• Asian-Australasian Journal of Animal Sciences
• /
• v.18 no.11
• /
• pp.1524-1528
• /
• 2005

Molecular genetic markers were used to detect chromosomal regions which contain economically important traits such as growth, carcass, and meat quality traits in pigs. A three generation resource population was constructed from a cross between Korean native boars and Landrace sows. A total of 240 F2 animals from intercross of F1 was produced. Phenotypic data on 17 traits, birth weight, body weights at 3, 5, 12, and 30 weeks of age, teat number, carcass weight, backfat thickness, body fat, backbone number, muscle pH, meat color, drip loss, cooking loss, water holding capacity, shear force, and intramuscular fat content were collected for F2 animals. Animals including grandparents (F0), parents (F1), and offspring (F2) were genotyped for 80 microsatellite markers covering from chromosome 1 to 10. Least squares regression interval mapping was used for quantitative trait loci (QTL) identification. Significance thresholds were determined by permutation tests. A total of 10 QTL were detected at 5% chromosome-wide significance levels for growth traits on SSCs 2, 4, 5, 6, and 8.

• 한국데이터정보과학회:학술대회논문집
• /
• 2003.05a
• /
• pp.41-47
• /
• 2003

한우 6번 염색체 유전자 지도에서 한우의 질을 높이기 위한 QTL(quantitative trait loci)분석을 실시하여 선별된 Loci 값을 Permutation Test를 이용하여 계산하였다. 한편, 경제적으로 주요한 한우의 특성부위(질적부위와 육량등)에 따른, 우수 경제형질 DNA marker를 K-평균 군집법을 실시 파악하였다. 이들 QTL과 K-평균법에 의해 한우의 염색체 6번, ILST035의 주요 경제 형질별 DNA marker들을 선별하여, Bootstrap BCa방법을 이용하여 각 DNA marker들의 신뢰구간을 구했다.

• Journal of Life Science
• /
• v.16 no.6
• /
• pp.949-954
• /
• 2006

Soybean [Glycine max (L.) Merr.] is an important crop, accounting for 48% of the world market in oil crops. Improvement of the quality and quantity of soybean seed constituents is one of the most important objectives in soybean breeding. Protein content and seed size are important properties to determine the quality of tofu and soy sprouts respectively. The objective of this study was to identify quantitative trait loci (QTLs) that control seed weight, protein and oil content in soybean. The 117 $F_{2:10}$ recombinant inbred lines (RlL) developed from a cross of 'Keunolkong' and 'Shinpaldalkong' were used. Narrow-sense heritability estimates based on a plot mean on seed weight, protein and oil content were 0.8, 0.78 and 0.71, respectively. Four independent QTLs for seed weight were identified from linkage group (LG) F, I and K. Five QTL for protein content were located on LG D1b, E, H, I and L. Oil content was related with six QTLs located on LG D1b, E, G, I, J and N. Protein and oil content have three common QTLs on LG D1b, E and I. Thus, we identified major loci improving soybean seed quality.

• KOREAN JOURNAL OF CROP SCIENCE
• /
• v.49 no.6
• /
• pp.539-545
• /
• 2004

The purpose of this study was to locate the quantitative trait loci (QTL) associated with quality properties in the recombinant inbred lines derived from the 'Milyang 23' and 'Gihobyeo' cross. Four quality-related traits; protein content, amylose content, fat acid content and sensory value were measured. Eight QTLs for protein content were detected on chromosomes 1 (two loci), 3, 6, 7 and 8 (three loci), each accounting for $6.0\%\~15.2\%$ of the phenotypic variation. Three QTLs for amylose content were detected on chromosomes 6 and 7 (two loci), each explaining from $7.3\%\;to\;24.4\%$ of the phenotypic variation. Six QTLs for fat acid content were detected on chromosomes 2 (two loci), 3, 6 (two loci) and 7, each explaining form $5.5\%\;to\;14.0\%$ of the phenotypic variation. Six QTLs for sensory value were detected on chromosomes 2, 6, 7(two loci) and 8 (two loci), each accounting for $5.5\%\~10.3\%$ of the phenotypic variation.

• Molecules and Cells
• /
• v.21 no.2
• /
• pp.192-196
• /
• 2006

Salt tolerance was evaluated at the young seedling stage of rice (Oryza sativa L.) using recombinant inbred lines (MG RILs) from a cross between Milyang 23 (japonica/indica) and Gihobyeo (japonica). 22 of 164 MG RILs were classified as tolerant with visual scores of 3.5-5.0 in 0.7% NaCl. Interval mapping of QTLs related to salt tolerance was conducted on the basis of the visual scores at the young seedling stage. Two QTLs, qST1 and qST3, conferring salt tolerance, were detected on chromosome 1 and 3, respectively, and the total phenotypic variance explained by the two QTLs was 36.9% in the MG RIL population. qST1 was the major QTL explaining 27.8% of the total phenotypic variation. qST1 was flanked by Est12~RZ569A, and qST3 was flanked by RG179~RZ596. The detection of new QTLs associated with salt tolerance will provide important information for the functional analysis of rice salt tolerance.

