scholarly journals Genetic analysis reveals candidate genes for activity QTL in the blind Mexican tetra,Astyanax mexicanus

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5189 ◽  
Author(s):  
Brian M. Carlson ◽  
Ian B. Klingler ◽  
Bradley J. Meyer ◽  
Joshua B. Gross
Keyword(s):  
Candidate Genes ◽  
Genetic Basis ◽  
Activity Patterns ◽  
Potential Candidate ◽  
Behavioral Phenotypes ◽  
Astyanax Mexicanus ◽  
Broad Array ◽  
Patterns Of Behavior ◽  
Surface Dwelling

Animal models provide useful tools for exploring the genetic basis of morphological, physiological and behavioral phenotypes. Cave-adapted species are particularly powerful models for a broad array of phenotypic changes with evolutionary, developmental and clinical relevance. Here, we explored the genetic underpinnings of previously characterized differences in locomotor activity patterns between the surface-dwelling and Pachón cave-dwelling populations ofAstyanax mexicanus.We identified multiple novel QTL underlying patterns in overall levels of activity (velocity), as well as spatial tank use (time spent near the top or bottom of the tank). Further, we demonstrated that different regions of the genome mediate distinct patterns in velocity and tank usage. We interrogated eight genomic intervals underlying these activity QTL distributed across six linkage groups. In addition, we employed transcriptomic data and draft genomic resources to generate and evaluate a list of 36 potential candidate genes. Interestingly, our data support the candidacy of a number of genes, but do not suggest that differences in the patterns of behavior observed here are the result of alterations to certain candidate genes described in other species (e.g., teleost multiple tissue opsins, melanopsins or members of the core circadian clockwork). This study expands our knowledge of the genetic architecture underlying activity differences in surface and cavefish. Future studies will help define the role of specific genes in shaping complex behavioral phenotypes inAstyanaxand other vertebrate taxa.

scholarly journals Identification of Multiple Gene Mutations Accounts for a new Genetic Architecture of Primary Ovarian Insufficiency

2016 ◽  
Vol 101 (12) ◽  
pp. 4541-4550 ◽  
Author(s):  
Justine Bouilly ◽  
Isabelle Beau ◽  
Sara Barraud ◽  
Valérie Bernard ◽  
Kemal Azibi ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Gene Mutations ◽  
Primary Ovarian Insufficiency ◽  
Potential Candidate ◽  
Missense Mutations ◽  
Ovarian Insufficiency ◽  
Monogenic Disorder ◽  
Gene Encoding ◽  
Multiple Loci

Context: Idiopathic primary ovarian insufficiency (POI) is a major cause of amenorrhea and infertility. POI affects 1% of women before age 40 years, and several genetic causes have been reported. To date, POI has been considered a monogenic disorder. Objective: The aim of this study was to identify novel gene variations and to investigate if individuals with POI harbor mutation in multiple loci. Patients and Methods: One hundred well-phenotyped POI patients were systematically screened for variants in 19 known POI loci (and potential candidate genes) using next-generation sequencing. Results: At least one rare protein-altering gene variant was identified in 19 patients, including missense mutations in new candidate genes, namely SMC1β and REC8 (involved in the cohesin complex) and LHX8, a gene encoding a transcription factor. Novel or recurrent deleterious mutations were also detected in the known POI candidate genes NOBOX, FOXL2, SOHLH1, FIGLA, GDF9, BMP15, and GALT. Seven patients harbor mutations in two loci, and this digenicity seems to influence the age of symptom onset. Conclusions: Genetic anomalies in women with POI are more frequent than previously believed. Digenic findings in several cases suggest that POI is not a purely monogenic disorder and points to a role of digenicity. The genotype-phenotype correlations in some kindreds suggest that a synergistic effect of several mutations may underlie the POI phenotype.

scholarly journals Genome-wide association studies of plant architecture-related traits and 100-seed weight in soybean landraces

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiaoli Zhang ◽  
Wentao Ding ◽  
Dong Xue ◽  
Xiangnan Li ◽  
Yang Zhou ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Seed Weight ◽  
Plant Architecture ◽  
Genetic Basis ◽  
Agronomic Traits ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Potential Candidate ◽  
Genome Wide ◽  
100 Seed Weight

