Population structure and selection signatures over generations in the composite Montana tropical ®

Abstract

Abstract Knowledge of population structure and breed composition is important for managing breed information within a breeding program. Composite Montana Tropical® was developed by crossing animals of four different biological types or racial groups. By using genomic data it is possible to conduct several studies of population structure and selection signatures. Pedigree and genotype data (51962 SNP) from 3215 Montana Tropical® animals were used to (1) predict the composition of biological groups in the pedigree and how this composition relates to generations within the composite breed; (2) characterize the distribution of runs of homozygosity (ROH) in relation to generations within the composite breed; (3) estimate and compare the inbreeding coefficient (F) based on information from genomic markers (FROH) and pedigree (FPED); (4) identify genomic regions of islands of ROH; and (5) identify related traits in each significant genomic region under selection. The population structure (PCA and ADMIXTURE) was not related to the racial composition of the pedigree and has a strong relationship with the number of generations within the breed. There was an increase in FROH as the number of equivalent generations increased. Estimates of FROH in the Montana Tropical® population also showed that from the equivalent generation five onwards, there was a reduced number of animals with FROH equal to zero. It is believed that using PCA results in a breed’s genetic improvement program to correct for population structure is an interesting alternative to replace the correction by NABC proportions based on pedigree. The population study showed selection signatures in regions of chromosomes 4, 6, 20 and 26. The frequency with which markers in homozygosity were observed increased with the generations within the breed, demonstrating that it is really a selection process that is occurring after the formation of the composite population. Most of these selection signature regions present carcass quality QTLs demonstrating that the objective of developing a breed of cattle for pasture production systems is being achieved at the genomic level over the generations of the breed.