Genomic approach to manage genetic variability in dairy farms

References

• Ablondi M, Sabbioni A, Stocco G, Cipolat-Gotet C, Dadousis C, Kaam J-Tv, Finocchiaro R, Summer A. 2022. Genetic diversity in the Italian Holstein dairy cattle based on pedigree and SNP data prior and after genomic selection. Front Vet Sci. 8:773985. doi: 10.3389/fvets.2021.773985.
   PubMed Web of Science ®Google Scholar
• Abreu AP, Macedo DB, Brito VN, Kaiser UB, Latronico AC. 2015. A new pathway in the control of the initiation of puberty: the MKRN3 gene. J Mol Endocrinol. 54(3):R131–R139. doi: 10.1530/JME-14-0315.
   PubMed Web of Science ®Google Scholar
• Abreu AP, Toro CA, Song YB, Navarro VM, Bosch MA, Eren A, Liang JN, Carroll RS, Latronico AC, Rønnekleiv OK. 2020. MKRN3 inhibits the reproductive axis through actions in kisspeptin-expressing neurons. J Clin Invest. 130(8):4486–4500.
   PubMed Web of Science ®Google Scholar
• ANAFIBJ – National statistics. 2022. Accessed Oct 18. http://www.anafi.it/it/pubblicazioni-statistiche/statistiche-nazionali.
   Google Scholar
• Andersson L. 2001. Genetic dissection of phenotypic diversity in farm animals. Nat Rev Genet. 2(2):130–138. doi: 10.1038/35052563.
   PubMed Web of Science ®Google Scholar
• Biscarini F, Cozzi P, Gaspa G, Marras G. 2019. detectRUNS: an R package to detect runs of homozygosity and heterozygosity in diploid genomes genomes. R package version 0.9.5. https://CRAN.R-project.org/package=detectRUNS.
   Google Scholar
• Boichard D, Ducrocq V, Fritz S. 2015. Sustainable dairy cattle selection in the genomic era. J Anim Breed Genet. 132(2):135–143. doi: 10.1111/jbg.12150.
   PubMed Web of Science ®Google Scholar
• Bovenhuis H, Van Arendonk JAM, Korver S. 1992. Associations between milk protein polymorphisms and milk production traits. J Dairy Sci. 75(9):2549–2559. doi: 10.3168/jds.S0022-0302(92)78017-5.
   PubMed Web of Science ®Google Scholar
• Brooke-Taylor S, Dwyer K, Woodford K, Kost N. 2017. Systematic review of the gastrointestinal effects of A1 compared with A2 β-casein. Adv Nutr. 8(5):739–748. doi: 10.3945/an.116.013953.
   PubMed Web of Science ®Google Scholar
• Caroli A, Bolla P, Budelli E, Barbieri G, Leone P. 2000. Effect of κ-casein E allele on clotting aptitude of Italian Friesian milk. Zootecnica e Nutrizione Animale. 26(3):127–130.
   Google Scholar
• Charlesworth D, Willis JH. 2009. The genetics of inbreeding depression. Nat Rev Genet. 10(11):783–796. doi: 10.1038/nrg2664.
   PubMed Web of Science ®Google Scholar
• Cole JB, Null DJ, VanRaden PM. 2016. Phenotypic and genetic effects of recessive haplotypes on yield, longevity, and fertility. J Dairy Sci. 99(9):7274–7288. doi: 10.3168/jds.2015-10777.
   PubMed Web of Science ®Google Scholar
• Collins FS, Guyer MS, Charkravarti A. 1997. Variations on a theme: cataloging human DNA sequence variation. Science. 278(5343):1580–1581. doi: 10.1126/science.278.5343.1580.
   PubMed Web of Science ®Google Scholar
• Comin A, Cassandro M, Chessa S, Ojala M, Dal Zotto R, de Marchi M, Carnier P, Gallo L, Pagnacco G, Bittante G. 2008. Effects of composite β- and κ-casein genotypes on milk coagulation, quality, and yield traits in italian holstein cows. J Dairy Sci. 91(10):4022–4027. doi: 10.3168/jds.2007-0546.
   PubMed Web of Science ®Google Scholar
• Dadousis C, Ablondi M, Cipolat-Gotet C, van Kaam J-T, Marusi M, Cassandro M, Sabbioni A, Summer A. 2022. Genomic inbreeding coefficients using imputed genotypes: assessing different estimators in Holstein-Friesian dairy cows. J Dairy Sci. 105(7):5926–5945. doi: 10.3168/jds.2021-21125.
   PubMed Web of Science ®Google Scholar
• Dickerson G, Hazel LN. 1944. Effectiveness of selection on progeny performance as a supplement to earlier culling in livestock. J Agric Res. 69(2):459–476.
