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.

The intermediate breeding material ‘JJ625LG’ was developed to diversify the grain shape characteristics of Korean japonica rice cultivars. ‘JJ625LG’ was derived from a cross between ‘HR30198-AC33 (DGS79),’ a japonica breeding material with extra-long and spindle-shaped grains, and ‘Boramchan,’ a high-yielding japonica cultivar with excellent cultivation stability and medium-short and semi-round grains. By employing both bulk and pedigree breeding methods, strong selection pressure was applied to eliminate undesirable traits inherited from ‘DGS79,’ such as very late heading, long awns, and susceptibility to lodging. Consequently, elite lines with long spindle-shaped grains on a japonica background were selected. These lines subsequently underwent yield performance and local adaptability tests, during which their agronomic traits were comprehensively evaluated, leading to the final selection of ‘JJ625LG.’ The heading date of ‘JJ625LG’ was August 16th, three days later than that of ‘Nampyeong’. Its culm length was similar to ‘Nampyeong.’ ‘JJ625LG’ exhibited a higher number of spikelets per panicle, fewer panicles per plant, and heavier 1,000-grain weight than brown rice. Additionally, it showed strong resistance to bacterial blight (races K1, K2, and K3) but was susceptible to viral diseases and insect pests, indicating the need for further improvement in these areas. Its grain yield was comparable to that of ‘Nampyeong.’ With a brown rice grain length of 6.34 mm, ‘JJ625LG’ was classified as a long-grain type and had a grain length-to-width ratio of 2.64, reflecting a spindle-shaped morphology. It carried the GW2-gs3-qSW5 allele combination associated with grain shape, which is a genetic profile not found in existing Korean japonica cultivars. Although its milling recovery rate was similar to that of ‘Nampyeong,’ the presence of many broken rice due to its long grain shape resulted in a lower percentage of head rice. The eating quality of ‘JJ625LG’ was excellent, with its grains exhibiting the sticky and soft texture typical of japonica rice and receiving high scores in sensory evaluation. As the first intermediate breeding material in Korea with long and spindle-shaped grains in a japonica background, ‘JJ625LG’ is expected to contribute significantly to diversifying the traditionally narrow grain shape spectrum of Korean japonica rice cultivars (Registration No. 10166).

‘Baeksoojeongchal’, a new naked waxy barley cultivar was developed from a cross between ‘Jinmichapssal’ and ‘Radiant’ at the National Institute of Crop Science, RDA in 2019. ‘Baeksoojeongchal’ is a white, waxy naked barley cultivar with a low browning reaction owing to the low levels of proanthocyanidin. Regional yield trials were conducted for ‘Baeksoojeongchal’ as the breeding line, ‘Jeonju135’ at four different regions between 2017 and 2019. The average heading date of ‘Baeksoojeongchal’ in the paddy field was April 20, which was a day later than that of ‘Saechal’. Maturing date of ‘Baeksoojeongchal’ in the paddy field was May 26, which was 2 days later than that of ‘Saechal’. It has a short culm length of 75 cm and a short spike length of 4.3 cm, with 48 grains per spike and a 1,000-grain weight of 29.5 g. Compared to ‘Saechal’, ‘Baeksoojeongchal’ shows weaker winter withering and has better tolerance to lodging. The incidence of BaYMV (Barley yellow mosaic virus) in ‘Baeksoojeongchal’ was similar to that in ‘Saechal’; in addition, it was susceptible to powdery mildew. The grain quality characteristics of ‘Baeksoojeongchal’ indicated a similar protein content (9.6%) and a lower proanthocyanidin content (0.011%) and whiteness (42.0) compared to that in ‘Saechal’. The average yield was 505 kg/10a in the paddy field, which was 7% higher than that of ‘Saechal’. ‘Baeksoojeongchal’ is the naked waxy barley cultivar with the most whiteness and low proanthocyanidin content; therefore this could contribute to the promotion of barley consumption, by avoiding reduction in consumer preference (Registration No. 9194).

A new covered barley cultivar ‘Hangang’ with resistance to barley yellow mosaic virus (BaYMV) and tolerance to cold was developed by crossing ‘Samkwangchal/Radiant’ at the National Institute of Crop Science, RDA in 2018. The regional yield trials were conducted for ‘Hangang’ as a breeding line ‘Jeonju498’ in five different regions from 2016 to 2018. The average heading date of ‘Hangang’ was April 22, which was one day earlier than that of ‘Olbori’. The maturing date of ‘Hangang’ was May 30, which was similar to that of ‘Olbori’. The culm length was 81 cm, which was shorter than that of ‘Olbori’, showing tolerance to lodging stress. ‘Hangang’ showed the spike length of 4.6 cm with 669 spikes per m², 54 grains per spike, and a weight of 33.5 g for 1,000 grains. Compared with ‘Olbori’, ‘Hangang’ showed stronger withering in winter (winter hardiness) and resistance to BaYMV. Among quality characteristics, ‘Hangang’ showed similar levels as those of ‘Olbori’ with respect to protein, β-glucan and amylose (10.7%, 4.6%, and 18.8%, respectively). However, ‘Hangang’ showed higher polyphenol content (1.69 mg/g) than the check cultivar. The yield of ‘Hangang’ in the regional yield trial was 611 kg/10a in upland, 502 kg/10a in paddy field, and an overall average of 567 kg/10a, which was 15%, 16% and 16% higher than that of the check cultivar, respectively. Therefore, ‘Hangang’ will be suitable cultivar when sowed in cold regions (Registration No. 8773).

