An B X, Xu L, Xia J W, Wang X Q, Miao J, Chang T P, Song M H, Ni J Q, Xu L Y, Zhang L P, Li J Y,Gao H J. 2020. Multiple association analysis of loci and candidate genes that regulate body size at three growth stages in Simmental beef cattle. BMC Genetics, 21, 32.
An J J, Rhee Y, Kim S H, Kim D M, Han D-H, Hwang J H, Jin Y-J, Cha B S, Baik J-H, Lee W T,Lim S-K. 2007. Peripheral effect of alpha-melanocyte-stimulating hormone on fatty acid oxidation in skeletal muscle. The Journal of biological chemistry, 282, 2862-2870.
Barbeira A N, Dickinson S P, Bonazzola R, Zheng J, Wheeler H E, Torres J M, Torstenson E S, Shah K P, Garcia T, Edwards T L, Stahl E A, Huckins L M, Nicolae D L, Cox N J,Im H K. 2018. Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics. Nature Communications, 9, 1825.
Berndt S I, Gustafsson S, Mägi R, Ganna A, Wheeler E, Feitosa M F, Justice A E, Monda K L, Croteau-Chonka D C, Day F R, Esko T, Fall T, Ferreira T, Gentilini D, Jackson A U, Luan J, Randall J C, Vedantam S, Willer C J, Winkler T W, Wood A R, Workalemahu T, Hu Y J, Lee S H, Liang L, Lin D Y, Min J L, Neale B M, Thorleifsson G, Yang J, Albrecht E, Amin N, Bragg-Gresham J L, Cadby G, den Heijer M, Eklund N, Fischer K, Goel A, Hottenga J J, Huffman J E, Jarick I, Johansson Å, Johnson T, Kanoni S, Kleber M E, König I R, Kristiansson K, Kutalik Z, Lamina C, Lecoeur C, Li G, Mangino M, McArdle W L, Medina-Gomez C, Müller-Nurasyid M, Ngwa J S, Nolte I M, Paternoster L, Pechlivanis S, Perola M, Peters M J, Preuss M, Rose L M, Shi J, Shungin D, Smith A V, Strawbridge R J, Surakka I, Teumer A, Trip M D, Tyrer J, Van Vliet-Ostaptchouk J V, Vandenput L, Waite L L, Zhao J H, Absher D, Asselbergs F W, Atalay M, Attwood A P, Balmforth A J, Basart H, Beilby J, Bonnycastle L L, Brambilla P, Bruinenberg M, Campbell H, Chasman D I, Chines P S, Collins F S, Connell J M, Cookson W O, de Faire U, de Vegt F, Dei M, Dimitriou M, Edkins S, Estrada K, Evans D M, Farrall M, Ferrario M M, Ferrières J, Franke L, Frau F, Gejman P V, Grallert H, Grönberg H, Gudnason V, Hall A S, Hall P, Hartikainen A L, Hayward C, Heard-Costa N L, Heath A C, Hebebrand J, Homuth G, Hu F B, Hunt S E, Hyppönen E, Iribarren C, Jacobs K B, Jansson J O, Jula A, Kähönen M, Kathiresan S, Kee F, Khaw K T, Kivimäki M, Koenig W, Kraja A T, Kumari M, Kuulasmaa K, Kuusisto J, Laitinen J H, Lakka T A, Langenberg C, Launer L J, Lind L, Lindström J, Liu J, Liuzzi A, Lokki M L, Lorentzon M, Madden P A, Magnusson P K, Manunta P, Marek D, März W, Mateo Leach I, McKnight B, Medland S E, Mihailov E, Milani L, Montgomery G W, Mooser V, Mühleisen T W, Munroe P B, Musk A W, Narisu N, Navis G, Nicholson G, Nohr E A, Ong K K, Oostra B A, Palmer C N, Palotie A, Peden J F, Pedersen N, Peters A, Polasek O, Pouta A, Pramstaller P P, Prokopenko I, Pütter C, Radhakrishnan A, Raitakari O, Rendon A, Rivadeneira F, Rudan I, Saaristo T E, Sambrook J G, Sanders A R, Sanna S, Saramies J, Schipf S, Schreiber S, Schunkert H, Shin S Y, Signorini S, Sinisalo J, Skrobek B, Soranzo N, Stančáková A, Stark K, Stephens J C, Stirrups K, Stolk R P, Stumvoll M, Swift A J, Theodoraki E V, Thorand B, Tregouet D A, Tremoli E, Van der Klauw M M, van Meurs J B, Vermeulen S H, Viikari J, Virtamo J, Vitart V, Waeber G, Wang