C. Alkan, B. P. Coe, and E. E. Eichler, Genome structural variation discovery and genotyping, Nat Rev Genet, vol.12, pp.363-376, 2011.

W. Barendse, A. Reverter, R. J. Bunch, B. E. Harrison, W. Barris et al., A validated whole-genome association study of efficient food conversion in cattle, Genetics, vol.176, pp.1893-1905, 2007.

P. Bellot, G. De-los-campos, and M. Perez-enciso, Can Deep Learning Improve Genomic Prediction of Complex Human Traits? Genetics, 2018.

D. M. Bickhart and G. E. Liu, The challenges and importance of structural variation detection in livestock, Front Genet, vol.5, p.37, 2014.

D. Boichard, M. Boussaha, A. Capitan, D. Rocha, C. Hozé et al., Experience from large scale use of the EuroGenomics custom SNP chip in cattle. Page 675 in Proc, Proc. World Congr. Genet. Appl. Livest. Prod, 2018.

S. Bolormaa, J. E. Pryce, A. Reverter, Y. Zhang, W. Barendse et al.,

, A multi-trait, meta-analysis for detecting pleiotropic polymorphisms for stature, fatness and reproduction in beef cattle, PLoS Genet, vol.10, 1004198.

A. C. Bouwman, H. D. Daetwyler, A. J. Chamberlain, C. H. Ponce, M. Sargolzaei et al., Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals, Nat Genet, vol.50, pp.362-367, 2018.

R. F. Brøndum, G. Su, L. Janss, G. Sahana, B. Guldbrandtsen et al., Quantitative trait loci markers derived from whole genome sequence data increases the reliability of genomic prediction, J Dairy Sci, vol.98, pp.4107-4116, 2015.

B. L. Browning and S. R. Browning, Genotype Imputation with Millions of Reference Samples, Am J Hum Genet, vol.98, pp.116-126, 2016.

C. J. Bult, J. A. Blake, C. L. Smith, J. A. Kadin, J. E. Richardson et al., Mouse Genome Database (MGD) 2019, Nucleic Acids Res, vol.47, pp.801-806, 2019.

M. P. Calus, M. E. Goddard, Y. C. Wientjes, P. J. Bowman, and B. J. Hayes, Multibreed genomic prediction using multitrait genomic residual maximum likelihood and multitask Bayesian variable selection, J Dairy Sci, vol.101, pp.4279-4294, 2018.

A. Capitan, A. Allais-bonnet, A. Pinton, B. Marquant-le-guienne, D. L. Bourhis et al., A 3.7 Mb deletion encompassing ZEB2 causes a novel polled and multisystemic syndrome in the progeny of a somatic mosaic bull, PLoS One, vol.7, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01019835

C. Charlier, W. Coppieters, F. Rollin, D. Desmecht, J. S. Agerholm et al., Highly effective SNP-based association mapping and management of recessive defects in livestock, Nat Genet, vol.40, pp.449-454, 2008.

A. Garcia-ruiz, J. B. Cole, P. M. Vanraden, G. R. Wiggans, F. J. Ruiz-lopez et al., Changes in genetic selection differentials and generation intervals in US Holstein dairy cattle as a result of genomic selection, Proc Natl Acad Sci U S A, vol.113, pp.3995-4004, 2016.

G. Project, C. , A. Auton, L. D. Brooks, R. M. Durbin et al., A global reference for human genetic variation, Nature, vol.526, pp.68-74, 2015.

M. Georges, C. Charlier, and B. Hayes, Harnessing genomic information for livestock improvement, Nat Rev Genet, vol.20, pp.135-156, 2019.

S. Goodwin, J. D. Mcpherson, and W. R. Mccombie, Coming of age: ten years of next-generation sequencing technologies, Nat Rev Genet, vol.17, pp.333-351, 2016.

E. H. Hay, Y. T. Utsunomiya, L. Xu, Y. Zhou, H. H. Neves et al., Genomic predictions combining SNP markers and copy number variations in Nellore cattle, BMC Genomics, vol.19, p.441, 2018.

B. Hayes, Overview of Statistical Methods for Genome-Wide Association Studies (GWAS), Methods Mol Biol, vol.1019, pp.149-169, 2013.

F. He, R. Pasam, F. Shi, S. Kant, G. Keeble-gagnere et al., Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome, Nat Genet, vol.51, pp.896-904, 2019.

J. T. Howard, J. E. Pryce, C. Baes, and C. Maltecca, Invited review: Inbreeding in the genomics era: Inbreeding, inbreeding depression, and management of genomic variability, J Dairy Sci, 2017.

C. Hoze, C. Escouflaire, M. Mesbah-uddin, A. Barbat, M. Boussaha et al.,

, Short Communication: A splice site mutation in CENPU is associated with recessive embryonic lethality in Holstein cattle

Y. Jiang, M. Xie, W. Chen, R. Talbot, J. F. Maddox et al.,

K. Hansen, R. A. Kristensen, P. Gibbs, C. C. Flicek, H. E. Warkup et al., The sheep genome illuminates biology of the rumen and lipid metabolism, vol.344, pp.1168-1173, 2014.

N. K. Kadri, P. D. Koks, and T. H. Meuwissen, Prediction of a deletion copy number variant by a dense SNP panel, Genet Sel Evol, vol.44, 2012.

N. K. Kadri, G. Sahana, C. Charlier, T. Iso-touru, B. Guldbrandtsen et al., A 660-Kb deletion with antagonistic effects on fertility and milk production segregates at high frequency in Nordic Red cattle: additional evidence for the common occurrence of balancing selection in livestock, PLoS Genet, vol.10, p.1004049, 2014.

K. E. Kemper, C. M. Reich, P. J. Bowman, C. J. Vander-jagt, A. J. Chamberlain et al., Improved precision of QTL mapping using a nonlinear Bayesian method in a multi-breed population leads to greater accuracy of across-breed genomic predictions, Genet Sel Evol, vol.47, p.29, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01303213

S. Kipp, D. Segelke, S. Schierenbeck, F. Reinhardt, R. Reents et al., Identification of a haplotype associated with cholesterol deficiency and increased juvenile mortality in Holstein cattle, J Dairy Sci, vol.99, pp.8915-8931, 2016.

D. Kolbehdari, Z. Wang, J. R. Grant, B. Murdoch, A. Prasad et al., A whole-genome scan to map quantitative trait loci for conformation and functional traits in Canadian Holstein bulls, J Dairy Sci, vol.91, pp.2844-2856, 2008.

M. Li, S. Tian, L. Jin, G. Zhou, Y. Li et al., Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars, Nat Genet, vol.45, pp.1431-1438, 2013.

W. Li, A. Sartelet, N. Tamma, W. Coppieters, M. Georges et al., Reverse genetic screen for loss-of-function mutations uncovers a frameshifting deletion in the melanophilin gene accountable for a distinctive coat color in Belgian Blue cattle, Anim Genet, vol.47, pp.110-113, 2016.

Y. Li, N. T. Klena, G. C. Gabriel, X. Liu, A. J. Kim et al., Global genetic analysis in mice unveils central role for cilia in congenital heart disease, Nature, vol.521, pp.520-524, 2015.

M. S. Lund, A. P. Roos, A. G. Vries, T. Druet, V. Ducrocq et al., A common reference population from four European Holstein populations increases reliability of genomic predictions, Genet Sel Evol, vol.43, p.43, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01191309

D. G. Macarthur, S. Balasubramanian, A. Frankish, N. Huang, J. Morris et al., A systematic survey of loss-of-function variants in human protein-coding genes, Science, vol.335, pp.823-828, 2012.

J. Marchini and B. Howie, Genotype imputation for genome-wide association studies, Nat Rev Genet, vol.11, pp.499-511, 2010.

J. Marchini, B. Howie, S. Myers, G. Mcvean, and P. Donnelly, A new multipoint method for genome-wide association studies by imputation of genotypes, Nat Genet, vol.39, pp.906-913, 2007.

