基于SSR标记的福建省闽楠代表性群体遗传多样性分析

doi:10.12302/j.issn.1000-2006.202111016

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南京林业大学学报（自然科学版） ›› 2022, Vol. 46 ›› Issue (4): 102-108.doi: 10.12302/j.issn.1000-2006.202111016

基于SSR标记的福建省闽楠代表性群体遗传多样性分析

冯一宁¹(), 李因刚², 祁铭¹, 周鹏燕¹, 周琦², 董乐¹, 徐立安¹^,^*()

1.南京林业大学,南方现代林业协同创新中心,江苏南京 210037
2.浙江省林业科学研究院,浙江杭州 310023

收稿日期:2021-01-26 修回日期:2021-09-08 出版日期:2022-07-30 发布日期:2022-08-01
通讯作者: 徐立安
基金资助:
浙江省省属科研院所扶持专项(2021F1065-1)

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

摘要/Abstract

摘要：

【目的】闽楠(Phoebe bournei)是珍贵的用材树种,被列为国家Ⅱ级重点保护野生植物。以福建省内保存较好的3个代表性闽楠自然群体为对象,研究其群体间及群体内的遗传变异水平及遗传结构特征,探究其成因,为闽楠天然群体的保护和利用提供依据。【方法】利用自行开发的18个多态性SSR标记,对3个群体共计88个样本进行检测,利用Popgene 32软件,分析群体的有效等位基因数(N_e)、观测杂合度(H_o)、期望杂合度(H_e)、基因分化系数(F_st))等,利用Structure软件研究群体的遗传结构。【结果】3个闽楠群体的平均期望杂合度为0.629,表明遗传多样性较丰富;3个群体的平均观测杂合度明显低于期望杂合度,群体内近交程度较高[近交系数(F)=0.280)],尤其是罗卜岩群体H_o/H_e差异大(0.399/0.608)、近交程度高(F=0.378);分子变异分析显示,闽楠的变异主要来源于群体内,群体间存在中等程度的分化(F_st=0.197)。聚类分析结果表明,3个群体闽楠样本可明显区分为两类,两类间存在明显的遗传分化,福建罗卜岩和福建顺昌群体为第Ⅰ类,且两者地理位置较近;福建政和与其距离较远,为第Ⅱ类。【结论】福建闽楠3个代表性群体具有较高的遗传多样性,但具有小群体特征,群体内近交程度较高,而地理隔离和人为活动使闽楠具有一定程度的遗传分化;应采取措施使群体内充分异交,以维持闽楠群体较高的遗传多样性。

关键词: 闽楠, SSR标记, 遗传多样性, 遗传分化, 遗传结构

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

中图分类号:

S722

冯一宁,李因刚,祁铭,等. 基于SSR标记的福建省闽楠代表性群体遗传多样性分析[J]. 南京林业大学学报（自然科学版）, 2022, 46(4): 102-108.

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 (Natural Science Edition), 2022, 46(4): 102-108.DOI: 10.12302/j.issn.1000-2006.202111016.

