山西谷子核心资源群体结构及主要农艺性状关联分析

doi:10.3864/j.issn.0578-1752.2019.22.013

摘要/Abstract

摘要：

【目的】分析山西谷子地方品种遗传多样性和群体遗传结构,筛选与谷子农艺性状相关联的分子标记,为谷子杂交组合亲本选配及分子标记辅助育种提供依据。【方法】利用96对SSR标记对595份山西谷子核心资源进行全基因组扫描,采用PowerMarker 3.25软件分析群体遗传多样性,利用STRUCTURE 2.3.4软件分析群体遗传结构,使用TASSEL 2.1软件中GLM（general linear model,Q）和MLM（mixed linear model,Q+K）2种方法,进行表型和标记关联分析。【结果】 96对SSR引物共扩增出828个等位变异,平均每对引物扩增到8.6个,变化范围为2—26;基因多样性指数变化范围为0.005—0.941,平均为0.610;多态信息量变化范围为0.005—0.938,平均为0.577;各位点杂合度变化范围为0—0.050,平均位点杂合度仅为0.016。群体结构分析将595份核心资源分为3个亚群。4 560个SSR位点成对组合中,共线性组合和非共线性组合之间都存在一定的连锁不平衡。D′统计概率（P<0.01）支持的LD成对位点1 955个,占全部位点组合的42.9%,D′平均值为0.23。通过GLM方法共检测到12个极显著性位点（P<0.01）,表型变异解释率为2.34%—13.94%,平均为6.33%,贡献率较高的等位变异位点是CAAS2050（R ²=13.94%）和B153（R ²=11.36%）;通过MLM方法共检测到9个极显著性位点（P<0.01）,表型变异解释率为2.80%—9.22%,平均为5.16%,贡献率较高的等位变异位点是P89（R ²=9.22%）和P3*（R ²=8.28%）;2种方法共同检测到的极显著性位点有7个。【结论】利用SSR标记分析了595份山西谷子核心资源的遗传多样性和群体遗传结构。2种关联分析模型中,GLM方法关联到12个标记与节数、株高、颈长、茎粗、穗长、穗粗、码数、码粒数、蛋白质含量9个性状相关;MLM方法关联到9个标记与节数、颈长、叶宽、茎粗、穗粗、码数、码粒数、千粒重8个性状相关。

关键词: 谷子, 山西, 地方品种, SSR, 遗传多样性, 连锁不平衡, 关联分析

Abstract:

【Objective】The objective of this study is to detect the SSR markers associated with agronomic trait and analyze genetic diversity and genetic structure of foxtail millet landrace in Shanxi province. The results will be helpful for hybridization combination of parent materials and molecular marker assisted breeding.【Method】96 SSR markers on 9 chromosomes were genome-wide screened for polymorphism in core collection of 595 accessions. PowerMarker 3.25 software was used to estimate the polymorphism information of population. Population structure was analyzed using STRUCTURE 2.3.4 software. Then the data were associated with 96 SSR markers by GLM (general linear model, Q) and MLM (mixed linear model, Q+K).【Result】Totally 828 alleles were found with 96 SSR markers and 8.6 alleles were revealed with each marker in average ranged from 2-26. The gene diversity was from 0.005 to 0.941, averagely 0.610. The polymorphism information content (PIC) value ranged from 0.005 to 0.938 with the mean of 0.577. Heterozygosity per locus on average was 0.016, ranging from 0 to 0.050. All the 595 accessions were divided into three subgroups by analysis of population genetic structure. There was linkage disequilibrium (LD) among linked loci and unlinked loci pairs, and 1 955 out of 4 560 loci pairs (42.9%) had significant LD (P < 0.01) with average D′ value of 0.23. A total of 12 locus found by GLM method significantly at the level of P<0.01 which explained 2.34%-13.94% of the phenotypic variance and the mean value was 6.33%. CAAS2050 (R ²=13.94%) and B153(R ²=11.36%) kept the max value. Meanwhile, 9 loci were found by MLM method significantly at the level of P<0.01 which explained 2.80%-9.22% of the phenotypic variance and the mean value was 5.16%. P89(R ²=9.22%) and P3*(R ²=8.28%) kept the max value. A total of 7 loci were detected in common by GLM and MLM. 【Conclusion】Genetic diversity and population structure of 595 accessions were analyzed through SSR markers. In the two association analysis models, 12 markers were associated with nine traits including stem node number, plant height, peduncle length, diameter of main stem, panicle length, panicle diameter, primary branch number per panicle, spikelet number per primary branch, protein content by GLM. Nine markers were associated with eight traits including stem node number, peduncle length, leaf width, diameter of main stem, panicle diameter, primary branch number per panicle, spikelet number per primary branch, 1000-grain weight by MLM.

Key words: foxtail millet, Shanxi, landrace, SSR, genetic diversity, linkage disequilibrium, association analysis

王海岗,温琪汾,穆志新,乔治军. 山西谷子核心资源群体结构及主要农艺性状关联分析[J]. 中国农业科学, 2019, 52(22): 4088-4099.

