"12","31","archive","1",,,"disk0/00/00/00/12","2011-05-17 07:57:46","2013-09-16 09:35:59","2011-05-17 07:57:46","article",,,"show","Library-ICRISAT@CGIAR.ORG",,,"","","","","","","","","","","0",,,"Dutta","S","","","","","","","Varshney","R K","","","","",,,,,"","",,,,,"","","University of Kalyani(Kalyani)","India","Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh]","pub","s1.2","","","public",,,,"<b>Agrotags</b>     - genetics | locus | polymorphism | genomes | genes | dna | planting | biodiversity | grain legumes | genotypes <br><b>Fishtags</b>    - NOT-AVAILABLE<br><b>Geopoliticaltags</b> - india | delhi | usa | maine | centre","This study was financially supported by the Pigeonpea Genomics Initiative
(PGI) of the Indian Council of Agricultural Research (ICAR), New Delhi under
the framework of Indo-US Agricultural Knowledge Initiative (AKI).
Contribution of Doug Cook was supported by the National Science
Foundation (NSF), USA. GK acknowledges fellowship support from
Department of Biotechnology, Government of India.","Background: Pigeonpea [Cajanus cajan (L.) Millspaugh], one of the most important food legumes of semi-arid
tropical and subtropical regions, has limited genomic resources, particularly expressed sequence based (genic)
markers. We report a comprehensive set of validated genic simple sequence repeat (SSR) markers using deep
transcriptome sequencing, and its application in genetic diversity analysis and mapping.
Results: In this study, 43,324 transcriptome shotgun assembly unigene contigs were assembled from 1.696 million
454 GS-FLX sequence reads of separate pooled cDNA libraries prepared from leaf, root, stem and immature seed of
two pigeonpea varieties, Asha and UPAS 120. A total of 3,771 genic-SSR loci, excluding homopolymeric and
compound repeats, were identified; of which 2,877 PCR primer pairs were designed for marker development.
Dinucleotide was the most common repeat motif with a frequency of 60.41%, followed by tri- (34.52%), hexa-
(2.62%), tetra- (1.67%) and pentanucleotide (0.76%) repeat motifs. Primers were synthesized and tested for 772 of
these loci with repeat lengths of ≥18 bp. Of these, 550 markers were validated for consistent amplification in eight
diverse pigeonpea varieties; 71 were found to be polymorphic on agarose gel electrophoresis. Genetic diversity
analysis was done on 22 pigeonpea varieties and eight wild species using 20 highly polymorphic genic-SSR
markers. The number of alleles at these loci ranged from 4-10 and the polymorphism information content values
ranged from 0.46 to 0.72. Neighbor-joining dendrogram showed distinct separation of the different groups of
pigeonpea cultivars and wild species. Deep transcriptome sequencing of the two parental lines helped in silico
identification of polymorphic genic-SSR loci to facilitate the rapid development of an intra-species reference
genetic map, a subset of which was validated for expected allelic segregation in the reference mapping
population.
Conclusion: We developed 550 validated genic-SSR markers in pigeonpea using deep transcriptome sequencing.
From these, 20 highly polymorphic markers were used to evaluate the genetic relationship among species of the
genus Cajanus. A comprehensive set of genic-SSR markers","2011","published",,"BMC Plant Biology","11","1","BioMed Central",,"17-29",,,,,,,,,,,"TRUE",,"14712229",,,,,,"","http://dx.doi.org/10.1186/1471-2229-11-17","http://scholar.google.co.in/scholar?as_q=%22Development+of+genic-SSR+markers+by+deep+transcriptome+sequencing+in+pigeonpea+%5BCajanus+cajan+%28L.%29+Millspaugh%5D%22&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_sauthors=&as_publication=","pub",,"Indian Council of Agricultural Research","",,,,,,"",,,,,,,"",,,,,"",,,,,"","",,,,,"","",,,,,
"12",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Kumawat","G","","",,,,,,,,,,,,,,,,,,,,,,,"Indian Institute of Pulses Research(Kanpur)","USA",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"National Science Foundation (NSF), USA",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"12",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Singh","B P","","",,,,,,,,,,,,,,,,,,,,,,,"Banaras Hindu University(Varanasi)",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Government of India - Department of Biotechnology",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"12",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Gupta","D K","","",,,,,,,,,,,,,,,,,,,,,,,"University of Agricultural Sciences(Dharwad)",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"12",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Singh","Sangeeta","","",,,,,,,,,,,,,,,,,,,,,,,"Panjabrao Deshmukh Krishi Vidyapeeth(Akola)",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"12",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Dogra","V","","",,,,,,,,,,,,,,,,,,,,,,,"ICRISAT(Patancheru)",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"12",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Gaikwad","K","","",,,,,,,,,,,,,,,,,,,,,,,"University of California(Davis)",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"12",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Sharma","T R","","",,,,,,,,,,,,,,,,,,,,,,,"IARI(New Delhi)",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"12",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Raje","R S","","",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"12",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Bandhopadhya","T K","","",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"12",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Datta","S","","",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"12",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Singh","M N","","",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"12",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Bashasab","F","","",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"12",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Kulwal","P","","",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"12",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Wanjari","K B","","",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"12",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Varshney","R K","","",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"12",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Cook","D R","","",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
"12",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,"Singh","N K","","",,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,