Articles
Next generation sequencing technologies for the development of molecular markers and the analysis of genome diversity in Capsicum spp.
Article number
1242_123
Pages
831 – 838
Language
English
Abstract
The accessibility and use of natural genetic variability in crops is essential for the management of genetic resources and the establishment of innovative breeding programs.
Nuclear whole-genome sequences of several cultivated and wild peppers have been recently generated in order to provide crucial information on the evolution, domestication and divergence of pepper species (Capsicum spp.). Despite next generation sequencing (NGS) technologies providing a significant advance in generation of high throughput data, the analysis of a large-scale data and of individuals is still a challenging task.
An alternative strategy to Whole Genome Sequencing is to generate a reduced representation of the genome using target enrichment strategies.
Among them, genotyping-by-sequencing (GBS) provides a rapid, highly informative, cost-effective tool for exploring genetic diversity on a genome-wide scale.
We applied GBS for SNP marker discovery in nuclear genomes and population structure analysis in a collection of cultivated and domesticated peppers.
Information generated in this study represents a first step towards future genome-wide association mapping studies and marker-assisted selection programs.
In addition, results from this analysis can be used to gain a better understanding of the genetic relationships within the Capsicum genus.
In order to provide a further contribution to that issue, we also determined the complete chloroplast DNA (cpDNA) sequence of 11 Capsicum accessions for a total of 8 species generally included in the C. annuum (7), C. baccatum (3) or C. pubescens/eximium complex (1). We performed comparative analysis and identified potential molecular markers able to discriminate among Capsicum species.
Nuclear whole-genome sequences of several cultivated and wild peppers have been recently generated in order to provide crucial information on the evolution, domestication and divergence of pepper species (Capsicum spp.). Despite next generation sequencing (NGS) technologies providing a significant advance in generation of high throughput data, the analysis of a large-scale data and of individuals is still a challenging task.
An alternative strategy to Whole Genome Sequencing is to generate a reduced representation of the genome using target enrichment strategies.
Among them, genotyping-by-sequencing (GBS) provides a rapid, highly informative, cost-effective tool for exploring genetic diversity on a genome-wide scale.
We applied GBS for SNP marker discovery in nuclear genomes and population structure analysis in a collection of cultivated and domesticated peppers.
Information generated in this study represents a first step towards future genome-wide association mapping studies and marker-assisted selection programs.
In addition, results from this analysis can be used to gain a better understanding of the genetic relationships within the Capsicum genus.
In order to provide a further contribution to that issue, we also determined the complete chloroplast DNA (cpDNA) sequence of 11 Capsicum accessions for a total of 8 species generally included in the C. annuum (7), C. baccatum (3) or C. pubescens/eximium complex (1). We performed comparative analysis and identified potential molecular markers able to discriminate among Capsicum species.
Authors
T. Cardi, N. D¿Agostino, C. Cantarella, V. Colonna, B. Greco, R. Tamburino, F. Taranto, N. Scotti, P. Tripodi
Keywords
pepper, breeding, genetic variability, Genotyping-by-Sequencing, chloroplast DNA
Groups involved
- Commission Banana
- Division Temperate Tree Fruits
- Division Vine and Berry Fruits
- Division Tropical and Subtropical Fruit and Nuts
- Division Ornamental Plants
- Division Vegetables, Roots and Tubers
- Division Horticulture for Development
- Division Plant Genetic Resources, Breeding and Biotechnology
- Commission Cultivar Registration
- Division Plant-Environment Interactions in Field Systems
- Division Postharvest and Quality Assurance
- Division Greenhouse and Indoor Production Horticulture
- Division Landscape and Urban Horticulture
- Division Horticulture for Human Health
- Division Precision Horticulture and Engineering
- Division Temperate Tree Nuts
- Commission Agroecology and Organic Farming Systems
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