Basis Of Phenotypic Variation Research Articles

BnVIR: bridging the genotype-phenotype gap to accelerate mining of candidate variations underlying agronomic traits in Brassica napus

BnVIR: bridging the genotype-phenotype gap to accelerate mining of candidate variations underlying agronomic traits in Brassica napus

Distribution of DGAT1 copy number variation in Chinese goats and its associations with milk production traits

Goat is an important sector for meat and dairy products. Diacylglycerol O-acyltransferase 1 (DGAT1), which is a key gene in milk production, has been recently detected to overlap with a novel copy number variation (CNV) in goats. CNVs could be genetic markers providing new insights into the genetic basis of phenotypic variation. Up to now, there are no reports on the DGAT1-related CNV (DGAT1 CNV) in Chinese goats. This study first detected the distribution of the DGAT1 CNV in Chinese seven goat breeds, finding substantial differences among dairy, meat, and fiber goats (P < 0.01). The association analysis between the DGAT1 CNV and milk production traits revealed significant associations: Xinong Sannen (XS) dairy goat with copy number loss type had higher freezing point depression (FPD) (P < 0.01) and milk solids-not-fat (SNF) content (P < 0.05). Overall, our study unraveled the distribution of DGAT1 CNV in Chinese goats for the first time and found the potential role of this CNV in the marker-assisted selection of dairy goat breeding.

LncRNAs in domesticated animals: from dog to livestock species

Animal genomes are pervasively transcribed into multiple RNA molecules, of which many will not be translated into proteins. One major component of this transcribed non-coding genome is the long non-coding RNAs (lncRNAs), which are defined as transcripts longer than 200 nucleotides with low coding-potential capabilities. Domestic animals constitute a unique resource for studying the genetic and epigenetic basis of phenotypic variations involving protein-coding and non-coding RNAs, such as lncRNAs. This review presents the current knowledge regarding transcriptome-based catalogues of lncRNAs in major domesticated animals (pets and livestock species), covering a broad phylogenetic scale (from dogs to chicken), and in comparison with human and mouse lncRNA catalogues. Furthermore, we describe different methods to extract known or discover novel lncRNAs and explore comparative genomics approaches to strengthen the annotation of lncRNAs. We then detail different strategies contributing to a better understanding of lncRNA functions, from genetic studies such as GWAS to molecular biology experiments and give some case examples in domestic animals. Finally, we discuss the limitations of current lncRNA annotations and suggest research directions to improve them and their functional characterisation.

The role of epigenetic regulation in adaptive phenotypic plasticity of plants

In recent decades, knowledge about the role of epigenetic regulation of gene expression in plant responses to external stimuli and in adaptation of plants to adverse environmental fluctuations have extended significantly. DNA methylation is considered as the main molecular mechanism that provides genomic information and contributes to the understanding of the molecular basis of phenotypic variations based on epigenetic modifications. Unfortunately, the vast majority of research in this area has been performed on the model species Arabidopsis thaliana. The development of the methylation-sensitive amplified polymorphism (MSAP) method has made it possible to implement the large-scale detection of DNA methylation alterations in wild non-model and agricultural plants with large and highly repetitive genomes in natural and manipulated habitats. The article presents current information on DNA methylation in species of natural communities and crops and its importance in plant development and adaptive phenotypic plasticity, along with brief reviews of current ideas about adaptive phenotypic plasticity and epigenetic regulation of gene expression. The great potential of further studies of the epigenetic role in phenotypic plasticity of a wide range of non-model species in natural populations and agrocenoses for understanding the molecular mechanisms of plant existence in the changing environment in onto- and phylogeny, directly related to the key tasks of forecasting the effects of global warming and crop selection, is emphasized. Specific taxa of the Ukrainian flora, which, in authors’ opinion, are promising and interesting for this type of research, are recommended.

