Bakanae disease, caused by various Fusarium species, poses a significant threat to global rice production, with its incidence increasing in major rice-producing regions. Currently, no rice varieties exhibit complete resistance to this disease. Enhancing resistance in rice cultivars could serve as a cost-effective and sustainable alternative to fungicide application. Developing resistant rice varieties may offer a practical solution to mitigate yield losses and reduce dependency on chemical treatments. ‘Jinokchal’ was derived from the cross between ‘Milyang299’, which harbors bakanae disease-resistant QTL qBK1. and ‘Baekokchal’ in 2014. A promising line, YR31624-5B-2, was then selected and designated as ‘Milyang366’ in 2019. The local adaptability test of ‘Milyang366’ was conducted at five locations from 2020 to 2022, and the cultivar was subsequently named ‘Jinokchal. ’ The heading date of ‘Jinokchal’ was August 13, classifying it as a medium-late maturing cultivar. The culm was 77 cm long and had 108 spikelets per panicle. The 1,000 grain-weight of brown rice is 22.7 g, which is heavier than that of ‘Sinseonchalbyeo’. This variety is resistant to blast, rice stripe virus, and bacterial blight, but susceptible to insect pests. The yield potential of ‘Jinokchal’ was approximately 497 kg/10a at the ordinary fertilizer level in the local adaptability test over three years. ‘Jinokchal’ is moderately resistant to bakanae disease and harbors the qBK1 gene derived from the tong-il type rice ‘Shingwang’ (Registration No. 8135).

In Asia, where climate change is increasing the damage caused by cold stress, it is crucial to cultivate varieties with enhanced cold tolerance. In this study, the Tongil variety ‘Hanareum2’ was crossed with the Japonica variety ‘Unkwang’ to improve plant growth ability at low temperatures during the seedling stage. This led to the development of 234 recombinant inbred line (RIL) populations, and a linkage map was constructed using 249 single nucleotide polymorphism (SNP) markers. The RIL populations were transplanted to the field one month earlier than the standard transplanting period, and plant height (PH), leaf number (LN), and dry weight (DW) were measured to identify quantitative trait loci (QTL) associated with plant growth ability at low temperatures during the seedling stage. QTLs related to cold tolerance, particularly those carrying the ‘Unkwang’ allele, were identified in the PH and DW traits. For PH, the QTLs qPH1, qPH5, and qPH8 were located on chromosomes 1, 5, and 8, respectively. Regarding DW, the QTLs qDW1, qDW8, and qDW9 were identified on chromosomes 1, 8, and 9. For the LN trait, qLN3 carrying the ‘Hanareum2’ allele was located on chromosome 3. If the identified QTLs are utilized, they can be incorporated into breeding programs for plant growth at low temperatures during the seedling stage.

To promote the expansion of rice consumption, we examined the nutritional components and qualities of five Tongil-type rice varieties. Regarding texture properties, ‘Dasan’ showed the highest viscosity at 0.43 kgf, whereas ‘Hanareum3’ displayed the lowest at 0.20 kgf. Regarding pasting properties, ‘Hanareum4’ exhibited the slowest aging speed of rice flour dough with a value of -42.34 RVU, and ‘Hanareum3’ had the slowest aging speed of cooked rice with a final viscosity of 258.62 RVU. Regarding proximate compositions, ‘Hanareum3’ had the highest crude ash content at 1.17 g/100 g, and ‘Hanareum2’ had the highest crude protein content at 8.39 g/100 g. Regarding amino acids, at 0.17–0.18%, ‘Dasan’ had a methionine content 0.13% lower than the other varieties. Regarding mineral contents, potassium, phosphorus, and magnesium contents were the highest in ‘Hanareum3’ at 263.08, 354.85, and 109.18 mg/100 g, respectively. ‘Dasan’ showed the highest contents of iron, manganese, and zinc, measured at 0.94, 2.17, and 1.43 mg/100 g, respectively. Of the 36 fatty acids measured, only 9 were confirmed. Myristic acid, linoleic acid, and alpha-linolenic acid were highest in ‘Hanareum3’ at 0.27, 9.91, and 0.48 mg/g, respectively. ‘Hanareum4’ had the highest levels of palmitic, stearic, and oleic acids, with contents of 6.69, 0.79, and 9.64 mg/g, respectively. Arachidic, eicosenoic, and lignoceric acids were detected at high levels in ‘Geumgang1,’ ‘Hanareum2,’ and ‘Dasan,’ with contents of 0.16, 0.13, and 0.3 mg/g, respectively.

