Genome‐wide variability and selection signatures in Italian island cattle breeds

Abstract

In the present study, a sample of 88 animals belonging to four local (Modicana, Sarda, Sardo-Bruna and Sardo-Modicana) and one cosmopolitan (Italian Brown Swiss) cattle breeds were genotyped with a medium density SNP beadchip and compared to investigate their genetic diversity and the existence of selection signatures. A total of 43 012 SNPs distributed across all 29 autosomal chromosomes were retained after data quality control. Basic population statistics, Wright fixation index and runs of homozygosity (ROH) analyses confirmed that the Italian Brown Swiss genome was shaped mainly by selection, as underlined by the low values of heterozygosity and minor allele frequency. As expected, local cattle exhibited a large within-breed genetic heterogeneity. The F comparison revealing the largest number of significant SNPs was Sardo-Bruna vs. Sardo-Modicana, whereas the smallest was observed for Italian Brown Swiss vs. Sardo-Modicana. Modicana exhibited the largest number of detected ROHs, whereas the smallest was observed for Sardo-Modicana. Signatures of selection were detected in genomic regions that harbor genes involved in milk production traits for Italian Brown Swiss and fitness traits for local breeds. According to the results of multi-dimensional scaling and the admixture analysis the Sardo-Bruna is more similar to the Sarda than to the Italian Brown Swiss breed. Moreover, the Sardo-Modicana is genetically closer to the Modicana than to the Sarda breed. Results of the present work confirm the usefulness of single nucleotide polymorphisms in deciphering the genetic architecture of livestock breeds.

Genome‐wide assessment of diversity and differentiation between original and modern Brown cattle populations

“…In the original Brown group (ORBR/BRHV), at the beginning of the island on BTA11, we found the ETAA1 gene, also reported within a ROH island in Sardo‐Bruna cattle (Cesarani et al . 2018), a local Italian Brown‐derived population, thus confirming previously reported data. In fact, the overlapping ROH islands among studies (Table ) provided good evidence that they are not artifacts, but potential genomic regions affected by selection (Mastrangelo et al .…”

“…as also reported by Cesarani et al . (2018), and related to a more recent inbreeding (Mastrangelo et al . 2016).…”

“…The analytical approach, using the allele frequency‐based inter‐population genetic differentiation ( F ST ) and intra‐population runs of homozygosity (ROHs), has been recently applied in several livestock species for the identification of genomic regions involved in phenotypic differences (Cesarani et al . 2018; Onzima et al . 2018; Elbeltagy et al .…”

Evolution and domestication of the Bovini species

“…2018), Sardinia (Cesarani et al . 2018), Sicily (Mastrangelo et al . 2014), northern Spain (Cañas‐Álvarez et al .…”

Genomic Tools for Effective Conservation of Livestock Breed Diversity

“…As selection is distinguished by local reductions in haplotype diversity, depending on the distribution of ROH patterns across the genome, results allow the identification of genomic regions that have been subjected to either recent and/or ancient selective pressure events [74,75]. These regions also allow, through gene ontology and enrichment analyses, identifying of candidate genes associated with selection for different traits, highlighting those of economic-interest in different livestock populations such as horses, cattle, sheep and poultry [76][77][78][79].…”