Uncovering the genetic diversity of yams (<i>Dioscorea</i> spp.) in China by combining phenotypic trait and molecular marker analyses

Cao, Tianxu; Sun, Jingyu; Shan, Nan; Wang, Putao; Zhu, Qianglong; Xiao, Yao; Zhang, Hongyu; Zhou, Qinghong; Huang, Yongji

doi:10.1002/ece3.7727

Cited by 16 publications

(16 citation statements)

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“…Microsatellite markers proved to be effective to characterise yam germplasms worldwide (Obidiegwu et al, 2009a; Obidiegwu et al, 2009b; Siqueira et al, 2011; Tostain et al, 2006; Tamiru et al, 2015; Arnau et al, 2017; Cao et al, 2021). The present study enabled the extraction of quite high numbers of microsatellites in different yam genomes.…”

Section: Discussionmentioning

confidence: 99%

“…In Dioscoreaceae , very few SSR markers have been experimentally (wet-lab) validated (Obidiegwu et al, 2009a; Obidiegwu et al, 2009b; Andris et al, 2010; Siqueira et al, 2011; Tostain et al, 2006; Tamiru et al, 2015; Arnau et al, 2017; Cao et al, 2021), most of which are from D. alata and D. rotundata . In other species such as rice (McCouch et al, 2002), sesame (Dossa et al, 2017), and cowpea ( Vigna unguiculata ) (Jasrotia et al, 2019), a large number of markers have been identified, experimentally characterised and available for genetic studies and breeding.…”

Section: Discussionmentioning

confidence: 99%

Section: Validating Selected Ssrsmentioning

confidence: 99%

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

Diouf

Zoclanclounon

Mboup

et al. 2023

Preprint

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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

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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

Diouf

Zoclanclounon

Mboup

et al. 2023

Preprint

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“…The markers commonly used in morphological characterization of different species of the genus Dioscorea are shape, color, length, and width of the leaf; the presence of wings; the color of the peel and of the pulp; and tuber weight (Wu et al 2019;Cao et al 2021;Chen et al 2022).…”

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confidence: 99%

“…In spite of the importance of phenotypic traits for germplasm characterization, they have the limitation of being subject to environmental variations (Cao et al 2021). An alternative to mitigate this problem is associating morphological and molecular markers (Agre et al 2021).…”

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confidence: 99%

Genetic diversity of yam (Dioscorea sp.) through morphological and molecular markers

Santos,

Gois,

Prata

et al. 2024

Preprint

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The aim of the present study was to evaluate the genetic diversity of genotypes of Dioscorea sp. originating from states of the Brazilian Northeast region (Sergipe, Bahia, Alagoas, and Paraíba) through morphological and molecular characterization. For this evaluation, 52 yam genotypes were collected from market locations and directly from rural growers. Morphological characterization made use of 31 morphological descriptors for the yam crop. The environmental coefficient of variation (CVe) of most of the descriptors evaluated was greater than the genotypic coefficient of variation (CVg), and heritability was high only for stem color (86.86%). The highest significant positive correlation was between the presence of the tuber and the presence of roots on the surface of the tuber (r = 1; p < 0.001). The genotypes were clustered in seven different groups based on the morphological descriptors evaluated. For molecular characterization, SSR (9) and ISSR (16) primers were used. The primers used were considered informative, showing high polymorphic information content; and 100% of the bands were polymorphic. Genetic diversity was estimated by the following parameters: number of alleles (2.00), effective number of alleles (1.30), expected heterozygosity (0.211), and the Shannon index (0.351). The 52 genotypes were clustered in seven groups according to the Jaccard distance. The genetic structure of the population in K = 2 reveals shared alleles among the genotypes of different geographic origins. Morphological and molecular characterization reveals the high genetic diversity among the 52 genotypes of Dioscorea sp. and low diversity among the collection sites.

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

Diouf,

Zoclanclounon,

Mboup

et al. 2024

The Plant Genome

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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.

show abstract

Uncovering the genetic diversity of yams (Dioscorea spp.) in China by combining phenotypic trait and molecular marker analyses

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 16 publications

References 50 publications

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

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

Genetic diversity of yam (Dioscorea sp.) through morphological and molecular markers

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

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