- These CNVRs together cover 2.8% of the bovine autosomes. - The assessment of the functional impact of CNVRs showed that rare CNVRs (MAF <. - Also, the role of CNVs in adaptive evolution is further exemplified by mean copy numbers of the AMY1 gene (which codes for amylase alpha1, an essential enzyme for starch digestion). - The 14,272 CNV calls were aggregated into 1755 CNV regions (CNVRs), based on at least 1 bp overlap, following Redon et al. - These CNVRs cover 2.8% of the autosomal genome se- quence Mb. - This region was reported to have a large number deletion and duplication calls by other cattle CNV studies based on UMD3.1, regardless of the studied breeds . - From the outside to the inside of the external circle: chromosome name. - Nextly, gene ontology analyses were performed to understand the functions of the genes that overlap with CNVRs. - of the 700 CNVRs were categorized as common, inter- mediate, and rare CNVRs, respectively.. - We further explored the allele frequencies by ap- plying Wright’s fixation index (Fst) [38] to characterize population structure [39] and detect loci that underwent selection [40], as done in Yali Xue et al. - We observed generally low r 2 , close to zero, re- gardless of the distance between CNVRs and SNPs (re- sults not shown). - The broad GWAS peak also indicate high LD in this regions, that matched with the findings from Qanbari et al. - To see whether CNVR 547 overlaps with regulatory elements, besides overlapping with the upstream region of the UGT2B4 gene directly, we called promoters and enhancers from ChipSeq data from Villar et al. - To summarize, our analyses imply that a high MAF of CNVR 547 might be due the select- ive sweep in the casein cluster or the consequence of direct selection on CNVR 547 itself due to the functional impact of the overlap with UGT2B4 and its enhancer.. - Nonetheless, we cannot exclude drift as a possible driver for the high allele frequency of the CNVR 547.. - Using CNVRs that are con- structed using the CNVs, we reported the functional im- pact and population genetic features of the CNVRs.. - Firstly, the SNP density in this region is a quarter of the genome-wide average SNP density in UMD3.1 (71 SNPs/Mb and 292 SNPs/. - Given that CNVR 1452 we found is a duplication locus, it might be a different mu- tation than the one found by Mesbah-Uddin et al. - 5) were filtered out in either of the popu- lations. - High LD can be obtained when the allele frequencies of the two loci match [76].. - Van Binsbergen et al. - Redon et al. - [28] and Locke et al. - Indeed, Cooper et al. - [61] and McCarroll et al. - Using commercial high-density SNP arrays, we identified 14,272 CNVs, that built 1755 CNVRs (cover ~ 2.8% of the bovine autosomes), and the CNVRs were further used as genetic loci this study. - Afterwards, the dis- tribution of the number of CNVs per individual was inspected using QQ plots (Additional file 2: Figure S7).. - The same filter on the distribution of the total length of CNVs per individual was applied and identified outlier samples (n = 11). - The CNVs were aggregated into CNV regions (CNVR) based on 1 bp overlap, following Redon et al. - The SDs detected by Feng et al. - Subsequently, CNVRs were classified depending on their functional impact, as done in Conrad et al. - following McCarroll et al. - The SNPs inside the CNVRs were masked to prevent a bias introduced during the phasing step, as done in Conrad et al. - To overlap the CNVR 547 and func- tional elements in bovine genomes, we used the data from Villar et al. - CNV: Copy number variation. - performed data collection and was involved in preparation of the manuscript. - MG is a member of the editorial board (Associate Editor) of BMC Genomics journal. - Structural variation in the human genome.. - Iafrate AJ, Feuk L, Rivera MN, Listewnik ML, Donahoe PK, Qi Y, et al.. - Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, et al. - Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, et al. - Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, et al.. - Eichler EE, Flint J, Gibson G, Kong A, Leal SM, Moore JH, et al. - Bochukova EG, Huang N, Keogh J, Henning E, Purmann C, Blaszczyk K, et