Linkage disequilibrium and population-structure analysis among Capsicum annuum L. cultivars for use in association mapping

Nimmakayala, Padma; Abburi, Venkata Lakshmi; Abburi, Lavanya; Alaparthi, Suresh Babu; Cantrell, Robert Stephen; Park, Minkyu; Choi, Doil; Hankins, Gerald R.; Malkaram, Sridhar A.; Reddy, Umesh K.

doi:10.1007/s00438-014-0827-3

Cited by 24 publications

(25 citation statements)

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“…A previous study on a collection of 96 Capsicum individuals genotyped by 176 SSRs reports a mean LD of 32.17 Mb [61]. Several factors are thought to influence LD in plants, such as genetic drift, mating system, high levels of selfing and the history of selection [62].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide SNP discovery and population structure analysis in pepper (Capsicum annuum) using genotyping by sequencing

et al. 2016

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BackgroundKnowledge on population structure and genetic diversity in vegetable crops is essential for association mapping studies and genomic selection. Genotyping by sequencing (GBS) represents an innovative method for large scale SNP detection and genotyping of genetic resources. Herein we used the GBS approach for the genome-wide identification of SNPs in a collection of Capsicum spp. accessions and for the assessment of the level of genetic diversity in a subset of 222 cultivated pepper (Capsicum annum) genotypes.ResultsGBS analysis generated a total of 7,568,894 master tags, of which 43.4% uniquely aligned to the reference genome CM334. A total of 108,591 SNP markers were identified, of which 105,184 were in C. annuum accessions. In order to explore the genetic diversity of C. annuum and to select a minimal core set representing most of the total genetic variation with minimum redundancy, a subset of 222 C. annuum accessions were analysed using 32,950 high quality SNPs. Based on Bayesian and Hierarchical clustering it was possible to divide the collection into three clusters. Cluster I had the majority of varieties and landraces mainly from Southern and Northern Italy, and from Eastern Europe, whereas clusters II and III comprised accessions of different geographical origins. Considering the genome-wide genetic variation among the accessions included in cluster I, a second round of Bayesian (K = 3) and Hierarchical (K = 2) clustering was performed. These analysis showed that genotypes were grouped not only based on geographical origin, but also on fruit-related features.ConclusionsGBS data has proven useful to assess the genetic diversity in a collection of C. annuum accessions. The high number of SNP markers, uniformly distributed on the 12 chromosomes, allowed the accessions to be distinguished according to geographical origin and fruit-related features. SNP markers and information on population structure developed in this study will undoubtedly support genome-wide association mapping studies and marker-assisted selection programs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3297-7) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Genome-wide SNP discovery and population structure analysis in pepper (Capsicum annuum) using genotyping by sequencing

et al. 2016

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“…FW (g), was collected for five plants. Quantitative analysis of capsaicin and dihydrocapsaicin content was performed using greenhouse-grown plants in three replications using the 1200 series HPLC system (Agilent Technologies, Santa Clara, CA) with a degasser, an autosampler, and a binary pump as described7.…”

Section: Methodsmentioning

confidence: 99%

“…Trade routes between Europe, Middle-East and Asia promoted additional introductions and reciprocal exchanges, so multiple introductions were rapidly cultivated in most tropical, Mediterranean and temperate regions of the world. In these secondary diversification centers, thousands of landraces have been selected for 4 to 5 centuries by growers to fit new environments and local consumption habits and trade, which has resulted in wide phenotypic diversity of pepper cultivars567.…”

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confidence: 99%

“…. An examination of population structure, diversity at the molecular level, linkage disequilibrium (LD) distribution across various chromosomes and quantitative trait loci (QTL) estimated by model-based association mapping would provide insights into the evolution of various traits among C. annuum cultivars7. LD distribution information across the C. annuum genome will help group SNPs into haplotypes and, their use in genome analysis can lead to understanding the consequences of selection and breeding histories across the collections of C. annuum L.…”

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Genome-wide Diversity and Association Mapping for Capsaicinoids and Fruit Weight in Capsicum annuum L