M. I. Mccarthy, G. R. Abecasis, L. R. Cardon, D. B. Goldstein, J. Little et al., Genomewide association studies for complex traits: consensus, uncertainty and challenges, Nat Rev Genet, vol.9, pp.356-369, 2008.

M. C. Mcclure, D. Bickhart, D. Null, P. Vanraden, L. Xu et al.,

C. P. Cole, T. S. Van-tassell, and . Sonstegard, Bovine exome sequence analysis and targeted SNP genotyping of recessive fertility defects BH1, HH2, and HH3 reveal a putative causative mutation in SMC2 for HH3, PLoS One, vol.9, 2014.

M. Mesbah-uddin, B. Guldbrandtsen, M. S. Lund, and G. Sahana, Genotype call for chromosomal deletions using readdepth from whole genome sequence variants in cattle. Page 662 in Proc, World Congr. Genet. Appl. Livest. Prod, 2018.

M. Mesbah-uddin, C. Hozé, P. Michot, A. Barbat, R. Lefebvre et al., A missense mutation (p.Tyr452Cys) in the CAD gene compromises reproductive success in French Normande cattle, J Dairy Sci, vol.102, pp.6340-6356, 2019.

T. Meuwissen and M. Goddard, Accurate prediction of genetic values for complex traits by whole-genome resequencing, Genetics, vol.185, pp.623-631, 2010.

T. H. Meuwissen, B. J. Hayes, and M. E. Goddard, Prediction of total genetic value using genome-wide dense marker maps, Genetics, vol.157, pp.1819-1829, 2001.

P. Michot, S. Chahory, A. Marete, C. Grohs, D. Dagios et al., A reverse genetic approach identifies an ancestral frameshift mutation in RP1 causing recessive progressive retinal degeneration in European cattle breeds, Genet Sel Evol, vol.48, p.56, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01479315

P. Michot, S. Fritz, A. Barbat, M. Boussaha, M. C. Deloche et al., A missense mutation in PFAS (phosphoribosylformylglycinamidine synthase) is likely causal for embryonic lethality associated with the MH1 haplotype in Montbeliarde dairy cattle, J Dairy Sci, vol.100, pp.8176-8187, 2017.

G. Moser, S. H. Lee, B. J. Hayes, M. E. Goddard, N. R. Wray et al., Simultaneous discovery, estimation and prediction analysis of complex traits using a bayesian mixture model, PLoS Genet, vol.11, 2015.

H. Pausch, R. Emmerling, H. Schwarzenbacher, and R. Fries, A multi-trait meta-analysis with imputed sequence variants reveals twelve QTL for mammary gland morphology in Fleckvieh cattle, Genet Sel Evol, vol.48, p.14, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01341348

H. Pausch, H. Schwarzenbacher, J. Burgstaller, K. Flisikowski, C. Wurmser et al., Homozygous haplotype deficiency reveals deleterious mutations compromising reproductive and rearing success in cattle, BMC Genomics, vol.16, p.312, 2015.

C. Pont, T. Leroy, M. Seidel, A. Tondelli, W. Duchemin et al., Tracing the ancestry of modern bread wheats, Nat Genet, vol.51, pp.905-911, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02154676

M. A. Rivas, M. Pirinen, D. F. Conrad, M. Lek, E. K. Tsang et al.,

J. B. Bustamante, M. J. Li, R. Daly, P. Guigo, K. Donnelly et al.,

T. Montgomery, D. G. Lappalainen, and . Macarthur, Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome, Science, vol.348, pp.666-669, 2015.

A. Roxström, E. Strandberg, B. Berglund, U. Emanuelson, and J. Philipsson, Genetic and Environmental Correlations Among Female Fertility Traits and Milk Production in Different Parities of Swedish Red and White Dairy Cattle, Acta Agriculturae Scandinavica, Section A -Animal Science, vol.51, pp.7-14, 2001.

G. Sahana, T. Iso-touru, X. Wu, U. S. Nielsen, D. J. De-koning et al., A 0.5-Mbp deletion on bovine chromosome 23 is a strong candidate for stillbirth in Nordic Red cattle, Genet Sel Evol, vol.48, p.35, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01341369

G. Sahana, U. S. Nielsen, G. P. Aamand, M. S. Lund, and B. Guldbrandtsen, Novel harmful recessive haplotypes identified for fertility traits in Nordic Holstein cattle, PLoS One, vol.8, 2013.

M. P. Sanchez, A. Govignon-gion, P. Croiseau, S. Fritz, C. Hoze et al., Within-breed and multi-breed GWAS on imputed whole-genome sequence variants reveal candidate mutations affecting milk protein composition in dairy cattle, Genet Sel Evol, vol.49, p.68, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01589691

M. Sargolzaei, J. P. Chesnais, and F. S. Schenkel, A new approach for efficient genotype imputation using information from relatives, BMC Genomics, vol.15, p.478, 2014.

L. R. Schaeffer, Strategy for applying genome-wide selection in dairy cattle, J Anim Breed Genet, vol.123, pp.218-223, 2006.

N. F. Schulman, G. Sahana, T. Iso-touru, S. D. Mckay, R. D. Schnabel et al., Mapping of fertility traits in Finnish Ayrshire by genome-wide association analysis, Anim Genet, vol.42, pp.263-269, 2011.

H. Schwarzenbacher, J. Burgstaller, F. R. Seefried, C. Wurmser, M. Hilbe et al., A missense mutation in TUBD1 is associated with high juvenile mortality in Braunvieh and Fleckvieh cattle, BMC Genomics, vol.17, p.400, 2016.

M. Slatkin, Linkage disequilibrium--understanding the evolutionary past and mapping the medical future, Nat Rev Genet, vol.9, pp.477-485, 2008.

P. Sørensen, S. M. Edwards, P. Jensen, . Vancouver, C. Bc et al., Using Sequence Variants in Linkage Disequilibrium with Causative Mutations to Improve Across-Breed Prediction in Dairy Cattle: A Simulation Study, Proc. 10th World Congress of Genetics Applied to Livestock Production, vol.6, pp.2553-2561, 2014.

I. Van-den-berg, T. H. Meuwissen, I. M. Macleod, and M. E. Goddard, Predicting the effect of reference population on the accuracy of within, across, and multibreed genomic prediction, J Dairy Sci, 2019.

E. M. Van-leeuwen, A. Kanterakis, P. Deelen, M. V. Kattenberg, C. Of-the-netherlands et al., Populationspecific genotype imputations using minimac or IMPUTE2, Nat Protoc, vol.10, pp.1285-1296, 2015.

P. M. Vanraden, K. M. Olson, D. J. Null, and J. L. Hutchison, Harmful recessive effects on fertility detected by absence of homozygous haplotypes, J Dairy Sci, vol.94, pp.6153-6161, 2011.

P. M. Vanraden, M. E. Tooker, J. R. O'connell, J. B. Cole, and D. M. Bickhart, Selecting sequence variants to improve genomic predictions for dairy cattle, Genet Sel Evol, vol.49, p.32, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01484834

C. J. Willer, Y. Li, and G. R. Abecasis, METAL: fast and efficient meta-analysis of genomewide association scans, Bioinformatics, vol.26, pp.2190-2191, 2010.

D. Boichard, C. Grohs, F. Bourgeois, F. Cerqueira, R. Faugeras et al.,

. Leveziel, Detection of genes influencing economic traits in three French dairy cattle breeds, Genet Sel Evol, vol.35, pp.77-101, 2003.
URL : https://hal.archives-ouvertes.fr/hal-00894436

D. Boichard, C. Grohs, P. Michot, C. Danchin-burge, A. Capitan et al., Prise en compte des anomalies génétiques en sélection : le cas des bovins, INRA Prod. Anim, vol.29, pp.351-358, 2016.