Bakanae disease, also known as the foolish seedling disease, caused by Gibberella fujikuroi, is a serious issue in Korea. Since 2007, there has been a rapid increase in the occurrence of bakanae disease; this has caused severe yield loss to rice farmers every year. The most reliable and economical solution for managing bakanae disease is to cultivate resistant varieties; however, there are only a few rice varieties in Korea that can withstand this disease. Therefore, this study aimed to evaluate the resistance of 61 major rice varieties which account for 89% of the total rice cultivation area. Only six varieties showed intermediate or higher resistance to bakanae disease; this included Anpyeong and Samkwang. The genetic inconsistency between the bioassay results and the allele types of 12 molecular markers (associated with four QTLs) ranged from 4.7% to 48.7%. Therefore, more accurate markers, such as gene-based markers, are essential for monitoring general breeding programs or gene pyramiding.

Bakanae disease is caused by several species of Fusarium and imposes serious limitations to rice production worldwide. The incidence of this disease is increasing in the top rice-growing countries. No rice variety has been found to be completely resistant to this disease. Thus, higher resistance to the disease may be a cost saving solution preferable to the application of fungicides. ‘Anpyeong’ was derived from the cross between ‘YR24982-9-1’ and ‘Saeilmi’ in 2012 and selected as the promising line, ‘YR30389-B-2GH-103’; it was further selected and designated as ‘Milyang 313’ in 2016. The local adaptability test for ‘Milyang 313’ was conducted at five locations from 2016 to 2018 and the cultivar was named ‘Anpyeong’. The heading date for the medium-late maturing cultivar ‘Anpyeong’ was August 13. The ‘Anpyeong’ culm was 77 cm long and had 115 spikelets per panicle. The brown rice 1,000 grain-weight was 22.2 g, which is higher than that of ‘Nampyeong’. This variety is resistant to blast disease and rice stripe virus, but susceptible to bacterial blight and insect pest. The potential ‘Anpyeong’ yield was approximately 562 kg/10 a at ordinary fertilizer level in the local adaptability test and for three years. ‘Anpyeong’ harboring the qBK1 gene derived from a tongil type rice ‘Shingwang’ is moderately resistant to bakanae disease (Registration No. 8135).

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.

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.

Limitation of genetic diversity in japonica rice breeding populations is often identified as a potential obstacle for the development of high yielding cultivars. The use of diverse germplasm in rice breeding has been suggested as one way of combating this problem. This study was conducted to improve the genetic diversity for rice, by developing an advanced backcross population derived from a backcross ‘Junam’ as recurrent parent and ‘IR72’ as a donor parent. Among them, we selected a promising line ‘YR24438-B-B-B-B-132’ containing bacterial blight resistance gene Xa4. Testing in the replicated yield trial in 2009, the ‘YR24438-B-B-B-B-132’ line was selected, and it was designated as ‘Milyang298’. The local adaptability test of ‘Milyang298’ was carried out at three locations from 2014 to 2016 and it was named ‘MY298BB’. The average culm length in the replicated yield trials was 87 cm, which is 15 cm taller than recurrent parent ‘Junam’. Number of spikelets per panicle was significantly lower than in ‘Junam’ but the number of tillers per hill was higher. This variety is resistant to bacterial blight race K1, K2, K3, and K3a.However ‘MY298BB’ showed early leaf senescence at the mature stage and the chlorophyll content of ‘MY298BB’ was significantly lower than that of the recurrent parent ‘Junam’. Moreover the grain filling ratio and yield were significantly lower in ‘MY298BB’ than those of recurrent parent ‘Junam’. Therefore, understanding the leaf senescence mechanism would be useful for improving yield potential in rice.

