Analysis on Genetic Diversity, Population Structure, and Linkage Disequilibrium of 273 Rice Germplasms

doi:10.16819/j.1001-7216.2021.0513

Abstract

Abstract:

【Objective】The assessment of genetic diversity and population structure of 273 rice germplasms would provide important references for breeding as well as association mapping. 【Method】In this study, genetic diversity, population structure, and linkage disequilibrium for 273 rice landraces and breeding materials from 14 countries were assayed based on genotyping with 214 markers. 【Result】The test population were classified into two subgroups (SG1 and SG2) and one mixed group(AD) through population structure analysis, and the results of UMPGA clustering analysis and principal component analysis were consistent with the results of population structure analysis. Genetic diversity analysis showed that a total of 524 alleles were detected with 214 markers, the number of alleles detected on each locus ranged from 2 to 5 with the average genetic diversity of 0.44 and the average polymorphism information content (PIC) of 0.355. The genetic diversity and PIC were higher in SG2 than those in SG1. Analysis of molecular variance showed that 34 percent of variation was attributed to the genetic variation among groups and 66 percent to the genetic variation within groups. There was significant genetic differentiation between SG1 and SG2 (F_st=0.725, P<0.01). Linkage disequilibrium analysis showed that there were linkage disequilibrium loci in each linkage group, and the minimum distances extended when linkage disequilibrium was attenuated to below 75% in SG1 and SG2 were 13.7 Mb and 90.5 kb, respectively. 【Conclusion】Given rich genetic variation, the population consisting of 273 rice germplasm resources is suitable for excellent alleles mining through association mapping.

Key words: rice germplasms, genetic diversity, population structure, linkage disequilibrium

摘要：

【目的】评估273份水稻种质资源的遗传多样性和群体结构,为今后利用这些水稻种质资源进行遗传育种和关联分析提供参考。【方法】利用214个分子标记对来自14个国家的273份水稻地方品种和育种材料进行基因型检测,分析其遗传多样性、群体结构、连锁不平衡程度。【结果】群体结构分析将供试群体划分为2个亚群(SG1、SG2)以及1个混合群(AD),聚类分析和主成分分析结果与群体结构分析结果一致;遗传多样性分析结果显示,214个标记共检测到524个等位变异,变幅为2~5个,平均遗传多样性指数为0.44,平均多态性信息含量（PIC）为0.355,SG2群遗传多样性指数和PIC高于SG1群;分子方差分析表明34％的变异来源于种群内,66％的变异来源于种群间,SG1与SG2群体间存在显著的遗传分化（F_st=0.725,P<0.01）;连锁不平衡分析结果显示,整个群体中存在较高程度连锁不平衡,平均r²为0.33,SG1和SG2中连锁不平衡衰减到75％以下所延伸的最小距离分别为13.7 Mb和90.5 kb。【结论】273份水稻种质资源群体内具有丰富的遗传变异,该群体适合通过关联作图来挖掘优异等位基因。

关键词: 水稻种质资源, 遗传多样性, 群体结构, 连锁不平衡

Junjie DONG, Yuxiang ZENG, Zhijuan JI, Yan LIANG, Changdeng YANG. Analysis on Genetic Diversity, Population Structure, and Linkage Disequilibrium of 273 Rice Germplasms[J]. Chinese Journal OF Rice Science, 2021, 35(2): 130-140.

董俊杰, 曾宇翔, 季芝娟, 梁燕, 杨长登. 273份水稻种质资源的遗传多样性、群体结构与连锁不平衡分析[J]. 中国水稻科学, 2021, 35(2): 130-140.

