Short Copy Number Variations Potentially Associated with Tonic Immobility Responses in Newly Hatched Chicks

Abe, Hideaki; Nagao, Kazuharu; Inoue‐Murayama, Miho

doi:10.1371/journal.pone.0080205

Cited by 9 publications

(4 citation statements)

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“…Intensive selection in a closed colony may help to maintain the frequency of deletion alleles and enable them to become prevalent in chicken breeds. Indeed, our previous study on array comparative hybridization demonstrated that commercial breeds of chicken have a considerable number of breed-specific CNV in their genomes [ 21 ]. Although many CNV loci are thought to be deleterious in the mammalian genome [ 22 ], the structural mutations identified in chicken NRG3 seem to be favored by positive selection.…”

Section: Discussionmentioning

confidence: 99%

Gene expression patterns of chicken neuregulin 3 in association with copy number variation and frameshift deletion

Abe

Aoya²,

Takeuchi

et al. 2017

BMC Genet

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BackgroundNeuregulin 3 (NRG3) plays a key role in central nervous system development and is a strong candidate for human mental disorders. Thus, genetic variation in NRG3 may have some impact on a variety of phenotypes in non-mammalian vertebrates. Recently, genome-wide screening for short insertions and deletions in chicken (Gallus gallus) genomes has provided useful information about structural variation in functionally important genes. NRG3 is one such gene that has a putative frameshift deletion in exon 2, resulting in premature termination of translation. Our aims were to characterize the structure of chicken NRG3 and to compare expression patterns between NRG3 isoforms.ResultsDepending on the presence or absence of the 2-bp deletion in chicken NRG3, 3 breeds (red junglefowl [RJF], Boris Brown [BB], and Hinai-jidori [HJ]) were genotyped using flanking primers. In the commercial breeds (BB and HJ), approximately 45% of individuals had at least one exon 2 allele with the 2-bp deletion, whereas there was no deletion allele in RJF. The lack of a homozygous mutant indicated the existence of duplicated NRG3 segments in the chicken genome. Indeed, highly conserved elements consisting of exon 1, intron 1, exon 2, and part of intron 2 were found in the reference RJF genome, and quantitative PCR detected copy number variation (CNV) between breeds as well as between individuals. The copy number of conserved elements was significantly higher in chicks harboring the 2-bp deletion in exon 2. We identified 7 novel transcript variants using total mRNA isolated from the amygdala. Novel isoforms were found to lack the exon 2 cassette, which probably harbored the premature termination codon. The relative transcription levels of the newly identified isoforms were almost the same between chick groups with and without the 2-bp deletion, while chicks with the deletion showed significant suppression of the expression of previously reported isoforms.ConclusionsA putative frameshift deletion and CNV in chicken NRG3 are structural mutations that occurred before the establishment of commercial chicken lines. Our results further suggest that the putative frameshift deletion in exon 2 may potentially affect the expression level of particular isoforms of chicken NRG3.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-017-0537-z) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Gene expression patterns of chicken neuregulin 3 in association with copy number variation and frameshift deletion

Abe

Aoya²,

Takeuchi

et al. 2017

BMC Genet

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“…There are many studies, mostly in chickens, that show associations between SVs and feathering phenotypes (Chen, Xi, et al., 2022; Derks et al., 2018; Domyan et al., 2016; Dong et al., 2018; Elferink et al., 2008; Li et al., 2020; Li, Lee, et al., 2021; Mou et al., 2011; Ng et al., 2012; Shen et al., 2023); comb, muff and beard traits (Dorshorst et al., 2015; Guo et al., 2016; Imsland et al., 2012; Moro et al., 2015; Sato et al., 2010; Wang et al., 2017; Wright et al., 2009; Yang et al., 2020, 2021); and egg production (Cui et al., 2006; Huang et al., 2018; Lan et al., 2021; Manoharan et al., 2021; Vinh et al., 2021). Although less common, there are also associations between SVs and behaviour and domestication (Abe et al., 2013; Chen, Bai, et al., 2022; Falker‐Gieske et al., 2023; Khatri et al., 2019; Komiyama et al., 2014; Krause et al., 2019; Rubin et al., 2010; Seol et al., 2019; Zhou et al., 2018; Zhu et al., 2021). Other uncommon traits associated with SVs are craniofacial deformities (Bai et al., 2018; Chang et al., 2014; Gu et al., 2017), fertility (Gu et al., 2017), muscle glycogen content (Liu et al., 2020), number of vertebrae (Xu et al., 2022) and aldehyde flavour (Yuan et al., 2022).…”

