中国板栗品种（系）DNA指纹图谱构建及其遗传多样性分析

doi:10.16420/j.issn.0513-353x.2021-0863

园艺学报 ›› 2022, Vol. 49 ›› Issue (11): 2313-2324.doi: 10.16420/j.issn.0513-353x.2021-0863

中国板栗品种（系）DNA指纹图谱构建及其遗传多样性分析

聂兴华¹^,², 李伊然², 田寿乐³, 王雪峰⁴, 苏淑钗¹, 曹庆芹², 邢宇²^,^*(), 秦岭²^,^*()

¹北京林业大学林学院，北京 100089
²北京农学院植物科学技术学院，农业应用新技术北京市重点实验室，北京 102206
³山东省农业科学院山东果树研究所，山东泰安 271000
⁴龙潭林场，江苏溧阳 213300

收稿日期:2022-04-26 修回日期:2022-07-28 出版日期:2022-11-25 发布日期:2022-11-25
通讯作者: 邢宇,秦岭 E-mail:xingyu@bua.edu.cn;qinlingbac@126.com
基金资助:
国家自然科学基金项目(31870671)

Construction of DNA Fingerprint Map and Analysis of Genetic Diversity for Chinese Chestnut Cultivars（Lines）

NIE Xinghua¹^,², LI Yiran², TIAN Shoule³, WANG Xuefeng⁴, SU Shuchai¹, CAO Qingqin², XING Yu²^,^*(), QIN Ling²^,^*()

¹College of Forestry，Beijing Forestry University，Beijing 100089，China
²Beijing Key Laboratory for Agricultural Application and New Technique，College of Plant Science and Technology，Beijing University of Agriculture，Beijing 102206，China
³Shandong Institute of Pomology，Shandong Academy of Agricultural Sciences，Tai’an，Shandong 271000，China
⁴Longtan Forest Farm，Liyang，Jiangsu 213300，China

Received:2022-04-26 Revised:2022-07-28 Online:2022-11-25 Published:2022-11-25
Contact: XING Yu,QIN Ling E-mail:xingyu@bua.edu.cn;qinlingbac@126.com

摘要/Abstract

摘要：

基于SSR荧光分子标记，对中国342个板栗品种（系）构建了DNA指纹图谱，并解析了各品种群间的亲缘关系和遗传分化特征。结果表明：（1）所有SSR标记多位点匹配后的PI和PIsibs值分别为4.960 × 10^-20和2.395 × 10^-8，显示本试验所选用的标记指纹识别潜力强;对342份品种（系）构建指纹图谱，共获得338个有唯一对应关系的指纹信息，其中舒城大红袍与焦扎、双合大红袍与CSB-1两两共享了一个指纹信息，结合主要植物学性状，推测其为同物异名品种;同时发现存在大于10个位点信息差异的19份同名资源，判定其为同名异物品种。（2）两两品种群的F_st平均值为0.0224（F_st< 0.05），表明品种群间遗传分化程度较低;对5个品种群进行了基因流（N_m）和AMOVA分析，遗传变异主要存在于个体内，占总变异的84%，各品种群间的平均基因流为6.592，表明资源间存在着广泛的基因交换，制约了各群体间的分化。（3）利用位点数据进行群体结构、主坐标和聚类树分析表明，板栗品种资源主要被划分为南、北两大品种群，确定了沿大别山山脉的湖北东北部、河南南部和安徽中北部、以及山东南部和江苏北部地区为分界带（混交地带）。

关键词: 板栗, SSR, 指纹图谱, 遗传多样性

Abstract:

