Abstract
Nucleotide sequence polymorphisms among R gene alleles influence the process of co-evolutionary interaction between host and pathogen by shaping the response of host plants towards invading pathogens. Here, we present the DNA sequence polymorphisms and diversities present among natural alleles of three rice bacterial blight resistance genes, Xa21, Xa26 and xa5. The diversity was examined across different wild relatives and cultivars of Oryza species. Functional significance of selected alleles was evaluated through semi-quantitative reverse transcription polymerase chain reaction and real time PCR. The greatest nucleotide diversity and singleton variable sites (SVS) were present in Xa26 (π = 0.01958; SVS = 182) followed by xa5 and Xa21 alleles. The highest frequency of single nucleotide polymorphisms were observed in Xa21 alleles and least in xa5. Transition bias was observed in all the genes and ‘G’ to ‘A’ transitions were more favored than other form of transitions. Neutrality tests failed to show the presence of selection at these loci, though negative Tajima’s D values indicate the presence of a rare form of polymorphisms. At the interspecies level, O. nivara exhibited more diversity than O. sativa. We have also identified two nearly identical resistant alleles of xa5 and two sequentially identical alleles of Xa21. The alleles of xa5 showed basal levels of expression while Xa21 alleles were functionally not expressed.
Highlights
Plants are constantly exposed to various biotic stresses like insect pests and pathogens and have evolved several mechanisms to guard themselves these stresses
There were a total of 196 mutations, 191 segregating sites, 113 parsimony informative sites, 64 insertions and deletions (InDel) events and 78 singleton variable sites within the entire sequenced region
The single nucleotide polymorphism (SNPs) frequency was higher in O. sativa with one SNP per 51.9 bp and one SNP per 55.25 bp in O. nivara
Summary
Plants are constantly exposed to various biotic stresses like insect pests and pathogens and have evolved several mechanisms to guard themselves these stresses. As pathogens challenge the fitness of the plant, they are regarded as natural selective agents shaping evolutionary dynamics of host-pathogen co-evolution [1, 2]. Infections by pathogens influence yield, morphology, grain quality and texture [3]. Bacterial blight (BB) is a major disease of rice caused by Xanthomonas oryzae pv. The annual yield loss by this disease is recorded. PLOS ONE | DOI:10.1371/journal.pone.0120186 March 25, 2015
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