基于SSR标记的白栎天然居群遗传多样性分析

doi:10.12302/j.issn.1000-2006.202004049

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南京林业大学学报（自然科学版） ›› 2021, Vol. 45 ›› Issue (1): 63-69.doi: 10.12302/j.issn.1000-2006.202004049

基于SSR标记的白栎天然居群遗传多样性分析

臧明月(), 李璇, 方炎明^*()

南京林业大学生物与环境学院,南方现代林业协同创新中心,亚热带森林生物多样性保护国家林业和草原局重点实验室,江苏南京 210037

收稿日期:2020-04-25 接受日期:2020-07-10 出版日期:2021-01-30 发布日期:2021-02-01
通讯作者: 方炎明
基金资助:
国家自然科学基金项目(31770699);国家自然科学基金项目(31370666);江苏高校优势学科建设工程资助项目(PAPD);南京林业大学2017年优秀博士学位论文创新基金项目(2170014)

Genetic diversity analysis among natural populations of Quercus fabri based on SSR markers

ZANG Mingyue(), LI Xuan, FANG Yanming^*()

Co-Innovation Center for the Sustainable Forestry in Southern China, Key Laboratory of National Administration of Forestry and Grassland on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China

Received:2020-04-25 Accepted:2020-07-10 Online:2021-01-30 Published:2021-02-01
Contact: FANG Yanming

摘要/Abstract

摘要：

【目的】利用SSR分子标记,对白栎天然居群进行遗传多样性分析,为其种质资源的合理开发与保护提供指导。【方法】采用筛选出的SSR引物对3个群体进行遗传多样性与遗传结构研究,并计算遗传参数;基于个体间的遗传距离进行主成分分析,运用GenAlEx 6.5进行遗传距离与地理距离的相关性Mantel检验,软件Arlequin 用于分子方差分析,聚类分析采用MEGA 7中的UPGMA法;同时,使用Structure软件中的贝叶斯聚类算法探究群体遗传结构。【结果】6对SSR引物共检测到75个等位基因,平均有效等位基因数、观察杂合度和期望杂合度分别为7.16、0.70和 0.80,Shannon信息指数为2.05。AMOVA表明,群体内部的分子变异率高达97.41%,而群体之间的遗传变异仅为2.59%。黄山(YM)与天目山(TM)群体间的基因流为12.908,显著高于其他群体之间的交流水平,而二者间有着最近的遗传距离为0.272。贝叶斯法与UPGMA法聚类结果一致,表明来自YM与TM的个体亲缘关系更近。【结论】白栎具有较高的遗传多样性水平,且不同居群间的水平相当。YM和TM居群的基因交流最为密切,遗传分化不明显。白栎绝大部分遗传变异来源于群体内部,对于该物种的保护应减少不合理的人为开发行为,以原地保护为主,同时开展种质资源的收集与遗传改良工作。

关键词: 白栎, SSR, 遗传多样性, 遗传结构

Abstract:

【Objective】 This study used simple-sequence repeat (SSR) markers to analyze the genetic diversity on Quercus fabri Hance from natural populations. The study provides important advice concerning the reasonable exploitation and utilization of this resource. 【Method】 The analysis of the genetic diversity and genetic structure of Q. fabri was performed using screened SSR molecular markers. The genetic parameters were calculated and the principal coordinate analysis was applied based on the genetic distance among individuals. The analysis of molecular variance was conducted using Arlequin software. GenAlEx 6.5 was used to test the correlation between the genetic distance and geographic distance. MEGA 7 was used for the UPGMA phylogenetic analysis, and Structure was employed to perform the Bayesian clustering analysis to explore the genetic structure. 【Result】 A total of 75 alleles were detected from six markers. The average number of effective alleles, observed heterozygosity, and expected heterozygosity were 7.16, 0.70 and 0.80, respectively. The Shannon’s information index was 2.05. AMOVA demonstrated that the genetic variation within populations (97.41%) accounted for the main percentage, with a negligible variation among populations (2.59%). The gene flow between Huangshan Mountain (YM) and Tianmushan Mountain (TM) was 12.908, which was much higher than that among other populations, and the genetic distance between the two populations was the closest (0.272). The results of the Bayesian clustering analysis were in accordance with the result of the UPGMA phylogenetic analysis, in that samples from the YM and TM populations had closer phylogenetic relationships. 【Conclusion】 There was a high and coincident level of genetic diversity among natural populations of Q. fabri. The genetic communication between YM and TM was the most frequent, and the genetic variation between these two spots was minor. For Q. fabri, the heritable variation within populations accounted for the majority of genetic variation. When collecting germplasm resources for the genetic improvement of this species, we should avoid unreasonable artificial exploitation. In addition, insitu conservation should be taken into consideration.