‘Dian’ was developed by crossing ‘Milyang85/Suwon335’, which has tolerance to lodging and high yield, and ‘Milyang122’, which has good brewing qualities, in 2003. The regional yield trials were conducted for ‘Dian’ as a breeding line ‘Iksan168’ in four different regions of Korea from 2012 to 2014. The heading and maturing dates of ‘Dian’ in paddy and upland fields were similar to ‘Hopum’. ‘Dian’ had a shorter culm length than ‘Hopum’ in paddy and upland fields, showing tolerance to lodging stress. The yield potential of ‘Dian’ was approximately 18% higher than that of ‘Hopum’ in the paddy fields, but there were no significant differences in the upland fields. ‘Dian’ had rym1 and rym5 genes and showed resistance to barley yellow mosaic virus (BaYMV), but was susceptible to powdery mildew. It also had good quality for brewing and was similar to ‘Hopum’. ‘Dian’ had a higher assortment ratio (94%) than ‘Hopum’ (89%). Regarding grain quality, ‘Dian’ was similar to ‘Hopum’ in protein content, β-glucan content, and husk rate. Concerning malt quality, ‘Dian’ showed a 71.6% extraction rate, 3.6% soluble protein content, and 33.0% Kolbach index, which are similar to the values of ‘Hopum’. Other malt qualities of ‘Dian’ include 185 WK (Windisch-Kolbach) diastatic power and 81.4% friability, which were lower than those of ‘Hopum’. Therefore, ‘Dian’ with high yield, tolerance to lodging, and resistance to BaYMV is considered to be stable for cultivation (Registration No. 8241).

‘Heugho’, a new cultivar developed in 2014, is a two-rowed hulled barley with black grains that was selected among doubled haploid lines produced by anther culture from a backcross between two cultivars. Black barley, which has black grains, was used as the donor parent and ‘Hopum’, which has an elite genotype, was used as the recurrent parent. Agricultural characteristics of the new cultivar such as heading date, lodging and disease resistance were similar to those of ‘Hopum’. The yield was approximately 3.8 ton/ha, which was also comparable to that of ‘Hopum’. In terms of grain quality, the thousand grain weights of ‘Heugho’ and ‘Hopum’ were similar at 44.9 g and 41.4 g, respectively. The malt quality of both cultivars, which was mainly determined by extract, diastatic power, Kolbach index, and soluble protein content, were also similar. The total polyphenol contents of ‘Heugho’ and ‘Hopum’ malts were 0.274% and 0.244%, and the anthocyanin contents were 37.1 µg/g and 16.5 µg/g, respectively. After malting, ‘Heugho’ had high antioxidant capacity, making it a functional food source for beer as well as tea. We expect that ‘Heugho’ will contribute to farmer’s income and regional economic activation associated with the barley processing industry(Registration No. 8239).

‘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).

‘Haepum’ is a bacterial blight-resistant, medium maturing rice cultivar with high grain quality. It was derived from a cross between ‘Iksan493’ (cultivar name ‘Jinbaek’) and the F₁ cross between ‘Iksan495’ (‘Dacheong’) and ‘Iksan496’ (‘Jungmo1005’). Of these three cultivars, ‘Jinbaek’ is a bacterial blight-resistant mid-late maturing rice cultivar with high grain quality, ‘Dacheong’ is a mid-late maturing rice cultivar with multiple resistance to disease and insects, and ‘Jungmo1005’ is a mid-late maturing rice cultivar with lodging tolerance. To develop fixed lines, the anther culture method was applied to F₁ plants. The cultivar ‘Haepum’ was selected using the pedigree method, yield trials, and local adaptability tests. The heading date of ‘Haepum’ was August 11^th, three days earlier than that of ‘Nampyeong’ cultivar. Haepum’ is a cultivar tolerant to lodging and it has short culms. Due to its low rate of viviparous germination, ‘Haepum’ could be useful for preventing pre-harvest sprouting in cultivation of medium maturing rice in the southern plain area of Korea. ‘Haepum’ carries two bacterial blight resistance genes (Xa3 and xa5), and in our study, it exhibited high-level and broad-spectrum resistance against bacterial blight, including K3a, the most virulent race in Korea. ‘Haepum’ is also resistant to the rice stripe virus and moderately resistant to rice blast. The yield of ‘Haepum’ was similar to that of ‘Nampyeong’. ‘Haepum’ showed excellent grain appearance and good taste of cooked rice, and therefore it could contribute to the development of bacterial blight-resistant rice cultivars of improved quality. ‘Haepum’ would be suitable for cultivation in the southern plain area of Korea as well as in bacterial blight-prone areas. (Registration No. 6068)

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.