Spatial variation in gene expression of Tasmanian devil facial tumors despite minimal host transcriptomic response to infection

BackgroundTransmissible cancers lie at the intersection of oncology and infectious disease, two traditionally divergent fields for which gene expression studies are particularly useful for identifying the molecular basis of phenotypic variation. In oncology, transcriptomics studies, which characterize the expression of thousands of genes, have identified processes leading to heterogeneity in cancer phenotypes and individual prognoses. More generally, transcriptomics studies of infectious diseases characterize interactions between host, pathogen, and environment to better predict population-level outcomes. Tasmanian devils have been impacted dramatically by a transmissible cancer (devil facial tumor disease; DFTD) that has led to widespread population declines. Despite initial predictions of extinction, populations have persisted at low levels, due in part to heterogeneity in host responses, particularly between sexes. However, the processes underlying this variation remain unknown.ResultsWe sequenced transcriptomes from healthy and DFTD-infected devils, as well as DFTD tumors, to characterize host responses to DFTD infection, identify differing host-tumor molecular interactions between sexes, and investigate the extent to which tumor gene expression varies among host populations. We found minimal variation in gene expression of devil lip tissues, either with respect to DFTD infection status or sex. However, 4088 genes were differentially expressed in tumors among our sampling localities. Pathways that were up- or downregulated in DFTD tumors relative to normal tissues exhibited the same patterns of expression with greater intensity in tumors from localities that experienced DFTD for longer. No mRNA sequence variants were associated with expression variation.ConclusionsExpression variation among localities may reflect morphological differences in tumors that alter ratios of normal-to-tumor cells within biopsies. Phenotypic variation in tumors may arise from environmental variation or differences in host immune response that were undetectable in lip biopsies, potentially reflecting variation in host-tumor coevolutionary relationships among sites that differ in the time since DFTD arrival.

Feasibility of Cultivating Artemisia afra Jacq. ex Willd in Côte d’Ivoire (Daloa) and Evaluation of Its Genetic Diversity on the Basis of Phenotypic Variations

In the southern African regions, Artemisia afra Jacq. ex Willd is one of the most popular and commonly used herbal medicines. In recent years, A. afra has received much attention from the scientific community and its use is being investigated in the modern diseases like diabetes, cardiovascular diseases, cancer, and respiratory diseases. This growth in popularity could pose a threat to the species due to intensive harvesting. Indeed, overexploitation is a growing problem for many medicinal species in Africa. To sustain the production and availability of A. afra , cultivation seems to be a good strategy and an alternative to collecting in the wild. Unlike A. annua L. (source of artemisinin), little information is available on the cultivation of A. Afra in West African countries. In this study, feasibility of cultivating A. Afra in Côte d’Ivoire was evaluated and the extent of its genetic diversity was assessed based on morphological variations. A. annua L. was used as control. The result showed for A. afra , 30 and 28.02% nursery and field mortality respectively, and 27.77% and 0% for A. annua . A. annua showed faster growth and development kinetics during the first 90 days after field transplantation. A. annua was relatively earlier (83 days to flowering on average) than A. afra (207.20 days to flowering on average). Contrary to A. annua , A. afra was sterile and did not give viable seeds, which poses a major problem of acclimatization in the environmental conditions of Côte d’Ivoire. Assessment of morphological traits revealed significant variations within and between species. Multivariate analysis showed important intra and interspecific genetic diversity. The plants of A. afra and A. annua were grouped separately and six major clusters were found: two clusters in A. annua (cluster I and II) and four clusters in A. afra (cluster III, IV, V and VI). These results show that further studies need to be considered to make cultivation of A. afra possible in Côte d’Ivoire with superior and genetically stable genotypes. Keywords: Artemisia afra , Artemisia annua , genetic diversity, cultivation DOI: 10.7176/JBAH/10-24-04 Publication date: December 31 st 2020

Identification, expression, and artificial selection of silkworm epigenetic modification enzymes

BackgroundUnderstanding the genetic basis of phenotype variations during domestication and breeding is of great interest. Epigenetics and epigenetic modification enzymes (EMEs) may play a role in phenotypic variations; however, no comprehensive study has been performed to date. Domesticated silkworm (Bombyx mori) may be utilized as a model in determining how EMEs influence domestication traits.ResultsWe identified 44 EMEs in the genome of silkworm (Bombyx mori) using homology searching. Phylogenetic analysis showed that genes in a subfamily among different animals were well clustered, and the expression pattern of EMEs is constant among Bombyx mori, Drosophila melanogaster, and Mus musculus. These are most highly expressed in brain, early embryo, and internal genitalia. By gene-related selective sweeping, we identified five BmEMEs under artificial selection during the domestication and breeding of silkworm. Among these selected genes, BmSuv4–20 and BmDNMT2 harbor selective mutations in their upstream regions that alter transcription factor-binding sites. Furthermore, these two genes are expressed higher in the testis and ovary of domesticated silkworm compared to wild silkworms, and correlations between their expression pattern and meiosis of the sperm and ova were observed.ConclusionsThe domestication of silkworm has induced artificial selection on epigenetic modification markers that may have led to phenotypic changes during domestication. We present a novel perspective to understand the genetic basis underlying animal domestication and breeding.

