High level of natural variation in a groundnut (<i>Arachis hypogaea</i> L.) germplasm collection assayed by selected informative SSR markers

Varshney, Rajeev K.; Mahendar, T.; Aruna, R.; Nigam, S. N.; Neelima, K.; Vadez, Vincent; Hoisington, David

doi:10.1111/j.1439-0523.2009.01638.x

Cited by 33 publications

(33 citation statements)

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“…The nature of this extra fragment remains to be determined. Amplification of more than one fragment by one primer pair in tetraploid groundnut accessions has been reported in several other studies [14,29,34]. While developing the genetic linkage map for tetraploid groundnut, Varshney and colleagues [32] identified duplicated loci in the segregating population for at least 5 markers and in case of the marker TC3G01 they identified 3 different scorable segregating loci in the population.…”

Section: Discussionmentioning

confidence: 87%

Genetic relationships among seven sections of genus Arachisstudied by using SSR markers

et al. 2010

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BackgroundThe genus Arachis, originated in South America, is divided into nine taxonomical sections comprising of 80 species. Most of the Arachis species are diploids (2n = 2x = 20) and the tetraploid species (2n = 2x = 40) are found in sections Arachis, Extranervosae and Rhizomatosae. Diploid species have great potential to be used as resistance sources for agronomic traits like pests and diseases, drought related traits and different life cycle spans. Understanding of genetic relationships among wild species and between wild and cultivated species will be useful for enhanced utilization of wild species in improving cultivated germplasm. The present study was undertaken to evaluate genetic relationships among species (96 accessions) belonging to seven sections of Arachis by using simple sequence repeat (SSR) markers developed from Arachis hypogaea genomic library and gene sequences from related genera of Arachis.ResultsThe average transferability rate of 101 SSR markers tested to section Arachis and six other sections was 81% and 59% respectively. Five markers (IPAHM 164, IPAHM 165, IPAHM 407a, IPAHM 409, and IPAHM 659) showed 100% transferability. Cluster analysis of allelic data from a subset of 32 SSR markers on 85 wild and 11 cultivated accessions grouped accessions according to their genome composition, sections and species to which they belong. A total of 109 species specific alleles were detected in different wild species, Arachis pusilla exhibited largest number of species specific alleles (15). Based on genetic distance analysis, the A-genome accession ICG 8200 (A. duranensis) and the B-genome accession ICG 8206 (A. ipaënsis) were found most closely related to A. hypogaea.ConclusionA set of cross species and cross section transferable SSR markers has been identified that will be useful for genetic studies of wild species of Arachis, including comparative genome mapping, germplasm analysis, population genetic structure and phylogenetic inferences among species. The present study provides strong support based on both genomic and genic markers, probably for the first time, on relationships of A. monticola and A. hypogaea as well as on the most probable donor of A and B-genomes of cultivated groundnut.

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Section: Discussionmentioning

confidence: 87%

Genetic relationships among seven sections of genus Arachisstudied by using SSR markers

et al. 2010

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“…Screening of 1,000 markers would provide just over 100 polymorphic markers useful for constructing a map. Also, allotetraploid peanut, having a large genome of around 3 9 10 9 bp (Varshney et al 2009b), comparable to that of the human genome, would require a large number of polymorphic markers to make maps sufficiently dense to permit mapbased cloning of genes controlling important traits. Consequently, application of LD mapping would be less time consuming, less expensive, would need minimal resources and will greatly accelerate the identification of potential loci associated with biotic and abiotic stresses.…”

