Analysis of nucleotide diversity among alleles of the major bacterial blight resistance gene Xa27 in cultivars of rice (Oryza sativa) and its wild relatives

Bimolata, Waikhom; Kumar, Anirudh; Sundaram, R. M.; Laha, G. S.; Qureshi, Insaf Ahmed; Reddy, G. Ashok; Ghazi, Irfan Ahmad

doi:10.1007/s00425-013-1891-3

Cited by 21 publications

(24 citation statements)

References 45 publications

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“…Comparison of transcript populations derived from R / S alleles (transcript is TALE activated) vs r / s (alleles transcript is not TALE activated) is in such cases an efficient method to identify TALE‐induced R or S candidate genes. However, allele mining has in the past uncovered pepper bs3 and rice xa27 alleles that due to frame‐shift mutations in their coding sequence are unable to induce defense reactions (Römer et al ., ; Bimolata et al ., ). Nonfunctional r alleles of this type are unable to induce a defense response even if these are transcriptionally activated by a given TALE.…”

Section: Cloning Of Tale‐activated Host S and R Genes – A Users Guidementioning

confidence: 97%

TAL effectors – pathogen strategies and plant resistance engineering

2014

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SummaryTranscription activator-like effectors (TALEs) from plant pathogenic Xanthomonas spp. and the related RipTALs from Ralstonia solanacearum are DNA-binding proteins with a modular DNA-binding domain. This domain is both predictable and programmable, which simplifies elucidation of TALE function in planta and facilitates generation of DNA-binding modules with desired specificity for biotechnological approaches. Recently identified TALE host target genes that either promote or stop bacterial disease provide new insights into how expression of TALE genes affects the plant-pathogen interaction. Since its elucidation the TALE code has been continuously refined and now provides a mature tool that, in combination with transcriptome profiling, allows rapid isolation of novel TALE target genes. The TALE code is also the basis for synthetic promoter-traps that mediate recognition of TALE or RipTAL proteins in engineered plants. In this review, we will summarize recent findings in plant-focused TALE research. In addition, we will provide an outline of the newly established gene isolation approach for TALE or RipTAL host target genes with an emphasis on potential pitfalls.

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Section: Cloning Of Tale‐activated Host S and R Genes – A Users Guidementioning

confidence: 97%

TAL effectors – pathogen strategies and plant resistance engineering

2014

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“…The cultivar Lota Sail had a recessive gene designated as xa28(t) for resistance to race 2. Bimolata [26] 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.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2014

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BackgroundBacterial 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.ResultsIn 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.ConclusionsThis 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.

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“…[36][37][38][39] Similar observations were made in the case of Xa21, Xa26, and xa5 alleles obtained from wild species. 40,41 Most of the alleles originating from five blast resistance genes showed non-synonymous (Ka) to synonymous (Ks) ratios ,1, indicating that they were under purifying selection, which was also evident from Tajima's D values.…”

Section: Discussionmentioning

confidence: 97%

Insights on Diversity of Leucine-Rich Repeat (LRR) Domain among Major Blast Resistance Genes of Rice

2016

Journal of Genomes and Exomes

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Rice blast is a continuous threat in rice ecosystems across the globe; its dynamics is becoming complex in the changing climatic conditions. Host resistance is still a viable option; hence, the exploration of resistance genes and their novel alleles is indispensable. The majority of the blast resistance genes belong to nucleotide-binding site and leucine-rich repeat (LRR) domain. In the present study, diverse LRR alleles of five major blast resistance genes (Pi2, Pi9, Pib, Pita, and Pi37) were cloned from 13 different Oryza species to determine the nucleotide diversity as well as to identify the single nucleotide polymorphisms, InDels, conserved domains, and protein functional sites. Although Pi9 and Pi2 are homologous genes, significant nucleotide variations and variants in the motifs distribution were observed. Among the five genes, Pi37 showed the highest nucleotide diversity and Pita showed the least diversity. The phylogenetic groups of alleles were correlated with the identified haplotypes. The motif (xxLxLxx) was present among all the alleles of blast R gene sequences across various Oryza species, indicating its importance. The appearance of post-translational modification sites in the protein sequences of these alleles also indicates its nature of involvement in host-pathogen interactions. The present study offers clues in further understanding the molecular evolution of the LRR domain of resistance genes, which is a key determinant of host-pathogen interactions.

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Analysis of nucleotide diversity among alleles of the major bacterial blight resistance gene Xa27 in cultivars of rice (Oryza sativa) and its wild relatives

Cited by 21 publications

References 45 publications

TAL effectors – pathogen strategies and plant resistance engineering

TAL effectors – pathogen strategies and plant resistance engineering

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

Insights on Diversity of Leucine-Rich Repeat (LRR) Domain among Major Blast Resistance Genes of Rice

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