The DNA fingerprint map of 342 chestnut cultivars（lines）was constructed using SSR fluorescent molecular markers as well as the genetic relationship and genetic differentiation were further illuminated among the cultivar groups in the current investigation. The results showed that：（1）The PI and and PIsibs values of all the markers combined were 4.960 × 10^-20and 2.395 × 10^-8，respectively，indicating that the 21 markers used in this study had excellent potential for fingerprint recognition. A total of 338 unique corresponding fingerprint information were obtained from 342 cultivars（lines）. Among them，‘Shucheng Dahongpao’shared only one fingerprint information with‘Jiaoza’，similarly for ‘Shuanghe Dahongpao’and‘CSB-1’. Combined with the main botanical traits，these cultivars（lines） were finally speculated to be synonym. Simultaneously，19 same-named cultivars（lines）with more than ten loci differences were identified as homonym. （2）The average F_st of each pairwise of chestnut cultivar groups was 0.0224（F_st < 0.05），which demonstrated that there was low genetic differentiation among cultivar groups. Subsequently，gene flow（N_m）and AMOVA were carried out on the five cultivar groups. The genetic variation of chestnut cultivars（lines）mainly was found in individuals，accounting for 84% of the total variation. The average gene flow among cultivar groups was 6.592，revealing extensive gene exchange and restricting differentiation among chestnut cultivar groups.（3）From analyzing the population structure，principal coordinates and cluster tree via the site data，it could be seen that all chestnut cultivars （lines）were mainly divided into two major groups，the north and the south. Meanwhile，a region of northeastern Hubei，southern Henan，and north-central Anhui along the Dabie Mountains and the southern Shandong，the northern Jiangsu constituted the boundary zone（mixed zone）of two groups.

Key words: Chinese chestnut, SSR, fingerprint map, genetic diversity

中图分类号:

S664.2

聂兴华, 李伊然, 田寿乐, 王雪峰, 苏淑钗, 曹庆芹, 邢宇, 秦岭. 中国板栗品种（系）DNA指纹图谱构建及其遗传多样性分析[J]. 园艺学报, 2022, 49(11): 2313-2324.

NIE Xinghua, LI Yiran, TIAN Shoule, WANG Xuefeng, SU Shuchai, CAO Qingqin, XING Yu, QIN Ling. Construction of DNA Fingerprint Map and Analysis of Genetic Diversity for Chinese Chestnut Cultivars（Lines）[J]. Acta Horticulturae Sinica, 2022, 49(11): 2313-2324.

图/表 9

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编号 Number	分子标记 Marker ID	基因库ID GenBank ID	正向引物序列（5′-3′） Forward primer	反向引物序列（5′-3′） Reverse primer	观察的重复序列 Observed-Motif
1	CmSI0396	290474606	AACTCCCACCACTCACATCC	TTTCGGACCATCCAGAACTC	CACACC
2	CmSI0509	290474647	CAAGTCCGATCCTTCCTCTG	AGCTGGGTTTTGAGTAGCGA	ACA
3	CmSI0561	290474702	CGTATAGGGTGGAAACGGAA	GGACAAGCAAATCACGGAAT	TCG
4	CmSI0614	290476556	TTGTGGTGAAGCTGACATCG	GGGTACTACCACAACATGCAG	GTT
5	CmSI0617	290475843	GCCTCAGCTGGTAACGAAGA	TCACATGGGCTTGTTGTAGC	GA
6	CmSI0658	290474781	AAAACGGTTTGTGGTGAAGC	GCCAACCAGTCAAGGGTACT	GTT
7	CmSI0702	290474818	GAAACACACCAGAGAGATGCAG	TTTTATACAGAGACATACTATCCTACACAG	TC
8	CmSI0735	290474842	ACGCCTTCAGTTGCTGTTTC	CAACGGTCTTACCCTTTGGA	AGAA
9	CmSI0742	290474850	GACGCTCCTCAGCTTTTGAC	TGCCGGTCAATTCTTCTTCT	AG
10	CmSI0800	290474899	TTATGGCAACCCTCCTGTTT	CTGAAATGATCGATGCTGCT	TC
11	CmSI0853	290474950	GGAGGAGGAGGAGCTCATTG	CCTTGGAGAGCTGCCAGTAG	TCT
12	CmSI0871	290474967	AGGGGGTGGAAGAACCTATG	AGATTGCAAGTGGGGAATTG	TCT
13	CmSI0881	290476058	TCCGACAAGCTACCGAGTCT	CCTAAATCAATCTTGCACCCATA	GA
14	CmSI0883	290476060	CAGCATCAGCACTCGTTCA	GGGATTGAGAGGATGAAGCA	AGC
15	CmSI0922	290475011	AATCTGAACCCCTCCGATCT	ACCAACAACATGTGCCAAAA	TTG
16	CmSI0930	290475019	CCATTTAGCATGCATAGTCATACC	GCAAGGATGTAGGTCGAATCA	ATAC
17	CmSI0938	290475031	CACGATTCCCACGATTCTTA	CGTCCAACTCCGTACTCTCC	GAC
18	CmSI0404	290474610	GTGCTACGACTACCGCTGCT	AGAATAACCTCGCGGTGAGA	ACA
19	CmSI0747	290474854	CATTCCAACAATGCACTCTCA	CGAGTTGGAGTCACCGAAGT	CTT
20	CmSI0809	290474901	GAGCGAGTCGAAGAAGGAAG	ATCTGCTTCGGCACCATCT	GGT
21	CmSI0933	290475025	AGGCCTCTTCTCCCTTGTGT	TCCTGTTCCTATGCTGCTCA	AGA

