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Xa1-mediated resistance to rice bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is triggered by transcription activator-like effectors (TALEs) and suppressed by interfering TALEs (iTALEs). TALEs interact with the rice transcription factor OsTFIIAγ1 or OsTFIIAγ5 (Xa5) to activate expression of target resistance and/or susceptibility genes. However, it is not clear whether OsTFIIAγ is involved in TALE-triggered and iTALE-suppressed Xa1-mediated resistance. In this study, genome-edited mutations in OsTFIIAγ5 or OsTFIIAγ1 of Xa1-containing rice ‘IRBB1’ and Xa1-transgenic plants of xa5-containing rice ‘IRBB5’ did not impair the activation or suppression of Xa1-mediated resistance. Correspondingly, the expression pattern of Xa1 in mutated OsTFIIAγ5 and OsTFIIAγ1 rice lines and ‘IRBB1’ rice was similar. In contrast, the expression of OsSWEET11 was repressed in rice lines mutated in OsTFIIAγ5 and OsTFIIAγ1. Bimolecular fluorescence complementation (BiFC) and co-immunoprecipitation assays showed that both TALE PthXo1 and iTALE Tal3a interacted with OsTFIIAγ1 and OsTFIIAγ5 in plant nuclei. These results indicated that TALE-triggered and iTALE-suppressed Xa1-mediated resistance to bacterial blight is independent of OsTFIIAγ1 or OsTFIIAγ5 in rice, and suggest that an unknown factor is potentially involved in the interaction of Xa1, TALEs and iTALEs.

Background Bacterial blight of cotton (BBC), which is caused by the bacterium Xanthomonas citri pv. malvacearum (Xcm), is a destructive disease in cotton. Transcription activator-like effectors (TALEs), encoded by tal-genes, play critical roles in the pathogenesis of xanthomonads. Characterized strains of cotton pathogenic Xcm harbor 8–12 different tal genes and only one of them is functionally decoded. Further identification of novel tal genes in Xcm strains with virulence contributions are prerequisite to decipher the Xcm-cotton interactions. Results In this study, we identified six tal genes in Xss-V2–18, a highly-virulent strain of Xcm from China, and assessed their role in BBC. RFLP-based Southern hybridization assays indicated that Xss-V2–18 harbors the six tal genes on a plasmid. The plasmid-encoded tal genes were isolated by cloning BamHI fragments and screening clones by colony hybridization. The tal genes were sequenced by inserting a Tn5 transposon in the DNA encoding the central repeat region (CRR) of each tal gene. Xcm TALome evolutionary relationship based on TALEs CRR revealed relatedness of Xss-V2–18 to MSCT1 and MS14003 from the United States. However, Tal2 of Xss-V2–18 differs at two repeat variable diresidues (RVDs) from Tal6 and Tal26 in MSCT1 and MS14003, respectively, inferred functional dissimilarity. The suicide vector pKMS1 was then used to construct tal deletion mutants in Xcm Xss-V2–18. The mutants were evaluated for pathogenicity in cotton based on symptomology and growth in planta. Four mutants showed attenuated virulence and all contained mutations in tal2. One tal2 mutant designated M2 was further investigated in complementation assays. When tal2 was introduced into Xcm M2 and expressed in trans, the mutant was complemented for both symptoms and growth in planta, thus indicating that tal2 functions as a virulence factor in Xcm Xss-V2–18. Conclusions Overall, the results demonstrated that Tal2 is a major pathogenicity factor in Xcm strain Xss-V2–18 that contributes significantly in BBC. This study provides a foundation for future efforts aimed at identifying susceptibility genes in cotton that are targeted by Tal2.

