Novel and stress relevant EST derived SSR markers developed and validated in peanut

Bosamia, T.C. and Mishra, G.P. and Thankappan, R. and Dobaria, J.R. (2015) Novel and stress relevant EST derived SSR markers developed and validated in peanut. PLoS ONE, 10 (6). pp. 1-19.

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Abstract

With the aim to increase the number of functional markers in resource poor crop like cultivated peanut (Arachis hypogaea), large numbers of available expressed sequence tags (ESTs) in the public databases, were employed for the development of novel EST derived simple sequence repeat (SSR) markers. From 16424 unigenes, 2784 (16.95%) SSRs containing unigenes having 3373 SSR motifs were identified. Of these, 2027 (72.81%) sequences were annotated and 4124 gene ontology terms were assigned. Among different SSR motif-classes, tri-nucleotide repeats (33.86%) were the most abundant followed by dinucleotide repeats (27.51%) while AG/CT (20.7%) and AAG/CTT (13.25%) were the most abundant repeat-motifs. A total of 2456 EST-SSR novel primer pairs were designed, of which 366 unigenes having relevance to various stresses and other functions, were PCR validated using a set of 11 diverse peanut genotypes. Of these, 340 (92.62%) primer pairs yielded clear and scorable PCR products and 39 (10.66%) primer pairs exhibited polymorphisms. Overall, the number of alleles per marker ranged from 1-12 with an average of 3.77 and the PIC ranged from 0.028 to 0.375 with an average of 0.325. The identified EST-SSRs not only enriched the existing molecular markers kitty, but would also facilitate the targeted research in marker-trait association for various stresses, inter-specific studies and genetic diversity analysis in peanut

Item Type: Article
Uncontrolled Keywords: Molecular genetics, Genetic markers, Genotypes, Genetic diversity
Author Affiliation: Crop Improvement Division, ICAR-Directorate of Groundnut Research, Junagadh, Gujarat, 362 001, India
Subjects: Crop Improvement
Divisions: Groundnut
Depositing User: Mr T L Gautham
Date Deposited: 06 Oct 2015 10:48
Last Modified: 06 Oct 2015 10:48
URI: http://eprints.icrisat.ac.in/id/eprint/13932

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