GWAS-Based Identification of Markers and Candidate Genes for Seed Setting Rate and Seed Yield in Leymus chinensis

doi:10.11733/j.issn.1007-0435.2026.08.006

Acta Agrestia Sinica ›› 2026, Vol. 34 ›› Issue (8): 2814-2825.DOI: 10.11733/j.issn.1007-0435.2026.08.006

GWAS-Based Identification of Markers and Candidate Genes for Seed Setting Rate and Seed Yield in Leymus chinensis

WEI Jia¹, LIU Zhen-zhen¹, XU Xin-xin¹, MU Lin-lin², DONG Hong-bin³, GAO Qiu³, HONG Jun³, WANG Jian-li², MA Xi-qing¹

1. College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China;
2. Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang Province 150086, China;
3. National Animal Husbandry Service, Beijing 100125, China

Received:2026-03-17 Revised:2026-04-02 Published:2026-08-04

基于GWAS挖掘羊草结实率及种子产量相关标记与候选基因

魏佳¹, 刘真真¹, 徐欣欣¹, 牟林林², 董弘斌³, 高秋³, 洪军³, 王建丽², 马西青¹

1. 中国农业大学草业科学与技术学院, 北京 100193;
2. 黑龙江省农业科学院草业研究所, 黑龙江哈尔滨 150086;
3. 全国畜牧总站, 北京 100125

通讯作者: 马西青,E-mail:ma2016@cau.edu.cn
作者简介:魏佳(2002-),女,汉族,河南新蔡人,博士研究生,主要从事草类育种与种子科学研究,E-mail:weijia_ke@126.com

Abstract

Abstract: Leymus chinensis is the main dominant species in the eastern Eurasian steppe， with significant ecological and production values. However， its low seed yield severely restricts its practical application. To identify the associated loci for the seed yield traits of L. chinensis and to discover key molecular markers， this study used 300 diverse accessions of L. chinensis as materials， measured five yield traits including spikelet number per spike， floret number per spikelet， total number of florets， seed number per spikelet and seed setting rate， and conducted a genome-wide association analysis （GWAS） using a mixed linear model. The results showed that seed number per spikelet exhibited the highest coefficient of variation （CV=0.52）， indicating substantial potential for genetic improvement. The seed setting rate was regulated by an independent genetic mechanism and was the key limiting factor for seed yield. GWAS analysis combined with gene functional annotation identified 120 key single nucleotide polymorphisms （SNPs） and identified EZ1 and multiple MADS-box and WRKY transcription factors as key candidate genes regulating seed yield. Based on 14 SNPs significantly associated with seed setting rate， 8 elite alleles were obtained. Notably， the CT genotype at the Lc5Ns_97563471 locus exhibited a high mean seed setting rate of 66.6%. This study revealed the genetic characteristics of L. chinensis seed yield being regulated by multiple genes， and the identified candidate genes and elite SNP loci can serve as direct targets for molecular marker-assisted breeding.

Key words: Leymus chinensis, Seed setting rate, Seed yield, Genome-wide association study, Superior allelic variation

摘要： 羊草（Leymus chinensis）是欧亚草原东部的主要建群种，生态与生产价值显著，但种子产量低严重制约其产业化应用。为定位羊草种子产量性状的关联位点，挖掘关键分子标记，本研究以300份羊草种质为材料，测定小穗数、每穗小花数、总小花数、每穗种子数及结实率5个产量性状，采用混合线性模型进行全基因组关联分析（Genome wide association study， GWAS），挖掘和羊草结实率性状相关的分子标记和候选基因。结果表明，每穗种子数变异幅度最大（CV=0.52），遗传改良潜力高；结实率是种子产量的关键限制因子，受独立的遗传机制调控。GWAS分析结合基因功能注释共筛选出120个关键单核苷酸多态性（Single nucleotide polymorphism，SNP）位点，并鉴定到调控种子产量的关键候选基因EZ1及多个MADS-box，WRKY类等转录因子。基于14个与结实率显著关联的SNP位点，共获得8个优异等位变异，其中，位点Lc5Ns_97563471的CT基因型结实率均值高达66.6%。本研究揭示了羊草种子产量受多基因调控的遗传特性，获得的候选基因及优异SNP位点可直接用于分子标记辅助育种。

关键词: 羊草, 结实率, 种子产量, 全基因组关联分析, 优异等位变异

CLC Number:

Q949.71+4.2

WEI Jia, LIU Zhen-zhen, XU Xin-xin, MU Lin-lin, DONG Hong-bin, GAO Qiu, HONG Jun, WANG Jian-li, MA Xi-qing. GWAS-Based Identification of Markers and Candidate Genes for Seed Setting Rate and Seed Yield in Leymus chinensis[J]. Acta Agrestia Sinica, 2026, 34(8): 2814-2825.

