Third Report on Chicken Genes and Chromosomes 2015

Wragg, David

doi:10.1159/000430927

Cited by 79 publications

(82 citation statements)

References 623 publications

(26 reference statements)

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“…The order of the genes on the chromosomes has been adjusted to highlight the similarities both between the chromosomes within each species, thus displaying the paralogon relationship, and between species, thus exposing the conservation of synteny. It is well known that intrachromosomal rearrangements happen frequently (Ocampo Daza et al 2012, Schmid et al 2015, so it is not surprising that some differences in gene order have arisen between the four chromosomes in each quartet, as well as between species for the corresponding chromosomal regions. The positions of the genes are shown below each box, and it can be seen that many of the genes are still in reasonably close proximity to one another.…”

Section: Discussionmentioning

confidence: 99%

Corticotropin-releasing hormone family evolution: five ancestral genes remain in some lineages

Cardoso¹,

Bergqvist²,

Félix³

et al. 2016

Journal of Molecular Endocrinology

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The evolution of the peptide family consisting of corticotropin-releasing hormone (CRH) and the three urocortins (UCN1-3) has been puzzling due to uneven evolutionary rates. Distinct gene duplication scenarios have been proposed in relation to the two basal rounds of vertebrate genome doubling (2R) and the teleost fish-specific genome doubling (3R). By analyses of sequences and chromosomal regions, including many neighboring gene families, we show here that the vertebrate progenitor had two peptide genes that served as the founders of separate subfamilies. Then, 2R resulted in a total of five members: one subfamily consists of CRH1, CRH2, and UCN1. The other subfamily contains UCN2 and UCN3. All five peptide genes are present in the slowly evolving genomes of the coelacanth Latimeria chalumnae (a lobe-finned fish), the spotted gar Lepisosteus oculatus (a basal ray-finned fish), and the elephant shark Callorhinchus milii (a cartilaginous fish). The CRH2 gene has been lost independently in placental mammals and in teleost fish, but is present in birds (except chicken), anole lizard, and the nonplacental mammals platypus and opossum. Teleost 3R resulted in an additional surviving duplicate only for crh1 in some teleosts including zebrafish (crh1a and crh1b). We have previously reported that the two vertebrate CRH/UCN receptors arose in 2R and that CRHR1 was duplicated in 3R. Thus, we can now conclude that this peptide-receptor system was quite complex in the ancestor of the jawed vertebrates with five CRH/UCN peptides and two receptors, and that crh and crhr1 were duplicated in the teleost fish tetraploidization.

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Section: Discussionmentioning

confidence: 99%

Corticotropin-releasing hormone family evolution: five ancestral genes remain in some lineages

Cardoso¹,

Bergqvist²,

Félix³

et al. 2016

Journal of Molecular Endocrinology

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“…Transcription of satellite DNA on avian lampbrush chromosomes: More examples About 60 avian genomes are available today 20 opening up additional opportunities for examining satellite DNA structure and transcription. For instance, Z-macrosatellite sequences (Z-amplicons) are transcribed during the lampbrush stage on chicken Z chromosome and on a number of macrochromosomes.…”

Section: Chicken Lampbrush Chromosomes: Example Of a Conserved Pattermentioning

confidence: 99%

“…Birds have relatively small genomes with a characteristic distribution of tandem repeats. 20 Specifically, sex W chromosome in chicken contains a number of tandemly repetitive families. 21 Another example is the germ-line restricted chromosome (GRC) in finches, largely consisting of highly repetitive DNA.…”

Section: Introductionmentioning

confidence: 99%

“…18,[24][25][26] Genomes of model organisms such as chicken (Gallus gallus) or clawed frog (Xenopus) are thoroughly characterized, enabling detailed studies of the tandem DNA repeats. 20,26,27 Birds and amphibians are of a special interest due to the widespread transcription of tandem repeats at the diplotene stage of oogenesis when chromosomes acquire specific lampbrush form. 18,19,24 Exceptionally large size of the lampbrush chromosomes and high rates of transcription during the lampbrush stage enables to study tandem repeats transcriptional activity with striking longitudinal resolution.…”

