Article
Biochemistry & Molecular Biology
Pirro G. Hysi, Massimo Mangino, Paraskevi Christofidou, Mario Falchi, Edward D. Karoly, Robert P. Mohney, Ana M. Valdes, Tim D. Spector, Cristina Menni
Summary: This study conducted a genome-wide association study on the levels of circulating metabolites in European subjects, identifying 202 unique genomic regions associated with 478 different metabolites. The replication study confirmed the robustness of these associations and discovered 74 novel genomic regions not previously associated with any metabolites.
Article
Microbiology
Changlong Chen, Shu Che, Zhou Dong, Jiayi Sui, Yu Tian, Yanyan Su, Meng Zhang, Wangwang Sun, Jiaqin Fan, Jianbo Xie, Hua Xie
Summary: Genome-wide association studies (GWAS) were conducted to identify the genetic basis of Pectobacterium spp. pathogenicity by analyzing genomic data and phenotypic measurements. The analysis revealed multiple loci associated with virulence and cellulase activity, as well as epistasis effects. This study provides valuable insights into the genetic mechanisms underlying Pectobacterium spp. pathogenicity.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Changlong Chen, Shu Che, Zhou Dong, Jiayi Sui, Yu Tian, Yanyan Su, Meng Zhang, Wangwang Sun, Jiaqin Fan, Jianbo Xie, Hua Xie
Summary: This study used genome-wide association studies to identify genetic basis of pathogenicity in Pectobacterium spp. by integrating genomic data with virulence and cellulase activity phenotypes. The analysis discovered significant loci associated with Pectobacterium virulence and cellulase activity, as well as identified epistasis loci pairs. Furthermore, the study confirmed the epistasis effects of AraC transcriptional regulator and nutrient transport-related genes in contributing to the virulence phenotype.
MICROBIOLOGY SPECTRUM
(2023)
Review
Multidisciplinary Sciences
David O. Enoma, Janet Bishung, Theresa Abiodun, Olubanke Ogunlana, Victor Chukwudi Osamor
Summary: This article discusses the applications and future trends of machine learning algorithms in genome-wide association studies (GWAS) to better understand the effects of population genetic variants. The study found that algorithms such as classification, regression, ensemble, and neural networks have been applied to GWAS and their application areas are comprehensively discussed.
JOURNAL OF KING SAUD UNIVERSITY SCIENCE
(2022)
Article
Plant Sciences
Guogen Zhang, Zhiyuan Bi, Jing Jiang, Jingbing Lu, Keyang Li, Di Bai, Xinchen Wang, Xueyu Zhao, Min Li, Xiuqin Zhao, Wensheng Wang, Jianlong Xu, Zhikang Li, Fan Zhang, Yingyao Shi
Summary: By utilizing genome-wide association and epistasis analysis (GWAES), the genetic basis of rice saline-alkali tolerance was studied. A total of 165 main-effect quantitative trait nucleotides (QTNs) and 124 additional epistatic QTNs were identified, explaining a significant portion of the phenotypic variation of saline-alkali tolerance. Most of these QTNs were located in genomic regions associated with saline-alkali tolerance or known genes. The finding of candidate genes and favorable haplotypes provides valuable information for genetic improvement of rice saline-alkali tolerance.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Yanwei Li, Ying Wang, Xinyi Wu, Jian Wang, Xiaohua Wu, Baogen Wang, Zhongfu Lu, Guojing Li
Summary: Fusarium wilt is a soil-borne disease that affects bottle gourd yield and fruit quality. Through GWAS analysis, potential candidate genes for FW resistance were identified, providing scientific evidence for breeding programs.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Multidisciplinary Sciences
Xiaoyu Liang, Xuewei Cao, Qiuying Sha, Shuanglin Zhang
Summary: The article introduces a novel multivariate method for phenome-wide association studies (PheWAS) and demonstrates its superiority through extensive simulation studies and real-life application. The proposed method involves hierarchical clustering, clustering linear combination, and false discovery rate control steps.
