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Genetic diversity of Juglans sigillata Dode germplasm in Yunnan Province, China, as revealed by SSRs

Published online by Cambridge University Press:  17 November 2020

Shaoyu Chen Open the ORCID record for Shaoyu Chen [Opens in a new window] ,
Tao Wu ,
Liangjun Xiao ,
Delu Ning  and
Li Pan
Shaoyu Chen*
Affiliation:
Yunnan Provincial Key Laboratory of Cultivation and Exploitation of Forest Plants, Yunnan Academy of Forestry and Grassland, Kunming650204, Yunnan, China
Tao Wu
Affiliation:
Yunnan Provincial Key Laboratory of Cultivation and Exploitation of Forest Plants, Yunnan Academy of Forestry and Grassland, Kunming650204, Yunnan, China
Liangjun Xiao
Affiliation:
Economic Forest Institute, Yunnan Academy of Forestry and Grassland, Kunming650204, Yunnan, China
Delu Ning
Affiliation:
Economic Forest Institute, Yunnan Academy of Forestry and Grassland, Kunming650204, Yunnan, China
Li Pan
Affiliation:
Economic Forest Institute, Yunnan Academy of Forestry and Grassland, Kunming650204, Yunnan, China
*
*Corresponding author. E-mail: [email protected]
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Abstract

Iron walnut, Juglans sigillata Dode, restricted to southwestern China, has its centre of distribution in Yunnan Province which has a varied climate, geography and rich plant diversity. Yunnan contains abundant J. sigillata germplasm. In this study, a provincial-scale set of walnut germplasm resources (14 populations comprising 1122 individuals) was evaluated for genetic diversity based on 20 simple sequence repeat (SSR) loci. The number of SSR alleles per locus ranged from 7 to 27, with an average of 17.55. Mean allelic richness and mean private allelic richness ranged from 3.40 to 4.62 and 0.11 to 0.36, with average of 3.93 and 0.30, respectively. Expected heterozygosity (He) varied from 0.26 to 0.78, with an average of 0.57. Polymorphism information content ranged from 0.22 to 0.79, with an average of 0.57. Genetic differentiation (FST) was 0.05, indicating that only 5% of total genetic variability was inter-populational, a finding supported by an analysis of molecular variance and STRUCTURE analysis. Relatively high gene flow (Nm = 6.70) was observed between populations. A unweighted pair-group method with arithmetic analysis classified the 14 populations into two major groups. Mantel testing uncovered a significant correlation between geographic distance and genetic distance (r = 0.33, P = 0.04). Overall, the research revealed a moderately high level of genetic diversity in the germplasm and low genetic differentiation among populations, which showed great potential for further development and exploitation of this resource.

Keywords

genetic differentiationgenetic diversityJuglans sigillata DodeSSR markersUPGMA clustering
Type
Research Article
Information
Plant Genetic Resources , Volume 18 , Issue 6 , December 2020 , pp. 417 - 426
Copyright
Copyright © The Author(s), 2020. Published by Cambridge University Press on behalf of NIAB

