Initial genomic characterization of Italian, Egyptian and Pakistani goat breeds.
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Parole chiave

Goat
ROH
Pakistan
Italy
Egypt

Abstract

Selection and breeding practices in goats have differed greatly among countries and populations.
These processes, together with natural selection and regional drift, have shaped the phenotypic
variability of goat breeds (Kim et al., 2015). The availability of improved genomic analysis tools for
this species may provide useful information on the history of selection, adaptation and
differentiation of goats from different areas of the world, that can be evaluated by the study of
gene frequencies and length of the Runs of Homozigosity (contiguous length of homozygous
genotypes, ROH; Purfield et al., 2012). In current study, we examined using a goat medium density
SNP chip animals from three different countries: Egypt (with lack of selection scheme), Italy (with
several standardized breeds; Nicoloso et al., 2015) and Pakistan (with several breeds showing
peculiar phenotypes) to produce a genomic landscape of goats breeds in these countries. A total
of 1,123 animals of 39 different populations, and 48,895 SNP markers were analyzed. Genotypes
were imputed on a country-based approach, and markers without known position in the genome
were excluded from the analysis. MDS and ADMIXTURE plots confirmed the good differentiation
among populations from the three countries. Runs of Homozygosity (ROH) were performed for
each country and population allowed the detection of genomic regions with high homozygosity
levels, common in at least two out of three sampling areas. These results provide new insights into
goat genome structure within and among breeds and countries. The detection of conserved
regions with different lengths may explain recent selection strategies or adaptation to different,
extreme environmental conditions. The research was funded by INNOVAGEN project. Support by
Iowa State University and the Ensminger funds for AE and AT as well as support by the Fulbright
Foundation for AE are gratefully acknowledged. Sampling from Pakistan was funded by PAK-USAID
project.

https://doi.org/10.13130/2283-3927/7048
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Riferimenti bibliografici

Kim, E-S, A R Elbeltagy, A M Aboul-Naga, B Rischkowsky, B Sayre, J M Mwacharo, and M F Rothschild., 2015. Multiple Genomic Signatures of Selection in Goats and Sheep Indigenous to a Hot Arid Environment. Heredity 116, 255–264.

Nicoloso, L., L. Bomba, L. Colli, R. Negrini, M. Milanesi, R. Mazza, T. Sechi, et al., 2015. Genetic Diversity of Italian Goat Breeds Assessed with a Medium-Density SNP Chip. Genetics Selection Evolution 47:62.

Purfield, Deirdre C, Donagh P Berry, Sinead McParland, and Daniel G Bradley., 2012. Runs of Homozygosity and Population History in Cattle. BMC Genetics 13:70.

This work is licensed under a CC BY-SA 4.0 international