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United States Department of Agriculture

Agricultural Research Service

Research Project: RESOURCE DEVELOPMENT FACILITATING BOVINE GENOME SEQUENCE USE TO IMPROVE CATTLE PRODUCTION EFFICIENCY, PRODUCT QUALITY & ENVIRONMENTAL IMPACT Title: Y are you not pregnant: identification of Y chromosome segments in female cattle with decreased reproductive efficiency

Authors
item McDaneld, Tara
item Kuehn, Larry
item Thomas, Milt -
item Snelling, Warren
item Sonstegard, Tad
item Matukumalli, Lakshmi -
item Smith, Timothy
item Pollak, Emil
item Keele, John

Submitted to: Journal of Animal Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 16, 2011
Publication Date: March 9, 2012
Citation: McDaneld, T.G., Kuehn, L.A., Thomas, M.G., Snelling, W.M., Sonstegard, T.S., Matukumalli, L.K., Smith, T.P., Pollak, E.J., Keele, J.W. 2012. Y are you not pregnant: identification of Y chromosome segments in female cattle with decreased reproductive efficiency. Journal of Animal Science. 90(7):2142-2151.

Interpretive Summary: Reproductive efficiency in cattle is an important element of the cow-calf component of the beef production industry. If the female does not become pregnant after breeding, she becomes a liability in the herd with no calf for the producer to market. As a result, reduction in unproductive periods in the reproductive female's life would significantly impact production costs. Therefore, we set out to identify regions of the genome that are associated with reproductive efficiency in beef cattle. Traditionally, heritability of reproductive traits is low, creating a challenge when identifying genomic regions that may harbor genetic markers that could be used for selection. With the development of high-density genetic marker arrays, it is possible to perform genome wide association studies for lowly heritable traits such as reproductive efficiency. However, high cost of genotyping with high-density genetic marker arrays can result in smaller sample sizes being genotyped limiting the power of the study. To overcome this, we have utilized DNA pooling of individual animals based on reproductive efficiency. Several populations have been evaluated for this study including commercial ranches and the USMARC population. Animals from the commercial ranches include populations from across the United States. DNA was pooled based on open/pregnant phenotype for each population. Equal concentrations of each individual sample were added to the respective pool to ensure that each animal is represented equally within the pool. Pools were then evaluated using a high-density array with 770,000 genetic markers. Utilizing pooling and the high-density genetic marker array, we surprisingly identified chromosome Y-associated material in low reproductive heifers. To assess these results, 6 chromosome Y genetic markers that were identified to be associated with reproduction were selected for further evaluation in individual animals that comprised each pool. Of the animals with low reproductive efficiency, 3-20% had at least 1 significant chromosome Y genetic marker. Additionally, none of the highly reproductive animals showed incidence of the chromosome Y genetic markers on an individual basis. This research is the first to identify a group of chromosome Y genetic markers that can be used to evaluate breeding females for reproductive potential and as a result can select against those females with a greater propensity for reproductive failure.

Technical Abstract: Reproductive efficiency is of economic importance in commercial beef cattle production, as failure to achieve pregnancy reduces the number of calves marketed. Identification of genetic markers with predictive merit for reproductive success would facilitate early selection of females and avoid inefficiencies associated with sub-fertile cows. To identify regions of the genome harboring variation affecting reproductive success, we applied a genome-wide association approach based on the >700,000 SNP markers genotyped by the Illumina BovineHD beadchip assay. To include the largest number of individuals possible under the available budget, cows from several populations were assigned to extremes for reproductive efficiency, and DNA was pooled within population and phenotype prior to genotyping. Surprisingly, pools prepared from DNA of low reproductive cattle returned fluorescence intensity data intermediate between fertile females and males for SNP mapped to the Y chromosome (i.e. male sex chromosome). The presence of Y-associated material in low reproductive heifers or cows was confirmed by Y-directed PCR, which revealed that 21-29% of females in the low reproductive category were positive by a Y chromosome PCR test normally used to sex embryos. The presence of Y chromosomal segments was further confirmed with application of additional Y-specific PCR amplicons, indicating the likelihood of the presence of some portion of male sex chromosome in female cattle in various beef cattle herds across the U.S. Discovery of this Y anomaly in low reproductive females may make an important contribution to management of reproductive failures in beef cattle operations.

Last Modified: 12/25/2014
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