Genome-wide variability and selection signatures in Italian island cattle breeds
| Autor: | Silvia Sorbolini, Donata Marletta, Gianni Battacone, Giuseppe Pulina, Giustino Gaspa, Andrea Criscione, N. P. P. Macciotta, Salvatore Bordonaro, Alberto Cesarani |
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| Jazyk: | angličtina |
| Rok vydání: | 2018 |
| Předmět: |
Gene Flow
0301 basic medicine Heterozygote admixture biodiversity genomics inbreeding indigenous breeds Single-nucleotide polymorphism Runs of Homozygosity Polymorphism Single Nucleotide Fixation index 03 medical and health sciences Genetics Animals Crosses Genetic Genetic diversity Genome biology Genetic Variation General Medicine biology.organism_classification Breed Pedigree 030104 developmental biology Evolutionary biology Animal Science and Zoology Cattle Sarda Brown Swiss Inbreeding |
| Popis: | 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 FST 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. |
| Databáze: | OpenAIRE |
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