Pérez-Enciso Miguel, Roussot Odile
Station d'Amelioration Génétique des Animaux, INRA, Castanet-Tolosan, France.
Genet Res. 2002 Jun;79(3):247-58. doi: 10.1017/s0016672302005645.
Amplified fragment length polymorphisms (AFLPs) are a widely used marker system: the technique is very cost-effective, easy and rapid, and reproducibly generates hundreds of markers. Unfortunately, AFLP alleles are typically scored as the presence or absence of a band and, thus, heterozygous and dominant homozygous genotypes cannot be distinguished. This results in a significant loss of information, especially as regards mapping of quantitative trait loci (QTLs). We present a Monte Carlo Markov Chain method that allows us to compute the identity by descent probabilities (IBD) in a general pedigree whose individuals have been typed for dominant markers. The method allows us to include the information provided by the fluorescent band intensities of the markers, the rationale being that homozygous individuals have on average higher band intensities than heterozygous individuals, as well as information from linked markers in each individual and its relatives. Once IBD probabilities are obtained, they can be combined into the QTL mapping strategy of choice. We illustrate the method with two simulated populations: an outbred population consisting of full sib families, and an F2 cross between inbred lines. Two marker spacings were considered, 5 or 20 cM, in the outbred population. There was almost no difference, for the practical purpose of QTL estimation, between AFLPs and biallelic codominant markers when the band density is taken into account, especially at the 5 cM spacing. The performance of AFLPs every 5 cM was also comparable to that of highly polymorphic markers (microsatellites) spaced every 20 cM. In economic terms, QTL mapping with a dense map of AFLPs is clearly better than microsatellite QTL mapping and little is lost in terms of accuracy of position. Nevertheless, at low marker densities, AFLPs or other biallelic markers result in very inaccurate estimates of QTL position.
扩增片段长度多态性（AFLP）是一种广泛应用的标记系统：该技术性价比高、操作简便快捷，可重复性地产生数百个标记。不幸的是，AFLP等位基因通常根据条带的有无进行计分，因此无法区分杂合子和显性纯合子基因型。这导致了大量信息的丢失，尤其是在数量性状基因座（QTL）定位方面。我们提出了一种蒙特卡罗马尔可夫链方法，该方法使我们能够在一个普通家系中计算同源概率（IBD），该家系中的个体已针对显性标记进行了分型。该方法使我们能够纳入由标记的荧光条带强度提供的信息，其基本原理是纯合个体的条带强度平均高于杂合个体，同时还能纳入每个个体及其亲属中连锁标记的信息。一旦获得IBD概率，就可以将它们整合到所选的QTL定位策略中。我们用两个模拟群体说明了该方法：一个由全同胞家系组成的远交群体，以及近交系之间的F2杂交群体。在远交群体中考虑了两种标记间距，即5或20厘摩。在考虑条带密度时，尤其是在5厘摩的间距下，对于QTL估计的实际目的而言，AFLP与双等位基因共显性标记之间几乎没有差异。每5厘摩的AFLP性能也与每20厘摩间隔的高多态性标记（微卫星）相当。从经济角度来看，使用密集的AFLP图谱进行QTL定位明显优于微卫星QTL定位，并且在位置准确性方面几乎没有损失。然而，在低标记密度下，AFLP或其他双等位基因标记会导致QTL位置的估计非常不准确。
