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The development of efficient, robust, and high-throughput SNP genotyping platforms is pivotal for crop genetics and breeding. Recently, SNP genotyping platforms based on target capture sequencing, which is very flexible in terms of the number of SNP markers, have been developed for maize, cassava, and fava bean. We aimed to develop a target capture sequencing SNP genotyping platform for rice. A target capture sequencing panel containing 2565 SNPs, including 1225 SNPs informative for japonica and 1339 SNPs informative for indica, was developed. This platform was used in diversity analysis of 50 rice varieties. Of the 2565 SNP markers, 2341 (91.3%) produced useful polymorphic genotype data, enabling the production of a phylogenetic tree of the 50 varieties. The mean number of markers polymorphic between any two varieties was 854. The platform was used for QTL mapping of preharvest sprouting (PHS) resistance in an F8 recombinant inbred line population derived from the cross Odae × Joun. A genetic map comprising 475 markers was constructed, and two QTLs for PHS resistance were identified on chromosomes 4 and 11. This system is a powerful tool for rice genetics and breeding and will facilitate QTL studies and gene mapping, germplasm diversity analysis, and marker-assisted selection.

Pre-harvest sprouting (PHS) leads to serious economic losses because of reductions in yield and quality. To analyze the quantitative trait loci (QTLs) for PHS resistance in japonica rice, PHS rates on panicles were measured in 160 recombinant inbred lines (RILs) derived from a cross between the temperate japonica varieties Odae (PHS resistant) and Unbong40 (PHS susceptible) under two different environmental conditions—field (summer) and greenhouse (winter) environments. Genome re-sequencing of the parental varieties detected 266,773 DNA polymorphisms including 248,255 single nucleotide polymorphisms and 18,518 insertions/deletions. We constructed a genetic map comprising 239 kompetitive allele-specific PCR and 49 cleaved amplified polymorphic sequence markers. In the field environment, two major QTLs, qPHS-3FD and qPHS-11FD, were identified on chromosomes 3 and 11, respectively, whereas three major QTLs, qPHS-3GH, qPHS-4GH, and qPHS-11GH, were identified on chromosomes 3, 4, and 11, respectively, in the greenhouse environment. qPHS-11GH and qPHS-11FD had similar locations on chromosome 11, suggesting the existence of a gene conferring stable PHS resistance effects under different environmental conditions. The QTLs identified in this study can be used to improve the PHS resistance of japonica varieties, and they may improve our understanding of the genetic basis of PHS resistance.

High-throughput molecular markers with high genotyping accuracy will be helpful for genetic analysis, mapping of interesting genes, and rice breeding program. To develop high-throughput and cost-effective molecular markers for Korean japonica rice varieties, which are closely-related genetically, we designed kompetitive allele-specific polymerase chain reaction (KASP) assays from the sequence data of 13 Korean japonica rice varieties. Of the 504 new KASP assays, 371 (73.6%) showed polymorphisms among the tested varieties. In addition to the 400 previously developed KASP markers, this resulted in 771 KASP markers being applicable for Korean japonica rice varieties. These KASP markers were used to map the quantitative trait loci (QTLs) for rice bakanae disease (BD) resistance. From the results of QTL mapping and determination of the mortality rate of BD in two F2:F3 populations, a major QTL, qFfR1-1, and a novel QTL, qFfR6, were revealed on chromosome 1 in the Junam/Nampyeong F2:F3 population and on chromosome 6 in the Saenuri/Nampyeong F2:F3 population, respectively. Further, the insertion/deletion markers in the qFfR1-1 region were developed to select BD-resistant japonica rice varieties. The 771 developed KASP markers will accelerate the molecular breeding in Korean japonica rice varieties, and the detected QTLs will be helpful in identifying candidate genes for BD resistance.

Producing good-quality, fine rice flour is more difficult than wheat flour because the rice grain is harder. The non-glutinous Japonica-type variety Seolgaeng, derived from N-methyl-N-nitrosourea (MNU) mutagenesis, and four other varieties, representing a range of amylose contents, were evaluated in this study. Dry-milled Seolgaeng rice flour exhibited an average particle size that is

