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Genetic diversity of the conserved motifs of six bacterial leaf blight resistance genes in a set of rice landraces

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Title Genetic diversity of the conserved motifs of six bacterial leaf blight resistance genes in a set of rice landraces
 
Creator Das, Basabdatta
Sengupta, Samik
Prasad, Manoj
Ghose, Tapas Kumar
 
Subject Genetic diversity
BLB resistance
DNA markers
Indian landraces
Rice
 
Description Accepted date: 10 July 2014
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.
The authors wish to thank Assam Agriculture University, Agricultural Training
Centre, Fulia, Rice Research Station, Chinsurah, National Bureau of Plant
Genetic Resources and State Agricultural Research Farm, Kashipur for
contributing the rice accessions. They also wish to thank the Department of
Science and Technology for providing the research funding through Bose
Institute and for providing the fellowship to Basabdatta Das. Thanks are also
due to the University of Calcutta for providing fellowship to Samik Sengupta.
Authors kindly acknowledge Muthamilarasan M of NIPGR, New Delhi for
critically reading the manuscript.
 
Date 2015-12-15T06:11:38Z
2015-12-15T06:11:38Z
2014
 
Type Article
 
Identifier BMC Genetics, 15: 82
1471-2164
http://172.16.0.77:8080/jspui/handle/123456789/401
http://www.biomedcentral.com/1471-2156/15/82
10.1186/1471-2156-15-82
 
Language en_US
 
Publisher BioMed Central Ltd