Early selection of grain quality traits in rice (Oryza sativa L.), is essential to improve the yield and quality of this staple crop. We analyzed four key traits—protein content, grain filling rate, height, and panicle length—in 85 Korean cultivars. Through whole- genome resequencing we identified 12,718,879 raw single nucleotide polymorphisms (SNPs); after PLINK-based quality control (bi-allelic selection, call rate≥0.90, MAF≥0.03), ~2.20 million high-quality SNPs remained for machine-learning (ML) pre-screening. To rank the features (without marker-level inference), we applied a liberal univariate PLINK case-control scan using the top and bottom 30% per trait. We also analyzed associations with a linear mixed model (GCTA v1.93.2, MLMA; fixed covariates: ecotype, PC1, PC2; random effect: GRM) to verify calibration under population structure; with n=85, no genome-wide significant hits were detected, and QQ-plots indicated adequate calibration (per-trait effective tests m≈1.54-1.57 million under stricter filters). The random forest feature importance prioritized 26, 51, 19, and 20 core SNPs for the four traits, respectively. Across the algorithms, the best models achieved mean accuracies of 81.8% (protein content), 81.0% (grain filling rate), 73.1% (height), and 94.0% (panicle length). All selected SNPs met the Fluidigm array design requirements, supporting its deployment as a compact, genotype-based panel for early selection and a practical step toward digital breeding in rice.

The rice cultivar ‘Chamdongjin’ was developed to enhance the disease resistance of ‘Sindongjin’. ‘Sindongjin’, developed by the RDA in 1999, is a mega-variety with a unique grain size and excellent taste, and has been cultivated in the largest area in Korea since 2018. As ‘Sindongjin’ has been cultivated in a large area recently, problems such as pest damage are increasing, and the necessity to develop alternative cultivars is emerging. Accordingly, the multiple disease-resistant, mid-late maturing rice cultivar ‘Chamdongjin’, carrying the bacterial blight resistance gene Xa21 into the genetic background of ‘Sindongjin’, was developed. ‘Chamdongjin’ was developed by the backcrossing method using the donor parent ‘HR27195-59-3-5-5’, harboring the bacterial blight resistance genes Xa3+Xa21 and the recurrent parent ‘Sindongjin’. ‘Chamdongjin’ was selected through the pedigree method, yield trials, and local adaptability tests, with a high selection pressure for agronomic trait similarities with ‘Sindongjin’. In order to effectively improve the disease resistance, marker-assisted selection for disease resistance genes and bioassays for bacterial blight, blast, and stripe virus were performed in parallel. ‘Chamdongjin’ was confirmed to have three disease-resistance genes, Xa3+Xa21+Stvb-i. Most of agronomic traits of ‘Chamdongjin’ were similar to ‘Sindongjin’, while ‘Chamdongjin’ showed enhanced disease resistance against bacterial blight and panicle blast compared to ‘Sindongjin’. ‘Chamdongjin’, like ‘Sindongjin’, possessed a grain size-related gene, the gs3 allele, and exhibited larger grains than general Korean japonica cultivars. In addition, ‘Chamdongjin’ showed a similar or higher level of palatability compared to ‘Sindognjin’, indicating the excellent quality characteristics. In the genetic background analysis using 787 KASP markers, ‘Chamdongjin’ showed 96.3% homozygosity with ‘Sindongjin’, indicating that it had a more similar genetic background to ‘Sindongjin’ than to other existing cultivars. ‘Chamgdongjin’ is expected to be widely cultivated as an alternative to ‘Sindongjin’, which could maintain the brand value while preventing the disease damage caused to ‘Sindongjin’ (Registration No. 9310).