Temperate japonica rice varieties exhibit wide variation in the phenotypes of several important agronomic traits, including disease resistance, pre-harvest sprouting resistance, plant architecture, and grain quality, indicating the presence of genes contributing to favorable agronomic traits. However, gene mapping and molecular breeding has been hampered as a result of the low genetic diversity among cultivars and scarcity of polymorphic DNA markers. Single nucleotide polymorphism (SNP)-based kompetitive allele-specific PCR (KASP) markers allow high-throughput genotyping for marker-assisted selection and quantitative trait loci (QTL) mapping within closely related populations. Previously, we identified 740,566 SNPs and developed 771 KASP markers for Korean temperate japonica rice varieties. However, additional markers were needed to provide sufficient genome coverage to support breeding programs. In this study, the 740,566 SNPs were categorized according to their predicted impacts on gene function. The high-impact, moderate-impact, modifier, and low-impact groups contained 703 (0.1%), 20,179 (2.7%), 699,866 (94.5%), and 19,818 (2.7%) SNPs, respectively. A subset of 357 SNPs from the high-impact group was selected for initial KASP marker development, resulting in 283 polymorphic KASP markers. After incorporation of the 283 markers with the 771 existing markers in a physical map, additional markers were developed to fill genomic regions with large gaps between markers, and 171 polymorphic KASP markers were successfully developed from 284 SNPs. Overall, a set of 1225 KASP markers was produced. The markers were evenly distributed across the rice genome, with average marker density of 3.3 KASP markers per Mbp. The 1225 KASP markers will facilitate QTL/gene mapping and marker-assisted selection in temperate japonica rice breeding programs.

We used a 135K rice microarray to identify genes involved in anthocyanin biosynthesis and metabolism in black rice. Using our multi-interaction screening method, we then screened 427 expression genes, 754 orthologous genes, and 416 pathway-network related genes associated with anthocyanin bio-synthesis. Finally, we identified eight candidate genes by comparing pathway-expression genes, including ortholog-ontology genes. To verify the candidate genes, each was mapped to the black rice genome, and functional predictions were confirmed via phylogenetic reconstructions using the candidate genes and their homologous proteins. While the eight genes identified by our method require further characterization and validation, our study demonstrates the power of multi-interaction screening after the initial identification of genes with microarrays.

The ‘Jungmo1017’ is a japonica rice variety developed from a cross between Suweon462 which has a good plant architecture, cold tolerance, moderately tolerant to leaf blast and bacterial blight and medium maturing habit, and Yeongdeog34 which has translucent milled rice and good milling properties, by the rice breeding team at NICS, RDA in 2011. The heading date of ‘Jungmo1017’ is August 16 and it is six days later than ‘Hwaseong’. ‘Jungmo1017’ has 65 cm of culm length which is 18 cm shorter than those of ‘Hwaseong’ and 93 spikelet per panicle. The pre-harvest sprouting rate of ‘Jungmo1017’ is 8.6% that is lower than 27.7% of ‘Hwaseong’ on local adaptability test (LAT). It showed resistance to blast diseases and moderately resistant to bacterial blight (K1 race) and stripe virus, but susceptible to other races (K2, K3 and K3a) of bacterial blight, viruses and planthoppers. The milled rice of this variety exhibits translucent, clear non-glutinous endosperm and medium short grain shape. It has better palatability index of cooked rice (0.53) than that of ‘Hwaseong’. ‘Jungmo1017’ showed lower protein content (6.4%) and amylose content (18.0%). ‘Jungmo1017’ could use aseptic-packaged cooked rice or processing cooked rice because its hardness of cooked rice is soft, setback and balance is low and palatability of cold and aseptic rice showed high score. The characters related to milling is better than those of ‘Hwaseong’. ‘Jungmo1017’ showed 5.01 MT/ha of milled rice productivity at 7 sites of middle plain, southern mid-mountainous and south-east coastal area in ordinary cultivation. ‘Jungmo1017’ could be adaptable to the middle plain area in Korea.

A recombinant inbred line (RIL) population derived from the cross between Ilpumbyeo (a Japonica of high eating quality) and Moroberekan (a tropical Japonica type of low eating quality) was used for mapping QTLs associated with grain physicochemical properties and eating quality traits in rice. A total of 182 recombinant inbred lines were evaluated for two physicochemical traits, alkali digestive value and amylose content, and five traits associated with eating quality including glossiness of cooked rice determined by Toyo-taste meter, and glossiness, stickiness, hardness and overall evaluation for taste evaluation by panels. A total of 30 QTLs associated with seven traits in 10 loci on chromosomes 1, 3, 5, 6, 10, and 12 were identified. The most critical regions for eating quality were on chromosomes 3, 5 and 6 by Ilpumbyeo alleles, whereas Moroberekan contributed a total of 6 loci on chromosomes 1, 10 and 12. The QTL region on chromosome 5 contains the novel alleles for eating quality from Ilpumbyeo. MAS using DNA markers tightly linked with those QTLs will be useful for breeding Japonica cultivars with high eating quality.

