Article
Agronomy
Zhenqi Shao, Jiabiao Shao, Xiaobo Huo, Wenlong Li, Youbin Kong, Hui Du, Xihuan Li, Caiying Zhang
Summary: This study identified closely associated SNPs and genes related to seed size and shape in soybean. These findings are important for understanding the genetic basis of soybean yield and breeding improvements.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Jae-Ryoung Park, Yoon-Hee Jang, Eun-Gyeong Kim, Sang-Sun Hur, Kyung-Min Kim, Deyong Ren
Summary: In this study, QTLs and candidate genes related to rice plant height regulation were identified, which can provide information and foundation for marker-assisted selection and breeding.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Agriculture, Dairy & Animal Science
B. Li, P. M. VanRaden, D. J. Null, J. R. O'Connell, J. B. Cole
Summary: This study aimed to identify potential quantitative trait loci (QTL) for 27 production, fitness, and conformation traits of Guernsey cattle through genome-wide association analyses, with a major QTL detected on BTA19 and the MYH10 gene within this region highly associated with milk production and body conformation traits. After fine mapping, only one significant SNP was found on BTA19 for most traits, with multiple independent significant SNPs identified for protein yield, dairy form, and stature. The haplotype hosting the major QTL on BTA19 was traced back to a US Guernsey born in 1954, indicating a long-term influence on the population.
JOURNAL OF DAIRY SCIENCE
(2021)
Review
Agronomy
Theo Meuwissen, Ben Hayes, Iona MacLeod, Michael Goddard
Summary: This review discusses the possibility of identifying causal variants for complex traits, stressing the importance of large and diverse samples, accurate genotypes, multiple phenotypes, annotation of genomic sites, and other types of evidence required for this task.
Article
Genetics & Heredity
Michael Scherer, Gilles Gasparoni, Souad Rahmouni, Tatiana Shashkova, Marion Arnoux, Edouard Louis, Arina Nostaeva, Diana Avalos, Emmanouil T. Dermitzakis, Yurii S. Aulchenko, Thomas Lengauer, Paul A. Lyons, Michel Georges, Joern Walter
Summary: This study introduces a computational framework called MAGAR for identifying methylation quantitative trait loci and distinguishing different cell type-specific effects. Experimental validation demonstrates that cell type-specific methQTLs are predominantly located in enhancer elements.
EPIGENETICS & CHROMATIN
(2021)
Article
Genetics & Heredity
Kexin Zhang, Jinpeng Wang, Fangfang Ding, Ruihui Shi, Wei Wang, Guofan Zhang, Li Li
Summary: Many marine ectotherms exhibit high phenotypic plasticity in response to rapid climate change by modulating gene expression levels, with some oysters showing regulatory relationships between different genes under heat stress, potentially serving as candidate biomarkers for predicting their persistence under future climate change scenarios.
Article
Multidisciplinary Sciences
Eugenia Annunzi, Loreta Cannito, Fabio Bellia, Francesca Mercante, Matteo Vismara, Beatrice Benatti, Alberto Di Domenico, Riccardo Palumbo, Walter Adriani, Bernardo Dell'Osso, Claudio D'Addario
Summary: This study investigated the epigenetic and genetic regulation of the oxytocin receptor, dopamine transporter, and serotonin transporter genes in relation to Internet addiction. The results showed significant changes in DNA methylation levels and their correlation with psychometric properties. These findings contribute to our understanding of the neurobiology of Internet addiction and offer potential biological predictors for early diagnosis and treatment.
SCIENTIFIC REPORTS
(2023)
Article
Plant Sciences
Rahul Chandnani, Changsoo Kim, Jinesh D. Patel, Hui Guo, Tariq Shehzad, Jason G. Wallace, Daohua He, Zhengsheng Zhang, Jeevan Adhikari, Sameer Khanal, Peng W. Chee, Andrew H. Paterson
Summary: This study investigated the genetic mapping of plant architecture, flowering time, and maturity traits in cotton, and identified a total of 27 QTLs associated with these traits. The findings suggest that this population structure can help reduce background noise and small effect QTLs, and the germplasm developed in this study may serve as potential pre-breeding material for improving cotton cultivars.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Oncology
Shaobo Li, Nicholas Mancuso, Catherine Metayer, Xiaomei Ma, Adam J. de Smith, Joseph L. Wiemels
Summary: This study investigated the associations between DNA methylation and birthweight in newborns of diverse genetic ancestries. The results showed that genetic variation affects DNA methylation levels and incorporating genetic effects improved the significance of associations. This study highlights the importance of considering genetic effects in epigenome-wide association studies, especially for multiethnic populations.
