Multi-environment trials (METs) are essential in plant breeding programs to evaluate crop productivity and adaptability in diverse environments. In this study, we demonstrated the practical use of METs to evaluate grain yield and yield-related traits using 276 Korean rice cultivars, divided into three maturity groups (81 early-, 90 medium-, and 105 medium–late-maturing cultivars) grown in three regions (Jeonju, Suwon, and Miryang) and two planting seasons (early and regular planting) for two years. Due to the narrow genetic variability of the commercial cultivars, which are cultivated in relatively similar environmental conditions, genotype-by-environment interaction (GEI) effects were not statistically significant. However, genotype and environment evaluation using GGE biplot analysis exhibited distinct patterns of mega-environment formation, winning genotypes, ranking genotypes, discriminating power, and representativeness according to the differences in planting seasons and regions. Moreover, the simultaneous selection of stable high-performance genotypes using a weighted average of absolute scores from the singular-value decomposition of the matrix of BLUPs (WAASB) and a multi-trait stability index (MTSI) revealed six recommended genotypes each for early-maturing (Manho, Namil, Unkwang, Odae 1ho, Sinunbong 1ho, and Jonong) and medium-maturing (Sobi, Cheongdam, Shinbaeg, Boramchal, Mimyeon, and Saemimyeon) cultivars, and four genotypes for medium–late-maturing cultivars (Hanmauem, Dami, Baegseolchal, and Hangangchalbyeo). The winning genotypes of each trait can be used as parents to develop regional specialty cultivars by fine-tuning favorable traits, and recommended genotypes can be utilized as elite climate-resilient parents that can aid breeders in improving yield potential and stability across the planting seasons and regions.

Forward genetic screens of induced mutant plant populations are powerful tools to identify genes underlying phenotypes of interest. Using traditional techniques, mapping causative mutations from forward screens is a lengthy, multi-step process, requiring the identification of a broad genetic region followed by candidate gene sequencing to characterize the causal variant. Mapping by whole genome sequencing accelerates the identification of causal mutations by simultaneously defining a mapping region and providing information on the induced genetic variants. In wheat, although the availability of a high-quality draft genome assembly facilitates mapping and mutation calling, whole genome resequencing remains prohibitively expensive due to its large genome. In the current study, we used exome sequencing as a complexity reduction strategy to detect mutations associated with a target phenotype. In a segregating wheat EMS population, we identified a clear peak region on chromosome arm 4BS associated with increased plant height. Although none of the significant SNPs seemed causative for the mutant phenotype, they were sufficient to identify a linked ~ 1.9 Mb deletion encompassing nine genes. These genes included Rht-B1, which is known to have a strong effect on plant height and is a strong candidate for the observed phenotype. We performed simulation experiments to determine the impacts of sequencing depth and bulk size and discuss the importance of considering each factor when designing mapping-by-sequencing experiments in wheat. This approach can accelerate the identification of candidate causal point mutations or linked deletions underlying important phenotypes.

Pre-harvest sprouting (PHS), induced by unexpected weather events, such as typhoons, at the late seed maturity stage, is becoming a serious threat to rice production, especially in the state of California, USA, Japan, and the Republic of Korea, where japonica varieties (mostly susceptible to PHS) are mainly cultivated. A projected economic loss by severe PHS in these three countries could range between 8–10 billion USD per year during the next 10 years. Here, we present promising rice germplasm with strong resistance to PHS that were selected from a diverse rice panel of accessions held in the International Rice Genebank (IRG) at the International Rice Research Institute (IRRI). To induce PHS, three panicle samples per accession were harvested at 20 and 30 days after flowering (DAF), respectively, and incubated at 100% relative humidity (RH), 30 °C in a growth chamber for 15 days. A genome-wide association (GWA) analysis using a 4.8 million single nucleotide polymorphisms (SNP) marker set was performed to identify loci and candidate genes conferring PHS resistance. Interestingly, two tropical japonica and four temperate japonica accessions showed outstanding PHS resistance as compared to tolerant indica accessions. Two major loci on chromosomes 1 and 4 were associated with PHS resistance. A priori candidate genes interactions with rice gene networks, which are based on the gene ontology (GO), co-expression, and other evidence, suggested that a key resistance mechanism is related to abscisic acid (ABA), gibberellic acid (GA), and auxin mediated signaling pathways.

Background: Producing rice flour of good quality by dry milling is necessary to reduce milling costs and promote the processed rice food industry. This study was conducted to evaluate the dry milling properties of Suweon 542, a floury endosperm mutant, and identify the chromosomal region responsible for the floury endosperm characteristics. Results: Compared with the wild type, after dry milling process, the grain hardness of Suweon 542 was significantly lower because of its round and loosely packed starch granules. Also, the flour of Suweon 542 had significantly smaller particles and less damaged starch than Namil and other rice cultivars and its particle size distribution was similar to a commercial wheat cultivar. Considering that the yield loss of Suweon 542 due to its floury endosperm was largely compensated for by an increased number of spikelets per panicle, Suweon 542 has potential value as a raw material for rice flour production. Association analysis using 70 genome-wide SSR markers and 94 F₂ plants derived from Suweon 542/Milyang 23 showed that markers on chromosome 5 explained a large portion of the variation in floury grains percentage (FGP). Further analysis with an increased number of SSR markers revealed that the floury endosperm of Suweon 542 was directed by a major recessive locus, flo7(t), located in the 19.33–19.86 Mbp region of chromosome 5, with RM18639 explaining 92.2% of FGP variation in the F₂ population. Conclusions: The floury endosperm of Suweon 542 is suitable for dry milling, with a small flour particle size and low damaged starch content. Further physical mapping of flo7(t), the floury endosperm locus of Suweon 542, would facilitate efficient breeding of rice cultivars with proper dry milling adaptability that can be used in the processed rice food industry.