图/表 8

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参考文献 22

[1]	傅立国, 金鉴明. 中国植物红皮书——稀有濒危植物[M]. 北京: 科学出版社, 1991:358-359.
	FU L G, JIN J M. China plant red data book:rare and endangered plants[M]. Beijing: Science Press, 1991: 358-359.
[2]	郑金兴, 黄锦学, 王珍珍, 等. 闽楠人工林细根寿命及其影响因素[J]. 生态学报, 2012, 32(23):7532-7539.
	ZHENG J X, HUANG J X, WANG Z Z, et al. Fine root longevity and controlling factors in a Phoebe bournei plantation[J]. Acta Ecol Sin, 2012, 32(23):7532-7539.DOI:10.5846/stxb201110231566.
[3]	唐星林, 刘光正, 姜姜, 等. 遮阴对闽楠一年生和三年生幼树叶绿素荧光特性及能量分配的影响[J]. 生态学杂志, 2020, 39(10):3247-3254.
	TANG X L, LIU G Z, JIANG J, et al. Effects of shading on the chlorophyll fluorescence characteristics and light energy partitioning of one-and three-year-old Phoebe bournei seedlings[J]. Chin J Ecol, 2020, 39(10):3247-3254.DOI:10.13292/j.1000-4890.202010.013.
[4]	何应会, 梁瑞龙, 蒋燚, 等. 珍贵树种闽楠研究进展及其发展对策[J]. 广西林业科学, 2013, 42(4):365-370.
	HE Y H, LIANG R L, JIANG Y, et al. Research progress of precious species Phoebe bournei and its development strategies[J]. Guangxi For Sci, 2013, 42(4):365-370.DOI:10.19692/j.cnki.gfs.2013.04.015.
[5]	陈星, 高子厚. DNA分子标记技术的研究与应用[J]. 分子植物育种, 2019, 17(6):1970-1977.
	CHEN X, GAO Z H. The study and application of DNA molecular marker technique[J]. Mol Plant Breed, 2019, 17(6):1970-1977.DOI:10.13271/j.mpb.017.001970.
[6]	WAHLSTEEN E. SSR markers distinguish critically endangered Acer campestre populations from cryptic invading gene pools[J]. Willdenowia, 2021, 51(1):115-125.DOI:10.3372/wi.51.51109.
[7]	LI Q Y, SU X J, MA H H, et al. Development of genic SSR marker resources from RNA-seq data in Camellia japonica and their application in the genus Camellia[J]. Sci Rep, 2021, 11(1):9919.DOI:10.1038/s41598-021-89350-w.
[8]	李新军, 黄敏仁, 潘惠新, 等. 林木基因组中的微卫星(SSR)及其应用[J]. 南京林业大学学报, 1999, 23(5):64-69.
	LI X J, HUANG M R, PAN H X, et al. Microsatellite markers and appication in the forestry genome[J]. J Nanjing For Univ, 1999, 23(5):64-69.DOI:10.3969/j.issn.1000-2006.1999.05.015.
[9]	程小毛, 黄晓霞. SSR标记开发及其在植物中的应用[J]. 中国农学通报, 2011, 27(5):304-307.
	CHENG X M, HUANG X X. Development and application of SSR markers in plants[J]. Chin Agric Sci Bull, 2011, 27(5):304-307.
[10]	江香梅, 温强, 叶金山, 等. 闽楠天然种群遗传多样性的RAPD分析[J]. 生态学报, 2009, 29(1):438-444.
	JIANG X M, WEN Q, YE J S, et al. RAPD analysis on genetic diversity in eight natural populations of Phoebe bournei from Fujian and Jiangxi Province,China[J]. Acta Ecol Sin, 2009, 29(1):438-444.DOI:10.3321/j.issn:1000-0933.2009.01.052.
[11]	李娟, 董利军, 林建勇, 等. 楠木树种种质资源的ISSR分析[J]. 分子植物育种, 2018, 16(19):6428-6435.
	LI J, DONG L J, LIN J Y, et al. The ISSR analysis of Phoebe nees germplasm resources[J]. Mol Plant Breed, 2018, 16(19):6428-6435.DOI:10.13271/j.mpb.016.006428.
[12]	GE Y J, LIU Y J, SHEN A H, et al. Fengshui forests conserve genetic diversity: a case study of Phoebe bournei (Hemsl.) Yang in Southern China[J]. Genet Mol Res, 2015, 14(1):1986-1993.DOI:10.4238/2015.March.20.8.
