Article
Biochemistry & Molecular Biology
Zachariah Gompert, Jeffrey L. Feder, Patrik Nosil
Summary: Understanding the impact of selection on the genome is crucial in biology. Indirect selection can affect functionally neutral genetic regions through statistical associations with genes under direct selection, leading to widespread genetic loci being impacted across the genome. This process, including unknown causal variants and genetic associations, makes aspects of evolution more predictable and has implications for evolutionary principles in both basic and applied science.
Article
Multidisciplinary Sciences
Sisay Kidane Alemu, Ayele Badebo Huluka, Kassahun Tesfaye, Teklehaimanot Haileselassie, Cristobal Uauy
Summary: This study conducted a genome wide association study of yellow rust resistance in 300 durum wheat accessions, identifying 11 SNPs significantly associated with resistance on chromosomes 1A, 1B, 2B, and 5A. Six of these SNPs consistently identified on chromosome 1B explained a significant portion of the phenotypic variation. Disease resistance related genes such as ABC transporters, RPM1, receptor kinases, and protein kinases were found at the identified resistance loci.
Article
Multidisciplinary Sciences
Philomin Juliana, Ravi Prakash Singh, Jesse Poland, Sandesh Shrestha, Julio Huerta-Espino, Velu Govindan, Suchismita Mondal, Leonardo Abdiel Crespo-Herrera, Uttam Kumar, Arun Kumar Joshi, Thomas Payne, Pradeep Kumar Bhati, Vipin Tomar, Franjel Consolacion, Jaime Amador Campos Serna
Summary: This study focused on improving wheat grain yield using genomic tools and identified GY-associated markers and LD-blocks, validating the feasibility of simultaneously improving yield potential and stress-resilience. The extensive resources presented in this study offer great opportunities to accelerate breeding for high-yielding and stress-resilient wheat varieties.
SCIENTIFIC REPORTS
(2021)
Article
Agronomy
Avjinder S. Kaler, Larry C. Purcell
Summary: This study identified and confirmed genetic regions, favorable alleles, and candidate genes associated with seed weight in soybean. The results of genome-wide association mapping can provide valuable resources for breeding for seed weight in soybean and improving quality in food industries.
Article
Plant Sciences
Wenchong Chen, Weiwu Yu, Ang Dong, Yanru Zeng, Huwei Yuan, Bingsong Zheng, Rongling Wu
Summary: This study utilizes advanced genotyping technologies to investigate the genetic structure of Torreya grandis, a species with high economic and ornamental values. A high-density linkage map is constructed, and the results suggest that the identified QTLs are relatively young and can be better utilized through clonal propagation.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Jessica Allingham, Wely B. Floriano
Summary: The study provides a comprehensive analysis of the IZUMO1 and JUNO gene sequences in over 2,000 humans, revealing different levels of genetic variation among human populations, with the JUNO gene showing distinct genetic differentiation in the African population compared to other groups. These findings support the potential of these genes as targets for controlling fertility.
Review
Plant Sciences
Muhammad Yasir, Hafiza Hamrah Kanwal, Quaid Hussain, Muhammad Waheed Riaz, Muhammad Sajjad, Junkang Rong, Yurong Jiang
Summary: Over the past two decades, high-density SNP arrays and DNA sequencing technology have been widely used in crop research, particularly in cotton crops. Genome-wide association studies (GWAS) have provided an important tool for uncovering the relationship between crop phenotypes and underlying genetics, helping to advance crop breeding and improvement.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Tilahun Mekonnen, Clay H. Sneller, Teklehaimanot Haileselassie, Cathrine Ziyomo, Bekele G. Abeyo, Stephen B. Goodwin, Dagnachew Lule, Kassahun Tesfaye
Summary: This study aimed to elucidate the genomic architecture of septoria tritici blotch (STB) resistance in an association panel of 178 bread wheat genotypes. Through phenotyping and genotyping, 53 loci associated with STB resistance were identified, with 33 putative quantitative trait loci (QTLs) confirmed. Population structure and principal component analyses revealed two sub-groups with high degrees of admixture.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Behavioral Sciences
Konstantinos Voskarides, Nefeli Giannopoulou, Rasha Eid, Konstantinos Parperis, Andreas Chatzittofis
Summary: Several studies have confirmed the association between autoimmune diseases and psychiatric disorders, with genetic evidence supporting this link. This study aimed to investigate the genetic linkage between genetic variants predisposing to autoimmune diseases and psychiatric disorders by constructing common haplotypes. The results showed multiple chromosomal regions containing genetic variants associated with both diseases, and specific genetic haplotypes were identified. Notably, six autoimmune diseases shared a common haplotype with psychiatric diseases at the HLA locus 6p21-22.