본 연구는 국내에서 육성되어 발아현미용으로 농가에 보급되고 있는 큰눈벼와 삼광벼의 발아현미 제품에 대하여 1~5 mm로 구분하여 발아싹을 틔운 다음 발아전의 일반현미와 싹길이에 따른 품질변화 양상을 구명할 목적으로 수행하였다. 일반성분인 단백질함량의 경우는 발아전 현미에 비하여 발아후의 싹길이에 따라서 약간 증가추세를 보였으나, 통계적 유의성은 인정되지 않았으며, 아밀로스의 경우 큰눈벼는 15~16%, 삼광벼는 17~18% 범위에서 유의적인 차이는 나타나지 않았다. 아울러 큰눈벼와 삼광벼 모두 발아과정에서 물리화학적 반응이 나타나 조직이 물러지고 호화가 진전되어 RVA로 측정한 결과, 호화점도 급격하게 낮아져 발아현미의 물성이 개선되어 밥맛을 향상되는 결과를 확인 할 수 있었다. 특히 밥맛과 관련이 깊은 치반점도(Setback)가 더욱 낮아지는 현상이 나타나 발아현미를 가공하게 되면 안정적으로 식감(밥맛)이 좋아지고 밥의 노화가 지연되어 밥맛이 오래 유지되는 결과를 얻을 수 있었다. 그러나 싹길이가 1 mm정도 신장된 발아현미의 호화점도 변화양상과 싹이 2~5 mm 이상 신장된 발아현미와의 호화점도 변화양상 차이가 없었다. GABA함량도 큰눈벼는 발아과정에서 3배 이상 증가되는 결과를 얻었으며, 삼광벼의 경우는 발아전 일반현미에서는 GABA함량의 활성이 나타나지 않아 $0.005{\mu}g/g$ 이었는데 발아현미에서는 $0.2428~0.2475{\mu}g/g$ 로 약 50배정도 명료하게 증가되었다. 발아현미의 경도는 발아전의 일반현미에 비하여 발아현미는 유의적으로 낮아졌으나, 싹길이가 2 mm 이상에서는 낮아지는 경향이 두드러지지 않았다. 결론적으로 발아현미를 가공할 때 싹길이는 2 mm 이하로 최대한 억제하면서 내부성분을 최대한 증가시키는 가공방법을 채택하는 것이 바람직할 것으로 사료되었다. 【The objective of this study was to evaluate quality properties including amylose, alkali digestion value (ADV), texture and GABA (Gamma Amino-Butyric Acid) of brown rice and 1~5 mm germinated brown rice of Keunnun and Samkwang culitvars. The protein content of germinated brown rice showed increasing tendency according to shoot length, however, the difference was not statistically significant. The amylose content of all samples ranged from 15.0% to 16.0% in Keunnun and 17.0% to 18.0% in Samkwang, without significant differences. Compared to regular brown rice, germinated brown rice from both cultivars demonstrated reduced gel consistency, which contributed to the improved cooked rice texture. Especially, germinated brown rice had significantly lower setback values, which is correlated with high palatability of cooked rice. However, there was no significant difference in gel consistency between 1 mm and 2~5 mm germinated brown rice. GABA content in Keunnun increased by 3~5 times after germination process. In Samkwang, GABA content increased by 50 times (from $0.005{\mu}g/g$ to $0.243{\sim}0.247{\mu}g/g$ ) after germination. The hardness of germinated brown rice was significantly lower than that of brown rice. However, there was no significant difference in hardness according to shoot length. Consequently, when processing germinate brown rice, it is recommended to maximize functional ingredients by germination while maintaining shoot length less than 2 mm.】

A set of five Korean rice cultivars and seven drought-tolerant indica lines were screened under irrigated non-stress and drought-stressed conditions in the 2011 and 2012 dry seasons at IRRI, Philippines. The drought-stressed experiment received mild to moderate stress. Under drought stress, 'IR86918-B-439-B' had the highest grain yield among all tested lines and 'Hanarembyeo' had the highest grain yield among the five Korean rice cultivars. 'IR86918-B-439-B' also had the highest yield under irrigated non-stress conditions. The grain yield of 'Hanareumbyeo' was similar to 'IR86918-B-439-B' under non-stress conditions. SSR marker analysis was performed using 125 SSR markers for detection of polymorphic markers between the Korean rice cultivars and the drought-tolerant indica lines, and for genetic diversity analysis. Twelve polymorphic markers were identified in the region of three major drought QTLs (DTY1.1, DTY2.2, DTY3.1) in two of the Korean rice cultivars and three of the drought-tolerant lines. These polymorphic markers will be useful as foreground genotyping markers for drought-QTL introgression in Korean rice genetic backgrounds.