Z, Widén E, Wild S H, Willemsen G, Winkelmann B R, Witteman J C, Wolffenbuttel B H, Wong A, Wright A F, Zillikens M C, Amouyel P, Boehm B O, Boerwinkle E, Boomsma D I, Caulfield M J, Chanock S J, Cupples L A, Cusi D, Dedoussis G V, Erdmann J, Eriksson J G, Franks P W, Froguel P, Gieger C, Gyllensten U, Hamsten A, Harris T B, Hengstenberg C, Hicks A A, Hingorani A, Hinney A, Hofman A, Hovingh K G, Hveem K, Illig T, Jarvelin M R, Jöckel K H, Keinanen-Kiukaanniemi S M, Kiemeney L A, Kuh D, Laakso M, Lehtimäki T, Levinson D F, Martin N G, Metspalu A, Morris A D, Nieminen M S, Njølstad I, Ohlsson C, Oldehinkel A J, Ouwehand W H, Palmer L J, Penninx B, Power C, Province M A, Psaty B M, Qi L, Rauramaa R, Ridker P M, Ripatti S, Salomaa V, Samani N J, Snieder H, Sørensen T I, Spector T D, Stefansson K, Tönjes A, Tuomilehto J, Uitterlinden A G, Uusitupa M, van der Harst P, Vollenweider P, Wallaschofski H, Wareham N J, Watkins H, Wichmann H E, Wilson J F, Abecasis G R, Assimes T L, Barroso I, Boehnke M, Borecki I B, Deloukas P, Fox C S, Frayling T, Groop L C, Haritunian T, Heid I M, Hunter D, Kaplan R C, Karpe F, Moffatt M F, Mohlke K L, O'Connell J R, Pawitan Y, Schadt E E, Schlessinger D, Steinthorsdottir V, Strachan D P, Thorsteinsdottir U, van Duijn C M, Visscher P M, Di Blasio A M, Hirschhorn J N, Lindgren C M, Morris A P, Meyre D, Scherag A, McCarthy M I, Speliotes E K, North K E, Loos R J,Ingelsson E. 2013. Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. Nature Genetics, 45, 501-512.
Billaut-Mulot O, Cocude C, Kolesnitchenko V, Truong M J, Chan E K, Hachula E, de la Tribonnière X, Capron A,Bahr G M. 2001. SS-56, a novel cellular target of autoantibody responses in Sjögren syndrome and systemic lupus erythematosus. The Journal of Clinical Investigation, 108, 861-869.
Bollag W B, Choudhary V, Zhong Q, Ding K-H, Xu J, Elsayed R, Yu K, Su Y, Bailey L J, Shi X-M, Elsalanty M, Johnson M H, McGee-Lawrence M E,Isales C M. 2018. Deletion of protein kinase D1 in osteoprogenitor cells results in decreased osteogenesis in vitro and reduced bone mineral density in vivo. Molecular and Cellular Endocrinology, 461, 22-31.
Boycott K M, Bonnemann C, Herz J, Neuert S, Beaulieu C, Scott J N, Venkatasubramanian A,Parboosingh J S. 2009. Mutations in VLDLR as a cause for autosomal recessive cerebellar ataxia with mental retardation (dysequilibrium syndrome). Journal of Child Neurology, 24, 1310-1315.
Browning B L, Zhou Y,Browning S R. 2018. A One-Penny Imputed Genome from Next-Generation Reference Panels. The American Journal of Human Genetics, 103, 338-348.
Chen Z, Chu S F, Xu X, Jiang J Y, Wang W Q, Shen H L, Li M X, Zhang H M, Mao Y J,Yang Z P. 2019. Analysis of longissimus muscle quality characteristics and associations with DNA methylation status in cattle. Genes Genomics, 41, 1147-1163.
Cheung V G,Spielman R S. 2002. The genetics of variation in gene expression. Nature Genetics, 32 Suppl, 522-525.
den Engelsman J, Boros S, Dankers P Y, Kamps B, Vree Egberts W T, Böde C S, Lane L A, Aquilina J A, Benesch J L, Robinson C V, de Jong W W,Boelens W C. 2009. The small heat-shock proteins HSPB2 and HSPB3 form well-defined heterooligomers in a unique 3 to 1 subunit ratio. Journal of Molecular Biology, 393, 1022-1032.
