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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Genome-wide SNP discovery and population structure analysis in pepper (Capsicum annuum) using genotyping by

F Taranto1, N D'Agostino1, B Greco1

  • 1Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria-Centro di ricerca per l'orticoltura (CREA-ORT), Via dei Cavalleggeri 25, 84098, Pontecagnano Faiano, SA, Italy.

BMC Genomics
|November 23, 2016
PubMed
Summary

Genotyping by sequencing (GBS) revealed genetic diversity in pepper (Capsicum annuum) accessions, grouping them by origin and fruit traits. This SNP marker data aids future breeding and selection programs.

Keywords:
Genotyping by sequencingPepperPopulation structureSingle nucleotide polymorphism

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Area of Science:

  • Plant genetics
  • Agricultural science
  • Genomics

Background:

  • Understanding population structure and genetic diversity in vegetable crops like pepper (Capsicum annuum) is crucial for advanced breeding techniques.
  • Genotyping by sequencing (GBS) offers an innovative approach for large-scale single nucleotide polymorphism (SNP) detection and genotyping of genetic resources.

Purpose of the Study:

  • To employ GBS for genome-wide SNP identification in Capsicum spp.
  • To assess genetic diversity within a subset of 222 cultivated pepper (Capsicum annuum) genotypes.
  • To identify a core set of genotypes representing maximum genetic variation with minimal redundancy.

Main Methods:

  • Genotyping by sequencing (GBS) was performed on Capsicum spp. accessions.
  • A subset of 222 C. annuum genotypes was analyzed using 32,950 high-quality SNPs.
  • Bayesian and Hierarchical clustering methods were applied to analyze population structure and genetic diversity.

Main Results:

  • GBS analysis identified over 108,000 SNP markers, with more than 105,000 in C. annuum.
  • Clustering analysis divided the 222 C. annuum accessions into three distinct groups based on geographical origin and fruit-related features.
  • Genotypes were successfully distinguished based on both geographical origin and fruit characteristics.

Conclusions:

  • GBS is effective for assessing genetic diversity in C. annuum collections.
  • The identified SNP markers and population structure information are valuable for genome-wide association mapping and marker-assisted selection.
  • This study provides essential genetic insights to support pepper breeding programs.