Novel dominant MPAN family with a complex genetic architecture as a basis for phenotypic variability.

ObjectiveOur aim was to study a Hungarian family with autosomal dominantly inherited neurodegeneration with brain iron accumulation (NBIA) with markedly different intrafamilial expressivity.MethodsTargeted sequencing and multiplex ligation-dependent probe amplification (MLPA) of known NBIA-associated genes were performed in many affected and unaffected members of the family. In addition, a trio whole-genome sequencing was performed to find a potential explanation of phenotypic variability. Neuropathologic analysis was performed in a single affected family member.ResultsThe clinical phenotype was characterized by 3 different syndromes—1 with rapidly progressive dystonia-parkinsonism with cognitive deterioration, 1 with mild parkinsonism associated with dementia, and 1 with predominantly psychiatric symptoms along with movement disorder. A heterozygous stop-gain variation in the C19Orf12 gene segregated with the phenotype. Targeted sequencing of all known NBIA genes, and MLPA of PLA2G6 and PANK2 genes, as well as whole-genome sequencing in a trio from the family, revealed a unique constellation of oligogenic burden in 3 NBIA-associated genes (C19Orf12 p.Trp112Ter, CP p.Val105PhefsTer5, and PLA2G6 dup(ex14)). Neuropathologic analysis of a single case (39-year-old man) showed a complex pattern of alpha-synucleinopathy and tauopathy, both involving subcortical and cortical areas and the hippocampus.ConclusionsOur study expands the number of cases reported with autosomal dominant mitochondrial membrane protein-associated neurodegeneration and emphasizes the complexity of the genetic architecture, which might contribute to intrafamilial phenotypic variability.

Ecological genomics of adaptation to unpredictability in experimental rotifer populations

Elucidating the genetic basis of phenotypic variation in response to different environments is key to understanding how populations evolve. Facultatively sexual rotifers can develop adaptive responses to fluctuating environments. In a previous evolution experiment, diapause-related traits changed rapidly in response to two selective regimes (predictable vs unpredictable) in laboratory populations of the rotifer Brachionus plicatilis. Here, we investigate the genomic basis of adaptation to environmental unpredictability in these experimental populations. We identified and genotyped genome-wide polymorphisms in 169 clones from both selective regimes after seven cycles of selection using genotyping by sequencing (GBS). Additionally, we used GBS data from the 270 field clones from which the laboratory populations were established. This GBS dataset was used to identify candidate SNPs under selection. A total of 76 SNPs showed divergent selection, three of which are candidates for being under selection in the particular unpredictable fluctuation pattern studied. Most of the remaining SNPs showed strong signals of adaptation to laboratory conditions. Furthermore, a genotype-phenotype association approach revealed five SNPs associated with two key life-history traits in the adaptation to unpredictability. Our results contribute to elucidating the genomic basis for adaptation to unpredictable environments and lay the groundwork for future evolution studies in rotifers.

Identifying favorable alleles for improving key agronomic traits in upland cotton