WANG HaiGang,WEN QiFen,MU ZhiXin,QIAO ZhiJun. Population Structure and Association Analysis of Main Agronomic Traits of Shanxi Core Collection in Foxtail Millet[J]. Scientia Agricultura Sinica, 2019, 52(22): 4088-4099.

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图/表 7

表1

96对SSR引物遗传多样性"

标记 Marker	染色体 Chromosome	基因型数 Genotype No.	等位基因数 Allele No.	基因多样性指数 Gene diversity	多态性信息含量 PIC	杂合度 Heterozygosity
In1-1	Chr.1	3	2	0.4955	0.3727	0.0183
In1-3	Chr.1	5	4	0.1810	0.1663	0.0200
In1-7	Chr.1	7	4	0.3955	0.3521	0.0267
In1-9	Chr.1	3	2	0.1113	0.1051	0.0083
CAAS1054	Chr.1	34	19	0.9051	0.8976	0.0283
P3*	Chr.1	27	15	0.8264	0.8072	0.0233
P88	Chr.1	27	14	0.8852	0.8756	0.0233
B153	Chr.1	13	10	0.7789	0.7477	0.0050
P58	Chr.1	14	8	0.7565	0.7184	0.0333
B218	Chr.1	18	9	0.8303	0.8084	0.0250
CAAS2006	Chr.2	11	5	0.7162	0.6675	0.0167
CAAS2010	Chr.2	13	6	0.6777	0.6269	0.0250
In2138	Chr.2	3	2	0.4867	0.3682	0.0267
In2184	Chr.2	4	4	0.1995	0.1815	0.0000
b242	Chr.2	10	9	0.7997	0.7730	0.0017
CAAS2050	Chr.2	11	6	0.6971	0.6435	0.0300
CAAS2030	Chr.2	6	4	0.5026	0.4165	0.0283
In2-11	Chr.2	3	2	0.0535	0.0521	0.0017
B169	Chr.2	23	18	0.9235	0.9182	0.0083
B249	Chr.2	24	22	0.9286	0.9241	0.0033
MPGD13	Chr.2	8	5	0.5607	0.4671	0.0067
b101	Chr.3	22	11	0.8607	0.8449	0.0233
B163	Chr.3	10	7	0.7193	0.6760	0.0067
B186	Chr.3	37	17	0.9182	0.9123	0.0383
P61*	Chr.3	6	4	0.6897	0.6299	0.0100
B225	Chr.3	26	16	0.8963	0.8869	0.0233
P98	Chr.3	9	6	0.5330	0.4808	0.0267
MPGD32	Chr.3	9	6	0.4217	0.3865	0.0150
MPGD44	Chr.3	8	6	0.4247	0.3914	0.0100
B224	Chr.3	47	25	0.9411	0.9379	0.0383
P78	Chr.3	14	9	0.7941	0.7657	0.0150
In4-3	Chr.4	5	4	0.4948	0.3796	0.0317
CAAS4019	Chr.4	7	5	0.4388	0.4096	0.0083
CAAS4033	Chr.4	14	8	0.8181	0.7936	0.0200
IN4-6	Chr.4	3	2	0.2608	0.2268	0.0117
IN4-7	Chr.4	6	4	0.2004	0.1909	0.0117
B109	Chr.4	38	26	0.8654	0.8533	0.0267
P2	Chr.4	28	18	0.9045	0.8970	0.0183
B247*	Chr.4	22	14	0.8866	0.8762	0.0167
P100**	Chr.4	8	7	0.5368	0.4883	0.0017
P89	Chr.4	24	17	0.8428	0.8246	0.0267
CAAS5048	Chr5	9	6	0.7318	0.6894	0.0050
In5-7	Chr.5	2	2	0.0099	0.0099	0.0000
In5-8	Chr.5	3	2	0.4382	0.3422	0.0283
CAAS5032	Chr.5	26	12	0.8911	0.8810	0.0300
b111	Chr.5	17	12	0.8842	0.8729	0.0100
P17X*	Chr.5	12	6	0.5827	0.5436	0.0200
B223	Chr.5	32	19	0.9141	0.9078	0.0317
B237	Chr.5	19	8	0.8512	0.8329	0.0267
B117	Chr.5	11	7	0.5355	0.4950	0.0233
MPGA51	Chr.5	5	4	0.2576	0.2367	0.0017
MPGD4	Chr.5	4	3	0.3705	0.3400	0.0117
In6-2	Chr.6	3	2	0.2733	0.2360	0.0133
CAAS6023	Chr.6	7	5	0.2109	0.1972	0.0067
In6-9	Chr.6	3	2	0.4986	0.3743	0.0400
In6-11	Chr.6	4	3	0.3183	0.2697	0.0017
CAAS6018	Chr.6	10	8	0.7108	0.6608	0.0117
CAAS6007	Chr.6	17	10	0.7759	0.7517	0.0183
B159	Chr.6	23	11	0.8445	0.8263	0.0233
P32	Chr.6	8	6	0.3231	0.2957	0.0050
P12X	Chr.6	18	12	0.8195	0.8004	0.0183
B250	Chr.6	35	20	0.8997	0.8917	0.0267
MPGA50	Chr.6	8	5	0.6601	0.6232	0.0150
In7-1	Chr.7	3	2	0.0050	0.0050	0.0017
CAAS7021	Chr.7	7	5	0.4033	0.3782	0.0050
SIMS14450	Chr.7	6	5	0.2846	0.2612	0.0117
CAAS7036	Chr.7	3	2	0.1569	0.1446	0.0150
In7-13	Chr.7	3	2	0.4911	0.3705	0.0500
P45	Chr.7	5	5	0.5788	0.4933	0.0000
B142	Chr.7	16	12	0.8185	0.7957	0.0100
B123	Chr.7	14	11	0.6491	0.6170	0.0083
P29	Chr.7	21	13	0.8830	0.8713	0.0150
B200	Chr.7	9	5	0.5637	0.5071	0.0083
B180	Chr.7	10	7	0.7220	0.6758	0.0067
SI 227	Chr.7	12	10	0.8304	0.8084	0.0050
In8-1	Chr.8	7	4	0.6511	0.5845	0.0183
P6	Chr.8	5	5	0.3672	0.3143	0.0000
CAAS8015	Chr.8	10	7	0.7853	0.7523	0.0100
CAAS8011	Chr.8	19	8	0.8140	0.7888	0.0250
B185	Chr.8	32	22	0.9234	0.9181	0.0183
B258	Chr.8	39	21	0.9211	0.9157	0.0300
J2（GTDZ7-1）	Chr.8	2	2	0.0099	0.0099	0.0000
P14	Chr.8	25	W	0.7974	0.7791	0.0150
B128	Chr.8	25	22	0.9309	0.9267	0.0050
b246	Chr.9	23	12	0.8797	0.8676	0.0333
CAAS9036	Chr.9	24	15	0.8811	0.8703	0.0183
b166	Chr.9	20	9	0.8320	0.8107	0.0267
CAAS9081	Chr.9	17	8	0.8058	0.7790	0.0250
CAAS9082	Chr.9	12	8	0.7926	0.7633	0.0083
CAAS9058	Chr.9	7	6	0.1620	0.1555	0.0100
P20*	Chr.9	15	11	0.7462	0.7074	0.0100
P41	Chr.9	11	9	0.7927	0.7623	0.0033
SIMS 298	Chr.9	4	3	0.4286	0.3423	0.0150
B145	Chr.9	9	6	0.5104	0.4788	0.0133
B212	Chr.9	3	3	0.0394	0.0390	0.0000
SI 110	Chr.9	5	5	0.1118	0.1093	0.0000
平均值 Mean		13	8.6	0.6097	0.5773	0.0159

