Miller Judith R, Hawthorne David
Department of Mathematics, Georgetown University, Washington, District of Columbia 20057, USA.
Genetics. 2005 Nov;171(3):1353-64. doi: 10.1534/genetics.104.035071. Epub 2005 Oct 6.
Given the relative ease of identifying genetic markers linked to QTL (compared to finding the loci themselves), it is natural to ask whether linked markers can be used to address questions concerning the contemporary dynamics and recent history of the QTL. In particular, can a marker allele found associated with a QTL allele in a QTL mapping study be used to track population dynamics or the history of the QTL allele? For this strategy to succeed, the marker-QTL haplotype must persist in the face of recombination over the relevant time frame. Here we investigate the dynamics of marker-QTL haplotype frequencies under recombination, population structure, and divergent selection to assess the potential utility of linked markers for a population genetic study of QTL. For two scenarios, described as "secondary contact" and "novel allele," we use both deterministic and stochastic methods to describe the influence of gene flow between habitats, the strength of divergent selection, and the genetic distance between a marker and the QTL on the persistence of marker-QTL haplotypes. We find that for most reasonable values of selection on a locus (s < or = 0.5) and migration (m > 1%) between differentially selected populations, haplotypes of typically spaced markers (5 cM) and QTL do not persist long enough (>100 generations) to provide accurate inference of the allelic state at the QTL.
鉴于识别与数量性状基因座（QTL）连锁的遗传标记相对容易（与找到基因座本身相比），自然而然会问，连锁标记是否可用于解决有关QTL当代动态和近期历史的问题。特别是，在QTL定位研究中发现与QTL等位基因相关的标记等位基因能否用于追踪种群动态或QTL等位基因的历史？要使这种策略成功，标记-QTL单倍型必须在相关时间范围内面对重组时持续存在。在这里，我们研究了在重组、种群结构和分歧选择下标记-QTL单倍型频率的动态，以评估连锁标记在QTL群体遗传学研究中的潜在效用。对于描述为“二次接触”和“新等位基因”的两种情况，我们使用确定性和随机方法来描述生境间基因流、分歧选择强度以及标记与QTL之间的遗传距离对标记-QTL单倍型持续性的影响。我们发现，对于在差异选择种群之间对一个基因座的大多数合理选择值（s≤0.5）和迁移率（m>1%），典型间隔标记（5厘摩）和QTL的单倍型不会持续足够长的时间（>100代）来提供对QTL等位基因状态的准确推断。
