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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #382414

Research Project: Improving Dairy Animals by Increasing Accuracy of Genomic Prediction, Evaluating New Traits, and Redefining Selection Goals

Location: Animal Genomics and Improvement Laboratory

Title: Accounting for X chromosome and allele frequencies in genomic inbreeding estimation

item NANI, JUAN - Oak Ridge Institute For Science And Education (ORISE)
item Vanraden, Paul

Submitted to: Journal of Dairy Science
Publication Type: Abstract Only
Publication Acceptance Date: 4/8/2021
Publication Date: 6/28/2021
Citation: Nani, J.P., Van Raden, P.M. 2021. Accounting for X chromosome and allele frequencies in genomic inbreeding estimation [abstract]. Journal of Dairy Science. 104(Suppl. 1):79–80(abstr. 205).

Interpretive Summary:

Technical Abstract: Breeders for many decades used pedigrees to limit increases in inbreeding (pedF), but genomic measures of relationship and inbreeding can provide more precise control. Previous calculations usually ignored influence of the X chromosome (BTX) when estimating relationships between two animals. For mating programs, excluding BTX can cause an increase in inbreeding by mating two individuals with the same X chromosome. Numbers of SNP markers located on BTX have increased recently in U.S. national evaluations. The X-specific region has 3.0% of the 79,060 SNPs used and those SNPs are coded as 100% homozygous in males, causing homozygosity of females to appear 3% less than males. Allele frequency also has an impact on computing genomic inbreeding (genF). Correlations were high between genomic inbreeding computed using 0.5 (genF_1) or base population (genF_2) allele frequencies for most but not all breeds. Also, average genF was higher for males than females. The genF_1 was further adjusted for BTX (genF_x) to obtain better correlations across breeds and sex and to make genF_x more similar to pedF. Haplotype-based inbreeding (hapF) was also estimated for comparison. Future inbreeding was estimated as half an animal’s relationship to a recent reference population using pedigree (EFI), 0.5 (genFI_1) or base frequencies (genFI_2) or adjusted for BTX markers (genFI_x). Definitions were compared for 3,280,753 genotyped animals of 5 breeds using a pedigree file of 86,924,013 animals. Smaller breeds were more sensitive to the use of different allele frequencies. Correlations with pedF were generally higher using genF_1 or genF_x compared to genF_2 (average correlations across breeds of 0.67, 0.67 and 0.54 respectively). Correlations with EFI were similar using genFI_1, genFI_2 or genFI_x (average correlations across breeds of 0.83, 0.84 and 0.83, respectively). Correlations of hapF with pedF were not higher than of genF_1 or genF_x with pedF (0.64). Use of genF_x and genFI_x did not affect the correlations within sexes but did improve the mean differences occurring between sexes. The adjustments allow simpler and more accurate comparisons of genomic and pedigree relationships.