scholarly journals Extensive hybridization reveals multiple coloration genes underlying a complex plumage phenotype

2020 ◽  
Author(s):  
Stepfanie M. Aguillon ◽  
Jennifer Walsh ◽  
Irby J. Lovette
Keyword(s):  
Genetic Basis ◽  
Important Target ◽  
Carotenoid Coloration ◽  
Genome Wide ◽  
Red Color ◽  
Color Differences ◽  
Genomic Regions ◽  
Carotenoid Pigmentation ◽  
Specific Control ◽  
Natural And Sexual Selection

ABSTRACTColoration is an important target of both natural and sexual selection. Discovering the genetic basis of color differences can help us to understand how this visually striking phenotype evolves. Hybridizing taxa with both clear color differences and shallow genomic divergences are unusually tractable for associating coloration phenotypes with their causal genotypes. Here, we leverage the extensive admixture between two common North American woodpeckers—yellow-shafted and red-shafted flickers—to identify the genomic bases of six distinct plumage patches involving both melanin and carotenoid pigments. Comparisons between flickers across ~8.5 million genome-wide SNPs show that these two forms differ at only a small proportion of the genome (mean FST = 0.007). Within the few highly differentiated genomic regions, we identify 408 SNPs significantly associated with four of the six plumage patches. These SNPs are linked to multiple genes known to be involved in melanin and carotenoid pigmentation. For example, a gene (CYP2J19) known to cause yellow to red color transitions in other birds is strongly associated with the yellow versus red differences in the wings and tail feathers of these flickers. Additionally, our analyses suggest novel links between known melanin genes and carotenoid coloration. Our finding of patch-specific control of plumage coloration adds to the growing body of literature suggesting color diversity in animals could be created through selection acting on novel combinations of coloration genes.

scholarly journals Extensive hybridization reveals multiple coloration genes underlying a complex plumage phenotype

2021 ◽  
Vol 288 (1943) ◽  
pp. 20201805
Author(s):  
Stepfanie M. Aguillon ◽  
Jennifer Walsh ◽  
Irby J. Lovette
Keyword(s):  
Genetic Basis ◽  
Carotenoid Pigments ◽  
Important Target ◽  
Carotenoid Coloration ◽  
Genome Wide ◽  
Growing Body ◽  
Genomic Regions ◽  
Carotenoid Pigmentation ◽  
Specific Control ◽  
Natural And Sexual Selection

Coloration is an important target of both natural and sexual selection. Discovering the genetic basis of colour differences can help us to understand how this visually striking phenotype evolves. Hybridizing taxa with both clear colour differences and shallow genomic divergences are unusually tractable for associating coloration phenotypes with their causal genotypes. Here, we leverage the extensive admixture between two common North American woodpeckers—yellow-shafted and red-shafted flickers—to identify the genomic bases of six distinct plumage patches involving both melanin and carotenoid pigments. Comparisons between flickers across approximately 7.25 million genome-wide SNPs show that these two forms differ at only a small proportion of the genome (mean F ST = 0.008). Within the few highly differentiated genomic regions, we identify 368 SNPs significantly associated with four of the six plumage patches. These SNPs are linked to multiple genes known to be involved in melanin and carotenoid pigmentation. For example, a gene ( CYP2J19 ) known to cause yellow to red colour transitions in other birds is strongly associated with the yellow versus red differences in the wing and tail feathers of these flickers. Additionally, our analyses suggest novel links between known melanin genes and carotenoid coloration. Our finding of patch-specific control of plumage coloration adds to the growing body of literature suggesting colour diversity in animals could be created through selection acting on novel combinations of coloration genes.

scholarly journals Behavior-dependent cis regulation reveals genes and pathways associated with bower building in cichlid fishes

2018 ◽  
Vol 115 (47) ◽  
pp. E11081-E11090 ◽  
Author(s):  
Ryan A. York ◽  
Chinar Patil ◽  
Kawther Abdilleh ◽  
Zachary V. Johnson ◽  
Matthew A. Conte ◽  
...  
Keyword(s):  
Gene Expression ◽  
Neural Plasticity ◽  
Genetic Basis ◽  
Specific Expression ◽  
Preferential Expression ◽  
Cichlid Fishes ◽  
Brain Gene Expression ◽  
Genome Wide ◽  
Allele Specific ◽  
Genomic Regions

