Article
Plant Sciences
Hui Xia, Ziyuan Hao, Yufang Shen, Zhonghua Tu, Lichun Yang, Yaxian Zong, Huogen Li
Summary: In this study, GWAS analysis identified multiple significant loci associated with growth trajectories in hybrid Liriodendron populations. These loci showed temporal variations in effect sizes and inheritance patterns potentially related to different growth and development stages. The identified loci can be beneficial for selecting superior genotypes and provide a foundation for future molecular-assisted breeding.
Article
Multidisciplinary Sciences
Wei-Yu Lin, Sarah E. Fordham, Nicola Sunter, Claire Elstob, Thahira Rahman, Elaine Willmore, Colin Shepherd, Gordon Strathdee, Tryfonia Mainou-Fowler, Rachel Piddock, Hannah Mearns, Timothy Barrow, Richard S. Houlston, Helen Marr, Jonathan Wallis, Geoffrey Summerfield, Scott Marshall, Andrew Pettitt, Christopher Pepper, Christopher Fegan, Francesco Forconi, Martin J. S. Dyer, Sandrine Jayne, April Sellors, Anna Schuh, Pauline Robbe, David Oscier, James Bailey, Syed Rais, Alison Bentley, Lynn Cawkwell, Paul Evans, Peter Hillmen, Guy Pratt, David J. Allsup, James M. Allan
Summary: Prognostication in CLL patients is challenging due to its heterogeneous clinical course. This study identifies two genomic locations associated with disease progression, highlighting the impact of constitutional genetic variation on CLL prognosis. Additionally, functional genes implicated in modulating key pathways in CLL pathogenesis are identified.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Fasil Tekola-Ayele, Xuehuo Zeng, Suvo Chatterjee, Marion Ouidir, Corina Lesseur, Ke Hao, Jia Chen, Markos Tesfaye, Carmen J. Marsit, Tsegaselassie Workalemahu, Ronald Wapner
Summary: Abnormal birthweight is associated with increased risk for cardiometabolic diseases in later life. This study integrated placental methylation and gene expression data with genetic loci associated with birthweight to identify functional genes involved in fetal growth regulation.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Garan Jones, Katerina Trajanoska, Adam J. Santanasto, Najada Stringa, Chia-Ling Kuo, Janice L. Atkins, Joshua R. Lewis, ThuyVy Duong, Shengjun Hong, Mary L. Biggs, Jian'an Luan, Chloe Sarnowski, Kathryn L. Lunetta, Toshiko Tanaka, Mary K. Wojczynski, Ryan Cvejkus, Maria Nethander, Sahar Ghasemi, Jingyun Yang, M. Carola Zillikens, Stefan Walter, Kamil Sicinski, Erika Kague, Cheryl L. Ackert-Bicknell, Dan E. Arking, B. Gwen Windham, Eric Boerwinkle, Megan L. Grove, Misa Graff, Dominik Spira, Ilja Demuth, Nathalie van der Velde, Lisette C. P. G. M. de Groot, Bruce M. Psaty, Michelle C. Odden, Alison E. Fohner, Claudia Langenberg, Nicholas J. Wareham, Stefania Bandinelli, Natasja M. van Schoor, Martijn Huisman, Qihua Tan, Joseph Zmuda, Dan Mellstrom, Magnus Karlsson, David A. Bennett, Aron S. Buchman, Philip L. De Jager, Andre G. Uitterlinden, Uwe Voelker, Thomas Kocher, Alexander Teumer, Leocadio Rodriguez-Manas, Francisco J. Garcia, Jose A. Carnicero, Pamela Herd, Lars Bertram, Claes Ohlsson, Joanne M. Murabito, David Melzer, George A. Kuchel, Luigi Ferrucci, David Karasik, Fernando Rivadeneira, Douglas P. Kiel, Luke C. Pilling
Summary: Low muscle strength is a heritable indicator of poor health in older people, with genetic loci associated with muscle weakness identified through genome-wide meta-analysis. Possible causal relationships with diabetes susceptibility, hematological parameters, and the immune system were also discovered using Mendelian randomization. The distinct mechanisms of muscle weakness from continuous strength were highlighted, shedding light on potential pathways involved in ageing.
NATURE COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Fenglei Sun, Yanlong Yang, Penglong Wang, Jun Ma, Xiongming Du
Summary: This study provides insights into the genetic basis of cotton yield under drought conditions and identifies potential candidate genes for breeding high-yield cotton varieties.
