A genome-wide linkage map for the house sparrow (Passer domesticus) provides insights into the evolutionary history of the avian genome

The house sparrow is an important model species for studying
physiological, ecological and evolutionary processes in wild populations.
Here, we present a medium density, genome wide linkage map for house
sparrow (Passer domesticus) that has aided the assembly of the house
sparrow reference genome, and that will provide an important resource for
ongoing mapping of genes controlling important traits in the ecology and
evolution of this species. Using a custom house sparrow 10K iSelect
Illumina SNP chip we have assigned 6498 SNPs to 29 autosomal linkage
groups, based on a mean of 430 informative meioses per SNP. The map was
constructed by combining the information from linkage with that of the
physical position of SNPs within scaffold sequences in an iterative
process. Averaged between the sexes; the linkage map had a total length of
2004 cM, with a longer map for females (2240 cM) than males (1801 cM).
Additionally, recombination rates also varied along the chromosomes.
Comparison of the linkage map to the reference genomes of zebra finch,
collared flycatcher and chicken, showed a chromosome fusion of the two
avian chromosomes 8 and 4A in house sparrow. Lastly, information from the
linkage map was utilized to conduct analysis of linkage disequilibrium
(LD) in eight populations with different effective population sizes (Ne)
in order to quantify the background level LD. Together, these results aid
the design of future association studies, facilitate the development of
new genomic tools and support the body of research that describes the
evolution of the avian genome.