Fan B, Onteru S K, Du Z Q, Garrick D J, Stalder K J,Rothschild M F. 2011. Genome-wide association study identifies Loci for body composition and structural soundness traits in pigs. Plos One, 6, e14726.
Fink T, Tiplady K, Lopdell T, Johnson T, Snell R G, Spelman R J, Davis S R,Littlejohn M D. 2017. Functional confirmation of PLAG1 as the candidate causative gene underlying major pleiotropic effects on body weight and milk characteristics. Scientific Reports, 7, 44793.
Gamazon E R, Wheeler H E, Shah K P, Mozaffari S V, Aquino-Michaels K, Carroll R J, Eyler A E, Denny J C, Nicolae D L, Cox N J,Im H K. 2015. A gene-based association method for mapping traits using reference transcriptome data. Nature Genetics, 47, 1091-1098.
Gheyas A A, Vallejo-Trujillo A, Kebede A, Lozano-Jaramillo M, Dessie T, Smith J,Hanotte O. 2021. Integrated Environmental and Genomic Analysis Reveals the Drivers of Local Adaptation in African Indigenous Chickens. Molcular Biology and Evolution, 38, 4268-4285.
Gusev A, Ko A, Shi H, Bhatia G, Chung W, Penninx B W, Jansen R, de Geus E J, Boomsma D I, Wright F A, Sullivan P F, Nikkola E, Alvarez M, Civelek M, Lusis A J, Lehtimäki T, Raitoharju E, Kähönen M, Seppälä I, Raitakari O T, Kuusisto J, Laakso M, Price A L, Pajukanta P,Pasaniuc B. 2016. Integrative approaches for large-scale transcriptome-wide association studies. Nature Genetics, 48, 245-252.
Gusev A, Mancuso N, Won H, Kousi M, Finucane H K, Reshef Y, Song L, Safi A, McCarroll S, Neale B M, Ophoff R A, O'Donovan M C, Crawford G E, Geschwind D H, Katsanis N, Sullivan P F, Pasaniuc B,Price A L. 2018. Transcriptome-wide association study of schizophrenia and chromatin activity yields mechanistic disease insights. Nature Genetics, 50, 538-548.
Hayes B J,Daetwyler H D. 2019. 1000 Bull Genomes Project to Map Simple and Complex Genetic Traits in Cattle: Applications and Outcomes. Annual Review of Animal Biosciences, 7, 89-102.
Higgins M G, Fitzsimons C, McClure M C, McKenna C, Conroy S, Kenny D A, McGee M, Waters S M,Morris D W. 2018. GWAS and eQTL analysis identifies a SNP associated with both residual feed intake and GFRA2 expression in beef cattle. Scientific Reports, 8, 14301.
Hiramoto K, Negishi M,Katoh H. 2006. Dock4 is regulated by RhoG and promotes Rac-dependent cell migration. Experimental Cell Research, 312, 4205-4216.
Hristov A C, Cope L, Di Cello F, Reyes M D, Singh M, Hillion J A, Belton A, Joseph B, Schuldenfrei A, Iacobuzio-Donahue C A, Maitra A,Resar L M. 2010. HMGA1 correlates with advanced tumor grade and decreased survival in pancreatic ductal adenocarcinoma. Modern Pathology, 23, 98-104.
Hu Y, Li M, Lu Q, Weng H, Wang J, Zekavat S M, Yu Z, Li B, Gu J, Muchnik S, Shi Y, Kunkle B W, Mukherjee S, Natarajan P, Naj A, Kuzma A, Zhao Y, Crane P K, Lu H,Zhao H. 2019. A statistical framework for cross-tissue transcriptome-wide association analysis. Nature Genetics, 51, 568-576.
J Joo J W, Sul J H, Han B, Ye C,Eskin E. 2014. Effectively identifying regulatory hotspots while capturing expression heterogeneity in gene expression studies. Genome Biology, 15, r61.
Jossin Y. 2020. Reelin Functions, Mechanisms of Action and Signaling Pathways During Brain Development and Maturation. Biomolecules, 10.
Kenny D, Murphy C P, Sleator R D, Judge M M, Evans R D,Berry D P. 2020. Animal-level factors associated with the achievement of desirable specifications in Irish beef carcasses graded using the EUROP classification system. Journal of Animal Science, 98, skaa191.