D. Boichard, F. Guillaume, A. Baur, P. Croiseau, M. N. Rossignol et al., Genomic selection in French dairy cattle, Animal Production Science, vol.52, pp.115-120, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01000202

J. Casper, A. S. Zweig, C. Villarreal, C. Tyner, M. L. Speir et al., The UCSC Genome Browser database, vol.46, pp.762-769, 2018.

C. Charlier, W. Coppieters, F. Rollin, D. Desmecht, J. S. Agerholm et al., Highly effective SNP-based association mapping and management of recessive defects in livestock, Nat Genet, vol.40, pp.449-454, 2008.

K. Chen, J. W. Wallis, M. D. Mclellan, D. E. Larson, J. M. Kalicki et al.,

X. Locke, R. S. Shi, T. J. Fulton, R. K. Ley, L. Wilson et al., BreakDancer: an algorithm for highresolution mapping of genomic structural variation, Nat Methods, vol.6, pp.677-681, 2009.

J. B. Cole, D. J. Null, and P. M. Vanraden, Phenotypic and genetic effects of recessive haplotypes on yield, longevity, and fertility, J Dairy Sci, vol.99, pp.7274-7288, 2016.

P. Cowin and J. Wysolmerski, Molecular mechanisms guiding embryonic mammary gland development, Cold Spring Harb Perspect Biol, vol.2, p.3251, 2010.

J. A. Cox, A. Lamora, S. L. Johnson, and M. M. Voigt, Novel role for carbamoyl phosphate synthetase 2 in cranial sensory circuit formation, Int J Dev Neurosci, vol.33, pp.41-48, 2014.

H. D. Daetwyler, A. Capitan, H. Pausch, P. Stothard, R. Van-binsbergen et al.,

C. Chamberlain, C. P. Anderson, I. Vantassell, M. E. Hulsegge, B. Goddard et al., Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle, Nat Genet, vol.46, pp.858-865, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01193853

E. V. Davydov, D. L. Goode, M. Sirota, G. M. Cooper, A. Sidow et al., Identifying a high fraction of the human genome to be under selective constraint using GERP++, PLoS Comput Biol, vol.6, 2010.

L. D. Fairbanks, M. Bofill, K. Ruckemann, and H. A. Simmonds, Importance of ribonucleotide availability to proliferating T-lymphocytes from healthy humans. Disproportionate expansion of pyrimidine pools and contrasting effects of de novo synthesis inhibitors, J Biol Chem, vol.270, pp.29682-29689, 1995.

D. R. Falk and D. Nash, Sex-linked auxotrophic and putative auxotrophic mutants of Drosophila melanogaster, Genetics, vol.76, pp.755-766, 1974.

D. M. Franks, T. Izumikawa, H. Kitagawa, K. Sugahara, and P. , Okkema. 2006. C. elegans pharyngeal morphogenesis requires both de novo synthesis of pyrimidines and synthesis of heparan sulfate proteoglycans, Dev Biol, vol.296, pp.409-420

S. Fritz, A. Capitan, A. Djari, S. C. Rodriguez, A. Barbat et al., Detection of haplotypes associated with prenatal death in dairy cattle and identification of deleterious mutations in GART, SHBG and SLC37A2, PLoS One, vol.8, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01000118

S. Fritz, C. Hoze, E. Rebours, A. Barbat, M. Bizard et al., An initiator codon mutation in SDE2 causes recessive embryonic lethality in Holstein cattle, J Dairy Sci, 2018.

J. R. Hens and J. J. Wysolmerski, Key stages of mammary gland development: molecular mechanisms involved in the formation of the embryonic mammary gland, Breast Cancer Res, vol.7, pp.220-224, 2005.

. Icar, Guidelines for Conformation Recording of Dairy Cattle, Beef Cattle and Dairy Goats. date accessed (10/25, 2018.

P. Kumar, S. Henikoff, and P. C. Ng, Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm, Nat Protoc, vol.4, pp.1073-1081, 2009.

M. Lek, K. J. Karczewski, E. V. Minikel, K. E. Samocha, E. Banks et al.,

G. Gabriel, S. J. Getz, C. M. Glatt, S. Hultman, M. Kathiresan et al.,

H. C. Tsuang, J. G. Watkins, M. J. Wilson, D. G. Daly, C. Macarthur et al., Analysis of proteincoding genetic variation in 60,706 humans, Nature, vol.536, pp.285-291, 2016.

R. Letaief, E. Rebours, C. Grohs, C. Meersseman, S. Fritz et al., Identification of copy number variation in French dairy and beef breeds using next-generation sequencing, Genet Sel Evol, vol.49, p.77, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01622967

H. Macias and L. Hinck, Mammary gland development, Wiley Interdiscip Rev Dev Biol, vol.1, pp.533-557, 2012.

A. Marchler-bauer, Y. Bo, L. Han, J. He, C. J. Lanczycki et al.,

S. H. Geer and . Bryant, CDD/SPARCLE: functional classification of proteins via subfamily domain architectures, Nucleic Acids Res, vol.45, pp.200-203, 2017.

A. Marete, M. S. Lund, D. Boichard, and Y. Ramayo-caldas, A system-based analysis of the genetic determinism of udder conformation and health phenotypes across three French dairy cattle breeds, PLoS One, vol.13, 2018.

L. K. Matukumalli, C. T. Lawley, R. D. Schnabel, J. F. Taylor, M. F. Allan et al., Development and characterization of a high density SNP genotyping assay for cattle, PLoS One, vol.4, 2009.

M. C. Mcclure, D. Bickhart, D. Null, P. Vanraden, L. Xu et al.,

C. P. Cole, T. S. Van-tassell, and . Sonstegard, Bovine exome sequence analysis and targeted SNP genotyping of recessive fertility defects BH1, HH2, and HH3 reveal a putative causative mutation in SMC2 for HH3, PLoS One, vol.9, 2014.

W. Mclaren, L. Gil, S. E. Hunt, H. S. Riat, G. R. Ritchie et al., The Ensembl Variant Effect Predictor, Genome Biol, vol.17, p.122, 2016.

F. Menzi, N. Besuchet-schmutz, M. Fragniere, S. Hofstetter, V. Jagannathan et al., A transposable element insertion in APOB causes cholesterol deficiency in Holstein cattle, Anim Genet, vol.47, pp.253-257, 2016.

P. Michot, S. Fritz, A. Barbat, M. Boussaha, M. C. Deloche et al., A missense mutation in PFAS (phosphoribosylformylglycinamidine synthase) is likely causal for embryonic lethality associated with the MH1 haplotype in Montbeliarde dairy cattle, J Dairy Sci, vol.100, pp.8176-8187, 2017.

A. D. Mitchell and N. J. Hoogenraad, De novo pyrimidine nucleotide biosynthesis in synchronized rat hepatoma (HTC) cells and mouse embryo fibroblast (3T3) cells, Exp Cell Res, vol.93, pp.105-110, 1975.

M. Moreno-morcillo, A. Grande-garcia, A. Ruiz-ramos, F. Cano-ochoa, J. Boskovic et al., Structural Insight into the Core of CAD, the Multifunctional Protein Leading De Novo Pyrimidine Biosynthesis, Structure, vol.25, pp.912-923, 2017.

B. G. Ng, L. A. Wolfe, M. Ichikawa, T. Markello, M. He et al., Biallelic mutations in CAD, impair de novo pyrimidine biosynthesis and decrease glycosylation precursors, Hum Mol Genet, vol.24, pp.3050-3057, 2015.

S. Norby, A specific nutritional requirement for pyrimidines in rudimentary mutants of Drosophila melanogaster, Hereditas, vol.66, pp.205-214, 1970.

S. Norby, The biochemical genetics of rudimentary mutants of Drosophila melanogaster. I. Aspartate carbamoyltransferase levels in complementing and non-complementing strains, Hereditas, vol.73, pp.11-16, 1973.

