Please wait a minute...
Journal of Integrative Agriculture  2016, Vol. 15 Issue (9): 1991-2001    DOI: 10.1016/S2095-3119(16)61364-3
Crop Genetics · Breeding · Germplasm Resources Advanced Online Publication | Current Issue | Archive | Adv Search |
Genetic diversity of pepper (Capsicum spp.) germplasm resources in China reflects selection for cultivar types and spatial distribution
ZHANG Xiao-min1*, ZHANG Zheng-hai1*, GU Xiao-zhen1, MAO Sheng-li1, LI Xi-xiang1, 2*, Joël Chadœuf3, Alain Palloix3#, WANG Li-hao1, ZHANG Bao-xi1
1 Key Laboratory of Vegetable Genetics and Physiology, Ministry of Agriculture/Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
2 National Gene Bank of Vegetables, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
3 Génétique et Amélioration des Fruits et Légumes, BP94, UR1052, PACA, INRA, Montfavet F-84143, France
Download:  PDF in ScienceDirect  
Export:  BibTeX | EndNote (RIS)      
Abstract      Pepper (Capsicum spp.) is an important vegetable crop in the world. Now the pepper in China contributes one-third of the world’s peppers production. Genetic diversity of the pepper germplasm of China is expected interesting to know. To explore the structure of genetic diversity in Chinese pepper germplasm resources and possible relationship with cultivar types or geographic origin, we sampled and compared 372 GenBank pepper accessions (local cultivars and landraces) from 31 provinces, autonomous regions and municipalities of China and 31 additional accessions from other countries. These accessions were genotyped using 28 simple sequence repeat (SSR) markers spanning the entire pepper genome. We then investigated the genetic structure of the sampled collection using model-based analysis in STRUCTURE v2.3.4 and examined genetic relationships by the unweighted pair-group method of mathematical averages (UPGMA) in MEGA. In addition to geographic origin, we evaluated eight plant and fruit traits. In total, 363 alleles were amplified using the 28 SSR primers. Gene diversity, polymorphism information content and heterozygosity of the 28 SSR loci were estimated as 0.09–0.92, 0.08–0.92 and 0.01–0.34, respectively. The UPGMA cluster analysis clearly distinguished Capsicum annuum L. from other cultivated pepper species. Population structure analysis of the 368 C. annuum accessions uncovered three genetic groups which also corresponded to distinct cultivar types with respect to the plant and fruit descriptors. The genetic structure was also related to the geographic origin of the landraces. Overall results indicate that genetic diversity of Chinese pepper landraces were structured by migration of genotypes followed by human selection for cultivar types in agreement with consumption modes and adaptation to the highly diversified agro-climatic conditions.
Keywords:  Capsicum spp. germplasm collection       genetic diversity        population structure        microsatellite  
Received: 04 August 2015   Online: 11 March 2016   Accepted:
Fund: 

This work was supported by the National Key Technology Research and Development Program of China (2011BAZ01732), the Project of the Ministry of Agriculture of China (CARS-25), the Core Research Budget of the Non-profit Governmental Research Institute, China (ICS, CAAS; 1610032011011), and the Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences (CAAS-ASTIP-IVFCAAS).

Corresponding Authors:  WANG Li-hao, Tel: +86-10-82109551, Fax: +86-10-62174123, E-mail: wanglihao@caas.cn   
About author:  ZHANG Xiao-min, Tel: +86-10-82109551, E-mail: zhangxiaomin1987@yeah.net;

Cite this article: 

ZHANG Xiao-min, ZHANG Zheng-hai, GU Xiao-zhen, MAO Sheng-li, LI Xi-xiang, Jo?l Chadoeuf, Alain Palloix, WANG Li-hao, ZHANG Bao-xi. 2016. Genetic diversity of pepper (Capsicum spp.) germplasm resources in China reflects selection for cultivar types and spatial distribution. Journal of Integrative Agriculture, 15(9): 1991-2001.

Aguilar-Meléndez A, Morrell P L, Roose M L, Kim S C. 2009. Genetic diversity and structure in semiwild and domesticated chili peppers (Capsicum annuum; Solanaceae) from Mexico. American Journal of Botany, 96, 1190–1202.

