scholarly journals Historical recombination variability contributes to deciphering the genetic basis of phenotypic traits

2019 ◽  
Author(s):  
Carlos Ruiz-Arenas ◽  
Alejandro Cáceres ◽  
Marcos López ◽  
Dolors Pelegrí-Sisó ◽  
Josefa González ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Genetic Variability ◽  
Genetic Basis ◽  
Potential Role ◽  
Selective Pressure ◽  
Real Data ◽  
Phenotypic Traits ◽  
Nonallelic Homologous Recombination ◽  
Historical Recombination

AbstractRecombination is a main source of genetic variability. However, the potential role of the variation generated by recombination in phenotypic traits, including diseases, remains unexplored as there is currently no method to infer chromosomal subpopulations based on recombination patterns differences. We developed recombClust, a method that uses SNP-phased data to detect differences in historic recombination in a chromosome population. We validated our method by performing simulations and by using real data to accurately predict the alleles of well known recombination modifiers, including common inversions in Drosophila melanogaster and human, and the chromosomes under selective pressure at the lactase locus in humans. We then applied recombClust to the complex human 1q21.1 region, where nonallelic homologous recombination produces deleterious phenotypes. We discovered and validated the presence of two different recombination histories in these regions that significantly associated with the differential expression of ANKRD35 in whole blood and that were in high linkage with variants previously associated with hypertension. By detecting differences in historic recombination, our method opens a way to assess the influence of recombination variation in phenotypic traits.

scholarly journals Functional Interactomes of Genes Showing Association with Type-2 Diabetes and Its Intermediate Phenotypic Traits Point towards Adipo-Centric Mechanisms in Its Pathophysiology

Biomolecules ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 601
Author(s):  
Aditya Saxena ◽  
Nitin Wahi ◽  
Anshul Kumar ◽  
Sandeep Kumar Mathur
Keyword(s):  
Type 2 Diabetes ◽  
Adipose Tissue ◽  
Network Analysis ◽  
Potential Role ◽  
Phenotypic Traits ◽  
Protein Protein Interaction ◽  
Cellular Processes ◽  
Antidiabetic Treatment

The pathogenic mechanisms causing type 2 diabetes (T2D) are still poorly understood; a greater awareness of its causation can lead to the development of newer and better antidiabetic drugs. In this study, we used a network-based approach to assess the cellular processes associated with protein–protein interaction subnetworks of glycemic traits—HOMA-β and HOMA-IR. Their subnetworks were further analyzed in terms of their overlap with the differentially expressed genes (DEGs) in pancreatic, muscle, and adipose tissue in diabetics. We found several DEGs in these tissues showing an overlap with the HOMA-β subnetwork, suggesting a role of these tissues in β-cell failure. Many genes in the HOMA-IR subnetwork too showed an overlap with the HOMA-β subnetwork. For understanding the functional theme of these subnetworks, a pathway-to-pathway complementary network analysis was done, which identified various adipose biology-related pathways, containing genes involved in both insulin secretion and action. In conclusion, network analysis of genes showing an association between T2D and its intermediate phenotypic traits suggests their potential role in beta cell failure. These genes enriched the adipo-centric pathways and were expressed in both pancreatic and adipose tissue and, therefore, might be one of the potential targets for future antidiabetic treatment.

Marine ‘Genetic Resources’ and the Potential Role of Protected Areas in Conserving Them

1983 ◽  
Vol 10 (1) ◽  
pp. 31-41 ◽  
Author(s):  
Nicholas V.C. Polunin
Keyword(s):  
Genetic Variability ◽  
Genetic Resources ◽  
Protected Areas ◽  
Potential Role ◽  
Environmental Concern ◽  
Marine Biota ◽  
Geographical Differences ◽  
Biotic Diversity

Marine genetic variability has been studied at all levels within the hierarchy of biological systems, and some major findings to date are briefly reviewed in this paper. Important conclusions are that many marine populations may be quite variable genetically, and that this variability is particularly high in species-rich communities such as those of coral reefs. It is generally thought that variability does change in relation to ecological variables, and thus must contribute to adaptation to environment. At the community level there are marked geographical differences not only in the composition of marine biota, but also in their richness. While the importance of threats to genetic resources cannot be quantified in relation either to one another and to other areas of environmental concern, it is clear that long-term measures such as the establishment of protected areas must be planned with genetic considerations in mind, as these resources are related to the survival of valuable species, and to the important theme of biotic diversity.

scholarly journals Identification of QTLs and Putative Candidate Gene Involved in Rhizome Enlargement of Asian lotus (Nelumbo Nucifera)

