Genomic Diversity and Novel Genome-wide Association with Fruit Morphology in Capsicum, from 746k Polymorphic Sites

Overview

Journal Sci Rep

Specialty Science

Date 2019 Jul 13

PMID 31296904

Citations 23

Authors

Vincenza Colonna

Nunzio DAgostino

Erik Garrison

Anders Albrechtsen

Jonas Meisner

Angelo Facchiano

Teodoro Cardi

Pasquale Tripodi

Affiliations

Soon will be listed here.

Abstract

Capsicum is one of the major vegetable crops grown worldwide. Current subdivision in clades and species is based on morphological traits and coarse sets of genetic markers. Broad variability of fruits has been driven by breeding programs and has been mainly studied by linkage analysis. We discovered 746k variable sites by sequencing 1.8% of the genome in a collection of 373 accessions belonging to 11 Capsicum species from 51 countries. We describe genomic variation at population-level, confirm major subdivision in clades and species, and show that the known major subdivision of C. annuum separates large and bulky fruits from small ones. In C. annuum, we identify four novel loci associated with phenotypes determining the fruit shape, including a non-synonymous mutation in the gene Longifolia 1-like (CA03g16080). Our collection covers all the economically important species of Capsicum widely used in breeding programs and represent the widest and largest study so far in terms of the number of species and number of genetic variants analyzed. We identified a large set of markers that can be used for population genetic studies and genetic association analyses. Our results provide a comprehensive and precise perspective on genomic variability in Capsicum at population-level and suggest that future fine genetic association studies will yield useful results for breeding.

Citing Articles

Genome-Wide Identification and Characterization of SNPs and InDels of var. from Mexico Based on Whole Genome Sequencing.

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Genomic structure and marker-trait association for plant and fruit traits in Capsicum chinense and Capsicum baccatum germplasm.

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Genome-wide association study and candidate gene identification for agronomic traits in 182 upward-growing fruits of C. frutescens and C. annuum.

Fu G, Yu S, Wu K, Yang M, Altaf M, Wu Z Sci Rep. 2024; 14(1):14691.

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Identification of CaPCR1, an OFP gene likely involved in pointed versus concave fruit tip regulation in pepper (Capsicum annuum L.) using recombinant inbred lines.

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