Article
Plant Sciences
Mingyang Quan, Xin Liu, Qingzhang Du, Liang Xiao, Wenjie Lu, Yuanyuan Fang, Peng Li, Li Ji, Deqiang Zhang
Summary: This study utilized a systems genetics approach to investigate the genetic architecture and regulatory pathways of photosynthesis and wood properties in Populus tomentosa, revealing coordinated regulatory networks for these two processes. A total of 222 significant single-nucleotide polymorphisms and 74 epistatic interactions were detected, providing insights into the transcriptional regulatory networks of candidate genes coordinating photosynthesis and wood properties. Furthermore, heterologous expression experiments demonstrated the regulatory roles of two pleiotropic genes in balancing photosynthesis and wood formation, which could aid in genetic breeding and molecular design in trees.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Biochemical Research Methods
Shanwen Sun, Benzhi Dong, Quan Zou
Summary: Genome-wide association studies (GWAS) have made significant progress in discovering genetic variants underlying complex human diseases and agriculturally important traits over the last decade. However, challenges such as detecting epistasis, SNPs with small effects, and distinguishing causal variants still exist. Advancements in statistical modeling and machine learning are driving improvements in GWAS analyses, while state-of-the-art tools are being developed to enhance signal detection and prioritize SNPs.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biotechnology & Applied Microbiology
Ruiqi Zhang, Fusheng Yao, Xue Cheng, Mengyuan Yang, Zhonghua Ning
Summary: This study determined the phenotype and heritability of egg yolk water content and conducted a genome-wide association study (GWAS) to understand the molecular mechanism underlying egg yolk moisture content. The results identified a series of single nucleotide polymorphisms (SNPs), candidate genes, and candidate regions related to egg yolk moisture content, providing insights on its molecular mechanism and potential for developing new egg traits.
Article
Plant Sciences
Jessica Delfini, Vania Moda-Cirino, Jose dos Santos Neto, Douglas Mariani Zeffa, Alison Fernando Nogueira, Luriam Aparecida Brandao Ribeiro, Paulo Mauricio Ruas, Paul Gepts, Leandro Simoes Azeredo Goncalves
Summary: This research aimed to identify Quantitative Trait Nucleotides (QTNs) associated with common bean productivity by evaluating ten morpho-agronomic traits in 178 Mesoamerican common bean domesticated accessions. They identified 64 stable QTNs detected by multiple methods or in multiple environments, with 39 showing significant phenotypic differences between their alleles. The accumulation of favorable alleles resulted in reduced plant height and increased nodules, seed weight, yield, pod insertion height, and number of pods per plant.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Aixia Yang, Xiaolei Ding, Yuan Feng, Ruiwen Zhao, Jianren Ye
Summary: This study compared the reproductivity and genetic variations of different strains of B. xylophilus in Liaoning Province and other parts of China. It found that the Liaoning isolates have higher reproductive ability at low temperatures and showed significant genetic differentiation from other isolates. Genome-wide association analysis identified SNPs closely related to low-temperature tolerance in genes responsible for environmental adaptation. These findings contribute to a better understanding of the prevalence and diffusion status of B. xylophilus in China.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Guang-Sheng Li, Feng Zhu, Fan Zhang, Fang-Xi Yang, Jin-Ping Hao, Zhuo-Cheng Hou
Summary: This study identified novel loci associated with feeding behavior traits in Pekin ducks through GWAS analysis. One locus on chromosome 2 was significantly related to daily meal times and meal feed intake, shedding light on the genetic mechanisms of feeding behavior patterns in ducks.
Review
Genetics & Heredity
Masato Akiyama
Summary: Genome-wide association studies have identified numerous genetic loci associated with complex traits, but interpreting these findings remains challenging, necessitating integrative analysis with various omics data.
JOURNAL OF HUMAN GENETICS
(2021)
Article
Agriculture, Dairy & Animal Science
Ruiqi Zhang, Xinghua Li, Ying Ma, Yuchen Liu, Yalan Zhang, Xue Cheng, Zhonghua Ning
Summary: This study aimed to identify significant single nucleotide polymorphism (SNP) sites and candidate genes related to thermogelled yolk texture in Hetian Dahei chicken (HTHD) flocks that can be used as genetic markers. The study found that 10 genes and some SNPs were associated with hardness of the thermogelled egg yolks, including RELCH gene participating in cholesterol transport and LRRK2 gene associated with gumminess. Moreover, 8 SNPs associated with resilience, 208 SNPs associated with chewiness, and 159 candidate genes were identified. The results provide a theoretical basis for breeding high-quality egg yolks using molecular marker-assisted selection.
