Second report on chicken genes and chromosomes 2005

Schmid, Michael; Nanda, Indrajit; Hoehn, Holger; Schartl, Manfred; Haaf, Thomas; Buerstedde, Jean-Marie; Arima, Hiroshi; Caldwell, Randolph B.; Weigend, Steffen; Burt, David W.; Smith, Jacqueline; Griffin, Darren K.; Masabanda, Julio S.; Groenen, Martien A. M.; Crooijmans, R.P.M.A.; Vignal, Alain; Fillon, Valérie; Morisson, Mireille; Pitel, Frédérique; Vignoles, M.; Garrigues, A.; Gellin, Joël; Rodionov, A. V.; Galkina, Svetlana; Лукина, Н. А.; Ben-Ari, Giora; Blum, Shula; Hillel, J.; Twito, T.; Lavi, U.; David, Lior; Feldman, Marcus W.; Delany, Mary E.; Conley, Catharine A.; Fowler, Velia M.; Hedges, S. Blair; Godbout, Roseline; Katyal, Sachin; Smith, Craig A.; Hudson, Quanah J.; Sinclair, Andrew H.; Mizuno, Shigeki

doi:10.1159/000084205

Cited by 147 publications

(182 citation statements)

References 348 publications

(366 reference statements)

Supporting

Mentioning

167

Contrasting

Unclassified

Order By: Relevance

“…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).…”

Section: Marker Analysismentioning

confidence: 59%

“…This has subsequently been confirmed through analyses of vertebrate genome sequence data, including chicken (Bourque et al 2005), the only bird that has had its genome sequenced to date (International Chicken Genome Sequencing Consortium 2004). Moreover, evidence for an unusually stable avian karyotype with few interchromosomal rearrangements has been obtained by cross-species chromosome painting or the use of other types of in situ hybridization probes (Shetty et al 1999;Shibusawa et al 2001Shibusawa et al , 2004aRaudsepp et al 2002;Guttenbach et al 2003;Kasai et al 2003;Derjusheva et al 2004;Schmid et al 2005;Itoh et al 1 2006; Fillon et al 2007;Griffin et al 2007;NishidaUmehara et al 2007). However, these experiments rarely have the resolution for detecting intrachromosomal or small-scale interchromosomal rearrangements.…”

mentioning

confidence: 99%

See 1 more Smart Citation

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

et al. 2008

View full text Add to dashboard Cite

By taking advantage of a recently developed reference marker set for avian genome analysis we have constructed a gene-based genetic map of the collared flycatcher, an important ''ecological model'' for studies of life-history evolution, sexual selection, speciation, and quantitative genetics. A pedigree of 322 birds from a natural population was genotyped for 384 single nucleotide polymorphisms (SNPs) from 170 protein-coding genes and 71 microsatellites. Altogether, 147 gene markers and 64 microsatellites form 33 linkage groups with a total genetic distance of 1787 cM. Male recombination rates are, on average, 22% higher than female rates (total distance 1982 vs. 1627 cM). The ability to anchor the collared flycatcher map with the chicken genome via the gene-based SNPs revealed an extraordinary degree of both synteny and gene-order conservation during avian evolution. The great majority of chicken chromosomes correspond to a single linkage group in collared flycatchers, with only a few cases of inter-and intrachromosomal rearrangements. The rate of chromosomal diversification, fissions/fusions, and inversions combined is thus considerably lower in birds (0.05/MY) than in mammals (0.6-2.0/MY). A dearth of repeat elements, known to promote chromosomal breakage, in avian genomes may contribute to their stability. The degree of genome stability is likely to have important consequences for general evolutionary patterns and may explain, for example, the comparatively slow rate by which genetic incompatibility among lineages of birds evolves.

