Identification of differential selection traces in two <scp>P</scp>olish cattle breeds

Gurgul, Artur; Pawlina, Klaudia; Frys-Żurek, Monika; Bugno‐Poniewierska, Monika

doi:10.1111/asj.12242

Cited by 4 publications

(1 citation statement)

References 31 publications

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“…Identification of hepatic DE genes in divergent cattle breeds that are specialized for either milk or meat production or raised as dual-purpose breeds might also have significant impact to detect signatures of selection for economically important dairy and beef production traits [57], as well as detecting potential genomic regions relevant to milk and beef production, which were in good agreement with known quantitative trait loci (QTLs) or candidate genes [58,59]. A recent study on genome-wide SNP analysis of Polish-HF and Polish-Red cattle identified 19 genomic regions encompassing 55 protein-coding genes and numerous quantitative trait loci, which potentially underlined some of the phenotypic traits [60].…”

Section: Discussionmentioning

confidence: 95%

Comparative Analysis of the Liver Transcriptome among Cattle Breeds Using RNA-seq

Pareek

Sachajko

Jaśkowski

et al. 2019

Veterinary Sciences

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Global gene expression in liver transcriptome varies among cattle breeds. The present investigation was aimed to identify the differentially expressed genes (DEGs), metabolic gene networks and metabolic pathways in bovine liver transcriptome of young bulls. In this study, we comparatively analyzed the bovine liver transcriptome of dairy (Polish Holstein Friesian (HF); n = 6), beef (Hereford; n = 6), and dual purpose (Polish-Red; n = 6) cattle breeds. This study identified 895, 338, and 571 significant (p < 0.01) differentially expressed (DE) gene-transcripts represented as 745, 265, and 498 hepatic DE genes through the Polish-Red versus Hereford, Polish-HF versus Hereford, and Polish-HF versus Polish-Red breeds comparisons, respectively. By combining all breeds comparisons, 75 hepatic DE genes (p < 0.01) were identified as commonly shared among all the three breed comparisons; 70, 160, and 38 hepatic DE genes were commonly shared between the following comparisons: (i) Polish-Red versus Hereford and Polish-HF versus Hereford; (ii) Polish-Red versus Hereford and Polish-HF versus Polish-Red; and (iii) Polish-HF versus Hereford and Polish-HF versus Polish-Red, respectively. A total of 440, 82, and 225 hepatic DE genes were uniquely observed for the Polish-Red versus Hereford, Polish-HF versus Hereford, and Polish-Red versus Polish-HF comparisons, respectively. Gene ontology (GO) analysis identified top-ranked enriched GO terms (p < 0.01) including 17, 16, and 31 functional groups and 151, 61, and 140 gene functions that were DE in all three breed liver transcriptome comparisons. Gene network analysis identified several potential metabolic pathways involved in glutamine family amino-acid, triglyceride synthesis, gluconeogenesis, p38MAPK cascade regulation, cholesterol biosynthesis (Polish-Red versus Hereford); IGF-receptor signaling, catecholamine transport, lipoprotein lipase, tyrosine kinase binding receptor (Polish-HF versus Hereford), and PGF-receptor binding, (Polish-HF versus Polish-Red). Validation results showed that the relative expression values were consistent to those obtained by RNA-seq, and significantly correlated between the quantitative reverse transcription PCR (RT-qPCR) and RNA-seq (Pearson’s r > 0.90). Our results provide new insights on bovine liver gene expressions among dairy versus dual versus beef breeds by identifying the large numbers of DEGs markers submitted to NCBI gene expression omnibus (GEO) accession number GSE114233, which can serve as useful genetic tools to develop the gene assays for trait-associated studies as well as, to effectively implement in genomics selection (GS) cattle breeding programs in Poland.

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Section: Discussionmentioning

confidence: 95%

Comparative Analysis of the Liver Transcriptome among Cattle Breeds Using RNA-seq

Pareek

Sachajko

Jaśkowski

et al. 2019

Veterinary Sciences

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Population Genomics of Animal Domestication and Breed Development

Wilkinson

Wiener

2018

Population Genomics

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Identification of genome‐wide selection signatures in the Limousin beef cattle breed

Gurgul

Szmatoła

Ropka‐Molik

et al. 2015

J Animal Breeding Genetics

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The study is aimed at identifying selection footprints within the genome of Limousin cattle. With the use of Extended Haplotype Homozygosity test, supplemented with correction for variation in recombination rates across the genome, we created map of selection footprints and detected 173 significant (p < 0.01) core haplotypes being potentially under positive selection. Within these regions, a number of candidate genes associated inter alia with skeletal muscle growth (GDF15, BMP7, BMP4 and TGFB3) or postmortem proteolysis and meat maturation (CAPN1 and CAPN5) were annotated. Noticeable clusters of selection footprints were detected on chromosomes 1, 4, 8 and 14, which are known to carry several quantitative trait loci for growth traits and meat quality. The study provides information about the genes and metabolic pathways potentially modified under the influence of directional selection, aimed at improving beef production characteristics in Limousin cattle.

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Identification of differential selection traces in two Polish cattle breeds

Cited by 4 publications

References 31 publications

Comparative Analysis of the Liver Transcriptome among Cattle Breeds Using RNA-seq

Comparative Analysis of the Liver Transcriptome among Cattle Breeds Using RNA-seq

Population Genomics of Animal Domestication and Breed Development

Identification of genome‐wide selection signatures in the Limousin beef cattle breed

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