Zhu Chengsong, Zhang Yuan-Ming
Section on Statistical Genomics, State Key Laboratory of Crop Genetics and Germplasm Enhancement/National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, China.
BMC Genet. 2007 Nov 29;8:82. doi: 10.1186/1471-2156-8-82.
Chromosomal region that causes distorted segregation ratios is referred to as segregation distortion locus (SDL). The distortion is caused either by differential representation of SDL genotypes in gametes before fertilization or by viability differences of SDL genotypes after fertilization but before genotype scoring. In both cases, observable phenotypes are distorted for marker loci in the chromosomal region close to the SDL. Under the quantitative genetics model for viability selection by proposing a continuous liability controlling the viability of individual, a simplex algorithm has been used to search for the solution in SDL mapping. However, they did not consider the effects of SDL on the construction of linkage maps.
We proposed a multipoint maximum-likelihood method to estimate the position and the effects of SDL under the liability model together with both selection coefficients of marker genotypes and recombination fractions. The method was implemented via an expectation and maximization (EM) algorithm. The superiority of the method proposed under the liability model over the previous methods was verified by a series of Monte Carlo simulation experiments, together with a working example derived from the MAPMAKER/QTL software.
Our results suggested that the new method can serve as a powerful alternative to existing methods for SDL mapping. Under the liability model, the new method can simultaneously estimate the position and the effects of SDL as well as the recombinant fractions between adjacent markers, and also be used to probe into the genetic mechanism for the bias of uncorrected map distance and to elucidate the relationship between the viability selection and genetic linkage.
导致分离比例扭曲的染色体区域被称为分离扭曲位点（SDL）。这种扭曲是由受精前配子中SDL基因型的差异代表性，或受精后但在基因型评分前SDL基因型的生存力差异引起的。在这两种情况下，靠近SDL的染色体区域中标记位点的可观察表型都会被扭曲。在通过提出一个控制个体生存力的连续阈值的生存力选择定量遗传模型下，一种单纯形算法已被用于在SDL定位中寻找解决方案。然而，他们没有考虑SDL对连锁图谱构建的影响。
我们提出了一种多点最大似然法，在阈值模型下，结合标记基因型的选择系数和重组率，来估计SDL的位置和效应。该方法通过期望最大化（EM）算法实现。通过一系列蒙特卡洛模拟实验以及一个源自MAPMAKER/QTL软件的实例，验证了在阈值模型下所提出的方法相对于先前方法的优越性。
我们结果表明，新方法可作为现有SDL定位方法的有力替代。在阈值模型下，新方法可以同时估计SDL的位置和效应以及相邻标记之间的重组率，还可用于探究未校正图谱距离偏差的遗传机制，并阐明生存力选择与遗传连锁之间的关系。
