Improving the salt tolerance of direct-seeding rice at the seed germination stage is a major breeding goal in many Asian rice-growing countries, where seedlings must often establish in soils with a high salt content. Thus, it is important to understand the genetic mechanisms of salt tolerance in rice and to screen for germplasm with salt tolerance at the seed germination stage. Here, we investigated seven seed germination-related traits under control and salt-stress conditions and conducted a genome-wide association study based on the re-sequencing of 478 diverse rice accessions. The analysis used a mixed linear model and was based on 6,361,920 single nucleotide polymorphisms in 478 rice accessions grouped into whole, indica, and non-indica panels. Eleven loci containing 22 significant salt tolerance-associated single nucleotide polymorphisms were identified based on the stress-susceptibility indices (SSIs) of vigor index (VI) and mean germination time (MGT). From the SSI of VI, six major loci were identified, explaining 20.2% of the phenotypic variation. From the SSI of MGT, five major loci were detected, explaining 26.4% of the phenotypic variation. Of these, seven loci on chromosomes 1, 5, 6, 11, and 12 were close to six previously identified quantitative gene loci/genes related to tolerance to salinity or other abiotic stresses. The strongest association region for the SSI of MGT was identified in a ~ 13.3 kb interval (15450039–15,463,330) on chromosome 1, near salt-tolerance quantitative trait loci controlling the Na+: K+ ratio, total Na+ uptake, and total K+ concentration. The strongest association region for the SSI of VI was detected in a ~ 164.2 kb interval (526662–690,854) on chromosome 2 harboring two nitrate transporter family genes (OsNRT2.1 and OsNRT2.2), which affect gene expression under salt stress. The haplotype analysis indicated that OsNRT2.2 was associated with subpopulation differentiation and its minor/rare tolerant haplotype was detected. These results provide valuable information for salt tolerance-related gene cloning and for understanding the genetic mechanisms of salt tolerance at the seed germination stage. This information will be useful to improve the salt tolerance of direct-seeding rice varieties by genomic selection or marker-assisted selection.

Rice (Oryza sativa. L) is more sensitive to drought stress than other cereals, and large genotypic variation in drought tolerance (DT) exists within the cultivated rice gene pool and its wild relatives. Selective introgression of DT donor segments into a drought-sensitive (DS) elite recurrent parent by backcrossing is an effective way to improve drought stress tolerance in rice. To dissect the molecular mechanisms underlying DT in rice, deep transcriptome sequencing was used to investigate transcriptome differences among a DT introgression line H471, the DT donor P28, and the drought-sensitive, recurrent parent HHZ under drought stress. The results revealed constitutively differential gene expression before stress and distinct global transcriptome reprogramming among the three genotypes under a time series of drought stress, consistent with their different genotypes and DT phenotypes. A set of genes with higher basal expression in both H471 and P28 compared with HHZ were functionally enriched in oxidoreductase and lyase activities, implying their positive role in intrinsic DT. Gene Ontology analysis indicated that common up-regulated genes in all three genotypes under mild drought stress were enriched in signaling transduction and transcription regulation. Meanwhile, diverse functional categories were characterized for the commonly drought-induced genes in response to severe drought stress. Further comparative transcriptome analysis between H471 and HHZ under drought stress found that introgression caused wide-range gene expression changes; most of the differentially expressed genes (DEGs) in H471 relative to HHZ under drought were beyond the identified introgressed regions, implying that introgression resulted in novel changes in expression. Co-expression analysis of these DEGs represented a complex regulatory network, including the jasmonic acid and gibberellin pathway, involved in drought stress tolerance in H471. Comprehensive gene expression profiles revealed that genotype-specific drought induced genes and genes with higher expression in the DT genotype under normal and drought conditions contribute jointly to DT improvement. The molecular genetic pathways of drought stress tolerance uncovered in this study, as well as the DEGs co-localized with DT-related QTLs and introgressed intervals, will serve as useful resources for further functional dissection of the molecular mechanisms of drought stress response in rice.

