Amylopectin branch-chain length distribution is a key determinant of rice starch functionality and eating quality, yet the genetic basis underlying specific chain fractions remains incompletely understood in diverse germplasm. In this study, amylopectin fine structure was quantified in 137 accessions of the Korean Rice Core Selection (KRICE_Core) using HPAEC-PAD, and genome-wide association studies were conducted with 2.1 million high-quality SNPs under the FarmCPU model. The short-chain distribution (SCD, DP 6-12) varied from 26.85% to 37.20%, whereas the intermediate-chain distribution (ICD, DP 12-24) ranged from 52.57% to 61.04%, and the two fractions showed a strong inverse correlation. GWAS identified two major loci on chromosomes 4 and 6, with the chromosome 6 region showing exceptionally strong association signals and co-localizing with
Rice yield is severely affected by phosphorus (P) deficiency, and plants have evolved various strategies to cope with this limitation. While some rice genotypes are adapted to low phosphate (Pi) availability, others remain sensitive to Pi deficiency. In this study, we conducted a genome-wide association study (GWAS) using a hydroponically cultivated population of 190 North Korean (NK) rice plants to identify genes associated with phosphorus use efficiency (PUE) and Pi deficiency tolerance. The rice plants were grown in Yoshida nutrient media with either full (10 mg/L) or low-P (1 mg/L) concentrations for 40 days. The phenotypic response to Pi deficiency was assessed at the seedling stage, followed by an evaluation of eight agricultural traits: chlorophyll content (SPAD), shoot length (SL), shoot fresh weight (SFW), shoot dry weight (SDW), root fresh weight (RFW), root dry weight (RDW), and tiller number (TN). The GWAS analysis revealed a total of 166 significant lead SNPs, with six located near known genes for Pi deficiency tolerance:
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Submergence damage to rice was reported as one of the major problems in rainfed lowland areas where the water remains. This study assessed the submergence tolerance of core collection during the seedling stage of the rice using dry seeds. Also, genome-wide association study (GWAS) combined with principal component analysis (PCA) and kinship matrix analysis was performed to identify quantitative trait loci (QTL) for submergence tolerance. Through this GWAS analysis, nine lead SNPs were confirmed to be associated with submergence tolerance, and a linkage disequilibrium (LD) decay analysis identified the 230 kb exploratory range for the detection of QTLs and candidate genes. Nine QTL were detected, on chromosomes 3 (
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At the reproductive development stage of rice (
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Salinity stress is one of the important abiotic stresses in crops. In this study, ten different concentrations of NaCl solutions were tested to determine the optimal level of NaCl concentration for salinity tolerance test at the germination stage in peanut, and 0.6% NaC1 was suitable for the test. A total of 249 peanut accessions were tested with 0.6% NaC1 and radical root lengths of the accessions were measured. The results showed that there were significant genetic variations on the tolerance to salinity stress among the tested accessions. Through a Genome-Wide Association Study (GWAS) using the Axiom_Arachis array with 58K SNPs, three putative SNPs with significant relation to radicle root length were identified on chromosomes Aradu.A03, Araip.B01, and Araip.B05.
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