A SNP based linkage map of the turkey genome reveals multiple intrachromosomal rearrangements between the Turkey and Chicken genomes

Abstract

BackgroundThe 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.ResultsEighteen 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.ConclusionOur 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.

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].…”

Karyotypes and recombination patterns of the Common Swift (Apus apus Linnaeus, 1758) and Eurasian Hobby (Falco subbuteo Linnaeus, 1758)

“…Unfortunately, only less than 10% of bird species have been karyotyped (Griffin and Burt 2014). Recombination traits have been studied in as few as nine species by cytological methods (see Table 1 and references therein) and in nine species by linkage analysis (Dawson et al 2007;Groenen et al 2009;Jaari et al 2009;Aslam et al 2010;Hansson et al 2010;Kawakami et al 2014;van Oers et al 2014).…”

Intrachromosomal rearrangements in two representatives of the genus Saltator (Thraupidae, Passeriformes) and the occurrence of heteromorphic Z chromosomes

“…This is the case in some Ratites, Galloanserae and Neoaves (Shetty et al 1999;Guttenbach et al 2003;Nanda et al 2008;Ellegren 2010). In contrast, genome sequencing has revealed the frequent occurrence of intrachromosomal rearrangements in birds, especially inversions (Aslam et al 2010;Volker et al 2010;Skinner and Griffin 2012). Actually, a large number of inversions is common in all sauropsids too, as well as in Testudines and Lepidosauromorpha (Alföldi et al 2011;Gunski et al 2013).…”