H. Pausch, H. Schwarzenbacher, J. Burgstaller, K. Flisikowski, C. Wurmser et al., Homozygous haplotype deficiency reveals deleterious mutations compromising reproductive and rearing success in cattle, BMC Genomics, vol.16, p.312, 2015.

C. Bovine-hapmap, R. A. Gibbs, J. F. Taylor, C. P. Van-tassell, W. Barendse et al.,

S. M. Hamernik, S. Kappes, L. K. Lien, J. C. Matukumalli, L. V. Mcewan et al.,

J. L. Sonstegard, B. Williams, L. Diallo, M. L. Hailemariam, C. A. Martinez et al.,

S. Muzny, A. Patil, Q. Lucas, M. P. Fu, R. Kent et al., Genomewide survey of SNP variation uncovers the genetic structure of cattle breeds, Science, vol.324, pp.528-532, 2009.

R. F. Brondum, B. Guldbrandtsen, G. Sahana, M. S. Lund, and G. Su, Strategies for imputation to whole genome sequence using a single or multi-breed reference population in cattle, BMC Genomics, vol.15, 2014.

R. F. Brondum, E. Rius-vilarrasa, I. Stranden, G. Su, B. Guldbrandtsen et al., Reliabilities of genomic prediction using combined reference data of the Nordic Red dairy cattle populations, J Dairy Sci, vol.94, pp.4700-4707, 2011.

B. Buitenhuis, N. A. Poulsen, G. Gebreyesus, and L. B. Larsen, Estimation of genetic parameters and detection of chromosomal regions affecting the major milk proteins and their post translational modifications in Danish Holstein and Danish Jersey cattle, BMC Genet, vol.17, p.114, 2016.

C. M. Carvalho and J. R. Lupski, Mechanisms underlying structural variant formation in genomic disorders, Nat Rev Genet, vol.17, pp.224-238, 2016.

C. Charlier, J. S. Agerholm, W. Coppieters, P. Karlskov-mortensen, W. Li et al., A deletion in the bovine FANCI gene compromises fertility by causing fetal death and brachyspina, PLoS One, vol.7, 2012.

C. Charlier, W. Li, C. Harland, M. Littlejohn, W. Coppieters et al., NGS-based reverse genetic screen for common embryonic lethal mutations compromising fertility in livestock, Genome Res, vol.26, pp.1333-1341, 2016.

,

K. Chen, L. Chen, X. Fan, J. Wallis, L. Ding et al., TIGRA: a targeted iterative graph routing assembler for breakpoint assembly, Genome Res, vol.24, pp.310-317, 2014.

L. Chen, A. J. Chamberlain, C. M. Reich, H. D. Daetwyler, and B. J. Hayes, Detection and validation of structural variations in bovine whole-genome sequence data, Genetics Selection Evolution, vol.49, issue.13, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01479142

J. B. Cole, D. J. Null, and P. M. Vanraden, Phenotypic and genetic effects of recessive haplotypes on yield, longevity, and fertility, J Dairy Sci, vol.99, pp.7274-7288, 2016.

J. B. Cole, B. Waurich, M. Wensch-dorendorf, D. M. Bickhart, and H. H. Swalve, A genome-wide association study of calf birth weight in Holstein cattle using single nucleotide polymorphisms and phenotypes predicted from auxiliary traits, J Dairy Sci, vol.97, pp.3156-3172, 2014.

J. B. Cole, G. R. Wiggans, L. Ma, T. S. Sonstegard, T. J. Lawlor et al.,

K. Matukumalli and Y. Da, Genome-wide association analysis of thirty one production, health, reproduction and body conformation traits in contemporary U.S. Holstein cows, BMC Genomics, vol.12, p.408, 2011.

D. F. Conrad, D. Pinto, R. Redon, L. Feuk, O. Gokcumen et al., Origins and functional impact of copy number variation in the human genome, Nature, vol.464, pp.704-712, 2010.

H. D. Daetwyler, A. Capitan, H. Pausch, P. Stothard, R. Van-binsbergen et al.,

C. Chamberlain, C. P. Anderson, I. Vantassell, M. E. Hulsegge, B. Goddard et al., Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle, Nat Genet, vol.46, pp.858-865, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01193853

M. E. Dickinson, A. M. Flenniken, X. Ji, L. Teboul, M. D. Wong et al.,

S. J. Hsu, S. Johnson, L. C. Kalaga, L. Keith, T. N. Lanoue et al., International Mouse Phenotyping

A. L. Mckerlie, M. Beaudet, S. A. Bucan, and . Murray, High-throughput discovery of novel developmental phenotypes, Nature, vol.537, pp.508-514, 2016.

L. Fang, G. Sahana, G. Su, Y. Yu, S. Zhang et al., Integrating Sequence-based GWAS and RNA-Seq Provides Novel Insights into the Genetic Basis of Mastitis and Milk Production in Dairy Cattle, Sci Rep, vol.7, 2017.

R. D. Finn, T. K. Attwood, P. C. Babbitt, A. Bateman, P. Bork et al., 2017-beyond protein family and domain annotations, vol.45, pp.190-199, 2017.

R. D. Finn, P. Coggill, R. Y. Eberhardt, S. R. Eddy, J. Mistry et al., The Pfam protein families database: towards a more sustainable future, Nucleic Acids Res, vol.44, pp.279-285, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01294685

R. E. Handsaker, J. M. Korn, J. Nemesh, and S. A. Mccarroll, Discovery and genotyping of genome structural polymorphism by sequencing on a population scale, Nat Genet, vol.43, pp.269-276, 2011.

R. E. Handsaker, V. Van-doren, J. R. Berman, G. Genovese, S. Kashin et al., Large multiallelic copy number variations in humans, Nat Genet, vol.47, pp.296-303, 2015.

P. J. Hastings, J. R. Lupski, S. M. Rosenberg, and G. Ira, Mechanisms of change in gene copy number, Nat Rev Genet, vol.10, pp.551-564, 2009.

Y. Hou, G. E. Liu, D. M. Bickhart, M. F. Cardone, K. Wang et al., Genomic characteristics of cattle copy number variations, BMC Genomics, vol.12, p.127, 2011.

J. T. Howard, S. D. Kachman, W. M. Snelling, E. J. Pollak, D. C. Ciobanu et al., Beef cattle body temperature during climatic stress: a genome-wide association study, Int J Biometeorol, vol.58, pp.1665-1672, 2014.

Z. L. Hu, C. A. Park, and J. M. Reecy, Developmental progress and current status of the Animal QTLdb, Nucleic Acids Res, vol.44, pp.827-833, 2016.

L. D. Hurst and N. G. Smith, Do essential genes evolve slowly?, Curr Biol, vol.9, pp.747-750, 1999.

S. Jansen, B. Aigner, H. Pausch, M. Wysocki, S. Eck et al., Assessment of the genomic variation in a cattle population by re-sequencing of key animals at low to medium coverage, BMC Genomics, vol.14, p.446, 2013.

N. K. Kadri, G. Sahana, C. Charlier, T. Iso-touru, B. Guldbrandtsen et al., A 660-Kb deletion with antagonistic effects on fertility and milk production segregates at high frequency in Nordic Red cattle: additional evidence for the common occurrence of balancing selection in livestock, PLoS Genet, vol.10, p.1004049, 2014.

M. Kanehisa, M. Furumichi, M. Tanabe, Y. Sato, and K. Morishima, KEGG: new perspectives on genomes, pathways, diseases and drugs, Nucleic Acids Res, vol.45, pp.353-361, 2017.

D. Karolchik, A. S. Hinrichs, T. S. Furey, K. M. Roskin, C. W. Sugnet et al., The UCSC Table Browser data retrieval tool, Nucleic Acids Res, vol.32, pp.493-496, 2004.

