Roldan Dana L, Gilbert Hélène, Henshall John M, Legarra Andrés, Elsen Jean-Michel
Instituto de Genética CICVyA-INTA Castelar, cc 1712, Buenos Aires, Argentina.
Genet Res (Camb). 2012 Aug;94(4):223-34. doi: 10.1017/S0016672312000407.
Recently, a Haley-Knott-type regression method using combined linkage disequilibrium and linkage analyses (LDLA) was proposed to map quantitative trait loci (QTLs). Chromosome of 5 and 25 cM with 0·25 and 0·05 cM, respectively, between markers were simulated. The differences between the LDLA approaches with regard to QTL position accuracy were very limited, with a significantly better mean square error (MSE) with the LDLA regression (LDLA_reg) in sparse map cases; the contrary was observed, but not significantly, in dense map situations. The computing time required for the LDLA variance components (LDLA_vc) model was much higher than the LDLA_reg model. The precision of QTL position estimation was compared for four numbers of half-sib families, four different family sizes and two experimental designs (half-sibs, and full- and half-sibs). Regarding the number of families, MSE values were lowest for 15 or 50 half-sib families, differences not being significant. We observed that the greater the number of progenies per sire, the more accurate the QTL position. However, for a fixed population size, reducing the number of families (e.g. using a small number of large full-sib families) could lead to less accuracy of estimated QTL position.
最近，一种结合连锁不平衡和连锁分析（LDLA）的海利-诺特型回归方法被提出来用于定位数量性状基因座（QTL）。分别模拟了标记间间距为5和25厘摩（cM）、标记密度分别为0·25和0·05厘摩的染色体。LDLA方法在QTL位置准确性方面的差异非常有限，在稀疏图谱情况下，LDLA回归（LDLA_reg）的均方误差（MSE）明显更好；在密集图谱情况下观察到相反的情况，但不显著。LDLA方差分量（LDLA_vc）模型所需的计算时间远高于LDLA_reg模型。针对四种半同胞家系数量、四种不同家系规模以及两种实验设计（半同胞，全同胞和半同胞），比较了QTL位置估计的精度。关于家系数量，15个或50个半同胞家系的MSE值最低，差异不显著。我们观察到每个父本的后代数量越多，QTL位置就越准确。然而，对于固定的群体大小，减少家系数量（例如使用少量大型全同胞家系）可能会导致估计的QTL位置准确性降低。