Key words: Quercus fabri Hance, simple-sequence repeats (SSR), genetic diversity, genetic structure

中图分类号:

臧明月,李璇,方炎明. 基于SSR标记的白栎天然居群遗传多样性分析[J]. 南京林业大学学报（自然科学版）, 2021, 45(1): 63-69.

ZANG Mingyue, LI Xuan, FANG Yanming. Genetic diversity analysis among natural populations of Quercus fabri based on SSR markers[J].Journal of Nanjing Forestry University (Natural Science Edition), 2021, 45(1): 63-69.DOI: 10.12302/j.issn.1000-2006.202004049.

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参考文献 33

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地点 locality	种群代号 population code	海拔/m altitude	经度/(°) E longitude	纬度/(°) N latitude	样本量 trees sampled
安徽黄山 Huangshan Mountain, Anhui	YM	1 864	118.08	30.10	30
浙江天目山 Tianmushan Mountain, Zhejiang	TM	459	119.44	30.32	30
江苏紫金山 Zijin Mountain, Jiangsu	PM	156	118.82	32.07	30

引物 primer	引物序列(5'-3') primer sequence (5'-3')	重复单位 repeat motif	等位基因大小/bp allele size	退火温度/℃ annealing temperature	标记荧光 fluorescent label
quru-GA-0M07	F:TTTAGCATCACATTTCCGTT	(GA)₁₉	209	50	5'-FAM
quru-GA-0M07	R:TTTTGTGTCATCCGGTATTA	(GA)₁₉	209	50	5'-FAM
MSQ16	F:GGAACAACTAGAGAGAAC	(TC)_n	170~250	53	5'-FAM
MSQ16	R:TTGCCTATCCTGCCCCGTAT	(TC)_n	170~250	53	5'-FAM
ssrQrZAG112	F:TTCTTGCTTTGGTGCGCG	(GA)₃₂	100	53	5'-HEX
ssrQrZAG112	R:GTGGTCAGAGACTCGGTAAGTATTC	(GA)₃₂	100	53	5'-HEX
QM67-3M1	F:TGGCTTATCCAATGTTTGTGATT	(GGA)₃(GGC)₄	150	52	5'-HEX
QM67-3M1	R:GCGTCGGTGGCGGCTTAGAGATT	(GGT)₄(GGC)(GGA)	150	52	5'-HEX
ssrQrZAG7	F:CAACTTGGTGTTCGGATCAA	(TC)₁₇	110~126	53	5'-FAM
ssrQrZAG7	R:GTGCATTTCTTTTATAGCATTCAC	(TC)₁₇	110~126	53	5'-FAM
ssrQpZAG110	F:GGAGGCTTCCTTCAACCTACT	(AG)₁₅	220~250	51	5'-HEX
ssrQpZAG110	R:GATCTCTTGTGTGCTGTATTT	(AG)₁₅	220~250	51	5'-HEX

位点 locus	N_a	N_e	H_o	H_e	I	G_st
quru-GA-0M07	15	9.72	0.63	0.90	2.46	0.020
MSQ16	16	8.46	0.61	0.87	2.39	0.044
ssrQrZAG112	9	2.89	0.78	0.65	1.43	0.079
QM67-3M1	8	3.65	0.76	0.73	1.57	0.013
ssrQrZAG7	20	13.83	0.79	0.93	2.79	0.010
ssrQpZAG110	7	4.39	0.62	0.77	1.65	0.011
平均mean	12.50	7.16	0.70	0.80	2.05	0.030

种群 population	N_a	N_e	H_o	H_e	I
YM	13.17	6.73	0.84	0.81	2.06
TM	11.67	6.81	0.74	0.79	1.96
PM	13.83	7.92	0.51	0.81	2.13
平均mean	12.89	7.16	0.70	0.80	2.05

方差来源 source of variation	自由度 df	平方和 sum of squares	方差分量 variance components	百分比/% percentage of variation
群体间 among populations	2	13.022	0.067	2.59
群体内 within populations	177	444.133	2.509	97.41
总计total	179	457.156	2.576	100.00

基于SSR标记的白栎天然居群遗传多样性分析

Genetic diversity analysis among natural populations of Quercus fabri based on SSR markers

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