魏佳, 刘真真, 徐欣欣, 牟林林, 董弘斌, 高秋, 洪军, 王建丽, 马西青. 基于GWAS挖掘羊草结实率及种子产量相关标记与候选基因[J]. 草地学报, 2026, 34(8): 2814-2825.

References

[1] HUANG Z H，ZHU J M，MU X J，et al. Pollen dispersion，pollen viability and pistil receptivity in Leymus chinensis[J]. Annals of Botany，2004，93（3）：295-301
[2] WANG J F，DONG D，ZHANG R，et al. Comprehensive evaluation of seed setting traits in 100Leymus chinensis germplasms from different regions[J]. Chinese Journal of Grassland，2025，47（10）：11-21王介繁，董笛，张然，等. 不同区域100份羊草种质结实性状的综合评价[J]. 中国草地学报，2025，47（10）：11-21
[3] LI Q，ZHANG Q F，CHENG L Q，et al. Progress of molecular biology of stress tolerance in sheepgrass[J]. Journal of Grassland and Forage Science，2018（6）：7-10李倩，张庆分，程丽琴，等. 羊草耐逆的分子生物学研究进展[J]. 草学，2018（6）：7-10
[4] SONG J M，CHU L S，LI H Y，et al. Research on the quantitative characteristics dynamics of reproductive ramets of Leymus chinensis populations under different habitats in Songnen Plain[J]. Acta Agrestia Sinica，2025，33（11）：3690-3697宋家敏，初丽爽，李海燕，等. 松嫩平原不同生境条件下羊草种群生殖株数量特征动态研究[J]. 草地学报，2025，33（11）：3690-3697
[5] YANG S，MU C S，LIN J X，et al. Summary of research on heading rate，seed setting rate and germination rate of Leymus chinensis[J]. Jilin Animal Husbandry and Veterinary Medicine，2018，39（2）：12-14杨双，穆春生，蔺吉祥，等. 羊草抽穗率、结实率和发芽率的研究概述[J]. 吉林畜牧兽医，2018，39（2）：12-14
[6] LIU G S，QI D M. Research progress on the biology of Leymus chinensis[J]. Acta Prataculturae Science，2004，13（5）：6-11刘公社，齐冬梅. 羊草生物学研究进展[J]. 草业学报，2004，13（5）：6-11
[7] CAI Y，LI Z Y，YU X H，et al. Effects of appropriate nitrogen fertilizer on seed productivity and forage quality of Leymus chinensis grassland in western Jilin Province[J]. Agriculture and Technology，2022，42（1）：16-20才源，李子勇，于新海，等. 适量氮肥对吉林西部人工建植羊草草原的种子产能与牧草品质影响的研究[J]. 农业与技术，2022，42（1）：16-20
[8] WANG Q，YANG Z P. Effects of mowing and fertilization on seed yield of Leymus chinensis in Inner Mongolia steppe[J]. Chinese Journal of Grassland，2022，44（12）：100-106王迁，杨兆平. 刈割和施肥对内蒙古典型草原羊草种子产量的影响[J]. 中国草地学报，2022，44（12）：100-106
[9] LIU Z D，CHAI F J，GAO H J，et al. Effects of trace elements on seed setting rate of Leymus chinensis[J]. Heilongjiang Agricultural Sciences，2019（8）：131-134刘泽东，柴凤久，高海娟，等. 施用微量元素对羊草结实率的影响[J]. 黑龙江农业科学，2019（8）：131-134
[10] CAO K，ZHOU Z K，WANG Q，et al. Genome-wide association study of 12 agronomic traits in peach[J]. Nature Communications，2016，7：13246
[11] WANG K X. Association analysis of maize ear-related traits and genomic selection breeding[D]. Urumqi：Xinjiang Agricultural University，2025：19-42汪凯翔. 玉米穗部相关性状关联分析与全基因组选择育种[D]. 乌鲁木齐：新疆农业大学，2025：19-42