编号 Number	分子标记 Marker ID	基因库ID GenBank ID	正向引物序列（5′-3′） Forward primer	反向引物序列（5′-3′） Reverse primer	观察的重复序列 Observed-Motif
1	CmSI0396	290474606	AACTCCCACCACTCACATCC	TTTCGGACCATCCAGAACTC	CACACC
2	CmSI0509	290474647	CAAGTCCGATCCTTCCTCTG	AGCTGGGTTTTGAGTAGCGA	ACA
3	CmSI0561	290474702	CGTATAGGGTGGAAACGGAA	GGACAAGCAAATCACGGAAT	TCG
4	CmSI0614	290476556	TTGTGGTGAAGCTGACATCG	GGGTACTACCACAACATGCAG	GTT
5	CmSI0617	290475843	GCCTCAGCTGGTAACGAAGA	TCACATGGGCTTGTTGTAGC	GA
6	CmSI0658	290474781	AAAACGGTTTGTGGTGAAGC	GCCAACCAGTCAAGGGTACT	GTT
7	CmSI0702	290474818	GAAACACACCAGAGAGATGCAG	TTTTATACAGAGACATACTATCCTACACAG	TC
8	CmSI0735	290474842	ACGCCTTCAGTTGCTGTTTC	CAACGGTCTTACCCTTTGGA	AGAA
9	CmSI0742	290474850	GACGCTCCTCAGCTTTTGAC	TGCCGGTCAATTCTTCTTCT	AG
10	CmSI0800	290474899	TTATGGCAACCCTCCTGTTT	CTGAAATGATCGATGCTGCT	TC
11	CmSI0853	290474950	GGAGGAGGAGGAGCTCATTG	CCTTGGAGAGCTGCCAGTAG	TCT
12	CmSI0871	290474967	AGGGGGTGGAAGAACCTATG	AGATTGCAAGTGGGGAATTG	TCT
13	CmSI0881	290476058	TCCGACAAGCTACCGAGTCT	CCTAAATCAATCTTGCACCCATA	GA
14	CmSI0883	290476060	CAGCATCAGCACTCGTTCA	GGGATTGAGAGGATGAAGCA	AGC
15	CmSI0922	290475011	AATCTGAACCCCTCCGATCT	ACCAACAACATGTGCCAAAA	TTG
16	CmSI0930	290475019	CCATTTAGCATGCATAGTCATACC	GCAAGGATGTAGGTCGAATCA	ATAC
17	CmSI0938	290475031	CACGATTCCCACGATTCTTA	CGTCCAACTCCGTACTCTCC	GAC
18	CmSI0404	290474610	GTGCTACGACTACCGCTGCT	AGAATAACCTCGCGGTGAGA	ACA
19	CmSI0747	290474854	CATTCCAACAATGCACTCTCA	CGAGTTGGAGTCACCGAAGT	CTT
20	CmSI0809	290474901	GAGCGAGTCGAAGAAGGAAG	ATCTGCTTCGGCACCATCT	GGT
21	CmSI0933	290475025	AGGCCTCTTCTCCCTTGTGT	TCCTGTTCCTATGCTGCTCA	AGA

