• Proceedings of the Korean Society of Crop Science Conference
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• 2019.04a
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• pp.128-128
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• 2019

• Korean Journal of Agricultural Science
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• v.41 no.1
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• pp.1-7
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• 2014

Ratooning ability is one of the major different traits from perennial to cultivated rice and annual type. We developed a set of 126 introgression lines derived from a cross between Hwayeong and W1944 (O. rufipogon) to gain an insight into the genetic factors underlying differences between common wild rice and cultivated rice. One IL, CR6 among the 126 ILs of $BC_3F_4$ showed a significant difference in rationing ability compared with Hwayeong. To further characterize the rationing ability, CR6 was selected and crossed to Hwayeong to produce three secondary populations, $BC_4F_2$, $BC_4F_3$ and $BC_5F_2$. In the Hwayeong background, the W1944 allele was associated with an increase in rationing ability. QTL analysis showed that the qRAT5 for rationing ability was linked to RM194 ($R^2$=6.6%, 19.6%, and 44.5% in the $BC_4F_2$, $BC_5F_2$, and $BC_5F_3$, respectively). The putative qRAT5 was also tightly linked to QTLs for spikelets per panicle and grain weight indicating that this region harbors a QTL cluster related to domestication. To our knowledge, this is the first report to map the major QTL for ratooning ability in rice. The SSR markers linked to qRAT5 would be useful in marker-assisted selection for breeding lines with enhanced ratooning ability.

• Journal of Life Science
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• v.14 no.2
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• pp.339-344
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• 2004

Identification of individual quantitative trait loci (QTL) is a prerequisite to application of marker-assisted selection for stern length. Two simple sequence repeat (SSR)-based linkage maps were constructed from recombination inbred line populations between cross of Keunolkong and Shinpaldalkong. Two parents used differed greatly in stem length, which were 30.57 cm and 49.75 cm in Keunolkong and Shinpaldalkong, respectively. Using the constructed maps, regression analysis and interval mapping were performed to identify QTLs conferring stem length. Four QTLs for stem length on linkage groups (LG) F, J, N and O were identified in the Keunolkong ${\times}$ Shinpaldalkong population and they totally explained 37.83% of variation for stem length. In the population, two major QTLs on LG J and O conditioning 14.25% and 10.68% of the phenotypic variation in stem length were determined and two QTLs with minor effect were detected on LG F and N. Identification of QTLs for stem length and mapping individual locus should facilitate to describe genetic mechanisms for stem length in different population. SSR markers tightly linked to QTLs for stem length allow to accelerate the elimination of deleterious genes and selection for desirable recombinants at early stage in crop breeding programs.

• Korean Journal of Breeding Science
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• v.40 no.3
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• pp.243-249
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• 2008

In the previous study, 141 $BC_3F_2$ lines from a cross between the Oryza sativa cv. Milyang 23 and O. glaberrima were used to identify favorable wild QTL alleles for yield component traits. In this study, we carried out QTL analysis of four grain morphology as well as four yield component traits using 141 $BC_3F_5$ lines from the same cross and compared QTLs detected in two different generations. The mean number of O. glaberrima segments in the 141 $BC_3F_5$ lines ranged from 1 to 13 with 2.69 and 5.71 of the average means of homozygous and heterozygous segments, respectively. There was a three-fold difference in the number of QTLs detected for four traits commonly evaluated in two generations (seven QTLs in the $BC_3F_5$ vs 21 in the $BC_3F_2$ population). The percentages of the phenotypic variance explained by QTLs in the BC3F5 population were similar to or less than those in the $BC_3F_2$ population. This is probably due to the difference in the genetic composition of two populations and the environmental effects. The locations of the QTLs commonly detected in both generations were in good agreement except for one QTL for spikelets per panicle. The yield QTL, yd3 was colocalized with the spikelets per panicle, spp3. Yield increase at this locus is due to the increase in spikelets per panicle, because both traits were associated with increase in spikelets per panicle and yield due to the presence of an O. glaberrima allele. Clusters of QTLs for grain morphology traits were observed in two chromosome regions. One cluster harboring five QTLs near SSR markers RM106 and RM263 was detected on chromosome 2. This population would serve as a foundation for development of the introgression line population from a cross between Milyang 23 and O. glaberrima.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.268-268
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• 2022

