Abstract
BackgroundEnvironmental variance (VE) is partially under genetic control, which means that the VE of individuals that share the same environment can differ because they have different genotypes. Previously, a divergent selection experiment for VE of litter size (LS) during 13 generations in rabbit yielded a successful response and revealed differences in resilience between the divergent lines. The aim of the current study was to identify signatures of selection in these divergent lines to better understand the molecular mechanisms and pathways that control VE of LS and animal resilience. Three methods (FST, ROH and varLD) were used to identify signatures of selection in a set of 473 genotypes from these rabbit lines (377) and a base population (96). A whole-genome sequencing (WGS) analysis was performed on 54 animals to detect genes with functional mutations.ResultsBy combining signatures of selection and WGS data, we detected 373 genes with functional mutations in their transcription units, among which 111 had functions related to the immune system, stress response, reproduction and embryo development, and/or carbohydrate and lipid metabolism. The genes TTC23L, FBXL20, GHDC, ENSOCUG00000031631, SLC18A1, CD300LG, MC2R, and ENSOCUG00000006264 were particularly relevant, since each one carried a functional mutation that was fixed in one of the rabbit lines and absent in the other line. In the 3ʹUTR region of the MC2R and ENSOCUG00000006264 genes, we detected a novel insertion/deletion (INDEL) variant.ConclusionsOur findings provide further evidence in favour of VE as a measure of animal resilience. Signatures of selection were identified for VE of LS in genes that have a functional mutation in their transcription units and are mostly implicated in the immune response and stress response pathways. However, the real implications of these genes for VE and animal resilience will need to be assessed through functional analyses.
Highlights
Environmental variance (VE) is partially under genetic control, which means that the VE of individuals that share the same environment can differ because they have different genotypes
The highest variation in LD patterns (VarLD) scores, 12.55 and 12.25, were obtained for OCU14 in the BaseHigh and Base-Low comparison, respectively. These three genomic regions were proposed as putative signatures of selection because their linkage disequilibrium (LD) patterns differed relative to the base population
By searching for the most relevant functional mutations, we found seven promising genes that contained an INDEL with the alternative allele fixed in one rabbit line and absent in the other (Table 2), i.e., TTC23L, FBXL20, GHDC, ENSOCUG00000031631, SLC18A1, CD300LG, MC2R, and ENSOCUG00000006264, and which are the most relevant for VE of litter size (LS)
Summary
Environmental variance (VE) is partially under genetic control, which means that the VE of individuals that share the same environment can differ because they have different genotypes. Several methods for the detection of signatures of selection have been proposed and are based on different assumptions according to the pattern of positive selection to be detected [14]: (1) reduction of the local genomic variability, (2) modification of the spectrums of allele frequency, or (3) variation of the linkage disequilibrium (LD). Because of these different assumptions, the three methods are not strongly correlated [15, 16] and, have to be used in conjunction to identify the largest possible number of signatures of selection
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