Abstract Background Plant architecture-related traits (e.g., plant height (PH), number of nodes on main stem (NN), branch number (BN) and stem diameter (DI)) and 100-seed weight (100-SW) are important agronomic traits and are closely related to soybean yield. However, the genetic basis and breeding potential of these important agronomic traits remain largely ambiguous in soybean (Glycine max (L.) Merr.). Results In this study, we collected 133 soybean landraces from China, phenotyped them in two years at two locations for the above five traits and conducted a genome-wide association study (GWAS) using 82,187 single nucleotide polymorphisms (SNPs). As a result, we found that a total of 59 SNPs were repeatedly detected in at least two environments. There were 12, 12, 4, 4 and 27 SNPs associated with PH, NN, BN, DI and 100-SW, respectively. Among these markers, seven SNPs (AX-90380587, AX-90406013, AX-90387160, AX-90317160, AX-90449770, AX-90460927 and AX-90520043) were large-effect markers for PH, NN, BN, DI and 100-SW, and 15 potential candidate genes were predicted to be in linkage disequilibrium (LD) decay distance or LD block. In addition, real-time quantitative PCR (qRT-PCR) analysis was performed on four 100-SW potential candidate genes, three of them showed significantly different expression levels between the extreme materials at the seed development stage. Therefore, Glyma.05 g127900, Glyma.05 g128000 and Glyma.05 g129000 were considered as candidate genes with 100-SW in soybean. Conclusions These findings shed light on the genetic basis of plant architecture-related traits and 100-SW in soybean, and candidate genes could be used for further positional cloning.

The Genetic Basis of the Pierre Robin Sequence

2006 ◽  
Vol 43 (2) ◽  
pp. 155-159 ◽  
Author(s):  
Linda P. Jakobsen ◽  
Mary A. Knudsen ◽  
James Lespinasse ◽  
Carmen García Ayuso ◽  
Carmen Ramos ◽  
...  
Keyword(s):  
Cleft Palate ◽  
Candidate Genes ◽  
Cleft Lip ◽  
Genetic Basis ◽  
Mendelian Inheritance ◽  
Potential Candidate ◽  
Pierre Robin Sequence ◽  
Gene Map ◽  
Robin Sequence ◽  
Pierre Robin

Objective The Pierre Robin Sequence (PRS) is subgroup of the cleft palate population. As with the etiology of cleft lip or palate, the etiology of PRS is generally unknown. Some factors are suggestive of a genetic basis for PRS. The purpose of this study was to compare genetic information on PRS available in the literature and in a cytogenetic database to facilitate focused genetic studies of PRS. Design After searching Medline for “pierre robin and genetics,” the Mendelian Cytogenetics Network database for “robin” and “pierre robin,” and two reviews from the Human Cytogenetics Database for “cleft palate” and “micrognathia,” a comparison of the data and a search in Online Mendelian Inheritance in Man (OMIM) Gene Map was performed to identify relevant candidate genes. Results The findings revealed consistency to a certain degree to loci 2q24.1-33.3, 4q32-qter, 11q21-23.1, and 17q21-24.3. A search in the OMIM Gene Map provided many candidate genes for PRS in these regions. The GAD67 on 2q31, the PVRL1 on 11q23-q24, and the SOX9 gene on 17q24.3-q25.1 are suggested to be of particular importance. Conclusion Candidate loci and a few potential candidate genes for PRS are proposed from the present study. This may enable researchers to focus their effort in the studies of PRS.

scholarly journals Pharmacokinetics and Pharmacogenetics of Apixaban

2020 ◽  
Vol 16 (5) ◽  
pp. 852-860
Author(s):  
A. V. Savinova ◽  
M. M. Petrova ◽  
N. A. Shnayder ◽  
E. N. Bochanova ◽  
R. F. Nasyrova
Keyword(s):  
Candidate Genes ◽  
Factor Xa ◽  
Potential Candidate ◽  
Beta Oxidation ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Vein Thrombosis ◽  
Genes Encoding ◽  
Deep Vein

