title: Utilization of in silico EST-SSR markers for diversity studies in castor (Ricinus communisL.).
abstract: Castor (Ricinus communisL.) a chief non-edible oilseed crop has numerous industrial applications. Systematic genetic diversity analysis utilizing DNA based markers has been quick and reliable method that ensures selection of diverse parents for exploitation of higher levels of heterosis in breeding programs. From NCBI database, 63,852 EST sequences of castor were mined. One thousand one hundred and five (1105) EST-SSRs and 1652 repeat motifs sequences were identified from 20,495 non-redundant unigene sequences. Repeat motifs consisted of 29.7 % mono nucleotide repeats, 24.8 % di nucleotide repeats, 27.27 % tri nucleotide repeats and 3.94 % tetra nucleotide repeats. Twenty eight primer pairs were chosen from SSR-containing ESTs to determine genetic diversity among 27 castor accessions. Twelve EST-SSRs showed polymorphism. Number of alleles detected were 2-3 with an average of 2.33 per locus. 150-400 bp was the size of an allele. Dendrogram analysis grouped the 27 accessions into two separate clusters. Genetic similarity coefficient of dendrogram ranged from 0.24 to 0.83. The polymorphic information content value of 0.28-0.49 revealed medium level of diversity in castor. Results of present study indicated that EST-SSRs to be efficient markers for genetic diversity studies. Knowledge on level of diversity existing in castor genotypes would be useful for breeders to plan efficient hybrid breeding programme.
authors.affiliation: Department of Crop Physiology, College of Agriculture, Rajendranagar, Hyderabad, 500030 India.
authors.forename: Ramesh
authors.identifier: 0000-0002-5730-6524
authors.initials: R
authors.lastname: Thatikunta
authors.affiliation: Department of Crop Physiology, College of Agriculture, Rajendranagar, Hyderabad, 500030 India.
authors.forename: A
authors.initials: A
authors.lastname: Siva Sankar
authors.affiliation: Department of Crop Physiology, College of Agriculture, Rajendranagar, Hyderabad, 500030 India.
authors.forename: J
authors.initials: J
authors.lastname: Sreelakshmi
authors.affiliation: Department of Crop Physiology, College of Agriculture, Rajendranagar, Hyderabad, 500030 India.
authors.forename: Gouthami
authors.initials: G
authors.lastname: Palle
authors.affiliation: Department of Crop Physiology, College of Agriculture, Rajendranagar, Hyderabad, 500030 India.
authors.forename: C
authors.initials: C
authors.lastname: Leela
authors.affiliation: Institute of Biotechnology, PJTSAU, Rajendranagar, Hyderabad, 500030 India.
authors.forename: Ch V
authors.initials: CV
authors.lastname: Durga Rani
authors.affiliation: SRTC, PJTSAU, Rajendranagar, Hyderabad, 500030 India.
authors.forename: V
authors.initials: V
authors.lastname: Gouri Shankar
authors.affiliation: Department of Crop Physiology, College of Agriculture, Rajendranagar, Hyderabad, 500030 India.
authors.forename: B
authors.initials: B
authors.lastname: Lavanya
authors.affiliation: Department of Plant Pathology, College of Agriculture, Rajendranagar, Hyderabad, 500030 India.
authors.forename: P
authors.initials: P
authors.lastname: Narayana Reddy
authors.affiliation: ICAR-Indian Institute of Oilseeds Research, Rajendranagar, Hyderabad, 500030 India.
authors.forename: M Y
authors.initials: MY
authors.lastname: Dudhe
keywords: Castor; EST–SSRs; Genetic diversity; Polymorphism