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450 results for “Candidate Genes”

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dryad36/100

Data from: Genomic islands of differentiation in two songbird species reveal candidate genes for hybrid female sterility

Hybrid sterility is a common first step in the evolution of postzygotic reproductive isolation. According to Haldane's Rule it affects predominantly the heterogametic sex. While the genetic basis of hybrid male sterility in organisms with heterogametic males has been studied for decades, the genetic basis of hybrid female sterility in organisms with heterogametic females has received much less attention. We investigated the genetic basis of reproductive isolation in two closely related avian species, the Common Nightingale (Luscinia megarhynchos) and the Thrush Nightingale (L. luscinia), that hybridize in a secondary contact zone and produce viable hybrid progeny. In accordance with Haldane's Rule, hybrid females are sterile, while hybrid males are fertile, allowing gene flow to occur between the species. Using transcriptomic data from multiple individuals of both nightingale species we identified genomic islands of high differentiation (FST) and of high divergence (Dxy), and we analyzed gene content and patterns of molecular evolution within these islands. Interestingly, we found that these islands were enriched for genes related to female meiosis and metabolism. The islands of high differentiation and divergence were also characterized by higher levels of linkage disequilibrium than the rest of the genome in both species indicating that they might be situated in genomic regions of low recombination. This study provides one of the first insights into genetic basis of hybrid female sterility in organisms with heterogametic females.

opencc-zeroDec 2016View details →

dryad36/100

Candidate-species delimitation in Desmognathus salamanders reveals gene flow across lineage boundaries, confounding phylogenetic estimation and clarifying hybrid zones

Dusky Salamanders (genus Desmognathus) currently comprise only 22 described, extant species. However, recent mitochondrial and nuclear estimates indicate the presence of up to 49 candidate species based on ecogeographic sampling. Previous studies also suggest a complex history of hybridization between these lineages. Studies in other groups suggest that disregarding admixture may affect both phylogenetic inference and clustering-based species-delimitation. With a dataset comprising 233 Anchored Hybrid Enrichment (AHE) loci sequenced for 896 Desmognathus specimens from all 49 candidate species, we test three hypotheses regarding i) species-level diversity, ii) hybridization and admixture, and iii) misleading phylogenetic inference. Using phylogenetic and population-clustering analyses considering gene flow, we find support for at least 47 candidate species in the phylogenomic dataset, some of which are newly characterized here while others represent combinations of previously named lineages that are collapsed in the current dataset. Within these, we observe significant phylogeographic structure, with up to 64 total geographic genetic lineages, many of which hybridize either narrowly at contact zones or extensively across ecological gradients. We find strong support for both recent admixture between terminal lineages and ancient hybridization across internal branches. This signal appears to distort concatenated phylogenetic inference, wherein more heavily admixed terminal specimens occupy apparently artifactual early diverging topological positions, occasionally to the extent of forming false clades of intermediate hybrids. Additional geographic and genetic sampling and more robust computational approaches will be needed to clarify taxonomy, and to reconstruct a network topology to display evolutionary relationships in a manner that is consistent with their complex history of reticulation. --

opencc-zeroFeb 2022View details →

dryad36/100

False and true positives in arthropod thermal adaptation candidate gene lists

Genome-wide studies are prone to false positives due to inherently low priors and statistical power. One approach to ameliorate this problem is to seek validation of reported candidate genes across independent studies: genes with repeatedly discovered effects are less likely to be false positives. Inversely, genes reported only as many times as expected by chance alone, while possibly representing novel discoveries, are also more likely to be false positives. We show that, across over 30 genome-wide studies that reported Drosophila and Daphnia genes with possible roles in thermal adaptation, the combined lists of candidate genes and orthologous groups are rapidly approaching the total number of genes and orthologous groups in the genome, respectively, consistent with the expectation of high frequency of false positives. The majority of these spurious candidates have been identified by one or a few studies, as expected by chance alone. In contrast, a noticeable minority of genes have been identified by numerous studies with the probabilities of such discoveries occurring by chance alone being exceedingly small. For this subset of genes, different studies are in agreement with each other despite differences in the ecological settings, genomic tools and methodology, and reporting thresholds. We provide a reference set of presumed true positives among Drosophila candidate genes and orthologous groups involved in response to changes in temperature, suitable for cross-validation purposes. Despite this approach being prone to false negatives, this list of presumed true positives includes several hundred genes, consistent with the "omnigenic" concept of genetic architecture of complex traits.

opencc-zeroMar 2022View details →

zenodo36/100

Raw data of metabolic pathways and candidate olfactory genes in Holotrichia parallela (Coleoptera: Scarabaeidae)