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References

Bayazit, S, Kazan, K, Gulbitti, V, Evik, C, Ayanoglu, H and Ergul, A (2007) AFLP analysis of genetic diversity in low chilling requiring Walnut (Juglans regia L.) genotypes from Hatay, Turkey. Scientia Horticulturae 111: 394–398.CrossRefGoogle Scholar
Botstein, D, White, RL, Skolnick, M and Davis, RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphism. American Journal of Human Genetics 32: 314–331.Google Scholar
Bussell, JD (1999) The distribution of random amplified polymorphic DNA (RAPD) diversity amongst populations of Isotoma petraea (Lobeliaceae). Molecular Ecology 8: 775–789.CrossRefGoogle Scholar
Chen, LH, Hu, TX, Zhang, F and Li, GH (2008) Genetic diversity of four Juglans Populations revealed by AFLP in Sichuan Province, China. Journal of Plant Ecology 32: 1362–1372, (In Chinese).Google Scholar
Chen, LN, Ma, QG, Chen, YK, Wang, BQ and Pei, D (2014) Identification of major walnut cultivars grown in China based on nut phenotypes and SSR markers. Scientia Horticulturae 168: 240–248.CrossRefGoogle Scholar
Chen, SY, Ning, DL, Wu, T, Xiao, LJ, Lin, HD, Zhu, YF, He, N and Pan, L (2017) Development of SSR markers in Juglans sigillata and its application in genetic diversity analysis. Journal of Northwest Forestry University 32: 91–96, (In Chinese).Google Scholar
Chen, SY, Wu, T and Xiao, LJ (2019) Genetic diversity and distribution characteristic of Juglans sigillata resources along Jinsha river in three parallel rivers belt of Yunnan. Journal of Southern Agriculture 50: 2656–2664, (In Chinese).Google Scholar
Evanno, G, Regnaut, S and Goudet, J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14: 2611–2620.CrossRefGoogle ScholarPubMed
Fan, ZY, Xi, XL, Fang, WL, Zhang, Y and Zhao, TS (2005) Breeding on three new promising and early fruiting walnut cultivars developed by species hybridization. Journal of Zhejiang Forestry College 22: 518–523, (In Chinese).Google Scholar
Fang, WL, Yang, ZB, Huang, Q, Zhang, XX, Fan, ZY and Qi, SL (1998) Selective breeding of precocious, prolific and quality walnut strains. Economic Forest Researches 16: 6–10, (In Chinese).Google Scholar
FAO (Food and Agricultural Organization of the United Nations) (2012) FAO Statistical Databases and DataSets. FAO (Food and Agricultural Organization of the United Nations). Available online: http://faostat.fao.org (accessed on 10 October 2020).Google Scholar
Feng, XJ, Yuan, XY, Sun, YW, Hu, YH, Zulfiqar, S, Ouyang, XH, Dang, M, Zhou, HJ, Woeste, K and Zhao, P (2018) Resources for studies of iron walnut (Juglans sigillata) gene expression, genetic diversity, and evolution. Tree Genetics & Genomes 14: 51.CrossRefGoogle Scholar
Fjellstrom, RG and Parfitt, DE (1994) Genetic diversity determined by restriction fragment length polymorphisms. Genome 37: 690–700.CrossRefGoogle ScholarPubMed
Frankham, R, Ballou, JD and Briscoe, DA (2002) Introduction to Conservation Genetics. Cambridge: Cambridge University Press.CrossRefGoogle Scholar
Gunn, BF, Aradhya, M, Salick, JM, Miller, AJ, Yang, YP, Liu, L and Hai, X (2010) Genetic variation in walnut (Juglans regia and J. sigillata; Juglandaceae): species distinctions, human impacts, and the conservation of agrobiodiversity in Yunnan, China. American Journal of Botany 97: 660–671.CrossRefGoogle Scholar
Hamrick, JL and Godt, MJW (1996) Effects of life history traits on genetic diversity in plant species. Philosophical Transactions of Royal Society of London B 351: 1291–1298.Google Scholar
Hamrick, JL and Loveless, MD (1989a) The genetic structure of tropical tree populations: associations with reproductive biology. In: Bock, JU, Linhart, YB (eds) Plant Evolutionary Ecology. Boulder: Westview Press, pp. 129–146.Google Scholar
Hamrick, JL and Loveless, MD (1992) Factors influencing levels of genetic diversity in woody plants species. New Forests 6: 95–124.CrossRefGoogle Scholar
