Patel et al.

genetics, relatively small genome size of 430 Mb (Causse

to all Indian and Philippine races of Xanthomonas

et al ., 1994; Kurata et al ., 1994), significant level of

oryzae pv. oryzae tested (Ikeda et al., 1990) and encodes

genetic polymorphism, large amount of well conserved

leucine-rich repeat (LRR) receptor kinase-like proteins. It

genetically diverse material and compatible wild species

is mapped on chromosome 11. The xa5 is the recessive

(Tanksley et al ., 1989; Wang et al ., 1992).

resistant locus which encodes the gamma subunit of

Severe loss in rice production occurs due to damage

transcription factor IIA (TFIIAγ) and mapped on the

by pathogens such as fungus, bacteria and pests. Major

short arm of chromosome 5. The xa13 is the recessive

diseases of rice are rice blast (Magnaporthe grisea) ,

resistant locus which specifically confers resistance to

Sheath blight ( Rhizoctonia solani) and bacterial leaf

the Philippine Xanthomonas oryzae pv. oryzae race 6.

blight (BLB) ( Xanthomonas oryzae pv. oryzae) (Xoo-

The xa13 gene was first discovered in the rice variety

family Pseudomonadaceae, a rod-shaped gram-negative

BJ1 and mapped on the long arm of rice chromosome

bacterium). Bacterial leaf blight (BLB) is one of the major

8 (Ogawa et al., 1987; Zhang et al., 1996; Sanchez et

biotic destructive diseases throughout the world (Khan,

al., 1998). The xa13 has been shown to be a mutation

1996). It causes leaf wilting, affects photosynthesis and

in the promoter region of a gene that is a homolog of

reduces 1000-grain weight and generally results in yield

the nodulin MtN3 (Chu et al ., 2006) . Xa4 is a dominant

loss upto 20-50%. The chemical control of bacterial leaf

resistant locus and mapped on the terminal region of long

blight is not effective. Therefore, the preferred strategy

arm of chromosome 11. The pyramided rice lines used

for disease management is through varietal resistance.

in this study, possess R genes viz , Xa4 , xa5 , xa13 , Xa21,

Plant disease resistance is often controlled by Mendelian

in the genetic background of popular rice cultivars, IR

genetics and follows a gene-for-gene relationship in many

64, Swarna, Lalat, Tapaswini, Pusa Basmati-1 and Samba

plant species and their pathogens (Flor, 1971). In rice,

Masuri.

single-gene resistance has been the primary means of

Detection and analysis of genetic variation can help us

control of bacterial leaf blight, but unfortunately, due to

to understand the molecular basis of various biological

continuous and large-scale use of single-gene resistance,

phenomena in plants. Since the entire plant Kingdom

there has been a shift in the virulence pattern of the

cannot be covered under sequencing projects, molecular

strains, leading to breakdown of resistance (Mew et al.,

markers and their correlation to phenotypes provide

1992). One method, to delay breakdown of resistance is

us with requisite landmarks for elucidation of genetic

to provide a broad-spectrum of resistance by combining

variation. Genetic or DNA based marker techniques

multiple genes (gene pyramiding) having complementary

such as, RAPD (random amplified polymorphic DNA),

resistance spectra, relative to the pathogen sub-

SSR (simple sequence repeats) and AFLP (amplified

populations, into a single plant genotype (Babujee and

fragment length polymorphism) are routinely being used

Gnanamanickam, 2000). Gene pyramiding would result

in ecological, evolutionary, taxonomical, phylogenic and

in genotypes with more durable resistance through both

genetic studies of plant sciences. The basis of RAPD

ordinary gene action and quantitative complementation

technique is differential PCR amplification of genomic

(Ogawa et al., 1987; Yoshimura et al., 1995). A total of

DNA. It deduces DNA polymorphisms produced by

thirty five bacterial leaf blight resistance genes have been

‘‘rearrangementsordeletionsatorbetweenoligonucleotide

identified in cultivated rice and the wild relatives (Nino-

primer binding sites in the genome’’ using short random

Lui et al. , 2006; Wang et al. , 2009). Eleven of them

oligonucleotide sequences (mostly ten bases long)

are recessive resistance genes including xa5 , xa8 , xa13 ,

(Williams et al ., 1991). RAPD analysis is simple, quick to

xa15 , xa19 , xa20 , xa24 , xa28 , xa31 and xa32 (Nino et

perform, requires only small amount of DNA, relatively

al. , 2006; Singh et al. , 2007; Rao, 2003) and some are

less expensive, no need of genome sequence information,

dominant genes such as Xa1, Xa2, Xa3, Xa4, Xa7, Xa10,

can be employed across species using universal primers

Xa11, Xa12, Xa14, Xa16, Xa17, Xa18, Xa21, Xa22 etc

and provides variation data at multiple loci (Williams

(Kinoshita, 1991; Lin et al., 1996; Chun et al., 2007).

et al ., 1991). Microsatellite or SSR are monotonous

Xa21 is a dominant resistant locus that confers resistance

repetitions of very short (one to five) nucleotide motifs,

428