References and Citations:

Papers and Abstracts on Making the QTLdb:

  1. Zhi-Liang Hu and Max Rothschild (2003). "A Frame-Work for Developing the Pig QTL Database". [The 13th North American Colloquium on Animal Cytogenetics & Gene Mapping. Louisville, Kentucky, July 13-17, 2003.] Cytogenet Genome Res 102:357.
  2. Zhi-Liang Hu, James Reecy and Max Rothschild (2005). "A Quantitative Trait Loci Resource and Comparison Tool for Pigs: PigQTLDB". Iowa State "Animal Industry 2005 Report".
  3. Zhi-Liang Hu, Svetlana Dracheva, Wonhee Jang, Donna Maglott, John Bastiaansen, Max F. Rothschild and James M. Reecy (2005). "PigQTLdb: A Pig QTL Database". Plant & Animal Genome XIV Conference, San Diego, CA, January 15-19, 2005.
  4. Zhi-Liang Hu, Svetlana Dracheva, Wonhee Jang, Donna Maglott, John Bastiaansen, Max F. Rothschild and James M. Reecy (2005). "A QTL Resource and Comparison Tool for Pigs: PigQTLDB". Mammalian Genome. (2005) Volume 16(10):792-800.
  5. Zhi-Liang Hu, Sean Humphray, Carol Scott, Stacey N. Meyers, Jane Rogers, Max F. Rothschild and James M. Reecy (2006). "Extension of PigQTLdb: Genome-wide Alignment of BAC FPC Maps and RH Maps for QTL Positional Gene Mining". Plant & Animal Genome XIV Conference, San Diego, CA, January 14-18, 2006.
  6. Zhi-Liang Hu, Eric Ryan Fritz and James M. Reecy (2007). AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond. Nucleic Acids Research, 2007, 35 (Database issue):D604-D609; doi:10.1093/nar/gkl946.
  7. Zhi-Liang Hu, Eric Ryan Fritz and James M. Reecy (2007). "Computer Demo: A Public Platform for QTL Comparisons and Integration with Diverse Types of Structural Genomic Information". Plant & Animal Genome XV Conference, San Diego, CA, January 13-17, 2007.
  8. Zhi-Liang Hu and James M. Reecy (2007). Animal QTLdb: Beyond a Repository - A Public Platform for QTL Comparisons and Integration with Diverse Types of Structural Genomic Information. Mammalian Genome, Volume 18, 1-4 (2007).
  9. Zhi-Liang Hu and James M. Reecy (2008). Extension Of Animal QTLdb (II): Alignment Of New Microsatellite Markers, SNPs And Microarray Elements To Cattle, Chicken And Pig QTL Maps And Comparative Mapping Tools For Positional Genome Information Mining. January 12-16, 2008, Town & Country Convention Center, San Diego, CA.
  10. Zhi-Liang Hu, Eric Ryan Fritz, Svetlana Dracheva, Behnam Abasht, Stacey N. Meyers, Denis M. Larkin John Bastiaansen, Carol Scott, Xiao-Ping Li, Wonhee Jang, Kwan-Suk Kim, Donna Maglott, Sean Humphray, Jonathan E. Beever, Susan J. Lamont, Harris A. Lewin, Shu-hong Zhao, Jane Rogers, Jill Maddox, Max F. Rothschild and James M. Reecy (2008). Animal QTLdb: A Tool Set to Warehouse and Compare Cattle, Pigs, Chicken and Sheep QTL Within and Between Species. International Society for Animal Genetics (ISAG), RAI Conference Centre, Amsterdam,The Netherlands. July 20-24, 2008.
  11. Zhi-Liang Hu, Cari Park, Eric Fritz, Mindy Dwindell, Mary Shimoyama, James M. Reecy (2009). Expanding the Utility of Animal QTLdb. Plant & Animal Genomes XVII Conference, January 10-14, 2009, Town & Country Convention Center, San Diego, CA.

Other publications that have cited our work:

  1. Fadiel, A., I. Anidi, and K.D. Eichenbaum (2005). Farm animal genomics and informatics: an update. Nucleic Acids Res. 2005; 33(19): 6308-6318.
  2. Demeure, O., D. Pomp, D. Milan, M. F. Rothschild and C. K. Tuggle. (2005). Mapping of 443 porcine EST improves the comparative maps for SSC1 and SSC7 with the human genome. Animal Genetics, 36: 381.
