Genotyping a Large Collection of Pepper (Capsicum Spp.) with SSR Loci Brings New Evidence for the Wild Origin of Cultivated C
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Genet Resour Crop Evol (2013) 60:2375–2390 DOI 10.1007/s10722-013-0006-0 RESEARCH ARTICLE 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 Maryse Nicolaı¨ • Me´lissa Cantet • Ve´ronique Lefebvre • Anne-Marie Sage-Palloix • Alain Palloix Received: 20 February 2013 / Accepted: 22 May 2013 / Published online: 8 August 2013 Ó Springer Science+Business Media Dordrecht 2013 Abstract Germplasm collections of cultivated distinct for plant and fruit descriptors corresponding to plants constitute the source for further genetic pro- cultivar types, showing that the genetic structure of gress. These collections gained further interest with this cultivated species was strongly impacted by the approaches for tracking allelic variants associated to long term human selection of landraces in primary as phenotypic variations within core collections. In order well as secondary diversification centres. We settled to explore the structure of genetic variation in pepper nested core-collections of 8, 16, 32, 64 and 128 C. (Capsicum spp.) and to select core-collections maxi- annuum accessions capturing from 37 to 90 % of the mizing the genetic and the phenotypic diversity, a genetic diversity for further sequencing efforts and pepper collection including 1,352 non redundant establishment of high throughput genotyping assays. accessions from 11 Capsicum species from 89 differ- By compiling phenotypic and genotypic data, a larger ent countries was genotyped using 28 microsatellite core-collection of 332 accessions was established, (SSR) markers spanning the whole genome. Model- capturing 97 % of the C. annuum genetic and pheno- based analysis structured the collection into 6 clusters, typic diversity for further genetic association studies. with 3 clusters separating the main species complexes, including cultivated species and wild relatives, Keywords Capsicum Á Core collection Á according to taxonomic classification (C. frutescens/ Cultivar types Á Germplasm collection Á C. chinense, C. baccatum, C. pubescens), and 3 Human selection Á Microsatellite additional clusters for C. annuum. The relationships between the cultivated C. annuum species and the wild relative (C. annnuum var. glabriusculum) was pre- Introduction cised. The 3 C. annuum clusters were significantly In plant breeding, genetic diversity is the essential source of genetic progress. This motivated the collec- Electronic supplementary material The online version of tion, maintenance and characterization of genetic this article (doi:10.1007/s10722-013-0006-0) contains supple- resources for most cultivated plant species by private, mentary material, which is available to authorized users. national and international initiatives since the early M. Nicolaı¨ Á M. Cantet Á V. Lefebvre Á 20th century. These plant Germplasm libraries of A.-M. Sage-Palloix Á A. Palloix (&) various sizes include wild accessions, landraces, Unite´ de Ge´ne´tique et Ame´lioration des Fruits et modern cultivars and related species of the crop of Le´gumes, INRA PACA, UR1052, CS 60094, 84140 Montfavet Cedex, France interest. Efforts in securing plant genetic resources for e-mail: [email protected] food and agriculture recently progressed worldwide, 123 2376 Genet Resour Crop Evol (2013) 60:2375–2390 since it is regarded as an essential resource to help the advantage of tracking genetic polymorphisms that farmers to respond to climate change (FAO 2010). control phenotype variations among large panels of Safeguarding wild accessions is an increasing priority accessions, giving access to multiple alleles and thus to prevent the loss of wild genotypes resulting from the increasing the efficiency of genetic resources exploi- reduction of natural wild habitats worldwide. Conser- tation. In these approaches, the main constraint relies vation of landraces and local cultivars is as well on the genetic structure of the population and the size crucial, since modern and highly performing cultivars of the accession panel under investigation. Testing for progressively replace the diversified and heteroge- statistical associations between the genotypes at the neous landraces worldwide, threatening the agricul- marker loci and the phenotypes in a sample of tural landscape with genetic erosion (Hammer et al. accessions is directly affected by the presence of 2003). For most cultivated species, the loss of genetic groups of related accessions with different allele variability started as soon as the domestication frequencies and may lead to false associations (Freed- process, and may have been worsened with migration man et al. 2004). Then, the core-collection