Kim D, Langmead B,Salzberg S L. 2015. HISAT: a fast spliced aligner with low memory requirements. Nature Methods, 12, 357-360.
Kim D, Shin H, Joung J-G, Lee S-Y,Kim J H. 2013. Intra-relation reconstruction from inter-relation: miRNA to gene expression. BMC Systems Biology, 7 Suppl 3, S8-S8.
Kim K S, Lee J J, Shin H Y, Choi B H, Lee C K, Kim J J, Cho B W,Kim T H. 2006. Association of melanocortin 4 receptor (MC4R) and high mobility group AT-hook 1 (HMGA1) polymorphisms with pig growth and fat deposition traits. Animal Genetics, 37, 419-421.
Kusuyama J, Komorizono A, Bandow K, Ohnishi T,Matsuguchi T. 2016. CXCL3 positively regulates adipogenic differentiation. Journal of Lipid Research, 57, 1806-1820.
Kwiatkowska A, Didier S, Fortin S, Chuang Y, White T, Berens M E, Rushing E, Eschbacher J, Tran N L, Chan A,Symons M. 2012. The small GTPase RhoG mediates glioblastoma cell invasion. Molecular Cancer, 11, 65.
LaValle C R, George K M, Sharlow E R, Lazo J S, Wipf P,Wang Q J. 2010. Protein kinase D as a potential new target for cancer therapy. Biochimica et Biophysica Acta, 1806, 183-192.
Lawrenson K, Li Q, Kar S, Seo J H, Tyrer J, Spindler T J, Lee J, Chen Y, Karst A, Drapkin R, Aben K K, Anton-Culver H, Antonenkova N, Baker H, Bandera E V, Bean Y, Beckmann M W, Berchuck A, Bisogna M, Bjorge L, Bogdanova N, Brinton L A, Brooks-Wilson A, Bruinsma F, Butzow R, Campbell I G, Carty K, Chang-Claude J, Chenevix-Trench G, Chen A, Chen Z, Cook L S, Cramer D W, Cunningham J M, Cybulski C, Dansonka-Mieszkowska A, Dennis J, Dicks E, Doherty J A, Dörk T, du Bois A, Dürst M, Eccles D, Easton D T, Edwards R P, Eilber U, Ekici A B, Fasching P A, Fridley B L, Gao Y T, Gentry-Maharaj A, Giles G G, Glasspool R, Goode E L, Goodman M T, Grownwald J, Harrington P, Harter P, Hasmad H N, Hein A, Heitz F, Hildebrandt M A, Hillemanns P, Hogdall E, Hogdall C, Hosono S, Iversen E S, Jakubowska A, James P, Jensen A, Ji B T, Karlan B Y, Kruger Kjaer S, Kelemen L E, Kellar M, Kelley J L, Kiemeney L A, Krakstad C, Kupryjanczyk J, Lambrechts D, Lambrechts S, Le N D, Lee A W, Lele S, Leminen A, Lester J, Levine D A, Liang D, Lissowska J, Lu K, Lubinski J, Lundvall L, Massuger L F, Matsuo K, McGuire V, McLaughlin J R, Nevanlinna H, McNeish I, Menon U, Modugno F, Moysich K B, Narod S A, Nedergaard L, Ness R B, Azmi M A, Odunsi K, Olson S H, Orlow I, Orsulic S, Weber R P, Pearce C L, Pejovic T, Pelttari L M, Permuth-Wey J, Phelan C M, Pike M C, Poole E M, Ramus S J, Risch H A, Rosen B, Rossing M A, Rothstein J H, Rudolph A, Runnebaum I B, Rzepecka I K, Salvesen H B, Schildkraut J M, Schwaab I, Sellers T A, Shu X O, Shvetsov Y B, Siddiqui N, Sieh W, Song H, Southey M C, Sucheston L, Tangen I L, Teo S H, Terry K L, Thompson P J, Timorek A, Tsai Y Y, Tworoger S S, van Altena A M, Van Nieuwenhuysen E, Vergote I, Vierkant R A, Wang-Gohrke S, Walsh C, Wentzensen N, Whittemore A S, Wicklund K G, Wilkens L R, Woo Y L, Wu X, Wu A H, Yang H, Zheng W, Ziogas A, Monteiro A, Pharoah P D, Gayther S A,Freedman M L. 2015. Cis-eQTL analysis and functional validation of candidate susceptibility genes for high-grade serous ovarian cancer. Nature Communications, 6, 8234.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G,Durbin R. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078-2079.
