Genomic inbreeding depression for climatic adaptation of tropical beef cattle

Inbreeding has the potential to negatively impact animal performance. Strategies to monitor and mitigate inbreeding depression require that it can be accurately estimated. Here, we used genomewide SNP data to explore 3 alternative measures of genomic inbreeding: the diagonal elements of the genomic relationship matrix (FGRM), the proportion of homozygous SNP (FHOM), and the proportion of the genome covered by runs of homozygosity (FROH). We used 2,111 Brahman (BR) and 2,550 Tropical Composite (TC) cattle with phenotypes recorded for 10 traits of relevance to tropical adaptation. We further explored 3 marker densities ranging from a high-density chip (729,068 SNP), a medium-density chip (71,726 SNP) specifically designed for Bos indicus cattle, and a low-density chip (18,860 SNP) associated with the measures of inbreeding. Measures of FGRM were highly correlated across the 3 SNP densities and negatively correlated with FHOM and FROH in the BR population. In both populations, there was a strong positive correlation for each measure of inbreeding across the 3 SNP panels. We found significant (P < 0.01) inbreeding depression for various traits, particularly when using the highest-density SNP chip in the BR population, where inbreeding was negatively associated with coat color and coat type such that inbred animals presented shorter, slicker, and lighter coats. Based on FGRM using the medium-density chip, we found that a 1% increase in inbreeding in the BR and TC populations was associated with a decrease of 0.514 and 0.579 kg BW, respectively, in yearlings. In the TC population, a 1% increase in FHOM was associated with a decrease in BCS of −0.636% (P < 0.001). The low-density chip, comprising SNP associated with inbreeding, captured genes, and regions with pleiotropic effects (P < 0.001). However, it did not improve our ability to identify inbreeding depression, relative to the use of higher-density panels. We conclude that where heterogeneous populations are present, such as in tropical environments where composite animals abound, measures of inbreeding that do not depend on allele frequencies, such as FHOM and FROH, are preferable for estimating genomic inbreeding. Finally, the sustainable intensification of livestock systems in tropical regions will rely on genetic safeguards to ensure that productivity is improved while also adapting animals to cope with climate change. The results of this study are a step toward achieving that goal

Real-time PCR genotyping and frequency of the myostatin F94L mutation in beef cattle breeds

This research developed two real-time PCR assays, employing high-resolution melt and allele-specific analysis to accurately genotype the F94L mutation in cattle. This mutation (g.433C > A) in the growth differentiation factor 8 or myostatin gene has recently been shown to be functionally associated with increased muscle mass and carcass yield in cattle. The F94L mutation is not, like other myostatin mutations, associated with reduced fertility and dystocia. It is therefore a candidate for introgression into other breeds to improve retail beef yield and the development of a simple and accurate test to genotype this specific mutation is warranted. Variations in the efficiency of enzyme cleavage compromised the accuracy of genotyping by published methods, potentially resulting in an overestimation of the frequency of the mutant allele. The frequency of the F94L mutation was determined by real-time PCR in 1140 animals from 15 breeds of cattle in Australia. The mutation was present in Simmental (0.8%), Piedmontese (2%), Droughtmaster (4%) and Limousin (94.2%) but not found in Salers, Angus, Poll Hereford, Hereford, Gelbvieh, Charolais, Jersey, Brahman, Holstein, Shorthorn or Maine Anjou. The low prevalence of F94L in all beef breeds except Limousin indicates the significant potential for this mutation to improve retail yield in Australian beef cattle. © 2009 The Animal Consortium

Comparison of metabolic, hematological, and peripheral blood leukocyte cytokine profiles of dairy cows and heifers during the periparturient period

The periparturient period presents major physiological challenges for the dairy cow. It is a period that is affected by metabolic stressors, major changes in endocrine status, and altered immune function, which together result in an increased risk of disease. Immunological, hematological, and metabolic profiles from the periparturient period of heifers (primipara) were compared with those of cows (pluripara) to test the hypothesis that at the time of calving they have qualitatively different peripheral blood profiles. Blood samples were collected from 22 Holstein-Friesian animals on 3 occasions: approximately 2wk before calving, within 24h after calving, and approximately 2wk after calving. Quantitative PCR was used to measure the expression of a selected set of cytokines and receptors by peripheral blood leukocytes. Additional analyses included hemoglobin concentration, red cell, platelet and white cell counts (total and differentiated), and clinical diagnostic biochemical profiles. Total leukocyte counts, neutrophils, and lymphocytes were higher in heifers than cows before calving and within 24h after calving. Alkaline phosphatase was consistently higher in heifers than cows and several significant differences were observed between the 2 groups with regards to cytokine and cytokine-receptor mRNA expression. The results warrant further investigation from the perspective of identifying risk factors for metabolic and parturient disease in dairy cattle