Hamrick, JL, Godt, MJW and Brown, AHD (1989b) Allozyme diversity in plant species. Plant Population Breeding & Genetic Resources 28: 43–63.Google Scholar
Hamrick, JL, Godt, MJW and Sherman-Broyles, LS (1995) Gene flow among plant populations: evidence from genetic markers. In: Hoch, DC, Stephnon, AG (eds) Experimental and Molecular Approaches to Plant Biosystematics. St Louis: Missouri Botanical Garden, pp. 215–232.Google Scholar
Huang, Y (2013) Analysis of Camellia meiocarpa genetic diversity based on SRAP markers. Scientia Silvae Sinicae 49: 43–50, (In Chinese).Google Scholar
Ji, AQ, Wang, YN, Wu, GL, Wu, WJ, Yang, HY and Wang, QH (2014) Genetic diversity and population structure of North China mountain walnut revealed by ISSR. American Journal of Plant Sciences 5: 3194–3202.CrossRefGoogle Scholar
Kalinowski, ST (2005) HP-RARE: a computer program for performing rarefaction on measures of allelic richness. Molecular Ecology Notes 5: 187–189.CrossRefGoogle Scholar
Li, GT, Ai, CX, Zhang, LS, Wei, HR and Liu, QZ (2011) ISSR Analysis of genetic diversity among seedling Walnut (Juglans Spp.) populations. Journal of Plant Genetic Resources 12: 640–645, (In Chinese).Google Scholar
Liu, XL, Chen, XS, Zhang, MY, Chen, XL, He, TM, Zhang, LJ and Zhang, CY (2008) Population genetic structure analysis of Juglans regia using SSR markers. Journal of Fruit Science 25: 526–530, (In Chinese).Google Scholar
Liu, BY, Liu, XL, Wei, HB and Gu, WY (2017) Genetic diversity of germplasm resources of Walnut in Qinghai. Journal of Northwest Forestry University 32: 130–135, (In Chinese).Google Scholar
Lu, B (2009) Characteristics and quality of Juglans sigillata. Nonwood Forest Research 27: 137–140, (In Chinese).Google Scholar
Lu, SJ, Lu, B, Wu, SB, Duan, LJ, Fan, LY and Yi, XY (2015) Analysis of the main economic characters of walnut nuts in Yunnan. Northern Horticulture 19: 18–21, (In Chinese).Google Scholar
Mantel, N (1967) The detection of disease clustering and a generalized regression approach. Cancer Research 27: 209.Google Scholar
Nazeer, A, Mir, JI, Mir, RR, Nazir, AR, Rizwan, R, Shabir, HW, Wajida, S, Hidayatullah, M and Sheikh, MA (2012) SSR And RAPD analysis of genetic diversity in walnut (Juglans regia L.) genotypes from jammu and Kashmir, India. Physiology and Molecular Biology of Plant 18: 149–160.Google Scholar
Nei, M (1973) Analysis of gene diversity in subdivided populations. Proceedings of the National Academy Sciences 70: 3321–3323.CrossRefGoogle ScholarPubMed
Ning, DL, Ma, QG, Zhang, Y, Wang, H, Lu, B and Pei, D (2011) FISH-AFLP analysis of genetic diversity on walnut cultivars in Yunnan Province. Forest Research 24: 189–193, (In Chinese).Google Scholar
Peakall, R and Smouse, PE (2012) GenALEx 6.5: genetic analysis in excel. Population genetic software for teaching and research-an update. Bioinformatics (Oxford, England) 28: 2537–2539.CrossRefGoogle ScholarPubMed
Potter, D, Gao, F, Aliello, G, Leslie, C and McGranahan, G (2002) Intersimple sequence repeat markers for fingerprinting and determining genetic relationship of Walnut (Juglans regia) cultivars. Journal of the American Society for Horticultural Science 127: 75–81.CrossRefGoogle Scholar
Pritchard, JK, Stephens, M, Rosenberg, NA and Donelly, P (2000) Association mapping in structured populations. The American Journal of Human Genetics 37: 170–181.CrossRefGoogle Scholar
Rohlf, FJ (2000) NTSYS-PC: Numerical Taxonomy and Multivariate Analysis System Version 2.1. Setauket New York: distribution by Exeter software.Google Scholar
Shah, UN, Mir, JI, Ahmed, N and Fazili, KM (2018) Assessment of germplasm diversity and genetic relationships among walnut (Juglans regia L.) genotypes through microsatellite markers. Journal of the Saudi Society of Agricultural Sciences 17: 339–350.CrossRefGoogle Scholar
Shamlu, F, Rezaei, M, Lawson, S, Ebrahimi, A, Biabani, A and Khan-Ahmadi, A (2018) Genetic diversity of superior Persian walnut genotypes in Azadshahr, Iran. Physiology and Molecular Biology of Plants 24: 939–949.CrossRefGoogle ScholarPubMed