Li S, Czubryt M P, McAnally J, Bassel-Duby R, Richardson J A, Wiebel F F, Nordheim A,Olson E N. 2005. Requirement for serum response factor for skeletal muscle growth and maturation revealed by tissue-specific gene deletion in mice. Proceedings of the National Academy Sciences of the United States of America, 102, 1082-1087.
Li Y D, Bai X, Liu X, Wang W J, Li Z W, Wang N, Xiao F, Gao H H, Guo H S, Li H,Wang S Z. 2022. Integration of genome-wide association study and selection signatures reveals genetic determinants for skeletal muscle production traits in an F2 chicken population. Journal of Integrative Agriculture, 21, 2065-2075.
Liao Y, Smyth G K,Shi W. 2014. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30, 923-930.
Littlejohn M D, Tiplady K, Fink T A, Lehnert K, Lopdell T, Johnson T, Couldrey C, Keehan M, Sherlock R G, Harland C, Scott A, Snell R G, Davis S R,Spelman R J. 2016. Sequence-based Association Analysis Reveals an MGST1 eQTL with Pleiotropic Effects on Bovine Milk Composition. Scientific Reports, 6, 25376.
Liu S L, Gao Y H, Canela-Xandri O, Wang S, Yu Y, Cai W, Li B, Xiang R, Chamberlain A J, Pairo-Castineira E, D'Mellow K, Rawlik K, Xia C, Yao Y, Navarro P, Rocha D, Li X, Yan Z, Li C, Rosen B D, Van Tassell C P, Vanraden P M, Zhang S, Ma L, Cole J B, Liu G E, Tenesa A,Fang L. 2022. A multi-tissue atlas of regulatory variants in cattle. Nature Genetics, 54, 1438-1447.
Liu X, Wang L G, Liang J, Yan H, Zhao K B, Li N, Zhang L C,Wang L X. 2014. Genome-Wide Association Study for Certain Carcass Traits and Organ Weights in a Large White×Minzhu Intercross Porcine Population. Journal of Integrative Agriculture, 13, 2721-2730.
Liu X X, Zhang J J, Xiong X W, Chen C Y, Xing Y Y, Duan Y Y, Xiao S J, Yang B,Ma J W. 2021. An Integrative Analysis of Transcriptome and GWAS Data to Identify Potential Candidate Genes Influencing Meat Quality Traits in Pigs. Frontiers in Genetics, 12, 748070.
Liu Y, Liu X L, Zheng Z W, Ma T T, Liu Y, Long H, Cheng H J, Fang M, Gong J, Li X Y, Zhao S H,Xu X W. 2020. Genome-wide analysis of expression QTL (eQTL) and allele-specific expression (ASE) in pig muscle identifies candidate genes for meat quality traits. Genetics Selection Evolution, 52, 59.
Ma J W, Yang J, Zhou L S, Ren J, Liu X X, Zhang H, Yang B, Zhang Z Y, Ma H B, Xie X H, Xing Y Y, Guo Y M,Huang L S. 2014. A splice mutation in the PHKG1 gene causes high glycogen content and low meat quality in pig skeletal muscle. Plos Genetics, 10, e1004710.
Madsen L,Kristiansen K. 2010. The importance of dietary modulation of cAMP and insulin signaling in adipose tissue and the development of obesity. Annals of the New York Academy of Sciences, 1190, 1-14.
Mei C G, Wang H C, Liao Q J, Wang L Z, Cheng G, Wang H B, Zhao C P, Zhao S C, Song J Z, Guang X M, Liu G E, Li A N, Wu X L, Wang C Z, Fang X D, Zhao X, Smith S B, Yang W C, Tian W Q, Gui L S, Zhang Y Y, Hill R A, Jiang Z L, Xin Y P, Jia C L, Sun X Z, Wang S H, Yang H M, Wang J, Zhu W J,Zan L S. 2018. Genetic Architecture and Selection of Chinese Cattle Revealed by Whole Genome Resequencing. Molecular Biology and Evolution, 35, 688-699.
Melillo R M, Pierantoni G M, Scala S, Battista S, Fedele M, Stella A, De Biasio M C, Chiappetta G, Fidanza V, Condorelli G, Santoro M, Croce C M, Viglietto G,Fusco A. 2001. Critical role of the HMGI(Y) proteins in adipocytic cell growth and differentiation. Molecular and Cellular Biology, 21, 2485-2495.
