• Asian-Australasian Journal of Animal Sciences
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• 제17권10호
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• pp.1350-1353
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• 2004

To further investigate the regions on porcine chromosome 7 that are responsible for economically important traits, phenotypic data from a total of 287 F2 individuals were collected and analyzed from 1998 to 2000. All animals were genotyped for eight microsatellite loci spanning the length of chromosome 7. QTL analysis was performed using interval mapping under the line-cross model. A permutation test was used to establish significance levels associated with QTL effects. Observed QTL effects were (chromosomewide significance, position of maximum significance in centimorgans): Birth weight (<0.01, 3); Carcass length (<0.05, 80); Longissimus muscle area (<0.01, 69); Skin percentage (<0.01, 69); Bone percentage (<0.01, 74); Fat depths at shoulder (<0.05, 54);Mean fat depth (<0.05, 81); Moisture in m. Longissimus Dorsi (<0.05, 88). Additional evidence was also found which suggested QTL for dressing percentage and fat depths at buttock. This study offers confirmation of several QTL affecting growth and carcass traits on SSC7 and provides an important step in the search for the actual major genes involved in the traits of economic interest.

• 한국수정란이식학회지
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• 제19권3호
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• pp.291-299
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• 2004

요크셔종과 버크셔종 교배 실험 집단을 활용하여 양적형질 유전자좌 (QTL)의 발현 특성 관련 유전 양식을 조사하였다. 총 512두의 F$_2$ 자손이 F$_1$간의 65교배 조합으로부터 생산되었으며 표현형 조사 기록은 일당증제량(ADG), 평균 등지방 두께(ABF), 10번째 등뼈 부위 등지방 두께(TRF) 및 등심단면적(LEA), 최후 척추부위 등지방 두께 (LRF)였다. 125종의 유전자 표지 (microsatellite)에 대한 3세대 개체별 유전자형이 분석되었으며 이들 정보를 통하여 최소자승 회귀 모형을 이용한 interval mapping 방법을 적용하였다. QTL의 유전양식 여부 검정에 대한 절차를 도식화하기 위해 귀무가설인 통상의 벤델리안 모형에 근거를 두고 수행하였다. 경험적 다중 검정 통계량에 대한 임계치는 단일 개개의 염색체 수준과 게놈 전반에 걸친 실험수준으로 유도하였으며, permutation에 의해 유도된 임계치의 유효성을 검증하기 위해 본 연구에 활용된 실험축 집단 구조와 유사한 simulation 집단 구조에 의해 산출된 결과들과 비교하여 유효성이 인정되었다. 본 연구에 활용된 실험축 집단구조와 Genome 전반에 걸친 QTL imprinting 여부를 조사한 결과 13종의 QTL 에 대한 imprinting이 확인되었으며 이들 중 9종의 QTL 유전 양식은 부계로부터 전달된 자손에게만 발현되는 것으로 추론되었다.

• Asian-Australasian Journal of Animal Sciences
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• 제19권12호
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• pp.1702-1705
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• 2006

A simulation study was conducted to evaluate a fine-mapping method exploiting population-wide linkage disequilibrium. Data were simulated according to the pedigree structure based on a large paternal half-sib family population with a total of 1,034 or 2,068 progeny. Twenty autosomes of 100 cM were generated with 5 cM or 1 cM marker intervals for all founder individuals in the pedigree, and marker alleles and a number of quantitative trait loci (QTL) explaining a total of 70% phenotypic variance were generated and randomly assigned across the whole chromosomes, assuming linkage equilibrium between the markers. The founder chromosomes were then descended through the pedigree to the current offspring generation, including recombinants that were generated by recombination between adjacent markers. Power to detect QTL was high for the QTL with at least moderate size, which was more pronounced with larger sample size and denser marker map. However, sample size contributed much more significantly to power to detect QTL than map density to the precise estimate of QTL position. No QTL was detected on the test chromosomes in which QTL was not assigned, which did not allow detection of false positive QTL. For the multiple QTL that were closely located, the estimates of the QTL positions were biased, except when the QTL were located on the right marker positions. Our fine mapping simulation results indicate that construction of dense maps and large sample size is needed to increase power to detect QTL and mapping precision for QTL position.

• 농업과학연구
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• 제39권4호
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• pp.477-482
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• 2012

Low-temperature germination is one of the major determinants for stable stand establishment in the rice direct seeding method in temperate regions and at high altitude areas. Quantitative trait loci (QTL) controlling low-temperature germinability in rice were identified using 96 introgression lines (ILs) derived from a cross between Oryza rufipogon and the Korean japonica cultivar, 'Hwaseongbyeo'. The germination rate at $15^{\circ}C$ was measured to represent low-temperature germination and used for QTL analysis. The germination rate at $15^{\circ}C$ for 7 days of Oryza rufipogon and Hwaseongbyeo was 93.3 and 28.7%, respectively, and that of progenies ranged from 0 to 48%. A linkage map was constructed using 135 simple sequence repeat (SSR) markers. Five putative QTLs associated with low-temperature germination were detected on chromosomes 1, 3, 4, 10 and 11. The QTL, qltg10 on chromosome 10 accounted for 19.2% of the total phenotypic variation for low-temperature germinability. Four additional QTL, accounted for 10.4 - 15.1% of the total phenotypic variation. The O. rufipogon alleles in all detected QTLs loci increased the low-temperature germination rate. No QTL associated with low temperature germinability has been detected near the qltg10 QTL in this study suggesting that qltg10 is a new QTL. The locus, qltg10 is of particular interest because of its independence from undesirable height and maturity effects. The DNA markers linked to the QTL for low temperature germinability would be useful in selecting lines with enhanced low temperature germinability in rice breeding program.

