Linkage Maps Used Supporting QTL Data Curations

CHIR1.1	Goat linkage map [Capra hircus; Breed=Yunnan black].
	Taxonomy ID=9925
Goat linkage map was produced with Carthagene on SNP genotype data on 94 RH clones from 5000 rads goat-hamster RH panel. . Available from .
Reference 2 Du Xiaoyong, Servin Bertrand, Womack James E, Cao Jianhua, Yu Mei, Dong Yang, Wang Wen, Zhao Shuhong, (2015). An update of the goat genome assembly using dense radiation hybrid maps allows detailed analysis of evolutionary rearrangements in Bovidae. BMC genomics, 15: 625.

MARC_cattle { Reference }	Cattle linkage map [Bos taurus; Breed=Gelbvieh, Simmental, Piedmontese, Longhorn, Nellore, Hereford, Angus].
	Taxonomy ID=9913
A 2990-cM bovine linkage map constructed with 1236 polymorphic DNA markers and 14 erythrocyte antigens. The map contains 627 new markers and 623 previously linked markers, providing a basis for integrating the four published bovine maps. . Available from MARC.
Reference 2 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.

MARC_pig { Reference }	Pig linkage map [Sus scrofa; Breed=Meishan, Minzhu, Duroc, White Chester].
	Taxonomy ID=9823
A high density comprehensive linkage map for pigs produced to date (1995) by Gary Rohrer et genotyping across a single reference population to yield 1042 linked loci in a scross breed family between Meishan, Minzhu, Duroc, and 4 American breeds including White Chester. The physical and genetic maps were integrated with 123 informative loci assigned previously by fluorescence in situ hybridization {FISH). Fourteen linkage groups span the entire length of each chromosome.. Available from MARC.
Reference 2 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.

NCCCWA { Reference }	Rainbow trout linkage map [Oncorhynchus mykiss; Breed=n/a].
	Taxonomy ID=8022
The current version of the physical map is composed of 167,989 clones of which 158,670 are assembled into contigs and 9,319 are singletons. The overall number of unique regions of conserved synteny identified through grouping of the rainbow trout BES into fingerprinting contigs was 2,259, 2,229, and 2,203 for stickleback, medaka, and zebrafish, respectively.. Available from NCCCWA.
Reference 2 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.

NIAIMap	Pig linkage map [Sus scrofa; Breed=G�ttingen miniature, Meishan].
	Taxonomy ID=9823
A Japaanese pig map using a boar of Göttingen miniature pig and two sows of Meishan pig as parents. In the construction of the family, two F1 males and 18 F1 females were intercrossed to generate 143 F2 offspring. The linkage maps of all the chromosomes except for chromosome 1 were found to be longer in females than in males. Concerning chromosome 1, the length of the linkage map showed no difference between females and males, which was attributed to low recombination rates between markers localized in the centromeric region in females. The average ratio of female-to-male recombination was calculated to be 1.55.. Available from ARKDB.
Reference 2 Mikawa S, Akita T, Hisamatsu N, Inage Y, Ito Y, Kobayashi E, Kusumoto H, Matsumoto T, Mikami H, Minezawa M, Miyake M, S et al. (1999). A linkage map of 243 DNA markers in an intercross of Göttingen miniature and Meishan pigs. Animal genetics, 30 (6): 407-17.

NordicMap	Pig linkage map [Sus scrofa; Breed=European Wild Boar and Large White].
	Taxonomy ID=9823
A comprehensive pig genetic linkage map by Leif Andersson group using a cross between the European Wild Boar and a domestic breed (Large White). The linkage map includes 77 type I loci informative for comparative mapping and 72 in situ mapped markers physically anchoring the linkage groups on chromosomes.. Available from DOI.
Reference 2 Ellegren H, Chowdhary B P, Johansson M, Marklund L, Fredholm M, Gustavsson I, Andersson L, (1994). A primary linkage map of the porcine genome reveals a low rate of genetic recombination. Genetics, 137 (4): 1089-100.