The damage caused by typhoons to rice production has been increasing. To reduce this damage, wind-tolerant rice breeding programs have been conducted at the Yeongdeok substation (YS) of the National Institute of Crop Science (NICS). This study was conducted to examine the effects of these wind-tolerant rice breeding programs. Under the wind-tolerance screening facility (WTSF), the wind-tolerance of 17 rice varieties bred at NICS (usual rice) and 20 rice varieties bred at YS (wind-tolerant rice) were analyzed by evaluating six traits: white spikelet (WS), white panicle (WP), degree of wind damage (DG), ratio of ripened grain (RRG) at control (RRG_C) and treatment (RRG_T), and reduction rate of RRG between control and treatment (RRG_R). Wind-tolerant rice showed more wind-tolerant characteristics than usual rice, such as lower WS, WP, DG, and RRG_R and higher RRG_T and RRG_C. In the principal component analysis, wind-tolerant rice showing a similar direction for RRG_T and RRG_C were located separately from the usual rice. The adaptability tests of wind-tolerant rice were conducted by evaluating eight yield-related traits in the wind-prone areas. Wind-tolerant rice was divided into three clusters by K-means clustering analysis using WP and RRG_T with the WTSF, RRG, and yield in the wind-prone areas. Among the three clusters, YC2 had the strongest wind tolerance performance, followed by YC3 showing moderate wind tolerance, and YC1 the weakest wind tolerance. ‘Sinbo’, a variety belonging to YC2, exhibited the strongest wind tolerance and high yield potential among all varieties. The wind-tolerant rice varieties bred at YS could be used practically to prevent wind damage and utilize breeding materials to enhance the wind tolerance of rice varieties.

The cultivation of early maturing rice in the Honam plain area of Korea is increasing to diversify the cropping systems. The cropping systems of this rice are usually classified as early, ordinary, and late cultivations based on transplanting time. The characteristics of varieties vary depending on the cultivations. To evaluate the performance of varieties and interpret the relationships between genotype and environment, nine yield and 17 panicle-related traits of six early maturing rice varieties (Jopyeong, Odae, Unkwang, Haedamssal, Jinkwang, and Haedeul) were characterized on early, ordinary, and late cultivations. Heading date was longer in order of early, ordinary, and late cultivations. The cumulative mean temperature of growth stage was similar for all cultivations. The variation in the number of spikelets per panicle (NS) was mainly due to the variety and the traits related with secondary rachis-branch were affected more by variety than the traits related to primary rachis-branch. The varieties with the highest yield were Haedamssal on early maturing cultivation and Unkwang on ordinary and late cultivations. Haedamssal displayed a panicle-number type plant architecture with relatively higher number of panicles per hill (PN) and average NS. Unkwang exhibited panicle-weight type with many NS and less PN. Additive main effects and multiplicative interaction analysis revealed that, NS and HD were mostly affected by genotype and environment, respectively. Among yield-related traits, NS contributed the most to enhanced yield of varieties in all cultivations. NS could be the target trait of breeding programs intended to improve the yield potential of early maturing rice adaptable to the Honam plain area. However, proper PN should be considered because PN, which was negatively correlated with NS, also affected the yield.

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.

‘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.

A doubled haploid (DH) lines derived from the cross between high-yielding japonica rice cultivars ‘Deuraechan’ and ‘Boramchan’ was developed to increase diversity of panicle and yield-related traits and select high-yielding lines. Panicle and yield-related traits of DH population consisting of 163 lines and 13 selected high-yielding lines were analyzed using correlation, principal component, and path analysis. Among panicle-related traits, number of spikelets on secondary rachis-branches (SRBs) was more highly correlated with and had more positive effect on number of spikelets (NS) than number of spikelets on primary rachis-branches (PRBs) per panicle. In the DH population, NS had the most positive effect on yield, whereas panicle number per hill (PN) was in the selected lines. PN was significantly positive correlated with ratio of ripened grain (RGG) in both case. The enhancement of ripening and increase of total spikelets number by increasing PN had more effect on yield than increase of total spiekelts number by increasing NS in the selected lines. Among 13 lines, four lines, AC60, AC152, AC156, and AC161 showed higher yield than Deuraechan (481 kg/10a) and Boramchan (558 kg/10a). Deuraechan exhibited panicle-weight type with low tiller and heavy panicles and Boramchan was slightly panicle-number type with more PN and higher RGG. Selected high-yielding lines showed medium characteristics of parents with improved yield potential. These elite lines could be utilized to develop high-yielding japonica rice.