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Pooling DNA to Investigate C attle I nfertility

Pooling DNA to Investigate C attle I nfertility. Tara McDaneld USDA/ARS Meat Animal Research Center Clay Center, NE, 68933, USA. Background. Reproductive efficiency Lifetime production of the cow Important element of cow-calf component of cattle industry

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Pooling DNA to Investigate C attle I nfertility

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  1. Pooling DNA to Investigate Cattle Infertility Tara McDaneld USDA/ARS Meat Animal Research Center Clay Center, NE, 68933, USA

  2. Background • Reproductive efficiency • Lifetime production of the cow • Important element of cow-calf component of cattle industry • Female becomes a liability in the herd with no calf for producer to market OR

  3. Objective • Identify regions of the genome associated with reproductive efficiency in beef cattle

  4. Challenges when evaluating reproductive traits • Low heritability (0.10-0.40) • Complex trait • Influenced by multiple genes • Creates difficulty when identifying genomic regions

  5. Tools for overcoming challenges Pooling 770 K SNP chip

  6. Steps in creating DNA pools • Extract DNA • Tissue • Blood • FTA cards • Determine quality and quantity • Pool equal amount of each individual • Properly mix pool to ensure consistency of individuals in pool

  7. 100 animals for each pool Each pool run in duplicate on 770 SNP chip

  8. Cattle populations • USMARC population • Genetically diverse populations • British and Continental breeds • 1000 females of low reproductive efficiency • 1000 females of high reproductive efficiency • 10 pools of 100 individuals for each phenotype

  9. Cattle populations • Central Florida population • Bos indicus influence • Brangus • Simbrah • Braford • Reproductive records from 2 breeding seasons • Open/open • Open/pregnant • Pregnant/open • Pregnant/pregnant

  10. Additional populations • Western Nebraska population • Records from 2007 born heifers • Records for three consecutive breeding seasons • Open females are culled after first failure • Milt Thomas at NMSU • Records from 7 small populations

  11. MARC population • Identified multiple regions across genome associated with reproductive efficiency • BTA 1, 9, 17 • Chromosome Y?

  12. Central Florida population • Identified multiple regions across genome associated with reproductive efficiency • BTA 5, 8, 9, 14, 17, and 20 • Chromosome Y

  13. Y SNP in males and females? Y SNP in the Central Florida Populations • Only see Y SNP in open and low reproductive pools 0 5000 15000 25000 35000 Red Intensity Bull Bull 00 01 10 11 00 01 10 11 00 01 10 11 Brangus Simbrah Braford

  14. Western Nebraska population • Identified multiple regions across genome associated with reproductive efficiency • BTA 1, 17, Y

  15. Additional populations • Identified multiple regions across genome associated with reproductive efficiency • BTA 5, 11, and Y

  16. SNP across the Y chromosome USMARC Central Florida -log10 P Value Western Nebraska Milt’s Position, Mb

  17. Why do we see Y SNP in the open females? • Can we determine which females that possess the Y SNP? • Evaluate individual females that make up open pool • Are all the open females contributing to the Y SNP?

  18. Y chromosome in the pools • Evaluate individuals of pools • PCR test specific to Y chromosome • PCR test is used to sex embryos • Only positive for males Bull Bull 1 2 3 4 5 6 7 8 9 10 11 12

  19. Y SNP in pools • Evaluate specific Y SNP on 770 K SNP chip • Developed PCR tests for Y SNP that are significant • We see different patterns in females that are positive for sexing PCR test (3-10% open females positive) • Different fragments of Y chromosome? Cow Cow Bull Bull 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21

  20. What is causing the Y SNP in females? • Undetected freemartins? • Females commonly calve on pasture • May miss calves that are born twins • Reproductive tracts are checked in Central Florida population at prebreeding check • Twins are recorded at USMARC

  21. Freemartins in pools? • Use PCR to test for genomic regions of Y in individuals that made up pool • Sexing PCR test Freemartin females Cow Cow Bull Bull

  22. Freemartins in pools? • Use PCR to test for Y SNP that are significant • All females that are positive for sexing primers are also positive for Y-SNP tests • Are freemartins the only cause of the Y? Freemartin females Cow Cow Bull Bull

  23. Conclusions • Identified regions of the genome associated with reproductive efficiency • Able to replicate these results in additional populations • Identified Y SNP in individuals of open pools that may contribute to low reproductive efficiency (approx. 3-29% of the open population)

  24. Current status • Evaluate Y-chromosome anomaly further • Fine map regions on autosomes identified in current project • Evaluate other chromosomal abnormalities

  25. Acknowledgements • MARC cattle operations • Central Florida Ranch • Western Nebraska Ranch • John Keele • Larry Kuehn • Warren Snelling • Milt Thomas and lab personal • Matt Spangler • Bonnie Long • Tammy Sorensen • Steve Simcox

  26. Thank You!

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