Characterization of a disease susceptibility locus for exploring an efficient way to improve rice resistance against bacterial blight

Genome-Wide Identification of the Rose SWEET Gene Family and Their Different Expression Profiles in Cold Response between Two Rose Species

Sugars Will Eventually be Exported Transporter (SWEET) gene family plays indispensable roles in plant physiological activities, development processes, and responses to biotic and abiotic stresses, but no information is known for roses. In this study, a total of 25 RcSWEET genes were identified in Rosa chinensis 'Old Blush' by genome-wide analysis and clustered into four subgroups based on their phylogenetic relationships. The genomic features, including gene structures, conserved motifs, and gene duplication among the chromosomes of RcSWEET genes, were characterized. Seventeen types of cis-acting elements among the RcSWEET genes were predicted to exhibit their potential regulatory roles during biotic and abiotic stress and hormone responses. Tissue-specific and cold-response expression profiles based on transcriptome data showed that SWEETs play widely varying roles in development and stress tolerance in two rose species. Moreover, the different expression patterns of cold-response SWEET genes were verified by qRT-PCR between the moderately cold-resistant species R. chinensis 'Old Blush' and the extremely cold-resistant species R. beggeriana. Especially, SWEET2a and SWEET10c exhibited species differences after cold treatment and were sharply upregulated in the leaves of R. beggeriana but not R. chinensis 'Old Blush', indicating that these two genes may be the crucial candidates that participate in cold tolerance in R. beggeriana. Our results provide the foundation for function analysis of the SWEET gene family in roses, and will contribute to the breeding of cold-tolerant varieties of roses.

Deployment of Genetic and Genomic Tools Toward Gaining a Better Understanding of Rice-Xanthomonas oryzae pv. oryzae Interactions for Development of Durable Bacterial Blight Resistant Rice

Rice is the most important food crop worldwide and sustainable rice production is important for ensuring global food security. Biotic stresses limit rice production significantly and among them, bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae (Xoo) is very important. BB reduces rice yields severely in the highly productive irrigated and rainfed lowland ecosystems and in recent years; the disease is spreading fast to other rice growing ecosystems as well. Being a vascular pathogen, Xoo interferes with a range of physiological and biochemical exchange processes in rice. The response of rice to Xoo involves specific interactions between resistance (R) genes of rice and avirulence (Avr) genes of Xoo, covering most of the resistance genes except the recessive ones. The genetic basis of resistance to BB in rice has been studied intensively, and at least 44 genes conferring resistance to BB have been identified, and many resistant rice cultivars and hybrids have been developed and released worldwide. However, the existence and emergence of new virulent isolates of Xoo in the realm of a rapidly changing climate necessitates identification of novel broad-spectrum resistance genes and intensification of gene-deployment strategies. This review discusses about the origin and occurrence of BB in rice, interactions between Xoo and rice, the important roles of resistance genes in plant's defense response, the contribution of rice resistance genes toward development of disease resistance varieties, identification and characterization of novel, and broad-spectrum BB resistance genes from wild species of Oryza and also presents a perspective on potential strategies to achieve the goal of sustainable disease management.

Engineering Broad-Spectrum Bacterial Blight Resistance by Simultaneously Disrupting Variable TALE-Binding Elements of Multiple Susceptibility Genes in Rice

Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial blight of rice, employs the transcription activator-like effectors (TALEs) to induce the expression of the OsSWEET family of putative sugar transporter genes, which function in conferring disease susceptibility (S) in rice plants. To engineer broad-spectrum bacterial blight resistance, we used CRISPR/Cas9-mediated gene editing to disrupt the TALE-binding elements (EBEs) of two S genes, OsSWEET11 and OsSWEET14, in rice cv. Kitaake, which harbors the recessive resistance allele of Xa25/OsSWEET13. The engineered rice line MS14K exhibited broad-spectrum resistance to most Xoo strains with a few exceptions, suggesting that the compatible strains may contain new TALEs. We identified two PthXo2-like TALEs, Tal5_LN18 and Tal7_PXO61, as major virulence factors in the compatible Xoo strains LN18 and PXO61, respectively, and found that Xoo encodes at least five types of PthXo2-like effectors. Given that PthXo2/PthXo2.1 target OsSWEET13 for transcriptional activation, the genomes of 3000 rice varieties were analyzed for EBE variationsin the OsSWEET13 promoter, and 10 Xa25-like haplotypes were identified. We found that Tal5_LN18 and Tal7_PXO61 bind slightly different EBE sequences in the OsSWEET13 promoter to activate its expression. CRISPR/Cas9 technology was then used to generate InDels in the EBE of the OsSWEET13 promoter in MS14K to creat a new germplasm with three edited OsSWEET EBEs and broad-spectrum resistance against all Xoo strains tested. Collectively, our findings illustrate how to disarm TALE-S co-evolved loci to generate broad-spectrum resistance through the loss of effector-triggered susceptibility in plants.

