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

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.

Genetic Architecture and Signatures of Selection in the Caqueteño Creole (Colombian Native Cattle)

“…It is worth mentioning that the approach to the selection of CAQ cattle has not been defined in relation to producing milk or meat; however, in some regions of the signatures of selection, we identified a slight trend of genes associated with growth and traits related to meat quality. For example, genomic regions related to meat production traits were identified in a recent study on the CAQ breed using the homozygosis island methodology [7].…”

“…In addition, replacing native vegetation (prairies) with plating forages sustained the breed's development in that region. Currently, the Criollo Caqueteño cattle have a low number of females with reproductive capacity [6][7][8]. With the development of next-generation sequencing (NGS) technologies, and single-nucleotide polymorphism (SNP) annotation, studies on population history, genetic diversity, and genome structure in domestic animals became possible [9][10][11][12][13].…”

Identification of ROH Islands Conserved through Generations in Pigs Belonging to the Nero Lucano Breed

“…According to several authors, the frequency and extension of ROH are affected by ancient or recent inbreeding events in the population and/or by the presence of genes under strong selection [20,21]. ROH islands are stretches of homozygous genomic sequences characterized by a very high frequency in a population.…”

Dissecting Selective Signatures and Candidate Genes in Grandparent Lines Subject to High Selection Pressure for Broiler Production and in a Local Russian Chicken Breed of Ushanka

“…The respective genomic inbreeding coefficient (F ROH ) was computed using data regarding the homozygous region count and length in the examined breed genomes [113]. This F ROH estimate was represented by the proportion of each individual's total length of ROH to the length of the autosomal SNP-covered reference genome [62,114,115].…”