Early selection of grain quality traits in rice (Oryza sativa L.), is essential to improve the yield and quality of this staple crop. We analyzed four key traits—protein content, grain filling rate, height, and panicle length—in 85 Korean cultivars. Through whole- genome resequencing we identified 12,718,879 raw single nucleotide polymorphisms (SNPs); after PLINK-based quality control (bi-allelic selection, call rate≥0.90, MAF≥0.03), ~2.20 million high-quality SNPs remained for machine-learning (ML) pre-screening. To rank the features (without marker-level inference), we applied a liberal univariate PLINK case-control scan using the top and bottom 30% per trait. We also analyzed associations with a linear mixed model (GCTA v1.93.2, MLMA; fixed covariates: ecotype, PC1, PC2; random effect: GRM) to verify calibration under population structure; with n=85, no genome-wide significant hits were detected, and QQ-plots indicated adequate calibration (per-trait effective tests m≈1.54-1.57 million under stricter filters). The random forest feature importance prioritized 26, 51, 19, and 20 core SNPs for the four traits, respectively. Across the algorithms, the best models achieved mean accuracies of 81.8% (protein content), 81.0% (grain filling rate), 73.1% (height), and 94.0% (panicle length). All selected SNPs met the Fluidigm array design requirements, supporting its deployment as a compact, genotype-based panel for early selection and a practical step toward digital breeding in rice.

Leaf size is closely related to photosynthesis and greatly affects rice productivity. Therefore, the search for quantitative trait Locus (QTL) that regulates leaf size is important for improving productivity through rice breeding. The F₉ recombinant inbred line (RIL) population from the cross between ‘Unbong 40’ (large leaves) and ‘Odae’ (ordinary size leaves) was grown in a test field, and the size traits of the flag leaves and 2nd leaves, along with stem and panicle length, were measured. Through QTL analysis of these traits, we detected 20 QTLs on chromosomes 1, 3, 6, 9, 11, and 12. In particular, the flag leaf length QTL qFLL3, the flag leaf area QTL qFLA3, the 2nd leaf length QTL q2LL3-2, and the 2nd leaf area QTL q2LA3 were clustered in the 149.0-161.6 cM region of chromosome 3, indicating that one QTL gene in this region may have pleiotropic effects that regulate the flag leaf length, flag leaf area, 2nd leaf length, and 2nd leaf area. In addition, the flag leaf width QTL qFLW9 and 2nd leaf width QTL q2LW9 were clustered in the 2.1-22.86 cM region on chromosome 9, which suggests that one QTL gene in this region may have pleiotropic effects that regulate both the flag leaf width and 2nd leaf width. These results serve as a valuable reference for breeding programs aiming to increase photosynthesis and yield by identifying QTLs for leaf size traits in Korean japonica rice.

To stably produce domestic wheat under water-scarce environmental conditions due to climate change, root characteristics with excellent water utilization rates are crucial. In this study, we analyzed the root and grain phenotypes of 37 domestic wheat varieties over a two-year period by combining the results of genetic mutations related to semi-dwarfing and grain size. Root length was positively correlated with maximum root depth (r=0.76**) and total seminal root length (r=0.54**), whereas it was negatively correlated with the number of roots (r=-0.33**) and root angles (r=-0.51**). The thousand-kernel weight was positively correlated with embryo width (r=0.34**) and embryo area (r=0.33**) but was not correlated with other root traits. Embryo length was positively correlated with the number of roots (r=0.34**) and coleoptile length (r=0.42**). Phenotypic analyses of roots and grains, along with genotypic analyses of semi-dwarfing (Rht-B1 and Rht-D1) and grain size (TaCWI-4A, TaCWI-5D, TaGW2-6A, TaSus2-2B) genes, revealed that the Rht-D1b genotype led to reduced root depth, increased root angles, and reduced coleoptile length. TaCwi-A1, TaCWI-5D, TaSus2-2B, and TaGW2-6A, possessing the alleles TaCwi-A1a, Hap-5D-C, Hap-L, and Hap-6A-G associated with a larger grain size, resulted in an increased number of roots and root depth. Domestic wheat varieties were categorized into three clusters based on root, grain, and coleoptile trait characteristics, with 15 varieties in Cluster I, 9 in Cluster II, and 13 in Cluster III. The results of this study can be utilized in basic research to develop varieties that can produce stable domestic wheat by selecting resources with excellent root growth and seed characteristics.

