Genomic Selection for Prediction of Fruit-Related Traits in Pepper (Capsicum spp.)

Frontiers in Plant Science
Ju-Pyo HongByoung-Cheorl Kang

Abstract

Pepper (Capsicum spp.) fruit-related traits are critical determinants of quality. These traits are controlled by quantitatively inherited genes for which marker-assisted selection (MAS) has proven insufficiently effective. Here, we evaluated the potential of genomic selection, in which genotype and phenotype data for a training population are used to predict phenotypes of a test population with only genotype data, for predicting fruit-related traits in pepper. We measured five fruit traits (fruit length, fruit shape, fruit width, fruit weight, and pericarp thickness) in 351 accessions from the pepper core collection, including 229 Capsicum annuum, 48 Capsicum baccatum, 48 Capsicum chinense, 25 Capsicum frutescens, and 1 Capsicum chacoense in 4 years at two different locations and genotyped these accessions using genotyping-by-sequencing. Among the whole core collection, considering its genetic distance and sexual incompatibility, we only included 302 C. annum complex (229 C. annuum, 48 C. chinense, and 25 C. frutescens) into further analysis. We used phenotypic and genotypic data to investigate genomic prediction models, marker density, and effects of population structure. Among 10 genomic prediction methods tested, Reproducing...Continue Reading

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Methods Mentioned

BETA
genotyping
PCA

Software Mentioned

Plink
R package “ poppr ”
GATK Haplotype Caller
Genome Analysis Toolkit ( GATK
RKHS
R package “ poppr
Net
R package “ ggplot2
VCFtools
GATK VariantFIltration

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