Genome-wide development of intra- and inter-specific transferable SSR markers and construction of a dynamic web resource for yam molecular breeding: Y2MD

Diouf Moussa, Bovys Zoclanclounon Yedomon Ange, Mboup Pape Adama Mboup, Diouf Diaga, Maledon Erick, Rivallan Ronan, Chair Hanâ, Dossa Komivi. 2023. Genome-wide development of intra- and inter-specific transferable SSR markers and construction of a dynamic web resource for yam molecular breeding: Y2MD. Plant Genome:e20428, 18 p.

Url - jeu de données - Entrepôt autre : https://y2md.ucad.sn/

Résumé : Microsatellite markers are widely used in population genetics and breeding. Despite the economic significance of yams in developing countries, there is a paucity of microsatellite markers, and as of now, no comprehensive microsatellite marker database exists. In this study, we conducted genome-wide microsatellite marker development across four yam species, identified cross-species transferable markers, and designed an easy-to-use web portal for the yam researchers. The screening of Dioscorea alata, Dioscorea rotundata, Dioscorea dumetorum, and Dioscorea zingiberensis genomes resulted in 318,713, 322,501, 307,040, and 253,856 microsatellites, respectively. Mono-, di-, and tri-nucleotides were the most important types of repeats in the different species, and a total of 864,128 primer pairs were designed. Furthermore, we identified 1170 cross-species transferable microsatellite markers. Among them, 17 out of 18 randomly selected were experimentally validated with good discriminatory power, regardless of the species and ploidy levels. Ultimately, we created and deployed a dynamic Yam Microsatellite Markers Database (Y2MD) available at https://y2md.ucad.sn/. Y2MD is embedded with various useful tools such as JBrowse, Blast, insilicoPCR, and SSR Finder to facilitate the exploitation of microsatellite markers in yams. This study represents the first comprehensive microsatellite marker mining across several yam species and will contribute to advancing yam genetic research and marker-assisted breeding. The released user-friendly database constitutes a valuable platform for yam researchers.

Mots-clés Agrovoc : marqueur génétique, Dioscorea rotundata, Dioscorea alata, microsatellite, phylogénie, locus des caractères quantitatifs, polymorphisme génétique, Dioscorea, génome, séquence nucléotidique, Dioscorea dumetorum, variation génétique, Dioscorea cayenensis, identification

Mots-clés géographiques Agrovoc : France

Classification Agris : F30 - Génétique et amélioration des plantes

Champ stratégique Cirad : CTS 2 (2019-) - Transitions agroécologiques

Agences de financement hors UE : Bill and Melinda Gates Foundation

Projets sur financement : (FRA) Enhancing Yam Breeding for Increased Productivity and Improved Quality in West Africa

Auteurs et affiliations

• Diouf Moussa, UCAD (SEN)
• Bovys Zoclanclounon Yedomon Ange, Jeonbuk National University (KOR)
• Mboup Pape Adama Mboup, UCAD (SEN)
• Diouf Diaga, UCAD (SEN)
• Maledon Erick, CIRAD-BIOS-UMR AGAP (GLP)
• Rivallan Ronan, CIRAD-BIOS-UMR AGAP (FRA)
• Chair Hanâ, CIRAD-BIOS-UMR AGAP (FRA)
• Dossa Komivi, CIRAD-BIOS-UMR AGAP (GLP) ORCID: 0000-0003-4894-6279 - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/608261/)

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