Article
Biochemical Research Methods
Dat Thanh Nguyen, Quan Hoang Nguyen, Nguyen Thuy Duong, Nam S. Vo
Summary: Despite the advancement of sequencing technology, SNP arrays remain the most cost-effective genotyping solution for large-scale genomic research. This study introduces a novel method called LmTag for tag SNP selection, which improves imputation performance and prioritizes highly functional SNP markers. It is particularly suitable for under-represented populations and non-model species in developing countries.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Zining Yang, Yaning Yang, Xu Steven Xu, Min Yuan
Summary: The paper introduces a novel two-step robust-efficient approach, the genetic model selection (GMS) method for quantitative trait analysis. GMS selects a genetic model by testing Hardy-Weinberg disequilibrium (HWD) with extremal samples of the population in the first step and then applies the corresponding genetic model-specific t-test in the second step, showing higher efficiency than existing methods.
Article
Agronomy
Scott H. Brainard, Shelby L. Ellison, Philipp W. Simon, Julie C. Dawson, Irwin L. Goldman
Summary: The genetic control of market class in carrots is mainly additive but also highly polygenic. Advancements in digital image analysis have made high-throughput quantification of root size and shape attributes possible, enabling the study of genetic control of root morphology. Combining digital image analysis with GWAS and GEBVs has provided novel insights into the genetic control of market class traits in carrots.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Genetics & Heredity
Ivan P. M. Gorlov, Christopher Amos
Summary: The X-chromosome has a lower density of GWAS-detected SNPs compared to autosomes, which cannot be explained by methodological bias. This lower density may be due to a real biological reason - a lower density of functional SNPs on the X-chromosome compared to autosomes. This hypothesis is supported by the analysis of overall SNP density and genic versus intergenic SNP densities.
Article
Multidisciplinary Sciences
Mauricio F. Landaeta, Carola Hernandez-Santoro, Francesca Search, Manuel Castillo, Claudio Bernal, Sergio A. Navarrete, Evie A. Wieters, Ricardo Beldade, Ana Navarro Campoi, Alejandro Perez-Matus
Summary: This study examines the discarded demersal community fauna in the artisanal and industrial crustacean fisheries along the southern Humboldt Current System from 2014 to 2019. It analyzes spatio-temporal patterns, species composition, and assemblages, and investigates the factors influencing biodiversity. The results show variations in species composition, assemblage segregation by depth and geographic zone, and interannual variations of biodiversity. Surface sea temperature, chlorophyll-a, or wind stress were not correlated with biodiversity.
Article
Genetics & Heredity
Juan Zhong, Jianping Xu, Ping Zhang
Summary: The study revealed geographic differentiation and genetic diversity of Amanita exitialis in southern China, with secondary homothallic reproduction and long-distance spore dispersal. Significant genetic differentiation was found among local populations, while an excess of heterozygous individuals was observed at both the local and total sample levels. The presence of three genetic clusters suggests divergence within this species in the geographic region.
Article
Forestry
Regiane Abjaud Estopa, Joao Gabriel Zanon Paludeto, Barbara Salomao Faria Muller, Ricardo Augusto de Oliveira, Camila Ferreira Azevedo, Marcos Deon Vilela de Resende, Evandro Vagner Tambarussi, Dario Grattapaglia
Summary: Genomic selection shows great potential for improving eucalypt tree breeding, especially for non-mainstream species. This study compared different genomic prediction models and found that they performed well in predicting wood quality traits and volume growth. The models outperformed the conventional pedigree-based approach, except for extractives content. Additionally, using a lower density SNP panel yielded similar predictive abilities and heritabilities compared to a higher density panel, but may not be economically advantageous.