Many behaviors are associated with heritable genetic variation [Kendler and Greenspan (2006) Am J Psychiatry 163:1683–1694]. Genetic mapping has revealed genomic regions or, in a few cases, specific genes explaining part of this variation [Bendesky and Bargmann (2011) Nat Rev Gen 12:809–820]. However, the genetic basis of behavioral evolution remains unclear. Here we investigate the evolution of an innate extended phenotype, bower building, among cichlid fishes of Lake Malawi. Males build bowers of two types, pits or castles, to attract females for mating. We performed comparative genome-wide analyses of 20 bower-building species and found that these phenotypes have evolved multiple times with thousands of genetic variants strongly associated with this behavior, suggesting a polygenic architecture. Remarkably, F1 hybrids of a pit-digging and a castle-building species perform sequential construction of first a pit and then a castle bower. Analysis of brain gene expression in these hybrids showed that genes near behavior-associated variants display behavior-dependent allele-specific expression with preferential expression of the pit-digging species allele during pit digging and of the castle-building species allele during castle building. These genes are highly enriched for functions related to neurodevelopment and neural plasticity. Our results suggest that natural behaviors are associated with complex genetic architectures that alter behavior via cis-regulatory differences whose effects on gene expression are specific to the behavior itself.

scholarly journals Genetic architecture and heritability of early-life telomere length in a wild passerine

2021 ◽  
Author(s):  
Michael Pepke ◽  
Thomas Kvalnes ◽  
Sarah Lundregan ◽  
Winnie Boner ◽  
Pat Monaghan ◽  
...  
Keyword(s):  
Body Size ◽  
Telomere Length ◽  
Early Life ◽  
Genetic Basis ◽  
Skeletal Development ◽  
Cellular Growth ◽  
Phenotypic Correlation ◽  
Animal Populations ◽  
Genome Wide ◽  
Genomic Regions

Early-life telomere length (TL) is associated with fitness in a range of organisms. Little is known about the genetic basis of variation in TL in wild animal populations, but to understand the evolutionary and ecological significance of TL it is important to quantify the relative importance of genetic and environmental variation in TL. In this study, we measured TL in 2746 house sparrow nestlings sampled across 20 years and used an animal model to show that there is a small heritable component of early-life TL (h2=0.04), but with a strong component of maternal inheritance. Variation in TL among individuals was mainly driven by environmental (year) variance, but also brood and parental effects. We did not find evidence for a negative genetic correlation underlying the observed negative phenotypic correlation between TL and structural body size. Thus, TL may evolve independently of body size and the negative phenotypic correlation is likely to be caused by non-genetic environmental effects. We further used genome‐wide association analysis to identify genomic regions associated with TL variation. We identified several putative genes underlying TL variation; these have been inferred to be involved in oxidative stress, cellular growth, skeletal development, cell differentiation and tumorigenesis in other species. Together, our results show that TL is a lowly heritable, polygenic trait which is strongly affected by environmental conditions in a free-living bird.

scholarly journals Genomic regions controlling shape variation in the first upper molar of the house mouse

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Luisa F Pallares ◽  
Ronan Ledevin ◽  
Sophie Pantalacci ◽  
Leslie M Turner ◽  
Eirikur Steingrimsson ◽  
...  
Keyword(s):  
Phenotypic Variation ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Shape Variation ◽  
Tooth Shape ◽  
Mus Musculus Musculus ◽  
Genome Wide ◽  
Genomic Regions ◽  
Hybrid Mice ◽  
Upper Molar

