Activity-directed selection of natural variants of a receptor kinase facilitates salt-tolerant rice breeding

Reduced the kinase activity of SALT INTOLERANCE 1 in a natural variant is better-suited to maintain the balance between growth and salt tolerance in rice.

Genome-Wide Association Study Identifies a Plant-Height-Associated Gene OsPG3 in a Population of Commercial Rice Varieties

Plant height is one of the most crucial components of plant structure. However, due to its complexity, the genetic architecture of rice plant height has not been fully elucidated. In this study, we performed a genome-wide association study (GWAS) to determine rice plant height using 178 commercial rice varieties and identified 37 loci associated with rice plant height (LAPH). Among these loci, in LAPH2, we identified a polygalacturonase gene, OsPG3, which was genetically and functionally associated with rice plant height. The rice plant exhibits a super dwarf phenotype when the knockout of the OsPG3 gene occurs via CRISPR-Cas9 gene-editing technology. RNA-Seq analysis indicated that OsPG3 modulates the expression of genes involved in phytohormone metabolism and cell-wall-biosynthesis pathways. Our findings suggest that OsPG3 plays a vital role in controlling rice plant height by regulating cell wall biosynthesis. Given that rice architecture is one of the most critical phenotypes in rice breeding, OsPG3 has potential in rice's molecular design breeding toward an ideal plant height.

Suppression of Rice Osa-miR444.2 Improves the Resistance to Sheath Blight in Rice Mediating through the Phytohormone Pathway

MicroRNAs (miRNAs) are a class of conserved small RNA with a length of 21-24 nucleotides in eukaryotes, which are involved in development and defense responses against biotic and abiotic stresses. By RNA-seq, Osa-miR444b.2 was identified to be induced after Rhizoctonia solani (R. solani) infection. In order to clarify the function of Osa-miR444b.2 responding to R. solani infection in rice, transgenic lines over-expressing and knocking out Osa-miR444b.2 were generated in the background of susceptible cultivar Xu3 and resistant cultivar YSBR1, respectively. Over-expressing Osa-miR444b.2 resulted in compromised resistance to R. solani. In contrast, the knocking out Osa-miR444b.2 lines exhibited improved resistance to R. solani. Furthermore, knocking out Osa-miR444b.2 resulted in increased height, tillers, smaller panicle, and decreased 1000-grain weight and primary branches. However, the transgenic lines over-expressing Osa-miR444b.2 showed decreased primary branches and tillers, but increased panicle length. These results indicated that Osa-miR444b.2 was also involved in regulating the agronomic traits in rice. The RNA-seq assay revealed that Osa-miR444b.2 mainly regulated the resistance to rice sheath blight disease by affecting the expression of plant hormone signaling pathways-related genes such as ET and IAA, and transcription factors such as WRKYs and F-boxes. Together, our results suggest that Osa-miR444b.2 negatively mediated the resistance to R. solani in rice, which will contribute to the cultivation of sheath blight resistant varieties.

Overexpression of OsOSM1 Enhances Resistance to Rice Sheath Blight

Sheath blight (SB), caused by Rhizoctonia solani, is one of the most destructive rice diseases worldwide. It has been difficult to generate SB-resistant varieties through conventional breeding because of the quantitative nature of rice resistance to SB. In this study, we found that overexpression of the OsOSM1 gene, encoding an osmotin protein belonging to the pathogenesis-related protein 5 family, is able to improve rice resistance to SB in field tests. Although there are two osmotin genes in rice, OsOSM1 is the one mainly expressed in leaf sheath at the booting stage, coinciding with the critical stage of SB development in the field. In addition, OsOSM1 expression is strongly induced by R. solani in SB-resistant rice variety YSBR1 but not in susceptible varieties, suggesting its involvement in SB resistance. Overexpression of OsOSM1 (OsOSM1ox) in susceptible variety Xudao 3 significantly increases resistance to SB in transgenic rice. The OsOSM1 mRNA levels in different transgenic lines are found to be positively correlated with their SB resistance levels. Intriguingly, although extremely high levels of OsOSM1 were detrimental to rice development, appropriately elevated levels of OsSOM1 were obtained that enhanced rice SB resistance without affecting rice development or grain yield. The OsSOM1 protein is localized on plasma membrane. OsOSM1 is upregulated by jasmonic acid (JA); furthermore, JA-responsive marker genes are induced in OsOSM1ox lines. These results suggest that the activation of JA signaling pathway may account for the increased resistance in transgenic OsOSM1ox lines. Taken together, our results demonstrate that OsOSM1 plays an important role in defense against rice SB disease and provides a new target for engineering resistance to SB.