• Molecules and Cells
• /
• v.37 no.2
• /
• pp.149-160
• /
• 2014

Plant breeders have focused on improving plant architecture as an effective means to increase crop yield. Here, we identify the main-effect quantitative trait loci (QTLs) for plant shape-related traits in rice (Oryza sativa) and find candidate genes by applying whole genome re-sequencing of two parental cultivars using next-generation sequencing. To identify QTLs influencing plant shape, we analyzed six traits: plant height, tiller number, panicle diameter, panicle length, flag leaf length, and flag leaf width. We performed QTL analysis with 178 $F_7$ recombinant inbred lines (RILs) from a cross of japonica rice line 'SNU-SG1' and indica rice line 'Milyang23'. Using 131 molecular markers, including 28 insertion/deletion markers, we identified 11 main- and 16 minor-effect QTLs for the six traits with a threshold LOD value > 2.8. Our sequence analysis identified fifty-four candidate genes for the main-effect QTLs. By further comparison of coding sequences and meta-expression profiles between japonica and indica rice varieties, we finally chose 15 strong candidate genes for the 11 main-effect QTLs. Our study shows that the whole-genome sequence data substantially enhanced the efficiency of polymorphic marker development for QTL fine-mapping and the identification of possible candidate genes. This yields useful genetic resources for breeding high-yielding rice cultivars with improved plant architecture.

• Journal of Life Science
• /
• v.18 no.12
• /
• pp.1665-1670
• /
• 2008

Soybean oil is an important source of vegetable oil for human food and nonfood applications and accounts for approximately 22% of the world's total edible oil production. Improvement of the quality and quantity of soybean seed oil constituents is one of the most important objectives in soybean breeding. The objective of this study was to identify quantitative trait loci (QTLs) that control oleic, linoleic, and linolenic acid contents in soybean. The 117 $F_{2:10}$ recombinant inbred lines (RIL) developed from a cross of 'Keunolkong' and 'Shinpaldalkong' were used. Narrow-sense heritability estimates based on a plot mean on seed weight, protein and oil content were 0.85, 0.82 and 0.81, respectively. Eight independent QTLs for oleic acid content were identified from linkage group (LG) A2, C1, D2, F, G, L, and O. Seven QTLs for linoleic acid content were located on LG D1b, E, H, I and L. Oil content was related with five QTLs located on LG C1, H, J, K, and L. Oleic, linoleic, and linolenic acid have two common QTLs on LG C1 and L. Thus, we identified major loci improving soybean oil quality.

• Genomics & Informatics
• /
• v.10 no.4
• /
• pp.234-238
• /
• 2012

Genetic epidemiology studies have established that the natural variation of gene expression profiles is heritable and has genetic bases. A number of proximal and remote DNA variations, known as expression quantitative trait loci (eQTLs), that are associated with the expression phenotypes have been identified, first in Epstein-Barr virus-transformed lymphoblastoid cell lines and later expanded to other cell and tissue types. Integration of the eQTL information and the network analysis of transcription modules may lead to a better understanding of gene expression regulation. As these network modules have relevance to biological or disease pathways, these findings may be useful in predicting disease susceptibility.

• BMB Reports
• /
• v.40 no.1
• /
• pp.95-99
• /
• 2007

Bovine coding region single nucleotide polymorphisms located proximal to quantitative trait loci were identified to facilitate bovine QTL fine mapping research. A total of 692,763 bovine SNPs was extracted from 39,432 UniGene clusters, and 53,446 candidate SNPs were found to be a depth >3. In order to validate the in silico SNPs experimentally, 186 animals representing 14 breeds and 100 mixed breeds were analyzed. Genotyping of 40 randomly selected candidate SNPs revealed that 43% of these SNPs ranged in frequency from 0.009 to 0.498. To identify non-synonymous SNPs and to correct for possible frameshift errors in the ESTs at the predicted SNP positions, we designed a program that determines coding regions by protein-sequence referencing, and identified 17,735 nsSNPs. The SNPs and bovine quantitative traits loci informations were integrated into a bovine SNP data: BcSNPdb (http://snugenome.snu.ac.kr/BtcSNP/). Currently there are 43 different kinds of quantitative traits available. Thus, these SNPs would serve as valuable resources for exploiting genomic variation that influence economically and agriculturally important traits in cows.

• Proceedings of the Korean Society of Crop Science Conference
• /
• 2017.06a
• /
• pp.116-116
• /
• 2017

Low-temperature is one of the environmental stress factors that affect plant growth and development and consequently limit crop productivity. The control of seed germination under low-temperature is organized by many genes which are called quantitative trait loci (QTLs). High germination rate for low-temperature is an important factor of growing rice. Previously, we identified a major QTL controlling low-temperature germinability in rice using 96 introgression lines (ILs) derived from a cross between Oryza rufipogon (Rufi) and the Korean japonica cultivar, 'Hwaseongbyeo (HS)'. A $BC_3F_7$ line (TR5) showed better low-temperature germinability than its recurrent parent. TR5 was crossed with HS to develop a segregating F2:3 populations for the target QTL. Six SSR markers polymorphic between HS and Rufi were used to screen and fine map the qLTG1. The qLTG1 on chromosome 1, which accounted for 55.5% of the total phenotypic variation, confirmed that Rufi allele enhanced the low-temperature germinability. Intervals between markers CRM16 and CRM15, four candidate genes were identified. The identified candidate genes, which are encoded by a protein of unknown function, showed their direct involvement on seed germination at low-temperature. To identify genes targeted by qLTG1, we investigated the expression profiles of these candidate genes and germination behavior of qLTG1 under different stress conditions and compared to HS, Rufi, and TR5 at $13{\pm}2^{\circ}C$ for 3 days after incubation. Furthermore, transgenic rice plants will also be developed to conduct a detailed investigation on low-temperature germinability. Hence, the QTL for low-temperature germinability would be useful in rice breeding programs especially in the development of lines possessing low-temperature germinability.