Kolbehdari D, Jansen G B, Schaeffer L R, Allen B O
Center for Genetic Improvement of Livestock, Department of Animal and Poultry Science, University of Guelph, Guelph, ON, Canada.
J Anim Breed Genet. 2006 Jun;123(3):191-7. doi: 10.1111/j.1439-0388.2006.00579.x.
The performance of several transmission disequilibrium tests (TDT) for detection of quantitative trait loci (QTL) in data structures typical of outbred livestock populations were investigated. Factorial mating designs were simulated with 10 sires mated to either 50 or 200 dams, each family having five or eight full sibs. A single marker and QTL, both bi-allelic, were simulated using a disequilibrium coefficient based on complete initial disequilibrium and 50 generations of recombination [i.e. D = D(0)(1 - theta)50], where theta is the recombination fraction between marker and QTL. The QTL explained either 10% (small QTL) or 30% (large QTL) of the genetic variance for a trait with heritability of 0.3. Methods were: TDT for QTL (Q-TDT; both parents known), 1-TDT (only one parent known) and sibling-based TDT (S-TDT; neither parent known, but sibs available). All were found to be effective tests for association and linkage between the QTL and a tightly linked marker (theta < 0.02) in these designs. For a large QTL, theta = 0.01, and five full sibs per family, the empirical power for Q-TDT, 1-TDT and S-TDT was 0.966, 0.602 and 0.974, respectively, in a large population, versus 0.700, 0.414 and 0.654, respectively, in a small population. For a small QTL effect, theta = 0.01, large population the empirical power of these tests were 0.709, 0.287 and 0.634. The power of Q-TDT, 1-TDT and S-TDT was satisfactory for large populations, for QTL with large effects and for five full sibs per family. The 1-TDT based on a linear model was more powerful than the normal 1-TDT. The empirical power for Q-TDT and 1-TDT with a linear model was 0.978 and 0.995 respectively. TDT based on analogous linear models, incorporating the polygenic covariance structure, provided only small increases in power compared with the usual TDT for QTL.
研究了几种用于检测远交家畜群体典型数据结构中数量性状基因座（QTL）的传递不平衡检验（TDT）的性能。模拟了析因交配设计，10头公牛与50头或200头母牛交配，每个家系有5个或8个全同胞。使用基于完全初始不平衡和50代重组的不平衡系数（即D = D(0)(1 - θ)50）模拟了一个单标记和一个QTL，二者均为双等位基因，其中θ是标记与QTL之间的重组率。对于遗传力为0.3的性状，该QTL解释了10%（小QTL）或30%（大QTL）的遗传方差。方法包括：用于QTL的TDT（Q - TDT；双亲均已知）、1 - TDT（仅一方亲本已知）和基于同胞的TDT（S - TDT；双亲均未知，但有同胞可用）。在这些设计中，所有方法都被发现是检测QTL与紧密连锁标记（θ < 0.02）之间关联和连锁的有效检验。对于一个大QTL，θ = 0.01，每个家系有5个全同胞，在大群体中，Q - TDT、1 - TDT和S - TDT的经验检验功效分别为0.966、0.602和0.974，而在小群体中分别为0.700、0.414和0.654。对于小QTL效应，θ = 0.01，在大群体中这些检验的经验检验功效分别为0.709、0.287和0.634。对于大群体、具有大效应的QTL以及每个家系有5个全同胞的情况，Q - TDT、1 - TDT和S - TDT的功效令人满意。基于线性模型的1 - TDT比常规的1 - TDT更具功效。具有线性模型的Q - TDT和1 - TDT的经验检验功效分别为0.978和0.995。与常规的QTL的TDT相比，纳入多基因协方差结构的类似线性模型的TDT在功效上仅略有提高。
