SSR marker development, genetic diversity and population structure analysis in oil tree species <i>Vernicia montana</i>

Zhao Pan; Li Danyang; Ma Jinlin; Liang Wenhui; Pang Xiaoming; Long Cui; Ma Jingyi; Guo Huihong

doi:10.12171/j.1000-1522.20210054

Journal of Beijing Forestry University > 2021 > 43(11): 50-61. > DOI: 10.12171/j.1000-1522.20210054

Zhao Pan, Li Danyang, Ma Jinlin, Liang Wenhui, Pang Xiaoming, Long Cui, Ma Jingyi, Guo Huihong. SSR marker development, genetic diversity and population structure analysis in oil tree species Vernicia montana[J]. Journal of Beijing Forestry University, 2021, 43(11): 50-61. DOI: 10.12171/j.1000-1522.20210054

Citation:

PDF (8614 KB)

SSR marker development, genetic diversity and population structure analysis in oil tree species Vernicia montana

1.
National Engineering Laboratory for Tree Breeding, School of Biological Sciences andBiotechnology, Beijing Forestry University, Beijing 100083, China
2.
Forestry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530002, Guangxi, China

More Information

Received Date: February 18, 2021
Revised Date: March 25, 2021
Available Online: October 15, 2021
Published Date: November 29, 2021

Graphical Abstract

Abstract

Abstract

Objective Vernicia montana, belonging to the genus Vernicia of Euphorbiaceae family, is an important industrial oil tree species, which has received great attention in recent years because it is much more resistant to wilt disease than V. fordii of same genus. However, the current researches on the molecular genetics of V. montana are still very limited due to its short cultivation history and inadequate management of germplasm resources. This study aimed to develop V. montana’s genome SSR markers, and then to carry out its germplasm identification, genetic diversity and population structure analyses.
Method Using RAD sequencing technology to obtain a simplified genome of V. montana to develop its SSR markers, based on the SSR markers, a series of methods including the analysis of molecular variance (AMOVA), the unweighted pair group method with arithmetic mean (UPGMA) clustering, principal coordinate analysis (PCoA) and population structure analysis were used to study 105 germplasm resources of V. montana from three different geographical distributions.
Result 17 polymorphic trinucleotide genomic-SSR markers were developed, which well distinguished all the tested 105 V. montana germplasms. A total of 85 private alleles were detected in 62 germplasms at 15 SSR loci. The AMOVA analysis revealed a moderate degree of genetic differentiation among the populations of V. montana; however, the genetic variation within the populations was much higher than that among the populations. Population structure analysis showed that four different gene pools were present in the three V. montana populations from different geographical distributions, and there was both evolutionary independence and a relatively high degree of genetic admixture among the populations, which was basically consistent with the results of UPGMA and PCoA analyses.
Conclusion The newly developed 17 SSR markers effectively identified 105 V. montana germplasms, and revealed the genetic diversity and population genetic structure of the germplasms, which would be very helpful for the conservation of germplasms and breeding program in V. montana.
- Vernicia montana,
- SSR marker,
- germplasm identification,
- genetic diversity,
- population structure

FullText(HTML)

References (55)

