Genetic diversity and population structure of Populus yunnanensis

doi:10.17520/biods.2019016

Abstract

Abstract:

Populus yunnanensis is an endemic tree species to Southwestern China. It is a typical southern Populus species that is fast-growing species with easy to clone propagules and is highly adaptable. It is important to research the genetic diversity and population structure of P. yunnanensis for the collection, preservation and utilization of the germplasm resources. In this study, 64 individuals were collected from six populations, spaning the main distribution areas of P. yunnanensis, including Zhaotong (ZT), Huize (HZ), Songming (SM), Eryuan (EY), Lashihai (LS) and Sichuan Meigu (MG). A total of 34 pairs of SSR primers and three pairs of cpDNA primers were used to determine out the genetic diversity and genetic structure. A total of 154 alleles were detected by SSR primers in P. yunnanensis. The average number of alleles was 4.529. The observed heterozygosity (Ho) and expected heterozygosity (He) were 0.552 and 0.472, respectively. And the average genetic differentiation coefficient (Fst) was 0.238. The average polymorphism information content (PIC) was 0.421 and the gene flow (Nm) was 0.806. The results of the DAPC, PCoA and UPGMA analyses showed that the six populations can be divided into three sub-categories: Group І included ZT, HZ and four individuals of SM. Group II included EY, LS and the six remaining individuals of SM; and group III included MG; SM population include mixed genetic components from І and ІІ. A total of 35 variable sites were detected in the three cpDNA combinations, forming 13 haplotypes. Among them, haplotype H5 was the most widely distributed in the population, while the remaining ones were of private haplotypes. Analysis of molecular variance (AMOVA) showed that genetic variation within the population was greater than between populations. The study clarifies that P. yunnanensis has geographical distribution characteristics and is suited to in situ conservation. As ZT population has the highest genetic diversity and contains seven chloroplast haplotypes, it should be given protection priority.

Key words: Populus yunnanensis, genetic diversity, genetic structure, molecular marker, SSR, cpDNA

Yahong Zhang, Huixia Jia, Zhibin Wang, Pei Sun, Demei Cao, Jianjun Hu. Genetic diversity and population structure of Populus yunnanensis[J]. Biodiv Sci, 2019, 27(4): 355-365.

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URL: https://www.biodiversity-science.net/EN/10.17520/biods.2019016

