基于SSR标记的青海蚕豆品种亲缘关系分析与指纹图谱构建

doi:10.3724/SP.J.1006.2025.44066

作物学报 ›› 2025, Vol. 51 ›› Issue (1): 79-90.doi: 10.3724/SP.J.1006.2025.44066

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

基于SSR标记的青海蚕豆品种亲缘关系分析与指纹图谱构建

郑栋¹^,²(), 周仙莉¹^,², 滕长才¹^,²^,^*(), 侯万伟¹^,²^,⁴, 张红岩¹^,², 刘玉皎¹^,³^,^*()

¹青海大学, 青海西宁 810016
²青海省农林科学院, 青海西宁 810016
³青海大学省部共建三江源生态与高原农牧业国家重点实验室, 青海西宁 810016
⁴国家农作物种质资源复份库, 青海西宁 810016

收稿日期:2024-04-19 接受日期:2024-09-18 出版日期:2025-01-12 网络出版日期:2024-10-10
通讯作者: *刘玉皎, E-mail: 13997058356@163.com; 滕长才, E-mail: 13299761531@163.com
作者简介:E-mail: 1304063128@qq.com
基金资助:
青海省重点研发与转化计划项目(2022-NK-109);财政部和农业农村部国家现代农业产业技术体系建设专项(CARS-08-G06)

Genetic relationship analysis and fingerprints construction of faba bean varieties in Qinghai province based on SSR markers

ZHENG Dong¹^,²(), ZHOU Xian-Li¹^,², TENG Chang-Cai¹^,²^,^*(), HOU Wan-Wei¹^,²^,⁴, ZHANG Hong-Yan¹^,², LIU Yu-Jiao¹^,³^,^*()

¹Qinghai University, Xining 810016, Qinghai, China
²Qinghai Academy of Agriculture and Forestry Sciences, Xining 810016, Qinghai, China
³State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, Qinghai, China
⁴National Crop Germplasm Resources Duplicate Library, Xining 810016, Qinghai, China

Received:2024-04-19 Accepted:2024-09-18 Published:2025-01-12 Published online:2024-10-10
Contact: *E-mail: 13997058356@163.com; E-mail: 13299761531@163.com
Supported by:
Key Research and Development and Transformation Plan of Qinghai Province(2022-NK-109);China Agriculture Research System of MOF and MARA(CARS-08-G06)

摘要/Abstract

摘要：

为明确青海蚕豆育成品种、高代品系和骨干亲本的群体结构与亲缘关系, 本研究利用46对多态性和稳定性好、重复性高的SSR引物对36个青海蚕豆主栽品种(品系)进行群体遗传学分析并构建了指纹图谱。结果表明, 通过毛细管电泳检测, 在46对引物中检测到262个等位位点, 各引物检测的多态性等位位点数(Na)为2~15, 平均等位位点数为5.696个, 平均每个位点检测到的有效等位基因数为2.988个, 范围为1.180~9.257; Shannon指数的变化范围为0.287~2.444, 均值为1.210; 多态性信息含量(polymorphism information content, PIC)值变化范围为0.141~0.883, 均值为0.553, 揭示了青海蚕豆品种丰富的遗传多样性。系统聚类将36份材料划分为4个亚群, 第I、II、III、IV亚群分别包括24、4、7、1份材料; 群体结构与主坐标分析将材料划分为2个亚群, 亚群I和亚群II分别包括17和19份材料, 与聚类分类结果有一定程度的交叉重合, 厘清了青海蚕豆主栽品种的群体遗传结构与亲缘关系。在此基础上, 筛选出4对核心引物, 构建了36份材料的指纹图谱, 并将相关信息储存在二维码中。青海蚕豆主栽品种指纹图谱的构建不仅为青海蚕豆品种鉴定提供了有效工具, 也为今后青海蚕豆品种亲本选配和新品种权保护提供了技术支撑。

关键词: 蚕豆, 青海, 主栽品种, SSR标记, 亲缘关系, 指纹图谱

Abstract:

To clarify the population structure and relationships among cultivated varieties, advanced lines, and backbone parents of faba bean in Qinghai province, forty-six pairs of SSR primers with high polymorphism, stability, and repeatability were used to analyze the genetic diversity of thirty-six varieties (lines) and construct genetic fingerprints. The results revealed that 262 alleles were detected using the forty-six primer pairs through capillary electrophoresis. The number of polymorphic alleles (Na) per primer ranged from two to fifteen, with an average of 5.696 alleles. The average number of effective alleles per locus was 2.988, ranging from 1.180 to 9.257. The Shannon index ranged from 0.287 to 2.444, with an average of 1.210. The polymorphism information content (PIC) varied from 0.141 to 0.883, with an average of 0.553, indicating rich genetic diversity among the faba bean varieties in Qinghai. Clustering analysis grouped the 36 materials into four subgroups: subgroup I (twenty-four materials), subgroup II (four materials), subgroup III (seven materials), and subgroup IV (one material). Population genetic structure and principal coordinate analyses divided the materials into two subgroups, with subgroup I containing seventeen materials and subgroup II containing nineteen materials. There was some overlap between the subgroups identified by clustering and those identified by population structure analysis, which clarified the genetic relationships and population structure of the main faba bean cultivars in Qinghai province. On this basis, four core primer pairs were selected to construct genetic fingerprints for the thirty-six materials, which were subsequently stored in a two-dimensional code. The fingerprinting of the main faba bean cultivars in Qinghai provides an effective tool for variety identification and offers technical support for parental selection and the protection of new varieties in future faba bean breeding programs in the region.

Key words: faba bean, Qinghai, main cultivars, SSR maker, genetic relationships, fingerprint

郑栋, 周仙莉, 滕长才, 侯万伟, 张红岩, 刘玉皎. 基于SSR标记的青海蚕豆品种亲缘关系分析与指纹图谱构建[J]. 作物学报, 2025, 51(1): 79-90.

ZHENG Dong, ZHOU Xian-Li, TENG Chang-Cai, HOU Wan-Wei, ZHANG Hong-Yan, LIU Yu-Jiao. Genetic relationship analysis and fingerprints construction of faba bean varieties in Qinghai province based on SSR markers[J]. Acta Agronomica Sinica, 2025, 51(1): 79-90.

图/表 8

表1

36份供试材料信息"

编号 No.	材料名称 Material name	材料来源 Material source	生长习性 Growth habit
1	青海1号 Qinghai 1	牛角蚕豆中系统选育 Systematic selection of Niujiao faba bean	无限 Indeterminacy
2	青海2号 Qinghai 2	—	无限 Indeterminacy
3	青海3号 Qinghai 3	拉萨1号×互助东和蚕豆 Lhasa 1×Huzhudonghe faba bean	无限 Indeterminacy
4	青海4号 Qinghai 4	—	无限 Indeterminacy
5	青海5号 Qinghai 5	—	无限 Indeterminacy
6	青海6号 Qinghai 6	—	无限 Indeterminacy
7	青海8号 Qinghai 8	农14×103 Nong 14×103	无限 Indeterminacy
8	青海11号 Qinghai 11	72-45×新西兰 72-45×New Zealand	无限 Indeterminacy
9	青海12号 Qinghai 12	青海3号×马牙//72-45×英国176 Qinghai 3×Maya//72-45×UK176	无限 Indeterminacy
10	青海13号Qinghai 13	马牙×戴韦 Maya×Divine	无限 Indeterminacy
11	青蚕14号Qingcan 14	72-45×日本寸蚕 72-45× Japanese Cuncan	无限 Indeterminacy
12	青蚕15号Qingcan 15	湟中落角×96-49 Huangzhongluojiao ×96-49	无限 Indeterminacy
13	青蚕16号Qingcan 16	马牙×Flip88-243FB Maya×Flip88-243FB	有限 Determinacy
14	青蚕17号Qingcan 17	透心绿系选 Systematic selection of Touxinlyu	无限 Indeterminacy
15	青蚕18号Qingcan 18	意大利蚕豆资源3290 Italian faba bean resource 3290	无限 Indeterminacy
16	青蚕19号Qingcan 19	云南新平绿豆×3290 Yunnanxinpinglyudou×3290	无限 Indeterminacy
17	青蚕20号Qingcan 20	云南新平绿豆×3290 Yunnanxinpinglyudou×3290	无限 Indeterminacy
18	青蚕21号Qingcan 21	130×意大利资源 166 130× Italian resource 166	无限 Indeterminacy
19	青蚕22号Qingcan 22	2005-00系选Systematic selection of 2005-00	无限 Indeterminacy
20	青蚕23号Qingcan 23	马牙×戴韦 Maya×Divine	无限 Indeterminacy
21	青蚕24号Qingcan 24	云122系选 Systematic selection of Yun 122	无限 Indeterminacy
22	青蚕25号Qingcan 25	马牙×戴韦 Maya×Divine	无限 Indeterminacy
23	青蚕26号Qingcan 26	—	无限 Indeterminacy
24	青蚕27号Qingcan 27	意大利资源 166 Italy resource 166	无限 Indeterminacy
25	青蚕28号Qingcan 28	意大利资源 166 Italy resource 166	无限 Indeterminacy
26	青蚕32号Qingcan 32	Y4系选 Systematic selection of Y4	有限 Determaincy
27	青蚕33号Qingcan 33	Y4×GF22	有限 Determaincy
28	RF12	2008F34黑有-7-1-16 2008F34 Heiyou-7-1-16	亚有限 Semi-determinacy
29	RF15	2008F34黑有-7-2-5 2008F34 Heiyou-7-2-5	亚有限 Semi-determinacy
30	RF22	2008F34黑有-7-4-11 2008F34 Heiyou-7-4-11	亚有限 Semi-determinacy
31	羊眼豆Yangyandou	甘肃农家种 Landrace of Gansu province	无限 Indeterminacy
32	沙珠玉紫蚕豆 Shazhuyu purple faba bean	农家种 Landrace	无限 Indeterminacy
33	RF19	2008F34黑有-7-3-7-1 2008F34 Heiyou-7-3-7-1	亚有限 Semi-determinacy
34	R4061	云122-3×2005-00 Yun 122-3×2005-00	无限 Indeterminacy
35	R4053	云122-3×2005-00 Yun 122-3×2005-00	无限 Indeterminacy
36	GF22	云南新平绿豆×3290 Yunnanxinpinglyudou×3290	无限 Indeterminacy

