Avian genome evolution: insights from a linkage map of the blue tit (Cyanistes caeruleus)

Abstract

We provide a first-generation linkage map of the blue tit (Cyanistes caeruleus), a passerine within the previously genetically uncharacterized family Paridae, which includes 91 orthologous loci with a single anchored position in the chicken (Gallus gallus) sequence assembly. The map consists of 18 linkage groups and covers 935 cM. There was highly conserved synteny between blue tit and chicken with the exception of a split on chromosome 1, potential splits on chromosome 4 and the translocation of two markers from chromosome 2 and 3, respectively, to chromosome 5. Gene order was very well conserved for the majority of chromosomes, an exception being chromosome 1 where multiple rearrangements were detected. Similar results were obtained in a comparison to the zebra finch (Taeniopygia guttata) genome assembly. The recombination rate in females was slightly higher than in males, implying a moderate degree of heterochiasmy in the blue tit. The map distance of the blue tit was B78% of that of the Wageningen chicken broiler population, and very similar to the Uppsala chicken mapping population, over homologous genome regions. Apart from providing insights into avian recombination and genome evolution, our blue tit linkage map forms a valuable genetic resource for ecological and evolutionary research in Paridae.

Pronounced inter- and intrachromosomal variation in linkage disequilibrium across the zebra finch genome

“…Whether this pattern will be found in other Passerines (which represent around half of all bird species) is unknown. There was no evidence of greater recombination rate at the ends of the macrochromosomes in linkage maps of either the Blue tit (Cyanistes caeruleus) or the Siberian Jay (Perisoreus infaustus), which we visualized by plotting the genetic distance (cM) against predicted physical positions (bp) (in zebra finch or chicken; Hansson et al 2009;Jaari et al 2009). However, this pattern may be obscured because in the absence of whole-genome sequences the true physical positions of the markers are unknown.…”

Pronounced Fixation, Strong Population Differentiation and Complex Population History in the Canary Islands Blue Tit Subspecies Complex

“…Summary statistics for all loci with their genomic location on the blue tit linkage map [30] and the zebra finch genome assembly [35] are given in Table S1 . All birds were molecularly sexed by amplifying a Z- and W-linked locus, TGZ-002 (D. Dawson, University of Sheffield, unpublished), and this information was used for interpreting the genotypes of the Z-linked microsatellites.…”

“…In blue tits, an extensive number of nuclear microsatellites have been developed [29] and a first generation linkage map has been constructed [30]. This enabled us chose a set of markers with known linkage map position for our analyses.…”

Immunocytological Analysis of Meiotic Recombination in the Gray Goose (<b><i>Anser anser</i></b>)

“…ber of recombination nodules per genome [Pigozzi and Solari, 1999a;Calderón and Pigozzi, 2006]. Genetic mapping revealed a significant sex difference in the length of the genetic map in both directions: it was longer in females in the blue tit [Hansson et al, 2010], great reed warbler [Hansson et al, 2005;Akesson et al, 2007], and Siberian jay [Jaari et al, 2009], and in males in chicken [Groenen et al, 2009], turkey [Aslam et al, 2010], and collared flycatcher [Backström et al, 2008;Kawakami et al, 2014;Smeds et al, 2016].…”