Nimmakayala

Abburi

Saminathan

et al. 2016

Sci Rep

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Accumulated capsaicinoid content and increased fruit size are traits resulting from Capsicum annuum domestication. In this study, we used a diverse collection of C. annuum to generate 66,960 SNPs using genotyping by sequencing. The study identified 1189 haplotypes containing 3413 SNPs. Length of individual linkage disequilibrium (LD) blocks varied along chromosomes, with regions of high and low LD interspersed with an average LD of 139 kb. Principal component analysis (PCA), Bayesian model based population structure analysis and an Euclidean tree built based on identity by state (IBS) indices revealed that the clustering pattern of diverse accessions are in agreement with capsaicin content (CA) and fruit weight (FW) classifications indicating the importance of these traits in shaping modern pepper genome. PCA and IBS were used in a mixed linear model of capsaicin and dihydrocapsaicin content and fruit weight to reduce spurious associations because of confounding effects of subpopulations in genome-wide association study (GWAS). Our GWAS results showed SNPs in Ankyrin-like protein, IKI3 family protein, ABC transporter G family and pentatricopeptide repeat protein are the major markers for capsaicinoids and of 16 SNPs strongly associated with FW in both years of the study, 7 are located in known fruit weight controlling genes.

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“…These maps formed the basis for the linkage mapping of numerous qualitative and quantitative horticultural traits such as fruit characters (size, shape, weight, color, carotenoid, anthocyan and capsaicinoid content, pendant/erect fruit habit), disease resistance (resistance to viruses, bacteria, nematodes and the oomycete Phytophthora capsici ), and male sterility, comprehensively reviewed by (Ramchiary et al 2014). First results of association mapping of fruit weight and capsaicinoid content have also been obtained (Nimmakayala et al 2014). Map-based cloning of the Bs3 gene for resistance to Xanthomonas campestris pv.…”

Section: Peppermentioning

confidence: 98%

The historical role of species from the Solanaceae plant family in genetic research

Gebhardt

2016

Theor Appl Genet

102

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Key message This article evaluates the main contributions of tomato, tobacco, petunia, potato, pepper and eggplant to classical and molecular plant genetics and genomics since the beginning of the twentieth century. AbstractSpecies from the Solanaceae family form integral parts of human civilizations as food sources and drugs since thousands of years, and, more recently, as ornamentals. Some Solanaceous species were subjects of classical and molecular genetic research over the last 100 years. The tomato was one of the principal models in twentieth century classical genetics and a pacemaker of genome analysis in plants including molecular linkage maps, positional cloning of disease resistance genes and quantitative trait loci (QTL). Besides that, tomato is the model for the genetics of fruit development and composition. Tobacco was the major model used to establish the principals and methods of plant somatic cell genetics including in vitro propagation of cells and tissues, totipotency of somatic cells, doubled haploid production and genetic transformation. Petunia was a model for elucidating the biochemical and genetic basis of flower color and development. The cultivated potato is the economically most important Solanaceous plant and ranks third after wheat and rice as one of the world’s great food crops. Potato is the model for studying the genetic basis of tuber development. Molecular genetics and genomics of potato, in particular association genetics, made valuable contributions to the genetic dissection of complex agronomic traits and the development of diagnostic markers for breeding applications. Pepper and eggplant are horticultural crops of worldwide relevance. Genetic and genomic research in pepper and eggplant mostly followed the tomato model. Comparative genome analysis of tomato, potato, pepper and eggplant contributed to the understanding of plant genome evolution.

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Linkage disequilibrium and population-structure analysis among Capsicum annuum L. cultivars for use in association mapping

Cited by 24 publications

References 48 publications

Genome-wide SNP discovery and population structure analysis in pepper (Capsicum annuum) using genotyping by sequencing

Genome-wide SNP discovery and population structure analysis in pepper (Capsicum annuum) using genotyping by sequencing

Genome-wide Diversity and Association Mapping for Capsaicinoids and Fruit Weight in Capsicum annuum L

The historical role of species from the Solanaceae plant family in genetic research

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