BackgroundGossypium hirsutum L. is grown worldwide and is the largest source of natural fiber crop. We focus on exploring the favorable alleles (FAs) for upland cotton varieties improvement, and further understanding the history of accessions selection and acumination of favorable allele during breeding.ResultsThe genetic basis of phenotypic variation has been studied. But the accumulation of favorable alleles in cotton breeding history in unknown, and potential favorable alleles to enhance key agronomic traits in the future cotton varieties have not yet been identified. Therefore, 419 upland cotton accessions were screened, representing a diversity of phenotypic variations of 7362 G. hirsutum, and 15 major traits were investigated in 6 environments. These accessions were categorized into 3 periods (early, medium, and modern) according to breeding history. All accessions were divided into two major groups using 299 polymorphic microsatellite markers: G1 (high fiber yield and quality, late maturity) and G2 (low fiber yield and quality, early maturity). The proportion of G1 genotype gradually increased from early to modern breeding periods. Furthermore, 21 markers (71 alleles) were significantly associated (−log P > 4) with 15 agronomic traits in multiple environments. Seventeen alleles were identified as FAs; these alleles accumulated more in the modern period than in other periods, consistent with their phenotypic variation trends in breeding history. Our results demonstrate that the favorable alleles accumulated through breeding effects, especially for common favorable alleles. However, the potential elite accessions could be rapidly screened by rare favorable alleles.ConclusionIn our study, genetic variation and genome-wide associations for 419 upland cotton accessions were analyzed. Two favorable allele types were identified during three breeding periods, providing important information for yield/quality improvement of upland cotton germplasm.

Time matters! Developmental shift in gene expression between the head and the trunk region of the cichlid fish Astatotilapia burtoni

BackgroundDifferential gene expression can be translated into differing phenotypic traits. Especially during embryogenesis, specific gene expression networks regulate the development of different body structures. Cichlid fishes, with their impressive phenotypic diversity and propensity to radiate, are an emerging model system in the genomics era. Here we set out to investigate gene expression throughout development in the well-studied cichlid fish Astatotilapia burtoni, native to Lake Tanganyika and its affluent rivers.ResultsCombining RNA-sequencing from different developmental time points as well as integrating adult gene expression data, we constructed a new genome annotation for A. burtoni comprising 103,253 transcripts (stemming from 52,584 genomic loci) as well as a new reference transcriptome set. We compared our transcriptome to the available reference genome, redefining transcripts and adding new annotations. We show that about half of these transcripts have coding potential. We also characterize transcripts that are not present in the genome assembly. Next, using our newly constructed comprehensive reference transcriptome, we characterized differential gene expression through time and showed that gene expression is shifted between different body parts. We constructed a gene expression network that identified connected genes responsible for particular phenotypes and made use of it to focus on genes under potential positive selection in A. burtoni, which were implicated in fin development and vision.ConclusionsWe provide new genomic resources for the cichlid fish Astatotilapia burtoni, which will contribute to its further establishment as a model system. Tracing gene expression through time, we identified gene networks underlying particular functions, which will help to understand the genetic basis of phenotypic diversity in cichlids.

Dissecting the human microbiome with single-cell genomics

Editorial summaryRecent advances in genome sequencing of single microbial cells enable the assignment of functional roles to members of the human microbiome that cannot currently be cultured. This approach can reveal the genomic basis of phenotypic variation between closely related strains and can be applied to the targeted study of immunogenic bacteria in disease.

Root Architecture Diversity and Meristem Dynamics in Different Populations of Arabidopsis thaliana.

Arabidopsis thaliana has been an excellent model system for molecular genetic approaches to development and physiology. More recently, the potential of studying various accessions collected from diverse habitats has been started to exploit. Col-0 has been the best-studied accession but we now know that several traits show significant divergences among them. In this work, we focused in the root that has become a key system for development. We studied root architecture and growth dynamics of 12 Arabidopsis accessions. Our data reveal a wide variability in root architecture and root length among accessions. We also found variability in the root apical meristem (RAM), explained mainly by cell size at the RAM transition domain and possibly by peculiar forms of organization at the stem cell niche in some accessions. Contrary to Col-0 reports, in some accessions the RAM size not always explains the variations in the root length; indicating that elongated cell size could be more relevant in the determination of root length than the RAM size itself. This study contributes to investigations dealing with understanding the molecular and cellular basis of phenotypic variation, the role of plasticity on adaptation, and the developmental mechanisms that may restrict phenotypic variation in response to contrasting environmental conditions.