CLINICAL EPIGENETICS
(2022)
Article
Biology
Dominik Karl Lagler, Elisabeth Hannemann, Kim Eck, Juergen Klawatsch, Doris Seichter, Ingolf Russ, Christian Mendel, Gesine Luehken, Stefan Krebs, Helmut Blum, Maulik Upadhyay, Ivica Medugorac
Summary: This study aimed to analyze natural tail length variation in Merinolandschaf and identify causal alleles for the short tail phenotype segregating within long-tailed breeds. The research discovered a SNP in the first exon of HOXB13 and a SINE element in the promoter of HOXB13 as potential candidates. These findings have implications for breeding shorter-tailed sheep, improving animal welfare, and understanding differential embryonic development.
COMMUNICATIONS BIOLOGY
(2022)
Article
Forestry
Suyun Wei, Guo Yang, Yonghua Yang, Tongming Yin
Summary: This study conducted a large-scale field trial on the progeny of Salix suchowensis and analyzed the genetic factors underlying plant growth. The results showed that stem height and ground diameter were controlled by four quantitative trait loci, with two of them exerting a pleiotropic effect. The pleiotropic effect was found to result from the co-localization of genes with independent effects on stem height and ground diameter. Furthermore, the study revealed that height and circumference growth involve different tissue activities.
Article
Plant Sciences
Rama Harinath Reddy Dadu, Ido Bar, Rebecca Ford, Prabhakaran Sambasivam, Janine Croser, Federico Ribalta, Sukhjiwan Kaur, Shimna Sudheesh, Dorin Gupta
Summary: This study identified major quantitative trait loci (QTL) regions on linkage group 5 and another QTL on LG2 that are associated with Ascochyta lentis resistance in lentils. The QTL regions contain putative candidate genes potentially involved in defense responses to fungal infection, which could aid in marker-assisted resistance selection in lentil breeding programs.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Dan-Dan Zhao, Yoon-Hee Jang, Muhammad Farooq, Jae-Ryoung Park, Eun-Gyeong Kim, Xiao-Xuan Du, Rahmatullah Jan, Kyung-Hwan Kim, Soo In Lee, Gang-Seob Lee, Kyung-Min Kim
Summary: In this study, QTLs related to rice plant architecture were identified using a genetic map and phenotypic data. Promising genes were further identified and a target gene was selected. This work is important for expanding our understanding of the genetic control of tiller angle and tiller crown width, as well as breeding ideal-type rice.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
Nagenahalli Dharmegowda Rathan, Deepmala Sehgal, Karthikeyan Thiyagarajan, Ravi Singh, Anju-Mahendru Singh, Velu Govindan
Summary: The study on nutritionally enhanced wheat identified new genomic regions controlling grain iron and zinc concentrations, leading to the discovery of pleiotropic QTL that could be used in wheat biofortification breeding to address micronutrient deficiency among wheat consumers. The in silico analysis revealed candidate genes involved in transporting small peptides and minerals as well as catalyzing phosphorylation processes, providing insights into the mechanisms of mineral uptake in wheat.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Yan Sun, Suhua Chang, Zhen Liu, Libo Zhang, Fan Wang, Weihua Yue, Hongqiang Sun, Zhaojun Ni, Xiangwen Chang, Yibing Zhang, Yang Chen, Jiqiang Liu, Lin Lu, Jie Shi
Summary: This study identified and replicated three novel genetic loci associated with the common risk of heroin, methamphetamine addiction, and alcoholism. These loci have functional effects on gene expression and brain structure, and may provide insights into the root cause of substance dependence, aiding in the development of prevention strategies for addiction disorders.
