Please wait a minute...
Journal of Integrative Agriculture  2019, Vol. 18 Issue (6): 1312-1320    DOI: 10.1016/S2095-3119(18)62132-X
Horticulture Advanced Online Publication | Current Issue | Archive | Adv Search |
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
Download:  PDF in ScienceDirect  
Export:  BibTeX | EndNote (RIS)      
Abstract  
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:
Fund: 
GU Xiao-zhen, E-mail: 913688646@qq.com; CAO Ya-cong, E-mail: caoyacong@caas.cn; * These authors contributed equally to this work.
Corresponding Authors:  Correspondence WANG Li-hao, E-mail: wanglihao@caas.cn; LI Xi-xiang, E-mail: lixixiang@caas.cn    

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.
[1] Niu Wang, Weidong Zhang, Zhenyu Zhong, Xiongbo Zhou, Xinran Shi, Xin Wang. FGF7 secreted from dermal papillae cell regulates the proliferation and differentiation of hair follicle stem cell[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3583-3597.
[2] Lichao Zhai, Shijia Song, Lihua Zhang, Jinan Huang, Lihua Lv, Zhiqiang Dong, Yongzeng Cui, Mengjing Zheng, Wanbin Hou, Jingting Zhang, Yanrong Yao, Yanhong Cui, Xiuling Jia. Subsoiling before winter wheat alleviates the kernel position effect of densely grown summer maize by delaying post-silking root–shoot senescence[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3384-3402.
[3] Tiantian Chen, Lei Li, Dan Liu, Yubing Tian, Lingli Li, Jianqi Zeng, Awais Rasheed, Shuanghe Cao, Xianchun Xia, Zhonghu He, Jindong Liu, Yong Zhang. Genome wide linkage mapping for black point resistance in a recombinant inbred line population of Zhongmai 578 and Jimai 22[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3311-3321.
[4] Zuxian Chen, Bingbing Zhao, Yingying Wang, Yuqing Du, Siyu Feng, Junsheng Zhang, Luxiang Zhao, Weiqiang Li, Yangbao Ding, Peirong Jiao. H5N1 avian influenza virus PB2 antagonizes duck IFN-β signaling pathway by targeting mitochondrial antiviral signaling protein[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3614-3625.
[5] Yang Sun, Yu Liu, Li Zhou, Xinyan Liu, Kun Wang, Xing Chen, Chuanqing Zhang, Yu Chen. Activity of fungicide cyclobutrifluram against Fusarium fujikuroi and mechanism of the pathogen resistance associated with point mutations in FfSdhB, FfSdhC2 and FfSdhD[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3511-3528.
[6] Yufeng Xiao, Meiqi Dong, Xian Wu, Shuang Liang, Ranhong Li, Hongyu Pan, Hao Zhang. Enrichment, domestication, degradation, adaptive mechanism, and nicosulfuron bioremediation of bacteria consortium YM2[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3529-3545.
[7] Yuxin He, Fei Deng, Chi Zhang, Qiuping Li, Xiaofan Huang, Chenyan He, Xiaofeng Ai, Yujie Yuan, Li Wang, Hong Cheng, Tao Wang, Youfeng Tao. Wei Zhou, Xiaolong Lei, Yong Chen, Wanjun Ren. Can a delayed sowing date improve the eating and cooking quality of mechanically transplanted rice in the Sichuan Basin, China?[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3368-3383.
[8] Dili Lai, Md. Nurul Huda, Yawen Xiao, Tanzim Jahan, Wei Li, Yuqi He, Kaixuan Zhang, Jianping Cheng, Jingjun Ruan, Meiliang Zhou. Evolutionary and expression analysis of sugar transporters from Tartary buckwheat revealed the potential function of FtERD23 in drought stress[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3334-3350.
[9] Zishuai Wang, Wangchang Li, Zhonglin Tang. Enhancing the genomic prediction accuracy of swine agricultural economic traits using an expanded one-hot encoding in CNN models[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3574-3582.
[10] Yunji Xu, Xuelian Weng, Shupeng Tang, Weiyang Zhang, Kuanyu Zhu, Guanglong Zhu, Hao Zhang, Zhiqin Wang, Jianchang Yang. Untargeted lipidomic analysis of milled rice under different alternate wetting and soil drying irrigation regimes[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3351-3367.
[11] Minghui Li, Yilan Chen, Siqiao Wang, Xueke Sun, Yongkun Du, Siyuan Liu, Ruiqi Li, Zejie Chang, Peiyang Ding, Gaiping Zhang. Plug-and-display nanoparticle immunization of the core epitope domain induces potent neutralizing antibody and cellular immune responses against PEDV[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3598-3613.
[12] Jing Zhou, Bingshuai Du, Yibo Cao, Kui Liu, Zhihua Ye, Yiming Huang, Lingyun Zhang. Genome-wide identification of sucrose transporter genes in Camellia oleifera and characterization of CoSUT4[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3494-3510.
[13] Yuheng Wang, Furong Kang, Bo Yu, Quan Long, Huaye Xiong, Jiawei Xie, Dong Li, Xiaojun Shi, Prakash Lakshmanan, Yueqiang Zhang, Fusuo Zhang. Magnesium supply is vital for improving fruit yield, fruit quality and magnesium balance in citrus orchards with increasingly acidic soil[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3641-3655.
[14] Mingxin Feng, Ying Hu, Xin Yang, Jingwen Li, Haochen Wang, Yujia Liu, Haijun Ma, Kai Li, Jiayin Shang, Yulin Fang, Jiangfei Meng. Uncovering the miRNA-mediated regulatory network involved in postharvest senescence of grape berries[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3465-3483.
[15] Li Liu, Yifeng Feng, Ziqi Han, Yaxiao Song, Jianhua Guo, Jing Yu, Zidun Wang, Hui Wang, Hua Gao, Yazhou Yang, Yuanji Wang, Zhengyang Zhao. Functional analysis of the xyloglucan endotransglycosylase/hydrolase gene MdXTH2 in apple fruit firmness formation[J]. >Journal of Integrative Agriculture, 2025, 24(9): 3418-3434.
No Suggested Reading articles found!