   Google Scholar
• Dinc H, Ozkan E, Koban E, Togan I. 2013. Beta-casein A1/A2, kappa-casein and beta-lactoglobulin polymorphisms in Turkish cattle breeds. Arch Anim Breed. 56(1):650–657. doi: 10.7482/0003-9438-56-065.
   Google Scholar
• Doekes HP, Veerkamp RF, Bijma P, De Jong G, Hiemstra SJ, Windig JJ. 2019. Inbreeding depression due to recent and ancient inbreeding in Dutch Holstein-Friesian dairy cattle. Genet Sel Evol. 51(1):54. doi: 10.1186/s12711-019-0497-z.
   PubMed Web of Science ®Google Scholar
• Egger-Danner C, Cole JB, Pryce JE, Gengler N, Heringstad B, Bradley A, Stock KF. 2015. Invited review: overview of new traits and phenotyping strategies in dairy cattle with a focus on functional traits. Animal. 9(2):191–207. doi: 10.1017/S1751731114002614.
   PubMed Web of Science ®Google Scholar
• Engelsma KA, Veerkamp RF, Calus MPL, Bijma P, Windig JJ. 2012. Pedigree‐and marker‐based methods in the estimation of genetic diversity in small groups of Holstein cattle. J Anim Breed Genet. 129(3):195–205. doi: 10.1111/j.1439-0388.2012.00987.x.
   PubMed Web of Science ®Google Scholar
• Falconer DS, Mackay TFC. 1983. Quantitative genetics. London: Longman.
   Google Scholar
• Farrell HM, Jr, Jimenez-Flores R, Bleck GT, Brown EM, Butler JE, Creamer LK, Hicks CL, Hollar CM, Ng-Kwai-Hang KF, Swaisgood HE. 2004. Nomenclature of the proteins of cows’ milk—Sixth revision. J Dairy Sci. 87(6):1641–1674. doi: 10.3168/jds.S0022-0302(04)73319-6.
   PubMed Web of Science ®Google Scholar
• Ferenčaković M, Sölkner J, Curik I. 2013. Estimating autozygosity from high-throughput information: effects of SNP density and genotyping errors. Genet Sel Evol. 45(1):42. doi: 10.1186/1297-9686-45-42.
   PubMedGoogle Scholar
• Georges M, Nielsen D, Mackinnon M, Mishra A, Okimoto R, Pasquino AT, Sargeant LS, Sorensen A, Steele MR, Zhao X. 1995. Mapping quantitative trait loci controlling milk production in dairy cattle by exploiting progeny testing. Genetics. 139(2):907–920. doi: 10.1093/genetics/139.2.907.
   PubMed Web of Science ®Google Scholar
• Ginger MR, Grigor MR. 1999. Comparative aspects of milk caseins. Comp Biochem Physiol B Biochem Mol Biol. 124(2):133–145. doi: 10.1016/S0305-0491(99)00110-8.
   PubMed Web of Science ®Google Scholar
• Hayes BJ, Visscher PM, Goddard ME. 2009. Increased accuracy of artificial selection by using the realized relationship matrix. Genet Res (Camb). 91(1):47–60. doi: 10.1017/S0016672308009981.
   PubMed Web of Science ®Google Scholar
• He M, Sun J, Jiang ZQ, Yang YX. 2017. Effects of cow’s milk beta-casein variants on symptoms of milk intolerance in Chinese adults: a multicentre, randomised controlled study. Nutr J. 16(1):72. doi: 10.1186/s12937-017-0275-0.
   PubMedGoogle Scholar
• Henderson CR. 1975. Best linear unbiased estimation and prediction under a selection model. Biometrics. 31(2):423–447. doi: 10.2307/2529430.
   PubMed Web of Science ®Google Scholar
• Hill WG, Weir BS. 2011. Variation in actual relationship as a consequence of Mendelian sampling and linkage. Genet Res (Camb). 93(1):47–64. doi: 10.1017/S0016672310000480.
   PubMed Web of Science ®Google Scholar
• Keller LF, Waller DM. 2002. Inbreeding effects in wild populations. Trends Ecol Evol. 17(5):230–241. doi: 10.1016/S0169-5347(02)02489-8.
   Web of Science ®Google Scholar
• Ketto IA, Knutsen TM, Øyaas J, Heringstad B, Ådnøy T, Devold TG, Skeie SB. 2017. Effects of milk protein polymorphism and composition, casein micelle size and salt distribution on the milk coagulation properties in Norwegian Red cattle. Int Dairy J. 70:55–64. doi: 10.1016/j.idairyj.2016.10.010.
