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

doi:10.12302/j.issn.1000-2006.202004049

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2021, Vol. 45 ›› Issue (1): 63-69.doi: 10.12302/j.issn.1000-2006.202004049

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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 E-mail:986084166@qq.com;jwu4@njfu.com.cn

Abstract

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

CLC Number:

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, 2021, 45(1): 63-69.

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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

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

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