Analysis of antennal transcriptome data caused the discovery of metabolic and signaling pathways and the identification of olfactory genes. According to KEGG pathway enrichment analysis, KEGG pathways and KEGG modules were annotated. Based on the FuncTree software analysis, the functional potential of H. parallela unigenes was visualized across different functional layers, including biological progress, KEGG module and KEGG pathway. We successfully identified a series of putative olfactory genes, including OBPs, CSPs SNMPs and ODEs. The relationship between H. parallela with other species was predicted and many olfactory genes with various functions were analyzed based on phylogenetic analysis. Heat maps and qRT-PCR experiments were performed to display and verify biased or specific expression profiles between sexes and between olfactory and non olfactory tissues.

opencc-by-4.0Dec 2018View details →

zenodo36/100

Genome-wide association studies identify candidate genes for coat color and mohair traits in the Iranian Markhoz goat

Illumina Caprine 53K SNPchip genotypes of 228 Iranian goats used for coat color and mohair traits GWAS

opencc-by-4.0Mar 2018View details →

zenodo36/100

Data: Genome-wide association study reveals white lupin candidate gene involved in anthracnose resistance

White lupin (Lupinus albus L.) is a re-emerging protein crop and promising alternative to soybean. Its cultivation, however, is severely threatened by anthracnose disease caused by the fungal pathogen Colletotrichum lupini. To dissect the genetic architecture for anthracnose resistance, genotyping-by-sequencing (GBS) was performed on white lupin accessions collected from the center of domestication and traditional cultivation regions. GBS resulted in 4,611 high-quality single-nucleotide polymorphisms (SNPs) for 181 accessions, which were combined with resistance data observed under controlled conditions to perform a genome-wide association study (GWAS). Obtained disease phenotypes were shown to highly correlate to overall three-year disease assessments under Swiss field conditions (r > 0.8). GWAS results identified two significant SNPs associated with anthracnose resistance on gene Lalb_Chr05_g0216161 encoding a RING zinc-finger E3 ubiquitin ligase which is potentially involved in plant immunity. Population analysis showed a remarkably fast linkage disequilibrium (LD) decay, weak population structure and grouping of commercial varieties with landraces, corresponding to the slow domestication history and scarcity of modern breeding efforts in white lupin. Together with 15 highly resistant accessions identified in the resistance assay, our findings show promise for further crop improvement. This study provides the basis for marker-assisted selection, genomic prediction and studies aimed at understanding anthracnose resistance mechanisms in white lupin and contributes to improving breeding programs worldwide.

opencc-by-4.0Sep 2021View details →

dryad36/100

Identification of quantitative trait loci and associated candidate genes for pregnancy success in Angus – Brahman crossbred heifers

Development of genomic tools to identify females with high genetic merit for reproductive function could increase the profitability and sustainability of beef production. Here, genome-wide association studies (GWAS) were performed on pregnancy outcome traits from a population of Angus – Brahman crossbred heifers. Furthermore, a validation GWAS was performed using data from another location. Heifers were genotyped with the Bovine GGP F250 array that contains ~250,000 SNPs. In the discovery population, heifers were bred in winter breeding seasons involving a single round of timed artificial insemination (AI) followed by natural mating for three months. Three phenotypes were analyzed: pregnancy outcome to first-service AI (PAI; n = 1481), pregnancy status at the end of the breeding season (PEBS; n = 1725), and pregnancy score (Pregscore where 1 = pregnant to first-service AI, 2 = pregnant to bull, 3 = not pregnant; n =1481). The heritability for PAI was estimated as 0.149. One large quantitative trait locus (QTL) that explained ~3% of the genetic variation for PAI was found on BTA7, in a region containing a cluster of γ-protocadherin genes and SLC25A2. Other QTLs explaining between 0.5-1% of the genetic variation were found on BTA12 and 25. The heritability of PEBS was estimated at 0.122. A large QTL on BTA7 was synonymous with the QTL for PAI, with minor QTL located on BTA5, 9, 10, 11, 19, and 20. Estimated heritability for Pregscore was 0.189. There was a large QTL on BTA7 synonymous with the other two traits as well as smaller QTLs on BTA1, 10, 15, 18, 19, and 20. The validation population for pregnancy status at the end of the breeding season were Angus-Brahman crossbred heifers bred by natural mating. In concordance with the discovery population, the large QTL on BTA7 and QTL on BTA10, 12 and 18 were identified. In summary, QTL and candidate SNPs associated with pregnancy outcomes in beef heifers were identified, including a large QTL associated with a group of protocadherin genes. Confirmation of these associations with larger populations could lead to the development of genomic estimates of reproductive function in beef cattle.

opencc-zeroSep 2023View details →

ClinicalTrials.gov36/100

Study in Healthy Adults to Evaluate Gene Activation After Vaccination With GlaxoSmithKline (GSK) Biologicals' Candidate Tuberculosis (TB) Vaccine GSK 692342

ClinicalTrials.gov study NCT01669096. IPD Sharing: YES. Countries: 1. Publications: 1.

controlledIPD-YESFeb 2026View details →

dryad36/100