Exploring evidence of positive selection signatures in cattle breeds selected for different traits
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Since domestication, the genome landscape of cattle has been changing due to natural and artificial selection forces resulting in several general and specialized cattle breeds of the world. Identifying genomic regions affected due to these forces in livestock gives an insight into the history of selection for economically important traits and genetic adaptation to specific environments of the populations under consideration. This study explores the genes/genomic regions under selection in relation to the phenotypes of Holstein, Hanwoo, and N’Dama cattle breeds using Tajima’s D, XP-CLR, and XP-EHH population statistical methods. The whole genomes of 10 Holstein (South Korea), 11 Hanwoo (South Korea), and 10 N’Dama (West Africa—Guinea) cattle breeds re-sequenced to ~11x coverage and retained 37 million SNPs were used for the study. Selection signature analysis revealed 441, 512, and 461 genes under selection from Holstein, Hanwoo, and N’Dama cattle breeds, respectively. Among all these, seven genes including ARFGAP3, SNORA70, and other RNA genes were common between the breeds. From each of the gene lists, significant functional annotation cluster terms including milk protein and thyroid hormone signaling pathway (Holstein), histone acetyltransferase activity (Hanwoo), and renin secretion (N’Dama) were enriched. Genes that are related to the phenotypes of the respective breeds were also identified. Moreover, significant breed-specific missense variants were identified in CSN3, PAPPA2 (Holstein), C1orf116 (Hanwoo), and COMMD1 (N’Dama) genes. The genes identified from this study provide an insight into the biological mechanisms and pathways that are important in cattle breeds selected for different traits of economic significance.
This work was supported by a grant from the Next-Generation BioGreen 21 Program (Project No. PJ01134905), Rural Development Administration (RDA), Republic of Korea.
MT conceived and designed the study, analyzed the data, and wrote the paper; WL, SJ, and JY helped analyzing the data; OH, TD, SK, OAM, SC, SJO, HKL, and HK designed the project; HK organized and supervised the project.
Compliance with ethical standards
Conflict of interest
On behalf of all authors, the corresponding author states that there is no conflict of interest.
- Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. Reference SourceGoogle Scholar
- Höglund JK, Guldbrandtsen B, Lund MS, Sahana G (2015) Identification of genomic regions associated with female fertility in Danish Jersey using whole genome sequence data. BMC Genet 16(1):1Google Scholar
- Kahoun J (1971) Heat tolerance in West African cattle. Ghana J Sci 11(1):19–26Google Scholar
- Kim J, Hanotte O, Mwai OA, Dessie T, Bashir S, Diallo B et al (2017) The genome landscape of indigenous African cattle. Genome Biol 18(34)Google Scholar
- Kucerova J, Matejicek A, Jandurová O, Sorensen P, Nemcova E, Stipkova M et al (2006) Milk protein genes CSN1S1, CSN2, CSN3, LGB and their relation to genetic values of milk production parameters in Czech Fleckvieh. Czech J Anim Sci 51(6):241Google Scholar
- Leak SG (1999) Tsetse biology and ecology: their role in the epidemiology and control of trypanosomosis. CABI publishing, WallingfordGoogle Scholar
- Mozdziak P (2006) Linking embryonic myogenesis to meat quantity and quality. Pol J Food Nutr Sci 15(2):117Google Scholar
- Ogunsanmi A, Taiwo V, Onawumi B, Mbagwu H, Okoronkwo C (2000) Correlation of physiological plasma lipid levels with resistance of cattle to trypanosomosis. Veterinarski arhiv 70(5):251–257Google Scholar
- Santana M, Ventura R, Utsunomiya Y, Neves H, Alexandre P, Oliveira Junior G et al (2015) A genomewide association mapping study using ultrasound-scanned information identifies potential genomic regions and candidate genes affecting carcass traits in Nellore cattle. J Anim Breed Genet 132(6):420–427PubMedCrossRefGoogle Scholar
- Zhang R (2016) Identification of candidate genes for porcine meat quality and investigation of effects of sulforaphane on porcine satellite cell. Rheinische Friedrich-Wilhelms-Universität Bonn, BonnGoogle Scholar