  3. K F Chen, C Knorr, K Bornemann-Kolatzki, J Ren, LS Huang, G A Rohrer, and B Brenig. (2005) Targeted oligonucleotide-mediated microsatellite identification (TOMMI) from large-insert library clones. BMC Genetics 2005, 6:54
  4. H. W. Raadsma A, B and I. Tammen (2005) Biotechnologies and their potential impact on animal breeding and production: a review. Animal Production Science, continuing Australian Journal of Experimental Agriculture, 45(8), 1021-1032
  5. Nonneman, D., T. P. L. Smith, B. A. Freking and G. A. Rohrer. (2005). Assignment of 12 genes to porcine chromosome 1 by linkage and radiation hybrid mapping. Animal Genetics, 36: 532.
  6. Alistair G. Reid and Susan M. Gribble (2005). SmartCapture and the frontiers of FISH technology. Chromosome Research. Vol. 13(8), 835-838
  7. W-S Liu, K. Eyer, H. Yasue, B. Roelofs, H. Hiraiwa, T Shimogiri, E. Landrito, and C. W. Beattie. (2005). A high-resolution radiation hybrid map for swine. J. Anim. Sci. Vol. 83, Suppl. 1/J. Dairy Sci. Vol. 88, Suppl. 1
  8. J. Estelle, A. Mercade, J.L. Noguera, M. Perez-Enciso, C. Ovilo, A. Sanchez and J.M. Folch (2005) Effect of the porcine IGF2-intron3-G3072A substitution in an outbred Large White population and in an Iberian x Landrace cross J. Anim. Sci. 2005. 83:2723-2728
  9. Martien A. M. Groenen (2005). Imprinted QTL in farm animals: a fortuity or a common phenomenon?. In: Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics, John Wiley & Sons, Ltd., Article Online Posting Date: November 15, 2005.
  10. Wimmers, K., I. Fiedler, T. Hardge, E. Murani, K. Schellander and S. Ponsuksili (2006). QTL for microstructural and biophysical muscle properties and body composition in pigs." BMC Genetics 7:15.
  11. Polineni P, Aragonda P, Xavier SR, Furuta R, Adelson DL (2006) The bovine QTL viewer: a web accessible database of bovine Quantitative Trait Loci. BMC Bioinformatics 2006, 7:283 (5 June 2006)
  12. T. Shimogiri, S. Kiuchi, H. Hiraiwa, T. Hayashi, Y. Takano, Y. Maeda and H. Yasue (2006) Assignment of 117 genes from HSA5 to the porcine IMpRH map and generation of a dense human-pig comparative map. Animal Genetics, 37(5):503.
  13. A. Tomas J. Casellas, O. Ramirez, G. Munoz J. L. Noguera, and A. Sanchez (2006) High amino acid variation in the intracellular domain of the pig prolactin receptor (PRLR) and its relation to ovulation rate and piglet survival traits J. Anim. Sci. 2006. 84:1991-1998
  14. A. Tomas, J. Casellas O. Ramirez, M. Perez-Enciso, M, C. Rodrigoez, J. L. Noguera and A. Sanchez (2006) Polymorphisms of the porcine dopamine?-hydroxylase gene and their relation to reproduction and piglet survivability in an Iberian-Meishan F2 intercross. Animal Genetics 37: 279
  15. K WIMMERS, N T NGU, E MURANI, K SCHELLANDER and S PONSUKSIL (2006) Linkage and expression analysis to elucidate the genetic background of muscle structure and meat quality in the pig Arch. Tierz., Dummerstorf (Archives Animal Breeding) 49 Special Issue, pp. 116-125.
  16. Zhu, Zhengmao; Li, Yong; Mo, Delin; Li, Kui; Zhao, Shuhong (2006). Molecular characterization and expression analysis of the porcine caveolin-3 gene. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 346 (1): 7-13 JUL 21 2006
  17. Chen, KF; Knorr, ; Bornemann-Kolatzki, ; Huang, LS; Rohrer, G; Brenig, B. (2006). Characterization of the PGK2 Associated Microsatellite S0719 on SSC7 Suitable for Parentage and QTL Diagnosis Animal Biotechnology, 17(1): 43-49
  18. Lin, C-L, D.G.J. Jennen, S. Ponsuksili, E. Tholen, D. Tesfaye, K. Schellander & K. Wimmers. (2006). Haplotype analysis of beta-actin gene for its association with sperm quality and boar fertility. J. Animal Breeding and Genetics. 123(6): 384
  19. Cepica, S., M. Masopust, A. Knoll, H. Bartenschlager, M. Yerle, G. A. Rohrer, H. Geldermann (2006) Linkage and RH mapping of 10 genes to a QTL region for fatness and muscling traits on pig chromosome X Animal Genetics. 37(6): 603
  20. Peng, Y. B., M. Yerle, B. Liu (2006) Mapping of nine porcine interferon regulatory factor genes Animal Genetics. Vol. 37 Issue 6 Page 600
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  23. G. Ottoa, R. Roehea, b, H. Looftc, L. Thoelkingc, P.W. Knapc, M.F. Rothschild, G.S. Plastowe and E. Kalm (2006). Associations of DNA markers with meat quality traits in pigs with emphasis on drip loss. Meat Science, 75(2):185-195.
