eprintid: 12 rev_number: 31 eprint_status: archive userid: 1 dir: disk0/00/00/00/12 datestamp: 2011-05-17 07:57:46 lastmod: 2013-09-16 09:35:59 status_changed: 2011-05-17 07:57:46 type: article metadata_visibility: show contact_email: Library-ICRISAT@CGIAR.ORG item_issues_count: 0 creators_name: Dutta, S creators_name: Kumawat, G creators_name: Singh, B P creators_name: Gupta, D K creators_name: Singh, Sangeeta creators_name: Dogra, V creators_name: Gaikwad, K creators_name: Sharma, T R creators_name: Raje, R S creators_name: Bandhopadhya, T K creators_name: Datta, S creators_name: Singh, M N creators_name: Bashasab, F creators_name: Kulwal, P creators_name: Wanjari, K B creators_name: Varshney, R K creators_name: Cook, D R creators_name: Singh, N K icrisatcreators_name: Varshney, R K affiliation: University of Kalyani(Kalyani) affiliation: Indian Institute of Pulses Research(Kanpur) affiliation: Banaras Hindu University(Varanasi) affiliation: University of Agricultural Sciences(Dharwad) affiliation: Panjabrao Deshmukh Krishi Vidyapeeth(Akola) affiliation: ICRISAT(Patancheru) affiliation: University of California(Davis) affiliation: IARI(New Delhi) country: India country: USA title: Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh] ispublished: pub subjects: s1.2 full_text_status: public agrotags: Agrotags - genetics | locus | polymorphism | genomes | genes | dna | planting | biodiversity | grain legumes | genotypes
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Geopoliticaltags - india | delhi | usa | maine | centre note: 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. abstract: 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 date: 2011 date_type: published publication: BMC Plant Biology volume: 11 number: 1 publisher: BioMed Central pagerange: 17-29 refereed: TRUE issn: 14712229 official_url: http://dx.doi.org/10.1186/1471-2229-11-17 related_url_url: 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= related_url_type: pub funders: Indian Council of Agricultural Research funders: National Science Foundation (NSF), USA funders: Government of India - Department of Biotechnology citation: Dutta, S and Kumawat, G and Singh, B P and Gupta, D K and Singh, Sangeeta and Dogra, V and Gaikwad, K and Sharma, T R and Raje, R S and Bandhopadhya, T K and Datta, S and Singh, M N and Bashasab, F and Kulwal, P and Wanjari, K B and Varshney, R K and Cook, D R and Singh, N K (2011) Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh]. BMC Plant Biology, 11 (1). pp. 17-29. ISSN 14712229 document_url: http://oar.icrisat.org/12/1/varsh-2011-aupay.pdf