scholarly journals The genetics and evolution of eye color in domestic pigeons (Columba livia)

PLoS Genetics ◽  
2021 ◽  
Vol 17 (8) ◽  
pp. e1009770
Author(s):  
Si Si ◽  
Xiao Xu ◽  
Yan Zhuang ◽  
Xiaodong Gao ◽  
Honghai Zhang ◽  
...  
Keyword(s):  
Glucose Transporter ◽  
Genome Wide Association Study ◽  
Stop Codon ◽  
Phylogenetic Analyses ◽  
Premature Stop Codon ◽  
Columba Livia ◽  
Eye Color ◽  
Iris Color ◽  
A Genome ◽  
Domestic Pigeons

The eye color of birds, generally referring to the color of the iris, results from both pigmentation and structural coloration. Avian iris colors exhibit striking interspecific and intraspecific variations that correspond to unique evolutionary and ecological histories. Here, we identified the genetic basis of pearl (white) iris color in domestic pigeons (Columba livia) to explore the largely unknown genetic mechanism underlying the evolution of avian iris coloration. Using a genome-wide association study (GWAS) in 92 pigeons, we mapped the pearl iris trait to a 9 kb region containing the facilitative glucose transporter gene SLC2A11B. A nonsense mutation (W49X) leading to a premature stop codon in SLC2A11B was identified as the causal variant. Transcriptome analysis suggested that SLC2A11B loss of function may downregulate the xanthophore-differentiation gene CSF1R and the key pteridine biosynthesis gene GCH1, thus resulting in the pearl iris phenotype. Coalescence and phylogenetic analyses indicated that the mutation originated approximately 5,400 years ago, coinciding with the onset of pigeon domestication, while positive selection was likely associated with artificial breeding. Within Aves, potentially impaired SLC2A11B was found in six species from six distinct lineages, four of which associated with their signature brown or blue eyes. Analysis of vertebrate SLC2A11B orthologs revealed relaxed selection in the avian clade, consistent with the scenario that during and after avian divergence from the reptilian ancestor, the SLC2A11B-involved development of dermal chromatophores likely degenerated in the presence of feather coverage. Our findings provide new insight into the mechanism of avian iris color variations and the evolution of pigmentation in vertebrates.

scholarly journals The Genetics and Evolution of Eye Color in Domestic Pigeons (Columba livia)

2020 ◽  
Author(s):  
Si Si ◽  
Xiao Xu ◽  
Yan Zhuang ◽  
Xiaodong Gao ◽  
Honghai Zhang ◽  
...  
Keyword(s):  
Glucose Transporter ◽  
Genome Wide Association Study ◽  
Stop Codon ◽  
Phylogenetic Analyses ◽  
Premature Stop Codon ◽  
Columba Livia ◽  
Eye Color ◽  
Iris Color ◽  
A Genome ◽  
Domestic Pigeons

The avian eye color, generally referred to the color of the iris, results from both pigments and structural coloration. Avian iris colors exhibit striking interspecific and, in some domestic species, intraspecific variations, suggesting unique evolutionary and ecological histories. Here we tackled the genetic basis of the pearl (white) iris color in domestic pigeons (Columba livia), to elucidate the largely unknown genetic mechanism underlying the evolution of avian iris coloration. Using a genome-wide association study (GWAS) in 92 pigeons, we mapped the pearl iris trait to a 9 kb region and a facilitative glucose transporter gene SLC2A11B. A nonsense mutation W49X leading to a premature stop codon in SLC2A11B was identified as the causal variant. Transcriptome analysis suggested that SLC2A11B loss-of-function may downregulate the xanthophore-differentiation gene CSF1R, and a key gene GCH1 involved in biosynthesis of pteridine, whose absence results in pearl iris. Coalescence and phylogenetic analyses indicated the mutation originated about 5,400 years ago coinciding with the onset of pigeon domestication, while positive selection was detected likely associated with artificial breeding. Within Aves, potentially impaired SLC2A11B was found in 10 species from six distinct lineages correlated to their signature brown or blue eyes. Analysis of vertebrate SLC2A11B orthologs revealed relaxed selection in the avian clade, consistent with the scenario that, during and after avian divergence from reptile ancestor, the SLC2A11B-involved development of dermal chromatophores likely degenerated due to feather coverage. Our findings provide new insight into the mechanism of avian iris color variations and the evolution of pigmentation in vertebrates.

