Abasht B, Lamont S J
Department of Animal Science, Iowa State University, Ames, IA 50011, USA.
Anim Genet. 2007 Oct;38(5):491-8. doi: 10.1111/j.1365-2052.2007.01642.x.
Genome-wide association studies have become possible in the chicken because of the recent availability of the complete genome sequence, a polymorphism map and high-density single nucleotide polymorphism (SNP) genotyping platforms. We used these tools to study the genetic basis of a very high level of heterosis that was previously observed for fatness in two F(2) populations established by crossing one outbred broiler (meat-type) sire with dams from two unrelated, highly inbred, light-bodied lines (Fayoumi and Leghorn). In each F(2) population, selective genotyping was carried out using phenotypically extreme males for abdominal fat percentage (AF) and about 3000 SNPs. Single-point association analysis of about 500 informative SNPs per cross showed significant association (P < 0.01) of 15 and 24 markers with AF in the Broiler x Fayoumi and Broiler x Leghorn crosses respectively. These SNPs were on 10 chromosomes (GGA1, 2, 3, 4, 7, 8, 10, 12, 15 and 27). Interestingly, of the 39 SNPs that were significantly associated with AF, there were about twice as many homozygous genotypes associated with higher AF that traced back to the inbred lines alleles, although the broiler line had on average higher AF. These SNPs are considered to be associated with QTL with cryptic alleles. This study reveals cryptic alleles as an important factor in heterosis for fatness observed in two chicken F(2) populations, and suggests epistasis as the common underlying mechanism for heterosis and cryptic allele expression. The results of this study also demonstrate the power of high marker-density SNP association studies in discovering QTL that were not detected by previous microsatellite-based genotyping studies.
由于鸡的全基因组序列、多态性图谱以及高密度单核苷酸多态性（SNP）基因分型平台的出现，全基因组关联研究在鸡中已成为可能。我们利用这些工具研究了在两个F₂群体中先前观察到的非常高的杂种优势的遗传基础，这两个群体是通过将一只远交肉鸡（肉用型）父本与来自两个不相关的、高度近交的轻型品系（法尤米鸡和来航鸡）的母本杂交而建立的。在每个F₂群体中，针对腹部脂肪百分比（AF）对表型极端的雄性进行选择性基因分型，并使用了约3000个SNP。每个杂交组合中约500个信息性SNP的单点关联分析表明，在肉鸡×法尤米鸡和肉鸡×来航鸡杂交组合中，分别有15个和24个标记与AF存在显著关联（P < 0.01）。这些SNP位于10条染色体上（鸡1号、2号、3号、4号、7号、8号、10号、12号、15号和27号染色体）。有趣的是，在与AF显著相关的39个SNP中，与较高AF相关的纯合基因型数量约为追溯到近交系等位基因的两倍，尽管肉鸡品系的AF平均较高。这些SNP被认为与具有隐性等位基因的数量性状位点（QTL）相关。本研究揭示了隐性等位基因是在两个鸡F₂群体中观察到的脂肪杂种优势的一个重要因素，并表明上位性是杂种优势和隐性等位基因表达的共同潜在机制。本研究结果还证明了高标记密度SNP关联研究在发现先前基于微卫星的基因分型研究未检测到的QTL方面的能力。
