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Genetic diversity and population structure of rice landraces from Eastern and North Eastern States of India
BACKGROUND: Adaptations to different habitats across the globe and consequent genetic variation within rice have resulted in more than 120,000 diverse accessions including landraces, which are vital genetic resources for agronomic and quality traits. In India the rice landraces of the states West Be...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3765237/ https://www.ncbi.nlm.nih.gov/pubmed/23945062 http://dx.doi.org/10.1186/1471-2156-14-71 |
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author | Das, Basabdatta Sengupta, Samik Parida, Swarup Kumar Roy, Bipasha Ghosh, Mrityunjay Prasad, Manoj Ghose, Tapas Kumar |
author_facet | Das, Basabdatta Sengupta, Samik Parida, Swarup Kumar Roy, Bipasha Ghosh, Mrityunjay Prasad, Manoj Ghose, Tapas Kumar |
author_sort | Das, Basabdatta |
collection | PubMed |
description | BACKGROUND: Adaptations to different habitats across the globe and consequent genetic variation within rice have resulted in more than 120,000 diverse accessions including landraces, which are vital genetic resources for agronomic and quality traits. In India the rice landraces of the states West Bengal, Assam, Mizoram, Manipur and Nagaland are worthy candidates for genetic assessment. Keeping the above in view, the present study was conducted with the aim to (i) calculate the genetic distances among the accessions of 83 landraces collected from these states along with 8 check accessions (total 91 accessions) using 23 previously mapped SSR markers and (ii) examine the population structure among the accessions using model-based clustering approach. RESULTS: Among the 91 accessions, 182 alleles were identified which included 51 rare and 27 null alleles. The average PIC value was 0.7467/marker. The non-aromatic landraces from West Bengal was most diverse with 154 alleles and an average PIC value of 0.8005/marker, followed by the aromatic landraces from West Bengal with 118 alleles and an average PIC value of 0.6524/marker, while the landraces from North East ranked third with 113 alleles and an average PIC value of 0.5745/marker. In the dendrogram distinct clusters consisting of predominantly aromatic landraces and predominantly North East Indian landraces were observed. The non-aromatic landraces from West Bengal were interspersed within these two clusters. The accessions were moderately structured, showing four sub-populations (A-D) with an Fst value of 0.398, 0.364, 0.206 and 0.281, respectively. The assigned clustering of accessions was well in agreement in both distance-based and model-based approaches. CONCLUSIONS: Each of the accessions could be identified unequivocally by the SSR profiles. Genetically the non aromatic landraces from West Bengal were most diverse followed by the aromatic landraces from the same state. The North Eastern accessions ranked third. Further, grouping of accessions based on their agronomic traits may serve as a resource for future studies, leading to the improvement of rice. Moreover in-situ preservation of the landraces is also a means of protection of biodiversity and cultural heritage. |
format | Online Article Text |
id | pubmed-3765237 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-37652372013-09-10 Genetic diversity and population structure of rice landraces from Eastern and North Eastern States of India Das, Basabdatta Sengupta, Samik Parida, Swarup Kumar Roy, Bipasha Ghosh, Mrityunjay Prasad, Manoj Ghose, Tapas Kumar BMC Genet Research Article BACKGROUND: Adaptations to different habitats across the globe and consequent genetic variation within rice have resulted in more than 120,000 diverse accessions including landraces, which are vital genetic resources for agronomic and quality traits. In India the rice landraces of the states West Bengal, Assam, Mizoram, Manipur and Nagaland are worthy candidates for genetic assessment. Keeping the above in view, the present study was conducted with the aim to (i) calculate the genetic distances among the accessions of 83 landraces collected from these states along with 8 check accessions (total 91 accessions) using 23 previously mapped SSR markers and (ii) examine the population structure among the accessions using model-based clustering approach. RESULTS: Among the 91 accessions, 182 alleles were identified which included 51 rare and 27 null alleles. The average PIC value was 0.7467/marker. The non-aromatic landraces from West Bengal was most diverse with 154 alleles and an average PIC value of 0.8005/marker, followed by the aromatic landraces from West Bengal with 118 alleles and an average PIC value of 0.6524/marker, while the landraces from North East ranked third with 113 alleles and an average PIC value of 0.5745/marker. In the dendrogram distinct clusters consisting of predominantly aromatic landraces and predominantly North East Indian landraces were observed. The non-aromatic landraces from West Bengal were interspersed within these two clusters. The accessions were moderately structured, showing four sub-populations (A-D) with an Fst value of 0.398, 0.364, 0.206 and 0.281, respectively. The assigned clustering of accessions was well in agreement in both distance-based and model-based approaches. CONCLUSIONS: Each of the accessions could be identified unequivocally by the SSR profiles. Genetically the non aromatic landraces from West Bengal were most diverse followed by the aromatic landraces from the same state. The North Eastern accessions ranked third. Further, grouping of accessions based on their agronomic traits may serve as a resource for future studies, leading to the improvement of rice. Moreover in-situ preservation of the landraces is also a means of protection of biodiversity and cultural heritage. BioMed Central 2013-08-15 /pmc/articles/PMC3765237/ /pubmed/23945062 http://dx.doi.org/10.1186/1471-2156-14-71 Text en Copyright © 2013 Das et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Das, Basabdatta Sengupta, Samik Parida, Swarup Kumar Roy, Bipasha Ghosh, Mrityunjay Prasad, Manoj Ghose, Tapas Kumar Genetic diversity and population structure of rice landraces from Eastern and North Eastern States of India |
title | Genetic diversity and population structure of rice landraces from Eastern and North Eastern States of India |
title_full | Genetic diversity and population structure of rice landraces from Eastern and North Eastern States of India |
title_fullStr | Genetic diversity and population structure of rice landraces from Eastern and North Eastern States of India |
title_full_unstemmed | Genetic diversity and population structure of rice landraces from Eastern and North Eastern States of India |
title_short | Genetic diversity and population structure of rice landraces from Eastern and North Eastern States of India |
title_sort | genetic diversity and population structure of rice landraces from eastern and north eastern states of india |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3765237/ https://www.ncbi.nlm.nih.gov/pubmed/23945062 http://dx.doi.org/10.1186/1471-2156-14-71 |
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