表1

表2

SSR位点多态性信息及鉴定概率"

标记 Marker	位点数 Number of alleles (Na)	主要位点频率 Major allele frequency (MAF)	有效位点数 Number of effective alleles (Ne)	Shannon’s 指数 Shannon’s diversity index (I)	Nei’s遗传多样性指数Nei’s gene diversity	多态信息含量 Polymorphism information content (PIC)	位点上的同一性概率 PI	相邻位点上的同一性概率 PI_sibs
4-37	6.000	0.529	2.558	1.180	0.609	0.546	0.216	0.500
3-54	3.000	0.618	2.181	0.920	0.542	0.480	0.271	0.547
6-118	2.000	0.600	1.923	0.673	0.480	0.365	0.386	0.606
1L-20	3.000	0.528	2.374	0.949	0.579	0.496	0.260	0.526
3-51	4.000	0.571	2.445	1.080	0.591	0.535	0.223	0.510
4-119	6.000	0.429	3.393	1.413	0.705	0.659	0.133	0.431
6-55	2.000	0.917	1.180	0.287	0.153	0.141	0.730	0.856
1S-113	6.000	0.457	3.165	1.360	0.684	0.635	0.149	0.445
2-28	4.000	0.486	2.360	0.979	0.576	0.486	0.270	0.529
1L-51	6.000	0.778	1.620	0.862	0.383	0.368	0.396	0.658
2-63	4.000	0.833	1.412	0.595	0.292	0.272	0.521	0.734
1L-73	7.000	0.412	4.014	1.609	0.751	0.719	0.094	0.398
1L-90	2.000	0.583	1.946	0.679	0.486	0.368	0.382	0.603
1S-68	3.000	0.771	1.610	0.696	0.379	0.347	0.417	0.665
1S-109	2.000	0.611	1.906	0.668	0.475	0.362	0.388	0.609
5-09	3.000	0.600	2.005	0.776	0.501	0.401	0.349	0.587
2-36	3.000	0.543	2.416	0.973	0.586	0.512	0.246	0.518
1L-15	6.000	0.361	3.904	1.496	0.744	0.702	0.107	0.405
6-14	13.000	0.278	7.200	2.251	0.861	0.849	0.032	0.327
4-42	7.000	0.457	2.981	1.357	0.664	0.609	0.168	0.460
1S-26	5.000	0.486	2.612	1.132	0.617	0.545	0.218	0.496
2-01	4.000	0.472	2.711	1.127	0.631	0.562	0.205	0.486
3-40	3.000	0.486	2.536	0.997	0.606	0.525	0.236	0.506
3-23	2.000	0.667	1.800	0.637	0.444	0.346	0.407	0.630
3-39	2.000	0.694	1.737	0.615	0.424	0.334	0.421	0.643
3-22	4.000	0.400	2.855	1.137	0.650	0.579	0.193	0.473
6-21	9.000	0.361	4.909	1.853	0.796	0.773	0.064	0.368
6-24	7.000	0.444	2.972	1.348	0.664	0.606	0.170	0.461
6-62	8.000	0.500	3.322	1.574	0.699	0.672	0.118	0.430
3-61	8.000	0.389	4.408	1.734	0.773	0.746	0.078	0.383
2-106	11.000	0.429	3.990	1.776	0.749	0.722	0.090	0.398
2-103	15.000	0.194	9.257	2.444	0.892	0.883	0.021	0.309
3-52	9.000	0.371	4.268	1.729	0.766	0.735	0.086	0.389
3-94	6.000	0.486	3.249	1.426	0.692	0.655	0.132	0.437
4-100	8.000	0.429	4.016	1.677	0.751	0.724	0.089	0.397
4-63	12.000	0.500	3.429	1.748	0.708	0.687	0.107	0.423
3-122	3.000	0.800	1.514	0.637	0.340	0.313	0.463	0.696
3-65	6.000	0.559	2.627	1.254	0.619	0.575	0.189	0.488
6-47	4.000	0.444	2.602	1.069	0.616	0.537	0.226	0.499
6-58	3.000	0.559	2.165	0.859	0.538	0.444	0.308	0.558
5-112	13.000	0.417	4.469	1.964	0.776	0.757	0.069	0.379
5-87	5.000	0.514	2.753	1.213	0.637	0.582	0.187	0.478
5-64	6.000	0.667	2.098	1.108	0.523	0.494	0.256	0.552
6-113	7.000	0.472	3.447	1.521	0.710	0.677	0.117	0.424
6-112	6.000	0.571	2.485	1.184	0.598	0.547	0.213	0.504
3-81	4.000	0.514	2.601	1.085	0.616	0.548	0.216	0.496
平均Mean	5.696	0.526	2.988	1.210	0.606	0.553	0.231	0.505

