Whole-genome SNP markers reveal runs of homozygosity in indigenous cattle breeds of Pakistan

References

• Curik I, Ferenčaković M, Sölkner JJLS. Inbreeding and runs of homozygosity: a possible solution to an old problem. Livest Sci. 2014;166:26–34.
   Web of Science ®Google Scholar
• Gibson J, Morton NE, Collins A. Extended tracts of homozygosity in outbred human populations. Hum Mol Genet. 2006;15(5):789–795.
   PubMed Web of Science ®Google Scholar
• Gurgul A, Szmatoła T, Topolski P, Jasielczuk I, Żukowski K, Bugno-Poniewierska M. The use of runs of homozygosity for estimation of recent inbreeding in Holstein cattle. J Appl Genet. 2016;57(4):527–530.
   PubMed Web of Science ®Google Scholar
• Purfield DC, Berry DP, McParland S, Bradley DG. Runs of homozygosity and population history in cattle. BMC Genet. 2012;13(1):70–11.
   PubMedGoogle Scholar
• Falconer D, Mackay T. Introduction to Quantitative Genetics. Harlow: Addison Wesley Longman; 1996.
   Google Scholar
• Peripolli E, Munari D, Silva M, Lima A, Irgang R, Baldi F. Runs of homozygosity: current knowledge and applications in livestock. Anim Genet. 2017;48(3):255–271.
   PubMed Web of Science ®Google Scholar
• Bosse M, Megens H, Madsen O, et al. Regions of homozygosity in the porcine genome: consequence of demography and the recombination landscape. PLOS Genet. 2012;8(11):e1003100.
   PubMed Web of Science ®Google Scholar
• Pemberton TJ, Absher D, Feldman MW, Myers RM, Rosenberg NA, Li JZ. Genomic patterns of homozygosity in worldwide human populations. Am J Hum Genet. 2012;91(2):275–292.
   PubMed Web of Science ®Google Scholar
• Forutan M, Mahyari SA, Baes C, Melzer N, Schenkel FS, Sargolzaei M. Inbreeding and runs of homozygosity before and after genomic selection in North American Holstein cattle. BMC Genom. 2018;19(1):1–12.
   PubMedGoogle Scholar
• Kim ES, Sonstegard TS, Rothschild MF. Recent artificial selection in US Jersey cattle impacts autozygosity levels of specific genomic regions. BMC Genom. 2015;16(1):1–10.
   PubMedGoogle Scholar
• Keller MC, Visscher PM, Goddard ME. Quantification of inbreeding due to distant ancestors and its detection using dense single nucleotide polymorphism data. Genetics. 2011;189(1):237–249.
   PubMed Web of Science ®Google Scholar
• Howrigan DP, Simonson MA, Keller MC. Detecting autozygosity through runs of homozygosity: a comparison of three autozygosity detection algorithms. BMC Genom. 2011;12(1):1–15.
   Google Scholar
• Gomez-Raya L, Rodríguez C, Barragán C, Silió L. Genomic inbreeding coefficients based on the distribution of the length of runs of homozygosity in a closed line of Iberian pigs. Genet Sel. 2015;47(1):1–15.
   PubMedGoogle Scholar
• Szmatoła T, Gurgul A, Ropka-Molik K, Jasielczuk I, Ząbek T, Bugno-Poniewierska M. Characteristics of runs of homozygosity in selected cattle breeds maintained in Poland. Livest Sci. 2016;188:72–80.
   Web of Science ®Google Scholar
• Xie R, Shi L, Liu J, et al. Genome-wide scan for runs of homozygosity identifies candidate genes in three pig breeds. Animals. 2019;9(8):518.
   Web of Science ®Google Scholar
• Pandey A, Sharma R, Singh Y, Prakash B, Ahlawat S. Genetic diversity studies of Kherigarh cattle based on microsatellite markers. J Genet. 2006;85(2):117–122.
   PubMed Web of Science ®Google Scholar
• Sharma R, Kishore A, Mukesh M, et al. Genetic diversity and relationship of Indian cattle inferred from microsatellite and mitochondrial DNA markers. BMC Genom. 2015;16(1):1–12.
   PubMedGoogle Scholar
• Purfield DC, McParland S, Wall E, Berry DP. The distribution of runs of homozygosity and selection signatures in six commercial meat sheep breeds. PLOS One. 2017;12(5):e0176780.