Michaelson J J, Loguercio S,Beyer A. 2009. Detection and interpretation of expression quantitative trait loci (eQTL). Methods, 48, 265-276.
Mombaerts P. 2004. Genes and ligands for odorant, vomeronasal and taste receptors. Nature Reviews Neuroscience, 5, 263-278.
Muniz M M M, Simielli Fonseca L F, Scalez D C B, Vega A S, Silva D, Ferro J A, Chardulo A L, Baldi F, Cánovas A,de Albuquerque L G. 2022. Characterization of novel lncRNA muscle expression profiles associated with meat quality in beef cattle. Evolutionary Applications, 15, 706-718.
Oh I H,Reddy E P. 1999. The myb gene family in cell growth, differentiation and apoptosis. Oncogene, 18, 3017-3033.
Oster H, Abraham D,Leitges M. 2006. Expression of the protein kinase D (PKD) family during mouse embryogenesis. Gene Expression Patterns, 6, 400-408.
Ozato K, Shin D M, Chang T H,Morse H C, 3rd. 2008. TRIM family proteins and their emerging roles in innate immunity. Nature Reviews Immunology, 8, 849-860.
Pertea M, Pertea G M, Antonescu C M, Chang T C, Mendell J T,Salzberg S L. 2015. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature biotechnological, 33, 290-295.
Pompura S L,Dominguez-Villar M. 2018. The PI3K/AKT signaling pathway in regulatory T-cell development, stability, and function. Journal of Leukocyte Biology, 103, 1065-1076.
Puig-Oliveras A, Revilla M, Castelló A, Fernández A I, Folch J M,Ballester M. 2016. Expression-based GWAS identifies variants, gene interactions and key regulators affecting intramuscular fatty acid content and composition in porcine meat. Scientific Reports, 6, 31803.
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira M A, Bender D, Maller J, Sklar P, de Bakker P I, Daly M J,Sham P C. 2007. PLINK: a tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics, 81, 559-575.
Purfield D C, Evans R D,Berry D P. 2019. Reaffirmation of known major genes and the identification of novel candidate genes associated with carcass-related metrics based on whole genome sequence within a large multi-breed cattle population. BMC Genomics, 20, 720.
Qiu T T, Qi X F, Cen J N,Chen Z X. 2012. Rap1GAP alters leukemia cell differentiation, apoptosis and invasion in vitro. Oncology Reports, 28, 622-628.
Rafter P, Gormley I C, Purfield D, Parnell A C, Naderi S,Berry D P. 2021. Genome-wide association analyses of carcass traits using copy number variants and raw intensity values of single nucleotide polymorphisms in cattle. BMC Genomics, 22, 757.
Rogne M,Taskén K. 2014. Compartmentalization of cAMP Signaling in Adipogenesis, Lipogenesis, and Lipolysis. Hormone and Metabolic Research, 46.
Shabalin A A. 2012. Matrix eQTL: ultra fast eQTL analysis via large matrix operations. Bioinformatics, 28, 1353-1358.
Signer-Hasler H, Flury C, Haase B, Burger D, Simianer H, Leeb T,Rieder S. 2012. A genome-wide association study reveals loci influencing height and other conformation traits in horses. Plos One, 7, e37282.
Spehr J, Gelis L, Osterloh M, Oberland S, Hatt H, Spehr M,Neuhaus E M. 2011. G Protein-coupled Receptor Signaling via Src Kinase Induces Endogenous Human Transient Receptor Potential Vanilloid Type 6 (TRPV6) Channel Activation*. Journal of Biological Chemistry, 286, 13184-13192.
Spencer J A,Misra R P. 1999. Expression of the SRF gene occurs through a Ras/Sp/SRF-mediated-mechanism in response to serum growth signals. Oncogene, 18, 7319-7327.
Stegle O, Parts L, Piipari M, Winn J,Durbin R. 2012. Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses. Nature protocols, 7, 500-507.
Sugiyama Y, Suzuki A, Kishikawa M, Akutsu R, Hirose T, Waye M M, Tsui S K, Yoshida S,Ohno S. 2000. Muscle develops a specific form of small heat shock protein complex composed of MKBP/HSPB2 and HSPB3 during myogenic differentiation. The Journal of Biological Chemistry, 275, 1095-1104.
