Genetic diversity analyses of Phoebe bournei representative populations in Fujian Province based on SSR markers

doi:10.12302/j.issn.1000-2006.202111016

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2022, Vol. 46 ›› Issue (4): 102-108.doi: 10.12302/j.issn.1000-2006.202111016

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Genetic diversity analyses of Phoebe bournei representative populations in Fujian Province based on SSR markers

FENG Yining¹(), LI Yingang², QI Ming¹, ZHOU Pengyan¹, ZHOU Qi², DONG Le¹, XU Li’an¹^,^*()

1. Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
2. Zhejiang Academy of Forestry,Hangzhou 310023,China

Received:2021-01-26 Revised:2021-09-08 Online:2022-07-30 Published:2022-08-01
Contact: XU Li’an E-mail:2312274295@qq.com;laxu@njfu.edu.cn

Abstract

Abstract:

【Objective】 Phoebe bournei is a precious timber tree, and listed as a national Class Ⅱ key-protected wild plant. This study aimed to understand the genetic variation levels and structural characteristics of the three representative and well-preserved natural populations (Luoboyan, Shunchang and Zhenghe) of P. bournei in Fujian Province, China, and explore the causes of genetic variation to provide a basis for the protection and utilization of natural populations. 【Method】 We used 18 self-developed polymorphic SSR markers to select 88 samples from the three populations. The effective number of alleles (N_e), observed heterozygosity (H_o), expected heterozygosity (H_e), and gene differentiation coefficient (F_st) were analyzed using Popgene 32 software. Besides, Structure software was used to study the genetic structure of the populations. 【Result】 The average expected heterozygosity of the three populations was 0.629, indicating the relatively rich genetic diversity of the three populations. In addition, the average observed heterozygosity of the three populations was significantly lower than expected, with a high inbreeding degree (F = 0.280). In particular, the H_o/H_e ratio of the Luobuyan population was large (0.399/0.608), with a high degree of inbreeding (0.378). The molecular variation analysis revealed that the variations in P. bournei populations were mainly from within, and a moderate degree of differentiation existed between populations (F_st = 0.197). The cluster analysis results indicated that the samples from the three populations could be divided into two groups, with an obvious genetic differentiation between them. Luoboyan and Shunchang populations comprised the first group because of their close geographical locations, and Zhenghe population formed the second because of being located distantly. 【Conclusion】 The three representative populations of P. bournei in Fujian Province had the high genetic diversity but small population characteristics, with a relatively high degree of inbreeding within the populations. However, geographical isolation and human activities had caused the P. bournei populations to attain a certain degree of genetic differentiations. Measures should be adopted to enable the full outcrossing of the populations to maintain the high genetic diversity of P. bournei.

Key words: Phoebe bournei, SSR markers, genetic diversity, genetic differentiation, genetic structure

CLC Number:

S722

FENG Yining, LI Yingang, QI Ming, ZHOU Pengyan, ZHOU Qi, DONG Le, XU Li’an. Genetic diversity analyses of Phoebe bournei representative populations in Fujian Province based on SSR markers[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY, 2022, 46(4): 102-108.

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采样群体 sampling population	样本数 sampling amount	经度/(°) longitude (E)	纬度/(°) altitude (N)	海拔/m latitude	年均气温/℃ annual average air temperature	年降水量/ mm annual average precipitation	平均胸径/cm average DBH	胸径范围/cm DBH range
福建罗卜岩LBY	33	117.24	26.26	604	12.5	1 926.9	14.35	1.5~42.0
福建顺昌SC	26	117.95	26.82	543	18.5	1 756.0	61.93	24.6~93.3
福建政和ZH	29	118.36	27.26	302	16.5	1 609.0	66.03	30.1~104.5

