In the present study, we conducted a detailed analysis of the genetic diversity and structural organization of 96 domestic Korean rice varieties (Oryza sativa L.) using 2,565 high-resolution TCS-based single nucleotide polymorphism (SNP) markers. Genetic structural variations were investigated using diversity indices, PCA, genetic similarity, and network analysis. Genetic diversity analysis revealed a significant expansion of the genetic foundation after the 1980s, marked by a sharp increase in the number of alleles (Na) from the 2000s. Despite this, high genetic homogeneity was maintained, with an average similarity of 77.7%. The observed 10% difference among same-cross varieties suggests that critical genetic variations are fixed by strong selection pressures for quality traits. Network analysis (85% similarity threshold) confirmed that the Korean rice breeding population followed a distinct core-periphery model (eight communities). The connected 84 varieties had a centrality range of 0.01 0.39. Core Variety Groups (e.g., ‘Junam’ and ‘Sindongjin’) exhibited the highest centrality (up to 0.39), indicating their extensive use as key breeding parents and their function as the central axis of the genetic network. Bridge Variety Groups (e.g., ‘Hwayeong’ and ‘Samkwang’) played an intermediary role linking clusters. Crucially, 12 ‘isolated accessions’ showed zero centrality (0.00), representing a genetic disconnect from the main pool. This quantitative network-based assessment provides essential fundamental data for breeders to select appropriate germplasms. Furthermore, the findings suggest that the current cultivar naming system, which inadequately reflects genetic relationships, requires reassessment, and that the establishment of objective management standards based on this research is warranted.

To diversify the grain quality characteristics of Korean varieties of japonica rice (Oryza sativa japonica), recombinant inbred lines were developed from a cross between the Korean cultivar “Boramchan” and the tropical japonica cultivar “Pecos” from the United States. Quantitative trait locus (QTL) analysis was performed to investigate the traits related to grain quality. Sixteen traits were evaluated, including five related to grain appearance, six associated with pasting properties and glossiness of cooked rice, and four related to eating texture. QTLs were detected on chromosomes 3, 5, 6, and 10, and candidate genes, including Hd1, qLTG3-1, GW5, and qGS10 were identified. The heading date-related gene Hd1 was associated with the following traits: head rice (HR), opaque rice (OR), damaged rice, pasting temperature, peak viscosity (PV), breakdown viscosity (BD), and glossiness. Most quality-related traits were influenced by allelic variation at Hd1, and the Hd1⁺ allele from “Boramchan”, which delays heading, positively affected both grain appearance and eating quality. The low-temperature germinability gene qLTG3-1 was identified as a candidate gene for broken rice and several pasting properties, including trough, final, and breakdown viscosities, and was shown to influence pasting characteristics depending on allelic variation. The grain shape gene GW5 was a candidate gene for HR and whiteness, whereas qGS10 was associated with OR, PV, BD, and setback viscosity. The GW5⁺ and qGS10^P alleles, derived from the slender grain shape of “Pecos,” contributed positively to both grain appearance and eating quality, indicating their potential as favorable alleles for improving grain shape and diversifying quality traits in Korean japonica rice. The results of this study demonstrate that key agronomic trait-related genes, such as heading and grain shape, significantly affect various quality-related traits, highlighting the potential of introducing and combining novel alleles to enhance grain quality in Korean japonica rice.

‘Boramchan’ is a high-yielding, mid-late maturing temperate japonica rice cultivar developed in Korea, while ‘Pecos’ is an early-maturing tropical japonica cultivar from the United States with medium-grain shape characteristics. In this study, quantitative trait loci (QTL) analysis was conducted on yield- and grain-related traits using recombinant inbred lines derived from a cross between ‘Boramchan’ and ‘Pecos’ in order to broaden the genetic diversity of these traits in Korean japonica rice varieties. QTLs for heading date were identified on chromosomes 3 and 6, with Hd6 and Hd1 proposed as candidate genes for this trait. The major heading date gene Hd1 exhibited pleiotropic effects, influencing not only the heading date (HD) but also multiple yield components, including culm length, panicle length, number of spikelets per panicle (NS), 1,000-grain weight (TGW), ratio of ripened grain (RRG), brown/rough rice ratio, and grain yield per plant. The minor heading date gene Hd6 showed a masking effect on HD and NS, depending on the allele type of Hd1. Allelic combinations of Hd1 and Hd6 allowed HD regulation for approximately 30 days. As more functional alleles associated with delayed heading accumulated, the values of yield-related traits gradually increased. Three QTLs for grain-related traits–qGL2, GW5, and qGS10–were identified on chromosomes 2, 5, and 10, respectively. GW5 was confirmed as a major gene with significant effects on phenotypic variation, influencing all grain-related traits, including grain length (GL), width (GW), thickness (GT), length to width ratio, and TGW. qGL2 was associated with GL and colocalized with qNS2, a QTL related to NS. qGS10 was identified as a QTL that affected GW, GT, and TGW. Allelic combinations of qGL2, GW5, and qGS10 influenced not only grain-related traits but also variation in yield-related traits. Combinations carrying the gw5^- allele from ‘Boramchan’ generally exhibited favorable characteristics in terms of yield potential. Furthermore, the introduction of qGL2^P and qGS10^P alleles from ‘Pecos’ contributed to the diversification of grain shape and showed positive effects on NS, RRG, and yield. Novel allele combinations, such as qGL2^P-gw5^--qGS10^B and qGL2^P-gw5^--qGS10^P are expected to enhance the genetic diversity of yield- and grain-related traits in Korean japonica rice varieties.