References

[1]	Xu W, Yang Q, Huai H Y, et al. Development of EST-SSR markers and investigation of genetic relatedness in tung tree[J]. Tree Genetics and Genomes, 2012, 8(4): 933−940. doi: 10.1007/s11295-012-0481-z
[2]	Zhang Q Y, Gao M, Wu L W, et al. Expression network of transcription factors in resistant and susceptible tung trees responding to Fusarium wilt disease[J]. Industrial Crops and Products, 2018, 122: 716−725. doi: 10.1016/j.indcrop.2018.05.041
[3]	Xu W, Yang Q, Huai H Y, et al. Microsatellite marker development in tung trees (Vernicia montana and V. fordii, Euphorbiaceae) [J]. American Journal of Botany, 2011, 98(8): e226−e228. doi: 10.3732/ajb.1100151
[4]	Chen Y H, Chen J H, Chang C Y, et al. Biodiesel production from tung (Vernicia montana) oil and its blending properties in different fatty acid compositions[J]. Bioresource Technology, 2010, 101(24): 9521−9526. doi: 10.1016/j.biortech.2010.06.117
[5]	He Z Q, Chapital D C, Cheng H N, et al. Application of tung oil to improve adhesion strength and water resistance of cottonseed meal and protein adhesives on maple veneer[J]. Industrial Crops and Products, 2014, 61: 398−402. doi: 10.1016/j.indcrop.2014.07.031
[6]	Chen Y C, Yin H F, Gao M, et al. Comparative transcriptomics atlases reveals different gene expression pattern related to Fusarium wilt disease resistance and susceptibility in two Vernicia species[J/OL]. Frontiers in Plant Science, 2016, 7: 1974 [2020−12−25]. http://doi.org/10.3389/fpls.2016.01974.
[7]	Zhang L L, Liu X L, Peng J H. Genetic diversity and geographic differentiation of tung tree, Vernicia fordii (Euphorbiaceae), a potential biodiesel plant species with low invasion risk[J/OL]. Agronomy, 2019, 9(7): 402 [2020−12−27]. http://doi.org/10.3390/agronomy9070402.
[8]	Zhang L L, Luo M C, You F M, et al. Development of microsatellite markers in tung tree (Vernicia fordii) using cassava genomic sequences[J]. Plant Molecular Biology Reporter, 2015, 33(4): 893−904. doi: 10.1007/s11105-014-0804-3
[9]	Luo X, Cao S Y, Hao Z X, et al. Analysis of genetic structure in a large sample of pomegranate (Punica granatum L.) using fluorescent SSR markers[J]. The Journal of Horticultural Science and Biotechnology, 2018, 93(6): 659−665. doi: 10.1080/14620316.2018.1432994
[10]	Agarwal M, Shrivastava N, Padh H. Advances in molecular marker techniques and their applications in plant sciences[J]. Plant Cell Reports, 2008, 27(4): 617−631. doi: 10.1007/s00299-008-0507-z
[11]	Francki M G, Walker E, Li D A, et al. High-density SNP mapping reveals closely linked QTL for resistance to Stagonospora nodorum blotch (SNB) in flag leaf and glume of hexaploid wheat[J]. Genome, 2018, 61(2): 145−149. doi: 10.1139/gen-2017-0203
[12]	Kalia R K, Rai M K, Kalia S, et al. Microsatellite markers: an overview of the recent progress in plants[J]. Euphytica, 2011, 177(3): 309−334. doi: 10.1007/s10681-010-0286-9
[13]	Lin E P, Zhuang H B, Yu J J, et al. Genome survey of Chinese fir (Cunninghamia lanceolata): identification of genomic SSRs and demonstration of their utility in genetic diversity analysis[J/OL]. Scientific Reports, 2020, 10(1): 4698 [2020−11−20]. http://doi.org/10.1038/s41598-020-61611-0.
[14]	Jain N, Patil G B, Bhargava P, et al. In Silico mining of EST-SSRs in Jatropha curcas L. towards assessing genetic polymorphism and marker development for selection of high oil yielding clones[J]. American Journal of Plant Sciences, 2014, 5(11): 1521−1541. doi: 10.4236/ajps.2014.511167
[15]	Chen Y N, Dai X G, Yin T M, et al. DNA fingerprinting of oil camellia cultivars with SSR markers[J/OL]. Tree Genetics and Genomes, 2016, 12(1): 7 [2021−01−02]. http://doi.org/10.1007/s11295-015-0966-7.
[16]	Bernard A, Barreneche T, Lheureux F, et al. Analysis of genetic diversity and structure in a worldwide walnut (Juglans regia L.) germplasm using SSR markers[J/OL]. PLoS One, 2018, 13(11): e0208021 [2021−01−15]. https://doi.org/10.1371/journal.pone.0208021.
[17]	Babu B K, Rani K L M, Sahu S, et al. Development and validation of whole genome-wide and genic microsatellite markers in oil palm (Elaeis guineensis Jacq.): first microsatellite database (OpSatdb)[J/OL]. Scientific Reports, 2019, 9: 1899 [2020−12−29]. http://doi.org/10.1038/s41598-018-37737-7.
[18]	Li D Y, Long C, Pang X M, et al. The newly developed genomic-SSR markers uncover the genetic characteristics and relationships of olive accessions[J/OL]. Peer J, 2020, 8: e8573 [2020−12−18]. http://doi.org/10.7717/peerj.8573.