W. J. Kent, BLAT--the BLAST-like alignment tool, Genome Res, vol.12, pp.656-664, 2002.

R. J. Kinsella, A. Kahari, S. Haider, J. Zamora, G. Proctor et al., Ensembl BioMarts: a hub for data retrieval across taxonomic space, Database (Oxford), 2011.

I. Lappalainen, J. Lopez, L. Skipper, T. Hefferon, J. D. Spalding et al., DbVar and DGVa: public archives for genomic structural variation, Nucleic Acids Res, vol.41, pp.936-941, 2013.

K. Lee, D. T. Nguyen, M. Choi, S. Y. Cha, J. H. Kim et al., Analysis of cattle olfactory subgenome: the first detail study on the characteristics of the complete olfactory receptor repertoire of a ruminant, BMC Genomics, vol.14, p.596, 2013.

H. Li and R. Durbin, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, vol.25, pp.1754-1760, 2009.

H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, pp.2078-2079, 2009.

G. E. Liu, Y. Hou, B. Zhu, M. F. Cardone, L. Jiang et al.,

C. P. Sonstegard, M. Van-tassell, E. E. Ventura, T. G. Eichler, J. W. Mcdaneld et al., Analysis of copy number variations among diverse cattle breeds, Genome Res, vol.20, pp.693-703, 2010.

F. Lobago, H. Gustafsson, M. Bekana, J. F. Beckers, and H. Kindahl, Clinical features and hormonal profiles of cloprostenol-induced early abortions in heifers monitored by ultrasonography, Acta Vet Scand, vol.48, p.23, 2006.

X. Mao, G. Sahana, D. J. De-koning, and B. Guldbrandtsen, Genome-wide association studies of growth traits in three dairy cattle breeds using whole-genome sequence data, J Anim Sci, vol.94, pp.1426-1437, 2016.

S. A. Mccarroll, F. G. Kuruvilla, J. M. Korn, S. Cawley, J. Nemesh et al., Integrated detection and populationgenetic analysis of SNPs and copy number variation, Nat Genet, vol.40, pp.1166-1174, 2008.

M. C. Mcclure, N. S. Morsci, R. D. Schnabel, J. W. Kim, P. Yao et al., A genome scan for quantitative trait loci influencing carcass, post-natal growth and reproductive traits in commercial Angus cattle, Anim Genet, vol.41, pp.597-607, 2010.

M. C. Mcclure, H. R. Ramey, M. M. Rolf, S. D. Mckay, J. E. Decker et al., Genome-wide association analysis for quantitative trait loci influencing Warner-Bratzler shear force in five taurine cattle breeds, Anim Genet, vol.43, pp.662-673, 2012.

A. Mckenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis et al., The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res, vol.20, pp.1297-1303, 2010.

W. Mclaren, L. Gil, S. E. Hunt, H. S. Riat, G. R. Ritchie et al., The Ensembl Variant Effect Predictor, Genome Biol, vol.17, p.122, 2016.

S. A. Miller, D. D. Dykes, and H. F. Polesky, A simple salting out procedure for extracting DNA from human nucleated cells, Nucleic Acids Res, vol.16, p.1215, 1988.

R. E. Mills, K. Walter, C. Stewart, R. E. Handsaker, K. Chen et al.,

T. Peckham, A. Rausch, X. Scally, M. P. Shi, A. M. Stromberg et al.,

M. A. Zhang, L. Batzer, G. T. Ding, G. Marth, J. Mcvean et al., Mapping copy number variation by populationscale genome sequencing, Nature, vol.470, pp.59-65, 2011.

Y. Niimura and M. Nei, Extensive gains and losses of olfactory receptor genes in mammalian evolution, PLoS One, vol.2, 2007.

S. Purcell, B. Neale, K. Todd-brown, L. Thomas, M. A. Ferreira et al., PLINK: a tool set for whole-genome association and population-based linkage analyses, Am J Hum Genet, vol.81, pp.559-575, 2007.

A. R. Quinlan and I. M. Hall, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, vol.26, pp.841-842, 2010.

. R-core-team, R: A language and environment for statistical computing. R Foundation for Statistical Computing, 2016.

R. Redon, S. Ishikawa, K. R. Fitch, L. Feuk, G. H. Perry et al., Global variation in copy number in the human genome, Nature, vol.444, pp.444-454, 2006.

R. Team, RStudio: Integrated Development Environment for R, 2016.

G. Sahana, B. Guldbrandtsen, and M. S. Lund, Genome-wide association study for calving traits in Danish and Swedish Holstein cattle, J Dairy Sci, vol.94, pp.479-486, 2011.

G. Sahana, T. Iso-touru, X. Wu, U. S. Nielsen, D. J. De-koning et al., A 0.5-Mbp deletion on bovine chromosome 23 is a strong candidate for stillbirth in Nordic Red cattle, Genet Sel Evol, vol.48, p.35, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01341369

M. Sandri, B. Stefanon, and J. J. Loor, Transcriptome profiles of whole blood in Italian Holstein and Italian Simmental lactating cows diverging for genetic merit for milk protein, J Dairy Sci, vol.98, pp.6119-6127, 2015.

E. Schutz, C. Wehrhahn, M. Wanjek, R. Bortfeld, W. E. Wemheuer et al., The Holstein Friesian Lethal Haplotype 5 (HH5) Results from a Complete Deletion of TBF1M and Cholesterol Deficiency (CDH) from an ERV-(LTR) Insertion into the Coding Region of APOB, PLoS One, vol.11, 2016.

W. M. Snelling, M. F. Allan, J. W. Keele, L. A. Kuehn, T. Mcdaneld et al., Genome-wide association study of growth in crossbred beef cattle, J Anim Sci, vol.88, pp.837-848, 2010.

P. H. Sudmant, T. Rausch, E. J. Gardner, R. E. Handsaker, A. Abyzov et al.,

Y. Kidd, E. W. Kong, S. Lameijer, P. Mccarthy, R. A. Flicek et al.,

C. Devine, E. E. Lee, J. O. Eichler, and . Korbel, An integrated map of structural variation in 2,504 human genomes, Nature, vol.526, pp.75-81, 2015.

D. Szklarczyk, A. Franceschini, S. Wyder, K. Forslund, D. Heller et al., STRING v10: protein-protein interaction networks, integrated over the tree of life, Nucleic Acids Res, vol.43, pp.447-452, 2015.

J. Van-ziffle, W. Yang, and F. F. Chehab, Homozygous deletion of six olfactory receptor genes in a subset of individuals with Beta-thalassemia, PLoS One, vol.6, 2011.

J. Weischenfeldt, O. Symmons, F. Spitz, and J. O. Korbel, Phenotypic impact of genomic structural variation: insights from and for human disease, Nat Rev Genet, vol.14, pp.125-138, 2013.

S. Wright, Evolution in Mendelian Populations, Genetics, vol.16, pp.97-159, 1931.

L. Xu, D. M. Bickhart, J. B. Cole, S. G. Schroeder, J. Song et al., Genomic signatures reveal new evidences for selection of important traits in domestic cattle, Mol Biol Evol, vol.32, pp.711-725, 2015.

L. Xu, J. B. Cole, D. M. Bickhart, Y. Hou, J. Song et al., , 2014.

, Genome wide CNV analysis reveals additional variants associated with milk production traits in Holsteins, BMC Genomics, vol.15, p.683

L. Xu, Y. Hou, D. M. Bickhart, Y. Zhou, H. A. Hay-el et al., Population-genetic properties of differentiated copy number variations in cattle, Sci Rep, vol.6, p.23161, 2016.

B. Yalcin, K. Wong, A. Agam, M. Goodson, T. M. Keane et al., Sequence-based characterization of structural variation in the mouse genome, Nature, vol.477, pp.326-329, 2011.

A. Yates, W. Akanni, M. R. Amode, D. Barrell, K. Billis et al., Nucleic Acids Res, vol.44, pp.710-716, 2016.

M. Zarrei, J. R. Macdonald, D. Merico, and S. W. Scherer, A copy number variation map of the human genome, Nat Rev Genet, vol.16, pp.172-183, 2015.

