Effects of inbreeding depression on milk production traits in Murrah buffaloes

Abstract

Inbreeding results in progeny with reduced heterozygosity, increasing the risk of inbreeding depression (ID), which reduces the average phenotypic value of traits of economic interest. Estimating the coefficient of inbreeding (F) and ID can support breeding programs, enabling the control and maintenance of genetic diversity and avoiding the effects of ID. The aim of this study is to estimate the F by different methods and to evaluate the effects of inbreeding on milk production traits in Murrah buffaloes. A total of 289 dairy buffaloes were genotyped for 90k with Axiom Buffalo Genotyping panel, and another 384 animals will be genotyped with the same panel. The effects of ID on 305-day milk yield, milk fat percent, and milk protein percent will be evaluated. The F will be estimated using genealogical (pedigree, FPED) records and genomic information (runs of homozygosity, FROH; genomic relationship matrix, GRM). The ID will be estimated by the regression of phenotypes on the F. The model for each trait will include the (1) fixed effect of group of contemporaries, (2) buffalo age at calving and each F (FPED, FROH, FGRM_Base, FGRM_Fixed) as covariables, and (3) random effects of genetic additive, permanent environment, and residual effects.