Gene Banks as Reservoirs to Detect Recent Selection: The Example of the Asturiana de los Valles Bovine Breed.

Simon Boitard,Kenza Bazi-Kabbaj,Natalia Sevane,Cyriel Paris,Bertrand Servin,Susana Dunner

doi:10.3389/fgene.2021.575405

Abstract

Gene banks, framed within the efforts for conserving animal genetic resources to ensure the adaptability of livestock production systems to population growth, income, and climate change challenges, have emerged as invaluable resources for biodiversity and scientific research. Allele frequency trajectories over the few last generations contain rich information about the selection history of populations, which cannot be obtained from classical selection scan approaches based on present time data only. Here we apply a new statistical approach taking advantage of genomic time series and a state of the art statistic (nSL) based on present time data to disentangle both old and recent signatures of selection in the Asturiana de los Valles cattle breed. This local Spanish originally multipurpose breed native to Asturias has been selected for beef production over the last few generations. With the use of SNP chip and whole-genome sequencing (WGS) data, we detect candidate regions under selection reflecting the effort of breeders to produce economically valuable beef individuals, e.g., by improving carcass and meat traits with genes such as MSTN, FLRT2, CRABP2, ZNF215, RBPMS2, OAZ2, or ZNF609, while maintaining the ability to thrive under a semi-intensive production system, with the selection of immune (GIMAP7, GIMAP4, GIMAP8, and TICAM1) or olfactory receptor (OR2D2, OR2D3, OR10A4, and 0R6A2) genes. This kind of information will allow us to take advantage of the invaluable resources provided by gene bank collections from local less competitive breeds, enabling the livestock industry to exploit the different mechanisms fine-tuned by natural and human-driven selection on different populations to improve productivity.

Highlights

Asturiana de los Valles is a Spanish cattle breed native to Asturias, in the north-western region of Spain.1 Being originally a multipurpose breed, it was selected for beef purposes over the last few generations
Selection Signatures Detected From the HMM Time Series Approach
The maximum likelihood estimation of effective population size in Asturiana de los Valles was equal to 408.3 animals, with a 95% confidence interval between 350 and 450

Summary

Introduction

Asturiana de los Valles is a Spanish cattle breed native to Asturias, in the north-western region of Spain. Being originally a multipurpose breed, it was selected for beef purposes over the last few generations. Being originally a multipurpose breed, it was selected for beef purposes over the last few generations To this aim, the selection of homozygous individuals for a disruptive mutation in the myostatin (MSTN) gene, associated with the muscular hypertrophy phenotype (Dunner et al, 2003), has led to a remarkable increase in the frequency of the nt821(del11) mutation in Asturiana de los Valles, as shown by a 93.6% frequency found in the animals belonging to the last generation (those born between 2014 and 2020, Aseava unpublished data). Gene banks allow for in vitro conservation of substantial inventories of germplasm and tissues They have emerged as invaluable resources for biodiversity and scientific research (Groeneveld et al, 2016), including reconstituting and enhancing the genetic variability of breeds (e.g., Blackburn et al, 2014; Kim et al, 2015). Far from representing breeds for one fixed point in time, gene bank collections have been shown to capture more diversity than some in-situ populations thanks to periodic resampling (e.g., Yue et al, 2015; Paiva et al, 2016)

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Conclusion