苦荞黄酮含量与SSR标记的关联分析

石桃雄; 黎瑞源; 潘凡; 黄娟; 朱丽伟; 汪燕; 梁成刚

doi:10.19303/j.issn.1008-0384.2021.08.003

苦荞黄酮含量与SSR标记的关联分析

doi: 10.19303/j.issn.1008-0384.2021.08.003

贵州师范大学荞麦产业技术研究中心，贵州　贵阳　550001

基金项目: 国家重点研发计划项目（2019YFD1001300, 2019YFD1001301）；国家自然科学基金项目（31960125）；贵州省科技支撑计划项目（黔科合ZC[2019]2298）；贵州省荞麦种质资源保育及创新重点实验室建设基金项目（黔教合KY[2017]002）；贵州师范大学博士启动基金项目（11904/0514027）

详细信息

作者简介:
石桃雄（1980−），女，博士，副教授，研究方向：荞麦种质资源保育及创新（E-mail: shitaoxiong@126.com）

黎瑞源（1980−），男，博士，副教授，研究方向：生物信息学（E-mail: ruiyuan_li@126.com）

通讯作者:
梁成刚（1985−），男，博士，副教授，研究方向：荞麦遗传育种（E-mail: jesselcg@163.com）

中图分类号: S 517
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出版历程
- 收稿日期: 2021-04-25
- 修回日期: 2021-06-29
- 网络出版日期: 2021-08-10
- 刊出日期: 2021-08-28

Correlation Between Flavonoids Content and SSR Markers of Tartary Buckwheat

Buckwheat Industry Technology Research Center, Guizhou Normal University, Guiyang, Guizhou　550001, China

摘要

摘要: 目的开展苦荞籽粒总黄酮含量与SSR标记的关联分析，挖掘与黄酮含量相关的分子标记，为高黄酮含量苦荞品种的遗传改良提供依据。方法以193份苦荞种质为供试材料，基于62对SSR引物分析了供试种质的遗传多样性，对总黄酮含量和SSR标记进行了关联分析。结果 193个种质籽粒总黄酮含量的变幅为1.04%～2.99%，变异系数为27.93%。62对引物在193个种质中共扩增出267个等位基因，每个SSR位点平均检测到2.45个有效等位基因，基因多样性为0.503，Shannon信息指数为0.942，观测杂合度为0.513，引物多态信息量为0.74。群体结构分析将193份种质划分为3个亚群。基于广义线性模型（GLM）共检测到5个与籽粒总黄酮含量显著关联的SSR标记，表型贡献率为6.3%～12.9%，其中标记TatG0124（12.9%）和S6853（8.5%）的表型贡献率较高。结论供试苦荞种质遗传多样性丰富，可用于苦荞重要农艺和品质性状的关联分析。TatG0124和SSR6853可能是控制籽粒黄酮含量的重要位点，对改良苦荞籽粒黄酮含量具有重要意义。
- 苦荞 /
- SSR标记 /
- 黄酮含量 /
- 遗传多样性 /
- 群体结构 /
- 关联分析
Abstract: Objective Correlation between the flavonoids content and associated markers was analyzed for genetic improvement studies on Tartary buckwheat. Method Sixty-two SSR primer pairs were used to assess the genetic diversity of 193 Tartary buckwheat germplasms. The SSR markers closely related to the total flavonoids content were selected by association analysis. Result The total flavonoids content of 193 Tartary buckwheat germplasms varied from 1.04% to 2.99% with a coefficient variation of 27.93%. Sixty-two pairs of SSR primers amplified 267 polymorphic sites with an average number of effective alleles of 2.45. The mean values of gene diversity, Shannon index, observed heterozygosity and polymorphism information content of SSR markers were 0.503, 0.942, 0.513 and 0.74, respectively. The population structure analysis divided the 193 germplasms into 3 subgroups. Five SSR markers were determined to be significantly associated with flavonoids content by the general linear model (GLM). The phenotypic variations ranged from 6.3% to 12.9% with TatG0124 at 12.9% and S6853 at 8.5% being the higher markers. Conclusion The germplasms used in this study were diverse in genetic variation and feasible for related genome-wide mapping on important traits of Tartary buckwheat. The loci, TatG0124 and S6853, appeared to closely associate with the flavonoids content of Tartary buckwheat and were considered to be potentially useful for breeding new varieties with high content of the functional components.
- Tartary buckwheat /
- SSR marker /
- flavonoids content /
- genetic diversity /
- population structure /
- correlation analysis