Albrecht E, Zhang D, Saftner R A, Stommel J R. 2012. Genetic diversity and population structure of Capsicum baccatum genetic resources. Genetic Resources and Crop Evolution, 59, 517–538.

Andrews J. 1984. Pepper - The Domesticated Capsicum. University of Texas Press, Austin, Texas.

Baral J B, Bosland P. 2002. An updated synthesis of the Capsicum genus. Capsicum and Eggplant Newsletter, 21, 11–21.

Cavalli-Sforza L L, Edwards A W. 1967. Phylogenetic analysis. Models and estimation procedures. American Journal of Human Genetics, 19, 233.

Chen H Z. 1688. Hua Jing. China. (in Chinese)

Chen X J, Chen J F, Di H, Lou Q F. 2006. RAPD diversity analysis of 5 domesticated species. Acta Horticulturae Sinica, 33, 751–756.

Cressie N. 1993. Statistics for Spatial Data. John Wiley and Sons, Chichester.

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.

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.

Kao L. 1591. Tsung Sheng Pa Chien. People’s Medical Publishing House, Beijing. p. 852. (in Chinese)

González-Jara P, Moreno-Letelier A, Fraile A, Piñero D, García-Arenal F. 2012. Impact of human management on the genetic variation of wild pepper Capsicum annuum var. glabriusculum. PLoS ONE, 6, 28715.

Hernández-Verdugo S, Luna-Reyes R, Oyama K. 2001. Genetic structure and differentiation of wild and domesticated populations of Capsicum annuum (Solanaceae) from Mexico. Plant System Evolution, 226, 129–142.

Hill T A, Ashrafi H, Wo S R C, Yao J, Stoffel K, Truco M J, Kozik A, Michelmore R W, Deynze A V. 2013. Characterization of Capsicum annuum genetic diversity and population structure based on parallel polymorphism discovery with a 30k unigene pepper GeneChip. PLOS ONE, 8, e56200.

Ibiza V P, Blanca J, Cañizares J, Nuez F. 2012. Taxonomy and genetic diversity of domesticated Capsicum species in the Andean region. Genetic Resources and Crop Evolution, l59, 1077–1088.

Ince A G, Karaca M, Onus AN. 2010. Genetic relationships within and between Capsicum species. Biochemistry Genetics, 48, 83–95.

Jeong H J, Jo Y D, Park S W, Kang B C. 2010. Identification of Capsicum species using SNP markers based on high resolution melting analysis. Genome, 53, 1029–1040.

Li L, Mark A, Friedl M A, Xin Q, Gray J, Pan Y, Frolking S. 2014. Mapping crop cycles in China using MODIS-EVI time series. Remote Sensing, 6, 2473–2493.

Li Y. 1984. History of Crops in China. China Science and Technology Publisher, Beijing. (in Chinese)

Luo Y D, Li J G, Li M F. 2006. Analysis of genetic diversity of Capsicum germplasm resources by using SSR markers. Biotechnology Bulletin, S1, 337–341.

Manly F J B. 2003. Randomization, Bootstrap and Monte-Carlo Methods in Biology. Chapman and Hall/CRC, Melbourne. p. 1991.

Nicolai 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, 2375–2390.

Pacheco-Olvera A, Hernandez-Verdugo S, Rocha-Ramírez V, Gonzalez-Rodríguez A, Oyama K. 2012. Genetic diversity and structure of pepper (Capsicum annuum L.) from Northwestern Mexico analyzed by microsatellite markers. Crop Science, 52, 231–241.

PGRI (Plant Genetic Resources Institute), AVRDC (Asian Vegetable Research and Development Center), CATIE (Center Agricultural Tropical de Investigacion Ensenanza). 1995. Descriptors for Capsicum (Capsicum spp.). International Plant Genetic Resources Institute, Rome, Italy.

Pickersgill B. 1991. Cytogenetics and evolution of Capsicum L. In: Tsuchiya T, Gupta P K, eds., Chromosome Engineering in Plants: Genetics, Breeding, Evolution. Elsevier,

Amsterdam. pp. 139–160.

