Genetic diversity analyses of Quercus acutissima based on SSR markers

doi:10.12302/j.issn.1000-2006.202101025

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2022, Vol. 46 ›› Issue (3): 109-116.doi: 10.12302/j.issn.1000-2006.202101025

Genetic diversity analyses of Quercus acutissima based on SSR markers

LYU Feng¹(), XIE Xiaoman¹^,², HAN Biao², LU Yizeng², WANG Lei², DONG Xin², WANG Yan², LU Lu², LIU Li¹, ZONG Shaoning², LI Wenqing¹^,²^,^*()

1. College of Life Science, Shandong Normal University, Ji’nan 250014, China
2. Shandong Forest and Grass Germplasm Resources Center, Ji’nan 250102, China

Received:2021-01-19 Accepted:2021-07-13 Online:2022-05-30 Published:2022-06-10
Contact: LI Wenqing E-mail:1148080865@qq.com;liwenqing0686@shandong.cn

Abstract

Abstract:

【Objective】To provide a theoretical basis for the protection and use of Quercus acutissima germplasm resources, 150 individuals of Q. acutissima from eight natural populations distributed in seven provinces of China were selected as the research objects. Their genetic diversity and genetic structure were analyzed based on SSR molecular markers.【Method】A total of 18 pairs of SSR primers were screened and used to study the genetic diversity, molecular variance, genetic distance and genetic structure of Q. acutissima populations and corresponding individuals using AMOVA analysis, principal component analysis, cluster analysis and structure analysis. Software such as GenAIEx 6.51, MEGA 7.0.26 and Structure 2.3.4 were used in the data analysis.【Result 】 The average number of alleles (N_a), effective alleles (N_e), the Shannon index (I) and observed heterozygosity (H_o) of the 18 SSR loci were 5.625, 4.104, 1.338 and 0.895, respectively. The average expected heterozygosity (H_e) was 0.645, and the 18 pairs of SSR primers that were screened showed abundant polymorphism. The genetic distance of the eight populations ranged from 0.222 to 1.587. The genetic consistency ranged from 0.205 to 0.801, the average coefficient of genetic differentiation (F_st) was 0.252, the average gene flow (N_m) was 1.140, and the average fixed index (F) was negative and was -0.441. The genetic diversity of the populations was high, the genetic differentiation was small, and there was heterozygote residues among the populations. A total of 98% of the variation came from within the population and 2% came from among the populations. UPGMA cluster analysis and structure analysis divided the eight populations into two groups, respectively. There were some differences in the individual composition of the two groups. The results of the principal component analysis were consistent with other results. The phenomena of cross introduction and gene introgression was present between the groups.【Conclusion】 The level of genetic diversity of Q. acutissima population is high, and the level of genetic differentiation is low. The genetic difference mainly exists in the population and presents the law of geographical variations in a southwest to northeast direction. For the protection of this species, areas with high genetic diversity should be protected as a priority, and the protection strategy of in situ conservation should be combined with ex situ breeding and preservation is proposed.

Key words: Quercus acutissima, natural population, simple-sequence-repeat (SSR), genetic diversity, genetic structure

CLC Number:

LYU Feng, XIE Xiaoman, HAN Biao, LU Yizeng, WANG Lei, DONG Xin, WANG Yan, LU Lu, LIU Li, ZONG Shaoning, LI Wenqing. Genetic diversity analyses of Quercus acutissima based on SSR markers[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY, 2022, 46(3): 109-116.

Figures/Tables 9

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编号 ID	群体 population	东经/(°) longitude (E)	北纬/(°) latitude (N)	样本个数 samples size
HN	河南南阳	113.23	32.49	12
LN	辽宁大连、鞍山	121.52	39.46	30
SX	山西运城	111.52	35.02	3
JD	山东1(鲁东)	121.20	36.86	19
YN	云南大理	100.92	25.35	3
LZN	山东2(鲁中南)	117.02	36.14	42
HB	河北秦皇岛	119.46	39.82	32
JS	江苏连云港、新沂、南京	118.34	34.20	9

位点 locus	引物序列(5'-3') primer sequence(5'-3')	退火温度/℃ annealing temperature	位点 locus	引物序列(5'-3') primer sequence(5'-3')	退火温度/℃ annealing temperature
MSQ13	F:TGGCTGCACCTATGGCTCTTAG R: ACACTCAGACCCACCATTTTTCC	54	QV11	F:ACCAATGTGAAAAGGGAAG R:TGGGTTTGGTTTCTTCTTCT	55
MSQ16	F:GGAACAACTAGAGAGAAC R:TTGCCTATCCTGCCCCGTAT	52	QV12	F:CAGCTCTGGATGGATATAATG R:ACATGCATGGAGAGAAATAGA	55
QM58TGT	F:GGTCAGTGTATTTTGTTGGT R:AAATGTATTTTGCTTGCTCA	52	QV14	F:AGAGCAATTCCCAACTAACTT R:TAGTTCAAGATCTGAGCCAAA	55
QpZAG36	F:GATCAAAATTTGGAATATTAAGAGAG R:ACTGTGGTGGTGAGTCT AACATGTAG	57	QrZAG112	F:TTCTTGCTTTGGTGCGCG R:GTGGTCAGAGACTCGGTAAGTATTC	45
QpZAG110	F:GGAGGCTTCCTTCAACCTACT R:GATCTCTTGTGTGCTGTATTT	49	QV3	F:TATCTTTTGTGGGGGAAGATA R:AGAAGGCCTCATCTTTCTTTA	55
QrZAG7	F:CAACTTGGTGTTCGGATCAA R:GTGCATTTCTTTTATAGCATTCAC	51	QV10	F:TGCCTTATTGTTGATGCTG R:CAAAATCCAAAAGGCCAAAC	55
QV4	F:ATTCATTTTTCTCCACCAAA R:CCATTATGATTGGATTAGGG	55	GA-1H14	F:GCTTGGGCTTGTTCCTACT R:CAACACTTCTCATGGATTAGAGA	58
QV6	F:CGCTTGCCACAATAGTAATAA R:AAGTACCAAAAATGACAATG	55	GA-Oi21	F:ATATGGTCCCGATTAATTC R: GGGCAACATTCAAATGTATCTA	50
QV8	F:CCTGCTTCCAATATTCTCATA R:GCAAAATCACTCATCAAGAAC	55	QM67-3Ml	F:GCGTCGGTGGCGGCTTAGAGATT R: TGGCTTATCCAATGTTTGTGATT	55