Q. Zhang, M. B.-guldbrandtsen, M. S. Bosse, G. Lund, and . Sahana, Runs of homozygosity and distribution of functional variants in the cattle genome, BMC Genomics, vol.16, p.542, 2015.

A. Abyzov, A. E. Urban, M. Snyder, and M. Gerstein, CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing, Genome Res, vol.21, pp.974-984, 2011.

Y. Benjamini and T. P. Speed, Summarizing and correcting the GC content bias in high-throughput sequencing, Nucleic Acids Res, vol.40, p.72, 2012.

D. M. Bickhart and G. E. Liu, The challenges and importance of structural variation detection in livestock, Front Genet, vol.5, p.37, 2014.

D. Boichard, M. Boussaha, A. Capitan, D. Rocha, C. Hozé et al., Experience from large scale use of the EuroGenomics custom SNP chip in cattle. Page 675 in Proc, Proc. World Congr. Genet. Appl. Livest. Prod, 2018.

M. Boussaha, D. Esquerre, J. Barbieri, A. Djari, A. Pinton et al., Genome-Wide Study of Structural Variants in Bovine Holstein, Montbeliarde and Normande Dairy Breeds, PLoS One, vol.10, p.135931, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01194172

A. C. Bouwman, H. D. Daetwyler, A. J. Chamberlain, C. H. Ponce, M. Sargolzaei et al., Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals, Nat Genet, vol.50, pp.362-367, 2018.

R. F. Brøndum, B. Guldbrandtsen, G. Sahana, M. S. Lund, and G. Su, Strategies for imputation to whole genome sequence using a single or multi-breed reference population in cattle, BMC Genomics, vol.15, 2014.

B. L. Browning and S. R. Browning, Genotype Imputation with Millions of Reference Samples, Am J Hum Genet, vol.98, pp.116-126, 2016.

C. C. Chang, C. C. Chow, L. C. Tellier, S. Vattikuti, S. M. Purcell et al., Second-generation PLINK: rising to the challenge of larger and richer datasets, Gigascience, vol.4, 2015.

C. Charlier, J. S. Agerholm, W. Coppieters, P. Karlskov-mortensen, W. Li et al., A deletion in the bovine FANCI gene compromises fertility by causing fetal death and brachyspina, PLoS One, vol.7, 2012.

L. Chen, A. J. Chamberlain, C. M. Reich, H. D. Daetwyler, and B. J. Hayes, Detection and validation of structural variations in bovine whole-genome sequence data, Genet Sel Evol, vol.49, issue.13, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01479142

D. F. Conrad, D. Pinto, R. Redon, L. Feuk, O. Gokcumen et al., Origins and functional impact of copy number variation in the human genome, Nature, vol.464, pp.704-712, 2010.

H. D. Daetwyler, A. Capitan, H. Pausch, P. Stothard, R. Van-binsbergen et al.,

C. Chamberlain, C. P. Anderson, I. Vantassell, M. E. Hulsegge, B. Goddard et al., Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle, Nat Genet, vol.46, pp.858-865, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01193853

P. Danecek, A. Auton, G. Abecasis, C. A. Albers, E. Banks et al., Genomes Project Analysis. 2011. The variant call format and VCFtools, Bioinformatics, vol.27, pp.2156-2158

S. Das, L. Forer, S. Schönherr, C. Sidore, A. E. Locke et al.,

C. Abecasis and . Fuchsberger, Next-generation genotype imputation service and methods, Nat Genet, vol.48, pp.1284-1287, 2016.

O. Delaneau, B. Howie, A. J. Cox, J. F. Zagury, and J. Marchini, Haplotype estimation using sequencing reads, Am J Hum Genet, vol.93, pp.687-696, 2013.

O. Delaneau, J. Marchini, C. G. Project, and C. G. Project, Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel, Nat Commun, vol.5, p.3934, 2014.

O. Delaneau, J. F. Zagury, and J. Marchini, Improved whole-chromosome phasing for disease and population genetic studies, Nat Methods, vol.10, pp.5-6, 2013.

Y. Gao, J. Jiang, S. Yang, Y. Hou, G. E. Liu et al., CNV discovery for milk composition traits in dairy cattle using whole genome resequencing, BMC Genomics, vol.18, p.265, 2017.

G. Project, C. , A. Auton, L. D. Brooks, R. M. Durbin et al., A global reference for human genetic variation, Nature, vol.526, pp.68-74, 2015.

R. E. Handsaker, J. M. Korn, J. Nemesh, and S. A. Mccarroll, Discovery and genotyping of genome structural polymorphism by sequencing on a population scale, Nat Genet, vol.43, pp.269-276, 2011.

R. E. Handsaker, V. Van-doren, J. R. Berman, G. Genovese, S. Kashin et al., Large multiallelic copy number variations in humans, Nat Genet, vol.47, pp.296-303, 2015.

R. Letaief, E. Rebours, C. Grohs, C. Meersseman, S. Fritz et al., Identification of copy number variation in French dairy and beef breeds using next-generation sequencing, Genet Sel Evol, vol.49, p.77, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01622967

H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., The Sequence Alignment/Map format and SAMtools, Bioinformatics, vol.25, pp.2078-2079, 2009.

A. Mckenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis et al., The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res, vol.20, pp.1297-1303, 2010.

M. Mesbah-uddin, T. B.-guldbrandtsen, J. Iso-touru, D. J. Vilkki, D. De-koning et al.,

, Genome-wide mapping of large deletions and their population-genetic properties in dairy cattle, DNA Res, vol.25, pp.49-59

M. Mesbah-uddin, B. Guldbrandtsen, M. S. Lund, and G. Sahana, Genotype call for chromosomal deletions using read-depth from whole genome sequence variants in cattle. Page 662 in Proc, World Congr. Genet. Appl. Livest. Prod, 2018.

M. Mielczarek, M. Fraszczak, R. Giannico, G. Minozzi, J. L. Williams et al., Analysis of copy number variations in Holstein-Friesian cow genomes based on whole-genome sequence data, J Dairy Sci, vol.100, pp.5515-5525, 2017.

H. Pausch, I. M. Macleod, R. Fries, R. Emmerling, P. J. Bowman et al., Evaluation of the accuracy of imputed sequence variant genotypes and their utility for causal variant detection in cattle, Genet Sel Evol, vol.49, p.24, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01479153

A. R. Quinlan and I. M. Hall, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, vol.26, pp.841-842, 2010.

. R-core-team, R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, 2014.

D. H. Shin, H. J. Lee, S. Cho, H. J. Kim, J. Y. Hwang et al., Deleted copy number variation of Hanwoo and Holstein using next generation sequencing at the population level, BMC Genomics, vol.15, p.240, 2014.

X. Wu, B. Guldbrandtsen, M. S. Lund, and G. Sahana, Association analysis for feet and legs disorders with wholegenome sequence variants in 3 dairy cattle breeds, J Dairy Sci, vol.99, pp.7221-7231, 2016.

Q. Zhang, M. P. Calus, M. Bosse, G. Sahana, M. S. Lund et al., Human-Mediated Introgression of Haplotypes in a Modern Dairy Cattle Breed, Genetics, vol.209, pp.1305-1317, 2018.

M. K. Abo-ismail, L. F. Brito, S. P. Miller, M. Sargolzaei, D. A. Grossi et al., Genome-wide association studies and genomic prediction of breeding values for calving performance and body conformation traits in Holstein cattle, Genet Sel Evol, vol.49, p.82, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01631052

Y. S. Aulchenko, S. Ripke, A. Isaacs, and C. M. Van-duijn, GenABEL: an R library for genome-wide association analysis, Bioinformatics, vol.23, pp.1294-1296, 2007.