Pickersgill B, Heiser C B, McNeill J. 1979. Numerical taxo-nomic studies of variation and domestication in some species of Capsicum. In: Hawkes J G, ed., The Biology and Taxonomy of the Solanaceae. Academic Press, New York. pp. 679–690.

Pritchard J K, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics, 155, 945–959.

Purseglove J M. 1968. Tropical Crops. vol. 2. John Wiley and Sons, New York.

Rodriguez J M, Berke T, Engle L, Nienhuis J. 1999. Variation among and within Capsicum species revealed by RAPD markers. Theoretical and Applied Genetics, 99, 147–156.

Somos A. 1984. The Paprika. Akademiai Kiado, Budapest. p. 302.

Tamura K, Dudley J, Nei M, Kumar S. 2004. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology Evolution, 24, 1596–1599.

Toquica S P, Rodriguez F, Martinez E, Duque M C, Tohme J. 2003. Molecular characterization by AFLPs of Capsicum germplasm from the Amazon department in Colombia. Genetic Resources and Crop Evolution, 50, 639–647.

Votava E J, Nabhan G P, Bosland P W. 2002. Genetic diversity and similarity revealed via molecular analysis among and within an in situ population and ex situ accessions of chiltepin (Capsicum annuum var. glabriusculum). Conservation Genetics, 3, 123–129.

Wackernagel H. 2003. Multivariate Geostatistics. Springer, Berlin. p. 899.

Walsh B M, Hoot S B. 2001. The phylogenetic relationships of Capsicum (Solanaceae) using DNA sequences from two non-coding regions: The chloroplast atpB-rbcL spacer region and nuclear waxy introns. International Journal of Plant Sciences, 162, 1409–1418.

Yi G, Lee J M, Lee S, Choi D, Kim B D. 2006. Exploitation of pepper EST-SSRs and an SSR-based linkage map. Theoretical and Applied Genetics, 114, 113–130.

Zhang B X, Wang L H, Mao S L, Zhang Z H. 2010. Research progress on pepper breeding and genetic during China’s Eleventh Five-year Plan. China Vegetables, 24, 1–9. (in Chinese)

Zheng N. 2006. Thought and discussion on the introduction Capsicum. Agricultural Archaeology, 4, 177–184.

Zhou J, Shen H L, Yang W C, Tan F, Wang Y L, Guo S. 2009. Analysis of genetic diversity of Capsicum germplasm by using SSR markers. Acta Agriculturae Boreali-Sinica, 24, 62–67. (in Chinese)