https://www.biodiversity-science.net/EN/Y2019/V27/I4/355

Figures/Tables 10

References 44

[1]	Allen G, Flores-Vergara M, Krasynanski S, Kumar S, Thompson WF (2006) A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide. Nature Protocols, 1, 2320-2325.
[2]	Bai WN, Zhang DY (2014) Current status and future directions in plant phylogeography. Chinese Bulletin of Life Sciences, 26, 125-137. (in Chinese with English abstract)
	[ 白伟宁, 张大勇 (2014) 植物亲缘地理学的研究现状与发展趋势. 生命科学, 26, 125-137.]
[3]	Bandelt HJ, Forster P, Röhl A (1999) Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution, 16, 37-48. DOI URL
[4]	Burland TG (2000) DNASTAR’s Lasergene sequence analysis software. Methods in Molecular Biology, 132, 71-91. DOI URL PMID
[5]	Chen K (2007) Genetic Relationships among Poplar Species in Section Tacamahaca Spach from Western Sichuan of China. PhD dissertation, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu. (in Chinese with English abstract)
	[ 陈珂 (2007) 川西青杨组(Section Tacamahaca Spach)不同种的亲缘关系分析. 博士学位论文, 中国科学院成都生物研究所, 成都.]
[6]	Chen XM, He ZH, Shi JR, Xia LQ, Rick W, Zhou Y, Jiang GL (2003) Genetic diversity of high quality winter wheat varieties (lines) based on SSR markers. Acta Agronomica Sinica, 29, 13-19. (in Chinese with English abstract)
	[ 陈新民, 何中虎, 史建荣, 夏兰芹, Ward Rick, 周阳, 蒋国梁 (2003) 利用SSR标记进行优质冬小麦品种(系)的遗传多样性研究. 作物学报, 29, 13-19.]
[7]	Chen XY (2000) Effects of habitat fragmentation on genetic structure of plant populations and implications for the biodiversity conservation. Acta Ecologica Sinica, 20, 884-892. (in Chinese with English abstract)
	[ 陈小勇 (2000) 生境片断化对植物种群遗传结构的影响及植物遗传多样性保护. 生态学报, 20, 884-892.]
[8]	Crandall KA, Templeton AR (1993) Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction. Genetics, 134, 959-969.
[9]	DiFazio S, Slavov G, Rodgers-Melnick E, Martin J, Schackwitz W, Priya R, Tuskan G (2011) Inferring the evolutionary history of Populus trichocarpa from whole genome resequencing data. BMC Proceedings, 5, O1.
[10]	Du QZ, Wang B, Wei ZZ, Zhang DQ, Li BL (2012) Genetic diversity and population structure of Chinese white poplar (Populus tomentosa) revealed by SSR markers. Journal of Heredity, 103, 853-862. DOI URL
[11]	Ferradini N, Lancioni H, Torricelli R, Russi L, Ragione ID, Cardinali I, Marconi G, Gramaccia M, Concezzi L, Achilli A, Veronesi F, Albertini E (2017) Characterization and phylogenetic analysis of ancient Italian landraces of pear. Frontiers in Plant Science, 8, 751. DOI URL
[12]	Golding GB (1987) The detection of deleterious selection using ancestors inferred from a phylogenetic history. Genetics Research, 49, 71-82. DOI URL
[13]	Gong GT (2004) The geographic distribution and origin of Populus L. Journal of Sichuan Forestry Science and Technology, 25(2), 25-30. (in Chinese with English abstract)
	[ 龚固堂 (2004) 杨属地理分布与起源初探. 四川林业科技, 25(2), 25-30.]
[14]	Hamrick JL, Godt MJW, Sherman-Broyles SL (1992) Factors influencing levels of genetic diversity in woody plant species. New Forests, 6, 95-124. DOI URL
[15]	He CZ, Che PY, Peng CY, Zhou XT, Duan AA, Wang DX, Xin PY (2010) A survey of research progress on gene resources of Populus yunnanensis. Journal of Southwest Forestry University, 30(1), 83-88. (in Chinese with English abstract)
	[ 何承忠, 车鹏燕, 周修涛, 段安安, 王德新, 辛培尧 (2010) 滇杨基因资源及其研究概况. 西南林业大学学报, 30(1), 83-88.]
[16]	He CZ, Zhang ZY, Duan AA, Feng XL (2009) Genetic Diversity Analysis of Populus yunnanensis by AFLP Markers. China Forestry Publishing House, Beijing. (in Chinese)
	[ 何承忠, 张志毅, 段安安, 冯夏莲 (2009) 滇杨基因资源遗传多样性的AFLP分析. 中国林业出版社, 北京.]
[17]	Jia HX, Ji HJ, Hu JJ, Lu MZ (2015) Fingerprints of SSR markers and ploidy detection for new Populus varieties. Scientia Silvae Sinicae, 51(2), 69-79. (in Chinese with English abstract)
	[ 贾会霞, 姬慧娟, 胡建军, 卢孟柱 (2015) 杨树新品种的SSR指纹图谱构建和倍性检测. 林业科学, 51(2), 69-79.] DOI
[18]	Jiang DC, Wu GL, Mao KS, Feng JJ (2015) Structure of genetic diversity in marginal populations of black poplar (Populus nigra L.). Biochemical Systematics and Ecology, 61, 297-302. DOI URL
[19]	Jombart T, Devillard S, Balloux F (2010) Discriminant analysis of principal components: A new method for the analysis of genetically structured populations. BMC Genetics, 11, 94.
[20]	Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33, 1870-1874. DOI URL
[21]	Peakall R, Smouse PE (2006) GENALEX 6: Genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6, 288-295. DOI URL
[22]	Peng YH (2006) Population Genetic Survey of Populus cathayana Rehd. Originating from eastern edge of Qinghai-Tibetan Plateau of China. PhD dissertation, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu. (in Chinese with English abstract)
	[ 彭幼红 (2006) 青藏高原东缘青杨(Populus cathayana Rehd.)遗传多样性研究. 博士学位论文, 中国科学院研究生院成都生物研究所, 成都.]