   Web of Science ®Google Scholar
• Kipp S, Segelke D, Schierenbeck S, Reinhardt F, Reents R, Wurmser C, Pausch H, Fries R, Thaller G, Tetens J, et al. 2016. Identification of a haplotype associated with cholesterol deficiency and increased juvenile mortality in Holstein cattle. J Dairy Sci. 99(11):8915–8931.,. doi: 10.3168/jds.2016-11118.
   PubMed Web of Science ®Google Scholar
• Longeri ML, Zaniboni L, Cozzi MC, Milanesi R, Bagnato A. 2021. Animal Bio Arkivi: establishment of a phenotype and tissue repository for farm animals and pets at the University of Milan. In ASPA Congress. Vol. 20. Taylor & Francis; p. 136.
   Google Scholar
• Lozada-Soto EA, Tiezzi F, Jiang J, Cole JB, VanRaden PM, Maltecca C. 2022. Genomic characterization of autozygosity and recent inbreeding trends in all major breeds of US dairy cattle. J Dairy Sci. 105(11):8956–8971. doi: 10.3168/jds.2022-22116.
   PubMed Web of Science ®Google Scholar
• MacLeod IM, Meuwissen THE, Hayes BJ, Goddard ME. 2009. A novel predictor of multilocus haplotype homozygosity: comparison with existing predictors. Genet Res (Camb). 91(6):413–426. doi: 10.1017/S0016672309990358.
   PubMed Web of Science ®Google Scholar
• Mariani P, Losi G, Russo V, Castagnetti GB, Grazia L, Morini D, Fossa E. 1976. Prove di caseificazione con latte caratterizzato dalle varianti A e B della k-caseina nella produzione del formaggio Parmigiano-Reggiano. Sci Tecn Latt-Cas. 27:208–27.
   Google Scholar
• Martikainen K, Sironen A, Uimari P. 2018. Estimation of intrachromosomal inbreeding depression on female fertility using runs of homozygosity in Finnish Ayrshire cattle. J Dairy Sci. 101(12):11097–11107. doi: 10.3168/jds.2018-14805.
   PubMed Web of Science ®Google Scholar
• Massella E, Piva S, Giacometti F, Liuzzo G, Zambrini AV, Serraino A. 2017. Evaluation of bovine beta casein polymorphism in two dairy farms located in northern Italy. Ital J Food Saf. 6(3):6904. doi: 10.4081/ijfs.2017.6904.
   PubMedGoogle Scholar
• Mastrangelo S, Sardina MT, Tolone M, Di Gerlando R, Sutera AM, Fontanesi L, Portolano B. 2018. Genome-wide identification of runs of homozygosity islands and associated genes in local dairy cattle breeds. Animal. 12(12):2480–2488. doi: 10.1017/S1751731118000629.
   PubMed Web of Science ®Google Scholar
• Mcdaniel BT. 2001. Uncontrolled Inbreeding. J Dairy Sci. 84: e 185–E186. doi: 10.3168/jds.S0022-0302(01)70214-7.
   Google Scholar
• McQuillan R, Leutenegger A-L, Abdel-Rahman R, Franklin CS, Pericic M, Barac-Lauc L, Smolej-Narancic N, Janicijevic B, Polasek O, Tenesa A, et al. 2008. Runs of homozygosity in European populations. Am J Hum Genet. 83(3):359–372. doi: 10.1016/j.ajhg.2008.08.007.
   PubMed Web of Science ®Google Scholar
• Mendes MO, de Morais MF, Rodrigues JF. 2019. A2A2 milk: brazilian consumers’ opinions and effect on sensory characteristics of Petit Suisse and Minas cheeses. LWT. 108:207–213.
   Web of Science ®Google Scholar
• Meuwissen THE, Hayes BJ, Goddard ME. 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics. 157(4):1819–1829. doi: 10.1093/genetics/157.4.1819.
   PubMed Web of Science ®Google Scholar
• Oliehoek PA, Bijma P. 2009. Effects of pedigree errors on the efficiency of conservation decisions. Genet Sel Evol. 41(1):9. doi: 10.1186/1297-9686-41-9.
   PubMedGoogle Scholar
• Ouborg NJ, Pertoldi C, Loeschcke V, Bijlsma RK, Hedrick PW. 2010. Conservation genetics in transition to conservation genomics. Trends Genet. 26(4):177–187. doi: 10.1016/j.tig.2010.01.001.
   PubMed Web of Science ®Google Scholar
• Pemberton TJ, Absher D, Feldman MW, Myers RM, Rosenberg NA, Li JZ. 2012. Genomic patterns of homozygosity in worldwide human populations. Am J Hum Genet. 91(2):275–292. doi: 10.1016/j.ajhg.2012.06.014.