2022 ◽  
Author(s):  
Yanling Liu ◽  
Heyun Song ◽  
Minghua Zhang ◽  
Dong Yang ◽  
Xianbao Deng ◽  
...  
Keyword(s):  
Aquatic Plant ◽  
Genetic Basis ◽  
Adaptive Strategy ◽  
Transgenic Potato ◽  
Phenotypic Traits ◽  
Storage Organ ◽  
Significant Qtls ◽  
Trait Variance ◽  
Putative Candidate Gene

Abstract Lotus (Nelumbo) is perennial aquatic plant with nutritional, pharmacological, and ornamental significance. Rhizome is an underground lotus stem that act as a storage organ and as a reproductive tissue for asexual production. The enlargement of lotus rhizome is an important adaptive strategy for surviving the cold winter. The aims of this study were to identify quantitative trait loci (QTLs) for rhizome enlargement traits including rhizome enlargement index (REI) and number of enlarged rhizome (NER), and to uncover candidate genes associated with these phenotypic traits. A high-density genetic linkage map was constructed, consisting of 2,935 markers binned from 236,840 SNPs. A total of 14 significant QTLs were detected for REI and NER, which explained 6.67–22.28% of trait variance. Three QTL regions were repeatedly identified in at least two years, and a major QTL, designated cqREI-LG2, with a rhizome-enlargement effect and about 20% of the phenotypic contribution was identified across the three climatic years. A candidate NnBEL6 gene located within the confidence interval of cqREI-LG2 was considered to be putatively involved in lotus rhizome enlargement. The expression of NnBEL6 was exclusively induced by rhizome swelling. Sequence comparison of NnBEL6 among lotus varieties revealed a functional Indel site in its promoter that likely initiates the rhizome enlargement process. Transgenic potato assay was used to confirm the role of NnBEL6 in inducing tuberization. The successful identification QTLs and functional validation of NnBEL6 gene reported in this study will enrich our knowledge on the genetic basis of rhizome enlargement in lotus.

scholarly journals IFT88 transports Gucy2d, a guanylyl cyclase, to maintain sensory cilia function in Drosophila

2020 ◽  
Author(s):  
Sascha Werner ◽  
Sihem Zitouni ◽  
Pilar Okenve-Ramos ◽  
Susana Mendonca ◽  
Anje Sporbert ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Guanylyl Cyclase ◽  
Potential Role ◽  
Late Onset ◽  
Intraflagellar Transport ◽  
Human Diseases ◽  
Evolutionarily Conserved ◽  
Sensory Cilia ◽  
Ciliated Neurons

Cilia are involved in a plethora of motility and sensory-related functions. Ciliary defects cause several ciliopathies, some of which with late-onset, suggesting cilia are actively maintained. While much is known about cilia assembly, little is understood about the mechanisms of their maintenance. Given that intraflagellar transport (IFT) is essential for cilium assembly, we investigated the role of one of its main players, IFT88, in ciliary maintenance. We show that DmIFT88, the Drosophila melanogaster orthologue of IFT88, continues to move along fully formed sensory cilia, and that its acute knockdown in the ciliated neurons of the adult affects sensory behaviour. We further identify DmGucy2d, the Drosophila guanylyl cyclase 2d, as a DmIFT88 cargo, whose loss also leads to defects in sensory behaviour maintenance. DmIFT88 binds to the intracellular part of DmGucy2d, a highly, evolutionarily conserved and mutated in several degenerative retina diseases, taking the cyclase into the cilia. Our results offer a novel mechanism for the maintenance of sensory cilia function and its potential role in human diseases.

scholarly journals One prophage WO gene rescues cytoplasmic incompatibility in Drosophila melanogaster

2018 ◽  
Vol 115 (19) ◽  
pp. 4987-4991 ◽  
Author(s):  
J. Dylan Shropshire ◽  
Jungmin On ◽  
Emily M. Layton ◽  
Helen Zhou ◽  
Seth R. Bordenstein
Keyword(s):  
Drosophila Melanogaster ◽  
Vector Control ◽  
Genetic Basis ◽  
Cytoplasmic Incompatibility ◽  
Embryo Rescue ◽  
Field Trials ◽  
Intracellular Bacteria ◽  
Fitness Advantage ◽  
Embryonic Death

Wolbachia are maternally inherited, intracellular bacteria at the forefront of vector control efforts to curb arbovirus transmission. In international field trials, the cytoplasmic incompatibility (CI) drive system of wMel Wolbachia is deployed to replace target vector populations, whereby a Wolbachia-induced modification of the sperm genome kills embryos. However, Wolbachia in the embryo rescue the sperm genome impairment, and therefore CI results in a strong fitness advantage for infected females that transmit the bacteria to offspring. The two genes responsible for the wMel-induced sperm modification of CI, cifA and cifB, were recently identified in the eukaryotic association module of prophage WO, but the genetic basis of rescue is unresolved. Here we use transgenic and cytological approaches to demonstrate that maternal cifA expression independently rescues CI and nullifies embryonic death caused by wMel Wolbachia in Drosophila melanogaster. Discovery of cifA as the rescue gene and previously one of two CI induction genes establishes a “Two-by-One” model that underpins the genetic basis of CI. Results highlight the central role of prophage WO in shaping Wolbachia phenotypes that are significant to arthropod evolution and vector control.