Protein is a major nutrient of food and has long been studied for nutritional and utility value. Among them, rice protein is attracting attention because of its hypoallergenic characteristics and nutritional value. Mutant DM225 with increased protein content was selected by EMS treatment on the weed rice Dharial. QTL analysis of Protein content was carried out using BC₂F₂ populations derived from a cross between "Hanareum2" as a recurrent parent and "DM225" as a donor parent. The protein content of populations was between 5~11%, with an average of 7.7%. To identify QTLs related to Protein content, 117 KASP markers(polymorphic ratio: 15%) showing polymorphisms between the parents were genotyped for the BC₂F₂ population. One QTL was detected between markers SK07 06 and SK07_10 on chromosome 7(LOD: 28.1). This QTL explained 71.4% of the phenotypic variance for Protein content. This QTL will be useful for protein-related rice breeding program.

• Journal of Life Science
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• v.19 no.9
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• pp.1239-1244
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• 2009

This study was conducted to clarify the genetic relationship between Calanthe discolor, C. sieboldii and variants, and the cause of flower color variations by using a molecular linkage map and a quantitative trait loci (QTL) analysis for flower and lip color in Calanthe species native to Korea. Twenty plants were included in three C. discolor and three C. sieboldii, and fourteen variants were obtained from their habitat, Jeju-do in Korea. The flowers of C. discolor were brownish red, the values of Commission Internationale de I'Eclairage (CIE) Lab were between 40 and 50. The flowers of C. sieboldii were yellowish, the values of CIE Lab were between 110 and 130. The variants had various mixed colors that were thought to have originated from natural hybridization between C. discolor and C. sieboldii, and the values of CIE Lab were between 50 and 70. The colors of the lips were usually divided into white and yellow. C. discolor had a white lip, C. sieboldii had a yellow one, and the variants had a white to yellow one. The CIE Lab value of each color was 90 in white and 110 to 120 in yellow lips. A molecular linkage mapping was constructed based on the segregation of 154 RAPD markers using a MAPL program. Sixteen linkage groups containing 66 markers were established. It covered a total map distance of 220.4 cM. The distance between adjacent markers ranged from 0 to 6.6 cM, with an average distance of 3.3 cM. These markers are thought to be closely associated with flower and lip color expression. Among the 16 molecular linkage groups, 3 QTLs had flower color trait loci and 1 QTL had lip color trait loci.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.92-92
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• 2017

Bakanae disease is one of the most serious and oldest problems of rice production, which was first described in 1828 in Japan. This disease has also been identified in Asia, Africa, North America, and Italy. Germinating rice seeds in seed boxes for mechanical transplantation has caused many problems associated with diseases, including bakanae disease. Bakanae disease has become a serious problem in the breeding of hybrid rice, which involves the increased use of raising plants in seed beds. The indica rice variety Shingwang was selected as resistant donor to bakanae disease. One hundred sixty nine NILs, YR28297 ($BC_6F_4$) generated by five backcrosses of Shingwang with the genetic background of susceptible japonica variety, Ilpum were used for QTL analysis. Rice bakanae disease pathogen, CF283, was mainly used in this study and inoculation and evaluation of bakanae disease was performed with the method of the large-scale screening method developed by Kim et al. (2014). SSR markers evenly distributed in the entire rice chromosomes were selected from the Gramene database (http://www.gramene.org), and the polymorphic markers were used for frame mapping of a $BC_5F_5$ resistant line. Here, we developed 168 near-isogenic rice lines (NILs, $BC_6F_4$) to locate a QTL for resistance against bakanae disease. The lines were derived from a cross between Shingwang, a highly resistant variety (indica), and Ilpum, a highly susceptible variety (japonica). The 24 markers representing the Shingwang allele in a bakanae disease-resistant NIL, YR24982-9-1 (parental line of the $BC_6F_4$ NILs), were located on chromosome 1, 2, 7, 8, 10, 11, and 12. Single marker analysis using an SSR marker, RM9, showed that a major QTL was located on chromosome 1. The QTL explained 65 % of the total phenotype variation in $BC_6F_4$ NILs. The major QTL designated qBK1 was mapped in 91 kb region between InDel15 and InDel21. The identification of qBK1 and the closely linked SSR marker, InDel18, could be useful for improving rice bakanae disease resistance in marker-assisted breeding.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.54 no.2
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• pp.165-171
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• 2009

