Original Article

Heredity (2014) 112, 307–316; doi:10.1038/hdy.2013.107; published online 23 October 2013

Replicated high-density genetic maps of two great tit populations reveal fine-scale genomic departures from sex-equal recombination rates
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K van Oers1,6, A W Santure2,6, I De Cauwer2,3,6, N EM van Bers1,4, R PMA Crooijmans4, B C Sheldon5, M E Visser1, J Slate2 and M AM Groenen4

  1. 1Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
  2. 2Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
  3. 3Laboratoire de Génétique et Evolution des Populations Végétales, UMR CNRS 8198, Bâtiment SN2, Université des Sciences et Technologies de Lille - Lille 1, Villeneuve d’Ascq Cedex, France
  4. 4Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, Wageningen, The Netherlands
  5. 5Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, UK

Correspondence: Dr K van Oers, Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, 6700 AB Wageningen, The Netherlands. E-mail: k.vanoers@nioo.knaw.nl

6These authors contributed equally to this work.

Received 28 May 2013; Accepted 16 September 2013
Advance online publication 23 October 2013

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Abstract

Linking variation in quantitative traits to variation in the genome is an important, but challenging task in the study of life-history evolution. Linkage maps provide a valuable tool for the unravelling of such trait−gene associations. Moreover, they give insight into recombination landscapes and between-species karyotype evolution. Here we used genotype data, generated from a 10k single-nucleotide polymorphism (SNP) chip, of over 2000 individuals to produce high-density linkage maps of the great tit (Parus major), a passerine bird that serves as a model species for ecological and evolutionary questions. We created independent maps from two distinct populations: a captive F2-cross from The Netherlands (NL) and a wild population from the United Kingdom (UK). The two maps contained 6554 SNPs in 32 linkage groups, spanning 2010cM and 1917cM for the NL and UK populations, respectively, and were similar in size and marker order. Subtle levels of heterochiasmy within and between chromosomes were remarkably consistent between the populations, suggesting that the local departures from sex-equal recombination rates have evolved. This key and surprising result would have been impossible to detect if only one population was mapped. A comparison with zebra finch Taeniopygia guttata, chicken Gallus gallus and the green anole lizard Anolis carolinensis genomes provided further insight into the evolution of avian karyotypes.

Keywords:

passerine; linkage map; heterochiasmy; chromosomal rearrangements; population comparison