Background: Soil salinity is one of the main environmental conditions that affects rice production. Identifying the genetic loci that affect rice salt tolerance (ST)-related traits at the seedling stage, especially under saline field conditions, is crucial for ST rice breeding by pyramiding ST genes that act at different developmental stages. Results: Large phenotypic variations were observed in 708 rice accessions, and yield and its related traits were considerably limited when exposed to salt stress. In a genome-wide association study (GWAS), 2255 marker-trait association signals were detected for all measured traits, and the significant SNPs were distributed in 903 genes. Of these, 43 genes processed same functional annotation, and the gene ontology terms “biological processes” and “molecular function” with the known genes responsive to salt stress in rice. Further haplotype analysis detected 15 promising candidates significantly associated with the target traits, including five known genes and 10 novel genes. We identified seven accessions carrying favorable haplotypes of four genes significantly associated with grain yield that performed well under saline stress conditions. Conclusions: Using high density SNPs within genes to conduct GWAS is an effective way to identify candidate genes for salt tolerance in rice. Five known genes (OsMYB6, OsGAMYB, OsHKT1;4, OsCTR3, and OsSUT1) and two newly identified genes (LOC_Os02g49700, LOC_Os03g28300) significantly associated with grain yield and its related traits under saline stress conditions were identified. These promising candidates provide valuable resources for validating potential ST-related genes and will facilitate rice breeding for salt tolerance through marker-assisted selection.

Grain appearance quality and milling quality are the main determinants of market value of rice. Breeding for improved grain quality is a major objective of rice breeding worldwide. Identification of genes/QTL controlling quality traits is the prerequisite for increasing breeding efficiency through marker-assisted selection. Here, we reported a genome-wide association study in indica rice to identify QTL associated with 10 appearance and milling quality related traits, including grain length, grain width, grain length to width ratio, grain thickness, thousand grain weight, degree of endosperm chalkiness, percentage of grains with chalkiness, brown rice rate, milled rice rate and head milled rice rate. A diversity panel consisting of 272 indica accessions collected worldwide was evaluated in four locations including Hangzhou, Jingzhou, Sanya and Shenzhen representing indica rice production environments in China and genotyped using genotyping-by-sequencing and Diversity Arrays Technology based on next-generation sequencing technique called DArTseq™. A wide range of variation was observed for all traits in all environments. A total of 16 different association analysis models were compared to determine the best model for each trait-environment combination. Association mapping based on 18,824 high quality markers yielded 38 QTL for the 10 traits. Five of the detected QTL corresponded to known genes or fine mapped QTL. Among the 33 novel QTL identified, qDEC1.1 (qGLWR1.1), qBRR2.2 (qGL2.1), qTGW2.1 (qGL2.2), qGW11.1 (qMRR11.1) and qGL7.1 affected multiple traits with relatively large effects and/or were detected in multiple environments. The research provided an insight of the genetic architecture of rice grain quality and important information for mining genes/QTL with large effects within indica accessions for rice breeding.

Prevalent irregular rainfall, flooding for weed control, and unleveled fields in the middle and lower reaches of the Yangtze River all contribute to flooding stress on germination and growth of direct‐seeded rice (Oryza sativa L.). Herein, some experiments were conducted so as to assess the effects of seed priming with selenium (Se) on the germination and growth of rice under hypoxia. The experiment was arranged in a completely randomized factorial design with two factors and five replicates. Factors included Se concentration (0, 30, and 60 μmol/L) and duration of flooding stress (0, 2, 4, and 8 days). The experimental results showed that Se accelerated seed germination and increased emergence index and final emergence percentage. Additionally, Se increased shoot and root lengths and dry weights, but high Se concentration (60 μmol/L) reduced 18‐day‐old seedling dry weight under long‐term flooding (8 days). Furthermore, Se reduced malondialdehyde content and increased starch hydrolysis efficiency in seeds, superoxide dismutase, peroxidase, catalase, and glutathione peroxidase activities and seedling soluble protein and total chlorophyll contents. Se improved seedling total Se and organic Se contents while increasing total dry weight and yield. Notably, the highest yield was obtained after a 4‐day flooding period. Although Se priming favored rice seedling emergence and growth under flooding conditions, Se concentrations equal or above 60 μmol/L increased the risk of seedling death during long‐term flooding (≥8 days).

A novel QTL cluster for appearance quality on Chr07 was identified using reciprocal introgression populations in different locations in China. Two secondary F ₂ populations validated QTL with significant effect on appearance quality.

One of the technology options that can help farmers cope with water scarcity at the field level is alternate wetting and drying (AWD). Limited information is available on the varietal responses to nitrogen, AWD, and their interactions. Field experiments were conducted at the International Rice Research Institute (IRRI) farm in 2009 dry season (DS), 2009 wet season (WS), and 2010 DS to determine genotypic responses and water use efficiency of rice under two N rates and two water management treatments. Grain yield was not significantly different between AWD and continuous flooding (CF) across the three seasons. Interactive effects among variety, water management, and N rate were not significant. The high yield was attributed to the significantly higher grain weight, which in turn was due to slower grain filling and high leaf N at the later stage of grain filling of CF. AWD treatments accelerated the grain filling rate, shortened grain filling period, and enhanced whole plant senescence. Under normal dry-season conditions, such as 2010 DS, AWD reduced water input by 24.5% than CF; however, it decreased grain yield by 6.9% due to accelerated leaf senescence. The study indicates that proper water management greatly contributes to grain yield in the late stage of grain filling, and it is critical for safe AWD technology.