A. C. Bouwman, H. D. Daetwyler, A. J. Chamberlain, C. H. Ponce, M. Sargolzaei et al., Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals, Nat Genet, vol.50, pp.362-367, 2018.

R. F. Brøndum, G. Su, L. Janss, G. Sahana, B. Guldbrandtsen et al., Quantitative trait loci markers derived from whole genome sequence data increases the reliability of genomic prediction, J Dairy Sci, vol.98, pp.4107-4116, 2015.

B. L. Browning and S. R. Browning, Genotype Imputation with Millions of Reference Samples, Am J Hum Genet, vol.98, pp.116-126, 2016.

Z. Cai, B. Guldbrandtsen, M. S. Lund, and G. Sahana, Prioritizing candidate genes post-GWAS using multiple sources of data for mastitis resistance in dairy cattle, BMC Genomics, vol.19, p.656, 2018.

S. Das, L. Forer, S. Schönherr, C. Sidore, A. E. Locke et al.,

C. Abecasis and . Fuchsberger, Next-generation genotype imputation service and methods, Nat Genet, vol.48, pp.1284-1287, 2016.

A. P. De-roos, B. J. Hayes, R. J. Spelman, and M. E. Goddard, Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle, Genetics, vol.179, pp.1503-1512, 2008.

O. Delaneau, B. Howie, A. J. Cox, J. F. Zagury, and J. Marchini, Haplotype estimation using sequencing reads, Am J Hum Genet, vol.93, pp.687-696, 2013.

O. Delaneau, J. Marchini, C. G. Project, and C. G. Project, Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel, Nat Commun, vol.5, p.3934, 2014.

C. G. Elsik, D. R. Unni, C. M. Diesh, A. Tayal, M. L. Emery et al., Bovine Genome Database: new tools for gleaning function from the Bos taurus genome, Nucleic Acids Res, vol.44, pp.834-839, 2016.

G. Gebreyesus, A. J. Buitenhuis, N. A. Poulsen, M. Visker, Q. Zhang et al.,

, Multi-population GWAS and enrichment analyses reveal novel genomic regions and promising candidate genes underlying bovine milk fatty acid composition, BMC Genomics, vol.20, p.178

J. K. Hoglund, B. Buitenhuis, B. Guldbrandtsen, M. S. Lund, and G. Sahana, Genome-wide association study for female fertility in Nordic Red cattle, BMC Genet, vol.16, p.110, 2015.

J. K. Hoglund, B. Guldbrandtsen, M. S. Lund, and G. Sahana, Identification of genomic regions associated with female fertility in Danish Jersey using whole genome sequence data, BMC Genet, vol.16, p.60, 2015.

J. K. Hoglund, G. Sahana, B. Guldbrandtsen, and M. S. Lund, Validation of associations for female fertility traits in Nordic Holstein, Nordic Red and Jersey dairy cattle, BMC Genet, vol.15, 2014.

T. Iso-touru, G. Sahana, B. Guldbrandtsen, M. S. Lund, and J. Vilkki, Genome-wide association analysis of milk yield traits in Nordic Red Cattle using imputed whole genome sequence variants, BMC Genet, vol.17, p.55, 2016.

J. G. Jardim, B. Guldbrandtsen, M. S. Lund, and G. Sahana, Association analysis for udder index and milking speed with imputed whole-genome sequence variants in Nordic Holstein cattle, J Dairy Sci, vol.101, pp.2199-2212, 2018.

L. Jiang, Z. Zheng, T. Qi, K. E. Kemper, N. R. Wray et al., A resource-efficient tool for mixed model association analysis of large-scale data, 2019.

N. K. Kadri, B. Guldbrandtsen, M. S. Lund, and G. Sahana, Genetic dissection of milk yield traits and mastitis resistance quantitative trait loci on chromosome 20 in dairy cattle, J Dairy Sci, vol.98, pp.9015-9025, 2015.

N. K. Kadri, G. Sahana, C. Charlier, T. Iso-touru, B. Guldbrandtsen et al., A 660-Kb deletion with antagonistic effects on fertility and milk production segregates at high frequency in Nordic Red cattle: additional evidence for the common occurrence of balancing selection in livestock, PLoS Genet, vol.10, p.1004049, 2014.

A. Marete, G. Sahana, S. Fritz, R. Lefebvre, A. Barbat et al., Genome-wide association study for milking speed in French Holstein cows, J Dairy Sci, vol.101, pp.6205-6219, 2018.

. Nav, NAV routine genetic evaluation of dairy cattle-data and genetic models. date accessed, 2013.

M. P. Sanchez, Y. Ramayo-caldas, V. Wolf, C. Laithier, M. E. Jabri et al., Sequence-based GWAS, network and pathway analyses reveal genes co-associated with milk cheese-making properties and milk composition in Montbeliarde cows, Genet Sel Evol, vol.51, p.34, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02176238

I. Van-den-berg, D. Boichard, B. Guldbrandtsen, and M. S. Lund, Using Sequence Variants in Linkage Disequilibrium with Causative Mutations to Improve Across-Breed Prediction in Dairy Cattle: A Simulation Study, G3 (Bethesda), vol.6, pp.2553-2561, 2016.

J. Yang, T. Ferreira, A. P. Morris, S. E. Medland, A. T. Replication et al., Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits, Nat Genet, vol.44, pp.361-363, 2012.

J. Yang, S. H. Lee, M. E. Goddard, and P. M. Visscher, GCTA: a tool for genome-wide complex trait analysis, Am J Hum Genet, vol.88, pp.76-82, 2011.

J. Yang, M. N. Weedon, S. Purcell, G. Lettre, K. Estrada et al.,

M. E. Mccarthy, P. M. Goddard, G. Visscher, and . Consortium, Genomic inflation factors under polygenic inheritance, Eur J Hum Genet, vol.19, pp.807-812, 2011.

D. R. Zerbino, P. Achuthan, W. Akanni, M. R. Amode, D. Barrell et al.,

L. Gil, L. Gordon, E. Haggerty, T. Haskell, O. G. Hourlier et al., Nucleic Acids Res, vol.46, pp.754-761, 2018.

A. V. Zimin, A. L. Delcher, L. Florea, D. R. Kelley, M. C. Schatz et al.,

G. Sonstegard, M. Marcais, P. Roberts, J. A. Subramanian, S. L. Yorke et al., Abstract We performed within-breed genomic prediction analyses using genomic best linear unbiased prediction (GBLUP) method. Besides Bovine50k BeadChip (50k) markers, in GBLUP, we used one or several (genetic) variance components to investigate the effect of imputed whole-genome sequence (WGS) variants and large chromosomal deletions (deletions), Genome Biol, vol.10, p.42, 2009.

D. Jersey, Nordic Red Dairy cattle (RDC) populations of artificial insemination bulls. In HOL, we observed same prediction accuracy (0.639) using either 50k (one-component model) or 50k and deletion markers (two-component model), JER

, FI associated markers (in two-component model) vs. that of only 50k markers (one-component model)

, Key words: genomic prediction, large deletion, fertility, GBLUP, dairy cattle 6.6 References

R. F. Brøndum, G. Su, L. Janss, G. Sahana, B. Guldbrandtsen et al., Quantitative trait loci markers derived from whole genome sequence data increases the reliability of genomic prediction, J Dairy Sci, vol.98, pp.4107-4116, 2015.

C. Charlier, J. S. Agerholm, W. Coppieters, P. Karlskov-mortensen, W. Li et al., A deletion in the bovine FANCI gene compromises fertility by causing fetal death and brachyspina, PLoS One, vol.7, 2012.

S. Das, L. Forer, S. Schönherr, C. Sidore, A. E. Locke et al.,

C. Abecasis and . Fuchsberger, Next-generation genotype imputation service and methods, Nat Genet, vol.48, pp.1284-1287, 2016.

