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

Abstract

Background: Microsatellite markers represent a low-cost and efficient tool for rapid genotyping as compared to single nucleotide polymorphism markers in laboratories with limited resources. For the economically important yam species widely cultivated in developing countries, very few microsatellite markers are available and no marker database has been developed to date. Herein, we conducted a genome-wide microsatellite marker development among four yam species, identified cross-species transferable markers, and designed an easy-to-use web portal for the yam breeder community. Results: The screening of yam genomes resulted in 318,713; 322,501; 307,040 and 253,856 microsatellites in Dioscorea alata, D. rotundata, D. dumetorum, and D. zingiberensis, 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, a subset of 17 markers were experimentally validated with good discriminatory power regarding the species and the ploidy levels. Ultimately, we created and deployed a dynamic Yam Microsatellite Markers Database (Y2MD) available at http://yamdb.42web.io/. Y2MD is embedded with various useful tools such as JBrowse, Blast, insilicoPCR, and SSR Finder to facilitate the exploitation of microsatellite markers in yams. Conclusions: The present work is the first comprehensive microsatellite marker mining across several yam species and will contribute to advance yam genetic research and marker-assisted breeding. The released user-friendly database constitutes a valuable platform for yam breeders, especially those in developing countries. Keywords: genotyping; Dioscoreacea; database; microsatellite; transferable markers