Section: Introductionmentioning

confidence: 99%

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Transcription of highly repetitive tandemly organized DNA in amphibians and birds: A historical overview and modern concepts

Trofimova

Krasikova

2016

RNA Biology

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Tandemly organized highly repetitive DNA sequences are crucial structural and functional elements of eukaryotic genomes. Despite extensive evidence, satellite DNA remains an enigmatic part of the eukaryotic genome, with biological role and significance of tandem repeat transcripts remaining rather obscure. Data on tandem repeats transcription in amphibian and avian model organisms is fragmentary despite their genomes being thoroughly characterized. Review systematically covers historical and modern data on transcription of amphibian and avian satellite DNA in somatic cells and during meiosis when chromosomes acquire special lampbrush form. We highlight how transcription of tandemly repetitive DNA sequences is organized in interphase nucleus and on lampbrush chromosomes. We offer LTR-activation hypotheses of widespread satellite DNA transcription initiation during oogenesis. Recent explanations are provided for the significance of high-yield production of non-coding RNA derived from tandemly organized highly repetitive DNA. In many cases the data on the transcription of satellite DNA can be extrapolated from lampbrush chromosomes to interphase chromosomes. Lampbrush chromosomes with applied novel technical approaches such as superresolution imaging, chromosome microdissection followed by high-throughput sequencing, dynamic observation in life-like conditions provide amazing opportunities for investigation mechanisms of the satellite DNA transcription.

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“…Efforts are continuing to comprehensively describe the chicken genome (Schmid et al, 2015). Recently, population genomics studies, which search for genetic signatures of selection in the genome (Akey, 2009), have been conducted using high density SNPs genotyping and whole genome sequencing techniques in the livestock genome (e.g., Rubin et al, 2010;Elferink et al, 2012;Fan et al, 2013;Qanbari et al, 2015).…”

Section: Discussionmentioning

confidence: 99%

Genetic Mapping of Quantitative Trait Loci for Egg Production and Egg Quality Traits in Chickens: a Review

Goto

Tsudzuki

2017

Jpn. Poult. Sci.

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Chickens display a wide spectrum of phenotypic variations in quantitative traits such as egg-related traits. Quantitative trait locus (QTL) analysis is a statistical method used to understand the relationship between phenotypic (trait measurements) and genotypic data (molecular markers). We have performed QTL analyses for egg-related traits using an original resource population based on the Japanese Large Game (Oh-Shamo) and the White Leghorn breeds of chickens. In this article, we summarize the results of our extensive QTL analyses for 11 and 66 traits for egg production and egg quality, respectively. We reveal that at least 30 QTL regions on 17 different chromosomes affect phenotypic variation in egg-related traits. Each locus had an age-specific effect on traits, and a variety in effects was also apparent, such as additive, dominance, and epistatic-interaction effects. Although genome-wide association study (GWAS) is suitable for gene-level resolution mapping of GWAS loci with additive effects, QTL mapping studies enable us to comprehensively understand genetic control, such as chromosomal regions, genetic contribution to phenotypic variance, mode of inheritance, and age-specificity of both common and rare alleles. QTL analyses also describe the relationship between genotypes and phenotypes in experimental populations. Accumulation of QTL information, including GWAS loci, is also useful for studies of population genomics approached without phenotypic data in order to validate the identified genomic signatures of positive selection. The combination of QTL studies and next-generation sequencing techniques with uncharacterized genetic resources will enhance current understanding of the relationship between genotypes and phenotypes in livestock animals.

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Third Report on Chicken Genes and Chromosomes 2015

Cited by 79 publications

References 623 publications

Corticotropin-releasing hormone family evolution: five ancestral genes remain in some lineages

Corticotropin-releasing hormone family evolution: five ancestral genes remain in some lineages

Transcription of highly repetitive tandemly organized DNA in amphibians and birds: A historical overview and modern concepts

Genetic Mapping of Quantitative Trait Loci for Egg Production and Egg Quality Traits in Chickens: a Review

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