Apixaban is oral anticoagulant, it is widely used in prevention of stroke in non-valvular atrial fibrillation and treatment of deep vein thrombosis and pulmonary embolism. Its main mechanism of action is through reversible inhibition of factor Xa. It specifically binds and inhibits both free and bound factor Xa which ultimately results in reduction in the levels of thrombin formation. Apixaban is mainly metabolized by CYP3A4 with minor contributions from CYP1A2, CYP2C8, CYP2C9, CYP2C19 and CYP2J2 isoenzymes. Some of the major metabolic pathways of apixaban include o-demethylation, hydroxylation, and sulfation, with o-demethylapixabansulphate being the major metabolite. The aim of this review is analysis of associated researches of single nucleotide variants (SNV) of CYP3A5 and SULT1A1 genes and search for new candidate genes reflecting effectiveness and safety of apixaban. The search for full-text publications in Russian and English languages containing key words “apixaban”, “pharmacokinetics”, “effectiveness”, “safety” was carried out amongst literature of the past twenty years with the use of eLibrary, PubMed, Web of Science, OMIM data bases. Pharmacokinetics and pharmacogenetics of apixaban are considered in this review. The hypothesis about CYP и SULT1A enzymes influence on apixaban metabolism was examined. To date, numerous SNVs of the CYP3A5 and SULT1A1 genes have been identified, but their potential influence on pharmacokinetics apixaban in clinical practice needs to be further studies. The role of SNVs of other genes encoding beta-oxidation enzymes of apixaban (CYP1A2, CYP2C8, CYP2C9, CYP2C19, CYP2J2) and transporter proteins (ABCB1, ABCG2) in its efficacy and safety are not well understood, and ABCB1 and ABCG2 genes may be potential candidate genes for studies of the drug safety.

scholarly journals Identification of genomic regions and candidate genes of functional importance for gastrointestinal parasite resistance traits in Djallonké sheep of Burkina Faso

2019 ◽  
Vol 62 (1) ◽  
pp. 313-323
Author(s):  
Isabel Álvarez ◽  
Iván Fernández ◽  
Albert Soudré ◽  
Amadou Traoré ◽  
Lucía Pérez-Pardal ◽  
...  
Keyword(s):  
Burkina Faso ◽  
Candidate Genes ◽  
Genetic Basis ◽  
Ovis Aries ◽  
Enrichment Score ◽  
Phenotypic Variance ◽  
Potential Candidate ◽  
Parasite Resistance ◽  
Functional Importance ◽  
Resistance Traits

Abstract. A total of 184 Djallonké lambs from Burkina Faso with phenotypes for packed-cell volume (PCV), log-transformed fecal egg count (lnFEC), and FAffa MAlan CHArt (FAMACHA©) eye scores were typed with the OvineSNP50 BeadChip of Illumina to contribute to the knowledge of the genetic basis of gastrointestinal (GIN) parasite resistance in sheep. Association analysis identified a total of 22 single-nucleotide polymorphisms (SNPs) related with PCV (6 SNPs), lnFEC (7), and FAMACHA scores (9) distributed among 14 Ovis aries chromosomes (OAR). The identified SNPs accounted for 18.76 % of the phenotypic variance for PCV, 21.24 % for lnFEC, and 34.38 % for FAMACHA scores. Analyses pointed out the importance of OAR2 for PCV, OAR3 for FAMACHA scores, and OAR6 for lnFEC. The 125 kb regions surrounding the identified SNPs overlapped with seven previously reported quantitative trait loci (QTLs) for the traits analyzed in the current work. The only chromosome harboring markers associated with the three traits studied was OAR2. In agreement with the literature, two different chromosomal areas on OAR2 can play a major role in the traits studied. Gene-annotation enrichment analysis allowed us to identify a total of 34 potential candidate genes for PCV (6 genes), lnFEC (4), and FAMACHA scores (24). Annotation analysis allowed us to identify one functional term cluster with a significant enrichment score (1.302). The cluster included five genes (TRIB3, CDK4, CSNK2A1, MARK1, and SPATA5) involved in immunity-related and cell-proliferation processes. Furthermore, this research suggests that the MBL2 gene can underlie a previously reported QTL for immunoglobulin A levels on OAR22 and confirms the importance of genes involved in growth and size (such as the ADAMTS17 gene on OAR18) for GIN resistance traits. Since association studies for the ascertainment of the genetic basis of GIN resistance may be affected by genotype–environment interactions, obtaining information from local sheep populations managed in harsh environments contributes to the identification of novel genomic areas of functional importance for GIN resistance for that trait.