Numerous loci of large effect have been shown to underlie phenotypic variation between species. However, loci with subtle effects are presumably more frequently involved in microevolutionary processes but have rarely been discovered. We explore the genetic basis of shape variation in the first upper molar of hybrid mice between Mus musculus musculus and M. m. domesticus. We performed the first genome-wide association study for molar shape and used 3D surface morphometrics to quantify subtle variation between individuals. We show that many loci of small effect underlie phenotypic variation, and identify five genomic regions associated with tooth shape; one region contained the gene microphthalmia-associated transcription factor Mitf that has previously been associated with tooth malformations. Using a panel of five mutant laboratory strains, we show the effect of the Mitf gene on tooth shape. This is the first report of a gene causing subtle but consistent variation in tooth shape resembling variation in nature.

scholarly journals Selection on a pleiotropic color gene block underpins early differentiation between two warbler species

2019 ◽  
Author(s):  
Silu Wang ◽  
Sievert Rohwer ◽  
Devin R. de Zwaan ◽  
David P. L Toews ◽  
Irby J. Lovette ◽  
...  
Keyword(s):  
Gene Flow ◽  
Genetic Basis ◽  
Early Stage ◽  
Population Substructure ◽  
Carotenoid Pigment ◽  
Single Nucleotide ◽  
Gene Block ◽  
Genome Wide ◽  
Genomic Regions ◽  
Divergence With Gene Flow

AbstractWhen one species gradually splits into two, divergent selection on specific traits can cause peaks of differentiation in the genomic regions encoding those traits. Whether speciation is initiated by strong selection on a few genomic regions with large effects or by more diffused selection on many regions with small effects remains controversial. Differentiated phenotypes between differentiating lineages are commonly involved in reproductive isolation, thus their genetic underpinnings are key to the genomics architecture of speciation. When two species hybridize, recombination over multiple generations can help reveal the genetic regions responsible for the differentiated phenotypes against a genomic background that has been homogenized via backcrossing and introgression. We used admixture mapping to investigate genomic differentiation and the genetic basis of differentiated plumage features (relative melanin and carotenoid pigment) between hybridizing sister species in the early stage of speciation: Townsend’s (Setophaga townsendi) and Hermit warblers (S. occidentalis). We found a few narrow and dispersed divergent regions between allopatric parental populations, consistent with the ‘divergence with gene flow’ model of speciation. One of the divergent peaks involves three genes known to affect pigmentation: ASIP, EIF2S2, and RALY (the ASIP-RALY gene block). After controlling for population substructure, we found that a single nucleotide polymorphism (SNP) inside the intron of RALY displays a strong pleiotropic association with cheek, crown, and breast coloration. In addition, we detect selection on the ASIP-RALY gene block, as the geographic cline of the RALY marker of this gene block has remained narrower than the plumage cline, which remained narrower than expected under neutral diffusion over two decades. Despite extensive gene flow between these species across much of the genome, the selection on ASIP-RALY gene block maintains stable genotypic and plumage difference between species allowing further differentiation to accumulate via linkage to its flanking genetic region or linkage-disequilibrium genome-wide.

Data Mining in Genome Wide Association Studies

2011 ◽  
pp. 465-471
Author(s):  
Tom Burr
Keyword(s):  
Data Mining ◽  
Genetic Basis ◽  
Association Studies ◽  
Causal Variant ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Common Diseases ◽  
Genome Wide ◽  
Genomic Regions

The genetic basis for some human diseases, in which one or a few genome regions increase the probability of acquiring the disease, is fairly well understood. For example, the risk for cystic fibrosis is linked to particular genomic regions. Identifying the genetic basis of more common diseases such as diabetes has proven to be more difficult, because many genome regions apparently are involved, and genetic effects are thought to depend in unknown ways on other factors, called covariates, such as diet and other environmental factors (Goldstein and Cavalleri, 2005). Genome-wide association studies (GWAS) aim to discover the genetic basis for a given disease. The main goal in a GWAS is to identify genetic variants, single nucleotide polymorphisms (SNPs) in particular, that show association with the phenotype, such as “disease present” or “disease absent” either because they are causal, or more likely, because they are statistically correlated with an unobserved causal variant (Goldstein and Cavalleri, 2005). A GWAS can analyze “by DNA site” or “by multiple DNA sites. ” In either case, data mining tools (Tachmazidou, Verzilli, and De Lorio, 2007) are proving to be quite useful for understanding the genetic causes for common diseases.