Section: Discussionmentioning

confidence: 99%

A first insight into population structure and linkage disequilibrium in the US peanut minicore collection

et al. 2011

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Knowledge of genetic diversity, population structure, and degree of linkage disequilibrium (LD) in target association mapping populations is of great importance and is a prerequisite for LD-based mapping. In the present study, 96 genotypes comprising 92 accessions of the US peanut minicore collection, a component line of the tetraploid variety Florunner, diploid progenitors A. duranensis (AA) and A. ipae¨nsis (BB), and synthetic amphidiploid accession TxAG-6 were investigated with 392 simple sequence repeat (SSR) marker bands amplified using 32 highly-polymorphic SSR primer pairs. Both distance-and model-based (Bayesian) cluster analysis revealed the presence of structured diversity. In general, the wild-species accessions and the synthetic amphidiploid grouped separately from most minicore accessions except for COC155, and were eliminated from most subsequent analyses. UPGMA analysis divided the population into four subgroups, two major subgroups representing subspecies fastigiata and hypogaea, a third group containing individuals from each subspecies or possibly of mixed ancestry, and a fourth group, either consisting of COC155 alone if wild species were excluded, or of COC155, the diploid species, and the synthetic amphidiploid. Modelbased clustering identified four subgroups-one each for fastigiata and hypogaea subspecies, a third consisting of individuals of both subspecies or of mixed ancestry predominantly from Africa or Asia, and a fourth group, consisting of individuals predominantly of var fastigiata, peruviana, and aequatoriana accessions from South America, including COC155. Analysis of molecular variance (AMOVA) revealed statistically-significant (P \ 0.0001) genetic variance of 16.87% among subgroups. A total of 4.85% of SSR marker pairs revealed significant LD (at r 2 C 0.1). Of the syntenic marker pairs separated by distances \ 10 cM, 11-20 cM, 21-50 cM, and [ 50 cM, 19.33, 5.19, 6.25 and 5.29% of marker pairs were found in strong LD (P B 0.01), in accord with LD extending to great distances in self pollinated crops. A threshold value of r 2 [ 0.035 was found to distinguish mean r 2 values of linkage distance groups statistically from the mean r 2 values of unlinked markers; LD was found to extend to 10 cM over the entire minicore collection by this criterion. However, there were large differences in r 2 values among marker pairs even among tightly-linked markers. The implications of these findings with regard to the possibility of using Vikas Belamkar-This work was performed in partial fulfillment of the requirements for the Master of Science degree.

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“…Multiple genetic studies have been carried out on crop legumes and their wild relatives including soybean (Glycine max; Vaughan & al., 2006;Li & al., 2010), peanut (Arachis hypogaea L.; Varshney & al., 2009), common bean (Phaseolus vulgaris; Mensack & al., 2011), lima bean (Phaseolus lunatus L.; Martínez-Castillo & al., 2006), pea (Pisum sativum L.), mungbean (Vigna radiata (L.) R. Wilczek, . However, the geographic sampling of the wild species in most of these previous studies is limited to certain countries and/or regions, and most used accessions from seed banks.…”

Section: Concept Strategies and Key Indicators Of The Assessmentsmentioning

confidence: 99%

Global legume diversity assessment: Concepts, key indicators, and strategies

Yahara

Javadi

Onoda

et al. 2013

TAXON

105

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While many plant species are considered threatened under anthropogenic pressure, it remains uncertain how rapidly we are losing plant species diversity. To fill this gap, we propose a Global Legume Diversity Assessment (GLDA) as the first step of a global plant diversity assessment. Here we describe the concept of GLDA and its feasibility by reviewing relevant approaches and data availability. We conclude that Fabaceae is a good proxy for overall angiosperm diversity in many habitats and that much relevant data for GLDA are available. As indicators of states, we propose comparison of species richness with phylogenetic and functional diversity to obtain an integrated picture of diversity. As indicators of trends, species loss rate and extinction risks should be assessed. Specimen records and plot data provide key resources for assessing legume diversity at a global scale, and distribution modeling based on these records provide key methods for assessing states and trends of legume diversity. GLDA has started in Asia, and we call for a truly global legume diversity assessment by wider geographic collaborations among various scientists.

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High level of natural variation in a groundnut (Arachis hypogaea L.) germplasm collection assayed by selected informative SSR markers

Cited by 33 publications

References 40 publications

Genetic relationships among seven sections of genus Arachisstudied by using SSR markers

Genetic relationships among seven sections of genus Arachisstudied by using SSR markers

A first insight into population structure and linkage disequilibrium in the US peanut minicore collection

Global legume diversity assessment: Concepts, key indicators, and strategies

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