PendeoMap { Reference }	Horse linkage map [Equus caballus; Breed=(mixed; n/a)].
	Taxonomy ID=9796
A comprehensive male linkage map was generated by adding 359 new, informative microsatellites to the International Equine Gene Map half-sibling reference families and by combining genotype data from three independent mapping resources: a full sibling family created at the Animal Health Trust in Newmarket, United Kingdom, eight half-sibling families from Sweden and two half-sibling families from the University of California, Davis. The map was constructed from a total of 766 markers distributed on the 31 equine chromosomes.. Available from DOI.
Reference 2 Penedo M C T, Millon L V, Bernoco D, Bailey E, Binns M, Cholewinski G, Ellis N, Flynn J, Gralak B, Guthrie A, Hasegawa et al. (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.

PiGMaP	Pig linkage map [Sus scrofa; Breed=n/a].
	Taxonomy ID=9823
A linkage map of the porcine genome has been developed by segregation analysis of 239 genetic markers. Eighty-one of these markers correspond to known genes. Linkage groups have been assigned to all 18 autosomes plus the X Chromosome (Chr). The work was by the PiGMaP consortium led by Alan Archibold and Max Rothschild.. Available from DOI.
Reference 2 Archibald A L, Haley C S, Brown J F, Couperwhite S, McQueen H A, Nicholson D, Coppieters W, Van de Weghe A, Stratil A, et al. (1995). The PiGMaP consortium linkage map of the pig (Sus scrofa). Mammalian genome, 6 (3): 157-75.

pigRH.2012	Pig linkage map [Sus scrofa; Breed=n/a].
	Taxonomy ID=9823
A genome-wide high density pig RH map for validating and improving the genome assembly 10.2. It was developed with segregation analysis of 239 genetic markers (81 of these markers correspond to known genes). Mapping information for 61 Type I loci (genes) enhances the contribution of the pig gene map to comparative gene mapping.. Available from Mammalian Genome .
Reference 2 Servin Bertrand, Faraut Thomas, Iannuccelli Nathalie, Zelenika Diana, Milan Denis, (2012). High-resolution autosomal radiation hybrid maps of the pig genome and their contribution to the genome sequence assembly. BMC genomics, 13 (): 585.

SM4.7 { Reference }	Sheep linkage map [Ovis aries; Breed=n/a].
	Taxonomy ID=9940
A medium-density sheep linkage map that contain over 1000 loci, by Jill Maddox et al. The map comprises 1093 markers representing 1062 unique loci (941 anonymous loci, 121 genes) and spans 3500 cM (sex-averaged) for the autosomes and 132 cM (female) on the X chromosome. There is an average spacing of 3.4 cM between autosomal loci and 8.3 cM between highly polymorphic [polymorphic information content (PIC) > or = 0.7] autosomal loci. . Available from .
Reference 2 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, Riffk et al. (2001). An enhanced linkage map of the sheep genome comprising more than 1000 loci. Genome Research, 11 (7): 1275-89.

Wageningen { Reference }	Chicken linkage map [Gallus gallus; Breed=Red Jungle fow, l/White Leghorn].
	Taxonomy ID=9031
An improved chicken consensus linkage map with 12,945 SNPs on the Wageningen (WU), East Lansing (EL), and Uppsala (UPP) mapping populations. The resolution of the chicken consensus linkage map has been dramatically improved in this study by genotyping 12,945 single nucleotide polymorphisms (SNPs) on three existing mapping populations in chicken: the Wageningen (WU), East Lansing (EL), and Uppsala (UPP) mapping populations. The current map consists of 34 linkage groups and covers at least 29 of the 38 autosomes.. Available from PUBLICATION.
Reference 2 Groenen Martien A M, Wahlberg Per, Foglio Mario, Cheng Hans H, Megens Hendrik-Jan, Crooijmans Richard P M A, Besnier Fr et al. (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.