Genomic and plumage variation in Vermivora hybrids

The Auk ◽  
2020 ◽  
Vol 137 (3) ◽  
Author(s):  
Marcella D Baiz ◽  
Gunnar R Kramer ◽  
Henry M Streby ◽  
Scott A Taylor ◽  
Irby J Lovette ◽  
...  
Keyword(s):  
Genetic Basis ◽  
First Generation ◽  
Parental Species ◽  
Face Mask ◽  
Mendelian Inheritance ◽  
Hybrid Index ◽  
Species Identity ◽  
Phenotypic Characters ◽  
Genomic Regions ◽  
Carotenoid Pigmentation

Abstract Hybrids with different combinations of traits can be used to identify genomic regions that underlie phenotypic characters important to species identity and recognition. Here, we explore links between genomic and plumage variation in Blue-winged Warbler x Golden-winged Warbler (Vermivora cyanoptera x V. chrysoptera) hybrids, which have traditionally been categorized into 2 discrete types. “Lawrence’s” hybrids are yellow overall, similar to Blue-winged Warblers, but exhibit the black throat patch and face mask of Golden-winged Warblers. “Brewster’s” hybrids are similar to Golden-winged Warblers, but lack the black throat patch and face mask, and sometimes have yellow on their underparts. Previous studies hypothesized that (1) first generation hybrids are of the Brewster’s type and can be distinguished by the amount of yellow on their underparts, and that (2) the throat patch/mask phenotype is consistent with Mendelian inheritance and controlled by variation in a locus near the Agouti-signaling protein (ASIP) gene. We addressed these hypotheses using whole genome re-sequencing of parental and hybrid individuals. We found that Brewster’s hybrids had genomic hybrid index scores indicating this phenotype can arise by majority ancestry from either parental species, that their plumage varied in levels of carotenoid pigmentation, and individuals captured in multiple years grew consistently less yellow over time. Variation in carotenoid pigmentation showed little relationship with genomic hybrid index score and is thus inconsistent with previous hypotheses that first generation hybrids can be distinguished by the amount of yellow in their plumage. Our results also confirm that variation near ASIP underlies the throat patch phenotype, which we refined to an ~10–15 Kb region upstream of the coding sequence. Overall, our results support the notion that traditional categorization of hybrids as either Lawrence’s or Brewster’s oversimplifies continuous variation in carotenoid pigmentation, and its inferred underlying genetic basis, and is based primarily on one discrete trait, which is the throat patch/mask phenotype.

scholarly journals Genetic architecture of root and shoot ionomes in rice (Oryza sativa L.)

2021 ◽  
Author(s):  
Joshua N. Cobb ◽  
Chen Chen ◽  
Yuxin Shi ◽  
Lyza G. Maron ◽  
Danni Liu ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Candidate Genes ◽  
Association Analysis ◽  
Phenotypic Variation ◽  
Genetic Variants ◽  
Genetic Basis ◽  
Living Environment ◽  
Mineral Nutrient ◽  
Genome Wide ◽  
Genomic Regions

Abstract Key message Association analysis for ionomic concentrations of 20 elements identified independent genetic factors underlying the root and shoot ionomes of rice, providing a platform for selecting and dissecting causal genetic variants. Abstract Understanding the genetic basis of mineral nutrient acquisition is key to fully describing how terrestrial organisms interact with the non-living environment. Rice (Oryza sativa L.) serves both as a model organism for genetic studies and as an important component of the global food system. Studies in rice ionomics have primarily focused on above ground tissues evaluated from field-grown plants. Here, we describe a comprehensive study of the genetic basis of the rice ionome in both roots and shoots of 6-week-old rice plants for 20 elements using a controlled hydroponics growth system. Building on the wealth of publicly available rice genomic resources, including a panel of 373 diverse rice lines, 4.8 M genome-wide single-nucleotide polymorphisms, single- and multi-marker analysis pipelines, an extensive tome of 321 candidate genes and legacy QTLs from across 15 years of rice genetics literature, we used genome-wide association analysis and biparental QTL analysis to identify 114 genomic regions associated with ionomic variation. The genetic basis for root and shoot ionomes was highly distinct; 78 loci were associated with roots and 36 loci with shoots, with no overlapping genomic regions for the same element across tissues. We further describe the distribution of phenotypic variation across haplotypes and identify candidate genes within highly significant regions associated with sulfur, manganese, cadmium, and molybdenum. Our analysis provides critical insight into the genetic basis of natural phenotypic variation for both root and shoot ionomes in rice and provides a comprehensive resource for dissecting and testing causal genetic variants.

