scholarly journals Genome-wide patterns of regulatory divergence revealed by introgression lines

2016 ◽  
Author(s):  
Rafael F Guerrero ◽  
Matthew W Hahn ◽  
Leonie C Moyle ◽  
Amanda L Posto
Keyword(s):  
Genetic Basis ◽  
Introgression Lines ◽  
Phenotypic Evolution ◽  
Solanum Pennellii ◽  
Interspecific Introgression ◽  
Regulatory Changes ◽  
Genome Wide ◽  
Cis And Trans ◽  
Hybrid Lines

Understanding the genetic basis for changes in transcriptional regulation is an important aspect of understanding phenotypic evolution. Using interspecific introgression lines, we infer the mechanisms of divergence in genome-wide patterns of gene expression between the nightshades Solanum pennellii and S. lycopersicum (domesticated tomato). We find that cis- and trans-regulatory changes have had qualitatively similar contributions to divergence in this clade, unlike results from other systems. Additionally, expression data from four tissues (shoot apex, ripe fruit, pollen, and seed) suggest that introgressed regions in these hybrid lines tend to be down-regulated, while background (non-introgressed) genes tend to be up-regulated. Finally, we find no evidence for an association between the magnitude of differential expression in NILs and previously determined sterility phenotypes. Our results contradict previous predictions of the predominant role of cis- over trans-regulatory divergence between species, and do not support a major role for gross genome-wide misregulation in reproductive isolation between these species.

scholarly journals Two loci contribute epistastically to heterospecific pollen rejection, a postmating isolating barrier between species

2016 ◽  
Author(s):  
Jennafer A. P. Hamlin ◽  
Natasha A. Sherman ◽  
Leonie C. Moyle
Keyword(s):  
Female Choice ◽  
Genetic Basis ◽  
Reproductive Tract ◽  
Interspecific Cross ◽  
Introgression Lines ◽  
Female Reproductive Tract ◽  
Solanum Pennellii ◽  
Heterospecific Pollen ◽  
Male Gametes ◽  
Pollen Rejection

ABSTRACTRecognition and rejection of heterospecific male gametes occurs in a broad range of taxa, although the complexity and redundancy of mechanisms underlying this postmating cryptic female choice is poorly understood. In plants, the arena for these interactions is the female reproductive tract (pistil), within which heterospecific pollen tube growth can be arrested via active molecular recognition. Unilateral incompatibility (UI) is one such pistil-mediated barrier in which pollen rejection occurs in only one direction of an interspecific cross. We investigated the genetic basis of pistil-side UI between Solanum species, with the specific goal of understanding the role and magnitude of epistasis between UI QTL. Using heterospecific introgression lines (ILs) between Solanum pennellii and S. lycopersicum, we assessed the individual and pairwise effects of three chromosomal regions (ui1.1, ui3.1, and ui12.1) previously associated with interspecific UI among Solanum species. Specifically, we pyramided ui12.1 with each of ui1.1 and ui3.1, and assessed the strength of UI pollen rejection in pyramided (double introgression) lines, compared to single introgression genotypes. We found that none of the three QTL individually showed UI rejection phenotypes, but lines combining ui3.1 and ui12.1 showed significant pistil-side pollen rejection. Furthermore, double introgression lines that combined different chromosomal regions overlapping ui3.1 differed significantly in their rate of UI, consistent with at least two genetic factors on chromosome three contributing quantitatively to interspecific pollen rejection. Together, our data indicate that loci on both chromosomes 3 and 12 are jointly required for the expression of UI between S. pennellii and S. lycopersicum suggesting that coordinated molecular interactions among a relatively few loci underlying the expression of this postmating prezygotic barrier. In addition, in conjunction with previous data, at least one of these loci appears to also contribute to conspecific self-incompatibility, consistent with a partially shared genetic basis between inter- and intraspecific mechanisms of postmating prezygotic female choice.

scholarly journals Incorporation of DNA methylation into eQTL mapping in African Americans

2020 ◽  
Author(s):  
Anmol Singh ◽  
Yizhen Zhong ◽  
Layan Nahlawi ◽  
C. Sehwan Park ◽  
Tanima De ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
African Americans ◽  
Genetic Basis ◽  
Critical Role ◽  
Eqtl Analysis ◽  
Biliary Cirrhosis ◽  
Eqtl Mapping ◽  
Genome Wide