‘Chamdongjin’ is a rice cultivar with a distinctively large grain size and good palatability, similar to ‘Sindongjin,’ which is a mega-cultivar in Korea. ‘Younghojinmi’ is a rice cultivar known for having the highest taste value among premium quality cultivars. In this study, we conducted quantitative trait loci (QTL) analysis of quality-related traits using recombinant inbred lines (RILs) derived from a cross between ‘Chamdongjin’ and ‘Younghojinmi’ to elucidate their genetic interactions. We analyzed 20 traits, including protein content, amylose content, glossiness of cooked rice, 7 traits related to grain appearance, 6 traits related to pasting properties, and 4 traits related to texture. Quality-related QTL were primarily detected on chromosome 3. In particular, GS3, one of the candidate genes for QTL, significantly influenced quality by affecting 14 different traits, including appearance traits such as head rice and the texture of cooked rice. Furthermore, RILs with the gs3 allele, which exhibited the large grains of ‘Chamdongjin,’ showed a lower protein content and higher amylose content than RILs with the GS3 allele. These lines also had lower head rice percentages and higher percentages of whiteness, opacity, and broken rice, indicating an inferior appearance quality. In terms of pasting properties, RILs with the gs3 allele showed a lower pasting temperature, peak viscosity, and breakdown, but a higher setback than RILs with the GS3 allele. Although the gs3 allele did not affect the glossiness, hardness, or toughness of the cooked rice, it resulted in higher adhesiveness and stickiness. Allelic alteration of the preharvest sprouting gene qLTG3-1 was found to affect seven quality-related traits, including pasting properties. Genes related to heading date (Hd18), culm length (SD1), and tiller number (OsTB1) were also associated with quality-related QTL. Alterations in the alleles of these genes caused variations in quality-related traits. Our identification of the association between quality-related traits and key agronomic genes is expected to support the effective development of rice cultivars with improved quality.

The rice cultivar ‘JJ644wx’ was developed to improve disease resistance and lodging tolerance of Korean japonica glutinous rice cultivars. ‘JJ644wx’ was derived from a cross between ‘HR27814-B-47-1-1’ (‘Sinjinbaek’), a multiple disease-resistant mid-late maturing elite line, and ‘HR29676-AC29’, a medium-maturing glutinous line with lodging tolerance. To shorten the breeding period, an anther culture method was applied to F₁ plants. ‘JJ644wx’ was selected through the pedigree method, yield trials, and local adaptability tests, with high selection pressure for disease resistance and lodging tolerance. The heading date of ‘JJ644wx’ was August 11th, four days later than that of ‘Sinseonchal’. ‘JJ644wx’ exhibited strong tolerance to lodging with a short culm length. The 1,000-grain weight of brown rice of ‘JJ644wx’ was heavier than that of ‘Sinseonchal’, and its yield was 553 kg/10a, which was 10% higher than that of ‘Sinseonchal’. ‘JJ644wx’ had a higher milling performance than ‘Sinseonchal’, but a lower head rice ratio due to a higher percentage of broken rice. ‘JJ644wx’ tended to be situated between ‘Sinseonchal’ and ‘Dongjinchal’ in terms of pasting and texture characteristics. ‘JJ644wx’ is the only Korean japonica glutinous rice cultivar resistant to the most virulent bacterial blight race, K3a; it also showed resistance to rice blast and stripe virus. ‘JJ644wx’ is expected to be a valuable resource that could contribute to improving the cultivation stability of Korean japonica glutinous rice in response to climate change (Registration No. 9606).

