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Genome-wide association study for stayability measures in Nellore-Angus crossbred cows.

ABSTRACT: Beef cow stayability is a complex, economically important trait often used as an indicator of a cow's potential lifetime productivity. Stayability is defined as capability of a cow to maintain a perfect record up to 6 yr of age. This age is commonly cited as a financial break-even point, where initial costs of cow development and maintenance are recovered by her cumulative net income from yearly calf receipts. Later-maturing Bos indicus-Bos taurus crossbred cows may experience reproductive difficulty early in life but have a high potential for a long reproductive life span. It was the objective of this study to identify genetic variants associated with measures of beef cow stayability. A population of B. indicus-B. taurus crossbred cows (n = 305) from central Texas was used. Phenotypes for various measures of stayability to 6 yr of age were produced by artificially imposing five different culling criteria on data from the population. Cows were scored either as a 1 (indicating a perfect record through 6 yr) or a 0 (indicating failure at or before 6 yr), under each criterion. Genome-wide association studies (GWAS) were conducted for each criterion using univariate procedures and prefitting the fixed effect of cow contemporary group. SNP associations for two criteria surpassed the false discovery threshold of 0.15, when a cow was scored as 0 upon her first failure to wean a calf, regardless of reason, through 6 yr (criterion 2), and when a cow was scored as 0 upon her first failure to give birth to a calf, through 6 yr (criterion 3). Associated SNP were found on bovine chromosomes (BTA) 1, 2, 5, 9, 18, and 21 for criterion 2 and on BTA 1, 5, 11, 15, and 24 for criterion 3. A critical region on BTA 5: 43-50 Mb was identified for each criterion. Due to the similarities to prior work, the tendency for B. indicus cattle to experience reproductive difficulties early in life, and due to the large proportion of cows that left the herd at an early age under these criteria, these results suggest that the associations are likely driven by an early life trait such as age at puberty or rate of heifer development.

SUBMITTER: Engle BN

PROVIDER: S-EPMC6140944 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BACKGROUND:Bovine respiratory disease complex (BRDC) is one of the most important sources of loss within the beef cattle industry in the USA. Steps have been taken to reduce the incidence of BRDC through vaccination. Despite the effectiveness of vaccines, large proportions of cattle still experience morbidity and mortality. Identification of genomic regions that are associated with variation in response to vaccination would allow for the selection of individuals genetically predisposed to respond to vaccination based on specific markers, while heritability and accuracy estimates would help facilitate genomic selection. This in turn may lead to selection for beef cattle herds that may have lower incidence rate of BRDC after vaccination. This study utilizes an Angus herd of more than 2000 head of cattle to identify these regions of association. RESULTS:Genome wide association studies were performed for viral neutralization antibody level and response to vaccination traits against four different viruses associated with BRDC: bovine viral diarrhea virus 1 and 2 (BVDV1 and BVDV2), bovine respiratory syncytial virus (BRSV), and bovine herpesvirus (BHV1). A total of six 1-Mb windows were associated with greater than 1% of the genetic variance for the analyzed vaccination response traits. Heritabilities ranged from 0.08 to 0.21 and prediction accuracy ranged from 0.01 to 0.33 across 7 different vaccination traits. CONCLUSIONS:Although six 1-Mb windows were identified as associated with 1% or greater genetic variance for viral neutralization antibody level and response to vaccination traits, few genes around these windows could readily be considered candidates. This indicates the need for further functional genomic annotation, as these regions appear to be gene deserts. Traits ranged from lowly to moderately heritable, which indicated the potential for selection of individuals that are genetically pre-disposed to respond to vaccination. The relatively low amount of genetic variance accounted for by any 1-Mb window indicated that viral neutralization antibody level and response to vaccination traits are polygenic in nature. Selection for these traits is possible, but likely to be slow due to the low heritabilities and absence of markers with high genetic variation associated with them.

Project description:BackgroundingStayability, which may be defined as the probability of a cow remaining in the herd until a reference age or at a specific number of calvings, is usually measured late in the animal's life. Thus, if used as selection criteria, it will increase the generation interval and consequently might decrease the annual genetic gain. Measuring stayability at an earlier age could be a reasonable strategy to avoid this problem. In this sense, a better understanding of the genetic architecture of this trait at different ages and/or at different calvings is important. This study was conducted to identify possible regions with major effects on stayability measured considering different numbers of calvings in Nellore cattle as well as pathways that can be involved in its expression throughout the female's productive life.ResultsThe top 10 most important SNP windows explained, on average, 17.60% of the genetic additive variance for stayability, varying between 13.70% (at the eighth calving) and 21% (at the fifth calving). These SNP windows were located on 17 chromosomes (1, 2, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 27, and 28), and they harbored a total of 176 annotated genes. The functional analyses of these genes, in general, indicate that the expression of stayability from the second to the sixth calving is mainly affected by genetic factors related to reproductive performance, and nervous and immune systems. At the seventh and eighth calvings, genes and pathways related to animal health, such as density bone and cancer, might be more relevant.ConclusionOur results indicate that part of the target genomic regions in selecting for stayability at earlier ages (from the 2th to the 6th calving) would be different than selecting for this trait at later ages (7th and 8th calvings). While the expression of stayability at earlier ages appeared to be more influenced by genetic factors linked to reproductive performance together with an overall health/immunity, at later ages genetic factors related to an overall animal health gain relevance. These results support that selecting for stayability at earlier ages (perhaps at the second calving) could be applied, having practical implications in breeding programs since it could drastically reduce the generation interval, accelerating the genetic progress.

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Genome-wide association study for stayability measures in Nellore-Angus crossbred cows.

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