BRAIN AND BEHAVIOR
(2023)
Article
Genetics & Heredity
Kunyan Zou, Ki-Seung Kim, Kipoong Kim, Dongwoo Kang, Yu-Hyeon Park, Hokeun Sun, Bo-Keun Ha, Jungmin Ha, Tae-Hwan Jun
Summary: This study evaluated the genetic diversity of 384 peanut germplasms using an Axiom_Arachis array with 58K SNPs, and identified five SNPs significantly associated with seed aspect ratio on chromosomes Aradu.A09, Aradu.A10, Araip.B08, and Araip.B09. The most significantly associated marker was AX-177640219 on chromosome Araip.B08. Additionally, the study found that the PEPC gene may have a strong causal effect on seed aspect ratio.
Editorial Material
Biochemistry & Molecular Biology
Zachariah Gompert, Jeffrey L. Feder, Patrik Nosil
Summary: This paper quantifies the genome-wide consequences of natural selection and addresses the effects of indirect selection due to the correlation of genetic regions. The critiques on the paper do not substantially affect the findings of the study.
Article
Clinical Neurology
Gie Ken-Dror, Ioana Cotlarciuc, Ida Martinelli, Elvira Grandone, Sini Hiltunen, Erik Lindgren, Maurizio Margaglione, Veronique Le Cam Duchez, Aude Bagan Triquenot, Marialuisa Zedde, Michelangelo Mancuso, Ynte M. Ruigrok, Thomas Marjot, Brad Worrall, Jennifer J. Majersik, Tiina M. Metso, Jukka Putaala, Elena Haapaniemi, Susanna M. Zuurbier, Matthijs C. Brouwer, Serena M. Passamonti, Maria Abbattista, Paolo Bucciarelli, Braxton D. Mitchell, Steven J. Kittner, Robin Lemmens, Christina Jern, Emanuela Pappalardo, Paolo Costa, Marina Colombi, Diana Aguiar de Sousa, Sofia Rodrigues, Patricia Canhao, Aleksander Tkach, Rosa Santacroce, Giovanni Favuzzi, Antonio Arauz, Donatella Colaizzo, Kostas Spengos, Amanda Hodge, Reina Ditta, Alessandro Pezzini, Stephanie Debette, Jonathan M. Coutinho, Vincent Thijs, Katarina Jood, Guillaume Pare, Turgut Tatlisumak, Jose M. Ferro, Pankaj Sharma
Summary: A genome-wide association study identified new genetic variants influencing susceptibility to CVT, with the discovery validated in an independent European cohort. These findings provide important new insights into the pathophysiology of CVT.
ANNALS OF NEUROLOGY
(2021)
Article
Biochemistry & Molecular Biology
Michael A. Hardigan, Anne Lorant, Dominique D. A. Pincot, Mitchell J. Feldmann, Randi A. Famula, Charlotte B. Acharya, Seonghee Lee, Sujeet Verma, Vance M. Whitaker, Nahla Bassil, Jason Zurn, Glenn S. Cole, Kevin Bird, Patrick P. Edger, Steven J. Knapp
Summary: The cultivated strawberry, originating from early 18th-century Europe, has undergone significant genomic changes over 300 years of breeding history, leading to global expansion in production. Research shows increased heterozygosity in interspecific hybrids, selective sweeps across the genome, and substantial allelic diversity in octoploid species. Despite genetic gains in modern cultivars, nucleotide diversity and heterozygosity are lower, suggesting potential trade-offs in agricultural selection.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Agronomy
Linfeng Chen, Shouping Yang, Susan Araya, Charles Quigley, Earl Taliercio, Rouf Mian, James E. Specht, Brian W. Diers, Qijian Song
Summary: Genotype imputation is a strategy to increase marker density of existing datasets without additional genotyping. This study compared the performance of different imputation software in soybean populations and found that AlphaPlantImpute had higher imputation accuracy. Factors such as linkage disequilibrium extent, minor allele frequency, and reference panel size were found to positively influence imputation accuracy.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Genetics & Heredity
Michal Marczyk, Agnieszka Macioszek, Joanna Tobiasz, Joanna Polanska, Joanna Zyla
Summary: The study evaluated the impact of different integration methods and linkage disequilibrium correction on multiple GSA algorithms, with CERNO and MAGENTA combined with Stouffer method showing the most efficiency. LD correction increased prioritization and specificity of enrichment outcomes for all tested algorithms. The best performance was observed when using Fisher or Stouffer integration with LD correction.