scholarly journals Investigations into a putative role for the novel BRASSIKIN pseudokinases in compatible pollen-stigma interactions in Arabidopsis thaliana

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Jennifer Doucet ◽  
Hyun Kyung Lee ◽  
Nethangi Udugama ◽  
Jianfeng Xu ◽  
Baoxiu Qi ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Stop Codon ◽  
Phylogenetic Analyses ◽  
Premature Stop Codon ◽  
The Novel ◽  
Specific Expression ◽  
Deletion Mutations ◽  
Brassicaceae Species ◽  
Compatible Pollen ◽  
Compatible Interactions

Abstract Background In the Brassicaceae, the early stages of compatible pollen-stigma interactions are tightly controlled with early checkpoints regulating pollen adhesion, hydration and germination, and pollen tube entry into the stigmatic surface. However, the early signalling events in the stigma which trigger these compatible interactions remain unknown. Results A set of stigma-expressed pseudokinase genes, termed BRASSIKINs (BKNs), were identified and found to be present in only core Brassicaceae genomes. In Arabidopsis thaliana Col-0, BKN1 displayed stigma-specific expression while the BKN2 gene was expressed in other tissues as well. CRISPR deletion mutations were generated for the two tandemly linked BKNs, and very mild hydration defects were observed for wild-type Col-0 pollen when placed on the bkn1/2 mutant stigmas. In further analyses, the predominant transcript for the stigma-specific BKN1 was found to have a premature stop codon in the Col-0 ecotype, but a survey of the 1001 Arabidopsis genomes uncovered three ecotypes that encoded a full-length BKN1 protein. Furthermore, phylogenetic analyses identified intact BKN1 orthologues in the closely related outcrossing Arabidopsis species, A. lyrata and A. halleri. Finally, the BKN pseudokinases were found to be plasma-membrane localized through the dual lipid modification of myristoylation and palmitoylation, and this localization would be consistent with a role in signaling complexes. Conclusion In this study, we have characterized the novel Brassicaceae-specific family of BKN pseudokinase genes, and examined the function of BKN1 and BKN2 in the context of pollen-stigma interactions in A. thaliana Col-0. Additionally, premature stop codons were identified in the predicted stigma specific BKN1 gene in a number of the 1001 A. thaliana ecotype genomes, and this was in contrast to the out-crossing Arabidopsis species which carried intact copies of BKN1. Thus, understanding the function of BKN1 in other Brassicaceae species will be a key direction for future studies.

scholarly journals Molecular parallelisms between pigmentation in the avian iris and the integument of ectothermic vertebrates

PLoS Genetics ◽  
2021 ◽  
Vol 17 (2) ◽  
pp. e1009404
Author(s):  
Pedro Andrade ◽  
Małgorzata A. Gazda ◽  
Pedro M. Araújo ◽  
Sandra Afonso ◽  
Jacob. A. Rasmussen ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Stop Codon ◽  
Expression Profiles ◽  
Single Gene ◽  
Skin Pigmentation ◽  
Premature Stop Codon ◽  
Gene Expression Profiles ◽  
Genomic Region ◽  
Pigment Cells ◽  
Eye Color

