Genome-Wide Association Study (GWAS) of Seed Yield and Size-Related Traits of Alfalfa (Medicago sativa L.)

doi:10.11733/j.issn.1007-0435.2024.08.009

Acta Agrestia Sinica ›› 2024, Vol. 32 ›› Issue (8): 2419-2427.DOI: 10.11733/j.issn.1007-0435.2024.08.009

Genome-Wide Association Study (GWAS) of Seed Yield and Size-Related Traits of Alfalfa (Medicago sativa L.)

XU Ming¹, JIANG Xue-qian², HE Fei², ZHANG Fan², YANG Tian-hui³, LONG Rui-cai², YANG Qing-chuan², CONG Li-li¹

1. College of Grassland Science, Qingdao Agricultural University, Qingdao, Shandong Province 266109, China;
2. Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
3. Institute of Animal Science, Ningxia Academy of Agricultural and Forestry Sciences, Yinchuan, Ningxia 750002, China

Received:2024-01-29 Revised:2024-03-22 Published:2024-09-07

紫花苜蓿种子产量与大小相关性状全基因组关联分析

徐明¹, 蒋学乾², 何飞², 张帆², 杨天辉³, 龙瑞才², 杨青川², 丛丽丽¹

1. 青岛农业大学草业学院, 山东青岛 266109;
2. 中国农业科学院北京畜牧兽医研究所, 北京 100193;
3. 宁夏农林科学院动物科学研究所, 宁夏银川 750002

通讯作者: 杨青川,E-mail:yangqingchuan@caas.cn;丛丽丽,E-mail:congli1985610@126.com
作者简介:徐明(1998-),男,汉族,山东烟台人,硕士研究生,主要从事紫花苜蓿育种方面的研究,E-mail:xuming199836@163.com
基金资助:
中国农业科学院科技创新工程项目(ASTIP-IAS14);国家牧草产业技术体系项目(CARS-34)资助

Abstract

Abstract: Alfalfa (Medicago sativa L.),as a leguminous forage with high nutritional value and good palatability,has been grown in more areas of China,and the demand of high-quality seeds is increasing year by year. Therefore,increasing the seed yield per unit area is of great significance to the development of alfalfa industry in China. In order to explore the genes related to the regulation of seed yield and shape,in this study,220 alfalfa seed materials collected from all over the world were used to evaluate their seed weight (SW),seed area (SA) and seed perimeter (SP) using Genome-wide association study (GWAS). Phenotypic analysis showed that the three traits had different degrees of variation,and the coefficients of variation were 10.96% (SW),8.31% (SA),and 4.43% (SP),respectively. Through GWAS,a total of 20 single nucleotide polymorphism (SNP) sites associated with three traits were found on 7 chromosomes. Haplotype analysis confirmed that there was a positive correlation between the number of excellent alleles and SW,SA and SP. Genes near these 20 significant SNPs were searched and labeled in the upstream and downstream 20 kb range,and finally 4 candidate genes related to seed yield and size were selected. The results of this study could provide new markers and candidate genes for molecular breeding to optimize alfalfa seed size and increase seed yield.

Key words: Alfalfa, GWAS, Seed size, Seed yield

摘要： 紫花苜蓿(Medicago sativa L.)作为一种营养价值高、适口性好的豆科牧草，在我国种植面积不断扩大，其优质种子的需求量也逐年增多。因此，提高单位面积的种子产量对我国紫花苜蓿产业的发展具有重要意义。为挖掘调控种子产量与外形的相关基因，本研究中，利用从世界各地收集的220份紫花苜蓿种子材料，对其种子重量(Seed weight，SW)、种子面积(Seed area，SA)、种子周长(Seed perimeter，SP)进行全基因组关联分析(Genome-wide association study，GWAS)。表型分析表明3个性状存在不同程度的变异，变异系数分别为10.96%(SW)，8.31%(SA)，4.43%(SP)。通过GWAS，共在7条染色体上发现20个与3个性状相关的单核苷酸多态性(Single nucleotide polymorphism，SNP)位点，单倍型分析证实了优异等位基因的数量与SW，SA和SP之间存在正相关性。对这20个显著SNP上下游各20 kb范围内的基因进行搜索注释，最终筛选到4个与种子产量和大小相关的候选基因。本研究的结果可为优化紫花苜蓿种子大小，提高种子产量的分子育种提供新的标记与候选基因。

关键词: 紫花苜蓿, 全基因组关联分析, 种子大小, 种子产量

CLC Number:

S963.22+3.3

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.

