been reported to significantly affect growth and development throughout the life cycle of the next generation. In this study, 10 RSA-related traits were evaluated in seedling stage from five independent hydroponic tests using seeds harvested from five different PREs. Based on the Wheat55K SNP array-based genetic map, quantitative trait loci (QTL) for these traits were detected in a recombinant inbred line population. Twenty-eight putative QTL for RSA-related traits were detected, covering thirteen chromosomal regions. A major QTL, QTrl.sicau-2SY-4D for total root length (TRL), which was likely independent of PREs, explained 15.81-38.48% of phenotypic variations and was located at 14.96-19.59 Mb on chromosome arm 4DS. Interestingly, it showed pleiotropic effects on TRL, root area, root volume, root forks, root dry weight, and shoot dry weight. The functional marker KASP-Rht-D1 for Rht-D1 was used to genotype 2SY population and remapping QTL for TRL showed that QTrl.sicau-2SY-4D was not linked to Rht-D1. The kompetitive allele-specific PCR (KASP) marker, KASP-AX-110527441 linked to this major QTL, was developed and used to successfully validate its effect in three different genetic populations. Further analysis suggested that the positive allele at QTrl.sicau-2SY-4D was mainly utilized in wheat breeding of northwest China where precipitation was significantly lower, indicating that wheat requires longer TRL to capture water and nutrients in arid or semi-arid regions due to deficient precipitation. Additionally, four genes (TraesCS4D03G0059800, TraesCS4D03G0057800, TraesCS4D03G0064000, and TraesCS4D03G0064400) possibly related to root development were predicted in physical interval of QTrl.sicau-2SY-4D. Taken together, these results enrich our understanding on the genetic basis of RSA and provide a potentially valuable TRL QTL for wheat breeding.

Keywords: Wheat55K SNP array; parental reproductive environment; precipitation; quantitative trait loci; total root length; wheat.