表1

图1

图2

图3

图4

表2

表3

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D' 值范围 D' value ranges	LD成对点数 Number of LD pairs
0—0.2	946
0.2—0.4	870
0.4—0.6	103
0.6—0.8	29
0.8—1	7

性状 Trait	位点 SSR loci	染色体 Chromosome	GLM				MLM
			2017		2018		2017		2018
			R²	P	R²	P	R²	P	R²	P
节数SN	P58	Chr.1	0.0572	6.42E-08	0.0597	1.73E-07
	B142	Chr.7							0.052	6.39E-05
株高PH	P58	Chr.1	0.0541	1.06E-07	0.0547	2.19E-07
颈长PL	CAAS6023	Chr.6	0.0558	3E-09	0.0517	1.77E-08			0.0298	8.8E-05
叶宽LW	In6-2	Chr.6							0.0444	4.34E-05
茎粗DMS	P3*	Chr.1	0.0774	1.04E-05	0.0977	4.95E-08			0.0828	3.73E-06
	In6-2	Chr.6	0.0458	2.91E-05	0.0498	8.95E-06			0.0445	5.1E-05
	P58	Chr.1					0.0522	3.73E-05
	P89	Chr.4					0.0922	1.3E-06
	B142	Chr.7							0.0628	6.19E-05
穗长PL	B153	Chr.1	0.0605	7.03E-07	0.0517	7.02E-06
	CAAS7036	Chr.7	0.0234	3.08E-05	0.0306	1.16E-06
穗粗PD	B142	Chr.7	0.068	1.37E-05	0.0646	5.05E-05
	B117	Chr.5					0.0457	6.4E-05
码数PBNP	CAAS2050	Chr.2	0.0514	3.48E-06	0.1394	3.59E-18			0.053	1.61E-06
	In2-11	Chr.2							0.028	1.82E-05
	In6-2	Chr.6	0.0258	5.04E-05	0.0277	3.55E-05
	B142	Chr.7	0.0583	9.36E-05	0.0772	1.14E-06
码粒数SNPB	B117	Chr.5	0.0559	4.73E-06	0.0439	9.4E-05	0.046	6.78E-05
千粒重GW	CAAS6023	Chr.6					0.0375	5.05E-05
蛋白含量PC	B153	Chr.1	0.1136	1.12E-12	0.1081	4.84E-11
	In1-7	Chr.1	0.0512	3.08E-07	0.0425	1.09E-05
	P14	Chr.8	0.0901	3.77E-07	0.1108	7.03E-09