will be events from original to secondary diversification sites optimized if it maximizes the genetic diversity found depending on the history of plant species exploitation in the whole collection and spans the full range of (Tang et al. 2010). Contrarily, thousands of years of phenotypic variation (Ranc et al. 2010, 2008). Thus, human selection in multiple environments and cultural preliminary analyses of the structure of the genetic contexts, provided new mutants and allele combina- diversity within the whole collection of accessions tions of agricultural interest but which had poor have to be performed together with an evaluation of probabilities to be retained under natural selection the range of phenotypic variation. This prerequisite pressure. The thousands of landraces and local culti- will further allow the selection of core-collections for vars originating from farmer selection in each crop SNP mining and for association or LD mapping. represent a wide source of diversity, particularly for Pepper (Capsicum spp.) is a complex of species alleles of agricultural interest and local adaptations originating from the intertropical America. The Cap- (i.e. quality traits, tolerance or resistance to biotic and sicum genus belongs to the Solanaceae family and abiotic stresses). Their contribution to further genetic includes 27 recognized species (Baral and Bosland progress and to the restoration of biodiversity in agro 2002). The taxonomic structure of the genus was systems is at least as promising as wild accessions, established from a multidisciplinary approach using related species or exogenous gene sources. numerical taxonomy, cross fertility and cytogenetics, Beyond the collection of these resources, their biochemical, geographical and ethnobotanical data exploitation depends on our ability to characterize (Pickersgill et al. 1979; Pickersgill 1991) providing them. The exhaustive phenotyping and genotyping of evidence for 5 distinct cultivated species: C. annuum large collections has rarely been performed. Within L., C. frutescens L., C. chinense Jacq., C. baccatum the plant breeding process, large screening tests focus L. and C. pubescens Ruiz et Pav., which originated on a particular trait in order to trap the alleles of from distinct domestication events and primary diver- interest. Then, segregating progenies are generated for sification centers, where related wild species still genetic analysis of the trait and the new alleles are coexist. Based on cross fertility and cytogenetics, the further introgressed into elite genitors in a cumulative cultivated and the wild species were grouped into genetic progress. More recently, approaches were 3 genetic pools. C. annuum, C. frutescens and developed to track the allelic variants associated to C. chinense form the first genetic pool (also named phenotypic variations directly within core collections the white flowered species) which was related to the of plant genotypes, i.e. subsamples of genotypes wild progenitor C. annuum var. glabriusculum (Dunal) which represent the genetic diversity of the crop with Heiser et Pickersgill, C. baccatum and the wild relative a minimal redundancy (Marita et al. 2000; Gupta et al. C. baccatum var. baccatum Esbaugh (C. microcarpum 2005; Zhu et al. 2008). Such core collections of Chodat et Hassl.) form the second genetic pool and reduced size are extremely useful for sequence C. pubescens together with the wild species C. eximium polymorphism mining and for associating these poly- Hunz. and C. cardenasii Heiser et Smith form the 3rd morphisms with phenotypic traits. Association map- genetic pool, those 2 pools being sexually isolated from ping or linkage disequilibrium (LD) mapping provide each other and from the first one. Since the 1990s, 123 Genet Resour Crop Evol (2013) 60:2375–2390 2377 genetic analyses using isozymes, nuclear and chloro- species whatever the markers used and generally higher plastic DNA markers confirmed this structure and than the polymorphism observed in other autogamous increased our knowledge of the relationships between solanaceae like tomato (Solanum lycopersicum L.), wild and domesticated species (Loaiza Figueroa et al. allowing intraspecific genetic mapping and cultivar 1989; Rodriguez et al. 1999; Walsh and Hoot 2001; identification. Structure of the genetic diversity within Toquica et al. 2003;Inceetal.2010; Jeong et al. 2010; species was rarely analysed, except by Moses and Ibiza et al. 2012). Genetic diversity was also explored in Umaharan (2012) who showed relationships between restricted geographic areas (mainly Mexico and Andean the phylogenetic clusters and geographic distribution of area) where cultivated species and wild relatives C. chinense, and Lefebvre et al. (2001) and Tam et al. coexist,