[19]	Baldoni L, Cultrera N G, Mariotti R, et al. A consensus list of microsatellite markers for olive genotyping[J]. Molecular Breeding, 2009, 24(3): 213−231. doi: 10.1007/s11032-009-9285-8
[20]	Beghè D, Molano J F G, Fabbri A, et al. Olive biodiversity in Colombia: a molecular study of local germplasm[J]. Scientia Horticulturae, 2015, 189: 122−131. doi: 10.1016/j.scienta.2015.04.003
[21]	广西林业科学研究所, 广西崇左县油桐试验站. “桂皱-27号”等四个千年桐高产优良无性系的选育[J]. 中国林业科学, 1977(1):41−45. Guangxi Forestry Research Institute, Guangxi Chongzuo Experimental Station of Tung tree. Breeding of high-yield and excellent clones of four V. montana including “Guizhou-27”[J]. Chinese Forestry Science, 1977(1): 41−45.
[22]	Nei M, Tajima F, Tateno Y. Accuracy of estimated phylogenetic trees from molecular data(II): gene frequency data[J]. Journal of Molecular Evolution, 1983, 19(2): 153−170. doi: 10.1007/BF02300753
[23]	Yu C, Zhang S G, Zhou C, et al. A likelihood ratio test of population Hardy-Weinberg equilibrium for case-control studies[J]. Genetic Epidemiology, 2009, 33(3): 275−280. doi: 10.1002/gepi.20381
[24]	Barchi L, Lanteri S, Portis E, et al. Identification of SNP and SSR markers in eggplant using RAD tag sequencing[J/OL]. BMC Genomics, 2011, 12: 304 [2021−01−01]. http://doi.org/10.1186/1471-2164-12-304.
[25]	Gao Y, Yin S, Liu C, et al. A rapid approach for SSR development in Amorphophallus paeoniifolius using RAD-seq[J]. Taiwania, 2018, 63(3): 281−285.
[26]	Poland J A, Brown P J, Sorrells M E, et al. Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach[J/OL]. PLoS One, 2012, 7(2): e32253 [2021−01−22]. https://doi.org/10.1371/journal.pone.0032253.
[27]	Feng J Y, Zhao S, Li M, et al. Genome-wide genetic diversity detection and population structure analysis in sweetpotato (Ipomoea batatas) using RAD-seq[J]. Genomics, 2020, 112(2): 1978−1987. doi: 10.1016/j.ygeno.2019.11.010
[28]	Dettori M T, Micali S, Giovinazzi J, et al. Mining microsatellites in the peach genome: development of new long-core SSR markers for genetic analyses in five Prunus species[J/OL]. SpringerPlus, 2015, 4(1): 337 [2020−12−12]. http://doi.org/10.1186/s40064-015-1098-0.
[29]	Song Q J, Fickus E W, Cregan P B. Characterization of trinucleotide SSR motifs in wheat[J]. Theoretical and Applied Genetics, 2002, 104(2−3): 286−293.
[30]	Song Q J, Marek L F, Shoemaker R C, et al. A new integrated genetic linkage map of the soybean[J]. Theoretical and Applied Genetics, 2004, 109(1): 122−128. doi: 10.1007/s00122-004-1602-3
[31]	Guo R, Landis J B, Moore M J, et al. Development and application of transcriptome-derived microsatellites in Actinidia eriantha (Actinidiaceae)[J/OL]. Frontiers in Plant Science, 2017, 8: 1383 [2021−01−12]. http://doi.org/10.3389/fpls.2017.01383.
[32]	Asadi A, Ebrahimi A, Rashidi-Monfared S, et al. Comprehensive functional analysis and mapping of SSR markers in the chickpea genome (Cicer arietinum L.)[J/OL]. Computational Biology and Chemistry, 2020, 84: 107169 [2020−12−15]. https://doi.org/10.1016/j.compbiolchem.2019.107169.
[33]	Delgado-Martinez F J, Amaya I, Sanchez-Sevilla J F, et al. Microsatellite marker-based identification and genetic relationships of olive cultivars from the Extremadura region of Spain[J]. Genetics and Molecular Research, 2012, 11(2): 918−932. doi: 10.4238/2012.April.10.7
[34]	Nachimuthu V V, Muthurajan R, Duraialaguraja S, et al. Analysis of population structure and genetic diversity in rice germplasm using SSR markers: an initiative towards association mapping of agronomic traits in Oryza sativa[J/OL]. Rice, 2015, 8: 30 [2021−01−04]. http://doi.org/10.1186/s12284-015-0062-5.
[35]	Vischi M, Chiabà C, Raranciuc S, et al. Genetic diversity of walnut (Juglans Regia L.) in the eastern Italian Alps[J/OL]. Forests, 2017, 8(3): 81 [2021−02−01]. http://doi.org/10.3390/f8030081.
[36]	Torokeldiev N, Ziehe M, Gailing O, et al. Genetic diversity and structure of natural Juglans regia L. populations in the southern Kyrgyz Republic revealed by nuclear SSR and EST-SSR markers[J/OL]. Tree Genetics and Genomes, 2019, 15(1): 5 [2021−01−10]. https://doi.org/10.1007/s11295-018-1311-8.
[37]	Balapanov I, Suprun I, Stepanov I, et al. Comparative analysis Crimean, Moldavian and Kuban Persian walnut collections genetic variability by SSR-markers[J]. Scientia Horticulturae, 2019, 253: 322−326. doi: 10.1016/j.scienta.2019.04.014
