Detection and validation of single feature polymorphisms in cowpea (Vigna unguiculata L. Walp) using a soybean genome array

Das, Sayan; Bhat, Prasanna R.; Sudhakar, Chinta; Ehlers, Jeffrey D.; Wanamaker, Steve; Roberts, Philip A.; Cui, Xinping; Close, Timothy J.

doi:10.1186/1471-2164-9-107

Cited by 38 publications

(31 citation statements)

References 35 publications

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“…For instance, the response to root knot nematode infection of resistant cowpea genotype CB46 and a susceptible near-isogenic line (null-Rk) were investigated at 3 and Schmutz et al (2010) 9 days post inoculation (Das et al 2010). Furthermore, GeneChip Soybean Genome Arrays identified single feature polymorphisms (SFPs) in cowpea (Das et al 2008) and pigeonpea (Saxena et al 2011).…”

Section: Hybridisation-based Gene Expression Profilingmentioning

confidence: 99%

Functional genomics to study stress responses in crop legumes: progress and prospects

Kudapa

Ramalingam

Nayakoti

et al. 2013

Functional Plant Biol.

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Abstract. Legumes are important food crops worldwide, contributing to more than 33% of human dietary protein. The production of crop legumes is frequently impacted by abiotic and biotic stresses. It is therefore important to identify genes conferring resistance to biotic stresses and tolerance to abiotic stresses that can be used to both understand molecular mechanisms of plant response to the environment and to accelerate crop improvement. Recent advances in genomics offer a range of approaches such as the sequencing of genomes and transcriptomes, gene expression microarray as well as RNA-seq based gene expression profiling, and map-based cloning for the identification and isolation of biotic and abiotic stressresponsive genes in several crop legumes. These candidate stress associated genes should provide insights into the molecular mechanisms of stress tolerance and ultimately help to develop legume varieties with improved stress tolerance and productivity under adverse conditions. This review provides an overview on recent advances in the functional genomics of crop legumes that includes the discovery as well as validation of candidate genes.

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Section: Hybridisation-based Gene Expression Profilingmentioning

confidence: 99%

Functional genomics to study stress responses in crop legumes: progress and prospects

Kudapa

Ramalingam

Nayakoti

et al. 2013

Functional Plant Biol.

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“…This array has been used to identify genes involved in Ascochyta blight resistance Pang 2005b, 2006) and tolerance to drought, cold, and salinity ). In the case of cowpea, by using RNA as a surrogate for DNA of cowpea with a readily available soybean genome array, 11% to 14.7% of all probe sets on the array showed present calls (Das et al 2008). These researchers enumerated 1,058 potential singlefeature polymorphisms (SFPs) between two parents of a RIL population segregating for several important traits.…”

Section: B Species-specific Genomic Resourcesmentioning

confidence: 99%

Legume Genomics and Breeding

Varshney

Thudi

May

et al. 2010

Plant Breeding Reviews

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“…The statistical method for analyzing HVPs was previously used for SFP analysis (Cui et al 2005;Das et al 2008) and mapping translocation breakpoints on 1RS (Bhat et al 2007). We utilized only scaled (scaling factor 500) and log 2 -transformed values from the PM probes.…”

Section: Plant Materialsmentioning

confidence: 99%

Comparative physical mapping between wheat chromosome arm 2BL and rice chromosome 4

Lee

Lee²,

Kim³

et al. 2010

Genetica

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Physical maps of chromosomes provide a framework for organizing and integrating diverse genetic information. DNA microarrays are a valuable technique for physical mapping and can also be used to facilitate the discovery of single feature polymorphisms (SFPs). Wheat chromosome arm 2BL was physically mapped using a Wheat Genome Array onto near-isogenic lines (NILs) with the aid of wheat-rice synteny and mapped wheat EST information. Using high variance probe set (HVP) analysis, 314 HVPs constituting genes present on 2BL were identified. The 314 HVPs were grouped into 3 categories: HVPs that match only rice chromosome 4 (298 HVPs), those that match only wheat ESTs mapped on 2BL (1), and those that match both rice chromosome 4 and wheat ESTs mapped on 2BL (15). All HVPs were converted into gene sets, which represented either unique rice gene models or mapped wheat ESTs that matched identified HVPs. Comparative physical maps were constructed for 16 wheat gene sets and 271 rice gene sets. Of the 271 rice gene sets, 257 were mapped to the 18-35 Mb regions on rice chromosome 4. Based on HVP analysis and sequence similarity between the gene models in the rice chromosomes and mapped wheat ESTs, the outermost rice gene model that limits the translocation breakpoint to orthologous regions was identified.

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Detection and validation of single feature polymorphisms in cowpea (Vigna unguiculata L. Walp) using a soybean genome array

Cited by 38 publications

References 35 publications

Functional genomics to study stress responses in crop legumes: progress and prospects

Functional genomics to study stress responses in crop legumes: progress and prospects

Legume Genomics and Breeding

Comparative physical mapping between wheat chromosome arm 2BL and rice chromosome 4

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