Genomic differentiation between Asturiana de los Valles, Avileña-Negra Ibérica, Bruna dels Pirineus, Morucha, Pirenaica, Retinta and Rubia Gallega cattle breeds

Abstract

The Spanish local beef cattle breeds have most likely common origin followed by a process of differentiation. This particular historical evolution has most probably left detectable signatures in the genome. The objective of this study was to identify genomic regions associated with differentiation processes in seven Spanish autochthonous populations (Asturiana de los Valles (AV), Avileña-Negra Ibérica (ANI), Bruna dels Pirineus (BP), Morucha (Mo), Pirenaica (Pi), Retinta (Re) and Rubia Gallega (RG)). The BovineHD 777K BeadChip was used on 342 individuals (AV, n=50; ANI, n=48; BP, n=50; Mo, n=50; Pi, n=48; Re, n=48; RG, n=48) chosen to be as unrelated as possible. We calculated the fixation index (F ST ) and performed a Bayesian analysis named SelEstim. The output of both procedures was very similar, although the Bayesian analysis provided a richer inference and allowed us to calculate significance thresholds by generating a pseudo-observed data set from the estimated posterior distributions. We identified a very large number of genomic regions, but when a very restrictive significance threshold was applied these regions were reduced to only 10. Among them, four regions can be highlighted because they comprised a large number of single nucleotide polymorphisms and showed extremely high signals (Kullback-Leiber divergence (KLD)>6). They are located in BTA 2 (5 575 950 to 10 152 228 base pairs (bp)), BTA 5 (17 596 734 to 18 850 702 bp), BTA 6 (37 853 912 to 39 441 548 bp) and BTA 18 (13 345 515 to 15 243 838 bp) and harbor, among others, the MSTN (Myostatin), KIT-LG (KIT Ligand), LAP3 (leucine aminopeptidase 3), NAPCG (non-SMC condensing I complex, subunit G), LCORL (ligand dependent nuclear receptor corepressor-like) and MC1R (Melanocortin 1 receptor) genes. Knowledge on these genomic regions allows to identify potential targets of recent selection and helps to define potential candidate genes associated with traits of interest, such as coat color, muscle development, fertility, growth, carcass and immunological response.

Mapping Recombination Rate on the Autosomal Chromosomes Based on the Persistency of Linkage Disequilibrium Phase Among Autochthonous Beef Cattle Populations in Spain

“…The similarity between estimates was within the same range than the reported between estimates of the recombination rate in human (Graffelman et al, 2007; Laayouni et al, 2011; Manu et al, 2018) and livestock (Petit et al, 2017; Shen et al, 2018) populations. Thus, somehow it confirms that similarities in the distribution of the recombination rate are achieved between closely related populations (Smukowski and Noor, 2011), such as the analyzed in this study (Cañas-Álvarez et al, 2015; González-Rodríguez et al, 2017). This similarity was even observed between pairs of populations that do not share any population (i. e. ANI-AV and BP-Pi), whose average correlation (0.52 ± 0.06) was only slightly lower than the average of the correlations between estimates from pairs that share (i.e.…”

“…The genomic data comprised the BovineHD Genotyping Beadchip (777,962 SNPs, Illumina) genotypes from 171 non-related triplets of sire, dam, and one offspring from seven breeds, being 25 Asturiana de los Valles (AV), 24 Avileña - Negra Ibérica (ANI), 25 Bruna dels Pirineus (BP), 25 Morucha (Mo), 24 Pirenaica (Pi), 24 Retinta (Re), and 24 Rubia Gallega (RG) triplets. This dataset has been used to analyze genetic differentiation (Cañas-Álvarez et al, 2015; Cañas-Álvarez et al, 2016; González-Rodríguez et al, 2017), signatures of selection (González-Rodríguez et al, 2016), and haplotype diversity (Mouresan et al, 2017). These breeds represent 72% of the total census of local beef breeds in Spain (Ministerio de Medio Ambiente y Medio Rural y Marino, 2010) and their production systems are extensive or semi-extensive.…”

Detection of selection signatures for agonistic behaviour in cattle

“…A similar result for the Asturiana de los Valles breed was also obtained by González‐Rodríguez et al. () using seven Spanish bovine beef breeds, suggesting that this breed has been used as terminal sire line and crossbred individuals are introduced into the receptor populations. However, it is difficult to embrace this argument in our case taking into account the presence of the Lidia breed, which is extremely isolated and with low effective population sizes (Cortés, Sevane, Baro, & Cañón, ).…”

“…Different studies have analysed genomic changes produced by the long‐term selection in most commercial bovine breeds (Pritchard, Pickrell, & Coop, ; Randhawa, ). As a consequence, several strong genomic signatures or hard sweeps belonging to traditional selected morphological traits (muscular hypertrophy, coat colour, presence/absence horns) have been reported (Druet, Pérez‐Pardal, Charlier, & Gautier, ; González‐Rodríguez et al., ). But so far, studies of selection signatures focused on behavioural features are limited.…”

Conservation status and historical relatedness of Italian cattle breeds

“…Towards this aim, detailed information on the genetic diversity and population structure of cattle breeds is needed to guide conservation decisions and the possible use of local cattle populations [ 4 , 8 , 10 ]. The genome-wide genetic diversity and population structure of Italian cattle breeds remain poorly studied compared to local breeds from other European countries, such as France [ 3 ], Spain [ 7 , 11 ], Russia [ 12 ] and, in general, of other worldwide cattle breeds [ 8 , 9 , 13 – 15 ]. Only a few Italian breeds have been characterized using medium-density single nucleotide polymorphism (SNP) arrays [ 16 ].…”