Summary: The genetic improvement of rice eating and cooking quality (ECQ) is an important goal in rice breeding. It is important to understand the genetic regulation of ECQ at the genomic level for effective breeding to improve ECQ. However, the mechanisms underlying the improvement of ECQ of indica and japonica cultivars in southern China remain unclear. In this study, 290 rice cultivars (155 indica and 135 japonica cultivars) bred in southern China in the past 30 years were collected. Physicochemical indicators, namely, apparent amylose content (AAC), protein content (PC), lipid content and taste value, were measured and correlation analysis was performed. A decrease in AAC and PC was a crucial factor for the ECQ improvement of the rice cultivars in southern China. Genome‐wide association analysis and selective domestication analysis preliminarily clarified that the comprehensive utilization of major and minor genes was an important genetic basis for improvement of ECQ. An elite allele, RAmy1A^A, with potential application in breeding to improve starch viscosity characteristics and ECQ, was mined. The Wx^b/OsmtSSB1L^T/OsDML4^G/RPBF^T/Du3^T and Wx^b/OsEro1^T/Glup3^G/OsNAC25^G/OsBEIIb^C/RAmy1A^A/FLO12^A gene modules, neither of which have been widely used, are proposed as the optimal allele combinations for ECQ improvement of indica and japonica cultivars in southern China. The results clarify the genetic regulation of rice ECQ improvement in southern China and provide novel genetic resources and breeding strategies for ECQ improvement in rice.

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.

Rice blast, caused by the Magnaporthe oryzae fungus, is one of the most devastating rice diseases worldwide. Developing resistant varieties by pyramiding different blast resistance (R) genes is an effective approach to control the disease. However, due to complex interactions among R genes and crop genetic backgrounds, different R-gene combinations may have varying effects on resistance. Here, we report the identification of two core R-gene combinations that will benefit the improvement of Geng (Japonica) rice blast resistance. We first evaluated 68 Geng rice cultivars at seedling stage by challenging with 58 M. oryzae isolates. To evaluate panicle blast resistance, we inoculated 190 Geng rice cultivars at boosting stage with five groups of mixed conidial suspensions (MCSs), with each containing 5–6 isolates. More than 60% cultivars displayed moderate or lower levels of susceptibility to panicle blast against the five MCSs. Most cultivars contained two to six R genes detected by the functional markers corresponding to 18 known R genes. Through multinomial logistics regression analysis, we found that Pi-zt, Pita, Pi3/5/I, and Pikh loci contributed significantly to seedling blast resistance, and Pita, Pi3/5/i, Pia, and Pit contributed significantly to panicle blast resistance. For gene combinations, Pita+Pi3/5/i and Pita+Pia yielded more stable pyramiding effects on panicle blast resistance against all five MCSs and were designated as core R-gene combinations. Up to 51.6% Geng cultivars in the Jiangsu area contained Pita, but less than 30% harbored either Pia or Pi3/5/i, leading to less cultivars containing Pita+Pia (15.8%) or Pita+Pi3/5/i (5.8%). Only a few varieties simultaneously contained Pia and Pi3/5/i, implying the opportunity to use hybrid breeding procedures to efficiently generate varieties with either Pita+Pia or Pita+Pi3/5/i. This study provides valuable information for breeders to develop Geng rice cultivars with high resistance to blast, especially panicle blast.

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.

Rice (Oryza sativa L.) bacterial leaf streak (BLS) caused by Xanthomonas oryzae pv. oryzicola (Xoc) seriously threatens rice production. This disease can be controlled by cultivating lines with appropriate resistance genes. To discover new resistance loci, a natural population of 246 sequenced backbone varieties of indica rice was inoculated with Xoc in the field, and their disease level was evaluated. The population structure, distribution of resistance phenotypes, and effect of combinations of resistance genes were analyzed in a genome-wide association study. On the basis of single nucleotide polymorphism data and disease phenotypes at the seedling stage, seven resistance loci (qBls1.1, qBls4.1, qBls5.1, qBls7.1, qBls8.1, qBls9.1, and qBls12.1) were identified to determine the superior haplotype of the corresponding loci, which showed stronger BLS resistance. The effects of combining loci were analyzed. As the number of superior haplotypes increased, BLS resistance tended to increase, indicating that BLS resistance can be significantly improved by pyramiding multiple resistance loci in ideal germplasm. This study provides new resistance loci and genetic resources for breeding BLS-resistant rice varieties. These genetic resources will be useful for the fine mapping of resistance loci, gene cloning, and the breeding of BLS-resistant varieties in follow-up research.