  24. Murá E, Muráová, Ponsuksili S, Schellander K, Wimmers K (2006). Molecular characterization and evidencing of the porcine CRH gene as a functional-positional candidate for growth and body composition. Biochemical and Biophysical Research Communications, Volume 342, Issue 2, pp394-405.
  25. K-T Leea, E-W Parka, S Moonc, H-S Parka, H-Y Kima, G-W Janga, B-H Choia, H.Y. Chunga, J-W Leea, I-C Cheonga, S-J Oha, H Kimc, D-S Suhb and T-H Kim (2006) Genomic sequence analysis of a potential QTL region for fat trait on pig chromosome 6. Genomics, 87(2): 218-224.
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  28. Banghua Shang and Linsheng Lian (2006) Application progress of microsatellite marker on genetics and breeding in pig. Modern Journal of Animal Husbandry and Veterinary Medicine, 2006 No.12 P.67-70
  29. Arch. Tierz., Dummerstorf Eduard MurÁi, Siriluck Ponsuksili, Karl Schellander and Klaus Wimmers (2006). Identification and characterization of an AFLP marker associated with carcass composition in the pig. Arch. Tierz., Dummerstorf, 49 (2006) 4, 413-414
  30. Max F. Rothschild, Zhi-Liang Hu & Zhihua Jiang (2007) Advances in QTL Mapping in Pigs. Int. J. Biol. Sci. 2007; 3:192-197.
  31. Kefei Chen, Tara Baxter, William M. Muir, Martien A. Groenen, Lawrence B. Schook (2007) Genetic Resources, Genome Mapping and Evolutionary Genomics of the Pig (Sus scrofa). Int. J. Biol. Sci. 2007; 3(3):153-165.
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  36. D. B. Edwards, C. W. Ernst, R. J. Tempelman, G. J. M. Rosa, N. E. Raney, M. D. Hoge and R. O. Bates (2007) QTL mapping in an F2 Duroc x Pietrain resource population: I. Growth traits. J. Anim Sci. 2008. 86:241-253.
  37. Micha Ron, Galit Israeli, Eyal Seroussi, Joel I Weller, Jeffrey P Gregg, Moshe Shani, and Juan F Medrano (2007). Combining mouse mammary gland gene expression and comparative mapping for the identification of candidate genes for QTL of milk production traits in cattle. BMC Genomics. 8: 183.
  38. D. W. Burt (2007). Emergence of the Chicken as a Model Organism: Implications for Agriculture and Biology. Poult Sci 2007. 86:1460-1471.
  39. S Ponsuksili, E Murani, C Walz, M Schwerin and K Wimmers (2007). Pre- and postnatal hepatic gene expression profiles of two pig breeds differing in body composition: insight into pathways of metabolic regulation. Physiol. Genomics 29: 267-279.
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  42. Alexander, L.J.; MacNeil, M.D.; Geary, T.W.; Snelling, W.M.; Rule, D.C.; Scanga, J.A (2007). Quantitative trait loci with additive effects on palatability and fatty acid composition of meat in a Wagyu-Limousin F2 population. Animal Genetics, Volume 38, Number 5, pp.506-513(8).
  43. Yu Gao, Ran Zhang, Xiaoxiang Hu and Ning Li (2007). Application of genomic technologies to the improvement of meat quality of farm animals. Meat Science Volume 77, Issue 1, September 2007, pp.36-45.
  44. E.C. Jorge, A. Figueira, M.C. Ledur, A.S.A.M.T. Moura and L.L. Coutinho (2007). Contributions and perspectives of chicken genomics in Brazil: from biological model to export commodity. World's Poultry Science Journal, 63:597-610
  45. Kirsty Jensen, Isabel K.F. de Miranda Santos and Elizabeth J. Glass (2007). Using genomic approaches to unravel livestock(host)-tick pathogen interactions. Trends in Parasitology. Volume 23, Issue 9, September 2007, Pages 439-444.