The rice recombinant inbred lines derived from Hanareum2 and Unkwang (HURILs) cross were used in genetic mapping and QTL analysis studies using the inclusive composite interval mapping (ICIM) method. In this study, we constructed the genetic map using 241 SNP markers based on the SNPs in the whole genome region between these varieties. As a result, the total genetic distance and average distances were 1,142 cM and 4.7 cM, respectively. Both heading date and plant height are important traits related to grain yield in rice. Twelve heading date QTLs were detected under natural condition in Korea. A major QTL qDTH3-2 for heading date and qCL1-2 for plant height explained 25.8~27.4% and 30.8~56.9% of the phenotypic variations in the HURIL populations. Four panicle traits, grain number (GN), panicle length (PL), number of panicle per plant (NPP), grain filling ratio (GFR) were evaluated for QTL effects in HURILs population during two years. Results showed that a total of twelve QTLs for GN, PL, NPP, and GFR were detected on chromosome 2, 3, 4, 6, 7, 8. A major QTL qGNP4 for GN was detected in HURIL populations with LOD score 7.7-19.3 and explained 6.7-17.69% of phenotypic variations. Twenty-five QTLs for the four traits TGW, GL, GW, and GT were identified in the HURIL populations for two years (2014~2015). The three QTLs, qTGW8, qGL8-2, and qGW8-2, shared the same interval between id8007093 and id8007764 on chromosome 8 with explained 4.8-4.1%, 4.2-6.8%, and 5.3-10.5% of phenotypic variations, respectively. Furthermore, two QTLs, qTGW3-2 and qGL3-2, were detected in the same chromosomal interval at the same position. These findings will benefit breeding design for development of high yielding variety in rice.

Rice stripe virus (RSV) is one of the major constraints in rice production which is transmitted by the small brown plant hopper, Laodelphax striatellus. Identifying new resistance genes from diverse sources is important for rice breeding programs to enhance the resistance level and/or to overcome the breakdown of resistance genes. This study was conducted to identify novel sources of resistance against RSV. We used five RSV resistant varieties that do not harbor Stv-bⁱ. The presence of known genes for RSV resistance was identified using the InDel7 marker for Stv-bⁱ, two Indel (Sid primer set) markers for Stv-b, and DNA sequence analysis for OsSOT1. We revealed that two varieties, 02428 (IT236925) and Tung Ting Wan Hien 1, are novel RSV resistance sources.

Rice tungro disease is a serious threat to rice production in South and Southeast Asian countries. Rice production in these countries has been intensified, often through continuous cultivation of rice. We conducted a screen of the resistance to tungro virus disease in Korean japonica rice. Dongjin, Hwaseong, and Sangju were varieties resistant to Rice tungro spherical virus (RTSV) but susceptible to Rice tungro bacilliform virus (RTBV). RTSV-resistant variety Sangju was crossed with RTSV-susceptible variety Unkwang to conduct a genetic analysis for RTSV resistance originating from Sangju. Evaluation of 201 F2 plants from the cross between Unkwang and Sangju showed that there were 85 plants showing resistance, and that 116 plants were susceptible, indicating a ratio fitting a 7:9 ratio ratio (χ² = 0.54; p = 0.46). Thus, the resistance to RTSV in Sangju might be controlled by two recessive genes. This result indicates that Sangju might serve as a useful genetic source for diversification of RTSV resistance and stabilization of resistance through gene pyramiding.

‘Hwaweon 6’ was developed from a cross between ‘Hwaseongbyeo’ and a wild species, Oryza minuta L. (Acc. No. 101154) based on marker-assisted selection and backcrossing. The recurrent parent ‘Hwaseongbyeo’ is a high grain quality cultivar with medium maturity. Hwaweon 6 is nearly isogenic to Hwaseongbyeo except a small O. minuta introgressed segment on chromosome 7 harboring genes related with spikelets per panicle. The preliminary and replicated yield trial was conducted at Chungnam National University and Chungcheongnamdo Agricultural Research & Extension (CARES), Yesan in 2009 and 2010. The local adaptability test was carried out by the National Seed Management Office (NSMO) in 2011 and 2012. This cultivar was registered to NSMO with a cultivar designated as Hwaweon 6. This cultivar averaged 80cm in culm length and has a medium growth duration. Milled rice of Hwaweon 6 is translucent and the grain quality traits are comparable to those of the recurrent parent. The average yield potential of Hwaweon 6 in grain was about 6.57 MT/ha at the ordinary fertilizer level for two years about 3.0% higher than that of Hwaseongbyeo due to an introgression of the quantitative trait locus (QTL) for spikelets per panicle (qSPP7) from O. minuta. This variety is comparable to Hwaseongbyeo in low temperature germinability and cold tolerance. The qSPP7 QTL would be useful in enhancing yield potential in rice breeding program.