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图 1 SSR引物TatG0124 （a）与S2234（b）在部分苦荞种质中的扩增结果

Figure 1. DNA fragments amplified by SSR primer TatG0124 (a) and S2234 (b) in part of Tartary buckwheat germplasms

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图 2 群体结构划分中ΔK随K值的变化率

Figure 2. ΔK of Ks in structure analysis

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图 3 193个苦荞种质的群体结构分析

Figure 3. Population structure analysis on 193 Tartary buckwheat germplasms

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表 1 基于62对SSR引物的193个苦荞种质的遗传多样性参数

Table 1. Genetic diversity indicators of 193 Tartary buckwheat germplasms based on 62 pairs of SSR primers

序号 Index	引物名称 Primer name	等位基因数 Na	有效等位基因数 Ne	Shannon信息指数 I	观察杂合度 Ho	基因多样性 He	多态信息量 PIC
1	S7582	4	2.253	0.918	0.932	0.556	0.82
2	S9023	5	4.120	1.497	0.813	0.757	0.90
3	S7676	3	1.451	0.519	0.005	0.311	0.58
4	S7622	3	1.418	0.568	0.130	0.295	0.61
5	S7678	4	3.110	1.224	0.802	0.678	0.77
6	S7642	4	3.501	1.320	0.578	0.714	0.81
7	S8993	3	2.196	0.858	0.865	0.545	0.73
8	S9065	5	2.309	1.002	0.771	0.567	0.79
9	S9095	3	1.442	0.532	0.328	0.307	0.77
10	S8951	3	1.696	0.727	0.151	0.410	0.64
11	S9007	3	2.813	1.063	0.188	0.644	0.73
12	S8983	3	1.759	0.736	0.109	0.432	0.64
13	S9045	3	1.099	0.206	0.000	0.09	0.66
14	S7606	3	2.089	0.802	0.839	0.521	0.73
15	S7662	3	1.709	0.721	0.109	0.415	0.65
16	S2218	5	2.400	1.012	0.844	0.583	0.72
17	S2298	3	1.833	0.753	0.479	0.455	0.80
18	S2314	3	1.241	0.389	0.026	0.194	0.56
19	S2158	5	3.401	1.351	0.797	0.706	0.82
20	S2214	4	3.486	1.314	0.438	0.713	0.81
21	S2252	3	1.840	0.749	0.469	0.457	0.66
22	S2288	4	2.471	1.033	0.875	0.595	0.74
23	S6827	4	1.875	0.814	0.417	0.467	0.67
24	S6865	3	2.038	0.780	0.766	0.509	0.60
25	S2234	5	3.378	1.348	0.870	0.704	0.83
26	S6871	5	2.274	0.938	0.901	0.560	0.77
27	S6821	5	3.136	1.230	0.672	0.681	0.82
28	S6873	4	2.752	1.187	0.266	0.637	0.85
29	S2216	6	2.695	1.193	0.948	0.629	0.87
30	S2310	5	2.173	0.879	0.88	0.540	0.70
31	S2312	7	1.535	0.784	0.094	0.349	0.85
32	S6853	7	3.615	1.453	0.953	0.723	0.88
33	S6805	4	1.350	0.470	0.271	0.259	0.80
34	S6891	3	1.244	0.366	0.000	0.196	0.20
35	S6875	4	2.178	0.863	0.880	0.541	0.78
36	S6789	4	1.505	0.698	0.125	0.335	0.79
37	S6843	3	1.299	0.464	0.078	0.230	0.79
38	S6859	4	1.582	0.664	0.036	0.368	0.72
39	S7654	5	2.811	1.151	0.438	0.644	0.78
40	S7668	4	2.219	0.893	0.813	0.549	0.61
41	S6819	5	3.461	1.325	0.734	0.711	0.80
42	S6811	3	2.105	0.796	0.964	0.525	0.53
43	S5216	3	1.021	0.065	0.000	0.021	0.67
44	S5196	3	2.128	0.82	0.870	0.530	0.57
45	S5166	4	2.300	0.922	0.875	0.565	0.79
46	S5176	3	1.134	0.252	0.000	0.118	0.69
47	S9013	4	2.544	1.026	0.964	0.607	0.73
48	S8963	4	1.065	0.165	0.005	0.061	0.52
49	S8969	3	1.321	0.489	0.135	0.243	0.59
50	S8947	4	1.295	0.412	0.219	0.228	0.71
51	S2304	4	2.228	0.951	0.214	0.551	0.82
52	TatG0242	8	7.283	2.031	0.747	0.863	0.91
53	TatG0164	4	2.248	0.923	0.124	0.555	0.78
54	TatG0227	6	2.625	1.148	0.916	0.619	0.83
55	TatG0272	4	2.391	1.096	0.202	0.582	0.79
56	TatG0188	5	2.542	1.118	0.006	0.607	0.79
57	TatG0124	6	4.437	1.573	0.787	0.775	0.89
58	TatG0004	8	4.684	1.744	0.433	0.787	0.91
59	TatG0156	6	4.370	1.562	0.899	0.771	0.88
60	TatG0214	5	3.526	1.390	0.579	0.716	0.87
61	TatG0184	9	4.248	1.699	0.646	0.765	0.91
62	TatG0175	5	3.851	1.421	0.944	0.740	0.85