Epigenetics is a reversible molecular mechanism that plays a critical role in many developmental, adaptive, and disease processes. DNA methylation has been shown to regulate gene expression and the advent of high throughput technologies has made genome-wide DNA methylation analysis possible. We investigated the effect of DNA methylation in eQTL mapping (methylation-adjusted eQTLs), by incorporating DNA methylation as a SNP-based covariate in eQTL mapping in African American derived hepatocytes. We found that the addition of DNA methylation uncovered new eQTLs and eGenes. Previously discovered eQTLs were significantly altered by the addition of DNA methylation data suggesting that methylation may modulate the association of SNPs to gene expression. We found that methylation-adjusted eQTLs which were less significant compared to PC-adjusted eQTLs were enriched in lipoprotein measurements (FDR = 0.0040), immune system disorders (FDR = 0.0042), and liver enzyme measurements (FDR = 0.047), suggesting a role of DNA methylation in regulating the genetic basis of these phenotypes. Our methylation-adjusted eQTL analysis also uncovered novel SNP-gene pairs. For example, our study found the SNP, rs11546996, was associated to PNKP. In a previous GWAS, this SNP was associated with primary biliary cirrhosis although the causal gene was thought to be SPIB. Our methylation-adjusted method potentially adds new understanding to the genetic basis of complex diseases that disproportionally affect African Americans.

scholarly journals Genomics of coloration in natural animal populations

2017 ◽  
Vol 372 (1724) ◽  
pp. 20160337 ◽  
Author(s):  
Luis M. San-Jose ◽  
Alexandre Roulin
Keyword(s):  
Genetic Basis ◽  
High Throughput Sequencing ◽  
Model Species ◽  
Animal Coloration ◽  
Sequencing Technologies ◽  
Animal Populations ◽  
Genome Wide ◽  
General Relevance ◽  
Genetic Structures

Animal coloration has traditionally been the target of genetic and evolutionary studies. However, until very recently, the study of the genetic basis of animal coloration has been mainly restricted to model species, whereas research on non-model species has been either neglected or mainly based on candidate approaches, and thereby limited by the knowledge obtained in model species. Recent high-throughput sequencing technologies allow us to overcome previous limitations, and open new avenues to study the genetic basis of animal coloration in a broader number of species and colour traits, and to address the general relevance of different genetic structures and their implications for the evolution of colour. In this review, we highlight aspects where genome-wide studies could be of major utility to fill in the gaps in our understanding of the biology and evolution of animal coloration. The new genomic approaches have been promptly adopted to study animal coloration although substantial work is still needed to consider a larger range of species and colour traits, such as those exhibiting continuous variation or based on reflective structures. We argue that a robust advancement in the study of animal coloration will also require large efforts to validate the functional role of the genes and variants discovered using genome-wide tools. This article is part of the themed issue ‘Animal coloration: production, perception, function and application’.

scholarly journals Unraveling cis and trans regulatory evolution during cotton domestication

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Ying Bao ◽  
Guanjing Hu ◽  
Corrinne E. Grover ◽  
Justin Conover ◽  
Daojun Yuan ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Sequence Evolution ◽  
Regulatory Evolution ◽  
Evolutionary Diversification ◽  
Regulatory Changes ◽  
Genome Wide ◽  
Network Properties ◽  
High Level ◽  
Cis And Trans ◽  
Allotetraploid Cotton

AbstractCis and trans regulatory divergence underlies phenotypic and evolutionary diversification. Relatively little is understood about the complexity of regulatory evolution accompanying crop domestication, particularly for polyploid plants. Here, we compare the fiber transcriptomes between wild and domesticated cotton (Gossypium hirsutum) and their reciprocal F1 hybrids, revealing genome-wide (~15%) and often compensatory cis and trans regulatory changes under divergence and domestication. The high level of trans evolution (54%–64%) observed is likely enabled by genomic redundancy following polyploidy. Our results reveal that regulatory variation is significantly associated with sequence evolution, inheritance of parental expression patterns, co-expression gene network properties, and genomic loci responsible for domestication traits. With respect to regulatory evolution, the two subgenomes of allotetraploid cotton are often uncoupled. Overall, our work underscores the complexity of regulatory evolution during fiber domestication and may facilitate new approaches for improving cotton and other polyploid plants.

scholarly journals Sex-specific evolution of a Drosophila sensory system via interacting cis- and trans-regulatory changes

2022 ◽  
Author(s):  
David M Luecke ◽  
Gavin R Rice ◽  
Artyom Kopp
Keyword(s):  
Sensory System ◽  
Phenotypic Evolution ◽  
Regulatory Evolution ◽  
Enhancer Activity ◽  
Epistatic Interactions ◽  
Regulatory Changes ◽  
Regulatory Architecture ◽  
Additive Component ◽  
Cis And Trans ◽  
Increased Activity