   PubMed Web of Science ®Google Scholar
• Poulsen NA, Bertelsen HP, Jensen HB, Gustavsson F, Glantz M, Månsson HL, Andrén A, Paulsson M, Bendixen C, Buitenhuis AJ, et al. 2013. The occurrence of noncoagulating milk and the association of bovine milk coagulation properties with genetic variants of the caseins in 3 Scandinavian dairy breeds. J Dairy Sci. 96(8):4830–4842. doi: 10.3168/jds.2012-6422.
   PubMed Web of Science ®Google Scholar
• Prinzenberg E, Krause I, Erhardt G. 1999. SSCP analysis at the bovine CSN3 locus discriminates six alleles corresponding to known protein variants (A, B, C, E, F, G) and three new DNA polymorphisms (H, I, A1). Anim Biotechnol. 10(1-2):49–62. doi: 10.1080/10495399909525921.
   PubMed Web of Science ®Google Scholar
• Purfield DC, Berry DP, McParland S, Bradley DG. 2012. Runs of homozygosity and population history in cattle. BMC Genet. 13(1):70. doi: 10.1186/1471-2156-13-70.
   PubMedGoogle Scholar
• Ribeiro LA, Baron EE, Martinez ML, Coutinho LL. 2000. PCR screening and allele frequency estimation of bovine leukocyte adhesion deficiency in Holstein and Gir cattle in Brazil. Genet Mol Biol. 23(4):831–834. doi: 10.1590/S1415-47572000000400021.
   Web of Science ®Google Scholar
• Sanchez M-P, Fritz S, Patry C, Delacroix-Buchet A, Boichard D. 2020. Frequencies of milk protein variants and haplotypes estimated from genotypes of more than 1 million bulls and cows of 12 French cattle breeds. J Dairy Sci. 103(10):9124–9141. doi: 10.3168/jds.2020-18492.
   PubMed Web of Science ®Google Scholar
• Schiavo G, Bovo S, Muñoz M, Ribani A, Alves E, Araújo JP, Bozzi R, Čandek-Potokar M, Charneca R, Fernandez AI, et al. 2021. Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds. Anim Genet. 52(2):155–170. doi: 10.1111/age.13045.
   PubMed Web of Science ®Google Scholar
• Stasio L, Mariani P. 2000. The role of protein polymorphism in the genetic improvement of milk production. Zootec Nutr Anim. 26(3):69–90.
   Google Scholar
• van den Berg G, Jtm E, de Koning PJ, Bovenhuis H. 1992. Genetic polymorphism of κ-casein and β-lactoglobulin in relation to milk composition and processing properties. Nederlands Melk En Zuiveltijdschrift. 46(3–4):145–168.
   Google Scholar
• Weigel KA. 2001. Controlling inbreeding in modern breeding programs. J Dairy Sci. 84: e 177–E184. doi: 10.3168/jds.S0022-0302(01)70213-5.
   PubMedGoogle Scholar
• Wickham H. 2016. ggplot2: elegant graphics for data analysis [Internet]. New York: Springer-Verlag. Accessed 2021 May 2. https://ggplot2.tidyverse.org.
   Google Scholar
• Wiggans GR, Cooper TA, VanRaden PM, Olson KM, Tooker ME. 2012. Use of the Illumina Bovine3K BeadChip in dairy genomic evaluation. J Dairy Sci. 95(3):1552–1558. doi: 10.3168/jds.2011-4985.
   PubMed Web of Science ®Google Scholar
• Wojdak-Maksymiec K. 2006. Associations between bovine lactoferrin gene polymorphism and somatic cell count in milk. Vet Med Praha. 51:14. doi: 10.17221/5512-VETMED.
   Google Scholar
• Xuan R, Chao T, Zhao X, Wang A, Chu Y, Li Q, Zhao Y, Ji Z, Wang J. 2022. Transcriptome profiling of the nonlactating mammary glands of dairy goats reveals the molecular genetic mechanism of mammary cell remodeling. J Dairy Sci. 105(6):5238–5260. doi: 10.3168/jds.2021-21039.
   PubMed Web of Science ®Google Scholar
• Yang A, Larsen T, Tume R. 1992. Carotenoid and retinol concentrations in serum, adipose tissue and liver and carotenoid transport in sheep, goats and cattle. Aust J Agric Res. 43(8):1809. doi: 10.1071/AR9921809.
   Google Scholar
• Zhang Q, Guldbrandtsen B, Bosse M, Lund MS, Sahana G. 2015. Runs of homozygosity and distribution of functional variants in the cattle genome. BMC Genomics. 16(1):542. doi: 10.1186/s12864-015-1715-x.
   PubMedGoogle Scholar