In rice more than 70 diseases caused by fungi, bacteria, viruses and nematodes are prevalent (Oryza sativa). The most devastating of them are the ones caused by Magnaporthe grisea (rice blast), Xanthomonas oryzae pv. oryzae (bacterial leaf blight, BLB) and Rhizoctonia solani (sheath blight). Improved agricultural practices, nutritional supplements, application of fungicides, bactericides and resistant cultivars had been used for disease control but no durable solution was available due to the breakdown of the resistance by high pathogenic variability. Hence, the search for resistant rice genotypes, particularly among the landraces, is in progress. According to Harlan  the extensive diverse array of rice landraces available worldwide are probable storehouses for novel alleles for many qualitative and quantitative traits. Harlan’s study emphasized that each landrace has certain unique properties or characteristics; such as early maturity, adaptation to particular soil types, resistance or tolerance to biotic and abiotic stresses, and in the end usage of the grains. India is home to many such unique landraces and the ones found in the ecological hotspots of the Indo-Burma region, and the Indian states of West Bengal, Assam, Nagaland, Mizoram and Manipur deserve special mention .
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 including Korea, Taiwan, Philippines, Indonesia, Thailand, India and China. Xanthomonas (from two Greek words; xanthos, meaning ‘yellow’, and monas, meaning ‘entity’) is a large genus of gram-negative and yellow-pigmented bacteria. Xoo enters rice leaf typically through the hydathodes at the leaf margin, multiplies in the intercellular spaces of the underlying epithelial tissue, and moves to the xylem vessels to cause systemic infection [3, 4].
Genes conferring resistance to the major classes of plant pathogens have been isolated from a variety of plant species and are termed ‘R genes’ . Comparison of the structural features and the sequences of the predicted proteins from the cloned ‘R genes’ from various plants have led to the identification of common domains which are conserved and show little variation. These conserved domains can be divided into five broad classes. They are the nucleotide-binding domain (NBD), the leucine rich repeat domain (LRR), the coiled coil domain (CC), the serine/threonine protein kinase domain and the detoxifying enzymes . A total of 38  BLB resistance genes (R genes) have been identified in rice, including Xa1, Xa2, Xa3/Xa26, Xa4, xa5, Xa6, Xa7, xa8, xa9, Xa10, Xa11, Xa12, xa13, Xa14, xa15, Xa16, Xa17, Xa18, xa19, xa20, Xa21, Xa22(t), Xa23, xa24(t), xa25/Xa25(t), Xa25, xa26(t), Xa27, xa28(t), Xa29(t), Xa30 (t), xa31(t), Xa32(t), xa33(t), xa34(t), Xa35(t), Xa36(t). The recessive resistance genes include xa5, xa8, xa9, xa13, xa15, xa19, xa20, xa24, xa25/Xa25(t), xa26(t), xa28(t), xa31(t), xa33(t), and xa34(t). Of the 37, 10 BLB resistance (R) genes have been mapped on rice chromosomes 4 (Xa1, Xa2, Xa12, Xa14 and Xa25), chromosome 5 (xa5), chromosome 6 (Xa7), chromosome 8 (xa13), and chromosome 11 (Xa3, Xa4, Xa10, Xa21, Xa22, and Xa23). The chromosomal locations for the rest of the BLB resistance genes still remain elusive. These R genes are known to act in a gene-for-gene manner and are the main sources for genetic improvement of rice for resistance to Xoo. Ten of the recessive R genes; xa5
, xa26, xa28
 and xa32
 occur naturally and confer race-specific resistance. The other 3, xa15
, xa19 and xa20
, were created by mutagenesis and each confers a wide spectrum of resistance to Xoo
[11, 13, 15].