[23]	Polzin T, Daneshmand SV (2003) On Steiner trees and minimum spanning trees in hypergraphs. Operations Research Letters, 31, 12-20. DOI URL
[24]	Posada D, Crandall KA (2001) Intraspecific gene genealogies: Trees grafting into networks. Trends in Ecology & Evolution, 16 , 37-45.
[25]	Qiu YX, Fu CX, Comes HP (2011) Plant molecular phylogeography in China and adjacent regions: Tracing the genetic imprints of Quaternary climate and environmental change in the world’s most diverse temperate flora. Molecular Phylogenetics and Evolution, 59, 225-244. DOI URL
[26]	Retief JD (1999) Phylogenetic analysis using PHYLIP. Methods in Molecular Biology, 132, 243-258.
[27]	Roy JK, Lakshmikumaran MS, Balyan HS, Gupta PK (2004) AFLP-based genetic diversity and its comparison with diversity based on SSR, SAMPL, and phenotypic traits in bread wheat. Biochemical Genetics, 42, 43-59. DOI URL
[28]	Rozas J, Sánchez-DelBarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19, 2496-2497. DOI URL
[29]	Schuelke M (2000) An economic method for the fluorescent labeling of PCR fragments. Nature Biotechnology, 18, 233-234.
[30]	Semerikova SA, Semerikov VL (2014) Molecular phylogenetic analysis of the genus Abies (Pinaceae) based on the nucleotide sequence of chloroplast DNA. Genetika, 50, 12-25.
[31]	Shang ZH, Yao AX (2002) Biological genetic diversity research methods and their protective measures. Journal of Ningxia Agricultural College, 23(1), 66-69. (in Chinese)
	[ 尚占环, 姚爱兴 (2002) 生物遗传多样性研究方法及其保护措施. 宁夏农学院学报, 23(1), 66-69.]
[32]	Shen XF, Wu ML, Liao BS, Liu ZX, Bai R, Xiao SM, Li XW, Zhang BL, Xu J, Chen SL (2017) Complete chloroplast genome sequence and phylogenetic analysis of the medicinal plant Artemisia annua. Molecules, 22, 1330. DOI URL
[33]	Tippmann HF (2004) Analysis for free: Comparing programs for sequence analysis. Briefings in Bioinformatics, 5, 82-87. DOI URL
[34]	Wan XQ, Zhang F, Zhong Y, Wang CL, Ding YH, Hu TX, Zhai MP, Qian ZL (2009) Conservation and application of the genetic resource of native poplars in Southwest China. Scientia Silvae Sinicae, 45(4), 139-144. (in Chinese with English abstract)
	[ 万雪琴, 张帆, 钟宇, 王长亮, 丁云海, 胡庭兴, 翟明普, 钱宗亮 (2009) 中国西南地区乡土杨树基因资源的保护与利用. 林业科学, 45(4), 139-144.] DOI
[35]	Wang J, Li ZJ, Guo QH, Ren GP, Wu YX (2011) Genetic variation within and between populations of a desert poplar (Populus euphratica) revealed by SSR markers. Annals of Forest Science, 68, 1143-1149. DOI URL
[36]	Wang JL, Gao QB, Fu PC, Gulzar K, Chen SL, Zhang FQ (2014) Phylogeography of Spiraea mongolica (Rosaceae) on the Qinghai-Tibetan Plateau and adjacent highlands. Acta Botanica Boreali-Occidentalia Sinica, 10, 1981-1991. (in Chinese with English abstract)
	[ 王久利, 高庆波, 付鹏程, Gulzar K, 陈世龙, 张发起 (2014) 青藏高原及其毗邻山区蒙古绣线菊谱系地理学研究. 西北植物学报, 34, 1981-1991.]
[37]	Xu WY (1988) Poplar. Heilongjiang People’s Publishing House. Harbin. (in Chinese)
	[ 徐纬英 (1988) 杨树. 黑龙江人民出版社, 哈尔滨.]
[38]	Yan LQ, Li JM, Yuan T, Zhou AP, Zong D, Li D, Xin PY, He CZ (2016) Genetic diversity analysis of Populus yunnanensis by SRAP markers. Biotechnology Bulletin, 32, 159-167. (in Chinese with English abstract)
	[ 颜璐茜, 李佳蔓, 员涛, 周安佩, 纵丹, 李旦, 辛培尧, 何承忠 (2016) 滇杨遗传多样性的SRAP分析. 生物技术通报, 32, 159-167.]
[39]	Yu SQ, Liu J, Fu DR, Liu DJ, Liu YQ (2003) Characteristics of Tacamahaca genes in the Western Sichuan Plateau. Journal of Zhejiang Forestry College, 20, 27-31. (in Chinese with English abstract)
	[ 余树全, 刘军, 付达荣, 刘大健, 刘友全 (2003) 川西高原青杨派基因资源特点. 浙江林学院学报, 20(1), 27-31.]
[40]	Závada T, Malik RJ, Kesseli RV (2017) Population structure in chicory (Cichorium intybus): A successful U. S. weed since the American revolutionary war. Ecology and Evolution, 7, 4209-4219. DOI URL
[41]	Zeng YF, Zhang JG, Abuduhamiti B, Wang WT, Jia ZQ (2018) Phylogeographic patterns of the desert poplar in Northwest China shaped by both geology and climatic oscillations. BMC Evolutionary Biology, 18, 75. DOI
[42]	Zhao N, Liu J (1994) Taxonomic studies on Populus L. in Southwestern China (II). Journal of Wuhan Botanical Research, 9, 225-232. (in Chinese with English abstract)
	[ 赵能, 刘军 (1994) 中国西南地区杨属的分类学研究(II). 武汉植物科学学报, 9, 225-232.]
[43]	Zheng HL, Fan LQ, Milne RI, Zhang L, Wang YL, Mao KS (2017) Species delimitation and lineage separation history of a species complex of aspens in China. Frontiers in Plant Science, 8, 375.
[44]	Zong D, Yuan T, Zhou AP, Liu DY, Zheng Y, Duan AA, He CZ (2014) Analysis of genetic background of 52 Populus yunnanensis superior trees by AFLP markers. Journal of Northwest Forestry University, 29, 103-108. (in Chinese with English abstract)
	[ 纵丹, 员涛, 周安佩, 刘东玉, 郑元, 段安安, 何承忠 (2014) 滇杨优树遗传多样性的AFLP分析. 西北林学院学报, 29, 103-108.]