Section: Identifying Associations Between Svs and Phenotypic Traitsmentioning

confidence: 99%

How structural variants shape avian phenotypes: Lessons from model systems

Recuerda,

Campagna

2024

Molecular Ecology

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Despite receiving significant recent attention, the relevance of structural variation (SV) in driving phenotypic diversity remains understudied, although recent advances in long‐read sequencing, bioinformatics and pangenomic approaches have enhanced SV detection. We review the role of SVs in shaping phenotypes in avian model systems, and identify some general patterns in SV type, length and their associated traits. We found that most of the avian SVs so far identified are short indels in chickens, which are frequently associated with changes in body weight and plumage colouration. Overall, we found that relatively short SVs are more frequently detected, likely due to a combination of their prevalence compared to large SVs, and a detection bias, stemming primarily from the widespread use of short‐read sequencing and associated analytical methods. SVs most commonly involve non‐coding regions, especially introns, and when patterns of inheritance were reported, SVs associated primarily with dominant discrete traits. We summarise several examples of phenotypic convergence across different species, mediated by different SVs in the same or different genes and different types of changes in the same gene that can lead to various phenotypes. Complex rearrangements and supergenes, which can simultaneously affect and link several genes, tend to have pleiotropic phenotypic effects. Additionally, SVs commonly co‐occur with single‐nucleotide polymorphisms, highlighting the need to consider all types of genetic changes to understand the basis of phenotypic traits. We end by summarising expectations for when long‐read technologies become commonly implemented in non‐model birds, likely leading to an increase in SV discovery and characterisation. The growing interest in this subject suggests an increase in our understanding of the phenotypic effects of SVs in upcoming years.

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“…There are many studies, mostly in chickens, on feathering phenotypes (45,(64)(65)(66)(67)(68)(69)(70)(71)(72); comb, muff and beard traits [73][74][75][76][77][78][79][80][81], and egg production [9][10][11]82,83]. Although less common, there are also associations between SVs and behavior and domestication [4,5,64,[84][85][86][87][88][89][90]. Other uncommon traits associated with SVs are craniofacial deformities [91,92], fertility [93], muscle glycogen content [94], number of vertebrae [95] and Aldehyde flavor [96].…”

Section: Phenotypic Traits Associated To Svsmentioning

confidence: 99%

How structural variants shape avian phenotypes: lessons from model systems

Recuerda,

Campagna

2023

Preprint

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Despite receiving significant recent attention, the relevance of Structural Variation (SV) in driving phenotypic diversity remains understudied. Advances in long-read sequencing, bioinformatics and pangenomic approaches, enhance SV detection. We review the role of SVs in shaping phenotypes in avian model systems, and identify general patterns in SV type, length, and their associated traits. Notably, most of the identified SVs are short indels in chickens, frequently associated with changes in body weight and plumage coloration. This review highlights how SVs underlie phenotypes in avian model systems and sets expectations for when long-read technologies become commonly implemented in non-model birds. The growing interest in this subject suggests an increase in our understanding of the phenotypic effects of SVs in upcoming years.

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Short Copy Number Variations Potentially Associated with Tonic Immobility Responses in Newly Hatched Chicks

Cited by 9 publications

References 36 publications

Gene expression patterns of chicken neuregulin 3 in association with copy number variation and frameshift deletion

Gene expression patterns of chicken neuregulin 3 in association with copy number variation and frameshift deletion

How structural variants shape avian phenotypes: Lessons from model systems

How structural variants shape avian phenotypes: lessons from model systems

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