分子标记 Marker ID	主要位点频率MAF	基因型数N_g	位点数 N_a	Shannon多样性指数I	观察杂合度H_o	期望杂合度H_e	基因流 N_m	多态信息含量 PIC	身份概率 PI	随机身份概率 PIsibs
CmSI0396	0.568	9	4	0.989	0.589	0.567	7.678	0.492	0.261	0.532
CmSI0509	0.477	13	6	1.179	0.542	0.646	4.987	0.583	0.188	0.474
CmSI0561	0.509	32	14	1.602	0.630	0.694	3.793	0.673	0.118	0.433
CmSI0617	0.325	30	9	1.713	0.714	0.778	3.482	0.744	0.081	0.381
CmSI0658	0.249	22	7	1.703	0.752	0.802	5.099	0.774	0.069	0.366
CmSI0702	0.412	26	11	1.409	0.647	0.702	3.202	0.655	0.140	0.434
CmSI0735	0.403	27	10	1.604	0.557	0.732	9.646	0.697	0.109	0.411
CmSI0742	0.422	20	13	1.346	0.627	0.689	6.857	0.633	0.151	0.443
CmSI0800	0.326	58	22	2.020	0.633	0.802	8.051	0.777	0.063	0.365
CmSI0809	0.270	24	10	1.824	0.624	0.809	2.930	0.762	0.063	0.362
CmSI0853	0.301	26	14	1.740	0.749	0.792	7.355	0.762	0.073	0.372
CmSI0871	0.597	15	11	0.920	0.522	0.527	11.653	0.448	0.306	0.563
CmSI0883	0.278	33	13	1.787	0.636	0.798	4.404	0.770	0.070	0.368
CmSI0933	0.646	10	7	0.936	0.493	0.514	10.042	0.459	0.294	0.567
CmSI0938	0.785	14	7	0.755	0.204	0.364	10.284	0.332	0.432	0.676
CmSI0922	0.254	38	12	1.944	0.738	0.833	7.656	0.811	0.049	0.346
CmSI0930	0.419	51	20	1.885	0.697	0.763	9.199	0.741	0.080	0.389
CmSI0881	0.324	24	8	1.760	0.493	0.798	6.470	0.756	0.068	0.368
CmSI0614	0.212	29	10	1.857	0.761	0.826	6.203	0.800	0.054	0.351
CmSI0404	0.839	6	4	0.781	0.224	0.388	2.285	0.254	0.400	0.656
CmSI0747	0.549	10	5	1.382	0.487	0.676	7.158	0.578	0.143	0.448
平均值Mean	0.436	24.619	10.333	1.483	0.587	0.690	6.592	0.643	0.153	0.443
组合 Combined	—	—	—	—	—	—	—	—	4.960 ×10^-20	2.395×10^-8

