<> "The repository administrator has not yet configured an RDF license."^^ . <> . . . "Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh]"^^ . "Background: Pigeonpea [Cajanus cajan (L.) Millspaugh], one of the most important food legumes of semi-arid\r\ntropical and subtropical regions, has limited genomic resources, particularly expressed sequence based (genic)\r\nmarkers. We report a comprehensive set of validated genic simple sequence repeat (SSR) markers using deep\r\ntranscriptome sequencing, and its application in genetic diversity analysis and mapping.\r\nResults: In this study, 43,324 transcriptome shotgun assembly unigene contigs were assembled from 1.696 million\r\n454 GS-FLX sequence reads of separate pooled cDNA libraries prepared from leaf, root, stem and immature seed of\r\ntwo pigeonpea varieties, Asha and UPAS 120. A total of 3,771 genic-SSR loci, excluding homopolymeric and\r\ncompound repeats, were identified; of which 2,877 PCR primer pairs were designed for marker development.\r\nDinucleotide was the most common repeat motif with a frequency of 60.41%, followed by tri- (34.52%), hexa-\r\n(2.62%), tetra- (1.67%) and pentanucleotide (0.76%) repeat motifs. Primers were synthesized and tested for 772 of\r\nthese loci with repeat lengths of ≥18 bp. Of these, 550 markers were validated for consistent amplification in eight\r\ndiverse pigeonpea varieties; 71 were found to be polymorphic on agarose gel electrophoresis. Genetic diversity\r\nanalysis was done on 22 pigeonpea varieties and eight wild species using 20 highly polymorphic genic-SSR\r\nmarkers. The number of alleles at these loci ranged from 4-10 and the polymorphism information content values\r\nranged from 0.46 to 0.72. Neighbor-joining dendrogram showed distinct separation of the different groups of\r\npigeonpea cultivars and wild species. Deep transcriptome sequencing of the two parental lines helped in silico\r\nidentification of polymorphic genic-SSR loci to facilitate the rapid development of an intra-species reference\r\ngenetic map, a subset of which was validated for expected allelic segregation in the reference mapping\r\npopulation.\r\nConclusion: We developed 550 validated genic-SSR markers in pigeonpea using deep transcriptome sequencing.\r\nFrom these, 20 highly polymorphic markers were used to evaluate the genetic relationship among species of the\r\ngenus Cajanus. A comprehensive set of genic-SSR markers"^^ . "2011" . . "11" . "1" . . "BioMed Central"^^ . . . "BMC Plant Biology"^^ . . . "14712229" . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . "M N"^^ . "Singh"^^ . "M N Singh"^^ . . "S"^^ . "Datta"^^ . "S Datta"^^ . . "T R"^^ . "Sharma"^^ . "T R Sharma"^^ . . "K"^^ . "Gaikwad"^^ . "K Gaikwad"^^ . . "N K"^^ . "Singh"^^ . "N K Singh"^^ . . "D R"^^ . "Cook"^^ . "D R Cook"^^ . . "K B"^^ . "Wanjari"^^ . "K B Wanjari"^^ . . "G"^^ . "Kumawat"^^ . "G Kumawat"^^ . . "B P"^^ . "Singh"^^ . "B P Singh"^^ . . "R S"^^ . "Raje"^^ . "R S Raje"^^ . . "F"^^ . "Bashasab"^^ . "F Bashasab"^^ . . "V"^^ . "Dogra"^^ . "V Dogra"^^ . . "P"^^ . "Kulwal"^^ . "P Kulwal"^^ . . "Sangeeta"^^ . "Singh"^^ . "Sangeeta Singh"^^ . . "T K"^^ . "Bandhopadhya"^^ . "T K Bandhopadhya"^^ . . "D K"^^ . "Gupta"^^ . "D K Gupta"^^ . . "R K"^^ . "Varshney"^^ . "R K Varshney"^^ . . "S"^^ . "Dutta"^^ . "S Dutta"^^ . . . . . . "Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh] (PDF)"^^ . . . . . . . . "varsh-2011-aupay.pdf"^^ . . . "Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh] (Image (JPEG))"^^ . . . . . . "preview.jpg"^^ . . "HTML Summary of #12 \n\nDevelopment of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh]\n\n" . "text/html" . . . "Pigeonpea"@en . .