基于55K SNP芯片的山西冬小麦种质资源遗传多样性分析

doi:10.3864/j.issn.0578-1752.2024.10.001

中国农业科学 ›› 2024, Vol. 57 ›› Issue (10): 1845-1856.doi: 10.3864/j.issn.0578-1752.2024.10.001

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

基于55K SNP芯片的山西冬小麦种质资源遗传多样性分析

雷梦林¹(), 刘霞¹, 王艳珍¹, 崔国庆¹, 穆志新¹, 刘龙龙¹, 李欣², 逯腊虎³, 李晓丽³, 张晓军²()

¹ 山西农业大学农业基因资源研究中心/农业农村部黄土高原作物基因资源与种质创制重点实验室/杂粮种质资源发掘与遗传改良山西省重点实验室，太原 030031
² 山西农业大学农学院/作物遗传与分子改良山西省重点实验室，山西太谷 030801
³ 山西农业大学小麦研究所，山西临汾 041000

收稿日期:2023-12-13 接受日期:2024-01-30 出版日期:2024-05-16 发布日期:2024-05-23
通信作者:
张晓军，E-mail：18636810904@163.com
联系方式: 雷梦林，E-mail：leimenglin35@163.com。
基金资助:
山西农业大学优秀博士启动项目(2023BQ96); 2023年小麦种业创新良种联合攻关项目(YZGG-02); 中央引导地方科技发展资金(YDZJSX20231C011); 山西省博士毕业生、博士后研究人员来晋工作奖励经费科研项目(SXBYKY2022089)

Genetic Diversity Analysis of Winter Wheat Germplasm Resources in Shanxi Province Based on 55K SNP Array

LEI MengLin¹(), LIU Xia¹, WANG YanZhen¹, CUI GuoQing¹, MU ZhiXin¹, LIU LongLong¹, LI Xin², LU LaHu³, LI XiaoLi³, ZHANG XiaoJun²()

¹ Center for Agricultural Genetic Resources Research, Shanxi Agricultural University/Key Laboratory of Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Taiyuan 030031
² College of Agriculture, Shanxi Agricultural University/Key Laboratory of Crop Genetics and Molecular Improvement of Shanxi Province, Taigu 030801, Shanxi
³ Institute of Wheat Research, Shanxi Agricultural University, Linfen 041000, Shanxi

Received:2023-12-13 Accepted:2024-01-30 Published:2024-05-16 Online:2024-05-23

摘要/Abstract

摘要：

【目的】分析山西省冬小麦种质资源的遗传多样性演变规律，为山西省小麦育种的亲本选配和品种选育提供更丰富多样的原始亲本材料。【方法】以山西省冬小麦323份地方品种和105份育成品种为自然群体，利用55K SNP芯片对428份自然群体进行全基因组扫描，分析品种间的遗传多样性、遗传结构、主成分、遗传聚类及亲缘关系。【结果】SNP位点在21条染色体上的分布范围为329—1 639个，平均值为1 152个；7个部分同源群中的分布范围为2 154—3 852个，平均值约为3 456个；基因组的分布规律为：B基因组>A基因组>D基因组；基因组注释多态性标记，在基因间区分布最多，约占50%，分析表明，SNP位点在21条染色体、7个同源群和3个基因组上均有覆盖，但分布各异，多态性比率为45.60%。整个群体的平均观测杂合度（0.0185）均低于平均期望杂合度（0.4992），整个自然群体的香农-威纳指数和多态性信息含量的变化幅度不大。对比自然群体多样性各参数，发现群体的遗传多样性不高，育成品种的遗传多样性比地方品种略高。群体结构分析将群体分为2个类群，第Ⅰ类群307份材料，以地方品种为主；第Ⅱ类群121份材料，以育成品种为主。主成分和聚类分析均将自然群体分为5个类群，第Ⅰ类群品种间的遗传距离平均值为0.21831，变幅为0.00127—0.72461；第Ⅱ类群品种间的遗传距离平均值为0.14619，变幅为0.00038—0.76489；第Ⅲ类群品种间的遗传距离平均值为0.16521，变幅为0.00049—0.43033；第Ⅳ类群品种间的遗传距离平均值为0.17643，变幅为0.00118—0.60496；第Ⅴ类群品种间的遗传距离平均值为0.12039，变幅为0.00042—0.37032，可见，山西省冬小麦品种间的遗传距离变异幅度较大，但平均遗传距离值较低，聚类分群明显，类群中部分品种的遗传关系较近。经对比，第Ⅰ类群和第Ⅳ类群的平均遗传距离均要高于第Ⅱ类群、第Ⅲ类群和第Ⅴ类群，第Ⅰ类群和第Ⅳ类群的遗传距离变幅大于第Ⅲ类群和第Ⅴ类群，可知，育成品种的遗传距离普遍大于地方品种。【结论】利用55K SNP芯片对山西省冬小麦种质资源进行遗传多样性分析，明确了山西省冬小麦育成品种和地方品种在基因组层面上的遗传多样性分布特点，育成品种通过外源基因的导入有利于品种的遗传多样性提高，地方品种的遗传多样性相对较低，同时，极少数品种的亲缘关系呈两极分化，在后续利用时应合理地区分利用。

关键词: 小麦, 地方品种, 育成品种, 遗传多样性, 55K SNP

Abstract:

【Objective】 Analyzing the evolutionary patterns of genetic diversity of wheat germplasm resources, providing richer and more diverse original parental materials for parental selection and variety selection in wheat breeding in Shanxi Province.【Method】 Using 323 landraces and 105 cultivated varieties as natural populations, a 55K SNP chip was used to perform whole genome scanning on 428 natural populations, analyzing genetic diversity, genetic structure, principal components, genetic clustering, and phylogenetic relationships among varieties. 【Result】 The distribution of SNP loci on 21 chromosomes ranged from 329 to 1 639, with an average of 1 152. The distribution range of 7 partially homologous groups is 2 154-3 852, with an average of approximately 3 456. The distribution pattern of the genome is: B genome>A genome>D genome. Genomic annotation polymorphism markers have the highest distribution among gene regions, accounting for about 50%. Analysis shows that SNP loci cover 21 chromosomes, 7 homologous groups and 3 genomes, but their distribution varies, with a polymorphism rate of 45.60%. The average observed heterozygosity of the entire population (0.0185) was lower than the expected heterozygosity (0.4992). The changes in the average shannon wiener index and polymorphism information content of the entire natural population were not significant. Comparing the diversity parameters of natural populations, it was found that the genetic diversity of the population is not high, the genetic diversity of cultivated varieties is slightly higher than that landraces. The population structure analysis of natural populations divides the population into two major groups. Group I has 307 materials, mainly landraces. Group Ⅱ has 121 materials, mainly cultivated varieties. The natural groups were divided into five groups by both principal component and cluster analysis. The average genetic distance between the varieties in group I is 0.21831, with a range of 0.00127-0.72461. The average genetic distance between varieties in group Ⅱ is 0.14619, with a range of 0.00038-0.76489. The varieties in group Ⅲ the average genetic distance between the varieties of group Ⅳ is 0.16521, with a range of 0.00049-0.43033. The average genetic distance between varieties of group Ⅳ is 0.17643, with a range of 0.00118-0.60496. The average genetic distance between varieties of group V is 0.12039, with a range of 0.00042-0.37032. It can be seen that the variation of genetic distance between wheat varieties is large in Shanxi Province. However, the average genetic distance value is low, the clustering classification differentiation is obvious. The genetic relationship between varieties in the middle of the group is relatively close. Comparison shows that the average genetic distance of group I and group Ⅳ is higher than that of group Ⅱ, group Ⅲ and group V. The genetic distance variation of group I and group Ⅳ is higher than that of group Ⅲ and group V. It can be seen that the genetic distance of cultivated varieties is generally greater than that of landraces.【Conclusion】 The 55K SNP chip was used to analyze the genetic diversity of Shanxi winter wheat germplasm resources, clarifying the distribution characteristics of genetic diversity at the genomic level between Shanxi wheat cultivated varieties and landraces. The introduction of exogenous genes into cultivated varieties is beneficial for improving genetic diversity, while the genetic diversity of landraces is relatively low. At the same time, the genetic relationships of very few varieties are polarized, so it should be rationally used differently in subsequent utilization.

Key words: wheat, landraces, cultivars, genetic diversity, 55K SNP

雷梦林, 刘霞, 王艳珍, 崔国庆, 穆志新, 刘龙龙, 李欣, 逯腊虎, 李晓丽, 张晓军. 基于55K SNP芯片的山西冬小麦种质资源遗传多样性分析[J]. 中国农业科学, 2024, 57(10): 1845-1856.

LEI MengLin, LIU Xia, WANG YanZhen, CUI GuoQing, MU ZhiXin, LIU LongLong, LI Xin, LU LaHu, LI XiaoLi, ZHANG XiaoJun. Genetic Diversity Analysis of Winter Wheat Germplasm Resources in Shanxi Province Based on 55K SNP Array[J]. Scientia Agricultura Sinica, 2024, 57(10): 1845-1856.

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参数 Parameter	数值 Value	育成品种+地方品种 Cultivars+Landraces	育成品种 Cultivars	地方品种 Landraces
观测杂合率Ho	平均值Mean	0.0185	0.0216	0.0175
	最大值Max	0.3710	0.3710	0.1923
	最小值Min	0.0022	0.0022	0.0050
期望杂合率He	平均值Mean	0.4992	0.4987	0.4994
	最大值Max	0.5000	0.5000	0.4999
	最小值Min	0.4964	0.4967	0.4964
香农-威纳指数SWI	平均值Mean	0.6923	0.6918	0.6925
	最大值Max	0.6931	0.6932	0.6930
	最小值Min	0.6895	0.6899	0.6895
多态性信息含量PIC	平均值Mean	0.3746	0.3743	0.3747
	最大值Max	0.3750	0.3750	0.3749
	最小值Min	0.3732	0.3733	0.3732

类群 Group	总数量 Total quantity	数量（频次）Quantity (frequency, %)
类群 Group	总数量 Total quantity	Q≥0.9	0.6<Q<0.9	Q≤0.6
Ⅰ	307	275 (89.57)	29 (9.45)	3 (0.98)
Ⅱ	121	79 (65.29)	32 (26.45)	10 (8.26)
Ⅰ+Ⅱ	428	354 (82.71)	61 (14.25)	13 (3.04)

基于55K SNP芯片的山西冬小麦种质资源遗传多样性分析

Genetic Diversity Analysis of Winter Wheat Germplasm Resources in Shanxi Province Based on 55K SNP Array

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