Sun D M, Yin Y Y, Guo C Z, Liu L X, Mao S Y, Zhu W Y,Liu J H. 2021. Transcriptomic analysis reveals the molecular mechanisms of rumen wall morphological and functional development induced by different solid diet introduction in a lamb model. Journal of Animal Science and Biotechnology, 12, 33.
Sutter N B, Bustamante C D, Chase K, Gray M M, Zhao K, Zhu L, Padhukasahasram B, Karlins E, Davis S, Jones P G, Quignon P, Johnson G S, Parker H G, Fretwell N, Mosher D S, Lawler D F, Satyaraj E, Nordborg M, Lark K G, Wayne R K,Ostrander E A. 2007. A single IGF1 allele is a major determinant of small size in dogs. Science, 316, 112-115.
Tao H, Aakula S, Abumrad N N,Hajri T. 2010. Peroxisome proliferator-activated receptor-gamma regulates the expression and function of very-low-density lipoprotein receptor. American Journal of Physiology Endocrinology and Metabolism, 298, E68-79.
Teng J Y, Gao Y H, Yin H W, Bai Z H, Liu S L, Zeng H N, Bai L J, Cai Z X, Zhao B R, Li X J, Xu Z T, Lin Q, Pan Z Y, Yang W J, Yu X S, Guan D L, Hou Y L, Keel B N, Rohrer G A, Lindholm-Perry A K, Oliver W T, Ballester M, Crespo-Piazuelo D, Quintanilla R, Canela-Xandri O, Rawlik K, Xia C, Yao Y L, Zhao Q Y, Yao W Y, Yang L, Li H C, Zhang H C, Liao W, Chen T S, Karlskov-Mortensen P, Fredholm M, Amills M, Clop A, Giuffra E, Wu J, Cai X D, Diao S Q, Pan X C, Wei C, Li J H, Cheng H, Wang S, Su G S, Sahana G, Lund M S, Dekkers J C M, Kramer L, Tuggle C K, Corbett R, Groenen M A M, Madsen O, Gòdia M, Rocha D, Charles M, Li C J, Pausch H, Hu X X, Frantz L, Luo Y L, Lin L, Zhou Z Y, Zhang Z, Chen Z T, Cui L L, Xiang R D, Shen X, Li P, Huang R H, Tang G Q, Li M Z, Zhao Y X, Yi G Q, Tang Z L, Jiang J C, Zhao F P, Yuan X L, Liu X H, Chen Y S, Xu X W, Zhao S H, Zhao P J, Haley C, Zhou H J, Wang Q S, Pan Y C, Ding X D, Ma L, Li J Q, Navarro P, Zhang Q, Li B J, Tenesa A, Li K, Liu G E, Zhang Z,Fang L Z. 2022. A compendium of genetic regulatory effects across pig tissues. bioRxiv.
Türkmen S, Hoffmann K, Demirhan O, Aruoba D, Humphrey N,Mundlos S. 2008. Cerebellar hypoplasia, with quadrupedal locomotion, caused by mutations in the very low-density lipoprotein receptor gene. European Journal of Human Genetics, 16, 1070-1074.
Vaittinen M, Kaminska D, Käkelä P, Eskelinen M, Kolehmainen M, Pihlajamäki J, Uusitupa M,Pulkkinen L. 2013. Down-regulation of calcineurin-like phosphoesterase domain containing 1 (CPPED1) expression improves glucose metabolism in vitro in adipocytes. Diabetes, 62.
van den Berg I, Hayes B J, Chamberlain A J,Goddard M E. 2019. Overlap between eQTL and QTL associated with production traits and fertility in dairy cattle. BMC Genomics, 20, 291.
Vásquez-Trincado C, Dunn J, Han J I, Hymms B, Tamaroff J, Patel M, Nguyen S, Dedio A, Wade K, Enigwe C, Nichtova Z, Lynch D R, Csordas G, McCormack S E,Seifert E L. 2022. Frataxin deficiency lowers lean mass and triggers the integrated stress response in skeletal muscle. JCI Insight, 7.
Wang L G, Zhang L C, Yan H, Liu X, Li N, Liang J, Pu L, Zhang Y B, Shi H B, Zhao K B,Wang L X. 2014. Genome-wide association studies identify the loci for 5 exterior traits in a Large White × Minzhu pig population. Plos One, 9, e103766.
Wang T Z, Niu Q H, Zhang T L, Zheng X, Li H, Gao X, Chen Y, Gao H, Zhang L, Liu G E, Li J,Xu L. 2022. Cis-eQTL Analysis and Functional Validation of Candidate Genes for Carcass Yield Traits in Beef Cattle. International Journal of Molecular Sciences, 23.
