Limits...
Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis.

Ma L, O'Connell JR, VanRaden PM, Shen B, Padhi A, Sun C, Bickhart DM, Cole JB, Null DJ, Liu GE, Da Y, Wiggans GR - PLoS Genet. (2015)

Bottom Line: Sex-specific GWAS analyses identified PRDM9 and CPLX1 to have significant effects on genome-wide recombination rate in both sexes.Two novel loci, NEK9 and REC114, were associated with recombination rate in both sexes, whereas three loci, MSH4, SMC3 and CEP55, affected recombination rate in females only.Given the largest sample size ever reported for such studies, our results reveal new insights into the understanding of cattle and mammalian recombination.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, United States of America.

ABSTRACT
Meiotic recombination is an essential biological process that generates genetic diversity and ensures proper segregation of chromosomes during meiosis. From a large USDA dairy cattle pedigree with over half a million genotyped animals, we extracted 186,927 three-generation families, identified over 8.5 million maternal and paternal recombination events, and constructed sex-specific recombination maps for 59,309 autosomal SNPs. The recombination map spans for 25.5 Morgans in males and 23.2 Morgans in females, for a total studied region of 2,516 Mb (986 kb/cM in males and 1,085 kb/cM in females). The male map is 10% longer than the female map and the sex difference is most pronounced in the subtelomeric regions. We identified 1,792 male and 1,885 female putative recombination hotspots, with 720 hotspots shared between sexes. These hotspots encompass 3% of the genome but account for 25% of the genome-wide recombination events in both sexes. During the past forty years, males showed a decreasing trend in recombination rate that coincided with the artificial selection for milk production. Sex-specific GWAS analyses identified PRDM9 and CPLX1 to have significant effects on genome-wide recombination rate in both sexes. Two novel loci, NEK9 and REC114, were associated with recombination rate in both sexes, whereas three loci, MSH4, SMC3 and CEP55, affected recombination rate in females only. Among the multiple PRDM9 paralogues on the bovine genome, our GWAS of recombination hotspot usage together with linkage analysis identified the PRDM9 paralogue on chromosome 1 to be associated in the U.S. Holstein data. Given the largest sample size ever reported for such studies, our results reveal new insights into the understanding of cattle and mammalian recombination.

No MeSH data available.


Related in: MedlinePlus

Genome-wide distribution of male and female recombination rates in SNP intervals of each chromosome.Male recombination rate was shown in the top half of the figure and female recombination rate was shown in the bottom by multiplying the original female recombination rate with ‒1. The dotted lines denote the threshold of 2.5 standard deviations plus the mean for recombination hotspot, 0.0023 for males and 0.0021 for females. Different colors were used to distinguish the 29 bovine autosomal chromosomes.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4634960&req=5

pgen.1005387.g003: Genome-wide distribution of male and female recombination rates in SNP intervals of each chromosome.Male recombination rate was shown in the top half of the figure and female recombination rate was shown in the bottom by multiplying the original female recombination rate with ‒1. The dotted lines denote the threshold of 2.5 standard deviations plus the mean for recombination hotspot, 0.0023 for males and 0.0021 for females. Different colors were used to distinguish the 29 bovine autosomal chromosomes.

Mentions: Cattle male and female recombination rates are unevenly distributed along the genome (Fig 3), consistent with the observations in humans and mice [9,11,12]. By defining hotspots as SNP intervals with recombination rate >2.5 standard deviations greater than the mean [29], we identified 1,792 hotspots for males and 1,885 hotspots for females, with 720 of them shared between sexes (i.e., 40.2% for males and 38.2% for females were shared). The difference in recombination rate in subtelomeric regions between males and females largely explains the low sharing of hotspots between the two sexes (Fig 3). The male recombination hotspots covered 3.0% of the physical length of the autosomes but accounted for 25.1% of the total male recombination events. The female hotspots comprised of 3.2% of the autosomes but accounted for 25.6% of the total recombination. The 720 shared hotspots accounted for a similar amount of the total recombination events in males (11.2%) and females (11.1%). The low sharing of hotspots between the two sexes (38.2% ~ 40.2%) could have allowed opportunity for sire selection for combined genetic material not as easily obtainable in females, noting that sire selection has been the primary genetic selection in dairy cattle and has been highly efficient.


Cattle Sex-Specific Recombination and Genetic Control from a Large Pedigree Analysis.

