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.

Popularly known as blue land crab, Cardisoma guanhumi is heavily exploited as food and considered as an important economic resource in Brazil. In recent decades, the species has experienced a sharp population decline by the loss and/or degradation of its natural habitat and overfishing. The present study aimed to investigate the genetic variation and connectivity among 154 specimens of C. guanhumi sampled along the coast of Pernambuco in five different levels of tropical mangroves conservation. Nine ISSR primers were used for assessing the genetic variation of the species. The genetic diversity observed in C. guanhumi was high reinforcing the condition of a resilient species, indicating a good conservation status of this resource in Pernambuco. The hypothesis of panmixia was rejected in favour of a heterogeneous distribution of the genotypes of C. guanhumi (ФST = 0.19) despite the high gene flow observed in the study region. Such difference could be attributed to the candidate loci being under positive selection and differentially distributed between the geographic regions assessed. The genetic structure showed a pattern of fine-scale genetic structuring better fitted to a model of selection-mediated geographic cline. Cluster analysis and candidate loci under positive selection suggested that the populations of C. guanhumi in the North-central and South coasts of Pernambuco might be different management units and must be managed independently. In conclusion, exhaustion of natural stocks upon which fishing is totally dependent will lead to serious ecological and sociocultural impacts.