表2

图1

图2

图3

表3

图4

表4

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引物 Primer	序列 Sequence (5°-3°)	简称Abbreviation	编码 Code (bp)
引物 Primer	序列 Sequence (5°-3°)	简称Abbreviation	0	1	2	3	4	5	6	7
6-21	F: GGCTGTTGCAATCAACTGG R: CGACCAGCTCCATCCTACAT	M1	—	136	292	301	306
3-52	F: TCACCCCCACTATTCTCACTG R: CCGCCCTCACTTTCAGTCTA	M2	—	253	267	272	278	290	295	306
1L-15	F: CGAGACTCGCGTCATTTGTA R: CATGGCGATCAAGTTCAGTG	M3	—	255	259	266	270
6-113	F: TTCTGCTTGAGGAAGCACCT R: CGGATCTTGTGGGTTGAAAG	M4	—	267	274	284	292

编号Number	材料名称 Material name	指纹编码 Fingerprint coding	编号Number	材料名称 Material name	指纹编码 Fingerprint coding
1	青海1号 Qinghai 1	23041313	19	青蚕22号 Qingcan 22	02020303
2	青海2号 Qinghai 2	03040303	20	青蚕23号 Qingcan 23	03040101
3	青海3号 Qinghai 3	24042403	21	青蚕24号 Qingcan 24	03030203
4	青海4号 Qinghai 4	24042302	22	青蚕25号 Qingcan 25	03030214
5	青海5号 Qinghai 5	04040203	23	青蚕26号 Qingcan 26	02040202
6	青海8号 Qinghai 8	14030313	24	青蚕27号 Qingcan 27	04060303
7	青海6号 Qinghai 6	03031313	25	青蚕28号 Qingcan 28	13051303
8	青海11号 Qinghai 11	03040103	26	青蚕32号 Qingcan 32	03460203
9	青海12号 Qinghai 12	23041313	27	青蚕33号 Qingcan 33	03450303
10	青海13号 Qinghai 13	04040123	28	RF12	03451203
11	青蚕14号 Qingcan 14	12040204	29	RF15	03040301
12	青蚕15号 Qingcan 15	04461304	30	RF22	03030301
13	青蚕16号 Qingcan 16	02040103	31	羊眼豆 Yangyandou	04020101
14	青蚕17号 Qingcan 17	03020303	32	沙珠玉紫蚕豆 Shazhuyu purple faba bean	01020201
15	青蚕18号 Qingcan 18	03010201	33	RF19	02030201
16	青蚕19号 Qingcan 19	02020302	34	R4061	03030303
17	青蚕20号 Qingcan 20	14070203	35	R4053	12030103
18	青蚕21号 Qingcan 21	04000303	36	GF22	03451203

基于SSR标记的青海蚕豆品种亲缘关系分析与指纹图谱构建

Genetic relationship analysis and fingerprints construction of faba bean varieties in Qinghai province based on SSR markers

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