[38]	Degirmenci F O, Acar P, Kaya Z. Consequences of habitat fragmentation on genetic diversity and structure of Salix alba L. populations in two major river systems of Turkey[J]. Tree Genetics and Genomes, 2019, 15(4): 59. doi: 10.1007/s11295-019-1365-2
[39]	Hmmam I, Mariotti R, Ruperti B, et al. Venetian olive (Olea europaea) germplasm: disclosing the genetic identity of locally grown cultivars suited for typical extra virgin oil productions[J]. Genetic Resources and Crop Evolution, 2018, 65(6): 1733−1750. doi: 10.1007/s10722-018-0650-5
[40]	Jones A G, Ardren W R. Methods of parentage analysis in natural populations[J]. Molecular Ecology, 2003, 12(10): 2511−2523. doi: 10.1046/j.1365-294X.2003.01928.x
[41]	Noormohammadi Z, Trujillo I, Belaj A, et al. Genetic structure of Iranian olive cultivars and their relationship with Mediterranean’s cultivars revealed by SSR markers[J]. Scientia Horticulturae, 2014, 178: 175−183. doi: 10.1016/j.scienta.2014.08.002
[42]	Mariotti R, Cultrera N G M, Mousavi S, et al. Development, evaluation, and validation of new EST-SSR markers in olive (Olea europaea L.)[J/OL]. Tree Genetics and Genomes, 2016, 12(6): 120 [2020−12−22]. http://doi.org/10.1007/s11295-016-1077-9.
[43]	Boucheffa S, Miazzi M M, di Rienzo V, et al. The coexistence of oleaster and traditional varieties affects genetic diversity and population structure in Algerian olive (Olea europaea) germplasm[J]. Genetic Resources and Crop Evolution, 2017, 64(2): 379−390. doi: 10.1007/s10722-016-0365-4
[44]	Li X, Li M, Hou L, et al. De Novo transcriptome assembly and population genetic analyses for an endangered Chinese endemic Acer miaotaiense (Aceraceae)[J/OL]. Genes, 2018, 9(8): 378 [2020−12−14]. https://doi.org/10.3390/genes9080378.
[45]	Wright S. Evolution and the genetics of populations[J]. Experimental Results and Evolutionary Deductions, 1977, 59: 815−826.
[46]	Ithnin M, Teh C K, Ratnam W. Genetic diversity of Elaeis oleifera (HBK) Cortes populations using cross species SSRs: implication’s for germplasm utilization and conservation[J/OL]. BMC Genetics, 2017, 18(1): 37 [2021−01−12]. http://doi.org/10.1186/s12863-017-0505-7.
[47]	Deng H W, Chen W M, Recker R R. Population admixture: detection by Hardy-Weinberg test and its quantitative effects on Linkage-Disequilibrium methods for localizing genes underlying complex traits[J]. Genetics, 2001, 157(2): 885−897. doi: 10.1093/genetics/157.2.885
[48]	Han H, Woeste K E, Hu Y H, et al. Genetic diversity and population structure of common walnut (Juglans regia) in China based on EST-SSRs and the nuclear gene phenylalanine ammonia-lyase (PAL)[J/OL]. Tree Genetics & Genomes, 2016, 12(6): 111 [2021−01−13]. http://doi.org/10.1007/s11295-016-1064-1.
[49]	周强, 周慧杰, 李史干, 等. 广西红水河流域生态经济区划初探[J]. 企业科技与发展, 2017(10):28−32. doi: 10.3969/j.issn.1674-0688.2017.10.010 Zhou Q, Zhou H J, Li S G, et al. A preliminary study on the ecological economic division of the Hongshui River Basin in Guangxi[J]. Technology and Development of Enterprise, 2017(10): 28−32. doi: 10.3969/j.issn.1674-0688.2017.10.010
[50]	Huang Y, Wang H, Xiao W H, et al. Contributions of climate change and anthropogenic activities to runoff change in the Hongshui River, southwest China[J/OL]. IOP Conference Series:Earth and Environmental Science, 2018, 191(1): 012143 [2021−01−22]. http://doi.org/10.1088/1755-1315/191/1/012143.
[51]	Lundqvist E, Andersson E. Genetic diversity in populations of plants with different breeding and dispersal strategies in a free-flowing boreal river system[J]. Hereditas, 2001, 135(1): 75−83.
[52]	Liu Y F, Wang Y, Huang H W. High interpopulation genetic differentiation and unidirectional linear migration patterns in Myricaria laxiflora (Tamaricaceae) , an endemic riparian plant in the three gorges valley of the Yangtze River[J]. American Journal of Botany, 2006, 93(2): 206−215. doi: 10.3732/ajb.93.2.206
[53]	Kikuchi S, Suzuki W, Sashimura N. Gene flow in an endangered willow Salix hukaoana (Salicaceae) in natural and fragmented riparian landscapes[J]. Conservation Genetics, 2011, 12(1): 79−89.
[54]	Wu Y, Yang Y D, Qadri R, et al. Development of SSR markers for coconut (Cocos nucifera L.) by selectively amplified microsatellite (SAM) and its applications[J]. Tropical Plant Biology, 2019, 12(1): 32−43. doi: 10.1007/s12042-018-9215-1
[55]	Emanuelli F, Lorenzi S, Grzeskowiak L, et al. Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape[J/OL]. BMC Plant Biology, 2013, 13(1): 39 [2021−02−22]. http://doi.org/10.1186/1471-2229-13-39.

