A high-resolution linkage map for the Z chromosome in chicken reveals hot spots for recombination

Abstract

A comprehensive linkage map for chicken chromosome Z was constructed as the result of a large-scale screening of single nucleotide polymorphisms (SNPs). A total of 308 SNPs were assigned to Z based on the genotype distribution among 182 birds representing several populations. A linkage map comprising 210 markers and spanning 200.9 cM was established by analyzing a small Red junglefowl/White Leghorn intercross. There was excellent agreement between the linkage map for Z and a recently released assembly of the chicken genome (May 2006). Almost all SNPs assigned to chromosome Z in the present study are on Z in the new genome assembly. The remaining 12 loci are all found on unassigned contigs that can now be assigned to Z. The average recombination rate was estimated at 2.7 cM/Mb but there was a very uneven distribution of recombination events with both cold and hot spots of recombination. The existence of one of the major hot spots of recombination, located around position 39.4 Mb, was supported by the observed pattern of linkage disequilibrium. Thirteen markers from unassigned contigs were shown to be located on chromosome W. Three of these contigs included genes that have homologues on chromosome Z. The preliminary assignment of three more genes to the gene-poor W chromosome may be important for studies on the mechanism of sex determination and dosage compensation in birds.

W chromosome expression responds to female-specific selection

“…Verification of femalespecific genes on genomic DNA samples, using PCR amplification, identified 12 previously unknown W-linked genes and confirmed four suspected W-linked genes (26,27) that have been misassembled in the current genome draft (WUGSC 2.1/galGal3). The alignment of the sequence data also revealed that three genes currently attributed to the W chromosome (ENSGALG00000013557, ENSGALG 00000013559, and ENSGALG00000022692) are not, in fact, female-limited.…”

A Gene-Based Genetic Linkage Map of the Collared Flycatcher (Ficedula albicollis) Reveals Extensive Synteny and Gene-Order Conservation During 100 Million Years of Avian Evolution

“…For the gene-based SNPs, a possible explanation of the absence of linkage is that they are located in regions of high recombination within conserved linkage groups. Given the observation that recombination rates tend to be elevated toward telomeric ends of avian chromosomes (International Chicken Genome Sequencing Consortium 2004; Schmid et al 2005;Wahlberg et al 2007), this explanation is supported by the fact that 6 of 9 unlinked genes are the most distal marker on chicken chromosomes in our marker set (at 2p, 3p, 4q, 5q, 10p, and 10q, respectively). Alternatively, they may indicate chromosomal rearrangements (see supplemental data).…”

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

“…Inter-specific recombination rates The blue tit linkage map intervals are shorter than the Wageningen chicken broiler population (Groenen et al, 2009), similar to the Uppsala chicken mapping population (Wahlberg et al, 2007;Groenen et al, 2009), and larger than the great reed warbler (cf. Dawson et al, 2007).…”

“…First, it could be a consequence of the low density of the passerine maps, and that the linkage groups of some species are located in low-recombining parts of the genome, such as the centromeres (Hulten, 1974;Lynn et al, 2000). The recombination rate differs in different parts of the chicken genome and, as in mammals, recombination hot spots occur (Wahlberg et al, 2007;Groenen et al, 2009). However, this and other passerine linkage mapping studies, and the chicken linkage map, have had good coverage over compared chromosomes and the estimated level of recombination should not reflect rates in local chromosomal segments.…”