位点 locus	样本量 sample size	N_a	N_e	I	H_o	H_e	F	F_st	N_m
QV8	5.500	3.625	2.675	0.985	0.742	0.514	-0.484	0.399	0.377
QV10	9.750	5.500	3.733	1.312	0.875	0.629	-0.458	0.298	0.589
MSQ13	3.000	3.125	2.771	0.911	0.750	0.495	-0.583	0.437	0.323
MSQ16	9.375	9.875	6.944	2.025	1.000	0.841	-0.193	0.070	3.312
QV11	8.625	4.500	3.429	1.292	1.000	0.691	-0.473	0.175	1.176
QrZAG7	13.625	6.250	3.916	1.451	0.875	0.673	-0.304	0.218	0.897
GA-1H14	5.750	7.250	5.889	1.654	0.875	0.719	-0.224	0.229	0.842
QV6	2.750	2.875	2.217	0.852	0.625	0.448	-0.397	0.511	0.240
QM67-3M1	8.750	2.000	1.778	0.632	0.875	0.444	-0.974	0.288	0.619
QPZAG36	2.375	3.125	2.764	0.936	0.750	0.503	-0.560	0.452	0.303
QRZAG112	11.625	4.875	3.670	1.356	1.000	0.711	-0.432	0.134	1.620
QPZAG110	11.625	8.625	5.292	1.713	1.000	0.749	-0.404	0.134	1.622
QV3	12.375	7.000	4.675	1.626	1.000	0.760	-0.335	0.108	2.073
QV4	8.500	5.375	3.791	1.398	1.000	0.709	-0.445	0.134	1.616
QM58TGT	12.375	13.125	9.547	2.267	1.000	0.861	-0.176	0.092	2.465
QV14	8.000	7.625	5.587	1.748	1.000	0.775	-0.333	0.141	1.525
GA-Oi21b	10.125	3.500	2.559	0.976	0.750	0.519	-0.460	0.397	0.380
QV12	2.500	3.000	2.643	0.949	1.000	0.579	-0.784	0.319	0.534
平均mean	8.146	5.625	4.104	1.338	0.895	0.645	-0.441	0.252	1.140

群体 popula- tion	样本量 sample size	N_a	N_e	I	H_o	H_e	F	P_PPL/%
HB	12.833	6.611	4.497	1.483	0.944	0.696	-0.403	94.44
HN	5.111	5.278	4.080	1.427	0.944	0.696	-0.389	94.44
JD	7.611	6.333	4.586	1.514	1.000	0.724	-0.437	100.00
JS	3.611	4.333	3.595	1.202	0.833	0.600	-0.432	83.33
LN	13.778	7.333	5.162	1.569	0.944	0.711	-0.372	94.44
LZN	19.556	10.389	6.405	1.929	0.996	0.805	-0.256	100.00
SX	1.278	2.444	2.407	0.831	0.778	0.491	-0.648	77.78
YN	1.389	2.278	2.102	0.748	0.722	0.441	-0.694	72.22
平均 mean	8.146	5.625	4.104	1.338	0.895	0.645	-0.441	89.58

变异来源 source of variation	自由度 df	均方和 SS	均方偏差 MS	变异方差分量 variance componets	方差分量占比/% percentage of variation
群体间among populations	7	77.171	11.024	0.113	2
群体内within populations	292	2 071.659	7.095	7.095	98
总计total	299	2 148.830	18.119	7.208	100

Genetic diversity analyses of Quercus acutissima based on SSR markers

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群体 population	HB	HN	JD	JS	LN	LZN	SX	YN
HB	—	0.501	0.657	0.624	0.775	0.755	0.314	0.246
HN	0.691	—	0.508	0.436	0.529	0.619	0.435	0.474
JD	0.420	0.677	—	0.555	0.751	0.775	0.347	0.291
JS	0.471	0.830	0.589	—	0.616	0.702	0.231	0.205
LN	0.255	0.637	0.286	0.484	—	0.801	0.321	0.281
LZN	0.281	0.480	0.255	0.354	0.222	—	0.413	0.343
SX	1.159	0.833	1.057	1.465	1.135	0.885	—	0.311
YN	1.403	0.746	1.235	1.587	1.271	1.071	1.167	—

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