闽楠群体遗传结构分析与核心种质库构建

doi:10.11707/j.1001-7488.LYKX20230138

Abstract

Abstract:

Objective: This study aims to provide a theoretical basis for scientific management, effective protection and efficient utilization of germplasm resources, by investigating population structure of collection germplasm resources of Phoebe bournei with SSR markers, and constructing a core collection of the germplasm resources. Method: A total of 33 pairs of SSR primers were used to investigate the genetic diversity and genetic structure of 425 individual trees of P. bournei belonging to 218 subfamilies collected from 27 provenances of five provinces (autonomous region), including Fujian, Jiangxi, Hunan, Zhejiang, and Guangxi. Genetic diversity parameters such as number of observed alleles (N_a), effective number of alleles (N_e), observed heterozygosity (H_o), Shannon’s information index (I), Nei’s diversity index (H) were calculated by combined DateTrans1.0 and Popgene32 software. The genetic structure of nine populations was analyzed using STRUCTURE 2.3.4 software. The core collection was constructed by using the method of grouping and stepwise clustering with the minimum distance. The genetic diversity parameters were examined by t-test, to verify the validity of the core collection for P. bournei. Result: According to the geographical distribution of germplasm sources, 218 families can be divided into 9 populations. A total of 130 alleles were detected at 33 SSR loci, and the average number of effective alleles (N_e) was 2.159, the average observed heterozygosity (H_o) was 0.224, the average expected heterozygosity (H_e) was 0.477, and the Shannon information index (I) average value was 0.841, indicating that there was the moderate genetic diversity in the germplasm resources of P. bournei. Genetic structure analysis classified nine populations into three groups. From the 425 original germplasm resources of P. bournei, 85 core germplasms and 340 reserved germplasms were obtained through stepwise cluster sampling. The core germplasms accounted for 20% of the original germplasms, and the retention rates of its N_a, N_e, H_o, H_e, I, and H were 92.318%, 103.803%, 116.652%, 105.052%, 103.341%, and 104.664%, respectively. The t-test analysis showed that there was no significant difference in the genetic diversity parameters between the core germplasm and the original germplasm, indicating that the core germplasm was able to fully represent the genetic diversity of the original germplasm. Conclusion: The core germplasm collection preserves the genetic diversity information of the original collection, which removes the genetic redundancy. The results are beneficial to the effective protection and scientific utilization of P. bournei resources and lay a solid foundation for further breeding in P. bournei.

Key words: Phoebe bournei, germplasm resources, SSR markers, genetic diversity, core collection

CLC Number:

S722.8

Junhong Zhang,Yang Wang,Shengcai Zhou,Xiaolin Wu,Renchao Wu,Qi Yang,Yuting Zhang,Zaikang Tong. Genetic Structure Analysis and Core Germplasm Collection Construction of Phoebe bournei Populations[J]. Scientia Silvae Sinicae, 2024, 60(1): 68-79.

Figures/Tables 10

Fig.1

Table 1

Table 2

The information of 33 pairs of SSR primers"

