Heterogeneity of a dwarf phenotype in Dutch traditional chicken breeds revealed by genomic analyses

Wu, Zhou; Bortoluzzi, Chiara; Derks, Martijn F.L.; Liu, Langqing; Bosse, Mirte; Hiemstra, S.J.; Groenen, M.A.M.; Crooijmans, R.P.M.A.

doi:10.1111/eva.13183

Cited by 10 publications

(20 citation statements)

References 94 publications

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“…Additionally, we identified a new candidate gene, RCBTB1 , whose mutation in the promoter region plays an important role in muscle and liver development ( Guo et al, 2004 ). For bone tissue, the most significant locus was 30 kb from the nearest novel lncRNA gene ( ENSGALG00000053256 ), associated with chicken body size ( Wu et al, 2021 ). We speculate that this may be a potential enhancer regulator, although few functional studies of this lncRNA have been performed.…”

Section: Discussionmentioning

confidence: 99%

Chicken chromatin accessibility atlas accelerates epigenetic annotation of birds and gene fine-mapping associated with growth traits

Zhu¹,

Wang²,

Li³

et al. 2023

Zoological Research

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The development of epigenetic maps, such as the ENCODE project in humans, provides resources for gene regulation studies and a reference for research of disease-related regulatory elements. However, epigenetic information, such as a bird-specific chromatin accessibility atlas, is currently lacking for the thousands of bird species currently described. The major genomic difference between birds and mammals is their shorter introns and intergenic distances, which seriously hinders the use of humans and mice as a reference for studying the function of important regulatory regions in birds. In this study, using chicken as a model bird species, we systematically compiled a chicken chromatin accessibility atlas using 53 Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) samples across 11 tissues. An average of 50 796 open chromatin regions were identified per sample, cumulatively accounting for 20.36% of the chicken genome. Tissue specificity was largely reflected by differences in intergenic and intronic peaks, with specific functional regulation achieved by two mechanisms: recruitment of several sequence-specific transcription factors and direct regulation of adjacent functional genes. By integrating data from genome-wide association studies, our results suggest that chicken body weight is driven by different regulatory variants active in growth-relevant tissues. We propose CAB39L (active in the duodenum), RCBTB1 (muscle and liver), and novel long non-coding RNA ENSGALG00000053256 (bone) as candidate genes regulating chicken body weight. Overall, this study demonstrates the value of epigenetic data in fine-mapping functional variants and provides a compendium of resources for further research on the epigenetics and evolution of birds and mammals.

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Section: Discussionmentioning

confidence: 99%

Chicken chromatin accessibility atlas accelerates epigenetic annotation of birds and gene fine-mapping associated with growth traits

Zhu¹,

Wang²,

Li³

et al. 2023

Zoological Research

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“…With the F ST , H p and XP-CLR with sliding window approaches, nine genes (PRDM16, ZNF382, ZNF461, ERGIC2, ENSCAFG00000033351, CCDC61, ALDH3A2, ENSCAFG00000011141, and ENSCAFG00000018533) were found to show selection signatures. Among these genes, PRDM16 was reported to be associated with growth traits in some species, such as bovine and chicken (Wang et al, 2010;Wu et al, 2021). It is known that PRDM16 controls a brown fat/skeletal muscle switch (Seale et al, 2008), and it might take a role in the growth of Mame Shiba Inu.…”

Section: Discussionmentioning

confidence: 99%

Whole Genome Sequencing Reveals Signatures for Artificial Selection for Different Sizes in Japanese Primitive Dog Breeds

et al. 2021

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Body size is an important trait in companion animals. Recently, a primitive Japanese dog breed, the Shiba Inu, has experienced artificial selection for smaller body size, resulting in the “Mame Shiba Inu” breed. To identify loci and genes that might explain the difference in the body size of these Shiba Inu dogs, we applied whole genome sequencing of pooled samples (pool-seq) on both Shiba Inu and Mame Shiba Inu. We identified a total of 13,618,261 unique SNPs in the genomes of these two breeds of dog. Using selective sweep approaches, including FST, Hp and XP-CLR with sliding windows, we identified a total of 12 genomic windows that show signatures of selection that overlap with nine genes (PRDM16, ZNF382, ZNF461, ERGIC2, ENSCAFG00000033351, CCDC61, ALDH3A2, ENSCAFG00000011141, and ENSCAFG00000018533). These results provide candidate genes and specific sites that might be associated with body size in dogs. Some of these genes are associated with body size in other mammals, but 8 of the 9 genes are novel candidate genes that need further study.

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“…In chickens, the dwarf phenotype is evaluated by different traits including, but not limited to, body weight, height, and shank length [ 6 , 7 ]. Based on physiological and genetic characteristics, four distinct types of dwarfism in chickens have been identified: sex-linked dwarfism, which has been well-studied and is caused by mutations in the growth hormone receptor gene ( GHR ) [ 8 , 9 ]; autosomal dwarfism, which is caused by a nonsense mutation in the transmembrane protein 263 gene ( TMEM263 ) [ 10 ]; the bantam phenotype, associated with the HMGA2 gene on chromosome 1 [ 11 ]; and creeper dwarfism due to a creeper allele described as a 25 kb deletion containing the IHH and non-homologous end-joining factor 1 ( NHEJ1 ) genes [ 12 , 13 ].…”

Section: Introductionmentioning

confidence: 99%

Genomics of Dwarfism in Italian Local Chicken Breeds

Perini

Cendron

et al. 2023

Genes

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The identification of the dwarf phenotype in chicken is based on body weight, height, and shank length, leaving the differentiation between dwarf and small breeds ambiguous. The aims of the present study were to characterize the sequence variations associated with the dwarf phenotype in three Italian chicken breeds and to investigate the genes associated with their phenotype. Five hundred and forty-one chickens from 23 local breeds (from 20 to 24 animals per breed) were sampled. All animals were genotyped with the 600 K chicken SNP array. Three breeds were described as “dwarf”, namely, Mericanel della Brianza (MERI), Mugellese (MUG), and Pepoi (PPP). We compared MERI, MUG, and PPP with the four heaviest breeds in the dataset by performing genome-wide association studies. Results showed significant SNPs associated with dwarfism in the MERI and MUG breeds, which shared a candidate genomic region on chromosome 1. Due to this similarity, MERI and MUG were analyzed together as a meta-population, observing significant SNPs in the LEMD3 and HMGA2 genes, which were previously reported as being responsible for dwarfism in different species. In conclusion, MERI and MUG breeds seem to share a genetic basis of dwarfism, which differentiates them from the small PPP breed.

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Heterogeneity of a dwarf phenotype in Dutch traditional chicken breeds revealed by genomic analyses

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 10 publications

References 94 publications

Chicken chromatin accessibility atlas accelerates epigenetic annotation of birds and gene fine-mapping associated with growth traits

Chicken chromatin accessibility atlas accelerates epigenetic annotation of birds and gene fine-mapping associated with growth traits

Whole Genome Sequencing Reveals Signatures for Artificial Selection for Different Sizes in Japanese Primitive Dog Breeds

Genomics of Dwarfism in Italian Local Chicken Breeds

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