Genetic Diversity Analysis and DNA Fingerprint Construction Based on SSR Markers for Xanthoceras sorbifolia

doi:10.13560/j.cnki.biotech.bull.1985.2023-1148

Abstract

Abstract:

【Objective】This work aims to quickly identify and utilize Xanthoceras sorbifolia germplasm resources, and explore the relationship of germplasm.【Method】Eleven primers with clear bands and good polymorphism were selected from 20 pairs of SSR primers. Fluorescence capillary electrophoresis technology was used for 29 X. sorbifolia varieties（lines）polymorphism detection. The neighbor-joining method was utilized for cluster analysis, while numerical and letter codes were assigned to create molecular identity cards. 【Result】A total of 66 alleles were detected, and each pair of primers detected 3-10 alleles with an average of 6. The Shannon information index（I）varied from 1.723 to 0.349，with an average of 1.16. The polymorphic information content（PIC）revealed by different primers ranged from 0.276 to 0.841，with an average of 0.66. The observed heterozygosity（Ho）ranged from 0.137 to 0.958, with an average of 0.739. The expected heterozygosity（He）ranged from 0.187 to 0.79, with an average of 0.648. Among the 11 loci, 7 loci had an average observed heterozygosity greater than the average expected heterozygosity. The genetic diversity coefficient varied from 0 to 1 with an average of 0.31. There were 15 individuals with a genetic similarity coefficient above 0.6, accounting for only 5.17% of the total data. At the genetic distance of 0.42, the 29 X. sorbifolia materials were divided into three categories by cluster analysis. Based on these results, the DNA fingerprint database composed of the digits 0 and 1 and the molecular identity card were established, which allowed unequivocal identification of all the varieties except a few unique ones. 【Conclusion】This indicates that the genetic diversity of the 29 germplasm resources of X. sorbifolia is relatively high, but there is also a certain degree of inbreeding. Molecular identity cards for X. sorbifolia using SSR markers is simple and feasible，which may provide technical support and scientific basis for genetic identification，rights protection，identity validation，traceability management，and new variety breeding of X. sorbifolia varieties.

Key words: Xanthoceras sorbifolia, varieties（lines）, fluorescent labeled SSR markers, genetic diversity, fingerprints, molecular identity card, clustering analysis

LI Si-qi, ZHANG Wen-chen, YANG Liu, FU Qing-xin, HONG Xin, ZHANG Hai-wang. Genetic Diversity Analysis and DNA Fingerprint Construction Based on SSR Markers for Xanthoceras sorbifolia[J]. Biotechnology Bulletin, 2024, 40(5): 74-83.

Figures/Tables 8

References 30

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编号 Code	材料名称 Accession	来源地 Origin	形态特征 Main characteristics
1	优系-1红	朝阳县	红花，三棱果型
2	优系-1黄	朝阳县	黄花，三棱果型
3	优系-1白	朝阳县	白花，平顶长方果型
4	优系-2红	朝阳县	红花，桃形果型
5	圆大硕种	彰武县	白花，奇数羽状复叶
6	悄然薄壳	彰武县	白花，果壳较薄
7	中石1号	彰武县	白花，平顶正方形果型
8	中石4号	彰武县	白花，小球果型
9	中石7号	彰武县	白花，三棱果型
10	中石9号	彰武县	白花，三棱果型
11	优系-2白	建平县	白花，桃形果型
12	优系-3白	建平县	白花，小球果型
13	优系-4白	建平县	白花，小球果型
14	优系-3红	朝阳县	红花，三棱果型
15	优系-2黄	朝阳县	黄花，平顶正方形果型
16	优系-4红	建平县	红花，三棱果型
17	优系-5白	义县	白花，三棱果型
18	辽红1号	建平县	红花，长尖果型
19	辽富1号	建平县	白花，扁球果型
20	优系-6白	建平县	白花，果大，丰产
21	优系-7白	建平县	白花，果大，丰产
22	优系-8白	建平县	白花，果大，丰产
23	优系-9白	建平县	白花，果大，丰产
24	优系-10白	建平县	白花，果大，丰产
25	优系-11白	建平县	白花，果大，丰产
26	优系-12白	建平县	白花，果大，丰产
27	优系-13白	建平县	白花，果大，丰产
28	优系-14白	建平县	白花，果大，丰产
29	辽冠1号	彰武县	白花，果实青色

