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Novel and Stress Relevant EST Derived SSR Markers Developed and Validated in Peanut
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. F...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457858/ https://www.ncbi.nlm.nih.gov/pubmed/26046991 http://dx.doi.org/10.1371/journal.pone.0129127 |
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author | Bosamia, Tejas C. Mishra, Gyan P. Thankappan, Radhakrishnan Dobaria, Jentilal R. |
author_facet | Bosamia, Tejas C. Mishra, Gyan P. Thankappan, Radhakrishnan Dobaria, Jentilal R. |
author_sort | Bosamia, Tejas C. |
collection | PubMed |
description | 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 di-nucleotide 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. |
format | Online Article Text |
id | pubmed-4457858 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-44578582015-06-09 Novel and Stress Relevant EST Derived SSR Markers Developed and Validated in Peanut Bosamia, Tejas C. Mishra, Gyan P. Thankappan, Radhakrishnan Dobaria, Jentilal R. PLoS One Research Article 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 di-nucleotide 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. Public Library of Science 2015-06-05 /pmc/articles/PMC4457858/ /pubmed/26046991 http://dx.doi.org/10.1371/journal.pone.0129127 Text en © 2015 Bosamia et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Bosamia, Tejas C. Mishra, Gyan P. Thankappan, Radhakrishnan Dobaria, Jentilal R. Novel and Stress Relevant EST Derived SSR Markers Developed and Validated in Peanut |
title | Novel and Stress Relevant EST Derived SSR Markers Developed and Validated in Peanut |
title_full | Novel and Stress Relevant EST Derived SSR Markers Developed and Validated in Peanut |
title_fullStr | Novel and Stress Relevant EST Derived SSR Markers Developed and Validated in Peanut |
title_full_unstemmed | Novel and Stress Relevant EST Derived SSR Markers Developed and Validated in Peanut |
title_short | Novel and Stress Relevant EST Derived SSR Markers Developed and Validated in Peanut |
title_sort | novel and stress relevant est derived ssr markers developed and validated in peanut |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4457858/ https://www.ncbi.nlm.nih.gov/pubmed/26046991 http://dx.doi.org/10.1371/journal.pone.0129127 |
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