Genetic linkage map of the zebra finch

Zebra finch
Male Zebra finch

Zebra finch (Taeniopygia guttata) belong to the order Passerines, which are one of the most widely studied taxonomic groups in evolutionary biology and ecology. Until only recently, studies in passerines were limited by a lack of available genomic resources and as such it had been difficult to identify genes responsible for variation in important traits. To help address this problem and complement the zebra finch genome sequence we developed a first generation linkage map for the zebra finch using SNPs.

The map revealed conserved synteny between zebra finch and chicken genomes. (the figure below shows almost 1:1 homology between chicken (Gga) and Zebra finch (Tgu) ten largest chromosomes, with a couple of exceptions). The map also identified a greater than expected number of intrachromosomal rearrangements between chicken and zebra finch, so gene order is different between the two birds.

Synteny of Chicken (right) and Zebrafinch (left) macrochromosomes
Synteny of Chicken (right) and Zebrafinch (left) macrochromosomes










Related publications
Stapley J, Birkhead TR, Burke T and Slate J. (2008) A linkage map of the zebra finch Taeniopygia guttata provides new insight into avian genome evolution. Genetics 179:651-667.
Slate J, Gratten J, Beraldi D, Stapley J, Hale M, Pemberton J. (2009) Gene mapping in the wild with SNPs: guidelines and future directions. Genetica 136:97-107.
Santure AW, Stapley J, Ball AD, Birkhead TR, Burke T and Slate J. (2010) On the use of large marker panels to estimate inbreeding and relatedness: empirical and simulation studies of a pedigreed zebra finch population typed at 771 loci. Molecular Ecology 19:1439-1451.
Ball A, Stapley J, Dawson DA, Birkhead, TR, Burke T and Slate J. (2010) A comparison of SNPs and microsatellites as linkage mapping markers: lessons from the zebra finch (Taeniopygia guttata). BMC Genomics 11:218
Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Kunstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TAF, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin Y-C, George J, Sweedler J, Southey B, Gunaratne P, Watson M, Nam K, Backstrom N, Smeds L, Nabholz B, Itoh Y, Whitney O, Pfenning AR, Howard J, Volker M, Skinner BM, Griffin DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente XS, Olender T, Lancet D, Smit AFA, Hubley R, Konkel MK, Walker JA, Batzer MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J, Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H, Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang S-P, Li X, Graves T, Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, and Wilson RK. (2010) The genome of a songbird, Nature, 464:757-762.
Ekblom R, Stapley J, Ball AD, Birkhead T, Burke T and Slate J. (2011) Genetic mapping of the major histocompatibility complex in the zebra finch (Taeniopygia guttata), Immunogenetics 63:523-530.