Figures/Tables 12

References 45

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编号Number	品种名Name	来源Origin	亚种Subspecies		编号 Number	品种名 Name	来源 Origin	亚种Subspecies
编号Number	品种名Name	来源Origin	先前研究Previous study	本研究Present study	编号 Number	品种名 Name	来源 Origin	先前研究Previous study	本研究Present study
WG7	文光	宁夏	粳	粳	WG139	谷光矮23	中国	籼	籼
WG17	低脚乌尖	台湾	籼	籼	WG156	胜利籼	湖南	籼	籼
WG28	金线稻	吉林	粳	粳	WG158	Baok	印尼	-	-
WG30	紫红	浙江	籼	籼	WG159	中山1号	广东	籼	籼
WG31	八十早	湖南	籼	籼	WG163	Bahagia	马来西亚	-	籼
WG32	黄丝晚谷	贵州	-	粳	WG166	草毛蛋	河南	籼	籼
WG33	冷水谷	中国	-	粳	WG167	田基度	广东	籼	籼
WG35	老红谷	安徽	粳	粳	WG172	顺德塘禾	广东	籼	籼
WG36	麻线谷	云南	-	粳	WG174	Jaya	印度	-	籼
WG37	银丝白	广西	籼	籼	WG175	RAJBHOG	-	-	-
WG39	黑稻	河南	-	粳	WG176	Cisadane	尼日利亚	-	籼
WG40	齐头谷	云南	籼	籼	WG177	BG90-2	斯里兰卡	-	粳
WG42	高山红	湖南	籼	籼	WG181	Rohini	印度	-	籼
WG43	皇帝稻	安徽	-	-	WG185	黄壳早廿日	江苏	粳	粳
WG44	公居73	云南	籼	籼	WG188	苏州青	江苏	粳	粳
WG45	小白板稻	中国	-	-	WG189	薄稻	中国	粳	粳
WG46	三粒寸	陕西	-	粳	WG190	铁杆青	江苏	-	粳
WG47	肥东塘稻	安徽	粳	-	WG191	江南晚	江苏	粳	粳
WG48	麻谷	四川	-	粳	WG192	缺儿糯	中国	-	粳
WG49	老虎稻	浙江	粳	粳	WG193	乌嘴糯	中国	籼	籼
WG50	白壳籼	安徽	籼	籼	WG194	大白糯	云南	粳	-
WG51	来安塘稻	安徽	粳	粳	WG195	毫变1	云南	-	籼
WG52	卫国	辽宁	粳	粳	WG196	扎缅尼1	云南	粳	籼
WG53	怀远塘稻	安徽	粳	粳	WG197	李材料	中国	-	籼
WG57	岩粘	贵州	籼	籼	WG203	雪禾矮早	云南	粳	籼
WG58	紫金兜	河南	籼	籼	WG206	黔农	贵州	籼	籼
WG59	麻酒谷	陕西	粳	粳	WG207	特矮	中国	-	籼
WG60	鸡油糯	贵州	-	粳	WG208	新桂矮	江苏	籼	籼
WG61	顺河早	贵州	籼	籼	WG210	丛腊矮	中国	-	籼
WG62	老白术	福建	籼	籼	WG211	B5580A	-	-	-
WG63	香谷	云南	-	粳	WG229	Resormain1	中国	-	籼
WG64	乌脚粘	陕西	籼	籼	WG259	高谷地米	中国	-	-
WG65	雪里青	浙江	粳	粳	WG260	信阳谷	中国	-	籼
WG66	大稻头	中国	-	粳	WG261	广丰宁	中国	-	-
WG67	黑芒稻	甘肃	粳	粳	WG262	白稻	中国	-	-
WG76	Unk2	中国	-	粳	WG263	小紫米	中国	-	籼
WG77	Unk3	中国	-	籼	WG264	汉阳里2	中国	-	籼
WG78	Camor	不详	-	籼	WG265	紫米	四川	-	籼
WG79	Unk5	中国	-	粳	WG268	赤壳糯	中国	-	粳
WG80	Unk6	中国	-	粳	WG269	泽谷	中国	-	籼
WG99	竹香稻	浙江	籼	籼	WG274	戈马列	-	-	-
WG104	白叶秋	西南	-	粳	WG275	红脚占	湖南	籼	籼
WG123	滇泷201	云南	籼	籼	WG276	砦塘	中国	-	籼
WG138	青谷矮	中国	籼	籼

