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Journal of Integrative Agriculture  2019, Vol. 18 Issue (6): 1312-1320    DOI: 10.1016/S2095-3119(18)62132-X
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Genetic diversity and population structure analysis of Capsicum germplasm accessions
GU Xiao-zhen1*, CAO Ya-cong1*, ZHANG Zheng-hai1, ZHANG Bao-xi1, ZHAO Hong1, ZHANG Xiao-min1, WANG Hai-ping1, 2, LI Xi-xiang1, 2, WANG Li-hao1
1 The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
2 National Mid-term Genebank for Vegetables, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
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Genetic diversity plays an essential role in plant breeding and utilization.  Pepper is an important vegetable and spice crop worldwide.  The genetic diversity of 1 904 accessions of pepper conserved at the National Mid-term Genebank for Vegetables, Beijing, China was analyzed based on 29 simple sequence repeat (SSR) markers, which were evenly distributed over 12 pepper chromosomes.  The pepper accessions were divided into two groups in a genetic structure analysis, and the two groups showed obvious differences in fruit type and geographical distribution.  We finally selected 248 accessions capturing 75.6% of the SSR alleles as the core collection for further research.  Insights into the genetic structure of pepper provide the basis for population-level gene mining and genetic improvement.
Keywords:  Capsicum       germplasm       SSR       genetic diversity              core collection  
Received: 06 July 2018   Accepted:
GU Xiao-zhen, E-mail:; CAO Ya-cong, E-mail:; * These authors contributed equally to this work.
Corresponding Authors:  Correspondence WANG Li-hao, E-mail:; LI Xi-xiang, E-mail:    

Cite this article: 

GU Xiao-zhen, CAO Ya-cong, ZHANG Zheng-hai, ZHANG Bao-xi, ZHAO Hong, ZHANG Xiao-min, WANG Hai-ping, LI Xi-xiang, WANG Li-hao. 2019. Genetic diversity and population structure analysis of Capsicum germplasm accessions. Journal of Integrative Agriculture, 18(6): 1312-1320.

Andrews J. 1984. Pepper: The Domesticated Capsicum. University of Texas Press, Austin, Texas. pp. 4–5.
Baral J B, Bosland P W. 2002. An updated synthesis of the Capsicum genus. Capsicum and Eggplant Newsletter, 21, 11–21.
Cavalli-Sforza L L, Edwards A W F. 1967. Phylogenetic analysis. Models and estimation procedures. American Journal of Human Genetics, 19, 233.
Cheng J, Qin C, Tang X, Zhou H, Hu Y, Zhao Z, Cui J, Li B, Wu Z, Yu J, Hu K. 2016. Development of a SNP array and its application to genetic mapping and diversity assessment in pepper (Capsicum spp.). Scientific Reports, 6, 33293.
Dong Y C, Cao Y S, Zhang X Y. 2003. Establishment of candidate core collections in Chinese common wheat germplasm. Journal of Plant Genetic Resources, 4, 1–8.
Evanno G, Regnaut S, Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14, 2611–2620.
Frankel O H. 1984. Genetic perspectives of germplasm conservation. In: Arber W, Llimensee K, Peacock W, Starlinger P, eds., Genetic Manipulation: Impact on Man and Society. Cambridge University Press, Cambridge. pp. 161–170.
Fulton T M, Chunwongse J, Tanksley S D. 1995. Microprep protocol for extraction of DNA from tomato and other herbaceous plants. Plant Molecular Biology Reporter, 13, 207–209.
Gouesnard B, Bataillon T M, Decoux G, Rozale C, Schoen D J, David J L. 2001. MSTRAT: An Algorithm for building germplasm core collections by maximizing allelic or phenotypic richness. Journal of Heredity, 92, 93–94.
Lee H Y, Ro N Y, Jeong H J, Jo J K, Ha Y, Jung A, Han J W, Venkatesh J, Kang B C. 2016. Genetic diversity and population structure analysis to construct a core collection from a large Capsicum germplasm. BMC Genetics, 17, 142.
Leroy T, Bellis F D, Legnate H, Musoli P, Kalonji A, Solorzano R G L, Cubry P. 2014. Developing core collections to optimize the management and the exploitation of diversity of the coffee Coffea canephora. Genetica, 142, 185–199.
Liu K, Muse S V. 2005. Power marker: An integrated analysis environment for genetic marker analysis. Bioinformatics, 21, 2128–2129.
Liu W F, Long H J, Cai R J. 2006. The utilization and research situation of Yunnan pepper germplasm resources. Journal of China Capsicum, 4, 10–12. (in Chinese)
Lv J, Qi J, Shi Q, Shen D, Zhang S, Shao G, Li H, Sun Z, Weng Y, Shang Y, Gu X, Li X, Zhu X, Zhang J, Treuren R, Dooijeweert W, Zhang Z, Huang S. 2012. Genetic diversity and population structure of cucumber (Cucumis sativus L.). PLoS ONE, 7, e46919.
Nicolaï M, Cantet M, Lefebvre V, Sage-Palloix A M, Palloix A. 2013. Genotyping a large collection of pepper (Capsicum spp.) with SSR loci brings new evidence for the wild origin of cultivated C. annuum and the structuring of genetic diversity by human selection of cultivar types. Genetic Resources and Crop Evolution, 60, 1–16.
Pickersgill B. 1969. The archaeological record of chili peppers (Capsicum spp.) and the sequence of plant domestation in Peru. American Antiquity, 34, 54–61.
Pritchard J K, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics, 155, 945–959.
Quenouille J, Saint-Felix L, Moury B, Palloix A. 2016. Diversity of genetic backgrounds modulating the durability of a major resistance gene. Analysis of a core collection of pepper landraces resistant to Potato virus Y. Molecular Plant Pathology, 17, 296–302.
Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology Evolution, 24, 1596–1599.
Thies J A, Fery R L. 2002. Evaluation of a core of the U.S. Capsicum germplasm collection for reaction to the northern root-knot nematode. Hortscience, 37, 805–810.
Wang L, Zheng J G, Lai Z X. 2003. RAPD analysis of genetic diversity in Capsicum annuum L. Journal of Fujian Agriculture and Forestry University, 32, 213–216.
Zheng N. 2006. Thought and discussion on the introduction Capsicum. Agricultural Archaeology, 4, 177–184. (in Chinese)
Zwendie Y, Tong N, Bosland P. 2004. Establishing a core collection of Capsicum using a cluster analysis with enlightened selection of accessions. Genetic Resource & Crop Evolution, 51, 147–151.
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