Shannon, CE and Weave, W (1959) The Mathematical Theory of Communication. Illiois: University of Illiois Press, pp. 20–29.Google Scholar
Slatkin, M and Barton, NH (1989) A comparison of three indirect methods for estimating average levels of gene flow. Evolution 43: 1349–1368.CrossRefGoogle ScholarPubMed
Templeton, AR (2010) Introduction to Conservation Genetics. Cambridge: Cambridge University Press. 56.Google Scholar
Testolin, R, Marrazzo, T, Cipriani, G, Quarta, R, Verde, I, Dettori, MT, Pancaldi, M and Sansavini, S (2000) Microsatellite DNA in peach (Prunus persica L. Batsch) and its use in fingerprinting and testing the genetic origin of cultivars. Genome 43: 512–520.CrossRefGoogle ScholarPubMed
Victory, ER, Glaubitz, JC, Rhodes, OE and Woeste, KE (2006) Genetic homogeneity in Juglans nigra (Juglandaceae) at nuclear microsatellites. American Journal of Botany 93: 118–126.CrossRefGoogle Scholar
Wang, H, Hao, JM, Wang, BQ and Pei, D (2007) SSR Analysis of genetic diversity of eight natural walnut populations in China. Scientia Silvae Sinicae 43: 120–124, (In Chinese).Google Scholar
Wang, H, Pei, D, Gu, RS and Wang, BQ (2008) Genetic diversity and structure of Walnut populations in Central and Southwest China revealed by microsatellite markers. Journal of the American Society for Horticultural Science 133: 197–203.CrossRefGoogle Scholar
Wang, H, Yan, YB, Zhang, JP and Pei, D (2009) Application of ITS sequence and SSR markers to study the relationship between Juglans regia And Juglans sigillata. Journal of Nanjing Forestry University: Natural Science Edition 33: 35–38, (In Chinese).Google Scholar
Wang, HX, Zhao, SG, Gao, Y, Zhang, ZH and Xuan, LC (2011) Genetic diversity of Juglans regia L. Cultivars revealed by AFLP analysis. Scientia Agricultura Sinica 44: 1434–1442, (In Chinese).Google Scholar
Wang, H, Pan, G, Ma, QG, Zhang, JP and Pei, D (2015) The genetic diversity and introgression of Juglans regia and Juglans sigillata in Tibet as revealed by SSR markers. Tree Genetics & Genomes 11: 1–11.CrossRefGoogle Scholar
Wen, YF, Han, WJ and Wu, S (2010) Plant genetic diversity and its influencing factors. Journal of Central South University of Forestry & Technology 30: 80–87, (In Chinese).Google Scholar
Wu, YM, Pei, D, Xi, SK and Li, JR (2000) A study on the genetic relationship among species in Juglans L. Using RAPD markers. Acta Horticulturae Sinica 27: 17–22, (In Chinese).Google Scholar
Xi, SK (1987) Gene resources of Juglans and genetic improvement of Juglans regia in China. Scientia Silvae Sinicae 23: 342–349, (In Chinese).Google Scholar
Xi, RT and Zhang, YP (1996) Fruit Trees of China: Walnut Volume. Beijing, China: Chinese Forestry Press. (In Chinese).Google Scholar
Xiao, LJ, Chen, SY, Ning, DL, Wu, T and He, N (2018) Study on the genetic diversity of germplasm resources of Juglans sigillata in Northwest Yunnan. Journal of Yunnan Agricultural University (Natural Science) 33: 597–604, (In Chinese).Google Scholar
Xu, YJ, Han, HB, Wang, H, Chen, NL, Ma, QG and Pei, D (2016) Phenotypic and genetic diversities of nuts of Walnut (Juglans regia) populations originated from seedlings in Daba Mountains. Scientia Silvae Sinicae 52: 111–118, (In Chinese).Google Scholar
Yang, E, Chen, SY, Zhang, Y, Fang, ZY and Xi, XL (2005) Comparison on effect between two methods of DNA extraction from leaves of Juglans sigillata. Journal of West China Forestry Science 34: 72–75, (In Chinese).Google Scholar
Yuan, XY, Sun, YW, Bai, XR, Dang, M, Feng, XJ, Zulfiqar, S and Zhao, P (2018) Population structure, genetic diversity, and gene introgression of two closely related walnuts (Juglans regia and J. sigillata) in southwestern China revealed by EST-SSR markers. Forests 9: 646.CrossRefGoogle Scholar
Zhao, TS, Fang, WL, Fan, ZY, Xi, XL and Zhang, Y (2007) Yunxin 90303, a promising new early walnut selection. Journal of Fruit Science 24: 252–253, (In Chinese).Google Scholar
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