• Asian-Australasian Journal of Animal Sciences
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• 제24권12호
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• pp.1644-1650
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• 2011

This study was conducted to detect quantitative trait loci (QTL) affecting meat quality in an $F_2$ reference population of Korean native pig and Landrace crossbreds. The three-generation mapping population was generated with 411 progeny from 38 $F_2$ full-sib families, and 133 genetic markers were used to produce a sex-average map of the 17 autosomes. The data set was analyzed using least squares Mendelian and parent-of-origin interval-mapping models. Lack-of-fit tests between models were used to characterize the QTL for mode of gene expressions. A total of 10 (32) QTL were detected at the 5% genome (chromosome)-wise level for the analyzed traits. Of the 42 QTL detected, 13 QTL were classified as Mendelian, 10 as paternal, 14 as maternal, and 5 as partial expressed QTL, respectively. Among the QTL detected at 5% genome-wise level, four QTL had Mendelian mode of inheritance on SSCs 5, 10, 12, and 13 for cooking loss, drip loss, crude lipid and crude protein, respectively; two QTL maternal inheritance for pH at 24-h and shear force on SSC11; three QTL paternal inheritance for CIE b and Hunter b on SSC9 and for cooking loss on SSC15; and one QTL partial expression for crude ash on SSC13, respectively. Most of the Mendelian QTL (9 of 13) had a dominant mode of gene action, suggesting potential utilization of heterosis for genetic improvement of meat quality within the cross population via marker-assisted selection.

• Genomics & Informatics
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• 제7권3호
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• pp.152-158
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• 2009

Although the genetic basis for bone mineral density (BMD) has been studied by many groups so far, genes responsible for this complex trait has not been completely revealed. In order to localize quantitative trait loci (QTLs) for BMD variation in Asian population, the study was designed using a group of Mongolian population, a genetically closed population with a homogeneous lifestyle. BMD was measured at the left and right wrists and ankles using DEXA in 1,082 participants from 142 families. Genotyping of 13 polymorphic microsatellite markers on chromosome 13 (average spacing 8-9 cM) and two-point and multipoint linkage analysis were performed. In two-point linkage analysis, we identified two markers, D13S175 (6.03 cM) and D13S265 (68.73 cM) that had LOD scores greater than 1 for left ankle (LOD=2.09, LOD=1.49, respectively). We also found a marker D13S175 (6.03 cM) with a high LOD for left wrist (LOD=1.49) and the markers D13S265 (68.73 cM) and D13S217 (17.21 cM) for the right wrist (LOD= 1.82, LOD= 1.62, respectively). Among these significant marker regions, only two regions at 17 cM (13p11) and 65 cM (13q21) for the right wrist overlapped with major QTLs reported in following multipoint linkage analysis (LOD= 1.7549, LOD=1.4462, respectively). This study provides the possible evidence of the presence of QTLs affecting right wrist BMD in Mongolian populations on 13p11 and 13q21. Modest evidence was also found for genes affecting left ankle and left wrist BMD on 13p13.

• 한국작물학회지
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• 제51권6호
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• pp.565-570
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• 2006

The viviparous germination (VG) with lodging caused the yield reduction and quality deterioration in rice. We carried out the evaluation of VG tolerance (on the 40th day after heading) and mapping QTLs associated with VG tolerance using the recombinant inbred lines (M/G RILs) from a cross between Milyang 23 (japonica/indica) and Gihobyeo (japonica). The VG rates of Milyang 23 and Gihobyeo were 0.0 and 7.0%, respectively. The averaged VG rate of 162 M/G RILs was 7.7%, and their range was from 0.0 to 50.9%. Of the 162 RILs, 144 lines were tolerant less than 10%, and 18 lines were susceptible more than 10%. Using the M/G RIL Map, three QTLs associated with the viviparous trait were detected on chromosome 2 (qVG 2-1 and qVG 2-2) and 8 (qVG 8). qVG 2-1 was linked to RM 32D and RZ 166, and had LOD score of 2.97. qVG 2-2 was tightly linked to E13M59.119-Pl and E13M59.M003-P2, and showed higher LOD score of 3.41. qVG 8 was linked to RM33 and TCT116, and had LOD score of 2.67. The total phenotypic variance explained by the three QTLs was about 24.4% of the total variance in the population. The detection of new QTLs associated with VG tolerance will provide important informations for the seed dormancy, low temperature germination, or comparative genetics.