MOLECULAR PSYCHIATRY
(2021)
Article
Mathematical & Computational Biology
Jingsi Ming, Jia Zhao, Can Yang
Summary: The technique of single-cell RNA-sequencing has allowed researchers to explore the cellular heterogeneity of complex tissues. In this study, a scalable framework called scPI was proposed to analyze scRNA-seq data. The scPI framework utilizes amortized variational inference and a nonlinear neural network to infer the low-dimensional representations of the data. Through analysis of real datasets, it was demonstrated that scPI can effectively handle various probabilistic models for scRNA-seq data in terms of scalability, missing value imputation, and cell type clustering.
STATISTICS IN BIOSCIENCES
(2023)
Article
Oncology
Fan Wang, Wonjong Moon, William Letsou, Yadav Sapkota, Zhaoming Wang, Cindy Im, Jessica L. Baedke, Leslie Robison, Yutaka Yasui
Summary: This study identified 13 rare high-risk loci for breast cancer, which exhibit significant risk increase when combined as haplotypes. The individual variants forming these rare haplotypes have smaller effects. Functional annotation revealed extensive cis-regulatory DNA elements in breast cancer-related cells underlying these replicated rare haplotypes.
Article
Substance Abuse
Henry R. R. Kranzler, Richard Feinn, Heng Xu, Brendan L. L. Ho, Divya Saini, Olivia R. R. Nicastro, Anya Jacoby, Sylvanus Toikumo, Joel Gelernter, Emily E. E. Hartwell, Rachel L. L. Kember
Summary: This study investigated the impact of genetic risk for substance use disorders (SUDs) on the onset and progression of substance use. The results showed that European-ancestry individuals and males had an earlier onset and quicker progression of substance use, and the polygenic risk scores (PRSs) had predictive value for substance use milestones and symptom progression. In African-ancestry individuals, PRSs also predicted some substance use milestones, albeit to a lesser extent due to a smaller discovery sample.
Article
Substance Abuse
Heng Xu, Sylvanus Toikumo, Richard C. Crist, Klaudia Glogowska, Zeal Jinwala, Joseph D. Deak, Amy C. Justice, Joel Gelernter, Emma C. Johnson, Henry R. Kranzler, Rachel L. Kember
Summary: This study used multi-trait analysis to identify novel loci associated with substance use disorders in European and African populations. The results showed that multi-trait analysis can improve the genetic modeling of substance use traits and uncover genes that were not previously linked to substance use. Additionally, it enhanced the effectiveness of polygenic risk scores.
Article
Substance Abuse
Michelle S. S. Naps, Shirley H. H. Leong, Emily E. E. Hartwell, Christopher T. T. Rentsch, Henry R. R. Kranzler
Summary: This study investigated the effects of topiramate, a medication used to treat alcohol use disorder, on serum bicarbonate concentrations. The study found that the effects of the medication on bicarbonate concentrations were similar regardless of the presence of alcohol use disorder or the dosage of topiramate. Therefore, it is recommended to monitor baseline and periodic serum bicarbonate concentrations during topiramate therapy.
ALCOHOL-CLINICAL AND EXPERIMENTAL RESEARCH
(2023)
Review
Substance Abuse
Henry R. Kranzler, Emily E. Hartwell
Summary: Chronic heavy alcohol use has negative impacts on neurotransmitter systems and causes various medical, psychiatric, and social problems. Evidence-based medications for treating alcohol use disorder (AUD) are not widely used in clinical practice. Pharmacogenetic approaches have gained interest but have not yet yielded strong enough results for routine clinical care.
ALCOHOL-CLINICAL AND EXPERIMENTAL RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Vidhya Kumaresan, Yolpanhchana Lim, Poorva Juneja, Allison E. Tipton, Giordano de Guglielmo, Lieselot L. G. Carrette, Marsida Kallupi, Lisa Maturin, Ying Liu, Olivier George, Huiping Zhang
Summary: Cocaine administration alters miRNA expression in the cortico-accumbal pathway, potentially impacting gene expression regulation during withdrawal. This study examined miRNA changes in this pathway during acute withdrawal and protracted abstinence from escalated cocaine intake. Results showed differential miRNA expression and pathways enriched in mRNA targets associated with addiction. The findings emphasize the importance of miRNA expression in addiction-related circuits and suggest the potential for developing biomarkers and therapies targeting abstinence-associated miRNAs.
