Journal of Animal Science and Technology

Korean Society of Animal Sciences and Technology (한국축산학회)
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Determination of Significance Threshold for Detecting QTL in Pigs

돼지의 QTL 검색을 위한 유의적 임계수준(Threshold) 결정

  • Lee, H.K. (National Livestock Research Institute) ;
  • Jeon, G.J. (Dept. of Genomic Engineering, Genomic Informatics Center, Hankyong National Univ.)
  • Published : 2002.02.28
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Abstract

Interval mapping using microsatellite markers was employed to detect quantitative trait loci (QTL) in the experimental cross between Berkshire and Yorkshire pigs. In order to derive critical values (CV) for test statistics for declaring significance of QTL, permutation test (PT) of Churchill and Doerge method(1994) and the analytical method(LK) of Lander and Kruglyak(1995) were used by each trait and chromosome. 525 $F_2$ progeny phenotypes of five traits(carcass weight, loin eye area, marbling score, cholesterol content, last back fat thickness) and genotypes of 125 markers covering the genome were used. Data were analyzed by line cross regression interval mapping with an F-test every by 1cM. PT CV were based on 10,000 permutations. CV at genome-wise test were 10.5 for LK and ranged from 8.1 to 8.3 for PT, depending on the trait. CV, differed substantially between methods, led to different numbers of quantitative trait loci (QTL) to be detected. PT results in the least stringent CV compared at the same % level.

양적형질 유전자좌위(Quantitative trait loci; QTL) 연관지도 작성을 위해 regression interval mapping method에 의해 Berkshire종과 Yorkshire종간 교배를 통해 생산된 $F_2$ 집단에서 실시하였다. 염색체내 QTL 위치를 결정하기 위해 regression 모델을 통해 계산된 검정통계량(F-statistic)에 대한 유의적인 threshold 수준의 설정은 permutation test 및 Lander와 kruglyak (1995)에 의해 제시된 방법으로 산출하였다. 525두 $F_2$ 개체에 대해 조사된 기록 중 5형질(도체중, 등심 단면적, 근내지방 교잡도, 콜레스테롤 함량, 척추 늑골 등지방 두께) 기록을 분석에 이용하였고 genome 전체에 걸친 125개의 microsatellite marker에 대해 3세대 집단 모두 개체에 대해 유전자형을 조사하였다. 회귀분석 모형에 따라 additive 및 dominance 효과를 추정하였으며 이때 모든 회귀계수 값과 F-검정 통계량은 각각 1cM 단위로 추정하였다. 각 형질별, 염색체별로 10,000회의 permutation에 의해 genome-wise 및 chromosome-wise threshold를 추정하였다. Lander와 Kruglyak(1995)에 의해 제시된 방법으로 산출된 threshold 값은 매우 높게 추정되어 이러한 threshold의 적용시 실제로 QTL 존재 여부를 인정할 수 있는 경우의 수가 permutation에 의해 유도된 threshold를 적용했을 때보다 상대적으로 적은 결과를 보였다. 5% genome-wise threshold의 경우 형질별로 다소 상이한 경향을 나타냈으며 분석에 활용된 5개 형질에 대해 총 4개의 QTL이 5% genome-wise 수준에서 검색되었다.

Keywords

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