Data_Sheet_1_A major quantitative trait locus for wheat total root length associated with precipitation distribution.xlsx

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.

优化根系构型（Root System Architecture, RSA）可帮助作物更好地获取水分与养分，并适应逆境环境。已有研究表明，亲本生殖环境（Parental Reproductive Environment, PRE）可显著影响子代整个生命周期的生长发育进程。本研究利用5种不同亲本生殖环境下收获的种子，通过5组独立的水培试验，对苗期10个与根系构型相关的性状进行了表型鉴定。基于小麦55K单核苷酸多态性（Single Nucleotide Polymorphism, SNP）芯片构建的遗传图谱，本研究在重组自交系（Recombinant Inbred Line, RIL）群体中检测到上述性状的定量性状位点（Quantitative Trait Locus, QTL）。共鉴定得到28个与根系构型相关性状的候选QTL，覆盖13个染色体区域。其中，与总根长（Total Root Length, TRL）相关的主效QTL QTrl.sicau-2SY-4D不受亲本生殖环境影响，可解释15.81%~38.48%的表型变异，定位于4DS染色体臂的14.96~19.59 Mb区间内。有趣的是，该QTL对总根长、根表面积、根体积、根分叉数、根干重及地上部干重均表现出多效性作用。利用针对Rht-D1的功能标记KASP-Rht-D1对2SY群体进行基因型分型，并重定位总根长的QTL，结果显示QTrl.sicau-2SY-4D与Rht-D1不存在连锁关系。本研究开发了与该主效QTL连锁的竞争等位基因特异性PCR（Kompetitive Allele-Specific PCR, KASP）标记KASP-AX-110527441，并在3个不同的遗传群体中成功验证了其效应。进一步分析显示，QTrl.sicau-2SY-4D的增效等位基因主要被应用于降水显著偏低的中国西北地区小麦育种中，这表明在降水匮乏的干旱或半干旱地区，小麦需要更长的总根长以获取水分与养分。此外，本研究在QTrl.sicau-2SY-4D的物理区间内预测到4个可能与根系发育相关的基因（TraesCS4D03G0059800、TraesCS4D03G0057800、TraesCS4D03G0064000、TraesCS4D03G0064400）。综上，本研究结果深化了人们对根系构型遗传基础的认识，并为小麦育种提供了一个具有潜在应用价值的总根长QTL。