   PubMed Web of Science ®Google Scholar
• Xu Z, Sun H, Zhang Z, et al. Assessment of autozygosity derived from runs of homozygosity in Jinhua pigs disclosed by sequencing data. Front Genet. 2019;10:274.
   PubMed Web of Science ®Google Scholar
• Decker JE, McKay SD, Rolf MM, et al. Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle. PLOS Genet. 2014;10(3):e1004254.
   PubMed Web of Science ®Google Scholar
• Dash S, Singh A, Bhatia A, et al. Evaluation of bovine high-density SNP genotyping array in indigenous dairy cattle breeds. Anim Biotechnol. 2018;29(2):129–135.
   PubMed Web of Science ®Google Scholar
• Chang CC, Chow CC, Tellier LC, Vattikuti S, Purcell SM, Lee J. Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience. 2015;4(1):7.
   PubMedGoogle Scholar
• Purcell S, Neale B, Todd-Brown K, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81(3):559–575.
   PubMed Web of Science ®Google Scholar
• Ferenčaković M, Hamzić E, Gredler B, et al. Estimates of autozygosity derived from runs of homozygosity: empirical evidence from selected cattle populations. J Anim Breed Genet. 2013;130(4):286–293.
   PubMed Web of Science ®Google Scholar
• Kirin M, McQuillan R, Franklin CS, Campbell H, McKeigue PM, Wilson JF. Genomic runs of homozygosity record population history and consanguinity. PLOS One. 2010;5(11):e13996.
   PubMed Web of Science ®Google Scholar
• McQuillan R, Leutenegger AL, Abdel-Rahman R, et al. Runs of homozygosity in European populations. Am J Hum Genet. 2008;83(3):359–372.
   PubMed Web of Science ®Google Scholar
• Dixit S, Singh S, Ganguly I, et al. Genome-wide runs of homozygosity revealed selection signatures in Bos indicus. Front Genet. 2020;11:92.
   PubMed Web of Science ®Google Scholar
• Mastrangelo S, Sardina M, Tolone M, et al. Genome-wide identification of runs of homozygosity islands and associated genes in local dairy cattle breeds. Animal. 2018;12(12):2480–2488.
   PubMed Web of Science ®Google Scholar
• Mastrangelo S, Tolone M, Sardina MT, et al. Genome-wide scan for runs of homozygosity identifies potential candidate genes associated with local adaptation in Valle del Belice sheep. Genet Sel. 2017;49(1):1–10.
   PubMedGoogle Scholar
• Zhao G, Zhang T, Liu Y, et al. Genome-wide assessment of runs of homozygosity in Chinese wagyu beef cattle. Anim. 2020;10(8):1425.
   Google Scholar
• Peripolli E, Stafuzza NB, Munari DP, et al. Assessment of runs of homozygosity islands and estimates of genomic inbreeding in Gyr (Bos indicus) dairy cattle. Anim Genet. 2018;19(1):1–13.
   Google Scholar
• Nothnagel M, Lu TT, Kayser M, Krawczak M. Genomic and geographic distribution of SNP-defined runs of homozygosity in Europeans. Hum Mol Genet. 2010;19(15):2927–2935.
   PubMed Web of Science ®Google Scholar
• Quilez J, Short AD, Martínez V, et al. A selective sweep of >8 Mb on chromosome 26 in the Boxer genome. BMC Genom. 2011;12(1):1–12.
   Google Scholar
• Ramey HR, Decker JE, McKay SD, Rolf MM, Schnabel RD, Taylor JF. Detection of selective sweeps in cattle using genome-wide SNP data. BMC Genom. 2013;14(1):1–18.
   PubMedGoogle Scholar
• Saravanan K, Panigrahi M, Kumar H, et al. Genomic scans for selection signatures revealed candidate genes for adaptation and production traits in a variety of cattle breeds. Genomics. 2021;113(3):955–963.
   PubMed Web of Science ®Google Scholar
• Makanjuola BO, Maltecca C, Miglior F, et al. Identification of unique ROH regions with unfavorable effects on production and fertility traits in Canadian Holsteins. Genet Sel Evol. 2021;53(1):1–11.
   PubMed Web of Science ®Google Scholar
• Ogorevc J, Kunej T, Razpet A, Dovc P. Database of cattle candidate genes and genetic markers for milk production and mastitis. Anim Genet. 2009;40(6):832–851.
   PubMed Web of Science ®Google Scholar
• Liu M, Li M, Wang S, et al. Association analysis of bovine Foxa2 gene single sequence variant and haplotype combinations with growth traits in Chinese cattle. Gene. 2014;536(2):385–392.