徐明, 蒋学乾, 何飞, 张帆, 杨天辉, 龙瑞才, 杨青川, 丛丽丽. 紫花苜蓿种子产量与大小相关性状全基因组关联分析[J]. 草地学报, 2024, 32(8): 2419-2427.

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References

[1] 孙启忠,柳茜,李峰,等. 我国古代苜蓿物种考述[J]. 草业学报,2018,27(8):155-174
[2] 杨富裕. 树立“饲草就是粮食”理念,大力发展饲草产业[J]. 草地学报,2023,31(2):311-313
[3] 李小云,余淑艳,黄薇,等. 覆膜对宁夏干旱区苜蓿种子产量及构成因素的影响[J]. 西北农林科技大学学报(自然科学版),2022,50(2):67-74
[4] 国家林草局国有林场和种苗管理司. 2023年度全国草种供需分析报告[EB/OL]. https://www.forestry.gov.cn/main/586/20221120/215148550687091.html.2022-11-20/2024-3-20
[5] 俞鸿,欧成明,王占军,等. 农艺措施对紫花苜蓿种子产量组分的影响[J]. 草地学报,2021,29(12):2853-2861
[6] 毛培胜,欧成明,贾志程,等. 我国牧草与草坪草种子生产技术的研究进展[J]. 中国草地学报,2023,45(1):1-11
[7] 王琴,李小云,黄淑迪,等. 株行距对宁夏干旱区苜蓿种子产量及构成因素的影响[J]. 中国草地学报,2023,45(8):31-40
[8] 陈涛. 灌溉与硼肥对河西地区紫花苜蓿和红豆草新品系种子产量及质量的影响[D]. 兰州:兰州大学,2023:18-44
[9] NYKIEL M,GIETLER M,FIDLER J,et al. Abiotic stress signaling and responses in plants[J]. Plants (Basel),2023,12(19):3405
[10] LIU H,ZHANG C,YANG J,et al. Hormone modulation of legume-rhizobial symbiosis[J]. Journal of Integrative Plant Biology,2018,60(8):632-648
[11] ZHAO L,LI M,MA X,et al. Transcriptome analysis and identification of abscisic acid and gibberellin-related genes during seed development of alfalfa (Medicago sativa L.)[J]. BMC Genomics,2022,23(1):651
[12] LÓPEZ-BUCIO J S,DUBROVSKY J G,RAYA-GONZLEZ J,et al. Arabidopsis thaliana mitogen-activated protein kinase 6 is involved in seed formation and modulation of primary and lateral root development[J]. Journal of Experimental Botany,2014,65(1):169-183
[13] HU J,WANG Y,FANG Y,et al. A rare allele of GS2 enhances grain size and grain yield in rice[J]. Molecular Plant,2015,8(10):1455-1465
[14] LIANG G,HE H,LI Y,et al. Molecular mechanism of microRNA396 mediating pistil development in arabidopsis[J]. Plant Physiology and Biochemistry,2014,164(1):249-258
[15] GUPTA P K,KULWAL P L,JAISWAL V. Association mapping in plants in the post-GWAS genomics era[J]. Advances in Genetics,2019(104):75-154
[16] 周艳春,刘建,徐安凯,等. 93份无芒雀麦种质资源产量性状的全基因组关联分析[J]. 草地学报,2020,28(3):623-632
[17] CHEN Y,NIU S,DENG X,et al. Genome-wide association study of leaf-related traits in tea plant in Guizhou based on genotyping-by-sequencing[J]. BMC Plant Biology,2023,23(1):1-19
[18] LIN S,MEDINA C A,NORBERG O S,et al. Genome-wide association studies identifying multiple loci associated with alfalfa forage quality[J]. Frontiers in Plant Science,2021(12):1-15
[19] YU L X,ZHENG P,BHAMIDIMARRI S,et al. The impact of genotyping-by-sequencing pipelines on SNP discovery and identification of markers associated with verticillium wilt resistance in autotetraploid alfalfa (Medicago sativa L.)[J]. Frontiers in Plant Science,2017(8):1-13
[20] YU L X. Identification of single-nucleotide polymorphic loci associated with biomass yield under water deficit in alfalfa (Medicago sativa L.) using genome-wide sequencing and association mapping[J]. Frontiers in Plant Science,2017(8):1-11
