Animal QTLdb Legacy Data Archive

Legacy Data The livestock genome analysis research have been evolving rapidly. As a result the utility of the traditional linkage-map-based QTL analysis methods/data used since mid-1990s is diminishing as sequence-based genome maps and SNP-based analysis are taking the stage. A total of 13,309 such data curated into the Animal QTLdb during 1999 and 2021 have been deposited into the Github.
GZIP Compressed file that contains 3,782 curated QTL mapped to Cattle Linkage Map (Reference: Kappes S M, Keele J W, Stone R T, McGraw R A, Sonstegard T S, Smith T P, Lopez-Corrales N L, Beattie C W, (1997). A second-generation linkage map of the bovine genome. Genome Research, 7 (3): 235-49.DOI: 10.1101/gr.7.3.235).
GZIP Compressed file that contains 2,701 curated QTL mapped to Chicken Linkage Map (Reference: Groenen Martien A M, Wahlberg Per, Foglio Mario, Cheng Hans H, Megens Hendrik-Jan, Crooijmans Richard P M A, Besnier Francois, Lathrop Mark, Muir William M, Wong Gane Ka-Shu, Gut Ivo, Andersson Leif, (2009). A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate. Genome Research, 19 (3): 510-9.DOI: 10.1101/gr.086538.108).
GZIP Compressed file that contains 31 curated QTL mapped to Horse Linkage Map (Reference: Penedo M C T, Millon L V, Bernoco D, Bailey E, Binns M, Cholewinski G, Ellis N, Flynn J, Gralak B, Guthrie A, Hasegawa T, Lindgren G, Lyons L A, Røed K H, Swinburne J E, Tozaki T, (2005). International Equine Gene Mapping Workshop Report: a comprehensive linkage map constructed with data from new markers and by merging four mapping resources. Cytogenetic and genome research, 111: 5-15.DOI: 10.1159/000085664).
GZIP Compressed file that contains 6,099 curated QTL mapped to Pig Linkage Map (Reference: Rohrer G A, Alexander L J, Hu Z-L, Smith T P, Keele J W, Beattie C W (1996). A comprehensive map of the porcine genome. Genome Research, 6 (5): 371-91.DOI: 10.1101/gr.6.5.371).
GZIP Compressed file that contains 592 curated QTL mapped to Sheep Linkage Map (Reference: Maddox J F, Davies K P, Crawford A M, Hulme D J, Vaiman D, Cribiu E P, Freking B A, Beh K J, Cockett N E, Kang N, Riffkin C D, Drinkwater R, Moore S S, Dodds K G, Lumsden J M, van Stijn T C, Phua S H, Adelson D L, Burkin H R, Broom J E, Buitkamp J, Cambridge L, Cushwa W T, Gerard E, Galloway S M, Harrison B, Hawken R J, Hiendleder S, Henry H M, Medrano J F, Paterson K A, Schibler L, Stone R T, van Hest B, (2001). An enhanced linkage map of the sheep genome comprising more than 1000 loci. Genome Research, 11 (7): 1275-89.DOI: 10.1101/
Rainbow trout
GZIP Compressed file that contains 104 curated QTL mapped to Rainbow trout Linkage Map (Reference: Palti Yniv, Genet Carine, Gao Guangtu, Hu Yuqin, You Frank M, Boussaha Mekki, Rexroad Caird E, Luo Ming-Cheng, (2012). A second generation integrated map of the rainbow trout (Oncorhynchus mykiss) genome: analysis of conserved synteny with model fish genomes. Marine biotechnology (New York, N.Y.), 14 (3): 343-57.DOI: 10.1007/s10126-011-9418-z).
The legacy data are deposited on GitHub
A note about phasing out the linkage-map based QTL data on QTLdb


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