An experiment of divergent selection for intramuscular fat was carried out at Universitat Politècnica de València. The high response of selection in intramuscular fat content, after nine generations of selection, and a multidimensional scaling analysis showed a high degree of genomic differentiation between the two divergent populations. Therefore, local genomic differences could link genomic regions, encompassing selective sweeps, to the trait used as selection criterion. In this sense, the aim of this study was to identify genomic regions related to intramuscular fat through three methods for detection of selection signatures and to generate a list of candidate genes. The methods implemented in this study were Wright’s fixation index, cross population composite likelihood ratio and cross population – extended haplotype homozygosity. Genomic data came from the 9th generation of the two populations divergently selected, 237 from Low line and 240 from High line. A high single nucleotide polymorphism (SNP) density array, Affymetrix Axiom OrcunSNP Array (around 200k SNPs), was used for genotyping samples. Several genomic regions distributed along rabbit chromosomes (OCU) were identified as signatures of selection (SNPs having a value above cut-off of 1%) within each method. In contrast, 8 genomic regions, harbouring 80 SNPs (OCU1, OCU3, OCU6, OCU7, OCU16 and OCU17), were identified by at least 2 methods and none by the 3 methods. In general, our results suggest that intramuscular fat selection influenced multiple genomic regions which can be a consequence of either only selection effect or the combined effect of selection and genetic drift. In addition, 73 genes were retrieved from the 8 selection signatures. After functional and enrichment analyses, the main genes into the selection signatures linked to energy, fatty acids, carbohydrates and lipid metabolic processes were ACER2, PLIN2, DENND4C, RPS6, RRAGA (OCU1), ST8SIA6, VIM (OCU16), RORA, GANC and PLA2G4B (OCU17). This genomic scan is the first study using rabbits from a divergent selection experiment. Our results pointed out a large polygenic component of the intramuscular fat content. Besides, promising positional candidate genes would be analysed in further studies in order to bear out their contributions to this trait and their feasible implications for rabbit breeding programmes.

在瓦伦西亚理工大学进行了肌内脂肪发散选择实验。在选择了9代后，对肌肉内脂肪含量的选择反应很高，并且多维缩放分析显示了两个不同群体之间的高度基因组分化。因此，局部基因组差异可以将包括选择性扫描在内的基因组区域链接到用作选择标准的性状。从这个意义上讲，本研究的目的是通过三种检测选择标记的方法来鉴定与肌内脂肪相关的基因组区域，并生成候选基因列表。这项研究中采用的方法是赖特的固定指数，跨群体复合似然比和跨群体-扩展单倍型纯合性。基因组数据来自不同选择的两个种群的第9代，低种群为237，高种群为240。高单核苷酸多态性（单核苷酸多态性密度阵列，Affymetrix Axiom OrcunSNP阵列（约200k SNP）用于基因分型。在每种方法中，沿着兔染色体（OCU）分布的几个基因组区域被确定为选择的特征（SNP的临界值高于1％）。相比之下，至少有2种方法鉴定了包含80个SNP的8个基因组区域（OCU1，OCU3，OCU6，OCU7，OCU16和OCU17），而没有通过3种方法鉴定出。一般而言，我们的结果表明，肌肉内脂肪选择影响多个基因组区域，这可能是选择效应或选择与遗传漂移共同作用的结果。此外，从8个选择标记中检索到73个基因。经过功能和富集分析后，主要的基因进入了与能量，脂肪酸，ACER2，PLIN2，DENND4C，RPS6，RRAGA（OCU1），ST8SIA6，VIM（OCU16），RORA，GANC和PLA2G4B（OCU17）。这项基因组扫描是首次使用来自不同选择实验的兔子的研究。我们的结果指出了肌内脂肪含量的一个很大的多基因成分。此外，有希望的位置候选基因将在进一步的研究中进行分析，以证明其对该特性的贡献及其对兔育种计划的可行意义。