引物名称 primer name	重复单元 repeat motif	引物序列(5'-3') primer sequence	长度/bp length	退火温度/℃ annealing temperature
ph_EST-SSR1	(CT)₃₂	GTGCTCTCTCTTGATTGTTCG	237	63
ph_EST-SSR2	(GA)₃₃	TAGCAGCAACTGAAGAGGA	410	62
ph_EST-SSR3	(CT)₃₆	TGTGGGATAGCCTTGATGTACTT	443	60
ph_EST-SSR4	(AG)₃₄	AAGTCCGATCTCGCAAAC	284	63
ph_EST-SSR5	(T)₆₀	AAACCATTAATTCCTCAACAGCA	445	63
ph_EST-SSR6	(GAA)₁₀	CGTCTTCGTTTCGCTACT	218	63
ph_EST-SSR7	(TTC)₁₀	TCTCGCCATCCTACTTCG	432	63
ph_EST-SSR8	(AG)₃₃	AGGTTCGTCGGAGTTAGG	333	63
ph_EST-SSR9	(CT)₃₆	ATGTGGGATAGCCTTGATGTACT	444	60
ph_EST-SSR10	(ATT)₁₄	TCGATTTGCAGAAGATAAGCC	449	63
ph_EST-SSR11	(TCT)₁₂	AGAGGGCCTGTGCGTACGTTT	352	63
ph_EST-SSR12	(GAA)₁₂	GCTAGAGCTCAAAGGATCCC	344	63
ph_EST-SSR13	(T)₂₅	GAAGTAGAAGAAGAAGATCCCT	230	63
ph_EST-SSR14	(AG)₃₅	GCCTGTGTTTGGAGTATGGA	229	63
ph_EST-SSR15	(CT)₃₁	GAGAAGGGCATCAACACCAAC	259	63
ph_EST-SSR16	(CT)₃₆	CTGCCATGTGGGATAGCCTTGAT	476	63
ph_EST-SSR17	(CTT)₁₀	AACAGGAGAAGGGAAGCAATGG	375	63
ph_EST-SSR18	(AGA)₁₁	AGTAATACCAGCAGTACCAGTC	126	63

引物 locus	N_a	N_e	H_o	H_e	PIC	F_st	N_m	HWE^*	I
ph_EST-SSR1	15	6.980	0.080	0.862	0.845	0.102	2.211	**	2.295
ph_EST-SSR2	19	7.333	0.307	0.869	0.854	0.104	2.157	**	2.443
ph_EST-SSR3	14	7.326	0.148	0.868	0.849	0.178	1.152	**	2.194
ph_EST-SSR4	8	3.350	0.466	0.706	0.774	0.421	0.344	**	1.474
ph_EST-SSR5	5	4.439	0.716	0.779	0.811	0.267	0.687	**	1.546
ph_EST-SSR6	12	5.367	0.136	0.818	0.792	0.079	2.926	**	1.970
ph_EST-SSR7	4	2.756	0.989	0.641	0.793	0.070	3.334	**	1.102
ph_EST-SSR8	18	10.130	0.216	0.906	0.893	0.122	1.794	**	2.523
ph_EST-SSR9	14	5.282	0.057	0.815	0.796	0.097	2.323	**	2.114
ph_EST-SSR10	9	4.823	0.148	0.797	0.764	0.470	0.282	**	1.777
ph_EST-SSR11	6	3.337	0.568	0.704	0.649	0.285	0.628	**	1.360
ph_EST-SSR12	7	2.893	0.773	0.658	0.605	0.081	2.852	**	1.306
ph_EST-SSR13	11	2.305	0.477	0.569	0.537	0.104	2.159	**	1.298
ph_EST-SSR14	7	3.832	0.523	0.743	0.701	0.258	0.719	**	1.577
ph_EST-SSR15	8	5.210	0.534	0.813	0.783	0.118	1.876	**	1.822
ph_EST-SSR16	10	5.210	0.330	0.813	0.783	0.335	0.497	**	1.866
ph_EST-SSR17	6	3.926	0.989	0.750	0.700	0.197	1.023	**	1.444
ph_EST-SSR18	10	4.999	0.671	0.805	0.773	0.260	0.713	**	1.773
平均mean	10.167	4.972	0.451	0.773	0.761	0.197	1.020	**	1.771

群体 population	N_a	N_e	H_o	H_e	AR	F
福建罗卜岩LBY	5.778	2.934	0.399	0.608	6.740	0.378
福建顺昌SC	6.167	3.379	0.440	0.638	7.444	0.310
福建政和ZH	6.944	3.293	0.521	0.641	6.610	0.143
群体水平population level	6.296	3.202	0.453	0.629	6.932	0.280
物种水平 species level	10.167	4.972	0.451	0.773	9.309	0.417

变异来源 sources of variation	方差分量 variance component	变异比例/% variation ratio	P
群体间 among population	6.413	28	0.010
群体内 within population	16.689	72	0.010
总计total	23.103	100

Genetic diversity analyses of Phoebe bournei representative populations in Fujian Province based on SSR markers

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