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The effect of divergent selection for intramuscular fat on the domestic rabbit genome

Published online by Cambridge University Press:  19 June 2020

B. S. Sosa-Madrid Open the ORCID record for B. S. Sosa-Madrid [Opens in a new window] ,
L. Varona Open the ORCID record for L. Varona [Opens in a new window] ,
A. Blasco Open the ORCID record for A. Blasco [Opens in a new window] ,
P. Hernández Open the ORCID record for P. Hernández [Opens in a new window] ,
C. Casto-Rebollo Open the ORCID record for C. Casto-Rebollo [Opens in a new window]  and
N. Ibáñez-Escriche Open the ORCID record for N. Ibáñez-Escriche [Opens in a new window]
B. S. Sosa-Madrid
Affiliation:
Institute for Animal Science and Technology, Universitat Politècnica de València, 46022Valencia, Spain
L. Varona
Affiliation:
Unidad de Genética Cuantitativa y Mejora Animal, Universidad de Zaragoza, Instituto Agroalimentario de Aragón (IA2), 50013Zaragoza, Spain
A. Blasco
Affiliation:
Institute for Animal Science and Technology, Universitat Politècnica de València, 46022Valencia, Spain
P. Hernández
Affiliation:
Institute for Animal Science and Technology, Universitat Politècnica de València, 46022Valencia, Spain
C. Casto-Rebollo
Affiliation:
Institute for Animal Science and Technology, Universitat Politècnica de València, 46022Valencia, Spain
N. Ibáñez-Escriche*
Affiliation:
Institute for Animal Science and Technology, Universitat Politècnica de València, 46022Valencia, Spain
*
†E-mail: noeibes@dca.upv.es
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Abstract

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.

Keywords

genome scangenomic divergencelagomorphmeat qualityselection signatures
Type
Research Article
Information
animal , Volume 14 , Issue 11 , November 2020 , pp. 2225 - 2235
Copyright
© The Author(s), 2020. Published by Cambridge University Press on behalf of The Animal Consortium

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