A total of 285 Korean rice cultivars were used for amylose content and genetic analyses using KASP markers related to the amylose content. We used three polymorphic KASP markers targeting the Waxy (Wx) gene and compared the genotyping efficiency with previously reported molecular markers. The rice cultivars were raised in Miryang, Korea, for one period. Genetic analysis of the rice cultivars revealed that the three KASP markers on the Wx gene were functional for genomic selection of SNPs related to amylose content variation. Therefore, the three KASP markers targeting different Wx alleles can be used for genomic selection. In addition, KASP markers were more efficient than previously reported molecular markers that target the same alleles. These findings can be beneficial for the breeding and genomic selection of high-quality rice in Korea.

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.

Rice doubled haploid (DH) lines derived from crosses of the indica cultivar 93-11 and japonica line Milyang352 were used in genetic mapping and QTL analysis studies of days to heading (DTH), an important trait that controls rice yield and biomass. QTL mapping was conducted using the inclusive composite interval mapping method. We used 234 single-nucleotide polymorphic markers in the whole-genome region, including 100 KASP markers and 134 Fluidigm markers, to construct a genetic map. DH populations were raised in Milyang, Korea, over three different periods. Two major DTH QTLs, qDTH3-1 and qDTH7, were detected under natural conditions in Milyang, and explained 14.88%~24.56% and 24.20%~37.39% of the phenotypic variation, respectively, in 93-11×Milyang352 DH populations. During three different rice cultivation periods, qDTH3-1 and qDTH7 were repeatedly detected with significant logarithm of the odds scores and phenotypic variability explained. The findings of this study will make a valuable contribution to breeding high-yielding and early-maturing rice in Korea.

This study was conducted to identify DNA markers related to resistance to herbicide containing mesotrione in Tongil type rice. Two Tongil type elite lines; Milyang154 and Suweon382, showed resistance to mesotrione, whereas the others were susceptible at 20 days after mesotrione application, and severe growth inhibition was observed in the remaining 13 lines. As a result of analysis of mesotrione resistance using 190 F₂ populations derived from a cross of Hanareum2 (susceptible) and Milyang154 (resistant), the mesotrione resistance locus was shown to be a single dominant gene with a 3:1 segregation ratio (X²=1.19, P=0.31). To identify a DNA marker closely linked to the mesotrione resistance gene, bulked segregant analysis (BSA) was adopted. The DNA marker RM3501 was identified on chromosome 2 with a recombinant value of 0.53 to the mesotrione resistance gene. Mst1(t) was located between SSR (simple sequence repeat) markers RM3501 and RM324 with a physical map distance of 10.2 Mb–11.4 Mb on chromosome 2. The band pattern of agarose gel electrophoresis of the SSR marker RM3501 showed the same segregation pattern with respect to mesotrione treatment in 20 Tongil type varieties and a BC₂F₂ segregation population derived from a cross between Unkwang (resistant) and Hanareum2 (susceptible). Thus, the RM3501 DNA marker could be used in breeding programs for Marker Assisted Selection in mesotrione resistant rice breeding.