Table 2 A sampling of non-model species for which robust linkage maps have been developed

From: Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits

Common name	Scientific name	Experimental design	Primary markers	References
Plants
Tomato	Lycopersicon esculentum and L. pennellii	Backcross and F2	RFLP	Bernatzky and Tanksley (1986)
Monkey flowers	Mimulus guttatus and M. platycalx	Backcross	RAPD	Lin and Ritland (1996)
Monkey flowers	M. cardinalis and M. lewisii	F2	RAPD	Bradshaw et al. (1998)
Monkey flowers	M. guttatus and M. nasutus	F2	AFLP	Fishman et al. (2001)
Shepherd's purse	Capsella bursa-pastoris	F2	RAPD	Linde et al. (2001)
Poplar	Populus deltoides, P. nigra and P. trichocarpa	Linkage analysis with two-way pseudo test cross design	AFLP	Cervera et al. (2001)
Western and Sierra columbines	Aquilegia formosa and A. pubescens	F2	AFLP	Hodges et al. (2002)
Sunflowers	Helianthus annuus and H. petiolaris	Backcross 2	Microsatellites	Rieseberg et al. (2003)
Lyrate rockcress	Arabidopsis lyrata	F2	CAPS markers	Kuittinen et al. (2004)
Pink shepherd's purse	Capsella rubella and C. grandiflora	F2	RFLPs, ESTs	Boivin et al. (2004)
Louisiana Iris	Iris fulva and I. brevicaulis	Backcross (recipcrocal)	IRRE retrotransposon display markers	Bouck et al. (2005)
Birch trees	Betula pendula	Full and half-sib families	AFLP	Pekkinen et al. (2005)
Bladder campion	Silene vulgaris	F2	AFLP	Bratteler et al. (2006)
Alpine pennycress	Thlaspi caerulescens	F3	AFLP	Assuncao et al. (2006)
Linanthus	Leptosiphon bicolor and L. jepsonii	F2, and reciprocal backcrosses	AFLP	Goodwillie et al. (2006)
Vertebrates
Fire-bellied toads	Bombina bombina and B. variegata	F2	SSCP	Nürnberger et al. (2003)
Tiger salamander	Ambystoma tigrinum and A. mexicanum	Backcross	AFLP	Voss and Shaffer (1997)
Tiger salamander	Ambystoma tigrinum and A. mexicanum	Backcross	PCR-based ESTs	Smith et al. (2005)
Tilapia	Oreochromis niloticus	Haploid embryos	AFLPs, microsatellites	Kocher et al. (1998)
Tilapia	Oreochromis niloticus and O. aureus	F2	Microsatellites, SNP	Lee et al. (2005)
Three-spined stickleback	Gasterosteus aculeatus	F2	Microsatellites	Peichel et al. (2001)
Atlantic salmon	Salmo salar	Half and full-sib family	AFLP	Moen et al. (2004)
Brown trout	Salmo trutta	Backcross	Microsatellites	Gharbi et al. (2006)
Mexican tetra (cavefish)	Astyanax mexicanus	Backcross	Microsatellites	Protas et al. (2006)
Turkey	Meleagris gallopavo	F2	Microsatellites, SNP	Reed et al. (2005)
Great reed warbler	Acrocephalus arundinaceus	Pedigree	Microsatellites	Hansson et al. (2005)
Passerine birds	—	Homology mapping	Microsatellites	Dawson et al. (2006)
Tammar wallaby	Macropus eugenii	Backcross	Microsatellites	Zenger et al. (2002)
Opossum	Monodelphis domestica	Backcross	Microsatellites	Samollow et al. (2004)
Hamadryas baboon	Papio hamadryas	Pedigree	Microsatellites	Rogers et al. (2000)
Red deer	Cervus elaphus	Pedigree	Microsatellites	Slate et al. (2002)
Soay sheep	Ovis aries	Pedigree	Microsatellites	Beraldi et al. (2006)
Oldfield mice	Peromyscus polionotus	F2	Microsatellites, SNP	Steiner et al. (in review)
Insects
Mosquito	Anopheles gambiae	Backcross	Microsatellites	Zheng et al. (1996)
Apple maggot fly	Rhagoletis pomonella	Single pair crosses	RFLP/SSCP	Roethele et al. (1997)
Ground crickets	Allonemobius fasciatus and A. socius	Backcross (bidirectional)	RAPD	Chu and Howard (1998)
Colorado potato beetle	Leptinotarsa decemlineata	Backcross	AFLP	Hawthorne (2001)
Pea aphids	Acyrthosiphon pisum	F2	AFLP	Hawthorne and Via (2001)
Hawaiian crickets	Laupala paranigra and L. kohalensis	F2	AFLP	Parsons and Shaw (2002)
Cactus fruit fly	Drosophila mojavensis	Backcross	Microsatellites	Staten et al. (2004)
Sulfur butterfly	Colias eurytheme and C. philodice	Backcross	AFLP	Wang and Porter (2004)
Corn borer	Ostrinia nubilalis	Backcross	AFLP	Dopman et al. (2004)
Red flour beetle	Tribolium castaneum	F2	AFLP	Zhong et al. (2004)
Heliconius butterfly	Heliconius melpomene	F2	AFLP	Jiggins et al. (2005)
Heliconius butterfly	Heliconius erato	Backcross	AFLP	Tobler et al. (2005)
Other invertebrates
Pacific oysters	Crassostrea gigas	Backcross	Microsatellites	Hubert and Hedgecock (2004)
Nematode	Pristionchus pacificus	F2	SSCP	Srinivasan et al. (2002)

Abbreviations: AFLP, amplified fragment length polymorphism; CAPS, cleaved amplified polymorphic sequences; IRRE, iris retroelement; RAPD, random amplification of polymorphic DNA; RFLP, restriction fragment length polymorphism; SNP, single-nucleotide polymorphism; SSCP, single strand conformation polymorphism.
Where more than one species name is provided, the linkage map was generated from interspecific crosses or backcrosses. The experimental design and predominate molecular marker used in the linkage map are given. For many of these species, newer linkage maps have been created using additional markers, or genome-sequencing projects are currently underway.

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Table 2 A sampling of non-model species for which robust linkage maps have been developed

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