编号 Code	材料名称 Accession	来源地 Origin	形态特征 Main characteristics
1	优系-1红	朝阳县	红花，三棱果型
2	优系-1黄	朝阳县	黄花，三棱果型
3	优系-1白	朝阳县	白花，平顶长方果型
4	优系-2红	朝阳县	红花，桃形果型
5	圆大硕种	彰武县	白花，奇数羽状复叶
6	悄然薄壳	彰武县	白花，果壳较薄
7	中石1号	彰武县	白花，平顶正方形果型
8	中石4号	彰武县	白花，小球果型
9	中石7号	彰武县	白花，三棱果型
10	中石9号	彰武县	白花，三棱果型
11	优系-2白	建平县	白花，桃形果型
12	优系-3白	建平县	白花，小球果型
13	优系-4白	建平县	白花，小球果型
14	优系-3红	朝阳县	红花，三棱果型
15	优系-2黄	朝阳县	黄花，平顶正方形果型
16	优系-4红	建平县	红花，三棱果型
17	优系-5白	义县	白花，三棱果型
18	辽红1号	建平县	红花，长尖果型
19	辽富1号	建平县	白花，扁球果型
20	优系-6白	建平县	白花，果大，丰产
21	优系-7白	建平县	白花，果大，丰产
22	优系-8白	建平县	白花，果大，丰产
23	优系-9白	建平县	白花，果大，丰产
24	优系-10白	建平县	白花，果大，丰产
25	优系-11白	建平县	白花，果大，丰产
26	优系-12白	建平县	白花，果大，丰产
27	优系-13白	建平县	白花，果大，丰产
28	优系-14白	建平县	白花，果大，丰产
29	辽冠1号	彰武县	白花，果实青色

序号No.	引物名称Primer name	5'标记荧光5' fluorescent marker
1	QXH002	5' FAM
2	QXH049	5' HEX
3	QXH177	5' HEX
4	QXH262	5' TAMRA
5	QXH274	5' FAM
6	QXH282	5' TAMRA
7	QXH365	5' FAM
8	QXHS371	5' TAMRA
9	QXH643	5' ROX
10	QBLB58	5' HEX
11	QBRS192	5' ROX

序号No.	引物名称Primer name	5'标记荧光5' fluorescent marker
1	QXH002	5' FAM
2	QXH049	5' HEX
3	QXH177	5' HEX
4	QXH262	5' TAMRA
5	QXH274	5' FAM
6	QXH282	5' TAMRA
7	QXH365	5' FAM
8	QXHS371	5' TAMRA
9	QXH643	5' ROX
10	QBLB58	5' HEX
11	QBRS192	5' ROX

位点 Locus	观测等位基因数 Number of alleles (Na)	有效等位基因数 Effective number of alleles (Ne)	Shannon 信息指数 Shannon information index (I)	观测杂合 Observed heterozygosity (Ho)	期望杂合 Expected heterozygosity (He)	固定指数 Fixation index (F)	多态信息含量 Polymorphic information content (PIC)
QXH002	3	2.591	0.950	0.942	0.602	-0.599	0.659
QXH049	5	3.521	1.297	0.884	0.706	-0.271	0.753
QXH177	7	3.309	1.338	0.863	0.697	-0.237	0.705
QXH262	8	4.579	1.648	0.838	0.780	-0.080	0.811
QXH274	10	4.845	1.723	0.958	0.790	-0.218	0.838
QXH282	6	3.616	1.333	0.884	0.711	-0.263	0.765
QXH365	4	2.322	0.959	0.340	0.560	0.396	0.601
QXHS371	5	1.933	0.759	0.440	0.444	-0.018	0.545
QXH643	8	4.614	1.623	0.905	0.778	-0.165	0.841
QBLB58	4	1.812	0.751	0.340	0.410	0.109	0.276
QBRS192	6	1.272	0.349	0.137	0.187	0.179	0.507