[12] LIU M C，ZHANG Y D，SHAW R K，et al. Genome-wide association study and prediction of tassel weight of tropical maize germplasm in multi-parent population[J]. International Journal of Molecular Sciences，2024，25（3）：1756
[13] BAI X H. Genome-wide association analysis of the grain numbers in the basal spikelets in wheat and mining of key candidate genes[D]. Taigu：Shanxi Agricultural University，2023：27-34白雄辉. 小麦穗基部结实粒数全基因组关联分析及关键候选基因的挖掘[D]. 太谷：山西农业大学，2023：27-34
[14] LI T，TANG S J，LI W，et al. Genome evolution and initial breeding of the Triticeae grass Leymus chinensis dominating the Eurasian Steppe[J]. Proceedings of the National Academy of Sciences of the United States of America，2023，120（44）：1-10
[15] YU H. Studies on the effects of optimal nitrogen application and irrigation time on seed yield and yield components of Leymus chinensis[D]. Changchun：Northeast Normal University，2010：1-2于辉. 羊草种子产量构成因子与产量最适调控时间的研究[D]. 长春：东北师范大学，2010：1-2
[16] WANG J. Study on the low seed setting percentage of Leymus chinensis based on photosynthetic product distribution[D]. Changchun：Northeast Normal University，2020：24-25王姣. 基于光合产物转运分配的羊草低结实率研究[D]. 长春：东北师范大学，2020：24-25
[17] CHEN Z，NIU J P，CAO X L，et al. Seed yield can be explained by altered yield components in field-grown western wheatgrass （Pascopyrum smithii Rydb.）[J]. Scientific Reports，2019，9：17976
[18] KIM J Y，SONG J T，SEO H S. The enhancer of zeste gene OsiEZ1is involved in ligule and seed development in rice[J]. Canadian Journal of Plant Science，2017：1068-1074
[19] MIZZOTTI C，MENDES M A，CAPORALI E，et al. The MADS box genes SEEDSTICK and ARABIDOPSIS Bsister play a maternal role in fertilization and seed development[J]. The Plant Journal，2012，70（3）：409-420
[20] YU Y F，CHU X，MA X J，et al. Genome-wide analysis of MADS-box gene family reveals CjSTK as a key regulator of seed abortion in Camellia japonica[J]. International Journal of Molecular Sciences，2024，25（11）：5770
[21] TANG J Q，TIAN X J，MEI E Y，et al. WRKY53 negatively regulates rice cold tolerance at the booting stage by fine-tuning anther gibberellin levels[J]. The Plant Cell，2022，34（11）：4495-4515
[22] TIAN C Y，BIAN X，LANG R B，et al. Association analysis of three breeding traits with SSR markers and exploration of elite alleles in sugarcane[J]. Acta Agronomica Sinica，2024，50（2）：310-324田春艳，边芯，郎荣斌，等. 甘蔗3个育种性状与SSR标记的关联分析及优异等位变异发掘[J]. 作物学报，2024，50（2）：310-324