A STUDY OF THE GENETIC BASIS OF THE SEXUAL DIMORPHISM FOR WING LENGTH IN DROSOPHILA MELANOGASTER

Genetics ◽  
1972 ◽  
Vol 72 (3) ◽  
pp. 475-487
Author(s):  
Margaret A Bird ◽  
H E Schaffer
Keyword(s):  
Drosophila Melanogaster ◽  
Sexual Dimorphism ◽  
Genetic Variability ◽  
Genetic Basis ◽  
Wing Length ◽  
Quantitative Character ◽  
Sex Dimorphism ◽  
Male Wing ◽  
The Difference ◽  
Chromosome Iii

ABSTRACT The genetic basis of a sexually dimorphic quantitative character in Drosophila melanogaster was investigated by means of two-way directional selection for increased and decreased differences between male and female wing length. The sex dimorphism (SD), defined as the mean wing length difference between the sexes, within families, provided the criterion for selection.—The two lines (High SD, Low SD) diverged rapidly during the 15 generations of selection, indicating the presence of extensive genetic variability for the genotype-sex interaction underlying the observed sexual dimorphism. There was evidence that genetic variability persisted in both lines when selection was relaxed. Most of the divergence between the two lines remained after 10 generations of relaxed selection.—The change in the level of sex dimorphism in the High line was due primarily to a decrease in male wing length; in the Low line most of the change in SD was the result of a decrease in female wing length. An overall reduction in wing length in both sexes in both lines is interpreted as an effect of inbreeding.—The distribution and nature of the genetic control underlying the SD characteristic of the two selection lines was investigated by chromosome substitution between selection lines using a marked inversion technique. The two lines differed by factors located on each of the three major chromosome pairs. Chromosome III had the greatest effect on the difference in SD level between lines, and showed an overall additive effect when present in homozygous versus heterozygous combination. Chromosome II had the least effect, with a significant dominance effect of the High II being evident when heterozygotes were compared with homozygotes. The effect of the X chromosome was intermediate. There was some evidence of interaction between non-homologous chromosomes.

POPDC proteins and cardiac function

2019 ◽  
Vol 47 (5) ◽  
pp. 1393-1404 ◽  
Author(s):  
Thomas Brand
Keyword(s):  
Potential Role ◽  
Striated Muscle ◽  
Short Review ◽  
Effector Proteins ◽  
Muscle Disease ◽  
Disease Genes ◽  
Protein Protein Interaction ◽  
Interaction Partners ◽  
And Function

Abstract The Popeye domain-containing gene family encodes a novel class of cAMP effector proteins in striated muscle tissue. In this short review, we first introduce the protein family and discuss their structure and function with an emphasis on their role in cyclic AMP signalling. Another focus of this review is the recently discovered role of POPDC genes as striated muscle disease genes, which have been associated with cardiac arrhythmia and muscular dystrophy. The pathological phenotypes observed in patients will be compared with phenotypes present in null and knockin mutations in zebrafish and mouse. A number of protein–protein interaction partners have been discovered and the potential role of POPDC proteins to control the subcellular localization and function of these interacting proteins will be discussed. Finally, we outline several areas, where research is urgently needed.

The Effect of Path Length and Display Size on Memory for Spatial Information

2012 ◽  
Vol 59 (3) ◽  
pp. 147-152 ◽  
Author(s):  
Katherine Guérard ◽  
Sébastien Tremblay
Keyword(s):  
Path Length ◽  
Potential Role ◽  
Spatial Information ◽  
Recall Performance ◽  
Minor Role ◽  
Length Effect ◽  
Serial Memory ◽  
Fixed Reference ◽  
A Minor

In serial memory for spatial information, some studies showed that recall performance suffers when the distance between successive locations increases relatively to the size of the display in which they are presented (the path length effect; e.g., Parmentier et al., 2005) but not when distance is increased by enlarging the size of the display (e.g., Smyth & Scholey, 1994). In the present study, we examined the effect of varying the absolute and relative distance between to-be-remembered items on memory for spatial information. We manipulated path length using small (15″) and large (64″) screens within the same design. In two experiments, we showed that distance was disruptive mainly when it is varied relatively to a fixed reference frame, though increasing the size of the display also had a small deleterious effect on recall. The insertion of a retention interval did not influence these effects, suggesting that rehearsal plays a minor role in mediating the effects of distance on serial spatial memory. We discuss the potential role of perceptual organization in light of the pattern of results.

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