Isolation and characterization of microsatellites for the yam Dioscorea cayenensis (Dioscoreaceae) and cross-amplification in D. rotundata

Silva, L R. G; Bajay, Miklos Maximiliano; Monteiro, Magali; Mezette, Thiago Fonseca; Nascimento, Wellington Ferreira do; Zucchi, Maria Imaculada; Pinheiro, José Baldin; Veasey, Elizabeth Ann

doi:10.4238/2014.april.14.5

Cited by 9 publications

(13 citation statements)

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“…The same dinucleotide predominance has been found for D. cayenensis (Silva et al, 2014) and D. alata (Tostain et al, 2006;Siqueira et al, 2011). Microsatellite loci of the perfect dinucleotide type are ideal for obtaining highly informative markers of high polymorphism levels, because mutation rates are higher in dinucleotides than in tri-or tetranucleotides and are therefore widely used in genetic studies (Ellegren, 2004).…”

Section: Discussionmentioning

confidence: 73%

“…Several SSR primers have been developed and used to assess the genetic diversity and structure of yam species, such as cultivated D. alata (Tostain et al, 2006;Sartie et al, 2012;Siqueira et al, 2011Siqueira et al, , 2014, D. trifida (Hochu et al, 2006;Nascimento et al, 2013), and D. cayenensis/D. rotundata (Tostain et al, 2007;Obidiegwu et al, 2009b;Sartie et al, 2012;Scarcelli et al, 2005Scarcelli et al, , 2013Mengesha et al, 2013;Silva et al, 2014). Recently, 14 SSR loci were developed for D. bulbifera accessions from China using the dual-suppression polymerase chain reaction (PCR) technique (Yan et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

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Genetic diversity among air yam (Dioscorea bulbifera) varieties based on single sequence repeat markers

Silva¹,

Siqueira²,

Carrasco³

et al. 2016

Genet. Mol. Res.

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ABSTRACT. Dioscorea is the largest genus in the Dioscoreaceae family, and includes a number of economically important species including the air yam, D. bulbifera L. This study aimed to develop new single sequence repeat primers and characterize the genetic diversity of local varieties that originated in several municipalities of Brazil. We developed an enriched genomic library for D. bulbifera resulting in seven primers, six of which were polymorphic, and added four polymorphic loci developed for other Dioscorea species. This resulted in 10 polymorphic primers to evaluate 42 air yam accessions. Thirtythree alleles (bands) were found, with an average of 3.3 alleles per locus. The discrimination power ranged from 0.113 to 0.834, with an average of 0.595. Both principal coordinate and cluster analyses (using the Jaccard Index) failed to clearly separate the accessions according to their origins. However, the 13 accessions from Conceição dos Ouros, Minas Gerais State were clustered above zero on the principal coordinate 2 axis, and were also clustered into one subgroup in the cluster analysis. Accessions from Ubatuba, São Paulo State were clustered below zero on the same principal coordinate 2 axis, except for one accession, although they were scattered in several subgroups in the cluster analysis. Therefore, we found little spatial structure in the accessions, although those from Conceição dos Ouros and Ubatuba exhibited some spatial structure, and that there is a considerable level of genetic diversity in D. bulbifera maintained by traditional farmers in Brazil.

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Section: Discussionmentioning

confidence: 73%

Section: Introductionmentioning

confidence: 99%

Genetic diversity among air yam (Dioscorea bulbifera) varieties based on single sequence repeat markers

Silva¹,

Siqueira²,

Carrasco³

et al. 2016

Genet. Mol. Res.

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“…Yam belongs to the Dioscoreaceae family and to the genus Dioscorea with more than 600 species, ten of which have rhizophores that are used as food (Lebot, 2009;Nascimento et al, 2015). The species Dioscorea rotundata and Dioscorea cayennensis (also known as Dioscorea cayennensis-rotundata complex) are the most cultivated in the world and account for 95% of yam world production (Obidiegwu et al, 2009;Silva et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

“…In Brazil, approximately 247,000 tons were produced on 25,700 hectares in 2014 (FAOSTAT, 2014). Approximately 90% of domestic production of Dioscorea species stems from the Northeast region, especially the states of Bahia, Paraíba, Pernambuco, Alagoas and Maranhão, where the yam crop represents an important agribusiness (Santos et al, 1998;Santos and Macedo, 2002;Santos et al, 2007a;Silva et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Agro-morphological diversity in yam genotypes from Recncavo of Bahia, Brazil

Moreira¹,

Afonso²,

Lêdo³

et al. 2017

Afr. J. Agric. Res.

