Genome-wide assessment of the population structure and genetic diversity of four Portuguese native sheep breeds

Abstract

As the effects of global warming become increasingly complex and difficult to manage, the conservation and sustainable use of locally adapted sheep breeds are gaining ground. Portuguese native sheep breeds are important reservoirs of genetic diversity, highly adapted to harsh environments and reared in low input production systems. Genomic data that would describe the breeds in detail and accelerate the selection of more resilient animals to be able to cope with climatic challenges are still lacking. Here, we sequenced the genomes of 37 animals from four Portuguese native sheep breeds (Campaniça, Bordaleira Serra da Estrela, Merino Branco and Merino Preto) and 19 crossbred sheep to make inferences on their genomic diversity and population structure. Mean genomic diversities were very similar across these breeds (.30 ≤ Ho ≤ .34; .30 ≤ He ≤ .35; 1.7 × 10–3 ≤ π ≤ 3.1 × 10–3) and the levels of inbreeding were negligible (.005 ≤ FIS ≤ .038). The Principal Components, Bayesian clustering and Treemix analyses split the Portuguese breeds in two main groups which are consistent with historical records: one comprising Campaniça and Serra da Estrela together with other European and transboundary dairy breeds; and another of the well-differentiated multi-purpose Merino and Merino-related breeds. Runs of homozygosity analyses yielded 1,690 ROH segments covering an average of 2.27 Gb across the genome in all individuals. The overall genome covered by ROH segments varied from 27,75 Mb in Serra da Estrela to 61,29 Mb in Campaniça. The phylogenetic analysis of sheep mitogenomes grouped the Portuguese native breeds within sub-haplogroup B1a along with two animals of the Akkaraman breed from Turkey. This result provides additional support to a direct influence of Southwest Asian sheep in local breeds from the Iberian Peninsula. Our study is a first step pertaining to the genomic characterization of Portuguese sheep breeds and the results emphasize the potential of genomic data as a valid tool to guide conservation efforts in locally adapted sheep breeds. In addition, the genomic data we generated can be used to identify markers for breed assignment and traceability of certified breed-products.

Genome-wide association study identifies genetic variants underlying footrot in Portuguese Merino sheep

“…The selection of SNPs to be used in the assay was based on whole-genome resequencing data from 39 Merino Branco, Merino Preto and crossbred animals sampled in the south of Portugal [ 36 ]. A total of 47,779 autosomal SNPs were used for genotyping (Figure S 1 ) of which 10,053 (21.04%) were exonic, 12,655 (26.49%) intronic, 15,616 (32.68%) intergenic, 6959 (14.56%) were in 3’ untranslated regions (UTR) and 2496 (5.22%) in 5’ UTRs (Figure S 1 ).…”

“…For the SNP panel design, whole-genome resequencing data obtained by Gaspar et al [ 36 ] for 39 sheep, including: 10 Merino Branco; 10 Merino Preto; and 19 crossbreds, was used. The criteria used for SNP selection and probe design were the following: i) minor allele frequency (MAF) > 1%; ii) call rate per SNP > 90%; iii) flanking region of 150 base pairs (bp) upstream and downstream of the SNP position; and iv) no variable positions allowed (SNPs or INDELs) within these flanking regions.…”

Genomic diversity of the locally developed Latvian Darkheaded sheep breed

“…Previously estimated heterozygosity levels for different native breeds from Southern Europe ranged between 0.30 and 0.398. Ho ranged from 0.30 to 0.42 for those from Central Europe, and Ho estimates derived from other studies on sheep breeds originating from northern regions ranged between 0.30 and 0.39 [ 11 , [36] , [37] , [38] , [39] , [40] , [41] ]. For example, the Lithuanian Blackface sheep, considered a modern improved breed with a population of approximately 9000 sheep, has been shown to harbor high genetic diversity, with an average H o of 0.41 [ 40 ].…”

“…Portuguese native sheep breeds were observed to be less inbred compared to LDS. Inbreeding levels among Portuguese breeds ranged from F ROH 0.01 for one of the most abundant local breeds, Bordaleira Serra da Estrela, to F ROH 0.023 in Campanica sheep [ 36 ].…”

ONE HEALTH APPROACH ON SARS-COV-2 – USING SHEEP AS SENTINEL ANIMALS TO INCREASE FUTURE PANDEMIC PREPAREDNESS – a pilot study

“…Sheep farming in Portugal has a long tradition especially in rural areas and therefore the selection has resulted in local native sheep breeds specialized for either meat, milk or wool [14]. One of the most important dairy sheep breeds is Serra da Estrela, inhabiting the Mountain region of the same name.…”