编号Number	品种名Name	来源Origin	亚种Subspecies		编号 Number	品种名 Name	来源 Origin	亚种Subspecies
编号Number	品种名Name	来源Origin	先前研究Previous study	本研究Present study	编号 Number	品种名 Name	来源 Origin	先前研究Previous study	本研究Present study
WG7	文光	宁夏	粳	粳	WG139	谷光矮23	中国	籼	籼
WG17	低脚乌尖	台湾	籼	籼	WG156	胜利籼	湖南	籼	籼
WG28	金线稻	吉林	粳	粳	WG158	Baok	印尼	-	-
WG30	紫红	浙江	籼	籼	WG159	中山1号	广东	籼	籼
WG31	八十早	湖南	籼	籼	WG163	Bahagia	马来西亚	-	籼
WG32	黄丝晚谷	贵州	-	粳	WG166	草毛蛋	河南	籼	籼
WG33	冷水谷	中国	-	粳	WG167	田基度	广东	籼	籼
WG35	老红谷	安徽	粳	粳	WG172	顺德塘禾	广东	籼	籼
WG36	麻线谷	云南	-	粳	WG174	Jaya	印度	-	籼
WG37	银丝白	广西	籼	籼	WG175	RAJBHOG	-	-	-
WG39	黑稻	河南	-	粳	WG176	Cisadane	尼日利亚	-	籼
WG40	齐头谷	云南	籼	籼	WG177	BG90-2	斯里兰卡	-	粳
WG42	高山红	湖南	籼	籼	WG181	Rohini	印度	-	籼
WG43	皇帝稻	安徽	-	-	WG185	黄壳早廿日	江苏	粳	粳
WG44	公居73	云南	籼	籼	WG188	苏州青	江苏	粳	粳
WG45	小白板稻	中国	-	-	WG189	薄稻	中国	粳	粳
WG46	三粒寸	陕西	-	粳	WG190	铁杆青	江苏	-	粳
WG47	肥东塘稻	安徽	粳	-	WG191	江南晚	江苏	粳	粳
WG48	麻谷	四川	-	粳	WG192	缺儿糯	中国	-	粳
WG49	老虎稻	浙江	粳	粳	WG193	乌嘴糯	中国	籼	籼
WG50	白壳籼	安徽	籼	籼	WG194	大白糯	云南	粳	-
WG51	来安塘稻	安徽	粳	粳	WG195	毫变1	云南	-	籼
WG52	卫国	辽宁	粳	粳	WG196	扎缅尼1	云南	粳	籼
WG53	怀远塘稻	安徽	粳	粳	WG197	李材料	中国	-	籼
WG57	岩粘	贵州	籼	籼	WG203	雪禾矮早	云南	粳	籼
WG58	紫金兜	河南	籼	籼	WG206	黔农	贵州	籼	籼
WG59	麻酒谷	陕西	粳	粳	WG207	特矮	中国	-	籼
WG60	鸡油糯	贵州	-	粳	WG208	新桂矮	江苏	籼	籼
WG61	顺河早	贵州	籼	籼	WG210	丛腊矮	中国	-	籼
WG62	老白术	福建	籼	籼	WG211	B5580A	-	-	-
WG63	香谷	云南	-	粳	WG229	Resormain1	中国	-	籼
WG64	乌脚粘	陕西	籼	籼	WG259	高谷地米	中国	-	-
WG65	雪里青	浙江	粳	粳	WG260	信阳谷	中国	-	籼
WG66	大稻头	中国	-	粳	WG261	广丰宁	中国	-	-
WG67	黑芒稻	甘肃	粳	粳	WG262	白稻	中国	-	-
WG76	Unk2	中国	-	粳	WG263	小紫米	中国	-	籼
WG77	Unk3	中国	-	籼	WG264	汉阳里2	中国	-	籼
WG78	Camor	不详	-	籼	WG265	紫米	四川	-	籼
WG79	Unk5	中国	-	粳	WG268	赤壳糯	中国	-	粳
WG80	Unk6	中国	-	粳	WG269	泽谷	中国	-	籼
WG99	竹香稻	浙江	籼	籼	WG274	戈马列	-	-	-
WG104	白叶秋	西南	-	粳	WG275	红脚占	湖南	籼	籼
WG123	滇泷201	云南	籼	籼	WG276	砦塘	中国	-	籼
WG138	青谷矮	中国	籼	籼

群体与亚群 Population and subgroup	品种份数 No. of varieties	多态性位点 Polymorphic locus		多态性信息含量 PIC		遗传多样性指数 Gene diversity
群体与亚群 Population and subgroup	品种份数 No. of varieties	总数 Overall	平均 Average	范围 Range	平均 Average	遗传多样性指数 Gene diversity
273份水稻材料Population	273	551	2.60	0.111~0.601	0.355	0.440
SG1	72	349	2.31	0.027~0.557	0.164	0.191
SG2	181	495	2.46	0.110~0.544	0.201	0.242
AD	20	516	2.40	0.090~0.661	0.364	0.445

群体与亚群 Population and subgroup	品种份数 No. of varieties	多态性位点 Polymorphic locus		多态性信息含量 PIC		遗传多样性指数 Gene diversity
群体与亚群 Population and subgroup	品种份数 No. of varieties	总数 Overall	平均 Average	范围 Range	平均 Average	遗传多样性指数 Gene diversity
273份水稻材料Population	273	551	2.60	0.111~0.601	0.355	0.440
SG1	72	349	2.31	0.027~0.557	0.164	0.191
SG2	181	495	2.46	0.110~0.544	0.201	0.242
AD	20	516	2.40	0.090~0.661	0.364	0.445

标记（染色体） Marker (Chr)	物理距离Physical site /MP	前引物（5'-3'） Forward primer	后引物（5'-3'） Reverse primer	退火温度Annealing temperature/℃	等位基因No. of alleles
D101D (1)	1.0	TGCTACTACTCACCTGCCATTCCG	GTCGCCAACTTTGACCTGTGATGT	55	3
D142C (1)	43.6	AGTGTAGTATTGGCTATTCGT	AGACTTTTCTCACCCTTCATA	47	3
D304B (3)	3.6	AACTACAGGACACCAGAAAAAT	TGAAAAGAAGCAGTAACAGAGC	50	4
D409A (4)	4.7	TTCCTCTTGTGTGTTTGTGTGA	CAGTGGCGACCATTATCTGTAC	55	3
D444 (4)	24.4	TTCAGAAACCACTTCCCCC	CCAAACCAAAATGCACTCG	55	3
D642 (6)	21.4	TAGCCCTTTATGTAGTTTGA	TTTGTTTGGTGAATGTAGCA	55	3
D657 (6)	28.3	GAGGAACACCAAGATGCCCAA	GACTTCGCTCTCAGCAACAGC	55	3
D757 (7)	28.5	TGTGGGCGAGGGATATAATA	CGATAACTACAAGCAAACCG	55	4
D1131 (11)	17.1	ATAAAAATGAATGGCGTGTCT	GCAAATGTAAGCCTGTAAGGA	48	3
D1149 (11)	24.1	TTCCCCTCATCTCTCCTCCT	TCAATCTACCGGCACACTCC	51	3