Development, cross-species/genera transferability of novel EST-SSR markers and their utility in revealing population structure and genetic diversity in sugarcane

Handle URI:
http://hdl.handle.net/10754/594214
Title:
Development, cross-species/genera transferability of novel EST-SSR markers and their utility in revealing population structure and genetic diversity in sugarcane
Authors:
Singh, Ram K.; Jena, Satya N.; Khan, Mohammad Suhail; Yadav, Sonia; Banarjee, Nandita; Raghuvanshi, Saurabh; Bhardwaj, Vasudha; Dattamajumder, Sanjay K.; Kapur, Raman; Solomon, Sushil; Swapna, M.; Srivastava, Sangeeta; Tyagi, Akhilesh K.
Abstract:
Sugarcane (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.
KAUST Department:
Center for Desert Agriculture
Citation:
Singh 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.
Publisher:
Elsevier BV
Journal:
Gene
Issue Date:
Jul-2013
DOI:
10.1016/j.gene.2013.03.125
PubMed ID:
23587912
Type:
Article
ISSN:
0378-1119
Sponsors:
The present work was financially supported by the Department of Biotechnology, Ministry of Science and Technology, Govt. of India, New Delhi.
Appears in Collections:
Articles; Center for Desert Agriculture

Full metadata record

DC FieldValue Language
dc.contributor.authorSingh, Ram K.en
dc.contributor.authorJena, Satya N.en
dc.contributor.authorKhan, Mohammad Suhailen
dc.contributor.authorYadav, Soniaen
dc.contributor.authorBanarjee, Nanditaen
dc.contributor.authorRaghuvanshi, Saurabhen
dc.contributor.authorBhardwaj, Vasudhaen
dc.contributor.authorDattamajumder, Sanjay K.en
dc.contributor.authorKapur, Ramanen
dc.contributor.authorSolomon, Sushilen
dc.contributor.authorSwapna, M.en
dc.contributor.authorSrivastava, Sangeetaen
dc.contributor.authorTyagi, Akhilesh K.en
dc.date.accessioned2016-01-19T14:43:25Zen
dc.date.available2016-01-19T14:43:25Zen
dc.date.issued2013-07en
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.en
dc.identifier.issn0378-1119en
dc.identifier.pmid23587912en
dc.identifier.doi10.1016/j.gene.2013.03.125en
dc.identifier.urihttp://hdl.handle.net/10754/594214en
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.en
dc.description.sponsorshipThe present work was financially supported by the Department of Biotechnology, Ministry of Science and Technology, Govt. of India, New Delhi.en
dc.publisherElsevier BVen
dc.subjectExpressed sequence tag (EST)en
dc.subjectPopulation structureen
dc.subjectSimple sequence repeat (SSR)en
dc.subjectSugarcaneen
dc.titleDevelopment, cross-species/genera transferability of novel EST-SSR markers and their utility in revealing population structure and genetic diversity in sugarcaneen
dc.typeArticleen
dc.contributor.departmentCenter for Desert Agricultureen
dc.identifier.journalGeneen
dc.contributor.institutionIndian Institute of Sugarcane Research (ICAR), Rai Bareli Road, Lucknow-226002, U.P., Indiaen
dc.contributor.institutionPlant Molecular Biology Laboratory, National Botanical Research Institute, Lucknow-226001, Indiaen
dc.contributor.institutionDepartment of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi-110021, Indiaen
dc.contributor.institutionNational Institute of Plant Genome Research, Aruna Asaf Ali Marg, P.O. Box No. 10531, New Delhi-110 067, Indiaen
kaust.authorKhan, Mohammad Suhailen

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