Zou X X. 2009. Genetics and Breeding of Pepper. Scientific Publisher, Beijing. (in Chinese)
[1] WANG Meng-qi, ZHANG Hong-rui, XI Yu-qiang, WANG Gao-ping, ZHAO Man, ZHANG Li-juan, GUO Xian-ru. Population genetic variation and historical dynamics of the natural enemy insect Propylea japonica (Coleoptera: Coccinellidae) in China[J]. >Journal of Integrative Agriculture, 2023, 22(8): 2456-2469.
[2] WANG Jie, LEI Qiu-xia, CAO Ding-guo, ZHOU Yan, HAN Hai-xia, LIU Wei, LI Da-peng, LI Fu-wei, LIU Jie. Whole genome SNPs among 8 chicken breeds enable identification of genetic signatures that underlie breed features[J]. >Journal of Integrative Agriculture, 2023, 22(7): 2200-2212.
[3] ZHANG Ying, CAO Yu-fen, HUO Hong-liang, XU Jia-yu, TIAN Lu-ming, DONG Xing-guang, QI Dan, LIU Chao. An assessment of the genetic diversity of pear (Pyrus L.) germplasm resources based on the fruit phenotypic traits[J]. >Journal of Integrative Agriculture, 2022, 21(8): 2275-2290.
[4] GUO Yi, GONG Ying, HE Yong-meng, YANG Bai-gao, ZHANG Wei-yi, CHEN Bo-er, HUANG Yong-fu, ZHAO Yong-ju, ZHANG Dan-ping, MA Yue-hui, CHU Ming-xing, E Guang-xin. Investigation of Mitochondrial DNA genetic diversity and phylogeny of goats worldwide[J]. >Journal of Integrative Agriculture, 2022, 21(6): 1830-1837.
[5] XU Xin, YE Jun-hua, YANG Ying-ying, LI Ruo-si, LI Zhen, WANG Shan, SUN Yan-fei, ZHANG Meng-chen, XU Qun, FENG Yue, WEI Xing-hua, YANG Yao-long. Genetic diversity analysis and GWAS reveal the adaptive loci of milling and appearance quality of japonica (oryza sativa L.) in Northeast China[J]. >Journal of Integrative Agriculture, 2022, 21(6): 1539-1550.
[6] WANG Fu-qiang, FAN Xiu-cai, ZHANG Ying, SUN Lei, LIU Chong-huai, JIANG Jian-fu. Establishment and application of an SNP molecular identification system for grape cultivars[J]. >Journal of Integrative Agriculture, 2022, 21(4): 1044-1057.
[7] LIU Lei, WANG Heng-bo, LI Yi-han, CHEN Shu-qi, WU Ming-xing, DOU Mei-jie, QI Yi-yin, FANG Jing-ping, ZHANG Ji-sen. Genome-wide development of interspecific microsatellite markers for Saccharum officinarum and Saccharum spontaneum[J]. >Journal of Integrative Agriculture, 2022, 21(11): 3230-3244.
[8] LIU Na, CHENG Fang-yun, GUO Xin, ZHONG Yuan. Development and application of microsatellite markers within transcription factors in flare tree peony (Paeonia rockii) based on next-generation and single-molecule long-read RNA-seq[J]. >Journal of Integrative Agriculture, 2021, 20(7): 1832-1848.
[9] DIAO Shu-qi, XU Zhi-ting, YE Shao-pan, HUANG Shu-wen, TENG Jin-yan, YUAN Xiao-long, CHEN Zan-mou, ZHANG Hao, LI Jia-qi, ZHANG Zhe. Exploring the genetic features and signatures of selection in South China indigenous pigs[J]. >Journal of Integrative Agriculture, 2021, 20(5): 1359-1371.
[10] GAO Yuan, WANG Da-jiang, WANG Kun, CONG Pei-hua, LI Lian-wen, PIAO Ji-cheng. Analysis of genetic diversity and structure across a wide range of germplasm reveals genetic relationships among seventeen species of Malus Mill. native to China [J]. >Journal of Integrative Agriculture, 2021, 20(12): 3186-3198.
[11] YANG Fang-yuan, GUO Jian-jun, LIU Ning, ZHANG Run-zhi.
Genetic structure of the invasive Colorado potato beetle Leptinotarsa decemlineata populations in China
[J]. >Journal of Integrative Agriculture, 2020, 19(2): 350-359.
[12] May Oo kHINE, brozenká MICHAELA, LIU Yan, Jiban kumar kUNDU, WANG Xi-feng. Molecular diversity of barley yellow dwarf virus-PAV from China and the Czech Republic[J]. >Journal of Integrative Agriculture, 2020, 19(11): 2736-2745.
[13] 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. Genetic diversity and population structure analysis of Capsicum germplasm accessions[J]. >Journal of Integrative Agriculture, 2019, 18(6): 1312-1320.
[14] WU Huai-heng, WAN Peng, HUANG Min-song, LEI Chao-liang. Microsatellites reveal strong genetic structure in the common cutworm, Spodoptera litura[J]. >Journal of Integrative Agriculture, 2019, 18(3): 636-643.
[15] WANG Chen, CHEN Yao-sheng, HAN Jian-lin, MO De-lin, LI Xiu-jin, LIU Xiao-hong. Mitochondrial DNA diversity and origin of indigenous pigs in South China and their contribution to western modern pig breeds[J]. >Journal of Integrative Agriculture, 2019, 18(10): 2338-2350.
No Suggested Reading articles found!