   PubMed Web of Science ®Google Scholar
• Kukučková V, Moravčíková N, Ferenčaković M, et al. Genomic characterization of Pinzgau cattle: genetic conservation and breeding perspectives. Conserv Genet. 2017;18(4):893–910.
   Web of Science ®Google Scholar
• Nalepa G, Rolfe M, Harper JW. Drug discovery in the ubiquitin-proteasome system. Nat Rev Drug Discov. 2006;5(7):596–613.
   PubMed Web of Science ®Google Scholar
• Sadri H, Giallongo F, Hristov A, et al. Effects of slow-release urea and rumen-protected methionine and histidine on mammalian target of rapamycin (mTOR) signaling and ubiquitin proteasome-related gene expression in skeletal muscle of dairy cows. J Dairy Sci. 2016;99(8):6702–6713.
   PubMed Web of Science ®Google Scholar
• Silva DB, Fonseca LF, Pinheiro DG, et al. Spliced genes in muscle from Nelore cattle and their association with carcass and meat quality. Sci Rep. 2020;10(1):1–13.
   PubMed Web of Science ®Google Scholar
• Ranganathan S, Simpson KJ, Shaw DC, Nicholas KR. The whey acidic protein family: a new signature motif and three-dimensional structure by comparative modeling. J Mol Graph. 1999;17(2):106–113.
   Google Scholar
• Bingle L, Singleton V, Bingle CD. The putative ovarian tumour marker gene HE4 (WFDC2), is expressed in normal tissues and undergoes complex alternative splicing to yield multiple protein isoforms. Oncogene. 2002;21(17):2768–2773.
   PubMed Web of Science ®Google Scholar
• Clauss A, Persson M, Lilja H, Lundwall Å. Three genes expressing Kunitz domains in the epididymis are related to genes of WFDC-type protease inhibitors and semen coagulum proteins in spite of lacking similarity between their protein products. BMC Biochem. 2011;12(1):55.
   PubMedGoogle Scholar
• Kirchhoff C, Habben I, Ivell R, Krull N. A major human epididymis-specific cDNA encodes a protein with sequence homology to extracellular proteinase inhibitors. Biol Reprod. 1991;45(2):350–357.
   PubMed Web of Science ®Google Scholar
• Kirchhoff C, Osterhoff C, Pera I, Schröter SJ. Function of human epididymal proteins in sperm maturation. Andrologia. 1998;30(4–5):225–232.
   PubMed Web of Science ®Google Scholar
• Moon S, Lee JW, Shin D, et al. A genome-wide scan for selective sweeps in racing horses. Asian-Australas J Anim Sci. 2015;28(11):1525–1531.
   PubMed Web of Science ®Google Scholar
• Fang X, Zhao Z, Jiang P, Yu H, Xiao H, Yang R. Identification of the bovine HSL gene expression profiles and its association with fatty acid composition and fat deposition traits. Meat Sci. 2017;131:107–118.
   PubMed Web of Science ®Google Scholar
• Jiang P, Xia L, Jin Z, et al. New function of the CD44 gene: lipid metabolism regulation in bovine mammary epithelial cells. J Dairy Sci. 2020;103(7):6661–6671.
   PubMed Web of Science ®Google Scholar
• Gao Y, Li S, Lai Z, et al. Analysis of long non-coding RNA and mRNA expression profiling in immature and mature bovine (Bos taurus) testes. Front Genet. 2019;10:646.
   PubMed Web of Science ®Google Scholar
• Liu S, Zhang J, Kherraf ZE, et al. CFAP61 is required for sperm flagellum formation and male fertility in human and mouse. bioRxiv. 2021.
   Google Scholar
• Ropka-Molik K, Żukowski K, Eckert R, et al. Whole transcriptome analysis of the porcine muscle tissue of breeds differing in muscularity and meat quality traits. Livest Sci. 2015;182:93–100.
   Web of Science ®Google Scholar
• Carvalho M, Baldi F, Santana M, et al. Identification of genomic regions related to tenderness in Nellore beef cattle. Adv Anim Vet Sci. 2017;8(s1):s42–s44.
   Google Scholar
• De León C, Manrique C, Martínez R, Rocha J. Genomic association study for adaptability traits in four Colombian cattle breeds. Genet Mol Res. 2019;18:GMR18373.
