BACKGROUND Ascites syndrome is a hypertensive, multifactorial, multigene trait affecting meat-type chickens imposing significant economic losses on the broiler industry. A region containing the CPQ gene has been previously identified as significantly affecting ascites phenotype. The region was discovered through whole genome resequencing focused on chicken chromosome 2. The association was confirmed through further genotyping in multiple broiler populations. RESULTS The whole genome resequencing analyses have now been extended to the current chicken genome assembly. DNA samples were pooled according to gender and phenotype and the pools subjected to next generation sequencing. Loci were identified as clusters of single nucleotide polymorphisms where frequencies of the polymorphisms differed between resistant and susceptible chickens. The chickens are an unselected line descended from a commercial elite broiler line. Regions identified were specific to one or both genders. The data identify a total of 28 regions as potential quantitative trait loci for ascites. The genes from these regions have been associated with hypertensive-related traits in human association studies. One region on chicken chromosome 28 contains the LRRTM4 gene. Additional genotyping for the LRRTM4 region demonstrates an epistatic interaction with the CPQ region for ascites phenotype. CONCLUSIONS The 28 regions identified were not previously identified in a multi-generational genome wide association study using 60k Single Nucleotide Polymorphism panels. This work demonstrates the utility of whole genome resequencing as a cost effective, direct, and efficient method for identifying specific gene regions affecting complex traits. The approach is applicable to any organism with a genome assembly and requires no a priori assumptions.

中文翻译：

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使用全基因组重测序鉴定和验证肉鸡腹水综合征数量性状位点。

背景技术腹水综合征是影响肉用鸡的高血压、多因素、多基因性状，给肉鸡业造成重大经济损失。含有 CPQ 基因的区域先前已被鉴定为显着影响腹水表型。该区域是通过针对鸡 2 号染色体的全基因组重测序发现的。通过对多个肉鸡群体的进一步基因分型证实了这种关联。结果全基因组重测序分析现已扩展到当前的鸡基因组组装。DNA 样本根据性别和表型进行合并，并对合并后的样本进行下一代测序。基因座被鉴定为单核苷酸多态性簇，其中抗性鸡和易感鸡之间的多态性频率不同。这些鸡是来自商业精英肉鸡品系的未经选择的品系。确定的区域特定于一种或两种性别。该数据总共确定了 28 个区域作为腹水的潜在数量性状位点。在人类关联研究中，这些区域的基因与高血压相关特征相关。鸡 28 号染色体上的一个区域含有 LRRTM4 基因。LRRTM4 区域的额外基因分型表明，腹水表型与 CPQ 区域存在上位相互作用。结论 所鉴定的 28 个区域是之前使用 60k 单核苷酸多态性组进行的多代全基因组关联研究中未鉴定过的。这项工作证明了全基因组重测序作为一种经济高效、直接且有效的方法来识别影响复杂性状的特定基因区域的实用性。该方法适用于任何具有基因组组装的生物体，并且不需要先验假设。