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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

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.

Keywords

QTL;Significance threshold;Permutation test;Pig

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