Birds exhibit striking variation in eye color that arises from interactions between specialized pigment cells named chromatophores. The types of chromatophores present in the avian iris are lacking from the integument of birds or mammals, but are remarkably similar to those found in the skin of ectothermic vertebrates. To investigate molecular mechanisms associated with eye coloration in birds, we took advantage of a Mendelian mutation found in domestic pigeons that alters the deposition of yellow pterin pigments in the iris. Using a combination of genome-wide association analysis and linkage information in pedigrees, we mapped variation in eye coloration in pigeons to a small genomic region of ~8.5kb. This interval contained a single gene, SLC2A11B, which has been previously implicated in skin pigmentation and chromatophore differentiation in fish. Loss of yellow pigmentation is likely caused by a point mutation that introduces a premature STOP codon and leads to lower expression of SLC2A11B through nonsense-mediated mRNA decay. There were no substantial changes in overall gene expression profiles between both iris types as well as in genes directly associated with pterin metabolism and/or chromatophore differentiation. Our findings demonstrate that SLC2A11B is required for the expression of pterin-based pigmentation in the avian iris. They further highlight common molecular mechanisms underlying the production of coloration in the iris of birds and skin of ectothermic vertebrates.

scholarly journals Two Genomic Loci Control Three Eye Colors in the Domestic Pigeon (Columba livia)

2021 ◽  
Author(s):  
Emily T. Maclary ◽  
Bridget Phillips ◽  
Ryan Wauer ◽  
Elena F. Boer ◽  
Rebecca Bruders ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Single Species ◽  
Columba Livia ◽  
Color Pattern ◽  
Color Variation ◽  
Domestic Pigeon ◽  
Eye Color ◽  
Solute Carrier ◽  
Neural Crest Migration ◽  
Domestic Pigeons

ABSTRACTThe iris of the eye shows striking color variation across vertebrate species, and may play important roles in crypsis and communication. The domestic pigeon (Columba livia) has three common iris colors, orange, pearl (white), and bull (dark brown), segregating in a single species, thereby providing a unique opportunity to identify the genetic basis of iris coloration. We used comparative genomics and genetic mapping in laboratory crosses to identify two candidate genes that control variation in iris color in domestic pigeons. We identified a nonsense mutation in the solute carrier SLC2A11B that is shared among all pigeons with pearl eye color, and a locus associated with bull eye color that includes EDNRB2, a gene involved in neural crest migration and pigment development. However, bull eye is likely controlled by a heterogeneous collection of alleles across pigeon breeds. We also found that the EDNRB2 region is associated with regionalized plumage depigmentation (piebalding). Our results establish a genetic link between iris and plumage color, two traits that were long known by pigeon breeders to co-occur, and demonstrate the importance of gene duplicates in establishing possibilities and constraints in the evolution of color and color pattern among vertebrates.

scholarly journals Two Genomic Loci Control Three Eye Colors in the Domestic Pigeon (Columba livia)

2021 ◽  
Author(s):  
Emily T Maclary ◽  
Bridget Phillips ◽  
Ryan Wauer ◽  
Elena F Boer ◽  
Rebecca Bruders ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Single Species ◽  
Columba Livia ◽  
Color Variation ◽  
Domestic Pigeon ◽  
Eye Color ◽  
Evolution Of Birds ◽  
Solute Carrier ◽  
Neural Crest Migration ◽  
Domestic Pigeons

Abstract The iris of the eye shows striking color variation across vertebrate species, and may play important roles in crypsis and communication. The domestic pigeon (Columba livia) has three common iris colors, orange, pearl (white), and bull (dark brown), segregating in a single species, thereby providing a unique opportunity to identify the genetic basis of iris coloration. We used comparative genomics and genetic mapping in laboratory crosses to identify two candidate genes that control variation in iris color in domestic pigeons. We identified a nonsense mutation in the solute carrier SLC2A11B that is shared among all pigeons with pearl eye color, and a locus associated with bull eye color that includes EDNRB2, a gene involved in neural crest migration and pigment development. However, bull eye is likely controlled by a heterogeneous collection of alleles across pigeon breeds. We also found that the EDNRB2 region is associated with regionalized plumage depigmentation (piebalding). Our study identifies two candidate genes for eye colors variation, and establishes a genetic link between iris and plumage color, two traits that vary widely in the evolution of birds and other vertebrates.

scholarly journals Novel genetic basis of resistance to Bt toxin Cry1Ac in Helicoverpa zea