Genetic Variation in the &lt;i&gt;FT1&lt;/i&gt; Locus Involved in Reproductive Onset in &lt;i&gt;Populus deltoides&lt;/i&gt;

The onset of reproduction is an important event in tree development and adaptation. Reproductive onset is controlled by the FT1 locus in poplar ( Populus sp .). However, sequence variation in this locus is not well understood. To enable large-scale polymorphism studies, the aim of this research was to identify sequence variation in the FT1 locus in a small population of Populus deltoides with varying reproductive onset. Gene specific primers were designed to amplify four exons and three introns of FT1 , from 14 genotypes. The sequence analysis showed 9 single nucleotide polymorphisms and 4 insertion-deletion sites located in introns of FT1 . Transcript expression analysis in two groups with different reproductive onset phenotypes showed FT1 transcript expressed higher in the early flowering genotypes than late flowering genotype. This information expands the understanding of the genetic basis of phenotypic variation in reproductive onset in Populus deltoides .

Differences in vocalisations, morphology and mtDNA support species status for New Zealand saddleback Philesturnus spp

Appropriate definitions of species limits are critical for scientific study and conservation management. Many subspecies of birds are defined on the basis of phenotypic variation. However, it has been suggested that following close examination many of these subspecies will be recognised as good species. North Island (NI) (Philesturnus rufusater) and South Island (SI) saddlebacks (P. carunculatus) differ in plumage and apparent vulnerability to introduced predators and, until recently, were considered subspecific. Here, we formally compare vocalisations, morphology and mtDNA between NI and SI saddlebacks. We show significant differences in male song and chatter calls which are fundamental saddleback vocalisations. A discriminant analysis correctly allocated 90% of birds based on significantly larger tarsus, weight and wing measurements in SI saddlebacks relative to NI saddlebacks. Finally, molecular data show c. 5% sequence divergence in mtDNA between the two groups. We concur with previous work elevating NI and SI saddleback to full species.

Genetic Diversity and Geographic Population Structure of Bovine Neospora caninum Determined by Microsatellite Genotyping Analysis

The cyst-forming protozoan parasite Neospora caninum is one of the main causes of bovine abortion worldwide and is of great economic importance in the cattle industry. Recent studies have revealed extensive genetic variation among N . caninum isolates based on microsatellite sequences (MSs). MSs may be suitable molecular markers for inferring the diversity of parasite populations, molecular epidemiology and the basis for phenotypic variations in N . caninum , which have been poorly defined. In this study, we evaluated nine MS markers using a panel of 11 N . caninum -derived reference isolates from around the world and 96 N . caninum bovine clinical samples and one ovine clinical sample collected from four countries on two continents, including Spain, Argentina, Germany and Scotland, over a 10-year period. These markers were used as molecular tools to investigate the genetic diversity, geographic distribution and population structure of N . caninum . Multilocus microsatellite genotyping based on 7 loci demonstrated high levels of genetic diversity in the samples from all of the different countries, with 96 microsatellite multilocus genotypes (MLGs) identified from 108 N . caninum samples. Geographic sub-structuring was present in the country populations according to pairwise F ST. Principal component analysis (PCA) and Neighbor Joining tree topologies also suggested MLG segregation partially associated with geographical origin. An analysis of the MLG relationships, using eBURST, confirmed that the close genetic relationship observed between the Spanish and Argentinean populations may be the result of parasite migration (i.e., the introduction of novel MLGs from Spain to South America) due to cattle movement. The eBURST relationships also revealed genetically different clusters associated with the abortion. The presence of linkage disequilibrium, the co-existence of specific MLGs to individual farms and eBURST MLG relationships suggest a predominant clonal propagation for Spanish N . caninum MLGs in cattle.

Allele-Specific Behavior of Molecular Networks: Understanding Small-Molecule Drug Response in Yeast

The study of systems genetics is changing the way the genetic and molecular basis of phenotypic variation, such as disease susceptibility and drug response, is being analyzed. Moreover, systems genetics aids in the translation of insights from systems biology into genetics. The use of systems genetics enables greater attention to be focused on the potential impact of genetic perturbations on the molecular states of networks that in turn affects complex traits. In this study, we developed models to detect allele-specific perturbations on interactions, in which a genetic locus with alternative alleles exerted a differing influence on an interaction. We utilized the models to investigate the dynamic behavior of an integrated molecular network undergoing genetic perturbations in yeast. Our results revealed the complexity of regulatory relationships between genetic loci and networks, in which different genetic loci perturb specific network modules. In addition, significant within-module functional coherence was found. We then used the network perturbation model to elucidate the underlying molecular mechanisms of individual differences in response to 100 diverse small molecule drugs. As a result, we identified sub-networks in the integrated network that responded to variations in DNA associated with response to diverse compounds and were significantly enriched for known drug targets. Literature mining results provided strong independent evidence for the effectiveness of these genetic perturbing networks in the elucidation of small-molecule responses in yeast.