al.. - Coe BP, Witherspoon K, Rosenfeld JA, van Bon BWM, Vulto-van Silfhout AT, Bosco P, et al. - Macé A, Tuke MA, Deelen P, Kristiansson K, Mattsson H, Nõukas M, et al.. - Marshall CR, Howrigan DP, Merico D, Thiruvahindrapuram B, Wu W, Greer DS, et al. - Gonzalez E, Kulkarni H, Bolivar H, Mangano A, Sanchez R, Catano G, et al.. - Perry GH, Dominy NJ, Claw KG, Lee AS, Fiegler H, Redon R, et al. - Rubin C-J, Megens H-J, Barrio AM, Maqbool K, Sayyab S, Schwochow D, et al. - Giuffra E, Tornsten A, Marklund S, Bongcam-rudlo E, Chardon P, Kijas MHJ, et al. - Durkin K, Coppieters W, Drögüller C, Ahariz N, Cambisano N, Druet T, et al.. - Xu L, Cole JB, Bickhart DM, Hou Y, Song J, VanRaden PM, et al. - Zhou Y, Connor EE, Wiggans GR, Lu Y, Tempelman RJ, Schroeder SG, et al.. - Durán Aguilar M, Román Ponce SI, Ruiz López FJ, González Padilla E, Vásquez Peláez CG, Bagnato A, et al. - Xu L, Hou Y, Bickhart DM, Zhou Y, Hay EHA, Song J, et al. - Bickhart DM, Xu L, Hutchison JL, Cole JB, Null DJ, Schroeder SG, et al.. - Upadhyay M, da Silva VH, Megens HJ, Visker MHPW, Ajmone-Marsan P, Bâlteanu VA, et al. - Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SFA, et al. - Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, et al. - Global variation in copy number in the human genome. - Jiang L, Jiang J, Yang J, Liu X, Wang J, Wang H, et al. - Prinsen RTMM, Strillacci MG, Schiavini F, Santus E, Rossoni A, Maurer V, et al. - Nandolo W, Utsunomiya YT, Mészáros G, Wurzinger M, Khayadzadeh N, Torrecilha RBP, et al. - Hou Y, Bickhart DM, Hvinden ML, Li C, Song J, Boichard DA, et al. - Famous individuals in the history of the Jersey and Holstein- Friesian breeds. - Jakobsson M, Scholz SW, Scheet P, Gibbs JR, Vanliere JM, Fung H, et al.. - A haplotype map of the human genome. - Xue Y, Sun D, Daly A, Yang F, Zhou X, Zhao M, et al. - Wade TD, Gordon S, Medland S, Bulik CM, Heath AC, Montgomery GW, et al. - Destito MCS, Souza MM, Cirillo CA, Ledda M, Zamboni A, Martin N, et al. - Dickinson ME, Flenniken AM, Ji X, Teboul L, Wong MD, White JK, et al. - Bouwman AC, Daetwyler HD, Chamberlain AJ, Ponce CH, Sargolzaei M, Schenkel FS, et al. - Strillacci MG, Gorla E, Cozzi MC, Vevey M, Genova F, Scienski K, et al. - Sharma A, Lee JS, Dang CG, Sudrajad P, Kim HC, Yeon SH, et al. - Visscher PM, Wray NR, Zhang Q, Sklar P, McCarthy MI, Brown MA, et al. - Developmental progress and current status of the animal QTLdb. - Qanbari S, Pimentel ECG, Tetens J, Thaller G, Lichtner P, Sharifi AR, et al. - Substrate specificity of the human UDP-glucuronosyltransferase UGT2B4 and UGT2B7. - Villar D, Berthelot C, Flicek P, Odom DT, Villar D, Berthelot C, et al. - Guryev V, Saar K, Adamovic T, Verheul M, Van Heesch SAAC, Cook S, et al.. - Conrad DF, Pinto D, Redon R, Feuk L, Gokcumen O, Zhang Y, et al. - Origins and functional impact of copy number variation in the human genome.. - Mesbah-Uddin M, Guldbrandtsen B, Iso-Touru T, Vilkki J, De Koning D-J, Boichard D, et al. - Boussaha M, Esquerré D, Barbieri J, Djari A, Pinton A, Letaief R, et al.. - McCarroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, Wysoker A, et al.. - Audano PA, Sulovari A, Graves-lindsay TA, Li YI, Wilson RK, Eichler EE, et al.. - Axelsson E, Ratnakumar A, Arendt ML, Maqbool K, Webster MT, Perloski M, et al. - Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, et al. - Mccarroll SA, Hadnott TN, Perry GH, Sabeti PC, Zody MC, Barrett JC, et al.. - Kato M, Kawaguchi T, Ishikawa S, Umeda T, Nakamichi R, Shapero MH, et al.. - Locke DP, Sharp AJ, Mccarroll SA, Mcgrath SD, Newman TL, Cheng Z, et al.. - within duplicated regions of the human genome. - Van Binsbergen R, Bink MCAM, Calus MPL, Van Eeuwijk FA, Hayes BJ, Hulsegge I, et al. - Gondo Y, Gardner JM, Nakatsu Y, Durham-pierre D, Deveaut SA, Kuper C, et al. - Feng X, Jiang J, Padhi A, Ning C, Fu J, Wang A, et al. - Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, et al.. - McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GRS, Thormann A, et al. - Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, Daverman R, et al.. - Purcell S, Neale B, Todd-brown K, Thomas L, Ferreira MAR, Bender D, et al.
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