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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #312639

Research Project: Improving Genetic Predictions in Dairy Animals Using Phenotypic and Genomic Information

Location: Animal Genomics and Improvement Laboratory

Title: Cattle sex-specific recombination and genetic control from a very large pedigree

Author
item Ma, Li - University Of Maryland
item O'connell, Jeffrey - University Of Maryland
item Vanraden, Paul
item Shen, Botong - University Of Maryland
item Padhi, Abinash - University Of Maryland
item Sun, Chuanyu - National Association Of Animal Breeders
item Bickhart, Derek
item Cole, John
item Null, Daniel
item Liu, Ge - George
item Da, Yang - University Of Minnesota
item Wiggans, George

Submitted to: PLoS Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/23/2015
Publication Date: 11/5/2015
Citation: Ma, L., O'Connell, J.R., Van Raden, P.M., Shen, B., Padhi, A., Sun, C., Bickhart, D.M., Cole, J.B., Null, D.J., Liu, G., Da, Y., Wiggans, G.R. 2015. Cattle sex-specific recombination and genetic control from a very large pedigree. PLoS Genetics. 11(11):e1005387.

Interpretive Summary: Recombination of chromosomes during meiosis is an essential biological process, providing new combinations of genetic variants that allow efficient selection and faster evolution. Crossovers contribute to genetic diversity by reshuffling maternal and paternal genetic alleles into the next generation. Locations are known to be non-random, and numbers of crossovers vary considerably across the species, gender, and even individuals. Using over a half million genotyped dairy cattle in a large pedigree, we identified over 8.5 million maternal and paternal crossover events in 186,927 three-generation Holstein families. The estimated male recombination map was 10% longer than the female map and spanned 25.5 and 23.2 Morgans, respectively, using 59,309 autosomal loci. Many hotspots of increased crossover rate and several genes influencing these were identified and compared to other species. Precise cattle linkage maps were constructed for use by researchers instead of the physical maps used currently.

Technical Abstract: Meiotic recombination is an essential biological process that generates novel genetic variants and ensures proper segregation of chromosomes during meiosis. From a large USDA dairy cattle pedigree with over half million genotyped animals, we extracted 186,927 three-generation families, identified over 8.5 million maternal and paternal crossover events, and constructed sex-specific recombination maps for 59,309 autosomal SNPs that spanned 25.5 and 23.2 Morgans in males and females respectively. The male map is 10% longer than the female map and the higher male recombination rate is most pronounced in the telomeric regions, although males and females exhibit similar recombination rates at other chromosomal locations. We identified 1,792 and 1,885 recombination hotspots for males and females respectively, with 720 of them shared between sexes. These recombination hotspots encompass about 3% of the genome but account for 25% of the genome-wide recombinations in both sexes. Strikingly, during the past forty years, both sexes showed a decreasing trend in recombination rate that coincided with the artificial selection for milk production in cattle. Using sex-specific GWAS analyses, we confirmed two genes, PRDM9 and CPLX1, and identified novel loci, NEK9 and REC114, to be associated with genome-wide recombination rate in both sexes. Three loci, MSH4, SMC3 and CEP55, were associated with recombination rate only in females. From GWAS of recombination hotspot usage, we clearly confirmed the cattle PRDM9 to be the paralogue on chromosome 1, despite a total of four paralogues in the cattle genome. Given the largest sample size ever reported for such studies, our results contribute large sample evidence to the understanding of mammalian recombination.