Conventional and molecular characterization of Trichophyton rubrum

Different studies illustrated that Trichophyton rubrum, among all species of Trichophyton, is the most prevalent and consequently the most important genus. T. rubrum as a worldwide filamentous pathogen fungus can infect human keratinized tissue (skin, nails and rarely hair), and causes dermatophytosis. Researchers use two general methods for the identification of dermatophytes namely, conventional methods on the basis of phenotype variations and molecular methods on the basis of molecular differences. Due to some limitations in traditional methods, in the recent years, molecular biological methods are regarded as useful in the exact and rapid recognition of dermatophytes. The present study identified nine clinical isolates and one ATCC as a control strain of T. rubrum by using both conventional and molecular methods. The molecular systematics method was used to elucidate genetic diversity among strains of T. rubrum and withinTrichophyton species. Morphological characteristics of all colonies T. rubrum quite varies among each other; we revealed that that conventional methods are generally prolonged and may be indecisive. However, molecular studies based on internal transcribed spacer(ITS) sequencing provides a very accurate result, which is more than 96% the similarity ofT. rubrum among all isolates, and more than 90% similarity within Trichophyton spp. Key words: Trichophyton rubrum, conventional method, internal transcribed spacer (ITS) regions, identification, dermatophytes.

Can AFLP genome scans detect small islands of differentiation? The case of shell sculpture variation in the periwinkle Echinolittorina hawaiiensis

Genome scans have identified candidate regions of the genome undergoing selection in a wide variety of organisms, yet have rarely been applied to broadly dispersing marine organisms experiencing divergent selection pressures, where high recombination rates can reduce the extent of linkage disequilibrium (LD) and the ability to detect genomic regions under selection. The broadly dispersing periwinkle Echinolittorina hawaiiensis exhibits a heritable shell sculpture polymorphism that is correlated with environmental variation. To elucidate the genetic basis of phenotypic variation, a genome scan using over 1000 AFLP loci was conducted on smooth and sculptured snails from divergent habitats at four replicate sites. Approximately 5% of loci were identified as outliers with Dfdist, whereas no outliers were identified by BayeScan. Closer examination of the Dfdist outliers supported the conclusion that these loci were false positives. These results highlight the importance of controlling for Type I error using multiple outlier detection approaches, multitest corrections and replicate population comparisons. Assuming shell phenotypes have a genetic basis, our failure to detect outliers suggests that the life history of the target species needs to be considered when designing a genome scan.

Ontogenetic Mechanisms Underlying a Geographic Size Cline in a Grasshopper, Romalea microptera

Abstract Geographic clines in body size have been described for many species, but relatively few investigations have tested hypotheses for the ontogenetic mechanisms maintaining geographic clines. We formalize and test the predictions for the role of ontogenetic mechanisms (e.g., hatching timing and size, juvenile developmental time, juvenile growth rate) in maintaining a longitudinal cline in adult body size of lubber grasshoppers [Romalea microptera (Beauvois)]. To obtain hatching timing and size, we collected eggs from wild females from several populations along the longitudinal gradient in 2 yr (2006 and 2007) and measured hatchling size and hatch date. To obtain juvenile developmental time and growth rates, we surveyed populations along the longitudinal gradient during 2 yr (2006 and 2007) and estimated developmental time and growth rates. We found the developmental time (hatching to fourth instar) and female growth rates increase from west to east along the cline. Patterns of hatching timing and hatching size were not consistent with the size cline. The size cline becomes evident in the third instar and is magnified in the fourth and fifth instars. Our data suggest that the size cline arises from some combination of clinal variation in developmental time and female growth rates; prolonged development and greater growth rates lead to larger mean size. Equally important, we found no evidence that differences in hatching time or size are ontogenetic causes of this cline. Our hypotheses for ontogenetic mechanisms producing an adult size cline should serve as a template for ecologists seeking to understand the ontogenetic basis of spatial variation in phenotypes.