Overexpression of OsPGIP1 Enhances Rice Resistance to Sheath Blight

Rice sheath blight (SB), caused by necrotrophic pathogen Rhizoctonia solani, is one of the most destructive rice diseases, and no major resistance genes are available. Polygalacturonase-inhibiting proteins (PGIP) are extracellular leucine-rich repeat proteins and play important roles in plant defense against different pathogenic fungi by counteracting secreted fungal polygalacturonases (PG). However, the role of PGIP in conferring resistance to rice SB remains to be thoroughly investigated. Here, we showed that OsPGIP1 is capable of inhibiting PG derived from R. solani. Our real-time reverse-transcription polymerase chain reaction results indicated that resistant rice 'YSBR1' and 'Jasmine 85' express significantly higher levels of OsPGIP1 than susceptible 'Lemont'. Our results also show that OsPGIP1 is most highly expressed at the late tillering stage in the sheath of YSBR1, coinciding with the critical stage of SB development in field. More importantly, the OsPGIP1 level is highly elevated by inoculation with R. solani in resistant cultivars but not in susceptible Lemont. Overexpression of OsPGIP1 significantly increased rice resistance to SB and inhibited tissue degradation caused by R. solani-secreted PG. Furthermore, OsPGIP1 overexpression did not affect rice agronomic traits or yield components. Together, our results not only demonstrate the important role of OsPGIP1 in combatting the rice SB disease but also provide a new avenue to the improvement of rice SB resistance by manipulating an endogenous gene.

Comparison and Confirmation of Quantitative Trait Loci Conferring Partial Resistance to Rice Sheath Blight on Chromosome 9

Sheath blight (SB), caused by Rhizoctonia solani, is one of the worst rice (Orzya sativa) diseases worldwide. Resistance to the SB disease in rice is a complex trait controlled by quantitative trait loci (QTLs). Through map integration, we found several previously identified SB resistance (SBR) QTLs reported in inconsistent regions on the long arm of chromosome 9. Five of them were detected on 'Jasmine 85' (J85), 'Minghui 63' (MH63), and 'Lemont' (LMNT) rice and were designated qSB-9^J85-1, qSB-9^J85-2, qSB-9^MH63-1, qSB-9^MH63-2, and qSB-9^LMNT, respectively, in the present study. To further verify and physically map the five potential SBR QTLs, we introduced these SBR QTLs into a common susceptible variety (LMNT) and developed a few chromosomal segment substitution lines through marker-assisted selection. After artificial inoculation with the SB fungus, we were able to validate qSB-9^J85-2 but not the other four SBR QTLs; whereas, on MH63, an SBR QTL designated qSB-9^MH63-3 was confirmed in the region defined by markers Y83 and Y91.8 that included qSB-9^J85-2, covering approximately 1,235 kb. Both qSB-9^J85-2 and qSB-9^MH63-3 appeared to be dominant resistance genes and contributed to similar levels to SB resistance, reducing SB disease severity by approximately 1.0 on a 0-to-9 SB disease rating system. After comparing with another confirmed SBR QTL (qSB-9^TQ) from 'Teqing' rice (TQ), we conclude that qSB-9^J85-2, qSB-9^MH63-3, and qSB-9^TQ are probably controlled by the same allelic resistance genes. These results will accelerate the utilization of this major SBR QTL and its map-based cloning.

[Identification and marker-assisted selection of two major quantitative genes controlling rice sheath blight resistance in backcross generations]

We constructed an F2 clonal population of intercross,Teqing/Lemont, and identified two quantitative trait loci (QTLs) contributing to rice sheath blight resistance on chromosome 9 and 11. The two QTLs were qSB-9 and qSB-11, respectively. From the population, three clonal lines were selected by markers' band types on both sides of these two QTLs, qSB-9 and qSB-11. Two were double-susceptible parent with homozygous susceptible alleles of these two loci,and the other was named as double-resistant parent,of which these two loci were all homozygous resistant alleles. These parents were separately backcrossed to recurrent parents, Teqing or Lemont. From BC2F1, marker-assisted selection was conducted in each proceeding generation and all back-crossed plants in BC2F1 and BC4F1 were inoculated by short toothpicks incubated with a strain, RH-9 of the fungus for identification of the resistance. Results suggested that these two QTLs were selected effectively in each backcross generation and their positions were also verified in identification of resistance to rice sheath blight. In seedling nursery of BC3F2 population, plants were selected through marker-assisted selection, and were separately mixed as homozygous lines of double-susceptible alleles on the background of Teqing, double-susceptible and double-resistant on the background of Lemont. The homozygous lines and their recurrent parents were simultaneously planted on experiment fields of Agriculture Collage of Yangzhou University and Lixiahe District Institute of Agricultural Science. The inoculation was performed by a random-block test with two replicates at each site. The results indicated that 1) The difference of sheath blight disease development was highly significant among materials under the same genetic background,and the order of disease seriousness among different homozygous lines were: double-susceptible line on the background of Lemont > double-susceptible line on the background of Teqing > Lemont > Teqing > double-resistant line on the background of Lemont; 2) When the resistant allele of qSB-9 or qSB-11 solely existed in a plant, its disease rating was reduced about 1.2 score, and 2.0 score when they simultaneously existed on the background of Lemont; 3) No significant interaction between the two QTLs controlling sheath blight resistance and environments was found. These studies have laid a strong groundwork in operation and application, of these QTLs contributing to rice sheath blight resistance.