A. Garcia-ruiz, J. B. Cole, P. M. Vanraden, G. R. Wiggans, F. J. Ruiz-lopez et al., Changes in genetic selection differentials and generation intervals in US Holstein dairy cattle as a result of genomic selection, Proc Natl Acad Sci U S A, vol.113, pp.3995-4004, 2016.

M. Georges, C. Charlier, and B. Hayes, Harnessing genomic information for livestock improvement, Nat Rev Genet, vol.20, pp.135-156, 2019.

E. H. Hay, Y. T. Utsunomiya, L. Xu, Y. Zhou, H. H. Neves et al., Genomic predictions combining SNP markers and copy number variations in Nellore cattle, BMC Genomics, vol.19, p.441, 2018.

N. K. Kadri, G. Sahana, C. Charlier, T. Iso-touru, B. Guldbrandtsen et al., A 660-Kb deletion with antagonistic effects on fertility and milk production segregates at high frequency in Nordic Red cattle: additional evidence for the common occurrence of balancing selection in livestock, PLoS Genet, vol.10, p.1004049, 2014.

A. Liu, M. S. Lund, D. Boichard, S. Fritz, E. Karaman et al., Using additional single nucleotide polymorphisms selected from whole genome sequence data for genomic prediction in Danish Jersey, Proceedings of the World Congress on Genetics Applied to Livestock Production, vol.11, p.586, 2018.

P. Ma, M. S. Lund, G. P. Aamand, and G. Su, Use of a Bayesian model including QTL markers increases prediction reliability when test animals are distant from the reference population, J Dairy Sci, 2019.

. Nav, NAV routine genetic evaluation of dairy cattle-data and genetic models. date accessed, 2013.

G. Sahana, T. Iso-touru, X. Wu, U. S. Nielsen, D. J. De-koning et al., A 0.5-Mbp deletion on bovine chromosome 23 is a strong candidate for stillbirth in Nordic Red cattle, Genet Sel Evol, vol.48, p.35, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01341369

G. Su, P. Ma, U. S. Nielsen, G. P. Aamand, G. Wiggans et al., Sharing reference data and including cows in the reference population improve genomic predictions in Danish Jersey, pp.1-9, 2015.

J. R. Thomasen, B. Guldbrandtsen, G. Su, R. F. Brøndum, and M. S. Lund, Reliabilities of genomic estimated breeding values in Danish Jersey, Animal, vol.6, pp.789-796, 2012.

P. M. Vanraden, Efficient methods to compute genomic predictions, J Dairy Sci, vol.91, pp.4414-4423, 2008.

J. Yang, S. H. Lee, M. E. Goddard, and P. M. Visscher, GCTA: a tool for genome-wide complex trait analysis, Am J Hum Genet, vol.88, pp.76-82, 2011.

V. A. Blomen, P. Majek, L. T. Jae, J. W. Bigenzahn, J. Nieuwenhuis et al., Gene essentiality and synthetic lethality in haploid human cells, vol.350, pp.1092-1096, 2015.
URL : https://hal.archives-ouvertes.fr/hal-02337430

,

D. Boichard, M. Boussaha, A. Capitan, D. Rocha, C. Hozé et al., Experience from large scale use of the EuroGenomics custom SNP chip in cattle. Page 675 in Proc, Proc. World Congr. Genet. Appl. Livest. Prod, 2018.

A. C. Bouwman, H. D. Daetwyler, A. J. Chamberlain, C. H. Ponce, M. Sargolzaei et al., Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals, Nat Genet, vol.50, pp.362-367, 2018.

R. F. Brøndum, E. Rius-vilarrasa, I. Stranden, G. Su, B. Guldbrandtsen et al., Reliabilities of genomic prediction using combined reference data of the Nordic Red dairy cattle populations, J Dairy Sci, vol.94, pp.4700-4707, 2011.

R. F. Brøndum, G. Su, L. Janss, G. Sahana, B. Guldbrandtsen et al., Quantitative trait loci markers derived from whole genome sequence data increases the reliability of genomic prediction, J Dairy Sci, vol.98, pp.4107-4116, 2015.

M. P. Calus, M. E. Goddard, Y. C. Wientjes, P. J. Bowman, and B. J. Hayes, Multibreed genomic prediction using multitrait genomic residual maximum likelihood and multitask Bayesian variable selection, J Dairy Sci, vol.101, pp.4279-4294, 2018.

S. Fritz, C. Hoze, E. Rebours, A. Barbat, M. Bizard et al., An initiator codon mutation in SDE2 causes recessive embryonic lethality in Holstein cattle, J Dairy Sci, 2018.

A. Garcia-ruiz, J. B. Cole, P. M. Vanraden, G. R. Wiggans, F. J. Ruiz-lopez et al., Changes in genetic selection differentials and generation intervals in US Holstein dairy cattle as a result of genomic selection, Proc Natl Acad Sci U S A, vol.113, pp.3995-4004, 2016.

M. Georges, C. Charlier, and B. Hayes, Harnessing genomic information for livestock improvement, Nat Rev Genet, vol.20, pp.135-156, 2019.

T. Hart, M. Chandrashekhar, M. Aregger, Z. Steinhart, K. R. Brown et al., High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities, Cell, vol.163, pp.1515-1526, 2015.

N. K. Kadri, G. Sahana, C. Charlier, T. Iso-touru, B. Guldbrandtsen et al., A 660-Kb deletion with antagonistic effects on fertility and milk production segregates at high frequency in Nordic Red cattle: additional evidence for the common occurrence of balancing selection in livestock, PLoS Genet, vol.10, p.1004049, 2014.

M. S. Lund, A. P. Roos, A. G. Vries, T. Druet, V. Ducrocq et al., A common reference population from four European Holstein populations increases reliability of genomic predictions, Genet Sel Evol, vol.43, p.43, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01191309

J. R. Meadows and K. Lindblad-toh, Dissecting evolution and disease using comparative vertebrate genomics, Nat Rev Genet, 2017.

T. Meuwissen and M. Goddard, Accurate prediction of genetic values for complex traits by whole-genome resequencing, Genetics, vol.185, pp.623-631, 2010.

P. Michot, S. Fritz, A. Barbat, M. Boussaha, M. C. Deloche et al., A missense mutation in PFAS (phosphoribosylformylglycinamidine synthase) is likely causal for embryonic lethality associated with the MH1 haplotype in Montbeliarde dairy cattle, J Dairy Sci, vol.100, pp.8176-8187, 2017.

, Online Mendelian Inheritance in Animals, 2018.

Y. Van-de-peer, E. Mizrachi, and K. Marchal, The evolutionary significance of polyploidy, Nat Rev Genet, vol.18, pp.411-424, 2017.

I. Van-den-berg, D. Boichard, B. Guldbrandtsen, and M. S. Lund, Using Sequence Variants in Linkage Disequilibrium with Causative Mutations to Improve Across-Breed Prediction in Dairy Cattle: A Simulation Study, G3 (Bethesda), vol.6, pp.2553-2561, 2016.

I. Van-den-berg, D. Boichard, M. S. Lund-;-i, T. H. Meuwissen, I. M. Macleod et al., Sequence variants selected from a multi-breed GWAS can improve the reliability of genomic predictions in dairy cattle, Genet Sel Evol, vol.48, p.83, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01479248

P. M. Vanraden, K. M. Olson, D. J. Null, and J. L. Hutchison, Harmful recessive effects on fertility detected by absence of homozygous haplotypes, J Dairy Sci, vol.94, pp.6153-6161, 2011.

T. Wang, K. Birsoy, N. W. Hughes, K. M. Krupczak, Y. Post et al., Identification and characterization of essential genes in the human genome, Science, vol.350, pp.1096-1101, 2015.

G. R. Wiggans, G. Su, T. A. Cooper, U. S. Nielsen, G. P. Aamand et al., Short communication: Improving accuracy of Jersey genomic evaluations in the United States and Denmark by sharing reference population bulls, J Dairy Sci, vol.98, pp.3508-3513, 2015.