Global socioeconomic developments create strong incentives for farmers to shift from transplanted to direct-seeded rice (DSR) as a means of intensification and economization(1). Rice production must increase to ensure food security(2) and the bulk of this increase will have to be achieved through intensification of cultivation, because expansion of cultivated areas is reaching sustainable limits(3). Anaerobic germination tolerance, which enables uniform germination and seedling establishment under submergence(4), is a key trait for the development of tropical DSR varieties(5,6). Here, we identify a trehalose-6-phosphate phosphatase gene, OsTPP7, as the genetic determinant in qAG-9-2, a major quantitative trait locus (QTL) for anaerobic germination tolerance(7). OsTPP7 is involved in trehalose-6-phosphate (T6P) metabolism, central to an energy sensor that determines anabolism or catabolism depending on local sucrose availability(8,9). OsTPP7 activity may increase sink strength in proliferating heterotrophic tissues by indicating low sugar availability through increased T6P turnover, thus enhancing starch mobilization to drive growth kinetics of the germinating embryo and elongating coleoptile, which consequently enhances anaerobic germination tolerance.

Highlight qEMF3, a novel QTL for the early-morning flowering trait to mitigate heat-induced spikelet sterility at flowering in rice, was identified using a wild rice, Oryza officinalis, as a genetic resource.

The major rice quantitative-trait locus Submergence 1 (Sub1) confers tolerance of submergence for about 2 weeks. To identify novel sources of tolerance, we have conducted a germplasm survey with allele-specific markers targeting SUB1A and SUB1C, two of the three transcription-factor genes within the Sub1 locus. The objective was to identify tolerant genotypes without the SUB1A gene or with the intolerant SUB1A-2 allele. The survey revealed that all tolerant genotypes possessed the tolerant Sub1 haplotype (SUB1A-1/SUB1C-1), whereas all accessions without the SUB1A gene were intolerant. Only the variety James Wee with the SUB1A-2 allele was moderately tolerant. However, some intolerant genotypes with the SUB1A-1 allele were identified and RT-PCR analyses were conducted to compare gene expression in tolerant and intolerant accessions. Initial analyses of leaf samples failed to reveal a clear association of SUB1A transcript abundance and tolerance. Temporal and spatial gene expression analyses subsequently showed that SUB1A expression in nodes and internodes associated best with tolerance across representative genotypes. In James Wee, transcript abundance was high in all tissues, suggesting that some level of tolerance might be conferred by high expression of the SUB1A-2 allele. To further assess tissue-specific expression, we have expressed the GUS reporter gene under the control of the SUB1A-1 promoter. The data revealed highly specific GUS expression at the base of the leaf sheath and in the leaf collar region. Specific expression in the growing part of rice leaves is well in agreement with the role of SUB1A in suppressing leaf elongation under submergence.

The development of rice genotypes with micronutrient-dense grains and disease resistance is one of the major priorities in rice improvement programs. We conducted Genome-wide association studies (GWAS) using a Multi-parent Advanced Generation Inter-Cross (MAGIC) Plus population to identify QTLs and SNP markers that could potentially be integrated in biofortification and disease resistance breeding. We evaluated 144 MAGIC Plus lines for agronomic and biofortification traits over two locations for two seasons, while disease resistance was screened for one season in the screen house. X-ray fluorescence technology was used to measure grain Fe and Zn concentrations. Genotyping was carried out by genotype by sequencing and a total of 14,242 SNP markers were used in the association analysis. We used Mixed linear model (MLM) with kinship and detected 57 significant genomic regions with a -log10 (P-value) ≥ 3.0. The PH1.1 and Zn7.1 were consistently identified in all the four environments, ten QTLs qDF3.1, qDF6.2 qDF9.1 qPH5.1 qGL3.1, qGW3.1, qGW11.1, and qZn6.2 were detected in two environments, while two major loci qBLB11.1 and qBLB5.1 were identified for Bacterial Leaf Blight (BLB) resistance. The associated SNP markers were found to co-locate with known major genes and QTLs such as OsMADS50 for days to flowering, osGA20ox2 for plant height, and GS3 for grain length. Similarly, Xa4 and xa5 genes were identified for BLB resistance and Pi5(t), Pi28(t), and Pi30(t) genes were identified for Blast resistance. A number of metal homeostasis genes OsMTP6, OsNAS3, OsMT2D, OsVIT1, and OsNRAMP7 were co-located with QTLs for Fe and Zn. The marker-trait relationships from Bayesian network analysis showed consistency with the results of GWAS. A number of promising candidate genes reported in our study can be further validated. We identified several QTLs/genes pyramided lines with high grain Zn and acceptable yield potential, which are a good resource for further evaluation to release as varieties as well as for use in breeding programs.

Salinity tolerance in rice is critical at reproductive stage because it ultimately determines grain yield. An F2 mapping population derived from a Sadri/FL478 cross was exposed to saline field conditions (6-8 dS m(-1)) after the active tillering stage to identify reproductive stage specific QTLs for salinity tolerance. Genetic linkage map was constructed using 123 microsatellite markers on 232 F2 progenies. Totally 35 QTLs for 11 traits under salinity stress were detected with LOD > 3, out of which 28 QTLs that explained from 5.9 to 30.0% phenotypic variation were found to be significant based on permutation test. Three major QTL clusters were found on chromosomes 2 (RM423-RM174), 4 (RM551-RM518) and 6 (RM20224-RM528) for multiple traits under salinity stress. Both parental lines contributed additively for QTLs identified for the yield components. A majority of the QTLs detected in our study are reported for the first time for reproductive stage salinity stress. Fine-mapping of selected putative QTLs will be the next step to facilitate marker-assisted backcrossing and to detect useful genes for salinity tolerance at the reproductive stage in rice.