引物 Primer	重复基元 Repeat motifs	上游引物 Forward primer sequence (5’-3’)	下游引物 Reverse primer sequence (5’-3’)	预计产物长度 Size/bp
E-MN3	(TGC)6	TTGGTGGTGATAAGGGTGGT	TCAAAGGAAGAAAGCGCAAG	154
E-MN7	(CAA)5	GTAGGGAAGGTGTTGCTGGT	TCTCAAATGCAGATGCCGTA	203
E-MN8	(GTT)6	TTTCCACCACCCAAATTCAT	ATGGTCTCCAAGACGACGAC	217
E-MN11	(ACACAA)4	TAAGCAACGAATCCATGCAA	TCCTTCCATCTGCGTCTTTT	178
E-MN17	(GGCTGG)4	CCATGCGTCTGAGCAGATTA	GGTCCACTGATGCTGGCTAT	241
E-MN19	(TG)7tatc(TATG)5	TGGACATGCACAAACCATCT	GGCAAAGAAAGGCATTGAAG	245
E-MN21	(AAT)6	TCACCAGCCCCATCTTATTC	TGCCAACACTCATCCCATTA	159
E-MN25	(AGTGC)4	ATTCATCGAAGCTGGATTGG	CATCCCATCGTCCCAAATAC	198
E-MN35	(TGT)7	ATCCTCGTCCTCATCCTCCT	GAAATCATCGCAGAAGCACA	250
E-MN46	(ATT)6	TGTCGCGTGTCAAGCACTAT	CCATCTGCAATTCTCGTCAG	225
E-MN47	(AAGGGA)4	TTGTCGGGTCAGACTCAGTG	CTTTCCATTTCCCCCATTCT	154
E-MN54	(TGA)6	CCCCAACATGGTTAGGAAGA	TGTGGAACAGTGGAAGTGGA	189
E-MN58	(TCT)5	CCATCTCTCCACGATCCCTA	TAATTTCAACGAGGGCCAAG	213
E-MN62	(AGA)5	AACAGCGGAAAGAATCAACG	TTTCACTTCGGCTTCGTCTT	229
E-MN66	(GGA)6	CTTGAGGGTTTGTCGTTGGT	TGATGGAGTTTGCTGAGGTG	213
E-MN71	(ACA)5	GGTAAGGCCTCTCCTCTGCT	GTTACTCGGGCGATGACAAT	203
E-MN88	(GCT)5	GCAAACACTCTCCCACCATT	CCCACTCTTGTCTTGCTTCC	202
E-MN89	(GAA)5	GGATCGGAAGGTGAAGATGA	CTCCGAAACGTTCCTATCCA	210
E-MN90	(GAA)5	GAGAACCCATGGTTGGTTTG	TTGCACCCTCGATTCTCTCT	208
G-MN102	(GATAAG)5	TTGCATCGTTGAGGAGCTGT	CAGAGTCGCCAATGTCGTCT	169
G-MN114	(CATT)5	ATGCTGACCGTGGTTCGATT	CATGTGAGCCCATTCCAGGT	208
G-MN120	(CCGGG)5	GGTGTGTCCAAGAGGTGTGT	ACTACCAACCGTGTGCATGT	260
G-MN134	(CATATC)5	TGTGCTGTATTTGGTCGCCT	CGATGGCTGGAACTGTGGAT	256
G-MN140	(TGGTTC)5	TGACCTCGGGAAGACACTCT	ATCTAGTAGGCAGCATGCGC	215
G-MN145	(AAGAGC)6	GAGGGAGCCATCCTTGATCG	TCCCTTGAGGAGACCAGGTT	198
G-MN146	(CCGAA)5	TGCGGTGATGGAGAAAGCAT	TGACAGATCCAAGGCAGCTG	195
G-MN150	(TCA)6	GAGCGATCCAAAGCCAATGC	ACCAAACTGCTCAGGGATCG	211
G-MN157	(AACCG)5	TGAGACCGAAAGCTTGGGAC	ACAACATGCATTTGGTGGGC	242
G-MN161	(GCAC)5	CAGCTCCCACCTCAAAACCT	GCGTCTGACTTGCAACTGTG	227
G-MN168	(ATGAGG)6	GTTGAAGAAGTCGGGGGAGG	GACTCCATTTCGCATTCGGC	165
G-MN174	(CTG)7	ACACCATTACTGCTGCTGCT	AGTACAGCCCATTGTCACCG	207
G-MN186	(CTCCAA)5	GAGCCGCACTTCAACTAGGT	GGAGTGGGAGTTGGAGTTGG	195
G-MN191	(TATCAC)5	GATGGCAGCTTCAACTTGGC	TCCCCAACTAGGTGGGATGT	237

Table 2

Table 3

Table 4

Fig.2

Table 5

Table 6

Table 7

Table 8

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群体 Population	地理来源 Geographic source	家系 Family	种质数量 Sample size
1 福建北部 Northern Fujian	政和Zhenghe	13, 14, 15, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88	18
	建瓯Jian’ou	10, 29, 30, 31, 32	5
	南平Nanping	124, 203, 204, 205, 206, 207, 208	7
	浦城Pucheng	67, 68, 69	3
	武夷山Wuyishan	2, 89, 90, 91	4
	松溪Songxi	3, 4, 12, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 118, 119, 121, 122, 123	26
2 福建中部 Central Fujian	三明Sanming	5, 6, 7, 196, 197, 198	6
	尤溪Youxi	46	1
	沙县Shaxian	8, 9, 71, 72, 73, 92, 93, 94, 95, 96, 97, 98	12
	泰宁Taining	57, 58, 59, 60, 61, 62, 63, 64, 65, 66	10
	将乐Jiangle	47, 48, 49, 50, 51, 52, 53, 54, 55, 56	10
	明溪Mingxi	43, 44, 45	3
	永安Yong’an	33, 34, 35, 36, 37, 38, 39, 40, 41, 42	10
3 福建南部 Southern Fujian	武平Wuping	199, 200, 201, 202	4
4 广西北部 Northern Guangxi	龙胜Longsheng	21, 22, 229	3
	兴安Xing’an	24, 25, 26, 27, 28	5
	三江Sanjiang	20	1
5 湖南西部 Western Hunan	邵阳Shaoyang	184, 185, 186	3
5 湖南西部 Western Hunan	永州Yongzhou	192, 193, 194, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 228	19
6 湖南东部 Eastern Hunan	炎陵Yanling	181, 182, 183	3
7 江西北部 Northern Jiangxi	上饶Shangrao	168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180	13
8 江西南部 Southern Jiangxi	赣州Ganzhou	156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167	12
	吉安Ji’an	125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155	23
	遂川Suichuan	137, 138, 139, 140, 141, 142, 143, 144	8
9 浙江南部 Southern Zhejiang	庆元Qingyuan	191, 225, 226, 227	4
	松阳Songyang	187, 188, 189, 190	4
	泰顺Taishun	209	1