种群 Population	代号 Code	样本量 Sample size	纬度 Latitude	经度 Longitude	海拔 Altitude (m)
昭通 Zhaotong	ZT	12	27°33°52″-27°38°29″ N	103°45°05″-103°46°43″ E	1,802-1,914
会泽 Huize	HZ	12	26°12°07″-26°23°42″ N	103°15°19″-103°24°09″ E	2,118-2,303
嵩明 Songming	SM	10	25°12°07″-25°17°42″ N	103°02°42″-103°03°43″ E	1,900-1,930
洱源 Eryuan	EY	12	26°05°56″-26°08°17″ N	99°58°13″-100°00°08″ E	2,056-2,060
拉市海 Lashihai	LS	12	26°51°03″-27°00°28″ N	100°08°58″-100°15°24″ E	2,418-2,657
美姑 Meigu	MG	6	28°19°40″-28°20°09″ N	103°08°22″-103°08°44″ E	1,944-2,027

种群 Population	代号 Code	样本量 Sample size	纬度 Latitude	经度 Longitude	海拔 Altitude (m)
昭通 Zhaotong	ZT	12	27°33°52″-27°38°29″ N	103°45°05″-103°46°43″ E	1,802-1,914
会泽 Huize	HZ	12	26°12°07″-26°23°42″ N	103°15°19″-103°24°09″ E	2,118-2,303
嵩明 Songming	SM	10	25°12°07″-25°17°42″ N	103°02°42″-103°03°43″ E	1,900-1,930
洱源 Eryuan	EY	12	26°05°56″-26°08°17″ N	99°58°13″-100°00°08″ E	2,056-2,060
拉市海 Lashihai	LS	12	26°51°03″-27°00°28″ N	100°08°58″-100°15°24″ E	2,418-2,657
美姑 Meigu	MG	6	28°19°40″-28°20°09″ N	103°08°22″-103°08°44″ E	1,944-2,027

名称 Name	区域 Primer area	正向序列 Forward primer sequence (5’-3’)	反向序列 Reverse primer sequence (5’-3’)
CO2	trnK	AGATGGAAAAAAGAGAGGATAGAGG	CAAATAATATCCAAATACCAAACCC
CO5	rpoC1	CGAATGGAAGACATAGACAAGT	AAGTGACCTTCGGGAGCTTCTC
CO9	atpF	TTGAAGTCCAGACAGAGCAGGTTAC	GGTCAAACAACTATTCAAAGTCCCT

名称 Name	区域 Primer area	正向序列 Forward primer sequence (5’-3’)	反向序列 Reverse primer sequence (5’-3’)
CO2	trnK	AGATGGAAAAAAGAGAGGATAGAGG	CAAATAATATCCAAATACCAAACCC
CO5	rpoC1	CGAATGGAAGACATAGACAAGT	AAGTGACCTTCGGGAGCTTCTC
CO9	atpF	TTGAAGTCCAGACAGAGCAGGTTAC	GGTCAAACAACTATTCAAAGTCCCT

种群 Popula-tion	等位基因Number of alleles (Na)	有效等位基因 Number of effective alleles (Ne)	观测杂合度Observed heterozygosity (Ho)	期望杂合度Expected heterozygosity (He)	Shannon’s 信息指数Shannon’s information content (I)	近交系数Inbreeding coefficient (F)	单倍型多态性 Haplotype diversity (h)	核苷酸多样性Nucleotide diversity (π)	单倍型组成(个体数) Haplotype composition (No. of individuals)
ZT	2.000	1.695	0.537	0.345	0.514	-0.439	0.864	0.00055	H1(3); H2(1); H3(1); H4(1); H5(4); H6(1); H7(1)
HZ	2.000	1.759	0.522	0.345	0.528	-0.432	-	-	H5(12)
SM	2.265	1.806	0.532	0.368	0.585	-0.313	-	-	H5(10)
EY	2.559	1.904	0.520	0.385	0.639	-0.190	0.455	0.00013	H5(9); H10(1); H11(1); H12(1)
LS	2.441	1.862	0.559	0.390	0.627	-0.260	0.378	0.00025	H5(10); H8(1); H9(1)
MG	1.794	1.623	0.495	0.324	0.473	-0.454	0.333	0.00017	H5(5); H13(1)
平均Mean	2.177	1.775	0.528	0.360	0.561	-0.341	0.402	0.00020