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Journal of Integrative Agriculture  2022, Vol. 21 Issue (11): 3131-3147    DOI: 10.1016/j.jia.2022.08.085
Special Issue: 麦类遗传育种合辑Triticeae Crops Genetics · Breeding · Germplasm Resources
Crop Science Advanced Online Publication | Current Issue | Archive | Adv Search |
Identification and validation of novel loci associated with wheat quality through a genome-wide association study

PU Zhi-en1*, YE Xue-ling3, 4*, LI Yang1, SHI Bing-xin1, GUO Zhu1, DAI Shou-fen2, MA Jian2, LIU Ze-hou4, JIANG Yun-feng2, LI Wei1, JIANG Qian-tao2, CHEN Guo-yue2, WEI Yu-ming2, ZHENG You-liang2 #br#

1 College of Agronomy, Sichuan Agricultural University, Chengdu 611130, P.R.China

2 Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, P.R.China

3 Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs/College of Food and Biological Engineering, Chengdu University, Chengdu 610106, P.R.China

4 Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, P.R.China

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摘要  了解小麦品质相关性状的遗传基础有助于对小麦品质进行改良,本实验测定了多环境下236份小麦种质资源(包括 160 个栽培品种和76个地方品种)的蛋白质含量(GPC)、淀粉含量(GSC)和湿面筋含量(WGC),并使用 55K小麦芯片进行了混合线性模型 (MLM)分析。结果共鉴定了 12 个稳定的 QTL/SNP,与GPC、GSC和WGC 相关的位点分别有3个、7个和2个 QTL,它们分别位于1B、1D、2A、2B、2D、3B、3D、5D 和 7D 染色体上;表型变异解释 (PVE) 范围从4.2 至10.7%。与之前报道的 QTL/基因相比,5 个 QTL(QGsc.sicau-1BLQGsc.sicau-1DSQGsc.sicau-2DL.1QGsc.sicau-2DL.2QWgc.sicau-5DL)是潜在的新位点。本实验着重关注了位于5D染色体上与湿面筋浓度相关的稳定QTL,并成功开发了SNP AX-108770574AX-108791420 两个KASP 标记。其中AX-108770574中含有A-等位基因和AX-108791420中含有T-等位基因的品种表型显着高于(P<0.01)含有湿面筋浓度G-等位基因或C-等位基因的地方品种,表明开发的KASP 标记可用于分子育种,改良小麦品质。

Abstract  Understanding the genetic basis of quality-related traits contributes to the improvement of grain protein concentration (GPC), grain starch concentration (GSC), and wet gluten concentration (WGC) in wheat, a genome-wide association study (GWAS) based on a mixed linear model (MLM) was performed on the 236 wheat accessions including 160 cultivars and 76 landraces using 55K single nucleotide polymorphism (SNP) array in multiple environments. A total of twelve stable QTL/SNPs were identified to control different quality traits in this populations at least two environments under stripe rust stress; three, seven and two QTLs associated with GPC, GSC, and WGC were characterized respectively and located on chromosomes 1B, 1D, 2A, 2B, 2D, 3B, 3D, 5D, and 7D with the range of phenotypic variation explained (PVE) from 4.2 to 10.7%. Compared with the previously reported QTLs/genes, five QTLs (QGsc.sicau-1BL, QGsc.sicau-1DS, QGsc.sicau-2DL.1, QGsc.sicau-2DL.2, QWgc.sicau-5DL) were potentially novel. KASP markers for SNPs AX-108770574 and AX-108791420 on chromosome on 5D associated with wet gluten concentration were successfully developed. Phenotype of the cultivars containing the A-allele in AX-108770574 and T-allele in AX-108791420 were extremely significantly (P<0.01) higher than that of the landraces containing the G-allele or C-allele of wet gluten concentration in each of the environments. The developed and validated KASP markers could be utilized in molecular breeding aiming to improve the quality in wheat.
Keywords:  cultivars        landraces        grain protein concentration (GPC)        grain starch concentration (GSC)        wet gluten concentration (WGC)        55K SNP       validation  
Received: 25 April 2021   Accepted: 01 July 2021
Fund: This work was supported by the National Key Research and Development Program of China (2017YFD0100900, 2016YFD0102000 and 2016YFD0100100), the International Science and Technology Cooperation and Exchanges Programs of Science and Technology Department of Sichuan Province, China (2019YFH0063), and the Sichuan Science and Technology Program, China (2022ZDZX0014).  
About author:  Correspondence ZHENG You-liang, Tel/Fax: +86-28-86290909, E-mail: * These authors contributed equally to this study.

