Lutz Vanessa, Stratz Patrick, Preuß Siegfried, Tetens Jens, Grashorn Michael A, Bessei Werner, Bennewitz Jörn
Institute of Animal Science, University of Hohenheim, 70599, Stuttgart, Germany.
Division of Functional Breeding, Department of Animal Sciences, Georg-August-University Göttingen, 37077, Göttingen, Germany.
Genet Sel Evol. 2017 Feb 3;49(1):18. doi: 10.1186/s12711-017-0287-4.
Feather pecking and aggressive pecking in laying hens are serious economic and welfare issues. In spite of extensive research on feather pecking during the last decades, the motivation for this behavior is still not clear. A small to moderate heritability has frequently been reported for these traits. Recently, we identified several single-nucleotide polymorphisms (SNPs) associated with feather pecking by mapping selection signatures in two divergent feather pecking lines. Here, we performed a genome-wide association analysis (GWAS) for feather pecking and aggressive pecking behavior, then combined the results with those from the recent selection signature experiment, and linked them to those obtained from a differential gene expression study.
A large F2 cross of 960 F2 hens was generated using the divergent lines as founders. Hens were phenotyped for feather pecks delivered (FPD), aggressive pecks delivered (APD), and aggressive pecks received (APR). Individuals were genotyped with the Illumina 60K chicken Infinium iSelect chip. After data filtering, 29,376 SNPs remained for analyses. Single-marker GWAS was performed using a Poisson model. The results were combined with those from the selection signature experiment using Fisher's combined probability test.
Numerous significant SNPs were identified for all traits but with low false discovery rates. Nearly all significant SNPs were located in clusters that spanned a maximum of 3 Mb and included at least two significant SNPs. For FPD, four clusters were identified, which increased to 13 based on the meta-analysis (FPD). Seven clusters were identified for APD and three for APR. Eight genes (of the 750 investigated genes located in the FPD clusters) were significantly differentially-expressed in the brain of hens from both lines. One gene, SLC12A9, and the positional candidate gene for APD, GNG2, may be linked to the monomanine signaling pathway, which is involved in feather pecking and aggressive behavior.
Combining the results from the GWAS with those of the selection signature experiment substantially increased the statistical power. The behavioral traits were controlled by many genes with small effects and no single SNP had effects large enough to justify its use in marker-assisted selection.
蛋鸡的啄羽和攻击啄行为是严重的经济和福利问题。尽管在过去几十年里对啄羽行为进行了广泛研究，但这种行为的动机仍不明确。这些性状的遗传力通常为低到中等。最近，我们通过在两个不同的啄羽品系中绘制选择标记，鉴定了几个与啄羽相关的单核苷酸多态性（SNP）。在此，我们对啄羽和攻击啄行为进行了全基因组关联分析（GWAS），然后将结果与最近的选择标记实验结果相结合，并将它们与差异基因表达研究获得的结果联系起来。
以这两个不同品系为亲本，培育了一个由960只F2母鸡组成的大型F2杂交群体。对母鸡的啄羽次数（FPD）、攻击啄次数（APD）和被攻击啄次数（APR）进行表型分析。使用Illumina 60K鸡Infinium iSelect芯片对个体进行基因分型。经过数据筛选，剩余29376个SNP用于分析。使用泊松模型进行单标记GWAS。使用Fisher联合概率检验将结果与选择标记实验的结果相结合。
所有性状均鉴定出大量显著的SNP，但错误发现率较低。几乎所有显著的SNP都位于跨度最大为3 Mb的簇中，且至少包括两个显著的SNP。对于FPD，鉴定出4个簇，基于荟萃分析（FPD）增加到13个。对于APD鉴定出7个簇，对于APR鉴定出3个簇。在两个品系母鸡的大脑中，位于FPD簇中的750个研究基因中有8个基因表达存在显著差异。一个基因SLC12A9以及APD的位置候选基因GNG2可能与单胺信号通路有关，该信号通路参与啄羽和攻击行为。
将GWAS结果与选择标记实验结果相结合，显著提高了统计效力。行为性状由许多效应较小的基因控制，没有单个SNP的效应大到足以证明其可用于标记辅助选择。
