A ∼ 4.1 kb deletion in IRX1 gene upstream is completely associated with rumplessness in Piao chicken

Zhang, Jinxin; Nie, Changsheng; Zhang, Xinye; Zhao, Xiurong; Jia, Yaxiong; Han, Jianlin; Chen, Yu; Wang, Liang; Lv, Xueze; Yang, Weijia; Li, Kaiyang; Zhang, Jianwei; Ning, Zhonghua; Bao, Haigang; Li, Junying; Zhao, Chunjiang; Qu, Lujiang

doi:10.1016/j.ygeno.2022.110515

Cited by 8 publications

(11 citation statements)

References 23 publications

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“…Early studies on mapping of the rumplessness trait in Piao through population comparisons have identified the associated region on chromosome 2 ( Wang et al 2021 ) and the candidate mutation, which is a structural variant ( Zhang et al 2022 ). While the specific role of this structural variation (SV) and its exact breakpoints weren’t explored in depth, the causal gene and the genetic mechanisms that underpin the trait's formation also remain undefined.…”

Section: Introductionmentioning

confidence: 99%

Mapping and Functional Dissection of the Rumpless Trait in Piao Chicken Identifies a Causal Loss of Function Mutation in the Novel Gene Rum

Guo,

Tian,

Song

et al. 2023

Molecular Biology and Evolution

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Rumpless chickens exhibit an abnormality in their tail development. The genetics and biology of this trait has been studied for decades to illustrate a broad variation in both the types of inheritance and the severity in the developmental defects of the tail. In this study, we created a backcross pedigree by intercrossing Piao (rumpless) with Xianju (normal) to investigate the genetic mechanisms and molecular basis of the rumpless trait in Piao chicken. Through genome-wide association and linkage analyses, the candidate region was fine-mapped to 798.5 kb (chromosome 2: 86.9 to 87.7 Mb). Whole-genome sequencing analyses identified a single variant, a 4.2 kb deletion, which was completely associated with the rumpless phenotype. Explorations of the expression data identified a novel causative gene, Rum, that produced a long, intronless transcript across the deletion. The expression of Rum is embryo-specific, and it regulates the expression of MSGN1, a key factor in regulating T-box transcription factors required for mesoderm formation and differentiation. These results provide genetic and molecular experimental evidence for a novel mechanism regulating tail development in chicken and report the likely causal mutation for the tail abnormity in the Piao chicken. The novel regulatory gene, Rum, will, due to its role in fundamental embryo development, be of interest for further explorations of a potential role in tail and skeletal development also in other vertebrates.

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Section: Introductionmentioning

confidence: 99%

Mapping and Functional Dissection of the Rumpless Trait in Piao Chicken Identifies a Causal Loss of Function Mutation in the Novel Gene Rum

Guo,

Tian,

Song

et al. 2023

Molecular Biology and Evolution

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“…A study found that the LINGO2 gene might be associated with rumplessness in Hongshan chicken ( Wang et al, 2018 ). Irx1 gene had been found to be associated with rumplessness in both Piao chicken ( Zhang et al, 2022 ) and Araucana Chicken ( Noorai et al, 2012 ). Other several candidate genes such as Irx2, Irx4, Il18, Hspb2, Cryab, Rum had also been identified in the study of rumplessness in Piao chicken ( Wang et al, 2021 ; Guo et al, 2023 ).…”

Section: Discussionmentioning

confidence: 99%

“…The genetic mechanism of the tailless trait in Hongshan chickens is helpful for improving their tail feather appearance and also for exploring the rich genetic resources of local chicken breeds in China. Abnormal tail appearance had also been found in other chicken breeds, among which Irx1, Irx4, Il18, Hspb2, Cryab, Rum genes have been found to be associated with rumplessness in Piao chickens ( Wang et al, 2021 ; Zhang et al, 2022 ; Guo et al, 2023 ). The deletion of 4,174 bp upstream of the IRX1 gene on chromosome 2 in Piao chickens was believed to be the cause of the rumplessness ( Zhang et al, 2022 ).…”

Section: Introductionmentioning

confidence: 87%

“…Abnormal tail appearance had also been found in other chicken breeds, among which Irx1, Irx4, Il18, Hspb2, Cryab, Rum genes have been found to be associated with rumplessness in Piao chickens ( Wang et al, 2021 ; Zhang et al, 2022 ; Guo et al, 2023 ). The deletion of 4,174 bp upstream of the IRX1 gene on chromosome 2 in Piao chickens was believed to be the cause of the rumplessness ( Zhang et al, 2022 ). The newly discovered embryo specific Rum gene associated with rumplessness could regulate the expression of MSGN1 gene, which played a crucial role in the formation and differentiation of the mesoderm, so the Rum gene was also believed to be related to abnormal tail in Piao chickens ( Guo et al, 2023 ).…”

Section: Introductionmentioning

confidence: 87%

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Molecular genetic foundation of a sex-linked tailless trait in Hongshan chicken by whole genome data analysis

Chen,

Wang,

Zhao

et al. 2024

Poultry Science

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“…Plumage colouration differences in European crow populations are associated with a 2.25-kb LTR retrotransposon insertion (Weissensteiner et al, 2020). Additionally, Suh et al ( 2018 In chickens, SV occurs in both coding and non-coding regions of the genome and the presence of these variants is positively correlated with chromosome size (Zhang et al, 2022). Furthermore, due to SVs involving larger stretches of the genome compared to SNPs, they have the potential to significantly impact phenotype (Chiang et al, 2017;Zhang et al, 2021).…”

Section: S Vs/phenot Ype a Sso Ciati On S In Non -Model B Irdsmentioning

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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A ∼ 4.1 kb deletion in IRX1 gene upstream is completely associated with rumplessness in Piao chicken

Cited by 8 publications

References 23 publications

Mapping and Functional Dissection of the Rumpless Trait in Piao Chicken Identifies a Causal Loss of Function Mutation in the Novel Gene Rum

Mapping and Functional Dissection of the Rumpless Trait in Piao Chicken Identifies a Causal Loss of Function Mutation in the Novel Gene Rum

Molecular genetic foundation of a sex-linked tailless trait in Hongshan chicken by whole genome data analysis

How structural variants shape avian phenotypes: Lessons from model systems

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