FRONTIERS IN GENETICS
(2021)
Letter
Hematology
Dean Bryant, Will Tapper, Nicola J. Weston-Bell, Arnold Bolomsky, Li Song, Shengtao Xu, Andrew R. Collins, Niklas Zojer, Surinder Singh Sahota
Article
Biochemical Research Methods
Clare Horscroft, Sarah Ennis, Reuben J. Pengelly, Timothy J. Sluckin, Andrew Collins
BRIEFINGS IN BIOINFORMATICS
(2019)
Article
Biochemical Research Methods
Reuben J. Pengelly, Andrew Collins
Review
Biotechnology & Applied Microbiology
Dareen Alyousfi, Diana Baralle, Andrew Collins
BRIEFINGS IN FUNCTIONAL GENOMICS
(2019)
Article
Multidisciplinary Sciences
Wai Yee Low, Rick Tearle, Derek M. Bickhart, Benjamin D. Rosen, Sarah B. Kingan, Thomas Swale, Francoise Thibaud-Nissen, Terence D. Murphy, Rachel Young, Lucas Lefevre, David A. Hume, Andrew Collins, Paolo Ajmone-Marsan, Timothy P. L. Smith, John L. Williams
NATURE COMMUNICATIONS
(2019)
Article
Biochemistry & Molecular Biology
Alejandra Vergara-Lope, Sarah Ennis, Igor Vorechovsky, Reuben J. Pengelly, Andrew Collins
EUROPEAN JOURNAL OF HUMAN GENETICS
(2019)
Article
Ecology
M. Reza Jabalameli, Clare Horscroft, Alejandra Vergara-Lope, Reuben J. Pengelly, Andrew Collins
Article
Multidisciplinary Sciences
Alejandra Vergara-Lope, M. Reza Jabalameli, Clare Horscroft, Sarah Ennis, Andrew Collins, Reuben J. Pengelly
Article
Oncology
Stuart J. Blakemore, Ruth Clifford, Helen Parker, Pavlos Antoniou, Ewa Stec-Dziedzic, Marta Larrayoz, Zadie Davis, Latha Kadalyayil, Andrew Colins, Pauline Robbe, Dimitris Vavoulis, Jade Forster, Louise Carr, Ricardo Morilla, Monica Else, Dean Bryant, Helen McCarthy, Renata J. Walewska, Andrew J. Steele, Jacqueline Chan, Graham Speight, Tanja Stankovic, Mark S. Cragg, Daniel Catovsky, David G. Oscier, Matthew J. J. Rose-Zerilli, Anna Schuh, Jonathan C. Strefford
Review
Biochemical Research Methods
Dareen Alyousfi, Diana Baralle, Andrew Collins
Summary: More than 50% of causal genetic variants underlying potential single gene disorders remain undiscovered, affecting clinical management without confirmed molecular diagnoses. The ESPP score has been developed to aid in filtering genome sequence data and identify genes with high potential for pathogenic disease-related variation. Recognizing gene essentiality can guide the identification of causal variants and improve genome sequence filtering.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Dentistry, Oral Surgery & Medicine
Alejandro Silva Espinosa, Julio Cesar Martinez, Yubahhaline Molina, Maria Alejandra Bermudez Gordillo, Daniel Ramos Hernandez, Daniela Zarate Rivera, Blanka Pacheco Olmos, Nathaly Ramirez, Liliana Arias, Andres Zarate, Q. Diana Marcela Diaz, Andrew Collins, Alvaro Mauricio Herrera Cepeda, Ignacio Briceno Balcazar
Summary: The study found that left cleft lip and palate and nonsyndromic forms were the most common types in the population, with the most frequent comorbidities being psychomotor retardation and heart disease. A low proportion of mothers were exposed to passive smoking during pregnancy, while low birth weight accounted for a significant number of cases.
CLEFT PALATE CRANIOFACIAL JOURNAL
(2022)
Article
Gastroenterology & Hepatology
Shreya Sharma, William J. Tapper, Andrew Collins, Zaed Z. R. Hamady
Summary: The study found that PDAC is associated with DM, particularly with NODM. The developed PRS models show good performance in identifying PDAC patients with NODM and long-standing DM, and can improve clinical risk assessment models.
Article
Genetics & Heredity
Daniel Uricoechea Patino, Andrew Collins, Oscar Julian Romero Garcia, Gustavo Santos Vecino, Jose Vicente Rodriguez Cuenca, Jaime E. Bernal, Escilda Benavides Benitez, Saray Vergara Munoz, Ignacio Briceno Balcazar
Summary: Analysis of mitochondrial DNA data from ancient human remains reveals high population heterogeneity among pre-Hispanic populations in Colombia.
Article
Hematology
Tomasz K. Wojdacz, Harindra E. Amarasinghe, Latha Kadalayil, Alice Beattie, Jade Forster, Stuart J. Blakemore, Helen Parker, Dean Bryant, Marta Larrayoz, Ruth Clifford, Pauline Robbe, Zadie A. Davis, Monica Else, Dena R. Howard, Basile Stamatopoulos, Andrew J. Steele, Richard Rosenquist, Andrew Collins, Andrew R. Pettitt, Peter Hillmen, Christoph Plass, Anna Schuh, Daniel Catovsky, David G. Oscier, Matthew J. J. Rose-Zerilli, Christopher C. Oakes, Jonathan C. Strefford
Article
Biochemical Research Methods
Reuben J. Pengelly, Alejandra Vergara-Lope, Dareen Alyousfi, M. Reza Jabalameli, Andrew Collins
BRIEFINGS IN BIOINFORMATICS
(2019)