Improving the salt-tolerance of direct-seeding rice at the seed germination stage is a major goal of breeders. Efficiently identifying salt tolerance loci will help researchers develop effective rice breeding strategies. In this study, six multi-locus genome-wide association studies (GWAS) methods (mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, pKWmEB, and ISIS EM-BLASSO) were applied to identify quantitative trait nucleotides (QTNs) for the salt tolerance traits of 478 rice accessions with 162,529 SNPs at the seed germination stage. Among the 371 QTNs detected by the six methods, 56 were identified by at least three methods. Among these 56 QTNs, 12, 6, 7, 4, 13, 12, and 12 were found to be associated with SSI-GI, SSI-VI, SSI-MGT, SSI-IR-24h, SSI-IR-48h, SSI-GR-5d, and SSI-GR-10d, respectively. Additionally, 66 candidate genes were identified in the vicinity of the 56 QTNs, and two of these genes (LOC_Os01g45760 and LOC_Os10g04860) are involved in auxin biosynthesis according to the enriched GO terms and KEGG pathways. This information will be useful for identifying the genes responsible for rice salt tolerance. A comparison of the six methods revealed that ISIS EM-BLASSO identified the most co-detected QTNs and performed best, with the smallest residual errors and highest computing speed, followed by FASTmrMLM, pLARmEB, mrMLM, pKWmEB, and FASTmrEMMA. Although multi-locus GWAS methods are superior to single-locus GWAS methods, their utility for identifying QTNs may be enhanced by adding a bin analysis to the models or by developing a hybrid method that merges the results from different methods.

Background: Sheath blight (ShB), caused by Rhizoctonia solani Kühn, is one of the most destructive rice diseases. Developing ShB-resistant rice cultivars represents the most economical and environmentally sound strategy for managing ShB. Results: To characterize the genetic basis for ShB resistance in rice, we conducted association studies for traits related to ShB resistance, namely culm length (CL), lesion height (LH), and relative lesion height (RLH). Combined a single locus genome-wide scan and a multi-locus method using 2,977,750 single-nucleotide polymorphisms to analyse 563 rice accessions, we detected 134, 562, and 75 suggestive associations with CL, LH, and RLH, respectively. The adjacent signals associated with RLH were merged into 27 suggestively associated loci (SALs) based on the estimated linkage disequilibrium blocks. More than 44% of detected RLH-SALs harboured multiple QTLs/genes associated with ShB resistance, while the other RLH-SALs were putative novel ShB resistance loci. A total of 261 ShB resistance putative functional genes were screened from 23 RLH-SALs according to bioinformatics and haplotype analyses. Some of the annotated genes were previously reported to encode defence-related and pathogenesis-related proteins, suggesting that quantitative resistance to ShB in rice is mediated by SA- and JA-dependent signalling pathways. Conclusions: Our findings may improve the application of germplasm resources as well as knowledge-based ShB management and the breeding of ShB-resistant rice cultivars.

A 1D/2D genome-wide association study strategy was adopted to investigate the genetic systems underlying the reciprocal adaptation of rice (Oryza sativa) and its bacterial pathogen, Xanthomonas oryzae pv. oryzae (Xoo) using the whole-genome sequencing and large-scale phenotyping data of 701 rice accessions and 23 diverse Xoo strains. Forty-seven Xoo virulence-related genes and 318 rice quantitative resistance genes (QR-genes) mainly located in 41 genomic regions, and genome-wide interactions between the detected virulence-related genes and QR genes were identified, including well-known resistance genes/virulence genes plus many previously uncharacterized ones. The relationship between rice and Xoo was characterized by strong differentiation among Xoo races corresponding to the subspecific differentiation of rice, by strong shifts toward increased resistance/virulence of rice/Xoo populations and by rich genetic diversity at the detected rice QR-genes and Xoo virulence genes, and by genome-wide interactions between many rice QR-genes and Xoo virulence genes in a multiple-to-multiple manner, presumably resulting either from direct protein–protein interactions or from genetic epistasis. The observed complex genetic interaction system between rice and Xoo likely exists in other crop–pathogen systems that would maintain high levels of diversity at their QR-loci/virulence-loci, resulting in dynamic coevolutionary consequences during their reciprocal adaptation.