位点 Locus	N_a	N_e	H_o	H_e	I	H	PIC
E-MN3	4.000	2.273	0.351	0.561	0.934	0.560	0.466
E-MN7	3.000	2.417	0.002	0.587	0.986	0.586	0.521
E-MN8	4.000	2.589	0.485	0.614	1.073	0.614	0.535
E-MN11	3.000	1.646	0.181	0.393	0.663	0.392	0.337
E-MN17	3.000	2.142	0.000	0.534	0.821	0.533	0.424
E-MN19	3.000	2.306	0.647	0.567	0.908	0.566	0.470
E-MN21	3.000	2.077	0.000	0.519	0.798	0.519	0.412
E-MN25	4.000	2.980	0.238	0.665	1.202	0.664	0.601
E-MN35	4.000	2.379	0.551	0.580	1.002	0.580	0.510
E-MN46	4.000	2.320	0.320	0.570	0.935	0.569	0.474
E-MN47	4.000	2.234	0.304	0.553	0.905	0.552	0.457
E-MN54	3.000	2.166	0.054	0.539	0.897	0.538	0.466
E-MN58	5.000	2.574	0.454	0.612	1.060	0.612	0.537
E-MN62	3.000	2.950	0.358	0.662	1.090	0.661	0.587
E-MN66	4.000	2.461	0.177	0.594	1.004	0.594	0.523
E-MN71	3.000	2.996	0.424	0.667	1.098	0.666	0.592
E-MN88	3.000	2.633	0.233	0.621	1.029	0.620	0.547
E-MN89	3.000	1.977	0.318	0.495	0.738	0.494	0.385
E-MN90	3.000	2.325	0.332	0.571	0.920	0.570	0.478
G-MN102	4.000	1.329	0.000	0.248	0.543	0.248	0.237
G-MN114	4.000	1.142	0.005	0.124	0.269	0.124	0.118
G-MN120	2.000	1.200	0.000	0.167	0.307	0.167	0.153
G-MN134	10.000	4.677	0.699	0.787	1.774	0.786	0.759
G-MN140	3.000	1.437	0.000	0.305	0.562	0.304	0.275
G-MN145	3.000	1.768	0.285	0.435	0.767	0.434	0.390
G-MN146	4.000	1.643	0.009	0.392	0.765	0.391	0.361
G-MN150	3.000	1.204	0.047	0.170	0.353	0.169	0.160
G-MN157	2.000	1.978	0.000	0.495	0.688	0.494	0.372
G-MN161	3.000	1.191	0.115	0.161	0.347	0.160	0.153
G-MN168	3.000	1.158	0.000	0.136	0.284	0.136	0.129
G-MN174	10.000	1.444	0.268	0.308	0.723	0.307	0.295
G-MN186	9.000	4.090	0.355	0.756	1.623	0.756	0.718
G-MN191	4.000	1.532	0.169	0.348	0.678	0.347	0.319
平均值Mean	3.939	2.159	0.224	0.477	0.841	0.476	0.417

