Two new structural mutations in the 5′ region of the ASIP gene cause diluted feather color phenotypes in Japanese quail

Robic, Annie; Morisson, Mireille; Leroux, Sophie; Gourichon, David; Vignal, Alain; Thébault, Noémie; Fillon, Valérie; Minvielle, Francis; Bed’Hom, Bertrand; Zerjal, Tatiana; Pitel, Frédérique

doi:10.1186/s12711-019-0458-6

Cited by 24 publications

(22 citation statements)

References 32 publications

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“…Large structural variations involving the entire ASIP gene have also been shown to cause the white coat color in Merino sheep and Saanen goats [ 44 – 46 ]. Structural variations that affect only the 5′-regulatory region of ASIP are also responsible for three characteristic mutant coat patterns in goats [ 46 ], namely Swiss markings ( A sm ), badgerface ( A b ) and peacock ( A pc ), and for color dilution in quails [ 47 ].…”

Section: Discussionmentioning

confidence: 99%

Variants at the ASIP locus contribute to coat color darkening in Nellore cattle

Trigo

Utsunomiya²,

Fortunato

et al. 2021

Genet Sel Evol

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Background Nellore cattle (Bos indicus) are well-known for their adaptation to warm and humid environments. Hair length and coat color may impact heat tolerance. The Nellore breed has been strongly selected for white coat, but bulls generally exhibit darker hair ranging from light grey to black on the head, neck, hump, and knees. Given the potential contribution of coat color variation to the adaptation of cattle populations to tropical and sub-tropical environments, our aim was to map positional and functional candidate genetic variants associated with darkness of hair coat (DHC) in Nellore bulls. Results We performed a genome-wide association study (GWAS) for DHC using data from 432 Nellore bulls that were genotyped for more than 777 k single nucleotide polymorphism (SNP) markers. A single major association signal was detected in the vicinity of the agouti signaling protein gene (ASIP). The analysis of whole-genome sequence (WGS) data from 21 bulls revealed functional variants that are associated with DHC, including a structural rearrangement involving ASIP (ASIP-SV1). We further characterized this structural variant using Oxford Nanopore sequencing data from 13 Australian Brahman heifers, which share ancestry with Nellore cattle; we found that this variant originates from a 1155-bp deletion followed by an insertion of a transposable element of more than 150 bp that may impact the recruitment of ASIP non-coding exons. Conclusions Our results indicate that the variant ASIP sequence causes darker coat pigmentation on specific parts of the body, most likely through a decreased expression of ASIP and consequently an increased production of eumelanin.

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Section: Discussionmentioning

confidence: 99%

Variants at the ASIP locus contribute to coat color darkening in Nellore cattle

Trigo

Utsunomiya²,

Fortunato

et al. 2021

Genet Sel Evol

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“…The study of epistasis can be interesting because epistatic interactions aid understanding of the functional relations of genes involved in the trait under study and sometimes can compensate for a lack of additive genome-wide studies in quantitative traits (Visscher et al 2012(Visscher et al , 2017Lee et al 2016). Distinct genes in chickens control plumage color traits (Li et al 2019a,b) and the genes associated with plumage pigmentation, such as melanocortin 1 receptor (MC1R; Kerje et al 2003;Hoque et al 2013;Zhang et al 2013;Ran et al 2016;Tu et al 2019;Yang et al 2019), tyrosinase (TYR;Yang et al 2019;Zheng et al 2020), premelanosome protein (PMEL; Kerje et al 2004;Abolins-Abols et al 2018;Zheng et al 2020), melanophilin (MLPH;Vaez et al 2008;Bed'hom et al 2012), Agouti signaling protein (ASIP; Robic et al 2019;Yang et al 2019), SRY-box (SOX families; Harris et al 2010;Gunnarsson et al 2011), solute carrier family member 2 (SLC45A2; Gunnarsson et al 2007;Zheng et al 2020) and endothelin B2 receptor (EDNRB2; Kinoshita et al 2014;Li et al 2015;Wu et al 2017;Xi et al 2020), are well known. Accordingly, multiple responsible genes have been reported for plumage color variation, but studies have focused on single loci with a major effect, rather than effective modifier loci with small or epistatic effects that influence plumage color more delicately.…”

Section: Introductionmentioning

confidence: 99%

New insights into genetics underlying of plumage color

et al. 2021

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Plumage color can be considered as a social signal in chickens and a breeding identification tool among breeders. The relationship between plumage color and trait groups of immunity, growth and fertility is still a controversial issue. This research aimed to determine the genome-wide additive and epistatic variants affecting plumage color variation in chickens using the chicken Illumina 60k high-density SNP array. Two scenarios of genome-wide additive association studies using all SNPs and independent SNPs were carried out. To perform epistatic association analysis, the LD pruning approach was used to reduce the complexity of the analysis. We detected seven novel significant loci using all of the SNPs in the model and 14 SNPs using the LD pruning approach associated with plumage color. Moreover, 89 significantly associated SNP-SNP interactions (P-value <10 −6 ) distributed in 25 chromosomes were identified, indicating that all of the signals together putatively influence the quantitative variation of plumage color. By annotating genes relevant to top SNPs, we have distinguished 18 potential candidate genes comprising HNF4beta, CKMT1B,

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“…To date, a number of researches about the genetic mechanism of plumage colour in avian have been reported (Domyan et al, 2014;Robic et al, 2019). In the present study, the mechanism of the formation of white plumage phenotype was explored in peafowl combined transcriptome analysis and RT-qPCR with resequencing data.…”

Section: Discussionmentioning

confidence: 89%

A High-Quality Assembly Reveals Genomic Characteristics, 1 Phylogenetic Status and Causal Genes for White Feather of 2 Indian Peafowl

Liu

Chen

Ouyang

et al. 2021

Preprint

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Background : Indian peafowl ( Pavo cristatus ) attracts people's attention because of the exclusively dazzling phenotypic characteristics. However, little is known about the phenotypic evolution and phylogeny of Indian peafowl at the whole-genome level. So far, there has been no report on the genetic mechanism of the formation of white feather in white feather peafowl. Results : This study assembled a draft genome of Indian peafowl with a genome size of 1.05 Gb (the sequencing depth is 362×), and N50 of the contig and scaffold was up to 6.2 Mb and 11.4 Mb, respectively. Compared with other birds, Indian peafowl changed in terms of metabolism, immunity, skeletal development and feather development, which provided a novel insight into the phenotypic evolution of peafowl, such as the large body size and feather morphologies. It was confirmed that the phylogeny of Indian peafowl was closer to that of turkey than that of chicken. Specially, it was identified that PMEL was a causal gene leading to the formation of white plumage in blue and white feather peafowl. Conclusions: This study provides a peafowl genome with high-quality as well as a novel understanding in the phenotypic evolution and phylogeny of peafowl among other birds. The results contribute a valuable reference genome to the study of the avian genome evolution. In addition, the discovery of the genetic mechanism of white plumage not only is a breakthrough in the exploration of peafowl plumage, but also provides clues and new ideas for further investigations of the avian plumage coloration and artificial breeding in peafowl.

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Two new structural mutations in the 5′ region of the ASIP gene cause diluted feather color phenotypes in Japanese quail

Cited by 24 publications

References 32 publications

Variants at the ASIP locus contribute to coat color darkening in Nellore cattle

Variants at the ASIP locus contribute to coat color darkening in Nellore cattle

New insights into genetics underlying of plumage color

A High-Quality Assembly Reveals Genomic Characteristics, 1 Phylogenetic Status and Causal Genes for White Feather of 2 Indian Peafowl

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