Identification of Runs of Homozygosity Islands and Genomic Estimated Inbreeding Values in Caqueteño Creole Cattle (Colombia)

Alejandra M Toro-Ospina; Ana C Herrera Rios; Gustavo Pimenta Schettini; Viviana H Vallejo Aristizabal; Wellington Bizarria Dos Santos; Cesar A Zapata; Edna Gicela Ortiz Morea

doi:10.3390/genes13071232

Identification of Runs of Homozygosity Islands and Genomic Estimated Inbreeding Values in Caqueteño Creole Cattle (Colombia)

Genes (Basel). 2022 Jul 12;13(7):1232. doi: 10.3390/genes13071232.

Authors

Alejandra M Toro-Ospina¹, Ana C Herrera Rios^{1

2}, Gustavo Pimenta Schettini³, Viviana H Vallejo Aristizabal¹, Wellington Bizarria Dos Santos⁴, Cesar A Zapata¹, Edna Gicela Ortiz Morea¹

Affiliations

¹ Amazonian Research Center CIMAZ-MACAGUAL, Laboratory of Agrobiotechnology, University of the Amazon, Florencia 180002, Colombia.
² Science and Humanities Faculty, Digital University Institute of Antioquia, IUDigital, Medellin, Antioquia 50010, Colombia.
³ Department of Animal and Poultry Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0002, USA.
⁴ School of Agricultural and Veterinary Sciences (FCAV), São Paulo State University (UNESP), Jaboticabal, Sao Paulo 14884-900, Brazil.

Abstract

The Caqueteño Creole (CAQ) is a native breed of cattle from the Caquetá department (Colombia), adapted to tropical conditions, which is extremely important to production systems in those regions. However, CAQ is poorly studied. In this sense, population structure studies associated with runs of homozygosity (ROH) analysis would allow for a better understanding of CAQ. Through ROH analysis, it is possible to reveal genetic relationships between individuals, measure genome inbreeding levels, and identify regions associated with traits of economic interest. Samples from a CAQ population (n = 127) were genotyped with the Bovine HD BeadChip (777,000 SNPs) and analyzed with the PLINK 1.9 program to estimate FROH and ROH islands. We highlighted a decrease in inbreeding frequency for FROH 4−8 Mb, 8−16 Mb, and >16 Mb classes, indicating inbreeding control in recent matings. We also found genomic hotspot regions on chromosomes 3, 5, 6, 8, 16, 20, and 22, where chromosome 20 harbored four hotspots. Genes in those regions were associated with fertility and immunity traits, muscle development, and environmental resistance, which may be present in the CAQ breed due to natural selection. This indicates potential for production systems in tropical regions. However, further studies are necessary to elucidate the CAQ production objective.

Keywords: cattle native; inbreeding; tropical.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Cattle / genetics
Colombia
Genome* / genetics
Genomics
Homozygote
Inbreeding*

Grants and funding

This work was part of a research project studying Experimental animal breeding genomics, for the breeding of the productive traits of cattle in the department of Caqueta, supported by Sistema General de Regalías (grant number 2018000100120).