群体Population	N_a	N_e	H_o	H_e	H	I
福建北部 Northern Fujian	3.636	2.049	0.227	0.462	0.460	0.797
福建南部Southern Fujian	2.455	1.968	0.280	0.474	0.444	0.713
福建中部Central Fujian	3.394	1.912	0.233	0.423	0.421	0.723
广西北部Northern Guangxi	2.758	1.830	0.157	0.421	0.409	0.692
湖南东部Eastern Hunan	2.364	1.924	0.263	0.408	0.374	0.623
湖南西部Western Hunan	3.455	2.287	0.248	0.516	0.510	0.892
江西北部Northern Jiangxi	2.242	1.621	0.218	0.313	0.306	0.504
江西南部Southern Jiangxi	2.788	1.957	0.201	0.406	0.404	0.674
浙江南部Southern Zhejiang	3.000	2.155	0.226	0.471	0.458	0.786
平均值Mean	2.899	1.967	0.228	0.433	0.421	0.712

取样比例 Sampling ratio	种质数目 Germplasm number	N_a	N_e	H_o	H_e	I	H
50	213	3.849	2.093	0.242	0.461	0.805	0.459
45	191	3.849	2.102	0.245	0.463	0.809	0.461
40	170	3.849	2.123	0.245	0.467	0.818	0.466
35	149	3.849	2.141	0.249	0.475	0.833	0.474
30	128	3.788	2.172	0.247	0.482	0.844	0.480
25	106	3.758	2.198	0.254	0.491	0.858	0.489
20	85	3.636	2.241	0.261	0.501	0.869	0.498
15	64	3.606	2.168	0.268	0.491	0.846	0.487
10	43	3.606	2.204	0.277	0.497	0.857	0.491

群体 Population	N_a	N_e	H_o	H_e	I	H
原始种质Original germplasms	3.939	2.159	0.224	0.477	0.841	0.476
核心种质Core germplasms	3.636	2.241	0.261	0.501	0.869	0.498
保留率Retention rate(%)	92.318	103.803	116.652	105.052	103.341	104.664
保留种质Reserved germplasms	3.909	2.122	0.215	0.465	0.819	0.465
保留率Retention rate(%)	99.241	98.300	95.804	97.568	97.360	97.647

Genetic Structure Analysis and Core Germplasm Collection Construction of Phoebe bournei Populations

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参数 Parameters	群体 Population	均值 Mean	标准差 Standard deviation	均值差值 Mean difference	t	P
N_a	原始种质Original germplasms	3.939	1.952	0.303	0.690	0.493
N_a	核心种质Core germplasms	3.636	1.597
N_e	原始种质Original germplasms	2.159	0.803	?0.082	?0.412	0.681
N_e	核心种质Core germplasms	2.241	0.821
H_o	原始种质Original germplasms	0.224	0.205	?0.038	?0.716	0.477
H_o	核心种质Core germplasms	0.261	0.223
H_e	原始种质Original germplasms	0.477	0.185	?0.024	?0.535	0.595
H_e	核心种质Core germplasms	0.501	0.185
I	原始种质Original germplasms	0.841	0.339	?0.028	?0.329	0.743
I	核心种质Core germplasms	0.869	0.363
H	原始种质Original germplasms	0.476	0.185	?0.022	?0.484	0.630
H	核心种质Core germplasms	0.498	0.184

类群 Group	分布区域 Distribution area	地理来源 Geographic source	家系 Family
第一类群（蓝色部分） The first group (blue part)	1 福建北部Northern Fujian	政和 Zhenghe	13, 87
		建瓯Jian’ou	29, 31
		南平Nanping	203, 204, 206, 207, 208
		松溪Songxi	3, 100, 101, 102, 103, 104, 105, 106, 107, 108, 111, 112, 114, 115, 116, 118, 119, 122
	2 福建中部Central Fujian	三明Sanming	5, 7, 196(2), 197, 198
		沙县Shaxian	9, 73, 94, 97
		将乐Jiangle	51
		明溪Mingxi	43
第二类群（绿色部分） The second group (green part)	3 福建南部Southern Fujian	武平Wuping	200, 201, 202
	5 湖南西部Western Hunan	邵阳Shaoyang	184, 186
		永州Yongzhou	192, 193, 210, 211, 212, 213, 215, 216, 217, 218(2), 219, 220, 222, 223(2), 228
	6 湖南东部Eastern Hunan	炎陵Yanling	181, 182, 183(2)
	8 江西南部Southern Jiangxi	吉安Ji’an	130, 147, 151
		遂川Suichuan	138, 141
	9 浙江南部Southern Zhejiang	庆元Qingyuan	191(2), 225, 226, 227(2)
		松阳Songyang	187, 188(2), 190
		泰顺Taishun	209
第三群类（红色部分） The third group (red part)	4 广西北部Northern Guangxi	兴安Xing’an	26
		三江Sanjiang	20
	7 江西北部Northern Jiangxi	上饶Shangrao	168, 172

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