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The aim of this study was to evaluate the diversity of yam genotypes concerning their agromorphological traits based on the Ward-modified location model (Ward-MLM) procedure. 209 genotypes from the commercial production area of the Recôncavo region in the state of Bahia, Brazil were used. Three agronomic traits (length, width and weight of the rhizophore) and two morphological traits (rhizophore shape and skin color) were evaluated. A considerable agro-morphological diversity was detected in the data for the 209 yam genotypes. The Ward-MLM procedure showed that the optimal number of groups according to the criteria of pseudo F and pseudo t 2 is four. The separation by genotype groups was associated with their origin from two regions with different soil and climatic conditions. The Ward-MLM procedure has shown its usefulness to detect diversity and cluster genotypes by simultaneous use of morphological and agronomic traits.

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“…Simple sequence repeat markers are very popular because they are codominant and multiallelic and, thus, are more informative than dominant markers (Zalapa et al, 2012). To date, only a few genomic SSR markers have been developed for D. cayenensis and the other Dioscorea species (Terauchi and Konuma, 1994; Mignouna et al, 2003; Mizuki et al, 2005; Tostain et al, 2006; Hochu et al, 2006; Siqueira et al, 2011; Silva et al, 2014) (Table 1). In the present work, we describe the development of genomic SSR markers for yellow Guinea yam ( D. cayenensis ) using the method of enriched microsatellite libraries and demonstrate their use in multiple Dioscorea species.…”

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confidence: 99%

Development of Genomic Simple Sequence Repeat Markers for Yam

et al. 2015

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Yam (Dioscorea spp.) is a major staple crop widely cultivated for its starchy tubers. To date, very few marker resources are publicly available as tools for genetic and genomic studies of this economically important crop. In this study, 90 simple sequence repeat (SSR) markers were developed from an enriched genomic library of yellow Guinea yam (D. cayenensis Lam.). Cross‐amplification revealed that 85 (94.4%) and 51 (56.7%) of these SSRs could be successfully transferred to the two major cultivated species of D. rotundata Poir. and D. alata L., respectively. Polymorphisms in 30 markers selected on the basis of reliability and reproducibility of DNA bands were evaluated using a panel of 12 D. cayenensis, 48 D. rotundata, and 48 D. alata accessions. Accordingly, number of alleles per locus ranged from 2 to 8 in D. cayenensis (mean = 3.9), 3 to 30 in D. rotundata (mean = 13.9), and 2 to 22 in D. alata (mean = 12.1). The average observed and expected heterozygosities were 0.156 and 0.634 (D. cayenensis), 0.326 and 0.853 (D. rotundata), and 0.247 and 0.836 (D. alata), respectively. Clustering based on six SSRs that were polymorphic in at least four of the five cultivated Dioscorea species studied, including D. cayenensis, D. rotundata, D. alata, D. dumetorum (Kunth) Pax., and D. bulbifera L., detected groups consistent with the phylogenetic relationships of the species except for D. dumetorum. These new SSR markers are invaluable resources for applications such as genetic diversity analysis and marker‐assisted breeding.

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Isolation and characterization of microsatellites for the yam Dioscorea cayenensis (Dioscoreaceae) and cross-amplification in D. rotundata

Cited by 9 publications

References 13 publications

Genetic diversity among air yam (Dioscorea bulbifera) varieties based on single sequence repeat markers

Genetic diversity among air yam (Dioscorea bulbifera) varieties based on single sequence repeat markers

Agro-morphological diversity in yam genotypes from Recncavo of Bahia, Brazil

Development of Genomic Simple Sequence Repeat Markers for Yam

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