The Gram-negative bacterium Xanthomonas translucens infects a wide range of gramineous plants with a notable impact on small grain cereals. However, genomics-informed intra-species population structure and virulence repertories of the pathogen have rarely been investigated. In this study, the complete genome sequences of seven X. translucens strains representing an entire set of genetic diversity of two pathovars X. translucens pv. undulosa and X. translucens pv. translucens is provided and compared with those of seven publicly available complete genomes of the pathogen. Organization of the 25 type III secretion system genes in all the 14 X. translucens strains was exactly the same, while TAL effector genes localized singly or in clusters across four loci in X. translucens pv. translucens and five to six loci in X. translucens pv. undulosa. Beside two previously unreported endogenous plasmids in X. translucens pv. undulosa, and variations in repeat variable diresidue (RVD) of the 14 strains, tal1a of X. translucens pv. translucens strain XtKm8 encode the new RVDs HE and YI which have not previously been reported in xanthomonads. Further, a number of truncated tal genes were predicted among the 14 genomes lacking conserved BamHI site at N-terminus and SphI site at C-terminus. Our data have doubled the number of complete genomes of X. translucens clarifying the population structure and genomics of the pathogen to pave the way in the small grain cereals industry for disease resistance breeding in the 21st century’s agriculture.

Excess Ni intake has harmful implications on human health, which include chronic bronchitis, reduced lung function, and cancer of lung and nasal sinuses. Like other toxic metals, higher Ni accumulation in grains leads to excess intake by humans when the contaminated grains are consumed as food. There is little information about the genetic factors that regulate Ni uptake in plants. To investigate genetic architecture of Ni uptake in leaf and translocation to grain, we performed a genome-wide association study with genotyping from 90 K array in a historical bread wheat diversity panel from Pakistan. We observed that Ni toxicity caused more than 50 % reductions in biological yield and grain yield, other agronomic traits were also partly or severely affected. Genetic association study helped identify 23 SNP-trait associations involved in Ni uptake in leaf and translocation to grains. These 23 SNPs covered 15 genomic loci at chromosomes 1A, 2D, 3B, 4A and 4B of wheat. The favorable alleles of these SNPs were randomly distributed in subpopulations indicating no selection pressure for this trait during breeding improvement. These regions had 283 low-confidence and 248 high-confidence protein coding genes. Among these, 156 were annotated using databases of wheat and closely related grass species. Since there is no previous report on genetic information of Ni uptake and translocation, these results provide sufficient grounds for further research of candidate genes and varietal development.

Xanthomonas translucens pv. cerealis (Xtc) causes bacterial leaf streak (BLS) of important cereal crops, including wheat (Triticum aestivum) and barley (Hordeum vulgare). Transcription activator-like effectors (TALEs) play vital roles in many plant diseases caused by Xanthomonas spp., however, TALEs have not been previously characterized in Xtc. In this study, the whole genome of NXtc01, a virulent strain of Xtc from Xinjiang, China, was sequenced and compared with genomes of other Xanthomonas spp. Xtc NXtc01 consists of a single 4,622,298 bp chromosome that encodes 4,004 genes. Alignment of the NXtc01 sequence with the draft genome of Xtc strain CFBP 2541 (United States) revealed a single giant inversion and differences in the location of two tal genes, which were designated tal1 and tal2. In NXtc01, both tal genes are located on the chromosome, whereas tal2 is plasmid-encoded in CFBP 2541. The repeat variable diresidues (RVDs) at the 12th and 13th sites within Tal2 repeat units were identical in both strains, whereas Tal1 showed differences in the third RVD. Xtc NXtc01 and CFBP 2541 encoded 35 and 33 non-TALE type III effectors (T3Es), respectively. tal1, tal2, and tal-free deletion mutants of Xtc NXtc01 were constructed and evaluated for virulence. The tal1 and tal-free deletion mutants were impaired with respect to symptom development and growth in wheat, suggesting that tal1 is a virulence factor in NXtc01. This was confirmed in gain-of-function experiments that showed the introduction of tal1, but not tal2, restored virulence to the tal-free mutant. Furthermore, we generated a hrcC deletion mutant of NXtc01; the hrcC mutant was non-pathogenic on wheat and unable to elicit a hypersensitive response in the non-host Nicotiana benthamiana. Our data provide a platform for exploring the roles of both TALEs and non-TALEs in promoting BLS on wheat.