Ma L, O'Connell JR, VanRaden PM, Shen B, Padhi A, Sun C, Bickhart DM, Cole JB, Null DJ, Liu GE, Da Y, Wiggans GR - PLoS Genet. (2015)

Genome-wide distribution of male and female recombination rates in SNP intervals of each chromosome.Male recombination rate was shown in the top half of the figure and female recombination rate was shown in the bottom by multiplying the original female recombination rate with ‒1. The dotted lines denote the threshold of 2.5 standard deviations plus the mean for recombination hotspot, 0.0023 for males and 0.0021 for females. Different colors were used to distinguish the 29 bovine autosomal chromosomes.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4634960&req=5

pgen.1005387.g003: Genome-wide distribution of male and female recombination rates in SNP intervals of each chromosome.Male recombination rate was shown in the top half of the figure and female recombination rate was shown in the bottom by multiplying the original female recombination rate with ‒1. The dotted lines denote the threshold of 2.5 standard deviations plus the mean for recombination hotspot, 0.0023 for males and 0.0021 for females. Different colors were used to distinguish the 29 bovine autosomal chromosomes.
Mentions: Cattle male and female recombination rates are unevenly distributed along the genome (Fig 3), consistent with the observations in humans and mice [9,11,12]. By defining hotspots as SNP intervals with recombination rate >2.5 standard deviations greater than the mean [29], we identified 1,792 hotspots for males and 1,885 hotspots for females, with 720 of them shared between sexes (i.e., 40.2% for males and 38.2% for females were shared). The difference in recombination rate in subtelomeric regions between males and females largely explains the low sharing of hotspots between the two sexes (Fig 3). The male recombination hotspots covered 3.0% of the physical length of the autosomes but accounted for 25.1% of the total male recombination events. The female hotspots comprised of 3.2% of the autosomes but accounted for 25.6% of the total recombination. The 720 shared hotspots accounted for a similar amount of the total recombination events in males (11.2%) and females (11.1%). The low sharing of hotspots between the two sexes (38.2% ~ 40.2%) could have allowed opportunity for sire selection for combined genetic material not as easily obtainable in females, noting that sire selection has been the primary genetic selection in dairy cattle and has been highly efficient.

Bottom Line: Sex-specific GWAS analyses identified PRDM9 and CPLX1 to have significant effects on genome-wide recombination rate in both sexes.Two novel loci, NEK9 and REC114, were associated with recombination rate in both sexes, whereas three loci, MSH4, SMC3 and CEP55, affected recombination rate in females only.Given the largest sample size ever reported for such studies, our results reveal new insights into the understanding of cattle and mammalian recombination.

View Article: PubMed Central - PubMed

Affiliation: Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, United States of America.

ABSTRACT
Meiotic recombination is an essential biological process that generates genetic diversity and ensures proper segregation of chromosomes during meiosis. From a large USDA dairy cattle pedigree with over half a million genotyped animals, we extracted 186,927 three-generation families, identified over 8.5 million maternal and paternal recombination events, and constructed sex-specific recombination maps for 59,309 autosomal SNPs. The recombination map spans for 25.5 Morgans in males and 23.2 Morgans in females, for a total studied region of 2,516 Mb (986 kb/cM in males and 1,085 kb/cM in females). The male map is 10% longer than the female map and the sex difference is most pronounced in the subtelomeric regions. We identified 1,792 male and 1,885 female putative recombination hotspots, with 720 hotspots shared between sexes. These hotspots encompass 3% of the genome but account for 25% of the genome-wide recombination events in both sexes. During the past forty years, males showed a decreasing trend in recombination rate that coincided with the artificial selection for milk production. Sex-specific GWAS analyses identified PRDM9 and CPLX1 to have significant effects on genome-wide recombination rate in both sexes. Two novel loci, NEK9 and REC114, were associated with recombination rate in both sexes, whereas three loci, MSH4, SMC3 and CEP55, affected recombination rate in females only. Among the multiple PRDM9 paralogues on the bovine genome, our GWAS of recombination hotspot usage together with linkage analysis identified the PRDM9 paralogue on chromosome 1 to be associated in the U.S. Holstein data. Given the largest sample size ever reported for such studies, our results reveal new insights into the understanding of cattle and mammalian recombination.

No MeSH data available.


Related in: MedlinePlus