Review
Developmental Biology
Trudy F. C. Mackay, Wen Huang
WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY
(2018)
Article
Ecology
Fabio Morgante, Wen Huang, Christian Maltecca, Trudy F. C. Mackay
Article
Genetics & Heredity
Daniel R. Matute, Aaron A. Comeault, Eric Earley, Antonio Serrato-Capuchina, David Peede, Anais Monroy-Eklund, Wen Huang, Corbin D. Jones, Trudy F. C. Mackay, Jerry A. Coyne
Article
Genetics & Heredity
Zhijun Dai, Nanye Long, Wen Huang
G3-GENES GENOMES GENETICS
(2020)
Article
Biotechnology & Applied Microbiology
Jinding Liu, Suxu Tan, Shuiqing Huang, Wen Huang
Article
Genetics & Heredity
Grace A. Parker, Nathan Kohn, Ally Spirina, Anna McMillen, Wen Huang, Trudy F. C. Mackay
G3-GENES GENOMES GENETICS
(2020)
Article
Genetics & Heredity
Aya Yanagawa, Wen Huang, Akihiko Yamamoto, Ayako Wada-Katsumata, Coby Schal, Trudy F. C. Mackay
G3-GENES GENOMES GENETICS
(2020)
Article
Genetics & Heredity
Fabio Morgante, Wen Huang, Peter Sorensen, Christian Maltecca, Trudy F. C. Mackay
G3-GENES GENOMES GENETICS
(2020)
Article
Multidisciplinary Sciences
Brandon M. Baker, Mary Anna Carbone, Wen Huang, Robert R. H. Anholt, Trudy F. C. Mackay
Summary: This study used Drosophila melanogaster to map the genetic basis of voluntary consumption of cocaine and methamphetamine. Significant phenotypic variation in drug consumption was found in both sexes, with genes associated with nervous system implicated. The genetic basis of voluntary drug consumption in fruit flies is polygenic and involves genes with human orthologs and sex-and drug-specific effects.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Genetics & Heredity
Ergi D. Ozsoy, Murat Yilmaz, Bahar Patlar, Guzin Emecen, Esra Durmaz, Michael M. Magwire, Shanshan Zhou, Wen Huang, Robert R. H. Anholt, Trudy F. C. Mackay
Summary: Epistasis, or gene-gene interaction, is common in mutations with large phenotypic effects in humans and model organisms, impacting various aspects of genetic studies. However, the significance of epistasis between alleles with small quantitative phenotypic effects remains controversial and challenging to assess. This study used the Drosophila melanogaster Genetic Reference Panel to evaluate the epistasis modifying the effects of mutations in two transcription factors, identifying candidate modifier loci affecting head morphology.
G3-GENES GENOMES GENETICS
(2021)
Article
Agriculture, Dairy & Animal Science
Rongrong Ding, Zhanwei Zhuang, Yibin Qiu, Donglin Ruan, Jie Wu, Jian Ye, Lu Cao, Shenping Zhou, Enqin Zheng, Wen Huang, Zhenfang Wu, Jie Yang
Summary: Backfat thickness (BFT) is an economically important trait in the pig industry, and genetic markers and candidate genes related to BFT were identified through genotyping and genome-wide association analysis in two Duroc populations. Most candidate genes can be directly used for genetic improvement through molecular markers. New insights gained from this study will contribute to genetic studies aiming to increase carcass lean meat percentage in pigs.
JOURNAL OF ANIMAL SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Jinding Liu, Fei Yin, Kun Lang, Wencai Jie, Suxu Tan, Rongjing Duan, Shuiqing Huang, Wen Huang
Summary: MetazExp is a database for gene expression and alternative splicing profiles based on 53,615 uniformly processed publicly available RNA-seq samples from 72 metazoan species. Users can conveniently query gene expression and alternative splicing profiles by gene IDs, symbols, functional terms, and sequence similarity, and flexibly customize experimental groups for differential and specific analyses. With data visualization tools and comprehensive links with external databases, users can efficiently explore results and gain insights.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biotechnology & Applied Microbiology
Jinding Liu, Kun Lang, Suxu Tan, Wencai Jie, Yihua Zhu, Shiqing Huang, Wen Huang
Summary: LivestockExp is a web-based database server for exploring gene expression and alternative splicing, containing a large number of livestock animals and RNA-seq samples. It provides diverse analysis modules and visualization tools, serving as a valuable data resource and analysis platform.
Article
Biochemistry & Molecular Biology
Jinding Liu, Yaru Zhang, Yiqing Zheng, Yali Zhu, Yapin Shi, Zhuoran Guan, Kun Lang, Danyu Shen, Wen Huang, Daolong Dou
Summary: PlantExp is a platform for plant gene expression and alternative splicing analysis based on public RNA-seq datasets. It provides online analysis tools and visualization tools to allow users to reanalyze public datasets and gain new research insights.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Plant Sciences
Zhiyuan Yin, Qingjie Yang, Danyu Shen, Jinding Liu, Wen Huang, Daolong Dou
Summary: Soybean is an important crop and the newly established SoyTIPdb database provides a valuable resource for researchers to explore structural variations caused by transposon insertions. The database contains processed whole-genome resequencing data from a wide range of soybean germplasm accessions, allowing for easy query and analysis.