Genetic Diversity Analysis of Populations of Polygonatum cyrtonema Hua Based on Two Types of DNA Barcode Sequences

doi:10.11924/j.issn.1000-6850.casb2025-0071

Abstract

Abstract:

In order to provide a theoretical basis for the breeding of Polygonatum cyrtonema Hua with high-quality, high-yield, 25 different populations in Hunan Province were collected for sequence feature analysis, population genetics analysis, genetic distance analysis and cluster analysis based on two DNA barcode sequences. The results showed that: (1) the length of ITS and psbA-trnH sequences were 688 -720 bp and 517 -531 bp, respectively. (2) Population evolution analysis revealed that ITS and psbA-trnH were neutral evolutionary genes, which were less affected by selection. The ITS sequence was greater than the psbA-trnH sequence in terms of haplotype number, haplotype diversity, and nucleotide polymorphism, indicating moderate genetic diversity. (3) Genetic distances of populations under ITS and psbA-trnH sequences were 0.0331-0.1433 and 0.0154-0.1294, respectively, indicating that the degree of population variation based on ITS sequence was greater than psbA-trnH sequence. (4) Both phylogenetic trees supported that all populations were divided into two groups, suggesting that the population of P. cyrtonema Hua from Hunan Province had two major branches. In total, there was a certain correlation between the genetic relationships of different populations and their geographical distribution.

Key words: Polygonatum cyrtonema Hua, population, DNA barcode, genetic diversity, system clustering

PENG Cuiying, LIANG Junsheng, LIAO Dezhi, WANG Xujun. Genetic Diversity Analysis of Populations of Polygonatum cyrtonema Hua Based on Two Types of DNA Barcode Sequences[J]. Chinese Agricultural Science Bulletin, 2025, 41(33): 67-73.

Figures/Tables 6

References 26

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代码	采集地	长度/bp		GC含量/%		GenBank登录号
代码	采集地	ITS	psbA-trnH	ITS	psbA-trnH	ITS	psbA-trnH
HNSM	石门县	707	522	69.73	34.48	OL818282	OL849964
HNSZ	桑植县	714	523	68.63	34.61	OL818283	OL849965
HNJS	吉首市	709	526	69.53	34.22	OL818284	OL849966
HNHY	花垣县	710	529	70.14	34.22	OL818285	OL849967
HNBJ	保靖县	714	523	69.33	34.80	OL818286	OL849968
HNNX	宁乡市	720	526	68.75	34.41	OL818287	OL849969
HNAH	安化县	715	527	69.65	33.97	OL818288	OL849970
HNXH	新晃县	715	523	69.37	34.03	OL818289	OL849971
HNLS	龙山县	708	520	69.35	34.04	OL818290	OL849972
HNMY	麻阳县	714	522	69.05	34.87	OL818291	OL849973
HNXN	新宁县	707	522	69.73	33.72	OL818292	OL849974
HNZJ	芷江县	713	525	70.27	33.90	OL818293	OL849975
HNCX	辰溪县	701	526	69.47	33.84	OL818294	OL849976
HNHT	会同县	703	524	68.71	34.35	OL818295	OL849977
HNTD	通道县	712	522	69.52	34.29	OL818296	OL849978
HNCB	城步县	705	522	69.36	34.48	OL818297	OL849979
HNXP	溆浦县	705	526	70.78	34.41	OL818298	OL849980
HNYL	沅陵县	708	526	70.20	34.03	OL818299	OL849981
HNLH	隆回县	707	525	69.17	35.05	OL818300	OL849982
HNSN	绥宁县	703	521	69.42	34.36	OL818301	OL849983
HNJZ	靖州县	711	517	69.76	36.17	OL818302	OL849984
HNLY	浏阳市	715	520	69.51	34.04	OL818303	OL849985
HNYS	永顺县	710	526	70.00	34.41	OL818304	OL849986
HNGZ	古丈县	710	531	69.72	33.71	OL818305	OL849987
HNTY	桃源县	688	518	69.48	37.26	OL818306	OL849988