scholarly journals The Genetic Basis of Tomato Aroma

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 226
Author(s):  
Matteo Martina ◽  
Yury Tikunov ◽  
Ezio Portis ◽  
Arnaud G. Bovy
Keyword(s):  
Candidate Genes ◽  
Genetic Basis ◽  
Tomato Fruit ◽  
Potential Candidate ◽  
Tomato Fruits ◽  
Vast Array ◽  
Solanum Lycopersicum L ◽  
Different Populations ◽  
Tomato Cultivars ◽  
Combining Information

Tomato (Solanum lycopersicum L.) aroma is determined by the interaction of volatile compounds (VOCs) released by the tomato fruits with receptors in the nose, leading to a sensorial impression, such as “sweet”, “smoky”, or “fruity” aroma. Of the more than 400 VOCs released by tomato fruits, 21 have been reported as main contributors to the perceived tomato aroma. These VOCs can be grouped in five clusters, according to their biosynthetic origins. In the last decades, a vast array of scientific studies has investigated the genetic component of tomato aroma in modern tomato cultivars and their relatives. In this paper we aim to collect, compare, integrate and summarize the available literature on flavour-related QTLs in tomato. Three hundred and fifty nine (359) QTLs associated with tomato fruit VOCs were physically mapped on the genome and investigated for the presence of potential candidate genes. This review makes it possible to (i) pinpoint potential donors described in literature for specific traits, (ii) highlight important QTL regions by combining information from different populations, and (iii) pinpoint potential candidate genes. This overview aims to be a valuable resource for researchers aiming to elucidate the genetics underlying tomato flavour and for breeders who aim to improve tomato aroma.

scholarly journals A chromosome-level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Wesley C. Warren ◽  
Tyler E. Boggs ◽  
Richard Borowsky ◽  
Brian M. Carlson ◽  
Estephany Ferrufino ◽  
...  
Keyword(s):  
Complex Traits ◽  
Fish Genome ◽  
Genetic Studies ◽  
Astyanax Mexicanus ◽  
Eye Size ◽  
Genome Wide ◽  
Surface Dwelling ◽  
Trait Locus ◽  
Chromosome Level

AbstractIdentifying the genetic factors that underlie complex traits is central to understanding the mechanistic underpinnings of evolution. Cave-dwelling Astyanax mexicanus populations are well adapted to subterranean life and many populations appear to have evolved troglomorphic traits independently, while the surface-dwelling populations can be used as a proxy for the ancestral form. Here we present a high-resolution, chromosome-level surface fish genome, enabling the first genome-wide comparison between surface fish and cavefish populations. Using this resource, we performed quantitative trait locus (QTL) mapping analyses and found new candidate genes for eye loss such as dusp26. We used CRISPR gene editing in A. mexicanus to confirm the essential role of a gene within an eye size QTL, rx3, in eye formation. We also generated the first genome-wide evaluation of deletion variability across cavefish populations to gain insight into this potential source of cave adaptation. The surface fish genome reference now provides a more complete resource for comparative, functional and genetic studies of drastic trait differences within a species.

Anti-Myelin Oligodendrocyte Glycoprotein Encephalomyelitis and Extensive Longitudinal Transverse Myelitis Associated with Compound Heterozygous NLRP3 Missense Mutations in a Young Child

2020 ◽  
Author(s):  
Deirdre O'Sullivan ◽  
Michael Moore ◽  
Susan Byrne ◽  
Andreas O. Reiff ◽  
Susanna Felsenstein
Keyword(s):  
Young Child ◽  
Genetic Basis ◽  
Transverse Myelitis ◽  
Acute Disseminated Encephalomyelitis ◽  
Myelin Oligodendrocyte Glycoprotein ◽  
Compound Heterozygous ◽  
Missense Mutations ◽  
Childhood Onset