The rice cultivar ‘Chamdongjin’ exhibits a distinctively large grain size and excellent eating quality but is weak with regard to pre-harvest sprouting (PHS), requiring genetic improvement. In contrast, the premium-quality rice cultivar ‘Younghojinmi’ exhibits strong PHS tolerance. This study conducted quantitative trait loci (QTL) analysis on PHS and low-temperature germinability (LTG) using recombinant inbred lines derived from a cross between ‘Chamdongjin’ and ‘Younghojinmi’ to elucidate the genetic factors. Thus, an elite line with improved PHS tolerance was selected. QTL analysis revealed that qPHS3 and qLTG3 were associated with PHS and LTG, respectively, and the candidate gene was identified as qLTG3-1. The loss-of-function allele qltg3-1 in ‘Younghojinmi’ enhanced PHS tolerance compared to the functional allele qLTG3-1 in ‘Chamdongjin,’ but it also showed a trade-off relationship by decreasing LTG. CY_RILs carrying qltg3-1 exhibited lower PHS and LTG rates of 17.9% and 41.6%, respectively, compared to 44.1% and 55.7%, respectively, for CY_RILs with qLTG3-1. The elite line, CY_RIL79, carrying qltg3-1, was selected from CY_RIL. This line was recognized for its PHS tolerance while maintaining the key agricultural traits of ‘Chamdongjin,’ thus designated ‘Jeonju697.’ ‘Jeonju697’ is expected to be utilized as a practical alternative for addressing the issue of enhancing PHS tolerance in ‘Chamdongjin’; however, considering its weak LTG, it is desirable to improve this trait through further breeding efforts.

‘Saebonghwang’ was developed as a mid-late ripening rice variety with good cultivation stability and yield in transplanting and under direct seeding cultivation. It was bred by backcrossing ‘Hopum’, which has excellent cultivation stability and adaptability to direct seeding, as a repeat parent, and ‘Hitomebore,’ a Japanese rice variety with excellent taste, as a donor. The heading date of ‘Saebonghwang’ was August 11 under ordinary planting, which is two days earlier than that of ‘Nampyeong’, and August 13 under wet-direct seeding cultivation, which is the same as that of ‘Dongan’. ‘Saebonghwang’ had a culm length of 74 cm under wet-direct seeding cultivation, which is larger than that of ‘Dongan’ (69 cm), and had good cultivation stability, including lodging resistance. ‘Saebonghwang’ is resistant to bacterial leaf blight and rice stripe virus and shows moderate resistance to rice blast. Furthermore, ‘Saebonghwang’ has better grain appearance, superior taste and better milling characteristics than ‘Nampyeong’. The yield of ‘Saebonghwang’ when cultivated under ordinary planting, wet-direct seeding, and double cropping was 5.65, 5.37, and 5.37 MT/ha, respectively. Under wet direct sowing by drone cultivation, ‘Saebonghwang’ showed good initial survival rate and cultivation stability. The yield was 4.49 MT/ha, slightly lower than that obtained under transplanted cultivation (5.03 MT/ha), but was not statistically different; therefore, ‘Saebonghwang’ was adjudged to be adaptable to drone wet-direct seeding. ‘Saebonghwang’ can be used in various ways to suit the working conditions of farms, increase farm work efficiency, and expand the area of wet direct-seeding cultivation (Registration No. 9171).

‘Yechan’ is a high grain quality mid-late maturing rice cultivar with lodging tolerance and multiple disease resistance. It was a derived from a cross between ‘Hopum’ and ‘Iksan537’ (cultivar name ‘Haepum’). ‘Hopum’ is a high grain quality mid-late maturing rice cultivar with strong lodging tolerance and ‘Haepum’ is a high grain quality medium maturing rice cultivar with multiple disease resistance. To shorten the breeding period, another culture method was applied to the F₁ plants. ‘Yechan’ was selected through the pedigree method, yield trials, and local adaptability tests, with a high selection pressure for grain quality, lodging, and disease resistance. The heading date of ‘Yechan’ was August 14, one day later than that of ‘Nampyeong’. ‘Yechan’ is a cultivar tolerant to lodging and it has short culms. It has multiple disease resistance against rice blast, rice stripe virus, and bacterial blight, including the K3a race, the most virulent race in Korea. The yield of ‘Yechan’ was similar to that of ‘Nampyeong’. ‘Yechan’ showed excellent grain appearance, superior taste when cooked, and enhanced milling performance; thus, we concluded that it could contribute to the improvement of Korean japonica rice cultivar quality. ‘Yechan’, a high grain quality mid-late maturing rice cultivar with lodging tolerance and multiple disease resistance, would be suitable for cultivation in the southern plain area in Korea and has been utilized in the breeding programs aimed at enhancing the grain quality and stability for the cultivation of Korean japonica rice (Registration No. 7647).