Recent advances in high-throughput sequencing technologies have enabled large-scale cost-effective genotypic analyses, and consequently, obtaining reliable phenotypic data has now become a major bottleneck in data-driven plant breeding. In order to construct a phenotype database for commercial rice varieties released by the National Institute of Crop Science, Rural Development Administration, we initiated a systematic phenotype evaluation project, with the aim of investigating the major agronomic traits of Korean rice varieties released during the period between 1979 and 2017. Despite the narrow genetic background, we found that the days to heading (DTH) and culm length (CL) of the 297 Korean rice varieties assessed exhibited wide phenotypic variation under different environments. Under normal planting cultivation in 2018, the DTH ranged from 48 to 104 days in Suwon, 46 to 111 days in Wanju, and 39 to 97 days in Miryang, with CL values ranging from 59 to 134 cm, 55 to 122 cm, and 57 to 106 cm, respectively. During early planting cultivation in 2019, the DTH ranged from 56 to 113 days (Suwon), 58 to 109 days (Wanju), and 58 to 100 days (Miryang), with corresponding CL values ranging from 63 to 119 cm, 55 to 93 cm, and 51 to 115 cm. Despite the difference of one month in planting dates in 2018 and 2019, DTH in the different years and regions showed highly significant positive correlations (r=0.90-0.98), whereas CL showed positive but weaker correlations (r=0.45-0.82). Furthermore, we detected a weak, although significant, correlation between DTH and CL in each environment (r=-0.18-0.35). Analyses of additive main effects and multiplicative interaction (AMMI) were conducted for DTH and CL to identify rice varieties with stable phenotypes under different environments. We anticipate that the findings of this study will provide a useful rice phenotype database to facilitate genotype-phenotype association studies and data-driven rice breeding.

Given that soil salinity significantly limits plant growth and production in agricultural land, research on salt stress is of particular agricultural relevance. In this study, for the purposes of functional screening of genes involved in salt stress responses, we selected approximately 651 transgenic Arabidopsis lines (157 independent full-length) from a transgenic Arabidopsis population overexpressing full-length Brassica rapa cDNAs. Initial screening indicated that the transgenic lines of 12 genes showed apparent salt tolerance phenotypes when exposed to NaCl at a concentration of 125 mM, among which, two genes (BrATL30 and BrZHD10) were selected for detailed characterization. The T₃ progeny of these transgenic lines exhibited accelerated seed germination, often accompanied by faster root growth and higher survival rate, compared with wild-type plants under salt stress. Additionally, in order to examine the agricultural potential of the two selected B. rapa genes, we constructed BrATL30- and BrZHD10-overexpressing Brassica napus transgenic plants (BrATL30-OX and BrZHD10-OX), which showed apparent high salt stress-tolerant phenotypes compared with wild-type plants. Furthermore, we found that the basal expression of several salt- and abiotic stress-responsive genes was higher in transgenic plants than in wild-type plants. Taken together, this study will provide two valuable functional genes related to salt stress tolerance.

The objective of this study was to identify quantitative trait loci (QTL) of spike length by association analysis with 94 doubled haploid wheat lines derived from Keumkang and Olgeuru. Days to heading date, culm length, spike length, and kernels per spike were evaluated in 2017 and 2018 in upland conditions. Culm length and spike length were biased short culm length and spike length (skewness=0.2 and 1.5, respectively). Kernel number per spike was biased low kernel number per spike (skewness=0.8). A genetic map was constructed with 170 microsatellite marker loci. One QTL was detected for spike length. The QTL on chromosome 4A, qSL-1 was detected by Xwmc283 and Xbarc327 explained 44.3% of the phenotypic variation. The QTL was applied to validate the relationship between genotypes of QTL and 29 Korean wheat cultivars grown for nine years under upland conditions. Korean wheat cultivars were classified into 5 types based on the combination of the two SSR markers. In Korean wheat cultivars, genotype b at Xbarc327, which was homozygous to Keumkang, had a shorter spike length (7.48 cm) than genotype c, which was different from the genotypes of Keumkang and Olgeuru, (8.45 cm). The two Korean wheat cultivars with genotypes ac at Xwmc283 and Xbarc327 had longer spike length (8.45 cm) than genotypes ba and bb (<7.42 cm).