‘Hwaweon 7’ was developed from a cross between the African upland cultivar, ‘Moroberekan’ and ‘Ilpumbyeo’ based on marker-aided backcross selection. The recurrent parent, Ilpumbyeo is a high grain quality cultivar with medium to late maturity. Hwaweon 7 is nearly isogenic to Ilpumbyeo except a small Moroberekan introgressed segment on chromosome 6 harboring genes related with spikelets per panicle and internode diameter. The preliminary and replicated yield trial was conducted at Chungnam National University and Chungcheongnamdo Agricultural Research & Extension (CARES), Yesan in 2010 and 2011. The local adaptability test was carried out by the National Seed Management Office (NSMO) in 2012 and 2013. This cultivar was registered to NSMO with a cultivar designated as “Hwaweon7”. This cultivar averaged 80cm in culm length and has a medium growth duration. Milled rice of “Hwaweon7” is translucent and the grain quality traits are comparable to those of the recurrent parent. The average yield potential of Hwaweon 7 in grain was about 6.48 MT/ha at the ordinary fertilizer level for two years about 5.1% higher than that of Ilpumbyeo due to increase in spikelets per panicle. This variety is tolerant to lodging and the tolerance is due to the APO1 gene controlling the base internode diameter on chromosome 6 introgressed from the donor parent, Moroberekan. The Apo1 gene would be useful in enhancing resistance to lodging in rice breeding program.

Grain size has a great impact on rice grain yield and is controlled by quantitative trait loci (QTL). Daeribbyeo 1 with big grain is widely used for genetic materials to develop varieties with diverse grain size. This study was conducted to identify genes controlling grain size traits of Daeribbyeo 1. An F_2:3 population derived from a cross between two japonica cultivars, Boseogheugchal and Daeribbyeo1, was used to identify QTL controlling grain shape traits. A total of 284 F₂ plants were measured for grain shape traits, grain length (GL), grain width (GW), grain thickness (GT), 1,000 grain weight (TGW), and two morphological traits, pericarp color and waxy endosperm. Sixty F₃ lines were selected based on the grain shape traits and marker genotypes and evaluated for grain shape traits. For marker analysis, SSR markers tightly linked to five known grain size genes and two QTLs were selected and used for genotyping. A total of 11 QTLs detected on chromosomes 2, 3, 4 and 6 explained phenotypic variation from 3.9% to 59.3%. qTGW2, qGW2 and qGT2 were detected in the same region between RM12811-RM12837 that are tightly linked with GW2 gene. qTGW3 and qGL3 were detected near GS3 gene. To know whether Daeribbyeo 1 has the same mutations in GW2 and GS3 as the various grain-size genotypes, GW2 and GS3 of two parents were sequenced. Daeribbyeo 1 had the same one base (A) deletion at a position 316 as ‘WY3’ in GW2 which results in the loss of function of GW2 gene. Boseogheugchal showed a C-to-A nonsense mutation in the second exon of GS3 gene that increased grain length. Interaction between GW2 and GS3 was not significant indicating that two genes controlled grain-size traits in additive pathway. The results from this study indicate that three QTLs GW2, qGT4 and qGL6 are associated with the grain size variation in Daeribbyeo 1 with GW2 as the major QTL.

‘Hwaweon3’ was developed from an interspecific cross between Hwayeongbyeo and a wild species, Oryza rufipogon L. (W1944) based on marker-aided selection and backcrossing. The recurrent parent ‘Hwayeongbyeo’ is a high grain quality cultivar with medium-maturity. ‘Hwaweon3’ is nearly isogenic to Hwayeongbyeo except a small O. rufipogon introgression on chromosomes 1, 8 and 12 harboring the QTL gene for cold tolerance. The preliminary and replicated yield trial was conducted at Chungnam National University in 2006 and 2007. The local adaptability test was carried out by the National Seed Management Office (NSMO) in 2008 and 2009. This cultivar was registered to NSMO with a cultivar designated as ‘Hwaweon3’. This cultivar averaged 78 cm in culm length and has a medium growth duration. This variety is resistant to stripe virus as the recurrent parent, and moderately resistant to leaf blast disease with durable resistance. Milled rice of ‘Hwaweon3’ is translucent and the grain quality traits are comparable to those of the recurrent parent. it has low protein content. The yield potential of ‘Hwaweon3’ in grain is about 7.23 MT/ha at the ordinary fertilizer level comparable to that of Hwayeongbyeo. ‘Hwaweon3’ performed better than Hwayeongbyeo in cold tolerance-related trait in the cold water-irrigated plot in the Chuncheon sub-station. This is mainly due to the introgressed segment from O. rufipogon on chromosome 1 harboring pe1.2 for panicle exsertion. ‘Hwaweon3’ could be used as a bridging line to enhance cold tolerance of japonica breeding lines.