Article
Agronomy
Chin Jian Yang, Olufunmilayo Ladejobi, Richard Mott, Wayne Powell, Ian Mackay
Summary: By modeling the distribution of allele frequency over the year of variety release, we have successfully identified major loci involved in historical breeding of winter wheat. Our study reveals that historical selection in winter wheat has mainly targeted yield improvement, but may have negative effects on traits such as flowering time, lodging, plant height and grain protein content. These findings provide important insights for guiding future breeding of winter wheat.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Biology
Jay Y. S. Hodgson, Michele M. Cutwa, Alex Collier, Kathryn S. Craven
Summary: Researchers developed and piloted an instructional scaffolding based on income tax return forms to help students calculate evolution equations. The study found that students improved their understanding of these equations after using the scaffolding. Suggestions for implementation of this exercise are also discussed.
AMERICAN BIOLOGY TEACHER
(2023)
Article
Biology
Rehab F. Almassabi, Rashid Mir, Jamsheed Javid, Faisel M. Abuduhier, Reema Almotairi, Marwan H. Alhelali, Naseh Algehainy, Basim S. O. Alsaedi, Salem Owaid Albalawi, Imadeldin Elfaki
Summary: Coronary artery disease (CAD) is a major cause of death and hospitalization worldwide, with a prevalence of 5.5% in Saudi Arabia. This study identified three genetic loci associated with CAD and found significantly increased TNF-alpha serum levels in CAD patients. These findings have implications for future genetic testing and prevention.
Article
Oncology
Ilaria Scarpelli, Valerie Beyer Stalder, Gerasimos Tsilimidos, Katrin Rapakko, Mariangela Costanza, Sabine Blum, Jacqueline Schoumans
Summary: Genetic testing is crucial in the diagnosis, prognosis, and treatment decisions for myelodysplastic neoplasms (MDS). This study compared chromosome banding analysis (CBA) with single nucleotide polymorphism (SNP) array testing in a large MDS cohort and found that SNP array provided a more refined cytogenetic IPSS-R score. This confirms the effectiveness of SNP array in MDS risk stratification and highlights the importance of assessing overall genomic complexity.
GENES CHROMOSOMES & CANCER
(2023)
Article
Medicine, General & Internal
Aadil Yousif, Rashid Mir, Jamsheed Javid, Jameel Barnawi, Mohammed M. Jalal, Malik A. Altayar, Salem Owaid Albalawi, Faisel M. Abuduhier
Summary: This study developed a T-ARMS-based PCR assay for genotyping ACE1-rs4646996 and ACE2-rs4240157 and investigated their association with coronary artery disease (CAD). The results showed significant differences in ACE1-rs4646996 and ACE2-rs4240157 genotypes between CAD patients and controls, and these genotypes were associated with CAD susceptibility. Additionally, ACE2 genotypes were found to be associated with hypertension, type 2 diabetes, and obesity. The findings suggest that the developed assay can be a potential molecular tool for genetic disease diagnosis, especially in resource-limited settings.
Article
Pharmacology & Pharmacy
Hanan Jadaan Ali, Haitham Mahmood Kadhim, Ammar Qassim Al-Fahad
Summary: This study examined the genetic variability in response to the drug montelukast in Iraqi asthmatic patients. The results showed that variations in the candidate genes of the leukotriene pathway did not contribute to the variability in clinical responses to montelukast.
JOURNAL OF PHARMACEUTICAL NEGATIVE RESULTS
(2022)
Article
Agronomy
Sofia Irene Deperi, Martin Enrique Tagliotti, Maria Cecilia Bedogni, Marcelo Atilio Huarte
Summary: The study found phenotypic variation in relative area under disease progress curve and yield parameters in potato germplasm. Association mapping on 159 genotypes identified significant associations related to late blight resistance in certain chromosomes, with potential implications for breeding programs.
Article
Biology
Rashid Mir, Imadeldin Elfaki, Jamsheed Javid, Jameel Barnawi, Malik A. Altayar, Salem Owaid Albalawi, Mohammed M. Jalal, Faris J. Tayeb, Aadil Yousif, Mohammad Fahad Ullah, Faisel M. AbuDuhier
Summary: Coronary artery disease (CAD) is a leading cause of death worldwide. This study aimed to investigate the association between genetic variants of eNOS, KLF-14, MTHFR, MiRNA-27a and CAD risk in the Saudi population. The results showed significant associations between certain gene variants and CAD susceptibility.