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Genetic diversity of the conserved motifs of six bacterial leaf blight resistance genes in a set of rice landraces
BACKGROUND: Bacterial leaf blight (BLB) caused by the vascular pathogen Xanthomonas oryzae pv. oryzae (Xoo) is one of the most serious diseases leading to crop failure in rice growing countries. A total of 37 resistance genes against Xoo has been identified in rice. Of these, ten BLB resistance gene...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2014
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4105243/ https://www.ncbi.nlm.nih.gov/pubmed/25016378 http://dx.doi.org/10.1186/1471-2156-15-82 |
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author | Das, Basabdatta Sengupta, Samik Prasad, Manoj Ghose, Tapas Kumar |
author_facet | Das, Basabdatta Sengupta, Samik Prasad, Manoj Ghose, Tapas Kumar |
author_sort | Das, Basabdatta |
collection | PubMed |
description | BACKGROUND: Bacterial leaf blight (BLB) caused by the vascular pathogen Xanthomonas oryzae pv. oryzae (Xoo) is one of the most serious diseases leading to crop failure in rice growing countries. A total of 37 resistance genes against Xoo has been identified in rice. Of these, ten BLB resistance genes have been mapped on rice chromosomes, while 6 have been cloned, sequenced and characterized. Diversity analysis at the resistance gene level of this disease is scanty, and the landraces from West Bengal and North Eastern states of India have received little attention so far. The objective of this study was to assess the genetic diversity at conserved domains of 6 BLB resistance genes in a set of 22 rice accessions including landraces and check genotypes collected from the states of Assam, Nagaland, Mizoram and West Bengal. RESULTS: In this study 34 pairs of primers were designed from conserved domains of 6 BLB resistance genes; Xa1, xa5, Xa21, Xa21(A1), Xa26 and Xa27. The designed primer pairs were used to generate PCR based polymorphic DNA profiles to detect and elucidate the genetic diversity of the six genes in the 22 diverse rice accessions of known disease phenotype. A total of 140 alleles were identified including 41 rare and 26 null alleles. The average polymorphism information content (PIC) value was 0.56/primer pair. The DNA profiles identified each of the rice landraces unequivocally. The amplified polymorphic DNA bands were used to calculate genetic similarity of the rice landraces in all possible pair combinations. The similarity among the rice accessions ranged from 18% to 89% and the dendrogram produced from the similarity values was divided into 2 major clusters. The conserved domains identified within the sequenced rare alleles include Leucine-Rich Repeat, BED-type zinc finger domain, sugar transferase domain and the domain of the carbohydrate esterase 4 superfamily. CONCLUSIONS: This study revealed high genetic diversity at conserved domains of six BLB resistance genes in a set of 22 rice accessions. The inclusion of more genotypes from remote ecological niches and hotspots holds promise for identification of further genetic diversity at the BLB resistance genes. |
format | Online Article Text |
id | pubmed-4105243 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2014 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-41052432014-07-31 Genetic diversity of the conserved motifs of six bacterial leaf blight resistance genes in a set of rice landraces Das, Basabdatta Sengupta, Samik Prasad, Manoj Ghose, Tapas Kumar BMC Genet Research Article BACKGROUND: Bacterial leaf blight (BLB) caused by the vascular pathogen Xanthomonas oryzae pv. oryzae (Xoo) is one of the most serious diseases leading to crop failure in rice growing countries. A total of 37 resistance genes against Xoo has been identified in rice. Of these, ten BLB resistance genes have been mapped on rice chromosomes, while 6 have been cloned, sequenced and characterized. Diversity analysis at the resistance gene level of this disease is scanty, and the landraces from West Bengal and North Eastern states of India have received little attention so far. The objective of this study was to assess the genetic diversity at conserved domains of 6 BLB resistance genes in a set of 22 rice accessions including landraces and check genotypes collected from the states of Assam, Nagaland, Mizoram and West Bengal. RESULTS: In this study 34 pairs of primers were designed from conserved domains of 6 BLB resistance genes; Xa1, xa5, Xa21, Xa21(A1), Xa26 and Xa27. The designed primer pairs were used to generate PCR based polymorphic DNA profiles to detect and elucidate the genetic diversity of the six genes in the 22 diverse rice accessions of known disease phenotype. A total of 140 alleles were identified including 41 rare and 26 null alleles. The average polymorphism information content (PIC) value was 0.56/primer pair. The DNA profiles identified each of the rice landraces unequivocally. The amplified polymorphic DNA bands were used to calculate genetic similarity of the rice landraces in all possible pair combinations. The similarity among the rice accessions ranged from 18% to 89% and the dendrogram produced from the similarity values was divided into 2 major clusters. The conserved domains identified within the sequenced rare alleles include Leucine-Rich Repeat, BED-type zinc finger domain, sugar transferase domain and the domain of the carbohydrate esterase 4 superfamily. CONCLUSIONS: This study revealed high genetic diversity at conserved domains of six BLB resistance genes in a set of 22 rice accessions. The inclusion of more genotypes from remote ecological niches and hotspots holds promise for identification of further genetic diversity at the BLB resistance genes. BioMed Central 2014-07-12 /pmc/articles/PMC4105243/ /pubmed/25016378 http://dx.doi.org/10.1186/1471-2156-15-82 Text en Copyright © 2014 Das et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/4.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Das, Basabdatta Sengupta, Samik Prasad, Manoj Ghose, Tapas Kumar Genetic diversity of the conserved motifs of six bacterial leaf blight resistance genes in a set of rice landraces |
title | Genetic diversity of the conserved motifs of six bacterial leaf blight resistance genes in a set of rice landraces |
title_full | Genetic diversity of the conserved motifs of six bacterial leaf blight resistance genes in a set of rice landraces |
title_fullStr | Genetic diversity of the conserved motifs of six bacterial leaf blight resistance genes in a set of rice landraces |
title_full_unstemmed | Genetic diversity of the conserved motifs of six bacterial leaf blight resistance genes in a set of rice landraces |
title_short | Genetic diversity of the conserved motifs of six bacterial leaf blight resistance genes in a set of rice landraces |
title_sort | genetic diversity of the conserved motifs of six bacterial leaf blight resistance genes in a set of rice landraces |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4105243/ https://www.ncbi.nlm.nih.gov/pubmed/25016378 http://dx.doi.org/10.1186/1471-2156-15-82 |
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