Abstract
Simple SummaryThis study aimed to evaluate the consistency of different methodologies and sources of information used to estimate inbreeding coefficients in small populations by analyzing the correlation between them in the Holstein population of Mexico and to choose the best option in order to aid breeding programs to improve the productive traits of Holstein cattle in small-specialized populations.This study aimed to identify inbreeding coefficient (F) estimators useful for improvement programs in a small Holstein population through the evaluation of different methodologies in the Mexican Holstein population. F was estimated as follows: (a) from pedigree information (Fped); (b) through runs of homozygosity (Froh); (c) from the number of observed and expected homozygotic SNP in the individuals (Fgeno); (d) through the genomic relationship matrix (Fmg). The study included information from 4277 animals with pedigree records and 100,806 SNP. The average and standard deviation values of F were 3.11 ± 2.30 for Fped, −0.02 ± 3.55 for Fgeno, 2.77 ± 0.71 for Froh and 3.03 ± 3.05 for Fmg. The correlations between coefficients varied from 0.30 between Fped and Froh, to 0.96 between Fgeno and Fmg. Differences in the level of inbreeding among the parent’s country of origin were found regardless of the method used. The correlations among genomic inbreeding coefficients were high; however, they were low with Fped, so further research on this topic is required.
Highlights
For many years, the Holstein breed has dominated the dairy industry
Artificial insemination, which has been intensively used in dairy cattle since the 1980s [1], along with embryo transfer, are useful tools in genetic improvement that have increased the rate of genetic progress, decreased generation intervals, increased selection accuracy and reduced the costs of progeny testing [2]
The number of complete generations calculated with the Pedig Software [16] was seven generations, and the from pedigree information (Fped) value calculated for this population was 3.11 ± 2.30%
Summary
Artificial insemination, which has been intensively used in dairy cattle since the 1980s [1], along with embryo transfer, are useful tools in genetic improvement that have increased the rate of genetic progress, decreased generation intervals, increased selection accuracy and reduced the costs of progeny testing [2]. Plus the use of genomic information has resulted in the selection of the generation of animals from a reduced number of families or individuals with high genetic values [3], increasing inbreeding and, decreasing the effective population size. Selection increases the frequency of homozygous regions in the genome, while at the same time decreasing the genetic diversity and affecting the phenotypic values for some productive features (inbreeding depression), lowering the yield per animal [4]. The inbreeding coefficient (F) is defined as the probability that at any locus of an individual, genes identical by descent are found [6]; in other words, it is the replica of a gene at the moment the embryo is generated from two parents with one or more common ancestors [6]
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