@prefix ep: .
@prefix rdfs: .
@prefix foaf: .
@prefix bibo: .
@prefix eprel: .
@prefix event: .
@prefix owl: .
@prefix cc: .
@prefix void: .
@prefix dc: .
@prefix epid: .
@prefix rdf: .
@prefix dct: .
@prefix geo: .
@prefix xsd: .
@prefix skos: .
<>
foaf:primaryTopic ;
rdfs:comment "The repository administrator has not yet configured an RDF license."^^xsd:string .
rdfs:label "varsh-2011-aupay.pdf"^^xsd:string .
rdfs:label "preview.jpg"^^xsd:string .
dc:format "text/html";
dc:title "HTML Summary of #12 \n\nDevelopment of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh]\n\n";
foaf:primaryTopic .
dct:hasPart ;
ep:hasFile ;
eprel:hasVersion ;
eprel:hasVolatileVersion ;
eprel:haspreviewThumbnailVersion ;
rdf:type bibo:Document,
ep:Document;
rdfs:label "Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh] (PDF)"^^xsd:string .
dct:hasPart ;
ep:hasFile ;
eprel:isVersionOf ;
eprel:isVolatileVersionOf ;
eprel:ispreviewThumbnailVersionOf ;
rdf:type ep:Document;
rdfs:label "Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh] (Image (JPEG))"^^xsd:string .
rdf:_1 ;
rdf:_2 ;
rdf:_3 ;
rdf:_4 ;
rdf:_5 ;
rdf:_6 ;
rdf:_7 ;
rdf:_8 ;
rdf:_9 ;
rdf:_10 ;
rdf:_11 ;
rdf:_12 ;
rdf:_13 ;
rdf:_14 ;
rdf:_15 ;
rdf:_16 ;
rdf:_17 ;
rdf:_18 .
bibo:abstract "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"^^xsd:string;
bibo:authorList ;
bibo:issue "1";
bibo:status ,
;
bibo:volume "11";
dc:hasVersion ;
dct:creator ,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
;
dct:date "2011";
dct:isPartOf ,
;
dct:publisher ;
dct:subject ;
dct:title "Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh]"^^xsd:string;
ep:hasDocument ,
;
ep:hasPublished ;
rdf:type bibo:AcademicArticle,
bibo:Article,
ep:ArticleEPrint,
ep:EPrint;
rdfs:seeAlso .
rdf:type skos:Concept;
skos:prefLabel "Pigeonpea"@en .
foaf:name "BioMed Central"^^xsd:string;
rdf:type foaf:Organization .
foaf:familyName "Bandhopadhya"^^xsd:string;
foaf:givenName "T K"^^xsd:string;
foaf:name "T K Bandhopadhya"^^xsd:string;
rdf:type foaf:Person .
foaf:familyName "Kumawat"^^xsd:string;
foaf:givenName "G"^^xsd:string;
foaf:name "G Kumawat"^^xsd:string;
rdf:type foaf:Person .
foaf:familyName "Singh"^^xsd:string;
foaf:givenName "Sangeeta"^^xsd:string;
foaf:name "Sangeeta Singh"^^xsd:string;
rdf:type foaf:Person .
foaf:familyName "Cook"^^xsd:string;
foaf:givenName "D R"^^xsd:string;
foaf:name "D R Cook"^^xsd:string;
rdf:type foaf:Person .
foaf:familyName "Datta"^^xsd:string;
foaf:givenName "S"^^xsd:string;
foaf:name "S Datta"^^xsd:string;
rdf:type foaf:Person .
foaf:familyName "Singh"^^xsd:string;
foaf:givenName "B P"^^xsd:string;
foaf:name "B P Singh"^^xsd:string;
rdf:type foaf:Person .
foaf:familyName "Kulwal"^^xsd:string;
foaf:givenName "P"^^xsd:string;
foaf:name "P Kulwal"^^xsd:string;
rdf:type foaf:Person .
foaf:familyName "Raje"^^xsd:string;
foaf:givenName "R S"^^xsd:string;
foaf:name "R S Raje"^^xsd:string;
rdf:type foaf:Person .
foaf:familyName "Bashasab"^^xsd:string;
foaf:givenName "F"^^xsd:string;
foaf:name "F Bashasab"^^xsd:string;
rdf:type foaf:Person .
foaf:familyName "Dogra"^^xsd:string;
foaf:givenName "V"^^xsd:string;
foaf:name "V Dogra"^^xsd:string;
rdf:type foaf:Person .
foaf:familyName "Wanjari"^^xsd:string;
foaf:givenName "K B"^^xsd:string;
foaf:name "K B Wanjari"^^xsd:string;
rdf:type foaf:Person .
foaf:familyName "Sharma"^^xsd:string;
foaf:givenName "T R"^^xsd:string;
foaf:name "T R Sharma"^^xsd:string;
rdf:type foaf:Person .
foaf:familyName "Gaikwad"^^xsd:string;
foaf:givenName "K"^^xsd:string;
foaf:name "K Gaikwad"^^xsd:string;
rdf:type foaf:Person .
foaf:familyName "Singh"^^xsd:string;
foaf:givenName "N K"^^xsd:string;
foaf:name "N K Singh"^^xsd:string;
rdf:type foaf:Person .
foaf:familyName "Varshney"^^xsd:string;
foaf:givenName "R K"^^xsd:string;
foaf:name "R K Varshney"^^xsd:string;
rdf:type foaf:Person .
foaf:familyName "Gupta"^^xsd:string;
foaf:givenName "D K"^^xsd:string;
foaf:name "D K Gupta"^^xsd:string;
rdf:type foaf:Person .
foaf:familyName "Singh"^^xsd:string;
foaf:givenName "M N"^^xsd:string;
foaf:name "M N Singh"^^xsd:string;
rdf:type foaf:Person .
foaf:familyName "Dutta"^^xsd:string;
foaf:givenName "S"^^xsd:string;
foaf:name "S Dutta"^^xsd:string;
rdf:type foaf:Person .
bibo:issn "14712229";
foaf:name "BMC Plant Biology"^^xsd:string;
owl:sameAs ;
rdf:type bibo:Collection .