[13]	时小东, 朱学慧, 盛玉珍, 等. 基于转录组序列的楠木SSR分子标记开发[J]. 林业科学, 2016, 52(11):71-78.
	SHI X D, ZHU X H, SHENG Y Z, et al. Development of SSR markers based on transcriptome sequence of Phoebe zhennan[J]. Sci Silvae Sin, 2016, 52(11):71-78.
[14]	刘丹, 刘斌, 曾钦朦, 等. 闽楠优良基因型遗传差异的SSR分析[J]. 森林与环境学报, 2019, 39(5):449-453.
	LIU D, LIU B, ZENG Q M, et al. Genetic diversity of the superior genotypes of Phoebe bournei using SSR markers[J]. J For Environ, 2019, 39(5):449-453.DOI:10.13324/j.cnki.jfcf.2019.05.001.
[15]	黄雨芹, 尹光天, 杨锦昌, 等. 基于SSR分子标记的闽楠(Phoebe bournei)核心种质的构建[J]. 分子植物育种, 2020, 18(8):2641-2648.
	HUANG Y Q, YIN G T, YANG J C, et al. Developing a mini core germplasm of Phoebe bournei based on SSR molecular marker[J]. Mol Plant Breed, 2020, 18(8):2641-2648.DOI:10.13271/j.mpb.018.002641.
[16]	祁铭, 周琦, 倪州献, 等. 基于SSR技术的古银杏群体遗传结构分析[J]. 生态学杂志, 2019, 38(9):2902-2910.
	QI M, ZHOU Q, NI Z X, et al. Genetic structure analysis of ancient Ginkgo biloba L.populations based on SSR markers[J]. Chin J Ecol, 2019, 38(9):2902-2910.DOI:10.13292/j.1000-4890.201909.017.
[17]	EVANNO G, REGNAUT S, GOUDET J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study[J]. Mol Ecol, 2005, 14(8):2611-2620.DOI:10.1111/j.1365-294X.2005.02553.x.
[18]	徐立安, 李新军, 潘惠新, 等. 用SSR研究栲树群体遗传结构[J]. 植物学报, 2001, 43(4):409-412.
	XU L, LI X J, PAN H X, et al. Study on population genetic structure in Castanopsis fargesii with microsatellite markers[J]. Bull Bota, 2001, 43(4):409-412.DOI:10.3321/j.issn:1672-9072.2001.04.015.
[19]	陈罡, 卜鹏图, 于世河, 等. 基于SSR标记的辽宁蒙古栎天然群体遗传多样性研究[J]. 沈阳农业大学学报, 2020, 51(6):727-733.
	CHEN G, BU P T, YU S H, et al. Study on genetic diversity of natural Quercus mongolica populations in Liaoning Province revealed by SSR markers[J]. J Shenyang Agric Univ, 2020, 51(6):727-733.DOI:10.3969/j.issn.1000-1700.2020.06.012.
[20]	ZHOU P Y, HUI L X, HUANG S J, et al. Study on the genetic structure based on geographic populations of the endangered tree species:Liriodendron chinense[J]. Forests, 2021, 12(7):917.DOI:10.3390/f12070917.
[21]	WRIGHT S. Evolution and the genetics of populations. Vol. 4. Variability within and among natural populations[M]. Chicago: University of Chicago Press, 1978:97-159,.
[22]	张馨方, 张树航, 李颖, 等. 基于SSR标记的板栗种质资源遗传多样性分析[J]. 分子植物育种, 2020, 18(15):5164-5175.
	ZHANG X F, ZHANG S H, LI Y, et al. Genetic diversity analysis of Castanea mollissima germplasm resources based on SSR markers[J]. Mol Plant Breed, 2020, 18(15):5164-5175.DOI:10.13271/j.mpb.018.005164.

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

基于SSR标记的福建省闽楠代表性群体遗传多样性分析

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

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[10]	陈兴彬, 徐海宁, 肖复明, 孙世武, 娄永峰, 邹元熹, 徐小强. 陈山红心杉1.5代种子园遗传多样性和子代父本分析[J]. 南京林业大学学报（自然科学版）, 2021, 45(3): 87-92.
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[13]	乔东亚, 王鹏, 王淑安, 李林芳, 高露璐, 杨如同, 汪庆, 李亚. 基于SNP标记的紫薇遗传多样性分析[J]. 南京林业大学学报（自然科学版）, 2020, 44(4): 18-25.
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