The evolution of gene expression via cis-regulatory changes is well established as a major driver of phenotypic evolution. However, relatively little is known about the influence of enhancer architecture and intergenic interactions on regulatory evolution. We address this question by examining chemosensory system evolution in Drosophila. D. prolongata males show a massively increased number of chemosensory bristles compared to females and males of sibling species. This increase is driven by sex-specific transformation of ancestrally mechanosensory organs. Consistent with this phenotype, the Pox neuro transcription factor (Poxn), which specifies chemosensory bristle identity, shows expanded expression in D. prolongata males. Poxn expression is controlled by non-additive interactions among widely dispersed enhancers. Although some D. prolongata Poxn enhancers show increased activity, the additive component of this increase is slight, suggesting most changes in Poxn expression are due to epistatic interactions between Poxn enhancers and trans-regulatory factors. Indeed, the expansion of D. prolongata Poxn enhancer activity is only observed in cells that express doublesex (dsx), the gene that controls sexual differentiation in Drosophila and also shows increased expression in D. prolongata males due to cis-regulatory changes. Although expanded dsx expression may contribute to increased activity of D. prolongata Poxn enhancers, this interaction is not sufficient to explain the full expansion of Poxn expression, suggesting that cis-trans interactions between Poxn, dsx, and additional unknown genes are necessary to produce the derived D. prolongata phenotype. Overall, our results demonstrate the importance of epistatic gene interactions for evolution, particularly when pivotal genes have complex regulatory architecture.

scholarly journals The genetic basis of psoriasis

2016 ◽  
Vol 14 (2) ◽  
pp. 197-207
Author(s):  
Nguyễn Thị Kim Liên ◽  
Nguyễn Huy Hoàng
Keyword(s):  
Genetic Basis ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Chromosome 6 ◽  
Disease Manifestation ◽  
Genome Wide ◽  
Increasing Risk ◽  
The Impact ◽  
Main Influence

Psoriasis is a chronic dermatitis disease. Although the disease is not dangerous but it affects patients’s life in many aspects and involving a large number of people in the world. Besides that, psoriasis related to many other diseases such as metabolic disorder, diabetes, cardiovascular disease or can develop into servere arthritis and psoriasis arthritis leading to joint deformities. HLAC gene located on chromosome 6 (locus PSORS1) is known to have an important role in the susceptibility of disease. Besides, investigations showed that psoriasis is controlled by many loci and genes. By using traditional methods and genome wide association studies (GWAS) have been identified 13 loci and many genes involved of disease. However, the role of each locus and gene influence to the susceptibility of disease, presentation of disease, time onset and the links with other diseases have not yet been defined clearly. Among the relevant loci, the PSORS1 locus still considered the main influence on the susceptibility of disease. Noteworthy, the factors of age, gender and race have influences to the disease manifestation of different loci. The studies also provides evidences of the relation of proriasis and increasing risk cardiovascular, hypertension, diabetes and other diseases. So that, by understanding the genetic basis of the disease, the doctors and patients can get orientation in prevention, treatment and minimizing the impact of the disease. In this article, we give a clearer view of the genetic basis of psoriasis.

scholarly journals Identification of a Missense Variant in MFSD12 Involved in Dilution of Phaeomelanin Leading to White or Cream Coat Color in Dogs

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 386 ◽  
Author(s):  
Benoit Hédan ◽  
Edouard Cadieu ◽  
Nadine Botherel ◽  
Caroline Dufaure de Citres ◽  
Anna Letko ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Coat Color ◽  
Association Studies ◽  
Missense Variant ◽  
White Coat ◽  
Genome Wide Association Studies ◽  
Chromosome 20 ◽  
Genome Wide ◽  
Domestication Process

White coat color in mammals has been selected several times during the domestication process. Numerous dog breeds are fixed for one form of white coat color that involves darkly pigmented skin. The genetic basis of this color, due to the absence of pigment in the hairs, was suggested to correspond to extreme dilution of the phaeomelanin, by both the expression of only phaeomelanin (locus E) and its extreme dilution (locus I). To go further, we performed genome-wide association studies (GWAS) using a multiple breed approach. The first GWAS, using 34 white dogs and 128 non-white dogs, including White Shepherds, Poodles, Cotons de Tulear and Bichons allowed us to identify two significantly associated loci on the locus E and a novel locus on chromosome 20. A second GWAS using 15 other breeds presenting extreme phaeomelanin dilution confirmed the position of locus I on the chromosome 20 (position 55 Mb pcorrected = 6 × 10−13). Using whole-genome sequencing, we identified a missense variant in the first exon of MFSD12, a gene recently identified to be involved in human, mouse and horse pigmentation. We confirmed the role of this variant in phaeomelanin dilution of numerous canine breeds, and the conserved role of MFSD12 in mammalian pigmentation.

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