Six BLB resistance genes, Xa1, xa5, Xa21, Xa21(A1), Xa26 and Xa27, have been cloned, sequenced and characterized. In 1967, Sakaguchi  identified Xa1 conforming a high level of specific resistance to race 1 strains of Xoo in Japan and mapped it on rice chromosome 4. The gene xa5 is a naturally occurring mutation that is most commonly found in the Aus-Boro group of rice varieties from the Bangladesh region of Asia [7, 17]. The predicted protein product of Xa21 carries LRRs in the extracellular region and a serine/threonine kinase domain in the cytoplasm . Xa21 is a member of a multigene family located on rice chromosome 11 [18, 19]. Seven Xa21 gene family members, designated A1, A2, B, C, D, E, and F, were cloned and grouped into two classes based on DNA sequence similarity . Xa26 is a dominant gene coding for a LRR receptor kinase protein. It is mapped to the long arm of chromosome 11 [11, 20] and was found in cultivar Mingui 63 which showed resistance against a number of Xoo strains both at seedling and at adult stage suggesting that it was not developmentally regulated . The Xa27 locus of rice conferred resistance to diverse strains of Xoo, including PXO99A, a strain isolated from rice variety IRBB27 by map-based cloning. Xa27 is an intron-less gene and encodes a protein of 113 amino acids.
Natural selection in the ecological niches of the world has generated landraces that are highly diverse for various quality, quantity and disease resistance traits controlling loci. It is important to identify and maintain this polymorphism to widen the genetic base of the commercially cultivated varieties and to reduce pathogen pressure. According to Glaszman et al.  study of local sequence variation reveals the multiple examples of mutation that have taken place due to adaptation towards specific drifts and selection pressure. This adaptive neo diversity superimposes on the ancestral diversity inherited from wild relatives and forms an important section in the passport data of various accessions. It is a tedious task to put the existing natural variation to commercial use. As a step towards that process Nordborg and Weigel  suggested the use of genome-wide association (GWA) mapping which associates the phenotype of interest to DNA sequence variation present in an individual’s genome determined by polymorphism at various loci. GWA mapping gives much higher resolution than linkage mapping because they involve studying associations in natural populations and reflect adaptive recombination events. This kind of mapping is very useful in self fertilized species like A. thaliana and rice . Further, in view of the challenge of assessing the diversity in large germplasm collections, the core collection concept was developed wherein diversity analysis will first be concentrated on a representative manageable sample before extending the study to a broad range of accessions . Such programs have been undertaken for rice and chickpea. In accordance with such postulates the objective of this study is to analyze a small set of phenotypically variable rice accessions from BLB disease hotspot for getting a birds-eye view of the existing diversity in 6 BLB resistant gene loci of those accessions.
Reports of diversity analysis of the BLB resistance genes are available. Ullah et al.,
 identified the presence of the genes Xa4, xa5, Xa7, and xa13 in 52 basmati landraces and five basmati cultivars using Polymerase Chain Reaction (PCR) based methods. They also found that the gene Xa7 was most prevalent among the cultivars and landraces while the genes xa5 and xa13 were confined to landraces only. Ten basmati landraces from their study had multiple resistance genes. Arif et al.,
 identified the BLB resistance gene Xa4 in 49 Pakistani rice lines. Lee et al.,
 identified three rice cultivars with resistance to various Phillipino Xoo strains. The cultivar Nep Bha Bong had a new recessive gene, designated as xa26(t) for moderate resistance to races 1, 2, and 3 and resistance to race 5. The cultivar Arai Raj had a dominant gene designated as Xa27(t) for resistance to race 2. The cultivar Lota Sail had a recessive gene designated as xa28(t) for resistance to race 2. Bimolata  analyzed the sequence variation in the functionally important domains of Xa27 across the Oryza species and found synonymous and non-synonymous mutations in addition to a number of InDels in non-coding regions of the gene. To the best of our knowledge, there is no report available on diversity of BLB resistance loci of rice landraces from the Indian states of Assam, Arunachal Pradesh, Nagaland, Mizoram, Manipur, Tripura and West Bengal.
In this study 34 pairs of primers were designed from conserved domains of the six 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 rice accessions collected from West Bengal and the North Eastern States of India.