• Asian-Australasian Journal of Animal Sciences
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• 제24권11호
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• pp.1525-1528
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• 2011

The purpose of this study was to detect SNPs that were responsible for a carcass trait in Hanwoo populations. A non-parametric model applying a restricted partition method (RPM) was used, which exploited a partitioning algorithm considering statistical criteria for multiple comparison testing. Phenotypic and genotypic data were obtained from the Hanwoo Improvement Center, National Agricultural Cooperation Federation, Korea, in which the pedigree structure comprised 229 steers from 16 paternal half-sib proven sires that were born in Namwon or Daegwanryong livestock testing station between spring of 2002 and fall of 2003. A carcass trait, longissimus dorsi muscle area for each steer was measured after slaughter at approximately 722 days. Three SNPs (19_1, 18_4 and 28_2) near the microsatellite marker ILSTS035 on BTA6, around which the quantitative trait loci (QTL) for meat quality were previously detected, were used in this study. The RPM analyses resulted in two significant interaction effects between SNPs (19_1 and 18_4) and (19_1 and 28_2) at ${\alpha}$ = 0.05 level. However, under a general linear (parametric) model no interaction effect between any pair of the three SNPs was detected, while only one main effect for SNP19_1 was found for the trait. Also, under another non-parametric model using a multifactor dimensionality reduction (MDR) method, only one interaction effect of the two SNPs (19_1 and 28_2) explained the trait significantly better than the parametric model with the main effect of SNP19_1. Our results suggest that RPM is a good alternative to model choices that can find associations of the interaction effects of multiple SNPs for quantitative traits in livestock species.

• 한국작물학회지
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• 제43권4호
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• pp.250-253
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• 1998

Somaclonal variation was observed in the field on doubled haploid plants derived from single pollen of a rice cultivar "Hwaseongbyeo". The variations of seven quantitative traits including plant height and one qualitative trait (pubescence) in 436 lines ($R_2$ generation) were analyzed. The number of lines which fell beyond the boundaries of the 95% confidence intervals of the check variety, Hwaseongbyeo was checked for each quantitative trait, and of those fertility showed the highest variation frequency (85.6%), followed by plant height (77.5%), flag leaf length (66.5%), grains per panicle (42.2%), days to heading (34.5%), panicle length (30.7%) and panicles per hill (22.7%). And the variations of quantitative traits except days to flowering appeared to move in the negative direction compared to "Hwaseongbyeo". Variability within lines was also observed for quantitative and qualitative traits. Twenty-nine $R_2$ lines (7%) segregated for pubescence and 130 $R_2$ lines (30%) showed variation with regard to fertility. This suggests that mutations usually occur before diploidization. Twenty-nine $R_2$ lines representing a wide spectrum of variation were chosen for RAPD analysis. The number of lines showing DNA polymorphism compared to Hwaseongbyeo ranged 0 from to 10 according to the primer used and this seems to indicate that specific loci have highly mutable genomic site.utable genomic site.

• 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.

• Journal of Animal Science and Technology
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• 제46권4호
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• pp.525-536
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• 2004

본 연구는 돼지의 염색체 7번에 존재하는 주요 경제형질에 관여하는 양적형질 유전자좌위(Quantitative trait loci; QTL)를 밝히기 위해 초성위체 표지인자를 이용하여 유전자지도(연관지도) 작성을 수행하였다. 기준집단의 조성은 이형접합성이 높은 기준집단을 조성하기 위하여 유전적 특성이 현격히 다른 우리나라의 재래돼지와 Landrace를 전형매 교배하여 생산된 $F_2$ 183두를 사용하였으며 기준집단에 대해 도축 24시간 후의 pH, 육색, 육즙손실량, 전단력, 가열감량, 조지방, 조회분, 수분, 조단백질 등 육질형질을 조사 및 분석하였다. 염색체 7번의 연관지도는 총 23개의 표지인자로 작성되었으며 암수평균 연관지도 길이는 154.6 cM 이었으며 수컷과 암컷의 연관지도 길이는 각각 169.2 cM과 141.4 cM로 수컷의 연관지도 길이가 암컷의 것보다 27.8 cM 더 길었다. 표지인자간의 최소간격은 SW175와 S0066 표지인자사이로 1.6 cM이었고, 최대간격은 SW2002와 SWR773표지인자사이로서 15.9 cM이었으며 평균간격은 7.02 cM이었다. 본 연구에서는 9개의 육질관련 형질 중 육색과 연관된 2개의 QTL이 확인되었는데 적색도(CIE-a)와 연관된 QTL은 45 cM 영역에서 1% 수준의 통계적 유의성을 나타내었고(Fig. 2), 이 영역에서 불과 3${\sim}$4 cM 떨어진 위치에서 황색도(CIE-b)와 연관된 QTL이 확인되었다. 향후에 본 연구에서 탐색된 QTL 영역에 대하여 고밀도의 유전자 지도 작성을 통하여 특정 형질과 연관된 부분을 계속해서 추적해 나간다면 육색형질을 조절하는 주유전자의 클로닝 및 특성 구명이 가능할 것으로 사료되며 궁극적으로는 돼지의 개량에 효율적으로 활용할 수 있는 표지인자(MAS)의 개발 등도 가능 할 것으로 사료된다.