Diagnostic kit for rice blight resistance

Blight-resistant rice lines are the most effective solution for bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo). Key resistance mechanisms involve SWEET genes as susceptibility factors. Bacterial transcription activator-like (TAL) effectors bind to effector-binding elements (EBEs) in SWEET gene promoters and induce SWEET genes. EBE variants that cannot be recognized by TAL effectors abrogate induction, causing resistance. Here we describe a diagnostic kit to enable analysis of bacterial blight in the field and identification of suitable resistant lines. Specifically, we include a SWEET promoter database, RT–PCR primers for detecting SWEET induction, engineered reporter rice lines to visualize SWEET protein accumulation and knock-out rice lines to identify virulence mechanisms in bacterial isolates. We also developed CRISPR–Cas9 genome-edited Kitaake rice to evaluate the efficacy of EBE mutations in resistance, software to predict the optimal resistance gene set for a specific geographic region, and two resistant ‘mega’ rice lines that will empower farmers to plant lines that are most likely to resist rice blight.

Strategic deployment of blight-resistant rice lines is enabled by a molecular diagnostic kit.

Effects of tillage managements and maize straw returning on soil microbiome using 16S rDNA sequencing

Agricultural practices could affect bacterial diversity and community structure by altering soil physical and chemical properties. Straw returning and tillage practices are widely used in agriculture, however, the effects of these agricultural practices on microbiomes are still unclear. In the present study, we compared the 18 bacterial communities of soil with different straw returning and tillage treatment combinations. The V3-V4 regions of the 16S ribosomal RNA were amplified and analyzed by high-throughput sequencing technology. The results showed that the bacterial communities were consistently dominated by Acidobacteria, Proteobacteria, Actinobacteria, and Chloroflexi. Short-term straw returning and tillage practices significantly altered the diversity, relative abundance and functions of the soil microbiome. Soil subjected to rotary tillage and straw returning (RTS) combination possessed the highest bacterial diversity and lowest ratio of G+/G- bacteria, indicating that RTS could be an efficient integrated management system to improve microbiome in the short term. Double verifications based on relative abundance and network analysis, revealed close relationships of Mycobacterium and Methylibium with RTS, indicating they could serve as biomarkers for RTS. Investigating microbial changes under different agricultural practices will provide valuable foundations for land sustainable utilization and increase crop yields.

Pooled DNA sequencing to identify SNPs associated with a major QTL for bacterial wilt resistance in Italian ryegrass (Lolium multiflorum Lam.)

SNPs and candidate genes associated with bacterial wilt resistance in Italian ryegrass were identified by sequencing the parental plants and pooled F₁ progeny of a segregating population. Italian ryegrass (Lolium multiflorum Lam.) is one of the most important forage grass species in temperate regions. Its yield, quality and persistency can significantly be reduced by bacterial wilt, a serious disease caused by Xanthomonas translucens pv. graminis. Although a major QTL for bacterial wilt resistance has previously been reported, detailed knowledge on underlying genes and DNA markers to allow for efficient resistance breeding strategies is currently not available. We used pooled DNA sequencing to characterize a major QTL for bacterial wilt resistance of Italian ryegrass and to develop inexpensive sequence-based markers to efficiently target resistance alleles for marker-assisted recurrent selection. From the mapping population segregating for the QTL, DNA of 44 of the most resistant and 44 of the most susceptible F₁ individuals was pooled and sequenced using the Illumina HiSeq 2000 platform. Allele frequencies of 18 × 10⁶ single nucleotide polymorphisms (SNP) were determined in the resistant and susceptible pool. A total of 271 SNPs on 140 scaffold sequences of the reference parental genome showed significantly different allele frequencies in both pools. We converted 44 selected SNPs to KASP™ markers, genetically mapped these proximal to the major QTL and thus validated their association with bacterial wilt resistance. This study highlights the power of pooled DNA sequencing to efficiently target binary traits in biparental mapping populations. It delivers genome sequence data, SNP markers and potential candidate genes which will allow to implement marker-assisted strategies to fix bacterial wilt resistance in outcrossing breeding populations of Italian ryegrass.

Natural variations in the promoter of OsSWEET13 and OsSWEET14 expand the range of resistance against Xanthomonas oryzae pv. oryzae

Bacterial blight, caused by Xanthomonas oryzae pv. oryzae (Xoo), is one of the major diseases that impact rice production in Asia. The bacteria use transcription activator-like effectors (TALEs) to hijack the host transcription machinery and activate key susceptibility (S) genes, specifically members of the SWEET sucrose uniporters through the recognition of effector-binding element (EBEs) in the promoter regions. However, natural variations in the EBEs that alter the binding affinity of TALEs usually prevent sufficient induction of SWEET genes, leading to resistance phenotypes. In this study, we identified candidate resistance alleles by mining a rice diversity panel for mutations in the promoter of OsSWEET13 and OsSWEET14, which are direct targets of three major TALEs PthXo2, PthXo3 and AvrXa7. We found natural variations at the EBE of both genes, which appeared to have emerged independently in at least three rice subspecies. For OsSWEET13, a 2-bp deletion at the 5th and 6th positions of the EBE, and a substitution at the 17th position appear to be sufficient to prevent activation by PthXo2. Similarly, a single nucleotide substitution at position 10 compromised the induction of OsSWEET14 by AvrXa7. These findings might increase our opportunities to reduce pathogen virulence by preventing the induction of SWEET transporters. Pyramiding variants along with other resistance genes may provide durable and broad-spectrum resistance to the disease.

