|
|
|
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 |
|
|
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.
|
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) |
No Suggested Reading articles found! |
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
|
Shared |
|
|
|
|
|
Discussed |
|
|
|
|