Center for Computational Biology, Beijing Forestry University, Beijing 100083, China.
Brief Bioinform. 2013 Jan;14(1):96-108. doi: 10.1093/bib/bbs011. Epub 2012 Apr 15.
An allotetraploid has four paired sets of chromosomes derived from different diploid species, whose meiotic behavior is qualitatively different from the underlying diploids. According to a traditional view, meiotic pairing occurs only between homologous chromosomes, but new evidence indicates that homoeologous chromosomes may also pair to a lesser extent compared with homolog pairing. Here, we describe and assess a unifying analytical framework that incorporates differential chromosomal pairing into a multilocus linkage model. The preferential pairing factor is used to quantify the probability difference of pairing occurring between homologous chromosomes and homoeologous chromosomes. The unifying framework allows simultaneous estimation of the linkage, genetic interference and preferential pairing factor using commonly existing multiplex markers. We compared the unifying approach and traditional approaches assuming random chromosomal pairing by analyzing marker data collected in a full-sib family of tetraploid switchgrass, a bioenergy species whose diploid origins are undefined, but with subgenomes that are genetically well differentiated. The unifying framework provides a better tool for estimating the meiotic linkage and constructing a genetic map for allotetraploids.
一个异源四倍体具有四对来自不同二倍体物种的同源染色体，其减数分裂行为与基础二倍体明显不同。根据传统观点，减数分裂配对仅发生在同源染色体之间，但新的证据表明，与同源配对相比，同系染色体之间也可能存在较小程度的配对。在这里，我们描述并评估了一个统一的分析框架，该框架将差异染色体配对纳入多点连锁模型中。优先配对因子用于量化同源染色体和同系染色体之间发生配对的概率差异。统一框架允许使用常用的多重标记同时估计连锁、遗传干扰和优先配对因子。我们通过分析四倍体柳枝稷全同胞家系中收集的标记数据，比较了统一方法和传统方法，其中四倍体柳枝稷的二倍体起源尚未确定，但亚基因组在遗传上有很好的分化。统一框架为估计异源四倍体的减数分裂连锁和构建遗传图谱提供了更好的工具。