Factores que afectan la expresión transitoria del gen GUS en yuca (Manihot esculenta Crantz)

La expresión transitoria es una métodología ampliamente utilizada para el estudio de genes. Sin embargo, hasta la fecha no existe un reporte en donde se utilice esta técnica en hojas de yuca de plantas adultas. Por esta razón este trabajo se centró en la determinación de algunos parámetros críticos para la expresión transitoria del gen GUS en yuca como son: la metodología para introducir la bacteria, la cepa de Agrobacterium, el tiempo post-inoculación, la introducción del gen VirG y la expresión del gen GUS en algunas variedades de yuca. Los resultados indicaron niveles más altos de expresión del gen GUS entre 5-7 días post-inoculación (dpi), agroinfiltrando con la cepa GV3101 y un incremento en la virulencia de esta cepa mediante la introducción del gen VirG. Por último se observaron diferentes niveles de expresión del gen GUS entre las variedades de yuca evaluadas, lo que indica que el factor genético es clave en la eficiencia de la agroinfiltración en este cultivo.

Rice Transcription Factor OsDOF11 Modulates Sugar Transport by Promoting Expression of Sucrose Transporter and SWEET Genes

Sucrose is produced in mesophyll cells and transferred into phloem cells before it is delivered long-distance to sink tissues. However, little is known about how sucrose transport is regulated in plants. Here, we identified a T-DNA insertional mutant of Oryza sativa DNA BINDING WITH ONE FINGER 11 (OsDOF11), which is expressed in the vascular cells of photosynthetic organs and in various sink tissues. The osdof11 mutant plants are semi-dwarf and have fewer tillers and smaller panicles as compared with wild-type (WT) plants. Although sucrose enhanced root elongation in young WT seedlings, this enhancement did not occur in osdof11 seedlings due to reduced sucrose uptake. Sugar transport rate analyses revealed that less sugar was transported in osdof11 plants than in the WT. Expression of four Sucrose Transporter (SUT) genes-OsSUT1, OsSUT3, OsSUT4, and OsSUT5-as well as two Sugars Will Eventually be Exported Transporters (SWEET) genes, OsSWEET11 and OsSWEET14, was altered in various organs of the mutant, including the leaves. Chromatin immunoprecipitation assays showed that OsDOF11 directly binds the promoter regions of SUT1, OsSWEET11, and OsSWEET14, indicating that the expression of these transporters responsible for sucrose transport via apoplastic loading is coordinately controlled by OsDOF11. We also observed that osdof11 mutant plants were less susceptible to infection by Xanthomonas oryzae pathovar oryzae, suggesting that OsDOF11 participates in sugar distribution during pathogenic invasion. Collectively, these results suggest that OsDOF11 modulates sugar transport by regulating the expression of both SUT and SWEET genes in rice.

Dominant and Recessive Major R Genes Lead to Different Types of Host Cell Death During Resistance to Xanthomonas oryzae in Rice

The bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is the most devastating bacterial disease of rice worldwide. A number of dominant major disease resistance (MR) genes and recessive MR genes against Xoo have been cloned and molecularly characterized in the last two decades. However, how these MR genes mediated-resistances occur at the cytological level is largely unknown. Here, by ultrastructural examination of xylem parenchyma cells, we show that resistances to Xoo conferred by dominant MR genes and recessive MR genes resulted in different types of programmed cell death (PCD). Three dominant MR genes Xa1, Xa4, and Xa21 and two recessive MR genes xa5 and xa13 that encode very different proteins were used in this study. We observed that Xa1-, Xa4-, and Xa21-mediated resistances to Xoo were associated mainly with autophagy-like cell death featured by the formation of autophagosome-like bodies in the xylem parenchyma cells. In contrast, the xa5- and xa13-mediated resistances to Xoo were associated mainly with vacuolar-mediated cell death characterized by tonoplast disruption of the xylem parenchyma cells. Application of autophagy inhibitor 3-methyladenine partially compromised Xa1-, Xa4-, and Xa21-mediated resistances, as did Na₂HPO₄ alkaline solution to xa5- and xa13-mediated resistances. These results suggest that autophagy-like cell death is a feature of the dominant MR gene-mediated resistance to Xoo and vacuolar-mediated cell death is a characteristic of the recessive MR gene-mediated resistance.