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

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

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

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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

Abstract

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

CLC Number:

S664.2

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.

Figures/Tables 9

References 28

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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

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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