SSR marker development, genetic diversity and population structure analysis of Bambara groundnut [Vigna subterranea (L.) Verdc.] landraces

Molosiwa, Odireleng O.; Aliyu, Siise; Stadler, Florian; Mayes, Katie; Massawe, Festo; Kilian, Andrzej; Mayes, Sean

doi:10.1007/s10722-015-0226-6

Cited by 55 publications

(83 citation statements)

References 20 publications

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“…Using these markers, an average of 2.5 and 2.4 alleles per locus for di- and tri-nucleotide SSRs, respectively, was observed (Table 6). Individual PIC values varied from 0.16 to 0.67, which is comparable to recent legume studies in pigeonpea [37], mungbean [38], and common bean [39], although lower than in cowpea [40] and bambara groundnut [41]. …”

Section: Resultssupporting

confidence: 83%

Development of Gene‐Based SSR Markers in Winged Bean (Psophocarpus tetragonolobus (L.) DC.) for Diversity Assessment

Wong

Tanzi

et al. 2017

Genes

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Winged bean (Psophocarpus tetragonolobus) is an herbaceous multipurpose legume grown in hot and humid countries as a pulse, vegetable (leaves and pods), or root tuber crop depending on local consumption preferences. In addition to its different nutrient-rich edible parts which could contribute to food and nutritional security, it is an efficient nitrogen fixer as a component of sustainable agricultural systems. Generating genetic resources and improved lines would help to accelerate the breeding improvement of this crop, as the lack of improved cultivars adapted to specific environments has been one of the limitations preventing wider use. A transcriptomic de novo assembly was constructed from four tissues: leaf, root, pod, and reproductive tissues from Malaysian accessions, comprising of 198,554 contigs with a N50 of 1462 bp. Of these, 138,958 (70.0%) could be annotated. Among 9682 genic simple sequence repeat (SSR) motifs identified (excluding monomer repeats), trinucleotide-repeats were the most abundant (4855), followed by di-nucleotide (4500) repeats. A total of 18 SSR markers targeting di- and tri-nucleotide repeats have been validated as polymorphic markers based on an initial assessment of nine genotypes originated from five countries. A cluster analysis revealed provisional clusters among this limited, yet diverse selection of germplasm. The developed assembly and validated genic SSRs in this study provide a foundation for a better understanding of the plant breeding system for the genetic improvement of winged bean.

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Section: Resultssupporting

confidence: 83%

Development of Gene‐Based SSR Markers in Winged Bean (Psophocarpus tetragonolobus (L.) DC.) for Diversity Assessment

Wong

Tanzi

et al. 2017

Genes

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“…Among these, Single Sequence Repeat (SSR) or microsatellite markers, which target tandem repeats of ditri-or tetra-nucleotide DNA motifs, are both highly polymorphic within populations and randomly distributed throughout the genome in both transcribed and nontranscribed sequences (Saghai-Maroof et al, 1994;Manzelli et al, 2007). SSR markers have been successfully used to evaluate genetic diversity in several crop species such as wheat (Fufa et al, 2005), Pennisetum purpureum (Azevedo et al, 2012), Capsicum (Nicolai et al, 2013), Sorghum (Cuevas et al, 2014), barley (Shakhatreh et al, 2015), Vigna subterranea (Molosiwa et al, 2015), maize (Salami et al, 2016) and some underutilized species such as buckwheat and wild melon (Roy et al, 2012;Zhang and Zao, 2013). For pearl millet characterization, several SSR markers were developed (Mariac et al, 2006;Stich et al, 2010;Nepolean et al, 2012) and used to evaluate its genetic diversity at the regional scale in west Africa.…”

Section: Introductionmentioning

confidence: 99%

Assessment of genetic diversity among cultivated Pearl millet (Pennisetum glaucum, Poaceae) accessions from Benin, West Africa

Adéoti¹,

Djèdatin²,

Ewedje³

et al. 2017

Afr. J. Biotechnol.

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Simple sequence repeat (SSR) molecular markers were used for genetic diversity analysis and population structure of the cultivated Pearl millet in Benin, West Africa. In order to assess the level of genetic diversity, 14 polymorphic SSR markers were used to screen 114 accessions from different agroecological zones in Benin. SSR markers were found to reveal a total of 57 alleles with an average of 4.071 allele per locus. Genetic diversity index varied from 0.099 to 0.633 with an average of 0.405. The average observed heterozygosity was found to reach 0.425. The analysis of molecular variance showed no real differentiation between regions. Only 5% of genetic variation was observed between samples collected from north-eastern and north-western region. A high level of variation (95%) was observed among accessions. Moreover, both principal component analysis (PCA) and the dendrogram obtained from the genetic distance among accessions revealed the absence of any specific structuration of accessions from each region under study. Our results confirmed diversity among cultivated Pearl millet in Benin and such diversity is not clustering according to geographical patterns.

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“…5 and 6). Here only the genotypic information was used to retrace geo-location associations of similar genetic profiles based on 20 microsatellites molecular markers (SSR) [37,46]. Five genetic profiles were identified from k-means on main principal components of the SSR response data.…”

Section: First Applicationsmentioning

confidence: 99%

Geospatial binding for transdisciplinary research in crop science: the GRASPgfs initiative

Leibovici

Anand

Santos

et al. 2017

Open geospatial data, softw. stand.

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The paper retraces the GRASPgfs endeavor (Geospatial Resource for Agricultural Species and Pests with integrated workflow modelling to support Global Food Security) between multiple disciplines around a common objective of facilitating research and model simulations for sustainable food security. Within this endeavor, the geospatial media has been the enabler for multidisciplinary research in crop modelling. Geospatial genetic-trait variations and associations with environmental forecasting were the main focus of the GRASPgfs. Designing the platform achieving this objective generated a transdisciplinary vision of modelling and forecasting for sustainable agriculture. Based on interoperability principles, seamless access as well as sharing for data, metadata and processing models, the design is described in this paper. This geospatial binding facilitates and supports new types of hypotheses and analysis as illustrated in the paper with a landscape genetic case study (bambara groundnut) and a crop disease modelling (eyespot disease). The approach and the eGRASP platform are generic enough to accommodate further complexity into the integrated modelling that this geospatial binding enables.

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SSR marker development, genetic diversity and population structure analysis of Bambara groundnut [Vigna subterranea (L.) Verdc.] landraces

Cited by 55 publications

References 20 publications

Development of Gene‐Based SSR Markers in Winged Bean (Psophocarpus tetragonolobus (L.) DC.) for Diversity Assessment

Development of Gene‐Based SSR Markers in Winged Bean (Psophocarpus tetragonolobus (L.) DC.) for Diversity Assessment

Assessment of genetic diversity among cultivated Pearl millet (Pennisetum glaucum, Poaceae) accessions from Benin, West Africa

Geospatial binding for transdisciplinary research in crop science: the GRASPgfs initiative

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