Cite this article: 

PU Zhi-en, YE Xue-ling, LI Yang, SHI Bing-xin, GUO Zhu, DAI Shou-fen, MA Jian, LIU Ze-hou, JIANG Yun-feng, LI Wei, JIANG Qian-tao, CHEN Guo-yue, WEI Yu-ming, ZHENG You-liang. 2022. Identification and validation of novel loci associated with wheat quality through a genome-wide association study. Journal of Integrative Agriculture, 21(11): 3131-3147.

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Characterization of wheat monogenic lines with known Sr genes and wheat cultivars for resistance to three new races of Puccinia graminis f. sp. tritici in China [J]. >Journal of Integrative Agriculture, 2023, 22(6): 1740-1749.

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[3] PAN Wen-jing, HAN Xue, HUANG Shi-yu, YU Jing-yao, ZHAO Ying, QU Ke-xin, ZHANG Ze-xin, YIN Zhen-gong, QI Hui-dong, YU Guo-long, ZHANG Yong, XIN Da-wei, ZHU Rong-sheng, LIU Chun-yan, WU Xiao-xia, JIANG Hong-wei, HU Zhen-bang, ZUO Yu-hu, CHEN Qing-shan, QI Zhao-ming. Identification of candidate genes related to soluble sugar contents in soybean seeds using multiple genetic analyses[J]. >Journal of Integrative Agriculture, 2022, 21(7): 1886-1902.
[4] DING Pu-yang, MO Zi-qiang, TANG Hua-ping, MU Yang, DENG Mei, JIANG Qian-tao, LIU Ya-xi, CHEN Guang-deng, CHEN Guo-yue, WANG Ji-rui, LI Wei, QI Peng-fei, JIANG Yun-feng, KANG Hou-yang, YAN Gui-jun, Wei Yu-ming, ZHENG You-liang, LAN Xiu-jin, MA Jian. A major and stable QTL for wheat spikelet number per spike validated in different genetic backgrounds[J]. >Journal of Integrative Agriculture, 2022, 21(6): 1551-1562.
[5] ZHANG Li-xin, LIU Wei, Mesfin Tsegaw, XU Xin, QI Yan-ping, Enoch Sapey, LIU Lu-ping, WU Ting-ting, SUN Shi, HAN Tian-fu. Principles and practices of the photo-thermal adaptability improvement in soybean[J]. >Journal of Integrative Agriculture, 2020, 19(2): 295-310.
[6] HUANG Cheng-dong, LIU Quan-qing, LI Xiao-lin, ZHANG Chao-chun. Effect of intercropping on maize grain yield and yield components[J]. >Journal of Integrative Agriculture, 2019, 18(8): 1690-1700.
[7] ZHOU Liang, MU Tai-hua, MA Meng-mei, ZHANG Ruo-fang, SUN Qing-hua, XU Yan-wen. Nutritional evaluation of different cultivars of potatoes (Solanum tuberosum L.) from China by grey relational analysis (GRA) and its application in potato steamed bread making[J]. >Journal of Integrative Agriculture, 2019, 18(1): 231-245.
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[9] CHANG Li-fang, LI Hui-hui, WU Xiao-yang, LU Yu-qing, ZHANG Jin-peng, YANG Xin-ming, LI Xiu-quan, LIU Wei-hua, LI Li-hui. Genetic characteristics of a wheat founder parent and a widely planted cultivar derived from the same cross[J]. >Journal of Integrative Agriculture, 2018, 17(04): 775-785.
[10] HE Ying-bin, ZHOU Yang-fan, CAI Wei-min, WANG Zhuo-zhuo, DUAN Ding-ding, LUO Shan-jun, CHEN Jing-zhu. Using a process-oriented methodology to precisely evaluate temperature suitability for potato growth in China using GIS[J]. >Journal of Integrative Agriculture, 2017, 16(07): 1520-1529.
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[13] WANG Yun-qi, XI Wen-xing, WANG Zhi-min, WANG Bin, XU Xue-xin, HAN Mei-kun, ZHOU Shun-li, ZHANG Ying-hua. Contribution of ear photosynthesis to grain yield under rainfed and irrigation conditions for winter wheat cultivars released in the past 30 years in North China Plain[J]. >Journal of Integrative Agriculture, 2016, 15(10): 2247-2256.
[14] Jan Bocianowski, Piotr Szulc, Anna Tratwal, Kamila Nowosad, Dariusz Piesik. The influence of potassium to mineral fertilizers on the maize health[J]. >Journal of Integrative Agriculture, 2016, 15(06): 1286-1292.
[15] SONG Wen-en, CHEN Shi-bao, LIU Ji-fang, CHEN Li, SONG Ning-ning, LI Ning, LIU Bin. Variation of Cd concentration in various rice cultivars and derivation of cadmium toxicity thresholds for paddy soil by species-sensitivity distribution[J]. >Journal of Integrative Agriculture, 2015, 14(9): 1845-1854.
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