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 Os06g0229800 (SSIIa). Haplotype analysis of SSIIa detected five non-synonymous SNPs defining five haplotypes. Hap1 and Hap5 were associated with increased SCD and reduced ICD, whereas indica-related haplotypes (Hap2-Hap4) showed the opposite trend, indicating that SSIIa allelic variation quantitatively shifts the balance between short and intermediate chain fractions. In a panel of 113 Korean-bred cultivars, Hap1 and Hap5 together accounted for > 99% of genotypes, suggesting strong directional selection for japonica-type SSIIa alleles during Korean breeding. These findings provide robust molecular targets for designing rice varieties with tailored starch architecture and cooking qualities.

Nitrogen is an essential nutrient for crop growth and development. Although the functions of several genes associated with nitrogen deficiency tolerance have been studied, many genetic components remain unknown. In this study, 190 North Korean (NK) rice genotypes were used to identify genes linked to nitrogen deficiency resistance. The NK population was hydroponically cultivated for 31 days under normal nitrogen (NN) and low nitrogen (LN) conditions. After this period, phenotypic evaluations were conducted on six agronomic traits (SPAD, shoot length, root length, shoot fresh weight, root fresh weight, and tiller number). A genome-wide association study (GWAS) was performed using the phenotypic values and resequencing data from 190 NK rice genotypes. As a result, 107 significant lead SNPs were identified. Among the genes related to these lead SNPs, 12 previously identified NUE-related genes for nitrogen use efficiency (NUE) and 6 unknown candidate genes exhibited significant differences in haplotype analysis. Nine of the 12 known genes (OsNPF4.1, OsNPF5.16, OsNPF6.1, OsNPF7.2, OsNPF7.7, OsAMT1.2, OsNRT1.3, OsAAP4, and OsLBD37) are involved in nitrogen uptake, while two (OsAAT1 and OsGS1;2) play a role in nitrogen assimilation, and one (OsNLP3) activates nitrate-responsive genes. This work demonstrates that the 190 NK rice genotypes analyzed harbor multiple critical genes involved in nitrogen uptake and identifies additional candidate genes associated with nitrogen deficiency tolerance. The genetic resources containing these known and novel genes for NUE could contribute to breeding rice varieties with high nitrogen deficiency tolerance (NDT).

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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 (qSUB3), 4 (qSUB4), 6 (qSUB6-1 and qSUB6-2), 11 (qSUB11-1, qSUB11-2 and qSUB11-3), and 12 (qSUB12-1 and qSUB12-2). Two candidate genes (Os03g0679300 and Os11g0517800) in the two QTL regions associated with submergence tolerance were detected. The results of this study provide associated SNPs in candidate genes for submergence condition and strategies for developing submergence condition in breeding programs.

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Cultivation of the medicinal herb Panax ginseng Meyer began by domesticating wild mountain ginsengs several hundred years ago in Korea. Elucidating the diversity of the maternally inherited plastid genome (plastome) in diverse ginseng collections including wild ginsengs would provide valuable information on ginseng breeding and cultivation history. We sequenced and compared the plastomes of 44 ginseng accessions collected from various Northeast Asian countries. The plastomes revealed 18 polymorphic sites, including 11 SNPs and 7 InDels, which portrayed less diversity than in the most closely related species, P. quinquefolius. We developed 10 kompetitive allele-specific PCR (KASP) markers and utilized them along with four previously developed InDel markers to characterize the genotypes of 203 ginseng accessions. Digital genotyping based on the developed KASP markers classified the accessions into 10 main and 2 branching haplotypes. Four InDel markers derived from different copy numbers of tandem repeats showed dynamic subgrouping within the haplotypes due to the occurrence of multi-alleles and reversible mutations. The digital haplotype genotyping (haplotyping) revealed that haplotype A, representing 60.1% of the accessions, might be the original plastome form without any SNP occurrence. Accumulation patterns of the variations suggest that nine main haplotypes (B-J) diverged independently by new SNP occurrences from the original plastome, and branching haplotypes may have derived from the first mutant lineage by additional SNP deposition. The digital haplotyping system based on plastome diversity deepens understanding of ginseng evolution and serves as a useful molecular breeding tool.

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  Cogent Food & Agriculture.2023;[Epub]     CrossRef
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