‘Sinjinbaek’ is a bacterial blight (BB)-resistant, mid-late maturing rice cultivar with high grain quality. To diversify the resistance genes and enhance the resistance of Korean rice cultivars against BB, ‘Sinjinbaek’ was developed from a cross between ‘Iksan493’ (cultivar name ‘Jinbaek’) and the F₁ cross between ‘Hopum’ and ‘HR24670-9-2-1’ (‘HR24670’). ‘Jinbaek’ is a BB-resistant cultivar with two BB resistance genes, Xa3 and xa5. ‘Hopum’ is a high grain quality cultivar with the Xa3 resistance gene. ‘HR24670’ is a near-isogenic line that carries the Xa21 gene, a resistance gene inherited from a wild rice species O. longistaminata, in the genetic background of japonica elite rice line ‘Suweon345’. ‘Sinjinbaek’ was selected through the pedigree method, yield trials, and local adaptability tests. Using bioassay for BB races and DNA markers for resistance genes, three resistance genes, Xa3, xa5, and Xa21, were pyramided in the ‘Sinjinbaek’ cultivar. ‘Sinjinbaek’ exhibited high-level and broad-spectrum resistance against BB, including the K3a race, the most virulent race in Korea. ‘Sinjinbaek’ is a mid-late maturing rice cultivar tolerant to lodging. It has multiple disease resistance against BB, rice blast, and stripe virus. The yield of ‘Sinjinbaek’ was similar to that of ‘Nampyeong’. ‘Sinjinbaek’ showed excellent grain appearance, good taste of cooked rice, and enhanced milling performance, and we concluded that it could contribute to improving the quality of BB-resistant cultivars. ‘Sinjinbaek’ was successfully introgressed with the Xa21 gene without the linkage drag negatively affecting its agronomic characteristics. ‘Sinjinbaek’ improved the resistance of Korean rice cultivars against BB by introgression of a new resistance gene, Xa21, as well as by pyramiding three resistance genes, Xa3, xa5, and Xa21. ‘Sinjinbaek’ would be suitable for the cultivation in BB-prone areas since it has been used in breeding programs for enhancing plants’ resistance to BB (Registration No. 7273).

It is reported that the absence of lipoxygenase-3 (LOX-3) may contribute to a reduction in stale flavor after the storage of rice. To improve the quality of stored rice of the Korean japonica rice cultivar, we conducted a breeding program to develop near-isogenic rice without LOX-3 in the genetic background of Saenuri, a mega variety of Korea. In the first step of the breeding program, we used a donor parent of LOX-3 null, Daw Dam, and a recurrent japonica parent, Sindongjin, to develop HR27873-AC12 by backcross (BC₁), color test for introgression of lox-3, and anther culture for rapid fixation. In the second step, we used the donor parent, HR27873-AC12, and the recurrent parent, Saenuri, to develop HR28896-31-3-1-1 by backcross (BC₁), marker-assisted selection (MAS) for lox-3, and phenotypic selection (PS) for agronomic traits. Finally, in the third step, we developed HR30960-186-2-1-2-1 (Jeonju624), derived from a cross between Saenuri and HR28896-31-3-1-1, by MAS for lox-3 and PS with high selection pressure for agronomic characteristics. Jeonju624 was confirmed with the introgression of lox-3 by molecular marker. Jeonju624 was a mid-late maturing rice with similar agronomic characteristics to Saenuri, lodging tolerance with short culm, erect plant architecture, and resistance to bacterial blight and rice stripe virus. The yield components of Jeonju624 were mostly similar to Saenuri, except for the 1,000-grain weight of brown rice. The appearance of the grain of Jeonju624 was better than that of Saenuri, and the characteristics of cooked rice were similar to those of Saenuri. In the genetic background analysis using 406 KASP (Kompetitive Allele-Specific PCR) markers, Jeonju624 was confirmed to be the near-isogenic line (NIL) of Saenuri with a 95.8% recovery rate. Jeonju624 is the NIL of Saenuri without LOX-3, and overcomes the linkage drag of Daw Dam with similar agronomic characteristics and genetic background to Saenuri. Jeonju624 can be utilized as a practical cultivar to improve the quality of stored rice, breeding material for the introgression of lox-3, and genetic material to elucidate the effect of introgressed genes.