GWAS-Based Identification of Markers and Candidate Genes for Seed Setting Rate and Seed Yield in Leymus chinensis

基于GWAS挖掘羊草结实率及种子产量相关标记与候选基因

PDF

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	YUAN Yu-tao, WU Li, CHEN Chen, ZHAO Zi-han, DING Zhong-yang, LIU Wen-hui, BAI Ma, ZHOU Qing-ping, CHEN You-jun. Key Influencing Traits and Path Analysis of Seed Setting Rate of Hulled Oats in the Northwestern Sichuan Alpine Region [J]. Acta Agrestia Sinica, 2026, 34(7): 2503-2514.
[2]	LIU Jin-yu, REN Shan, ZHANG Hai-zhen, WANG Yue, ZHOU Ai-min. Comparative Study on Physiological Responses of Leymus chinensis and Elymus dahuricus to Salt and Alkali Stress [J]. Acta Agrestia Sinica, 2026, 34(7): 2515-2527.
[3]	FAN Tai-lian, WU Rui, LIANG Guo-ling, LIU Wen-hui, HU Ze-long, WANG Wen-hu, HAN Ming-mei. Comprehensive Analyses of the Combined Effects of Nitrogen Application Rate and Sowing Density on the Agronomic Traits and Seed Yield of ‘Qingyan No.2’ Oats [J]. Acta Agrestia Sinica, 2026, 34(5): 1932-1941.
[4]	WEI Kong-tao, CAO Quan, ZHANG Zheng-she, ZHANG Chun-ping, YU Yang, ZHOU Ze, ZHANG Xue, WANG Xin-xin, YUE Si-yu, DONG Quan-min. Study on the Yield-Related Traits and Influencing Factors of Hay and Seed Yield in Different Oat （Avena sativa L.） Varieties [J]. Acta Agrestia Sinica, 2026, 34(2): 531-542.
[5]	YAN Yu-ting, GAO Jie, ZHAO Mu-qier, GE Gen-tu, JIA Yu-shan, WANG Zhi-jun, NA Ya. Investigation and Analysis of the Effects of Regional and Planting Patterns on Economic Benefit of Leymus chinensis [J]. Acta Agrestia Sinica, 2025, 33(6): 1947-1960.
[6]	WANG Xin-yao, LIU Yi-xin, SUI Xiao-qing, LANG Meng-qing, JIN Lian-wu. Effects of Spray Mepiquat-Chloride on Leaf Cells， Agronomic Traits and Seed Yield Formation in Alfalfa [J]. Acta Agrestia Sinica, 2025, 33(6): 1972-1981.
[7]	LUO Jun-jie, XIAO Yan-zi, HOU Mei-ling, XU Li-jun, HU Meng-jie, LU Na, ZHANG Xiao-lin, ZHANG Jia-xu, AN Xin. Effects of Different Additives on Quality and Vitamin Content of Mixed Silage of Alfalfa and Leymus chinensis [J]. Acta Agrestia Sinica, 2025, 33(3): 992-1000.
[8]	WANG Jie-fan, LI Jian-hui, ZHANG Sheng-yuan, DONG Di, ZHANG Ran, WANG Si-ning, LIU Yue-han, LI Xiao-xia, SHI Feng-ling. Cloning， Expression Pattern Analysis and Subcellular Localization of LcPDS gene in Leymus chinensis [J]. Acta Agrestia Sinica, 2025, 33(11): 3550-3558.
[9]	LI Qi, LABA Zhuoma, LIU Wen-hui, QI Hui-fang, LI Si-da, LIU Kai-qiang, WU Rui. Study on the Production Performance and Agronomic Traits of Elymus sibiricus [J]. Acta Agrestia Sinica, 2025, 33(11): 3676-3689.
[10]	SONG Jia-min, CHU Li-shuang, LI Hai-yan, YANG Yun-fei, LAN Li-shi, YOU Cheng-cheng. Research on the Quantitative Characteristics Dynamics of Reproductive Ramets of Leymus chinensis Populations under Different Habitats in Songnen Plain [J]. Acta Agrestia Sinica, 2025, 33(11): 3690-3697.
[11]	DU Jin-shan, PU Jun-yu, HUANG Jing, QIAO Jian-xia, SU Ying-jia, XING Zhi-xian, HONG Yi-nan, ZHONG Xiao-lan, WANG Xin-sheng, LIU Ke-si. Effects of Temperate Leymus chinensis Steppe Degradation on the Root Morphological Traits of Leymus chinensis [J]. Acta Agrestia Sinica, 2025, 33(10): 3147-3154.
[12]	YU Shuai, FENG Guang-yan, SU Xiao-li, ZHANG Xian-fang, ZUO Su-tian, ZHANG Xin-quan. Multiple Analyses of the Relationship between Agronomic Traits and Yield Formation in 17 Varieties/Lines of Lolium multiflorum [J]. Acta Agrestia Sinica, 2024, 32(9): 2862-2874.
[13]	XIAO Ai-ping, WANG Yu, WANG Bin, WANG Teng-fei, LAN Jian. Effects of Different Fertilizers and Levels on Light Energy Radiation and Seed Yield of Astragalus Adsurgens Population [J]. Acta Agrestia Sinica, 2024, 32(9): 2899-2909.
[14]	XU Ming, JIANG Xue-qian, HE Fei, ZHANG Fan, YANG Tian-hui, LONG Rui-cai, YANG Qing-chuan, CONG Li-li. Genome-Wide Association Study (GWAS) of Seed Yield and Size-Related Traits of Alfalfa (Medicago sativa L.) [J]. Acta Agrestia Sinica, 2024, 32(8): 2419-2427.
[15]	BAI Yan-yan, WANG Chu, CHEN Fen, LI Cai-ying, LI Chen-yan, LI Mao-na, SUN Yan. Effects of Nitrogen Application Amount and Frequency on Seed Yield and Nitrogen Use Efficiency of Buffalograss [J]. Acta Agrestia Sinica, 2024, 32(8): 2630-2637.