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表 2 苦荞种质各亚群的遗传多样性指数

Table 2. Genetic diversity indicators for each Tartary buckwheat subgroup

亚群 Subgroup	样本数 N	等位基因数 Na	有效等位基因数 Ne	Shannon信息指数 I	观察杂合度 Ho	基因多样性 He
POP1	88	4.21	2.42	0.943	0.493	0.513
POP2	90	3.74	2.33	0.870	0.502	0.484
POP3	15	2.95	2.27	0.800	0.576	0.468

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表 3 各亚群成对Fst系数（下三角）和Nei’s遗传距离（上三角）

Table 3. Pairwise estimated Fst (below diagonal) and Nei’s genetic distance (above diagonal) for subgroups

亚群 Subgroup	POP 1	POP 2	POP 3
POP1		0.065	0.076
POP2	0.030		0.026
POP3	0.037	0.014
注：全部Fst差异显著（P＜0.001）。 Note: All Fst values are significant （P＜0.001）.

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表 4 显著LD的SSR标记成对组合数的比例和D'（标准不平衡系数）

Table 4. Percentage and D' (standardized disequilibrium) value of pairs with significant LD

群体与亚群 Population and subgroup	种质数 No. of germplasms	LD的SSR标记成对组合数 No. of SSR marker pairs in LD	LD的SSR标记成对组合所占比例 Percentage of SSR marker pairs in LD	D’
群体 Population	193	644	34.06	0.277
Pop1	88	90	4.76	0.412
Pop2	90	206	10.89	0.304
Pop3	15	97	5.13	0.493

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表 5 与苦荞籽粒黄酮含量显著相关的SSR标记

Table 5. SSR markers significantly associated with flavonoids content in Tartary buckwheat grains

SSR标记 SSR marker	F值 F value	显著水平 P	表型贡献率 R²/ %
S2310	3.146	0.0095	7.9
S2304	2.423	0.0373	6.3
TatG0124	1.848	0.0401	12.9
S2312	2.157	0.0402	7.7
S6853	2.066	0.0415	8.5

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