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A SNP Based Linkage Map of the Turkey Genome Reveals Multiple Intrachromosomal Rearrangements Between the Turkey and Chicken Genomes

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A SNP Based Linkage Map of the Turkey Genome Reveals Multiple Intrachromosomal Rearrangements Between the Turkey and Chicken Genomes

Muhammad L Aslam et al. BMC Genomics.

Abstract

Background: The turkey (Meleagris gallopavo) is an important agricultural species that is the second largest contributor to the world's poultry meat production. The genomic resources of turkey provide turkey breeders with tools needed for the genetic improvement of commercial breeds of turkey for economically important traits. A linkage map of turkey is essential not only for the mapping of quantitative trait loci, but also as a framework to enable the assignment of sequence contigs to specific chromosomes. Comparative genomics with chicken provides insight into mechanisms of genome evolution and helps in identifying rare genomic events such as genomic rearrangements and duplications/deletions.

Results: Eighteen full sib families, comprising 1008 (35 F1 and 973 F2) birds, were genotyped for 775 single nucleotide polymorphisms (SNPs). Of the 775 SNPs, 570 were informative and used to construct a linkage map in turkey. The final map contains 531 markers in 28 linkage groups. The total genetic distance covered by these linkage groups is 2,324 centimorgans (cM) with the largest linkage group (81 loci) measuring 326 cM. Average marker interval for all markers across the 28 linkage groups is 4.6 cM. Comparative mapping of turkey and chicken revealed two inter-, and 57 intrachromosomal rearrangements between these two species.

Conclusion: Our turkey genetic map of 531 markers reveals a genome length of 2,324 cM. Our linkage map provides an improvement of previously published maps because of the more even distribution of the markers and because the map is completely based on SNP markers enabling easier and faster genotyping assays than the microsatellitemarkers used in previous linkage maps. Turkey and chicken are shown to have a highly conserved genomic structure with a relatively low number of inter-, and intrachromosomal rearrangements.

Figures

Figure 1
Figure 1
Inter and intra chromosomal rearrangements between turkey and chicken. Linkage maps of turkey chromosomes MGA3, MGA6 and MGA4, MGA9 showing inter and intra chromosomal rearrangements (fission, fusion and inversions,) with their syntenic chicken chromosomes GGA2 and GGA4 (maps based on physical position of SNPs in chicken genome).
Figure 2
Figure 2
Intrachromosomal rearrangements between turkey and chicken involving nearly a complete chromosome arm. Turkey chromosomes MGA10 and MGA20 (genetic linkage maps) showing intrachromosomal rearrangements (Inversions) compared to the syntenic chicken chromosomes GGA8 and GGA18 (maps based on physical position of SNPs in chicken genome).
Figure 3
Figure 3
Distribution of recombination rates and sequence motif densities across the turkey chromosomes. Recombination rate cM/Mb was correlated with chromosome length (Mb) and CpG/Mb was correlated with recombination rate (cM/Mb). All remaining sequence motifs (CCCCCCC, CCTCCCT, CTCF and CTCTCCC) were correlated with chromosome length (cM).

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