Selection for environmental variance of litter size in rabbits involves genes in pathways controlling animal resilience

Abstract

Background 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. 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. Results By 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. Conclusions Our 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.

Comparative analysis of genomic inbreeding parameters and runs of homozygosity islands in several fancy and meat rabbit breeds

“…This might suggest again that fancy rabbit breeds should be considered apart from other rabbit lines where inbreeding is usually avoided to maintain high production performances. Runs of homozygosity were also investigated in rabbits by Casto-Rebollo et al (2021) for another purpose. These authors used ROH to identify signatures of divergent selection in a rabbit population from which divergent lines for environmental variance of litter size were established.…”

“…Runs of homozygosity were also investigated in rabbits by Casto‐Rebollo et al ( 2021 ) for another purpose. These authors used ROH to identify signatures of divergent selection in a rabbit population from which divergent lines for environmental variance of litter size were established.…”

Differential patterns in runs of homozygosity in two mice lines under divergent selection for environmental variability for birth weight

“…These are directly related to higher profitability and improvement in animal welfare (Bolet et al, 2007;Poigner et al, 2000). Recently, Casto-Rebollo et al (2021) have shown that selection to modify the environmental variance of litter size involve genes with a functional mutation in their transcription units and are mostly implicated in the immune response and stress response pathways. More uniform animals would be less affected by unappreciable environments environment changes thus keeping their performance, which is a sign of robustness.…”

Dietary hydrolyzed soya lecithin affects feed intake, abundance of bacteria in the caecum, fatty acid composition and area of adipocytes in pre‐mating primiparous V‐line female rabbit

“…One of the powerful tools to sustain livestock production to feed the rapidly developing populations is to enhance their reproductive potential (Roszkos et al, 2020). Rabbit does can give birth to two to nine kittens in each pregnancy (Casto-Rebollo et al, 2021); therefore, the high reproductive rate of rabbits could provide animal protein source to feed the growing human populations. Nutrition plays a crucial role in reproduction (Attia et al, 2018).…”