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

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.

Estimation of direct and maternal genetic effects and annotation of potential candidate genes for weight and meat quality traits in a genotyped outdoor dual-purpose cattle breed

“…The gene HS3ST1 (a potential candidate gene for direct genetic effects on BWT) and the genes ZNF609 , PECAM1 , and TEX2 genes (potential candidate genes for maternal genetic effects on BWT) were associated with carcass and body weight traits in beef cattle ( Kim, et al, 2011 ; Naserkheil et al, 2020 ; Bruscadin et al, 2021 ). In a selection signature segment on BTA10, Boitard et al (2021) also detected ZNF609 as a candidate gene for carcass traits in a beef cattle population. SMG6 , a potential candidate gene for the maternal genetic effect on 200dW, was significantly associated with rib eye area in beef cattle ( Wang et al, 2020 ).…”

Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines

“…One important point to outline is that these 18 regions under convergent selection could not have been detected by comparing the two modern lines, as convergent selection does not increase population differentiation. Besides, these signatures are likely too recent to be detected with other standard approaches based on local changes in genetic diversity or LD [ 11 , 39 ]. Regions that were selected only in LWS or LWD left a small signature of excessive differentiation between lines, but this signal was too small to be detected with high confidence.…”

“…In contrast to studies on ancient DNA time series, which document evolution over a very long time scale starting from the initial domestication [ 8 ], gene bank collections capture the evolution of genetic diversity over the last few decades via recurrent re-sampling of populations over this period [ 9 ]. The resulting short-term genomic time series allow detection of loci that have been selected as a result of recent selection objectives [ 10 ], thereby distinguishing them from those that had been selected before this modern intensive breeding period [ 11 ]. These data also inform us about the evolution of the effective population size or inbreeding over this recent period [ 10 , 12 , 13 ].…”

Selection and Drift: A Comparison between Historic and Recent Dutch Friesian Cattle and Recent Holstein Friesian Using WGS Data

“…Our results revealed that the Dutch gene bank has stored material containing genetic diversity that has been lost in vivo by selection and drift. Gene bank collections have been shown to capture more diversity than some in situ populations thanks to periodic resampling [59][60][61]. It is also important that the gene bank pool stores genetic variation existing in the whole population.…”