AbstractAcute disseminated encephalomyelitis in association with extensive longitudinal transverse myelitis is reported in a young child with positive anti-myelin oligodendrocyte glycoprotein (MOG) antibody with heterozygous NLRP3 missense mutations; p.(Arg488Lys) and p.(Ser159Ile). This case may well present an exceptional coincidence, but may describe a yet unrecognized feature of the spectrum of childhood onset cryopyrinopathies that contribute to the understanding of the genetic basis for anti-MOG antibody positive encephalomyelitis. Based on this observation, a larger scale study investigating the role of NLRP3 and other inflammasomes in this entity would provide important pathophysiological insights and potentially novel avenues for treatment.

scholarly journals Meta-QTL analysis and identification of candidate genes for quality, abiotic and biotic stress in durum wheat

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jose Miguel Soriano ◽  
Pasqualina Colasuonno ◽  
Ilaria Marcotuli ◽  
Agata Gadaleta
Keyword(s):  
Molecular Markers ◽  
Abiotic Stress ◽  
Durum Wheat ◽  
Candidate Genes ◽  
Biotic Stress ◽  
Qtl Analysis ◽  
Complex Traits ◽  
Genetic Basis ◽  
Agronomic Traits ◽  
Plant Performance

AbstractThe genetic improvement of durum wheat and enhancement of plant performance often depend on the identification of stable quantitative trait loci (QTL) and closely linked molecular markers. This is essential for better understanding the genetic basis of important agronomic traits and identifying an effective method for improving selection efficiency in breeding programmes. Meta-QTL analysis is a useful approach for dissecting the genetic basis of complex traits, providing broader allelic coverage and higher mapping resolution for the identification of putative molecular markers to be used in marker-assisted selection. In the present study, extensive QTL meta-analysis was conducted on 45 traits of durum wheat, including quality and biotic and abiotic stress-related traits. A total of 368 QTL distributed on all 14 chromosomes of genomes A and B were projected: 171 corresponded to quality-related traits, 127 to abiotic stress and 71 to biotic stress, of which 318 were grouped in 85 meta-QTL (MQTL), 24 remained as single QTL and 26 were not assigned to any MQTL. The number of MQTL per chromosome ranged from 4 in chromosomes 1A and 6A to 9 in chromosome 7B; chromosomes 3A and 7A showed the highest number of individual QTL (4), and chromosome 7B the highest number of undefined QTL (4). The recently published genome sequence of durum wheat was used to search for candidate genes within the MQTL peaks. This work will facilitate cloning and pyramiding of QTL to develop new cultivars with specific quantitative traits and speed up breeding programs.

scholarly journals Vulnerability to climate change of a microendemic lizard species from the central Andes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
A. Laspiur ◽  
J. C. Santos ◽  
S. M. Medina ◽  
J. E. Pizarro ◽  
E. A. Sanabria ◽  
...  
Keyword(s):  
Climate Change ◽  
Species Distribution Models ◽  
Activity Patterns ◽  
Geographic Range ◽  
Behavioral Thermoregulation ◽  
Rapid Loss ◽  
Distribution Models ◽  
Lizard Species ◽  
Vulnerability To Climate Change

AbstractGiven the rapid loss of biodiversity as consequence of climate change, greater knowledge of ecophysiological and natural history traits are crucial to determine which environmental factors induce stress and drive the decline of threatened species. Liolaemus montanezi (Liolaemidae), a xeric-adapted lizard occurring only in a small geographic range in west-central Argentina, constitutes an excellent model for studies on the threats of climate change on such microendemic species. We describe field data on activity patterns, use of microhabitat, behavioral thermoregulation, and physiology to produce species distribution models (SDMs) based on climate and ecophysiological data. Liolaemus montanezi inhabits a thermally harsh environment which remarkably impacts their activity and thermoregulation. The species shows a daily bimodal pattern of activity and mostly occupies shaded microenvironments. Although the individuals thermoregulate at body temperatures below their thermal preference they avoid high-temperature microenvironments probably to avoid overheating. The population currently persists because of the important role of the habitat physiognomy and not because of niche tracking, seemingly prevented by major rivers that form boundaries of their geographic range. We found evidence of habitat opportunities in the current range and adjacent areas that will likely remain suitable to the year 2070, reinforcing the relevance of the river floodplain for the species’ avoidance of extinction.

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