2021 ◽  
Author(s):  
Kyle M Benowitz ◽  
Carson W Allan ◽  
Benjamin A Degain ◽  
Xianchun Li ◽  
Jeffrey A Fabrick ◽  
...  
Keyword(s):  
Helicoverpa Zea ◽  
Genetic Basis ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
Pest Resistance ◽  
The United States ◽  
Chromosome 13 ◽  
Bt Toxin ◽  
Bt Toxins ◽  
A Genome

Crops genetically engineered to produce insecticidal proteins from the bacterium Bacillus thuringiensis (Bt) have advanced pest management, but their benefits are diminished when pests evolve resistance. Elucidating the genetic basis of pest resistance to Bt toxins can improve resistance monitoring, resistance management, and design of new insecticides. Here, we investigated the genetic basis of resistance to Bt toxin Cry1Ac in the lepidopteran Helicoverpa zea, one of the most damaging crop pests in the United States. To facilitate this research, we built the first chromosome-level genome assembly for this species. Using a genome-wide association study, fine-scale mapping, and RNA-seq, we identified a 250kb QTL on chromosome 13 that was strongly associated with resistance in a strain of H. zea that had been selected for resistance in the field and lab. This QTL contains no genes with a previously reported role in resistance or susceptibility to Bt toxins. However, within this QTL, we discovered a premature stop codon in a kinesin gene. We hypothesize that this mutation contributes to resistance. The results indicate the mutation on chromosome 13 was necessary but not sufficient for resistance, and therefore conclude that mutations in more than one gene contributed to resistance. Moreover, we found no changes in gene sequence or expression consistently associated with resistance for 11 genes previously implicated in lepidopteran resistance to Cry1Ac. Thus, the results reveal a novel and polygenic basis of resistance and extend the list of genes contributing to pest resistance to Bt toxins.

Ectopic Transcript Analysis Indicates that Allelic Exclusion is an Important Cause of Type I Protein C Deficiency in Patients with Nonsense and Frameshift Mutations in the PROC Gene

1996 ◽  
Vol 75 (06) ◽  
pp. 870-876 ◽  
Author(s):  
José Manuel Soria ◽  
Lutz-Peter Berg ◽  
Jordi Fontcuberta ◽  
Vijay V Kakkar ◽  
Xavier Estivill ◽  
...  
Keyword(s):  
Splice Site ◽  
Protein C ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
Allelic Exclusion ◽  
Polymorphism Analysis ◽  
Type I ◽  
Protein C Deficiency ◽  
Nonsense Mutations ◽  
Stop Codons

SummaryNonsense mutations, deletions and splice site mutations are a common cause of type I protein C deficiency. Either directly or indirectly by altering the reading frame, these' lesions generate or may generate premature stop codons and could therefore be expected to result in premature termination of translation. In this study, the possibility that such mutations could instead exert their pathological effects at an earlier stage in the expression pathway, through “allelic exclusion” at the RNA level, was investigated. Protein C (PROC) mRNA was analysed in seven Spanish type I protein C deficient patients heterozygous for two nonsense mutations, a 7bp deletion, a 2bp insertion and three splice site mutations. Ectopic RNA transcripts from patient and control lymphocytes were analysed by RT-PCR and direct sequencing of amplified PROC cDNA fragments. The nonsense mutations and the deletion were absent from the cDNAs indicating that only mRNA derived from the normal allele had been expressed. Similarly for the splice site mutations, only normal PROC cDNAs were obtained. In one case, exclusion of the mutated allele could be confirmed by polymorphism analysis. In contrast to these six mutations, the 2 bp insertion was not associated with loss of mRNA from the mutated allele. In this case, cDNA analysis revealed the absence of 19 bases from the PROC mRNA consistent with the generation and utilization of a cryptic splice site 3’ to the site of mutation, which would result in a frameshift and a premature stop codon. It is concluded that allelic exclusion is a common causative mechanism in those cases of type I protein C deficiency which result from mutations that introduce premature stop codons

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