The objective of this study was to characterize the main-effect QTLs, epistatic QTLs and QTL-by-environment interactions (QE), which are involved in the control of protein content. A population of 120 doubled haploid (DH) lines derived from a cross between 'Samgang' and 'Nagdong', was planted and determined for protein content over three years. Based on the population and a genetic linkage map of 172 markers, QTL analysis was conducted by WinQTLcart 2.5 and QTLMAPPER. Three main-effect QTLs affecting protein content of brown rice were detected from 2004 to 2006 on chromosomes 1 and 11. The qPC11.2 was repeatedly detected across two years. Seven pairs of epistatic loci were identified on eight chromosomes for protein content and collectively explained 39.15% of phenotype variation. These results suggest that epistatic effects might be an even more important component of the genetic basis for protein content and that the segregation of the DH lines for protein content could be largely explained by a few main-effect QTLs and many epistatic loci.

• Horticultural Science & Technology
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• v.35 no.2
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• pp.149-164
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• 2017

Next generation sequencing (NGS) technologies have led to the rapid accumulation of genome sequences through whole-genome sequencing and re-sequencing of crop species. Genomic resources provide the opportunity for a new revolution in plant breeding by facilitating the dissection of complex traits. Among vegetable crops, reference genomes have been sequenced and assembled for several species in the Solanaceae and Cucurbitaceae families, including tomato, pepper, cucumber, watermelon, and melon. These reference genomes have been leveraged for re-sequencing of diverse germplasm collections to explore genome-wide sequence variations, especially single nucleotide polymorphisms (SNPs). The use of genome-wide SNPs and high-throughput genotyping methods has led to the development of new strategies for dissecting complex quantitative traits, such as genome-wide association study (GWAS). In addition, the use of multi-parent populations, including nested association mapping (NAM) and multiparent advanced generation intercross (MAGIC) populations, has helped increase the accuracy of quantitative trait loci (QTL) detection. Consequently, a number of QTL have been discovered for agronomically important traits, such as disease resistance and fruit traits, with high mapping resolution. The molecular markers for these QTL represent a useful resource for enhancing selection efficiency via marker-assisted selection (MAS) in vegetable breeding programs. In this review, we discuss current genomic resources and marker-trait association analysis to facilitate genome-assisted breeding in vegetable species in the Solanaceae and Cucurbitaceae families.

• Journal of Life Science
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• v.17 no.5 s.85
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• pp.599-605
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• 2007

Seed and pod numbers are the main yield components in soybean. Selection for increased yield potential is main goal of plant breeding. The objective of this study was to identify quantitative trait loci(QTLs) that control pod number per plant, seed number per plant and pod in soybean. The 117 $F_{2:10}$ recombinant inbred lines(RILs) developed from a cross of 'Keunolkong' and 'Shinpaldalkong' were used. Two independent QTLs for pod number per plant were identified from linkage group(LG) F and L. Two QTLs for seed number per plant were located on LG F and L. Seed number per pod was related with three QTLs located on LG D1a, D1b and F. Pod and seed number per plant have two common QTLs on LG F and L.