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Open Access Highly Accessed Research article

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

Basabdatta Das1, Samik Sengupta2, Manoj Prasad3 and Tapas Kumar Ghose1*

Author Affiliations

1 Division of Plant Biology, Bose Institute, Main Campus, 93/1 A.P.C. Road, 700009 Kolkata, West Bengal, India

2 Department of Horticulture, Institute of Agricultural Science, University of Calcutta, 35, Balligunge Circular Road, 700029 Kolkata, West Bengal, India

3 National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, 110067 New Delhi, India

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BMC Genetics 2014, 15:82  doi:10.1186/1471-2156-15-82

Published: 12 July 2014



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.


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.


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.

Genetic diversity; BLB resistance; DNA markers; Indian landraces; Rice