scholarly journals Genome Wide Association Study Pinpoints Key Agronomic QTLs in African Rice Oryza glaberrima

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Philippe Cubry ◽  
Hélène Pidon ◽  
Kim Nhung Ta ◽  
Christine Tranchant-Dubreuil ◽  
Anne-Céline Thuillet ◽  
...  
Keyword(s):  
Association Study ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Oryza Glaberrima ◽  
Rice Yellow Mottle Virus ◽  
Adaptive Variation ◽  
African Rice ◽  
Genome Wide ◽  
Genomic Regions

Abstract Background African rice, Oryza glaberrima, is an invaluable resource for rice cultivation and for the improvement of biotic and abiotic resistance properties. Since its domestication in the inner Niger delta ca. 2500 years BP, African rice has colonized a variety of ecologically and climatically diverse regions. However, little is known about the genetic basis of quantitative traits and adaptive variation of agricultural interest for this species. Results Using a reference set of 163 fully re-sequenced accessions, we report the results of a Genome Wide Association Study carried out for African rice. We investigated a diverse panel of traits, including flowering date, panicle architecture and resistance to Rice yellow mottle virus. For this, we devised a pipeline using complementary statistical association methods. First, using flowering time as a target trait, we found several association peaks, one of which co-localised with a well described gene in the Asian rice flowering pathway, OsGi, and identified new genomic regions that would deserve more study. Then we applied our pipeline to panicle- and resistance-related traits, highlighting some interesting genomic regions and candidate genes. Lastly, using a high-resolution climate database, we performed an association analysis based on climatic variables, searching for genomic regions that might be involved in adaptation to climatic variations. Conclusion Our results collectively provide insights into the extent to which adaptive variation is governed by sequence diversity within the O. glaberrima genome, paving the way for in-depth studies of the genetic basis of traits of interest that might be useful to the rice breeding community.

scholarly journals Parallel Genetic Origin of Foot Feathering in Birds

2020 ◽  
Vol 37 (9) ◽  
pp. 2465-2476
Author(s):  
Chiara Bortoluzzi ◽  
Hendrik-Jan Megens ◽  
Mirte Bosse ◽  
Martijn F L Derks ◽  
Bert Dibbits ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Parallel Evolution ◽  
Ectopic Expression ◽  
Genetic Origin ◽  
Animal Evolution ◽  
Transcription Regulator ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions ◽  
Feather Development

Abstract Understanding the genetic basis of similar phenotypes shared between lineages is a long-lasting research interest. Even though animal evolution offers many examples of parallelism, for many phenotypes little is known about the underlying genes and mutations. We here use a combination of whole-genome sequencing, expression analyses, and comparative genomics to study the parallel genetic origin of ptilopody (Pti) in chicken. Ptilopody (or foot feathering) is a polygenic trait that can be observed in domesticated and wild avian species and is characterized by the partial or complete development of feathers on the ankle and feet. In domesticated birds, ptilopody is easily selected to fixation, though extensive variation in the type and level of feather development is often observed. By means of a genome-wide association analysis, we identified two genomic regions associated with ptilopody. At one of the loci, we identified a 17-kb deletion affecting PITX1 expression, a gene known to encode a transcription regulator of hindlimb identity and development. Similarly to pigeon, at the second loci, we observed ectopic expression of TBX5, a gene involved in forelimb identity and a key determinant of foot feather development. We also observed that the trait evolved only once as foot-feathered birds share the same haplotype upstream TBX5. Our findings indicate that in chicken and pigeon ptilopody is determined by the same set of genes that affect similar molecular pathways. Our study confirms that ptilopody has evolved through parallel evolution in chicken and pigeon.

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