title: Development, cross-species/genera transferability of novel EST-SSR markers and their utility in revealing population structure and genetic diversity in sugarcane.
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.
authors.affiliation: Indian Institute of Sugarcane Research (ICAR), Rai Bareli Road, Lucknow-226002, U.P., India. ikrps@yahoo.com
authors.forename: Ram K
authors.initials: RK
authors.lastname: Singh
authors.forename: Satya N
authors.initials: SN
authors.lastname: Jena
authors.forename: Suhail
authors.initials: S
authors.lastname: Khan
authors.forename: Sonia
authors.initials: S
authors.lastname: Yadav
authors.forename: Nandita
authors.initials: N
authors.lastname: Banarjee
authors.forename: Saurabh
authors.initials: S
authors.lastname: Raghuvanshi
authors.forename: Vasudha
authors.initials: V
authors.lastname: Bhardwaj
authors.forename: Sanjay K
authors.initials: SK
authors.lastname: Dattamajumder
authors.forename: Raman
authors.initials: R
authors.lastname: Kapur
authors.forename: Sushil
authors.initials: S
authors.lastname: Solomon
authors.forename: M
authors.initials: M
authors.lastname: Swapna
authors.forename: Sangeeta
authors.initials: S
authors.lastname: Srivastava
authors.forename: Akhilesh K
authors.initials: AK
authors.lastname: Tyagi
mesh_terms: D020121:5' Untranslated Regions; D001483:Base Sequence; D003001:Cloning, Molecular; D018744:DNA, Plant / Q000235:genetics; D020224:Expressed Sequence Tags; D005787:Gene Frequency; D005819:Genetic Markers; D014644:Genetic Variation; D018745:Genome, Plant; D005838:Genotype; D018895:Microsatellite Repeats; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D031786:Saccharum / Q000145:classification / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid
chemical_list: D020121:5' Untranslated Regions; D018744:DNA, Plant; D005819:Genetic Markers