• 생명과학회지
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• 제31권6호
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• pp.568-573
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• 2021

본 연구는 전장 유전체 연관성 분석(genome-wide association study, GWAS)을 통해 ERp29의 mRNA 발현과 관련된 유전좌위(expression quantitative trait loci, eQTL)을 식별하는 것을 목표로 하였다. 대상 유전자는 ERp29이다. ERp29는 소포체(ER)의 lumen에 단백질의 folding & assembly 기능을 가진 분자 chaperone 단백질로서 소포체 스트레스에 의해 발현량이 증가하며, 분비 단백질의 생합성에 관여한다. 최근 연구 결과 발암과 연관성이 알려지면서 주목을 받고 있다. 총 373명의 유럽인의 genome을 대상으로 GWAS 분석 결과, ERp29 유전자 발현은 정소와 뇌에서 강하게 발현하는 long noncoding RNA (LncRNA) LOC105372577과 관계가 있었다. 즉, 3개의 eQTL: rs6138266 (p<4.172e10-9), rs62193420 (p<1.173e10-8), rs6138267 (p<2.041e10-8)와 연관성이 깊은 것으로 밝혀졌다. ERp29의 발현과 연관이 있는 것으로 확인된 3개의 eQTL을 사용한 transcriptome-wide association study (TWAS) 결과 osteosarcoma amplified 9 (OS9) 발현과 유의한 연관성을 보이며 OS9 유전자의 up-stream에 upstream of transcription factor 1 (USF1)이 결합할 수 있는 것을 알았다.

• 농업과학연구
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• 제42권4호
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• pp.397-406
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• 2015

Quantitative traits are mostly controlled by a large number of genes. Some of these genes tend to have a large effect on quantitative traits in cattle and are known as major genes primarily located at quantitative trait loci (QTL). The genetic merit of animals can be estimated by genomic selection, which uses genome-wide SNP panels and statistical methods that capture the effects of large numbers of SNPs simultaneously. In practice, the accuracy of genomic predictions will depend on the size and structure of reference and training population, the effective population size, the density of marker and the genetic architecture of the traits such as number of loci affecting the traits and distribution of their effects. In this review, we focus on the structure of Hanwoo reference and training population in terms of accuracy of genomic prediction and we then discuss of genetic architecture of intramuscular fat(IMF) and marbling score(MS) to estimate genomic breeding value in real small size of reference population.

• Asian-Australasian Journal of Animal Sciences
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• 제28권11호
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• pp.1525-1531
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• 2015

Using next-generation sequencing, we conducted a genome-wide scan of selective sweeps associated with selection toward genetic improvement in Thoroughbreds. We investigated potential phenotypic consequence of putative candidate loci by candidate gene association mapping for the finishing time in 240 Thoroughbred horses. We found a significant association with the trait for Ral GApase alpha 2 (RALGAP2) that regulates a variety of cellular processes of signal trafficking. Neighboring genes around RALGAP2 included insulinoma-associated 1 (INSM1), pallid (PLDN), and Ras and Rab interactor 2 (RIN2) genes have similar roles in signal trafficking, suggesting that a co-evolving gene cluster located on the chromosome 22 is under strong artificial selection in racehorses.