Genetic diversity and population structure analysis to construct a core collection from a large Capsicum germplasm

Area of Science:

• Plant genetics
• Crop improvement
• Molecular diversity analysis

Background:

• Conserving genetic diversity is crucial for developing new crop varieties.
• Large germplasm collections often lack detailed information on population structure and diversity.
• A well-defined core collection simplifies access to genetic resources and utilization of hidden diversity in Capsicum.

Purpose of the Study:

• To explore genetic diversity and population structure within a large Capsicum germplasm collection.
• To develop an optimal strategy for constructing a core collection.
• To establish a representative core collection for Capsicum breeding and research.

Main Methods:

• Genotyping of 3,821 Capsicum accessions using 48 transcriptome-based single nucleotide polymorphisms (SNPs).
• Population structure and phylogenetic analyses to understand genetic relationships and origins.
• Evaluation of five sampling strategies for core collection construction.
• Selection of a core collection (CC240) based on allelic variation and 32 phenotypic traits.

Main Results:

• Capsicum annuum exhibited the highest genetic diversity, while C. galapagoense showed the lowest.
• Population structure analysis identified 10 clusters, and phylogenetic analysis revealed five distinct groups.
• The developed core collection (CC240) comprises 240 accessions (5.2%) and shows high genetic diversity (I=0.95) and evenness (J'=0.80).
• CC240 represents a broad range of phenotypic variation (MD=9.45%, CR=98.40%).

Conclusions:

• A representative core collection (CC240) of 240 Capsicum accessions was successfully established.
• This core collection was selected using genome-wide distributed SNP markers and phenotypic data.
• CC240 serves as a valuable resource for future genetic association and functional studies in pepper breeding.