   Web of Science ®Google Scholar
• Sharma U, Banerjee P, Joshi J, Kapoor P, Vijh R. Identification of quantitative trait loci for fat percentage in buffaloes. Indian J Anim Sci. 2018;88:714–723.
   Web of Science ®Google Scholar
• Illa SK, Mukherjee S, Nath S, Mukherjee A. Genome-wide scanning for signatures of selection revealed the putative genomic regions and candidate genes controlling milk composition and coat color traits in Sahiwal cattle. Front Genet. 2021;12:699422.
   PubMed Web of Science ®Google Scholar
• MacLean JA II. Ruminant Trophoblast Kunitz Domain Proteins. Missouri (MO): University of Missouri-Columbia; 2000.
   Google Scholar
• Chen Z, Yao Y, Ma P, Wang Q, Pan Y. Haplotype-based genome-wide association study identifies loci and candidate genes for milk yield in Holsteins. PLOS One. 2018;13(2):e0192695.
   PubMed Web of Science ®Google Scholar
• Oliveira M, Mello B, Gonella-Diaza A, et al. Unravelling the role of 17β-estradiol on advancing uterine luteolytic cascade in cattle. Domest Anim Endocrinol. 2022;78:106653.
   PubMed Web of Science ®Google Scholar
• Sorbolini S, Marras G, Gaspa G, et al. Detection of selection signatures in Piemontese and Marchigiana cattle, two breeds with similar production aptitudes but different selection histories. Genet Sel. 2015;47(1):1–13.
   PubMedGoogle Scholar
• Zhang W, Yang F, Zhu Z, et al. Cellular DNAJA3, a novel VP1-interacting protein, inhibits foot-and-mouth disease virus replication by inducing lysosomal degradation of VP1 and attenuating its antagonistic role in the beta interferon signaling pathway. J Virol. 2019;93(13):e00588-19.
   PubMed Web of Science ®Google Scholar
• Mohammadi A, Alijani S, Rafat SA, Abdollahi-Arpanahi R. Genome-wide association study and pathway analysis for female fertility traits in Iranian Holstein cattle. Ann Anim Sci. 2020;20(3):825–851.
   Web of Science ®Google Scholar
• Boitard S, Paris C, Sevane N, Servin B, Bazi-Kabbaj K, Dunner S. Gene banks as reservoirs to detect recent selection: the example of the Asturiana de los Valles bovine breed. Front Genet. 2021;12:575405.
   PubMed Web of Science ®Google Scholar
• Li H. Patterns of Genomic Variation and Whole Genome Association Studies of Economically Important Traits in Cattle; 2012.
   Google Scholar
• Caroni P, Rothenfluh A, McGlynn E, Schneider C. S-cyclophilin. New member of the cyclophilin family associated with the secretory pathway. J Biol Chem. 1991;266(17):10739–10742.
   PubMed Web of Science ®Google Scholar
• Carlton J, Bujny M, Peter BJ, et al. Sorting nexin-1 mediates tubular endosome-to-TGN transport through coincidence sensing of high- curvature membranes and 3-phosphoinositides. Curr Biol. 2004;14(20):1791–1800.
   PubMed Web of Science ®Google Scholar
• Haft CR, de la Luz Sierra M, Barr VA, Haft DH, Taylor SI. Identification of a family of sorting nexin molecules and characterization of their association with receptors. Mol Cell Biol. 1998;18(12):7278–7287.
   PubMed Web of Science ®Google Scholar
• Tizioto PC, Decker JE, Taylor JF, et al. Genome scan for meat quality traits in Nelore beef cattle. Physiol Genomics. 2013;45(21):1012–1020. doi:10.1152/physiolgenomics.00066.2013.
   PubMed Web of Science ®Google Scholar
• Sun SX, Zhang LJ, Wang CF, Zhong JF, Li Q, Zhang JB. Study on genetic diagnosis for IRAK2 gene associated with mastitis in Chinese Holstein cattle. Heilongjiang Ann Sci Vet Med. 2012;21:94–96.
   Google Scholar
• Lin S, Wan Z, Zhang J, Xu L, Han B, Sun D. Genome-wide association studies for the concentration of albumin in colostrum and serum in Chinese Holstein. Animals. 2020;10(12):2211.
   Web of Science ®Google Scholar
• Zhou X, Zhuang Z, Wang W, et al. OGG1 is essential in oxidative stress induced DNA demethylation. Cell Signal. 2016;28(9):1163–1171.
   PubMed Web of Science ®Google Scholar