Identification of functional mutations associated with environmental variance of litter size in rabbits

Abstract

Background: Environmental variance (V E) is partly under genetic control and has recently been proposed as a measure of resilience. Unravelling the genetic background of the V E of complex traits could help to improve resilience of livestock and stabilize their production across farming systems. The objective of this study was to identify genes and functional mutations associated with variation in V E of litter size (LS) in rabbits. To achieve this, we combined the results of a genome-wide association study (GWAS) and a whole-genome sequencing (WGS) analysis using data from two divergently selected rabbit lines for high and low V E of LS. These lines differ in terms of biomarkers of immune response and mortality. Moreover, rabbits with a lower V E of LS were found to be more resilient to infections than animals with a higher V E of LS. Results: By using two GWAS approaches (single-marker regression and Bayesian multiple-marker regression), we identified four genomic regions associated with V E of LS, on chromosomes 3, 7, 10, and 14. We detected 38 genes in the associated genomic regions and, using WGS, we identified 129 variants in the splicing, UTR, and coding (missense and frameshift effects) regions of 16 of these 38 genes. These genes were related to the immune system, the development of sensory structures, and stress responses. All of these variants (except one) segregated in one of the rabbit lines and were absent (n = 91) or fixed in the other one (n = 37). The fixed variants were in the HDAC9, ITGB8, MIS18A, ENSOCUG00000021276 and URB1 genes. We also identified a 1-bp deletion in the 3′UTR region of the HUNK gene that was fixed in the low V E line and absent in the high V E line. Conclusions: This is the first study that combines GWAS and WGS analyses to study the genetic basis of V E. The new candidate genes and functional mutations identified in this study suggest that the V E of LS is under the control of functions related to the immune system, stress response, and the nervous system. These findings could also explain differences in resilience between rabbits with homogeneous and heterogeneous V E of litter size.

Inflammatory Correlated Response in Two Lines of Rabbit Selected Divergently for Litter Size Environmental Variability

“…Recently a genome-wide association study was performed on our lines, identifying several genes with functionality in the immune system and stress [47]. This finding corroborates the decisive role of the immune system in the environmental variation of litter size.…”

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

“…We used three methods to identify signatures of selection in combination with whole-genome sequencing (WGS) analysis to highlight the genes with functional mutations. This study complements a previous GWAS for V E of LS using the same rabbit lines [ 11 ].…”

“…By combining the three methods, ROH, F ST and VarLD, we were able to identify most of the selection forces that affect the trait of interest, and we considered these 134 true signatures of selection as independent patterns of positive selection for V E of LS. However, only one F ST window on OCU3 (51–51.75 Mb) agreed with a variance-controlling locus (vQTL), which was previously identified in a GWAS [ 11 ] that used the same animals from the base and the generation 11 populations. The three genes ( SLIT3 , FOXI1 , and FGF18 ) with functional mutations located in this vQTL could be the most relevant genes that play a role in the control of V E of LS.…”

“…WGS data were pre-processed following Elston et al [ 25 ] with the following steps: (1) indexation to the reference genome (OryCun v2.0.103), (2) removal of adapters and low-quality read ends, (3) alignment to OryCun v2.0.103, and (4) identification of duplicates. Then, variant calling was performed using the GATK Best Practices pipeline [ 26 ] in three steps: (5) creation of raw VCF files for the high and low V E of LS lines, (6) variant filtering, and (7) variant annotation (for further information see Casto-Rebollo et al [ 11 ]).…”

“…Genome-wide associations studies (GWAS) for V E in livestock have identified candidate genes that are involved in the immune response, which boosts the inflammatory response [9][10][11]. In rabbit lines that were divergently selected for V E of LS, Casto-Rebollo et al [11] identified functional mutations in candidate genes that are involved in the immune system, the nervous system, and the development of sensory structures. However, V E is a complex trait with a low heritability [12] and low phenotype accuracy, which makes the identification of all the loci that affect V E by GWAS only, difficult [13].…”