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dc.contributor.authorSingh, Ram K.
dc.contributor.authorJena, Satya N.
dc.contributor.authorKhan, Mohammad Suhail
dc.contributor.authorYadav, Sonia
dc.contributor.authorBanarjee, Nandita
dc.contributor.authorRaghuvanshi, Saurabh
dc.contributor.authorBhardwaj, Vasudha
dc.contributor.authorDattamajumder, Sanjay K.
dc.contributor.authorKapur, Raman
dc.contributor.authorSolomon, Sushil
dc.contributor.authorSwapna, M.
dc.contributor.authorSrivastava, Sangeeta
dc.contributor.authorTyagi, Akhilesh K.
dc.date.accessioned2016-01-19T14:43:25Z
dc.date.available2016-01-19T14:43:25Z
dc.date.issued2013-07
dc.identifier.citationSingh RK, Jena SN, Khan S, Yadav S, Banarjee N, et al. (2013) Development, cross-species/genera transferability of novel EST-SSR markers and their utility in revealing population structure and genetic diversity in sugarcane. Gene 524: 309–329. Available: http://dx.doi.org/10.1016/j.gene.2013.03.125.
dc.identifier.issn0378-1119
dc.identifier.pmid23587912
dc.identifier.doi10.1016/j.gene.2013.03.125
dc.identifier.urihttp://hdl.handle.net/10754/594214
dc.description.abstractSugarcane (Saccharum spp. hybrid) with complex polyploid genome requires a large number of informative DNA markers for various applications in genetics and breeding. Despite the great advances in genomic technology, it is observed in several crop species, especially in sugarcane, the availability of molecular tools such as microsatellite markers are limited. Now-a-days EST-SSR markers are preferred to genomic SSR (gSSR) as they represent only the functional part of the genome, which can be easily associated with desired trait. The present study was taken up with a new set of 351 EST-SSRs developed from the 4085 non redundant EST sequences of two Indian sugarcane cultivars. Among these EST-SSRs, TNR containing motifs were predominant with a frequency of 51.6%. Thirty percent EST-SSRs showed homology with annotated protein. A high frequency of SSRs was found in the 5'UTR and in the ORF (about 27%) and a low frequency was observed in the 3'UTR (about 8%). Two hundred twenty-seven EST-SSRs were evaluated, in sugarcane, allied genera of sugarcane and cereals, and 134 of these have revealed polymorphism with a range of PIC value 0.12 to 0.99. The cross transferability rate ranged from 87.0% to 93.4% in Saccharum complex, 80.0% to 87.0% in allied genera, and 76.0% to 80.0% in cereals. Cloning and sequencing of EST-SSR size variant amplicons revealed that the variation in the number of repeat-units was the main source of EST-SSR fragment polymorphism. When 124 sugarcane accessions were analyzed for population structure using model-based approach, seven genetically distinct groups or admixtures thereof were observed in sugarcane. Results of principal coordinate analysis or UPGMA to evaluate genetic relationships delineated also the 124 accessions into seven groups. Thus, a high level of polymorphism adequate genetic diversity and population structure assayed with the EST-SSR markers not only suggested their utility in various applications in genetics and genomics in sugarcane but also enriched the microsatellite marker resources in sugarcane. © 2013 Elsevier B.V.
dc.description.sponsorshipThe present work was financially supported by the Department of Biotechnology, Ministry of Science and Technology, Govt. of India, New Delhi.
dc.publisherElsevier BV
dc.subjectExpressed sequence tag (EST)
dc.subjectPopulation structure
dc.subjectSimple sequence repeat (SSR)
dc.subjectSugarcane
dc.titleDevelopment, cross-species/genera transferability of novel EST-SSR markers and their utility in revealing population structure and genetic diversity in sugarcane
dc.typeArticle
dc.contributor.departmentDesert Agriculture Initiative
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.identifier.journalGene
dc.contributor.institutionIndian Institute of Sugarcane Research (ICAR), Rai Bareli Road, Lucknow-226002, U.P., India
dc.contributor.institutionPlant Molecular Biology Laboratory, National Botanical Research Institute, Lucknow-226001, India
dc.contributor.institutionDepartment of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi-110021, India
dc.contributor.institutionNational Institute of Plant Genome Research, Aruna Asaf Ali Marg, P.O. Box No. 10531, New Delhi-110 067, India
kaust.personKhan, Mohammad Suhail


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