Rice sheath blight (ShB), which is caused by Rhizoctonia solani, has become the most serious rice disease in China. Yangdao 4, a cultivar with partial resistance to ShB, was crossed with Lemont, a susceptible cultivar, to develop mapping populations that were used to analyze quantitative trait loci (QTL) that confer resistance to ShB. QTL analysis were performed in 3 environments (E1-E3) using 2 F2 and 1 F2:3 populations, respectively. Three traits were recorded to evaluate ShB resistance, including disease rating (DR), lesion height (LH), and percentage of lesion height (PLH). Based on field evaluation of ShB resistance and the 2 genetic maps constructed, we identified a total of 8 QTLs for DR (4 in E1, 4 in E2, and 3 in E3), 6 QTLs for LH (1 in E1, 3 in E2, and 2 in E3), and 7 QTLs for PLH (1 in E1, 4 in E2, and 2 in E3). Sixteen of the ShB-QTLs co-localized as 6 clusters on chromosomes 3, 7, 11, and 12. Four of the 6 clusters contained ShB-QTLs that were detected in 2 environments, while the other 2 clusters with ShB-QTLs were detected in 1 environment. Three ShB-QTLs (qSBD-3-2, qSBL-3-1, and qSBPL-3-1) were delimited to a 581-kb region flanked by markers D333B and D334 on chromosome 3. The resistance alleles of Yangdao 4 at the qSBD-3-2 locus decreased DR by 0.68 and 0.79 in E2 and E3, respectively.

Bakanae disease, caused by the fungus Fusarium fujikuroi, occurs widely throughout Asia and Europe and sporadically in other rice production areas. Recent changes in climate and cropping patterns have aggravated this disease. To gain a better understanding of the molecular mechanisms of rice bakanae disease resistance, we employed a 6-plex tandem mass tag approach for relative quantitative proteomic comparison of infected and uninfected rice seedlings 7 days post-inoculation with two genotypes: the resistant genotype 93–11 and the susceptible genotype Nipponbare. In total, 123 (77.2% up-regulated, 22.8% down-regulated) and 91 (94.5% up-regulated, 5.5% down-regulated) differentially expressed proteins (DEPs) accumulated in 93–11 and Nipponbare, respectively. Only 11 DEPs were both shared by the two genotypes. Clustering results showed that the protein regulation trends for the two genotypes were highly contrasting, which suggested obviously different interaction mechanisms of the host and the pathogen between 93 and 11 and Nipponbare. Further analysis showed that a noticeable aquaporin, PIP2–2, was sharply upregulated with a fold change (FC) of 109.2 in 93–11, which might be related to pathogen defense and the execution of bakanae disease resistance. Certain antifungal proteins were regulated in both 93–11 and Nipponbare with moderate FCs. These proteins might participate in protecting the cellular integrity required for basic growth of the susceptible genotype. Correlation analysis between the transcriptome and proteome revealed that Pearson correlation coefficients of R = 0.677 (P = 0.0005) and R = − 0.097 (P = 0.702) were obtained for 93–11 and Nipponbare, respectively. Our findings raised an intriguing result that a significant positive correlation only in the resistant genotype, while no correlation was found in the susceptible genotype. The differences in codon usage was hypothesized for the cause of the result. Quantitative proteomic analysis of the rice genotypes 93-11and Nipponbare after F. fujikuroi infection revealed that the aquaporin protein PIP2–2 might execute bakanae disease resistance. The difference in the correlation between the transcriptome and proteome might be due to the differences in codon usage between 93-11and Nipponbare. Overall, the protein regulation trends observed under bakanae disease stress are highly contrasting, and the molecular mechanisms of disease defense are obviously different between 93 and 11 and Nipponbare. In summary, these findings deepen our understanding of the functions of proteins induced by bakanae disease and the mechanisms of rice bakanae disease resistance.

Five physiological and eleven yield traits of two pairs of sister lines generated from a high generation with similar genetic background (SLs) for purple pericarp were investigated to explore the reasons behind low-yield production of colored rice. Of the five physiological traits examined, except grain anthocyanin content, there were generally similar trends between the P (purple-pericarp) lines and the corresponding W (white-pericarp) lines over two seasons (in the year 2009 and 2010 separately). The results demonstrated that the chlorophyll content of flag leaves, the net photosynthetic rate of flag leaves, and the grain anthocyanin content could be easily influenced by the environment. The physiological functions of the traits for the P lines were more active than those of the corresponding W lines in the year 2010. The grain anthocyanin content of the P lines was much greater in the year 2010 than in the year 2009 during the growth period. The investigation of yield traits revealed that the P lines had reduced 1000-grain weight, yield per plot and grain/brown rice thickness compared to the W lines. A difference comparison of these traits and a source-sink and transportation relationship analysis for these SLs suggested that small sink size was a key reason behind yield reduction of purple pericarp rice.