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Journal of Integrative Agriculture  2023, Vol. 22 Issue (9): 2617-2631    DOI: 10.1016/j.jia.2023.04.017
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Dissecting the genetic basis of grain color and pre-harvest sprouting resistance in common wheat by association analysis

YAN Sheng-nan*, YU Zhao-yu*, GAO Wei, WANG Xu-yang, CAO Jia-jia, LU Jie, MA Chuan-xi, CHANG Cheng#, ZHANG Hai-ping#

Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Affairs/College of Agronomy, Anhui Agricultural University, Hefei 230036, P.R.China
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摘要  

收获前穗发芽对小麦的品质和产量产生不利影响。籽粒颜色与小麦穗发芽抗性密切相关。然而,两者的遗传关系尚不清楚。本研究采用90K芯片对168个籽粒颜色和穗发芽抗性差异显著的小麦品种进行基因分型。基于混合线性模型的全基因组关联分析显示,67SNP标记(分布于29个位点与籽粒颜色显著关联,其中包括17个潜在的新位点,解释1.1-17.0%的表型变异。另外,100SNP标记(分布于54个位点)与穗发芽抗性显著关联,其中包括31个潜在的新位点,解释1.1-14.7%的表型变异。随后对籽粒颜色和穗发芽抗性的共定位位点Qgc.ahau-2B.3/Qphs.ahau-2B.42B和穗发芽抗性位点Qphs.ahau-5B.4(5B)分别开发CAPS标记2B-4485B-301利用171份中国微核心种质进一步验证了上述2CAPS标记与籽粒颜色和穗发芽抗性相关性。此外,基于小麦公共表达数据库、转录组测序数据以及基因等位变异分析结果,将编码谷氧还蛋白glutaredoxinTraesCS5B02G545100基因确定为Qphs.ahau-5B.4位点的潜在候选基因。进一步基于TraesCS5B02G545100基因CDS区域的SNP (T/C)变异,本文开发了一个CAPS标记CAPS-356利用411/红芒春21重组自交系(RILs)的高密度遗传连锁图谱检测到CAPS-356标记与一个新的穗发芽抗性QTL共定位,进一步支持了TraesCS5B02G545100Qphs.ahau-5B.4位点的潜在候选基因的假设。本文结果为Qphs.ahau-5B.4的图位克隆和白皮抗穗发芽品种的培育提供了有价值的参考信息。



Abstract  Pre-harvest sprouting (PHS) adversely affects wheat quality and yield, and grain color (GC) is associated with PHS resistance.  However, the genetic relationship between GC and PHS resistance remains unclear.  In this study, 168 wheat varieties (lines) with significant differences in GC and PHS resistance were genotyped using an Illumina 90K iSelect SNP array.  Genome-wide association study (GWAS) based on a mixed linear model showed that 67 marker-trait associations (MTAs) assigned to 29 loci, including 17 potentially novel loci, were significantly associated with GC, which explained 1.1–17.0% of the phenotypic variation.  In addition, 100 MTAs belonging to 54 loci, including 31 novel loci, were significantly associated with PHS resistance, which accounted for 1.1–14.7% of the phenotypic variation.  Subsequently, two cleaved amplified polymorphic sequences (CAPS) markers, 2B-448 on chromosome 2B and 5B-301 on chromosome 5B, were developed from the representative SNPs of the major common loci Qgc.ahau-2B.3/Qphs.ahau-2B.4 controlling GC/PHS resistance and PHS resistance locus Qphs.ahau-5B.4, respectively.  Further validation in 171 Chinese mini-core collections confirmed significant correlations of the two CAPS markers with GC and PHS resistance phenotypes under different environments (P<0.05).  Furthermore, the wheat public expression database, transcriptomic sequencing, and gene allelic variation analysis identified TraesCS5B02G545100, which encodes glutaredoxin, as a potential candidate gene linked to Qphs.ahau-5B.4.  The new CAPS marker CAPS-356 was then developed based on the SNP (T/C) in the coding sequences (CDS) region of TraesCS5B02G545100.  The high-density linkage map of the Jing 411/Hongmangchun 21 recombinant inbred lines (RILs) constructed based on specific locus amplified fragment sequencing markers showed that CAPS-356 collocated with a novel QTL for PHS resistance, supporting the role of TraesCS5B02G545100 as the potential candidate gene linked to Qphs.ahau-5B.4.  These results provide valuable information for the map-based cloning of Qphs.ahau-5B.4 and breeding of PHS resistant white-grained varieties.
Keywords:  common wheat        grain color        PHS resistance        GWAS        90K SNP        CAPS marker  
Received: 28 November 2022   Accepted: 16 March 2023
Fund: This work was supported by grants from the University Synergy Innovation Program of Anhui Province, China (GXXT-2021-058), the National Natural Science Foundation of China (Joint Fund Projects, U20A2033), the Natural Science Foundation of Anhui Province, China (2108085MC98), the Jiangsu Collaborative Innovation Center for Modern Crop Production, China (JCIC-MCP), the key scientific and technological breakthroughs of Anhui Province (2021d06050003), and the joint key project of improved wheat variety of Anhui Province, China (21803003).
About author:  YAN Sheng-nan, E-mail: 3104764960@qq.com; YU Zhao-yu, E-mail: 1053550020@qq.com; #Correspondence ZHANG Hai-ping, E-mail: zhhp20@163.com; CHANG Cheng, E-mail: changtgw@126.com * These authors contributed equally to this study.

Cite this article: 

YAN Sheng-nan, YU Zhao-yu, GAO Wei, WANG Xu-yang, CAO Jia-jia, LU Jie, MA Chuan-xi, CHANG Cheng, ZHANG Hai-ping. 2023. Dissecting the genetic basis of grain color and pre-harvest sprouting resistance in common wheat by association analysis. Journal of Integrative Agriculture, 22(9): 2617-2631.

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[1] SUN Yan, LI Yu-hua, ZHAO Chang-heng, TENG Jun, WANG Yong-hui , WANG Tian-qi, SHI Xiao-yuan, LIU Zi-wen, LI Hai-jing, WANG Ji-jing, WANG Wen-wen, NING Chao, WANG Chang-fa, ZHANG Qin. Genome-wide association study for numbers of vertebrae in Dezhou donkey population reveals new candidate genes[J]. >Journal of Integrative Agriculture, 2023, 22(10): 3159-3169.
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