Rice panicle architecture is an important factor affecting yield potential. Korean rice cultivars have a narrow genetic background for panicle architecture. To enhance the yield potential of Korean rice cultivars, we developed and characterized rice lines with new panicle architecture. Rice with improved panicle architecture has clustered spikelets and dense panicles (CD type). CD rice was derived from a cross between “Binhae Col.#1” carrying dense panicles, and “ARC10319” that has the clustered spikelets gene (Cl). CD rice lines had short and semi-erect panicles with two to five high density spikelets clustered at the tips of primary and secondary rachis branches. CD rice lines had dramatically increased numbers of spikelets; almost twice as many as those of Korean rice cultivars. The increase in spikelet number was mainly caused by the increased spikelets and branches on secondary rachises compared to those on primary rachises. The increase in spikelet number was expected to enhance the yield of CD rice by expanding sink capacity. However, the yield of selected lines; CD9, CD27, CD34, and CD39, did not reach the level of the Korean high-yielding cultivars “Boramchan” and “Hanareum2,” due to the reduction in panicle number and grain weight, and poor ripening. Although no substantial yield increase was observed in CD rice, the panicle architecture of CD rice, clustered spikelets, and dense panicles could be new genetic resources as breeding material for diversifying panicle architecture and enhancing yield potential.

To enhance rice yield and diversify grain quality of Korean japonica rice, we developed japonica rice line with long and spindle-shaped grain. Korean japonica rice cultivars have narrow genetic background of grain size and shape. Most of cultivars show medium-short and semi-round grain. To diversify the genetic background for grain, we developed Jeonju625, japonica rice line with long and spindle-shaped grain, derived from a cross between DSG79, the breeding material with extra-long and spindle-shaped grain, and Boramchan, japonica super high-yielding cultivar with medium-short and semi-round grain. Jeonju625 had GW2gs3qSW5+qGL3 allele type for grain-related genes, which conferred extra-long and spindle-shaped grain. The grain length and ratio of length to width of brown rice of Jeonju625 was 7.06 mm and 2.72, respectively. Jeonju625 was improved the deteriorated traits of DGS79, very late heading, long culm, long awn, droopy flag leaves, and susceptibility to lodging, by strong selection pressure focused on field breeding. The milled rice yield of Jeonju625 was 559 kg/10a, which was similar level of Boramchan (552 kg/10a) and 29% enhanced yield compared to DSG79. Jeonju625 had suitable characteristics for cooked rice. Jeongju625 showed lower protein contents and better glossiness and palatability of cooked rice than Boramchan and Hanareum2. Elite japonica rice line, Jeonju625, with extra-long and spindle-shaped grain showed good characteristics for rice yield and grain quality. Jeonju625 could be utilized practical cultivar and breeding material for enhancing rice yield and diversifying grain quality.

To diversify the grain size and shape of japonica rice, we developed the Breeding Materials with Diverse Grain Size and Shape (BM_DGS) and characterized the grain and yield-related traits. We used the donor parents Jizi1560 and Jizi1581, japonica germplasm with extremely large grain size. Four cross combinations between the each donor parents and Korean high yielding japonica rice cultivars, Deuraechan and Boramchan, were constructed and anther culture method was applied. Among 290 doubled haploid lines, we selected 91 elite lines with diverse grain size and shape and designated to the BM_DGS. The grain size and shape of BM_DGS exhibited beyond the characteristics of previously developed Korean rice cultivars. The alleles of major grain-related genes, GW2, GS3, and qSW5, in BM_DGS showed two types, wild type or loss-of-function mutant type. The loss-of-function mutant alleles, gw2, gs3, and qSw5, had an effect on increasing grain size. The phenotypic variation of grain length was mostly controlled by GS3 alleles, and grain width and thickness were influenced by the combinations of GW2 and qSW5 alleles. 1,000-grain weight was determined by the combinations of GW2, GS3, and qSW5. The grain-related genes influenced the phenotypic variation of yield-related traits. The result of this study could be useful to elucidate the relationship between the grain-related genes and agronomic traits. And the BM_DGS are being utilized in the breeding programs to diversify the grain size and shape in japonica rice.