• Molecules and Cells
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• 제21권2호
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• pp.192-196
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• 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.

• Asian-Australasian Journal of Animal Sciences
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• 제17권9호
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• pp.1210-1213
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• 2004

Quantitative trait loci (QTL) mapping can be applied to detect chromosomal locations that control economic traits in farm animals. Teat number has been considered as one of the most important factors to evaluate mothering ability of sow. Especially, teat number is more important when the number is less than the litter size. This study was conducted to identify QTL affecting teat number in the Korean native pig${\times}$Landrace resource family. A total of 240 animals was genotyped for 132 polymorphic microsatellites covering the 18 pig autosomes. Mean and standard deviation of teat number in $F_2$animals is 13.46${\pm}$1.40. QTL was analyzed using F2 QTL Analysis Servlet of QTL express. A QTL for teat number on SSC9 was significant at the 1% chromosome-wide level and three suggestive QTL were detected on SSC3, 7 and 14. All QTL detected in this study had additive effect and Landrace alleles were associated with higher teat number in comparison with Korean native pig for three of four QTL.

• 생명과학회지
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• 제14권2호
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• pp.339-344
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• 2004

콩에서 경장과 연관된 DNA 표지인자를 개발하여 품종육성에 활용함으로서 육종효율 증진에 기여하고자 수행하였다. 본 시험은 육성된 큰올콩과 신팔달콩의 RIL 계통 및 SSR marker를 이용하여 유전자지도를 작성하고, 이를 바탕으로 경장과 관련된 양적형질 유전자좌(QTt)를 탐색하였다. 시험재료로 이용된 큰올콩과 신팔달콩은 경장이 각각 30.57 cm와 49.75 cm로 매우 큰 차이를 보였다. 경장과 연관된 QTL은 개별마커들과의 분산분석 결과, 연관군 F, J, N 및 O에서 전체변이의 37.83%를 설명할 수 있는 4개의 QTL을 탐색하였다. 특히, 연관군 J와 O에서 각각 14.25%와 10.68%를 설명할 수 있는 주요 QTL을 확인하였다. 따라서 경장 관련 QTL중 연관군 J와 O에서 확인된 주요 QTL은 품종 육성과정에서 경장 관련 선발 마커로서 활용가치가 높은 것으로 판단된다.

• Asian-Australasian Journal of Animal Sciences
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• 제18권12호
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• pp.1675-1683
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• 2005

In the process of crossbreeding, the linkage disequilibria between the quantitative trait loci (QTL) and their linked markers were reduced gradually with increasing generations. To study the potential of QTL mapping using the crossbred population, we presented a mixed effect model that treated the mean allelic value of the different founder populations as the fixed effect and the allelic deviation from the population mean as random effect. It was assumed that there were fifty QTLs having effect on the trait variation, the population mean and variance were divided to each QTL in founder generation in our model. Only the additive effect was considered in this model for simulation. Six schemes (S1-S6) of crossbreeding were studied. The selection index was used to evaluate the synthetic breeding value of two traits of the individual in the scheme of S2, S4 and S6, and the individuals with high selection index were chosen as the parents of the next generation. Random selection was used in the scheme of S1, S3 and S5. In this study, we premised a QTL explained 40% of the genetic variance was located in a region of 20 cM by the linkage analysis previously. The log likelihood ratio (log LR) was calculated to determine the presence of a QTL at the particular chromosomal position in each of the generations from the fourth to twentieth. The profiles of log LR and the number of the highest log LR located in the region of 5, 10 and 20 cM were compared between different generations and schemes. The profiles and the correct number reduced gradually with the generations increasing in the schemes of S2, S4 and S6, but both of them increased in the schemes of S1, S3 and S5. From the results, we concluded that the crossbreeding population undergoing random selection was suitable for improving the resolution of QTL mapping. Even experiencing index selection, there was still enough variation existing within the crossbred population before the fourteenth generation that could be used to refine the location of QTL in the chromosome region.

• Journal of Plant Biotechnology
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• 제43권1호
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• pp.76-81
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• 2016

We performed a molecular marker-based analysis of quantitative trait loci for traits that determine the quality of appearance of grains using 120 doubled haploid lines developed by anther culture from the F1 cross between 'Cheongcheong' (Oryza sativa L. ssp. Indica) and 'Nagdong' (Oryza sativa L. ssp. Japonica). We therefore calculated the alkali digestion value (ADV), used to indirectly measure gelatinization temperature, to evaluate the quality of cooked rice in 2013 and 2014. The ADV score of frequency distribution was higher milled rice than brown rice. In total, nine different quantitative trait loci (QTLs) were found on 5 chromosomes in 2013 and 2014. Also, chromosome 5, 8 were detected over two years. We conclude that selected molecular markers from this QTL analysis could be exploited in future rice quality. In conclusion, we investigated ADV of brown and milled rice in CNDH population. This study found nine QTLs related to the ADV of brown and milled rice. The detected one marker can be used to select lines with desirable eating-quality traits because ADV is closely associated with the eating quality of cooked rice. Therefore, it will be useful to collect resources and distinguishable in many varieties for rice breeding program.

• Molecules and Cells
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• 제37권2호
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• pp.149-160
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• 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.