Cited By

Cited by

Periodical cited type(8)

1.	颜欢欢. 不同基质对千年桐容器苗光合生理特征的影响. 福建林业科技. 2024(02): 31-36 .
2.	赵永树，张世超，杨澜，谢佳鑫，刘明，杨汉波，辜云杰，彭建，刘闵豪. 基于SSR标记的四川楠木种源（家系）遗传多样性分析. 四川林业科技. 2024(03): 1-8 .
3.	王芝懿，李振芳，彭婵，陈英，张新叶. 基于荧光SSR标记的紫薇遗传多样性分析. 南京林业大学学报(自然科学版). 2023(02): 61-69 .
4.	赵慧琪，李栋梁，赵慧琳，吴芳芳，黄赛，张永豪，张浪，杨珺，任军方. 海南岛火焰兰SSR标记开发、遗传多样性与群体结构分析. 分子植物育种. 2023(07): 2300-2310 .
5.	侯佳音，冯树香，代嵩华，闫淑芳. 7种观赏桃新种质的TP-M13-SSR分子标记鉴定及亲缘关系分析. 北京林业大学学报. 2023(08): 132-141 . 本站查看
6.	莫长明，谢文娟，郭文锋，张燕玲，黄江，张馨丹，李忠，唐其，马小军. 罗汉果遗传多样性与群体结构及核心种质研究. 中草药. 2023(18): 6040-6054 .
7.	黄彬，黄建建，汤优令，周文才，汪雁楠，田仟仟，龚春，舒惠理，温强. 江西省浙江红山茶及近缘种群体遗传多样性的SSR分析. 江西农业大学学报. 2023(05): 1084-1095 .
8.	秦英之，车佳航，尹跃，饶书培，安巍，戴国礼，陈金焕. 基于全长转录组信息的枸杞SSR标记开发. 植物遗传资源学报. 2022(06): 1816-1827 .

Other cited types(8)

Get Citation

PDF

XML

Article views (1106) PDF downloads (81) Cited by(16)

Turn off MathJax

Article Contents

Abstract

References

SSR marker development, genetic diversity and population structure analysis in oil tree species Vernicia montana

Abstract

References

Cited by

Periodical cited type(8)

Other cited types(8)

Catalog

Export File

Citation

Format

Content