Dioscorea alata orthologous groups identified by comparative genomics approach

Yams are important tubers widely consumed in developing countries in various forms, mainly boiled, pounded and fried. Tuber quality is a key criterion for acceptance by the various actors in the value chain. However, the genetics of yam tuber quality has not yet been comprehensively investigated. Given this lack of knowledge, we used population genomics and candidate gene association approaches to unravel the genetic basis of the three main quality attributes of boiled yam, namely texture, starch content and colour indices. We re-sequenced the whole genome of 127 yam genotypes with different quality attributes, and performed an enrichment of the already available functional genome annotation using comparative genomics. Population genomics analysis highlighted three main genetic groups and 1,053 genes under selection. We focused this work on three known quality trait-related pathways: pectin, starch content and flavonoid biosynthesis, and inventoried in the genome all the structural genes related to those pathways by comparative genomics. We improved the functional annotation of the three pathways with 48% more genes. A total of 18 candidate genes containing genetic variants significantly associated with the target traits were detected, including eight genes that were also found under selection. The texture-related candidate genes were distributed between the pectin and starch pathways. Overall, the use of comparative genomics has allowed the generation of an unprecedented genomic resource. The improved functional annotation of the yam genome is a promising predictive tool for identifying other core genes associated with any trait of interest to meet the growing need and diversified demands for yams. To complement the set of Dioscorea alata annotated genes, a comparative genomics approach was employed using a comparison of 45 genomes of species from diverse plant lineages. The species were chosen based on their genomes, phylogenetic distribution along the tree of viridiplantae and in the use of plant-models. They belong to the monocotyledons and dicotyledons, encompassing 17 different clades. The orthology analysis resulted in a total of 58,916 ortholous groups (OG) from 1,706,645 proteins. The OG were first used in this study to complement the set of genes in pathways involved in yam tuber quality.

Bibliographic Details

Main Authors:	Zotta Mota Ana, Dossa Komivi, Lechaudel Mathieu, Cornet Denis, Mournet Pierre, Lopez David, Chaïr Hana
Other Authors:	Cornet, Denis
Format:	Omic data biblioteca
Language:	English
Published:	CIRAD Dataverse
Subjects:	Agricultural Sciences, Computer and Information Science, Comparative genomics, Dioscorea,
Online Access:	https://doi.org/10.18167/DVN1/A4OYRU
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