show abstract

Section: Marker Analysismentioning

confidence: 59%

mentioning

confidence: 99%

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

et al. 2008

View full text Add to dashboard Cite

show abstract

“…NA denotes data were unavailable or not shown. (Groenen et al, 2009), substantially smaller than the 4200 cM previously estimated using 2261 markers (Schmid et al, 2005). However, obtaining enough markers to detect fine-scale recombination is resourceintensive, thereby producing maps that range in scale from kilobases (hereafter referred to as 'fine scale'), to hundreds of kilobases (hereafter referred to as 'intermediate scale'), to tens of megabases (hereafter referred to as 'broad scale'), to whole genomes.…”

Section: How Does the Methodology By Which Recombination Is Measured mentioning

confidence: 97%

Recombination rate variation in closely related species

2011

View full text Add to dashboard Cite

Despite their importance to successful meiosis and various evolutionary processes, meiotic recombination rates sometimes vary within species or between closely related species. For example, humans and chimpanzees share virtually no recombination hotspot locations in the surveyed portion of the genomes. However, conservation of recombination rates between closely related species has also been documented, raising an apparent contradiction. Here, we evaluate how and why conflicting patterns of recombination rate conservation and divergence may be observed, with particular emphasis on features that affect recombination, and the scale and method with which recombination is surveyed. Additionally, we review recent studies identifying features influencing fine-scale and broad-scale recombination patterns and informing how quickly recombination rates evolve, how changes in recombination impact selection and evolution in natural populations, and more broadly, which forces influence genome evolution.

show abstract

“…Fluorescent in situ hybridization (FISH) of the chicken-specific probes on chicken and quail metaphase chromosomes first confirmed the predicted pericentric inversions on chromosomes 1, 2, and 4 (Shibusawa et al 2001;Schmid et al 2005;Kayang et al 2006). However, precise FISH mapping is tricky in birds, even on macrochromosomes.…”

Section: Introductionmentioning

confidence: 89%

“…The total number of chromosomes is the same in both species (2n078). Furthermore, a high degree of syntenic conservation has been demonstrated using different approaches, such as comparative gene mapping (Shibusawa et al 2001;Schmid et al 2005;Galkina et al 2006;Kayang et al 2006), chromosome painting (Schmid et al 2000;Guttenbach et al 2003), and linkage analysis (Kayang et al 2006;Sasazaki et al 2006). The conservation of both macro-and microchromosomes suggests the absence of interchromosomal rearrangements accompanying the divergence of the chicken and Japanese quail.…”

Section: Introductionmentioning

confidence: 99%

Centromere positions in chicken and Japanese quail chromosomes: de novo centromere formation versus pericentric inversions

et al. 2012

View full text Add to dashboard Cite

Chicken (Gallus gallus domesticus, GGA) and Japanese quail (Coturnix coturnix japonica, CCO) karyotypes are very similar. They have identical chromosome number (2n078) and show a high degree of synteny. Centromere positions on the majority of orthologous chromosomes are different in these two species. To explore the nature of this divergence, we used highresolution comparative fluorescent in situ hybridization mapping on giant lampbrush chromosomes (LBCs) from growing oocytes. We applied 41 BAC clones specific for GGA1, 2, 3, 11, 12, 13, 14, and 15 to chicken and quail LBCs. This approach allowed us to rule out a pericentric inversion earlier proposed to explain the difference between GGA1 and CCO1. In addition to a well-established large-scale pericentric inversion that discriminates GGA2 and CCO2, we identified another, smaller one in the large inverted region. For the first time, we described in detail inversions that distinguish GGA3 from CCO3 and GGA11 from CCO11. Despite the newly identified and confirmed inversions, our data suggest that, in chicken and Japanese quail, the difference in centromere positions is not mainly caused by pericentric inversions but is instead due to centromere repositioning events and the formation of new centromeres. We also consider the formation of short arms of quail microchromosomes by heterochromatin accumulation as a third scenario that could explain the discrepancy in centromeric indexes.

show abstract

Second report on chicken genes and chromosomes 2005

Cited by 147 publications

References 348 publications

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

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

Recombination rate variation in closely related species

Centromere positions in chicken and Japanese quail chromosomes: de novo centromere formation versus pericentric inversions

Contact Info

Product

Resources

About