  46. Craig R.G. Lewis, Tahar Ait-Ali, Mary Clapperton, Alan L. Archibald, Stephen Bishop (2007). Genetic Perspectives on Host Responses to Porcine Reproductive and Respiratory Syndrome (PRRS). Viral Immunology. September 2007, 20(3): 343-358.
  47. P. Karlskov-Mortensen, Z.-L. Hu, J. Gorodkin, J. M. Reecy and M. Fredholm (2007) Identification of 10 882 porcine microsatellite sequences and virtual mapping of 4528 of these sequences. Animal Genetics, Volume 38 Issue 4, pp401-405.
  48. E. M. Sellner, J. W. Kim, M. C. McClure, K. H. Taylor, R. D. Schnabel and J. F. Taylor (2007) BOARD-INVITED REVIEW: Applications of genomic information in livestock. J. Anim Sci. 2007. 85:3148-3158.
  49. Izabela Szczerbal, Li Lin, Monika Stachowiak, Agata Chmurzynska, Mariusz Mackowski, Andreas Winter, Krzysztof Flisikowski, Ruedi Fries, Marek Switonski (2007). Cytogenetic mapping of DGAT1, PPARA, ADIPOR1 and CREB genes in the pig. J Appl Genet 48(1), 2007, pp. 73-76
  50. Stephanie D McKay, Robert D Schnabel, Brenda M Murdoch, Lakshmi K Matukumalli, Jan Aerts, Wouter Coppieters, Denny Crews, Emmanuel Dias Neto, Clare A Gill, Chuan Gao, Hideyuki Mannen, Paul Stothard, Zhiquan Wang, Curt P Van Tassell, John L Williams, Jeremy F Taylor, and Stephen S Moore (2007). Whole genome linkage disequilibrium maps in cattle. BMC Genetics, 2007; 8: 74
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  53. GONG Yuan-Fang, LU Xin, WANG Zhi-Peng, LI Shan, QIU Xiao-Tian, ZHANG Qin (2008). Detection of quantitative trait loci affecting haematological traits on swine chromosomes 2, 7 and 8. Prog. Biochem. Biophys., 35(11):1291-1297.
  54. Xiaoping Li, Zhi-Liang Hu, S-J. Moon, K-T Do, Y-K Ha, H. Kim, M. J. Byun, B-H Choi, M. F. Rothschild, J. M. Reecy and K-S. Kim (2007). Development and characterization of an in silico Coding Gene SNP map in pigs. Animal Genetics, 39(4): 446 - 450.
  55. Huirong Mao, Yuanmei Guo, Guangcheng Yang, Bin Yang, Jun Ren, Sanfeng Liu, Huashui Ai, Junwu Ma, Bertram Brenig, and Lusheng Huang (2008). A genome-wide scan for quantitative trait loci affecting limb bone lengths and areal bone mineral density of the distal femur in a White Duroc ×Erhualian F2 population. BMC Genet. 9:63.
  56. W.-S. Liu, H. Yasue, K. Eyer, H. Hiraiwa, T. Shimogiri, B. Roelofs, E. Landrito, J. Ekstrand, M. Treat, N. Paes, M. Lemos, A.C. Griffith, M.L. Davis, S.N. Meyers, M. Yerle, D. Milan, J.E. Beever, L.B. Schook, C.W. Beattie (2008) High-resolution comprehensive radiation hybrid maps of the porcine chromosomes 2p and 9p compared with the human chromosome 11. Cytogenet Genome Res ;120:157-163.
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  60. Qinghua Nie, Meixia Fang, Liang Xie, Min Zhou, Zhangmin Liang, Ziping Luo, Guohuang Wang, Wensen Bi, Canjian Liang, Wei Zhang, and Xiquan Zhang (2008) The PIT1 gene polymorphisms were associated with chicken growth traits. BMC Genet. 2008; 9: 20. doi: 10.1186/1471-2156-9-20.
  61. E. Lipkin1, R. Tal-Stein, A. Friedmann and M. Soller (2008). Effect of Quantitative Trait Loci for Milk Protein Percentage on Milk Protein Yield and Milk Yield in Israeli Holstein Dairy Cattle. J. Dairy Sci. 2008. 91:1614-1627. doi:10.3168/jds.2007-0655.
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(Compiled by Zhiliang Hu)

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