Wang Y N, Zhang F, Mukiibi R, Chen L H, Vinsky M, Plastow G, Basarab J, Stothard P,Li C. 2020. Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: II: carcass merit traits. BMC Genomics, 21, 38.
Ward C J, Hogan M C, Rossetti S, Walker D, Sneddon T, Wang X, Kubly V, Cunningham J M, Bacallao R, Ishibashi M, Milliner D S, Torres V E,Harris P C. 2002. The gene mutated in autosomal recessive polycystic kidney disease encodes a large, receptor-like protein. Nature Genetics, 30, 259-269.
Wen X Q, Lee Y J, Luca F,Pique-Regi R. 2016. Efficient Integrative Multi-SNP Association Analysis via Deterministic Approximation of Posteriors. The American Journal of Human Genetics, 98, 1114-1129.
Wu P X, Zhou J, Wang K, Chen D J, Yang X D, Liu Y H, Jiang A A, Shen L Y, Jin L, Xiao W H, Jiang Y Z, Li M Z, Zhu L, Zeng Y S, Xu X, Qiu X T, Li X W,Tang G Q. 2021. Identifying SNPs associated with birth weight and days to 100 kg traits in Yorkshire pigs based on genotyping-by-sequencing. Journal of Integrative Agriculture, 20, 2483-2490.
Xia W, Zhu X W, Mo X B, Wu L F, Wu J, Guo Y F, Zeng K Q, Wang M J, Lin X, Qiu Y H, Wang L, He P, Xie F F, Bing P F, Lu X, Liu Y Z, Yi N J, Deng F Y,Lei S F. 2017. Integrative multi-omics analysis revealed SNP-lncRNA-mRNA (SLM) networks in human peripheral blood mononuclear cells. Human Genetics, 136, 451-462.
Yang J, Lee S H, Goddard M E,Visscher P M. 2011. GCTA: a tool for genome-wide complex trait analysis. The American Journal of Human Genetics, 88, 76-82.
Yang J, Zaitlen N A, Goddard M E, Visscher P M,Price A L. 2014. Advantages and pitfalls in the application of mixed-model association methods. Nature Genetics, 46, 100-106.
Yang Y, Mishra V K, Chen M, Duffee E, Dimmitt R,Harmon C M. 2013. Molecular characterization of human melanocortin-5 receptor ligand-receptor interaction. Biochemistry, 52, 1737-1745.
Yu G, Wang L G, Han Y,He Q Y. 2012. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS, 16, 284-287.
Yu J N, Wang G X, Chen Z Y, Wan L, Zhou J, Cai J Y, Liu X,Wang Y. 2022. Deficit of PKHD1L1 in the dentate gyrus increases seizure susceptibility in mice. Human Molecular Genetics.
Zhang H M, Xia H L, Jiang H R, Mao Y J, Qu K X, Huang B Z, Gong Y C,Yang Z P. 2018. Longissimus dorsi muscle transcriptomic analysis of Yunling and Chinese simmental cattle differing in intramuscular fat content and fatty acid composition. Genome, 61, 549-558.
Zhang W, Xu L, Gao H J, Wu Y, Gao X, Zhang L P, Zhu B, Song Y X, Bao J, Li J Y,Chen Y. 2016. Detection of candidate genes for growth and carcass traits using genome-wide association strategy in Chinese Simmental beef cattle. Animal Production Science, 58.
Zhang Z, Bae Y E, Bradley J R, Wu L,Wu C. 2022. SUMMIT: An integrative approach for better transcriptomic data imputation improves causal gene identification. Nature Communications, 13, 6336.
Zhang Z, Chen Z T, Diao S Q, Ye S P, Wang J Y, Gao N, Yuan X L, Chen Z M, Zhang H,Li J Q. 2021. Identifying the complex genetic architecture of growth and fatness traits in a Duroc pig population. Journal of Integrative Agriculture, 20, 1607-1614.
Zhuo D X, Zhang X W, Jin B, Zhang Z, Xie B S, Wu C L, Gong K,Mao Z B. 2013. CSTP1, a novel protein phosphatase, blocks cell cycle, promotes cell apoptosis, and suppresses tumor growth of bladder cancer by directly dephosphorylating Akt at Ser473 site. Plos One, 8, e65679.
|