分子标记 Marker ID	主要位点频率MAF	基因型数N_g	位点数 N_a	Shannon多样性指数I	观察杂合度H_o	期望杂合度H_e	基因流 N_m	多态信息含量 PIC	身份概率 PI	随机身份概率 PIsibs
CmSI0396	0.568	9	4	0.989	0.589	0.567	7.678	0.492	0.261	0.532
CmSI0509	0.477	13	6	1.179	0.542	0.646	4.987	0.583	0.188	0.474
CmSI0561	0.509	32	14	1.602	0.630	0.694	3.793	0.673	0.118	0.433
CmSI0617	0.325	30	9	1.713	0.714	0.778	3.482	0.744	0.081	0.381
CmSI0658	0.249	22	7	1.703	0.752	0.802	5.099	0.774	0.069	0.366
CmSI0702	0.412	26	11	1.409	0.647	0.702	3.202	0.655	0.140	0.434
CmSI0735	0.403	27	10	1.604	0.557	0.732	9.646	0.697	0.109	0.411
CmSI0742	0.422	20	13	1.346	0.627	0.689	6.857	0.633	0.151	0.443
CmSI0800	0.326	58	22	2.020	0.633	0.802	8.051	0.777	0.063	0.365
CmSI0809	0.270	24	10	1.824	0.624	0.809	2.930	0.762	0.063	0.362
CmSI0853	0.301	26	14	1.740	0.749	0.792	7.355	0.762	0.073	0.372
CmSI0871	0.597	15	11	0.920	0.522	0.527	11.653	0.448	0.306	0.563
CmSI0883	0.278	33	13	1.787	0.636	0.798	4.404	0.770	0.070	0.368
CmSI0933	0.646	10	7	0.936	0.493	0.514	10.042	0.459	0.294	0.567
CmSI0938	0.785	14	7	0.755	0.204	0.364	10.284	0.332	0.432	0.676
CmSI0922	0.254	38	12	1.944	0.738	0.833	7.656	0.811	0.049	0.346
CmSI0930	0.419	51	20	1.885	0.697	0.763	9.199	0.741	0.080	0.389
CmSI0881	0.324	24	8	1.760	0.493	0.798	6.470	0.756	0.068	0.368
CmSI0614	0.212	29	10	1.857	0.761	0.826	6.203	0.800	0.054	0.351
CmSI0404	0.839	6	4	0.781	0.224	0.388	2.285	0.254	0.400	0.656
CmSI0747	0.549	10	5	1.382	0.487	0.676	7.158	0.578	0.143	0.448
平均值Mean	0.436	24.619	10.333	1.483	0.587	0.690	6.592	0.643	0.153	0.443
组合 Combined	—	—	—	—	—	—	—	—	4.960 ×10^-20	2.395×10^-8

群体 Pop	样品数 Sample	位点数 N_a	有效等位位点 N_e	Shannon’s 多样性指数 I	观察杂合度 H_o	期望杂合度 H_e
Pop1（华北品种群North China group）	190	8.714 ± 0.772	3.675 ± 0.282	1.450 ± 0.083	0.577 ± 0.032	0.685 ± 0.030
Pop2（西北品种群Northwest China group）	10	4.857 ± 0.347	3.286 ± 0.210	1.289 ± 0.080	0.595 ± 0.044	0.658 ± 0.032
Pop3（长江中下游品种群Middle and lower reaches of the Yangtze River group）	100	7.810 ± 0.699	3.320 ± 0.294	1.347 ± 0.094	0.601 ± 0.042	0.642 ± 0.035
Pop4（东南品种群 Southeast China group）	18	6.286 ± 0.522	3.593 ± 0.339	1.391 ± 0.096	0.582 ± 0.050	0.662 ± 0.035
Pop5（西南品种群 Southwest China group）	24	6.381 ± 0.567	3.368 ± 0.309	1.462 ± 0.091	0.585 ± 0.043	0.703 ± 0.029

中国板栗品种（系）DNA指纹图谱构建及其遗传多样性分析

Construction of DNA Fingerprint Map and Analysis of Genetic Diversity for Chinese Chestnut Cultivars（Lines）

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变异来源 Source of variance	自由度 df	方差总和 SS	平均方差 MS	变异组分 Variance component	变异百分率/% Variation	P
种群间Among Pops	4	134.102	33.526	0.249	3	< 0.001
个体间Among Indiv	337	2722.196	8.078	0.965	13	< 0.001
个体内Within Indiv	342	2102.500	6.148	6.148	84	< 0.010
总量Total	683	4958.798		7.362	100

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中国板栗品种（系）DNA指纹图谱构建及其遗传多样性分析

Construction of DNA Fingerprint Map and Analysis of Genetic Diversity for Chinese Chestnut Cultivars（Lines）

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