Exploring genome-wide differentiation and signatures of selection in Italian and North American Holstein populations.

Autor:	Persichilli C; Department of Agricultural, Environmental and Food Sciences, University of Molise, Via A. De sanctis, 86100 Campobasso (CB), Italy., Senczuk G; Department of Agricultural, Environmental and Food Sciences, University of Molise, Via A. De sanctis, 86100 Campobasso (CB), Italy. Electronic address: g.senczuk@unimol.it., Mastrangelo S; Department of Agricultural, Food and Forest Sciences, University of Palermo, Viale delle Scienze, 90128 Palermo (PA), Italy., Marusi M; National Association of Italian Holstein, Brown and Jersey Breeders, Via Bergamo, 292, 26100 Cremona (CR), Italy., van Kaam JT; National Association of Italian Holstein, Brown and Jersey Breeders, Via Bergamo, 292, 26100 Cremona (CR), Italy., Finocchiaro R; National Association of Italian Holstein, Brown and Jersey Breeders, Via Bergamo, 292, 26100 Cremona (CR), Italy., Di Civita M; Department of Agricultural, Environmental and Food Sciences, University of Molise, Via A. De sanctis, 86100 Campobasso (CB), Italy., Cassandro M; National Association of Italian Holstein, Brown and Jersey Breeders, Via Bergamo, 292, 26100 Cremona (CR), Italy; Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università 16, 35020 Legnaro (PD), Italy., Pilla F; Department of Agricultural, Environmental and Food Sciences, University of Molise, Via A. De sanctis, 86100 Campobasso (CB), Italy.
Jazyk:	angličtina
Zdroj:	Journal of dairy science [J Dairy Sci] 2023 Aug; Vol. 106 (8), pp. 5537-5553. Date of Electronic Publication: 2023 Jun 07.
DOI:	10.3168/jds.2022-22159
Abstrakt:	Among Italian dairy cattle, the Holstein is the most reared breed for the production of Parmigiano Reggiano protected designation of origin cheese, which represents one of the most renowned products in the entire Italian dairy industry. In this work, we used a medium-density genome-wide data set consisting of 79,464 imputed SNPs to study the genetic structure of Italian Holstein breed, including the population reared in the area of Parmigiano Reggiano cheese production, and assessing its distinctiveness from the North American population. Multidimensional scaling and ADMIXTURE approaches were used to explore the genetic structure among populations. We also investigated putative genomic regions under selection among these 3 populations by combining 4 different statistical methods based either on allele frequencies (single marker and window-based) or extended haplotype homozygosity (EHH; standardized log-ratio of integrated EHH and cross-population EHH). The genetic structure results allowed us to clearly distinguish the 3 Holstein populations; however, the most remarkable difference was observed between Italian and North American stock. Selection signature analyses identified several significant SNPs falling within or closer to genes with known roles in several traits such as milk quality, resistance to disease, and fertility. In particular, a total of 22 genes related to milk production have been identified using the 2 allele frequency approaches. Among these, a convergent signal has been found in the VPS8 gene which resulted to be involved in milk traits, whereas other genes (CYP7B1, KSR2, C4A, LIPE, DCDC1, GPR20, and ST3GAL1) resulted to be associated with quantitative trait loci related to milk yield and composition in terms of fat and protein percentage. In contrast, a total of 7 genomic regions were identified combining the results of standardized log-ratio of integrated EHH and cross-population EHH. In these regions candidate genes for milk traits were also identified. Moreover, this was also confirmed by the enrichment analyses in which we found that the majority of the significantly enriched quantitative trait loci were linked to milk traits, whereas the gene ontology and pathway enrichment analysis pointed to molecular functions and biological processes involved in AA transmembrane transport and methane metabolism pathway. This study provides information on the genetic structure of the examined populations, showing that they are distinguishable from each other. Furthermore, the selection signature analyses can be considered as a starting point for future studies in the identification of causal mutations and consequent implementation of more practical application. (© 2023, The Authors. Published by Elsevier Inc. and Fass Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)
Databáze:	MEDLINE
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