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

Abstract

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

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.

Figures/Tables 6

Table 1

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Table 2

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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)

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

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