Review
Substance Abuse
Juliana I. Byanyima, Xinyi Li, Sianneh A. Vesslee, Henry R. Kranzler, Zhenhao Shi, Corinde E. Wiers
Summary: Opioid use disorder (OUD) is a chronic condition with serious adverse consequences, including high incarceration rates and overdose-related fatalities. Medications used for OUD treatment have been shown to cause metabolic impairments, but the effects vary depending on the individual's metabolic condition. Further research is needed to determine the best approach for reducing the risk of metabolic disorders in OUD treatment.
CURRENT ADDICTION REPORTS
(2023)
Article
Substance Abuse
Frances L. Wang, Brian M. Hicks, Hang Zhou, Henry R. Kranzler, Joel Gelernter, Robert A. Zucker
Summary: Genome-wide association studies (GWAS) have identified hundreds of loci associated with alcohol-related traits. This study aims to evaluate the usefulness of a polygenic risk score (PRS) for problematic alcohol use (PAU), and the results show that PAU PRS can predict heavy drinking and alcohol problems even after accounting for family history of AUD and prior drinking history.
DRUG AND ALCOHOL DEPENDENCE
(2023)
Article
Biology
William Letsou, Fan Wang, Wonjong Moon, Cindy Im, Yadav Sapkota, Leslie L. Robison, Yutaka Yasui
Summary: This study found that common variants are associated with small but significant differences in breast cancer risk, supporting the polygenic model of inherited predisposition. Using a novel algorithm, the researchers showed that rare haplotypes may refine the association of breast cancer risk with common germline alleles. These findings provide insight into the genetic risk factors for breast cancer.
LIFE SCIENCE ALLIANCE
(2023)
Letter
Biochemistry & Molecular Biology
Yiming Chao, Yang Xiang, Jiashun Xiao, Weizhong Zheng, Mo R. Ebrahimkhani, Can Yang, Angela Ruohao Wu, Pentao Liu, Yuanhua Huang, Ryohichi Sugimura
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2023)
Article
Biochemical Research Methods
Xinyi Yu, Jiashun Xiao, Mingxuan Cai, Yuling Jiao, Xiang Wan, Jin Liu, Can Yang
Summary: The findings from genome-wide association studies have greatly helped us understand the genetic basis of human complex traits and diseases. However, several major challenges still need to be addressed, including the unknown biological functions of most GWAS hits and the identification of genetic risk variants with weak effects. To overcome these challenges, we propose a powerful and adaptive latent model (PALM) that integrates functional annotations with GWAS summary statistics.
Article
Psychology, Clinical
Zachary L. Mannes, Ofir Livne, Justin Knox, Deborah S. Hasin, Henry R. Kranzler
Summary: This study aims to examine the prevalence and clinical correlates of opioid withdrawal syndrome (OWS) among adults in the U.S. who engage in non-medical use of prescription opioids (NMOU). Results revealed that OWS is prevalent among individuals with NMOU and is associated with psychiatric disorders and opioid use disorder (OUD).
AMERICAN JOURNAL OF DRUG AND ALCOHOL ABUSE
(2023)
Article
Biochemical Research Methods
Chen Li, Ting-Fung Chan, Can Yang, Zhixiang Lin
Summary: The study introduces a method called stVAE, based on the variational autoencoder framework, to deconvolve the cell-type composition of cellular resolution spatial transcriptomic datasets. It accurately identifies spatial patterns of cell types and their relative proportions across spots.
Article
Substance Abuse
Carrie M. Mintz, Justin Knox, Sarah M. Hartz, Deborah S. Hasin, Silvia S. Martins, Henry R. Kranzler, Emily Greene, Elvin H. Geng, Richard A. Grucza, Laura J. Bierut
Summary: This study analyzed demographic disparities in the implementation of SBIRT for unhealthy alcohol use. The results showed that gender, age, race, and insurance status were factors that influenced the likelihood of screening and intervention. Addressing these disparities and reducing attrition from treatment could improve outcomes for individuals with unhealthy alcohol use.
ALCOHOL-CLINICAL AND EXPERIMENTAL RESEARCH
(2023)