[21] MEDINA C A,HAWKINS C,LIU X P,et al. Genome-wide association and prediction of traits related to salt tolerance in autotetraploid alfalfa (Medicago sativa L.)[J]. International Journal of Molecular Sciences,2020,21(9):3361
[22] 严勇亮,张恒,张金波,等. 春小麦主要籽粒性状的全基因组关联分析[J]. 麦类作物学报,2022,42(10):1182-1191
[23] 杨丹丹,李小林,吕莹,等. 云南水稻新品系重要农艺性状全基因组关联分析[J]. 西南农业学报,2023,36(9):1825-1834
[24] CHEN H,ZENG Y,YANG Y,et al. Allele-aware chromosome-level genome assembly and efficient transgene-free genome editing for the autotetraploid cultivated alfalfa[J]. Nature Communications,2020,11(1):1-11
[25] CHEN L,HE F,LONG R,et al. A global alfalfa diversity panel reveals genomic selection signatures in Chinese varieties and genomic associations with root development[J]. Journal of Integrative Plant Biology,2021,63(11):1937-1951
[26] HUANG M,LIU X,ZHOU Y,et al. BLINK:a package for the next level of genome-wide association studies with both individuals and markers in the millions[J]. Gigascience,2019,8(2):1-12
[27] XU C,WU T,YUAN S,et al. Can soybean cultivars with larger seed size produce more protein,lipids,and seed yield? A meta-analysis[J]. Foods,2022,11(24):40-59
[28] AMBIKA S,MANONMANI V,SOMASUNDARAM G. Review on effect of seed size on seedling vigour and seed yield[J]. Research Journal of Seed Science,2014,7(2):31-38
[29] 尹淑英. 紫花苜蓿的种子功能性状及SSR分子标记的遗传多样性[D]. 兰州:兰州大学,2018:19-26
[30] WANG J,ZHANG Z. GAPIT version 3:boosting power and accuracy for genomic association and prediction[J]. Genomics Proteomics Bioinformatics,2021,19(4):629-640
[31] MORRIS E R,CHEVALIER D,WALKER J C. DAWDLE,a forkhead-associated domain gene,regulates multiple aspects of plant development[J]. Plant Physiology,2006,141(3):932-941
[32] KAPAZOGLOU A,ENGINEER C,DROSOU V,et al. The study of two barley type I-like MADS-box genes as potential targets of epigenetic regulation during seed development[J]. BMC Plant Biology,2012,12:166
[33] LAFON-PLACETTE C,KÖHLER C. Embryo and endosperm,partners in seed development[J]. Current Opinion in Plant Biology,2014(17):64-69
[34] ZHANG J,ZHANG Z,ZHANG R,et al. Type I MADS-box transcription factor TaMADS-GS regulates grain size by stabilizing cytokinin signalling during endosperm cellularization in wheat[J]. Plant Biotechnology Journal,2024,22(1):200-215
[35] HUANGFU L,CHEN R,LU Y,et al. OsCOMT,encoding a caffeic acid O-methyltransferase in melatonin biosynthesis,increases rice grain yield through dual regulation of leaf senescence and vascular development[J]. Plant Biotechnology Journal,2022,20(6):1122-1139
[36] BAJAJ D,SAXENA M S,KUJUR A,et al,Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea[J]. Journal of Experimental Botany,2015,66(5):1271-1290(责任编辑刘婷婷)第32卷第8期 Vol.32 No. 8草地学报 ACTAAGRESTIASINICA 2024年 8月

Genome-Wide Association Study (GWAS) of Seed Yield and Size-Related Traits of Alfalfa (Medicago sativa L.)

紫花苜蓿种子产量与大小相关性状全基因组关联分析

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