代码	采集地	长度/bp		GC含量/%		GenBank登录号
代码	采集地	ITS	psbA-trnH	ITS	psbA-trnH	ITS	psbA-trnH
HNSM	石门县	707	522	69.73	34.48	OL818282	OL849964
HNSZ	桑植县	714	523	68.63	34.61	OL818283	OL849965
HNJS	吉首市	709	526	69.53	34.22	OL818284	OL849966
HNHY	花垣县	710	529	70.14	34.22	OL818285	OL849967
HNBJ	保靖县	714	523	69.33	34.80	OL818286	OL849968
HNNX	宁乡市	720	526	68.75	34.41	OL818287	OL849969
HNAH	安化县	715	527	69.65	33.97	OL818288	OL849970
HNXH	新晃县	715	523	69.37	34.03	OL818289	OL849971
HNLS	龙山县	708	520	69.35	34.04	OL818290	OL849972
HNMY	麻阳县	714	522	69.05	34.87	OL818291	OL849973
HNXN	新宁县	707	522	69.73	33.72	OL818292	OL849974
HNZJ	芷江县	713	525	70.27	33.90	OL818293	OL849975
HNCX	辰溪县	701	526	69.47	33.84	OL818294	OL849976
HNHT	会同县	703	524	68.71	34.35	OL818295	OL849977
HNTD	通道县	712	522	69.52	34.29	OL818296	OL849978
HNCB	城步县	705	522	69.36	34.48	OL818297	OL849979
HNXP	溆浦县	705	526	70.78	34.41	OL818298	OL849980
HNYL	沅陵县	708	526	70.20	34.03	OL818299	OL849981
HNLH	隆回县	707	525	69.17	35.05	OL818300	OL849982
HNSN	绥宁县	703	521	69.42	34.36	OL818301	OL849983
HNJZ	靖州县	711	517	69.76	36.17	OL818302	OL849984
HNLY	浏阳市	715	520	69.51	34.04	OL818303	OL849985
HNYS	永顺县	710	526	70.00	34.41	OL818304	OL849986
HNGZ	古丈县	710	531	69.72	33.71	OL818305	OL849987
HNTY	桃源县	688	518	69.48	37.26	OL818306	OL849988

序列特征	ITS	psbA-trnH
序列长度变幅/bp	688~720	517~531
保守位点/个	453	369
变异位点/个	393	175
简约信息位点/个	152	81
单一多态位点/个	138	90
插入缺失位点/个	17	13
A碱基占比/%	19.32	32.35
T碱基占比/%	12.77	34.02
C碱基占比/%	35.26	18.41
G碱基占比/%	32.65	15.22
T + A变幅/%	27.33~32.46	64.37~68.06
G + C变幅/%	62.22~72.44	34.34~36.156
碱基转换	3	2
碱基颠换	6	3
转换/颠换值	0.5	0.67

序列特征	ITS	psbA-trnH
序列长度变幅/bp	688~720	517~531
保守位点/个	453	369
变异位点/个	393	175
简约信息位点/个	152	81
单一多态位点/个	138	90
插入缺失位点/个	17	13
A碱基占比/%	19.32	32.35
T碱基占比/%	12.77	34.02
C碱基占比/%	35.26	18.41
G碱基占比/%	32.65	15.22
T + A变幅/%	27.33~32.46	64.37~68.06
G + C变幅/%	62.22~72.44	34.34~36.156
碱基转换	3	2
碱基颠换	6	3
转换/颠换值	0.5	0.67

检测类型	检测指标	ITS	psbA-trnH
群体动态Fu and Li’s test	FLD*值	-0.8749	0.8864
	总突变位点数	32	14
	特殊突变位点数Eta(s)	17	4
	单倍型数，H值	11	6
	单倍型多样性，Hd值	0.8790	0.8010
	核苷酸多态性，Pi值	0.0252	0.0083
	多态位点数，S值	31	13
	核苷酸平均差异数，K值	7.5700	4.4480
	扩展系数，S/K	4.0951	2.9227
	Tajima's D值	-0.7368	1.7543
Strobeck's统计	单倍型数等于或低于h的概率	0.1821	0.1397
重组分析	Rm值	2	1
多样性分析	π值	0.01	0.01