Article
Plant Sciences
Xiaohui Song, Guozhong Zhu, Sen Hou, Yamei Ren, Muhammad Waqas Amjid, Weixi Li, Wangzhen Guo
Summary: Genome-wide association analysis was conducted on fiber quality parameters in cotton, identifying 67 stable quantitative trait loci (QTLs) related to fiber length, strength, and micronaire. Transcriptome analysis revealed candidate genes involved in crucial processes like sugar metabolism and cytoskeleton organization, providing new insights for improving fiber quality in cotton.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Agriculture, Dairy & Animal Science
Hanhan Yang, Yunlei Li, Jingwei Yuan, Aixin Ni, Hui Ma, Yuanmei Wang, Yunhe Zong, Jinmeng Zhao, Sihua Jin, Yanyan Sun, Jilan Chen
Summary: The genetic parameters for egg production and clutch-related traits in indigenous Beijing-You chickens were estimated in this study. The results showed that the age at first egg for Beijing-You chickens was 174.45 days and had a high heritability of 0.62. The clutch traits were moderately to highly heritable, while the average pause length had a very low heritability.
Article
Multidisciplinary Sciences
Ruidong Xiang, Iona M. MacLeod, Hans D. Daetwyler, Gerben de Jong, Erin O'Connor, Chris Schrooten, Amanda J. Chamberlain, Michael E. Goddard
Summary: This study presents a method for fine-mapping potentially causal mutations by integrating functional, evolutionary, and pleiotropic information and developing a custom genotyping array. The custom array, containing variants with biological functions, outperformed the standard array in predicting genetic values for multiple traits in dairy cattle populations across different countries. This highlights the potential improvement in genomic prediction by utilizing mutations with functional, evolutionary, and pleiotropic consequences.
NATURE COMMUNICATIONS
(2021)
Article
Agriculture, Dairy & Animal Science
K. Kaseja, S. Mucha, J. Yates, E. Smith, G. Banos, J. Conington
Summary: This study investigated the genetic background of health and production traits in the UK Texel sheep population using phenotypic and SNP data. Results identified significant SNPs associated with birth weight, weaning weight, and scan weight. The study also found other SNPs related to animal health and production traits. The results suggest that these traits have a complex genetic architecture.
Article
Plant Sciences
Minkyung Kim, Thuy Tien Phan Nguyen, Joon-Hyung Ahn, Gi-Jun Kim, Sung-Chur Sim
Summary: This study utilized GWAS to identify significant QTL for tomato fruit traits, with the discovery of potential novel QTL. The results not only contribute to genetic dissection of tomato fruit traits, but also offer valuable resources for improving fruit traits through molecular tools.
HORTICULTURE RESEARCH
(2021)
Article
Genetics & Heredity
Guimin Gao, Peter N. Fiorica, Julian McClellan, Alvaro N. Barbeira, James L. Li, Olufunmilayo I. Olopade, Hae Kyung Im, Dezheng Huo
Summary: GWAS has identified over 200 genomic loci associated with breast cancer risk, but the specific causal genes in most of these loci have not been identified. Using TWAS and multi-tissue data, we discovered candidate genes associated with breast cancer, including new loci.
AMERICAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Genetics & Heredity
Ammarah Ghaffar, Dale R. Nyholt
Summary: We developed a method named GIDEE to prioritize trait-relevant tissues by combining GWAS summary statistic data with tissue-specific eQTL data. The best-performing GIDEE method ranked the known trait-relevant tissue first multiple times across nine training datasets. Application of the GIDEE approach to test datasets provided important prioritization of tissues relevant to the trait's regulatory architecture.
FRONTIERS IN GENETICS
(2023)
Article
Plant Sciences
Zhibo Qu, Ying Wu, Die Hu, Ting Li, Hangyu Liang, Fan Ye, Jiquan Xue, Shutu Xu
Summary: This study dissected the genetic basis of maize grain size using genome-wide association analysis and identified 139 loci associated with the trait. Transcriptome data revealed differential expression of 15 candidate genes involved in regulating peroxidase activity, oxidoreductase, and leaf senescence.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Wei Liang Andre Tan, Laercio Ribeiro Porto Neto, Antonio Reverter, Michael McGowan, Marina Rufino Salinas Fortes
Summary: This study conducted genome-wide association analyses using sequence-level data targeting seven bull production and fertility traits in a multi-breed population of 6,422 tropically adapted bulls. The study identified genetic variants and candidate genes associated with these traits, highlighting the highly polygenic nature of the traits and significant results across the genome.
Article
Multidisciplinary Sciences
Muhammad Moaeen-ud-Din, Raja Danish Muner, Muhammad Sajjad Khan
Summary: This study aimed to identify genomic regions influencing growth and body conformation traits among Punjab goat breeds by performing GWAS using 50K SNP Chip. We identified a number of highly significant SNPs and candidate genes associated with growth and body conformation traits, indicating their potential role in body growth. Pleiotropic effects were also observed for some SNPs for body weight and conformation traits.
SCIENTIFIC REPORTS
(2022)
Article
Biotechnology & Applied Microbiology
Xiaodong Tan, Ranran Liu, Yonghong Zhang, Xicai Wang, Jie Wang, Hailong Wang, Guiping Zhao, Maiqing Zheng, Jie Wen
Summary: In chickens with FLHS, a genome-wide dysregulated DNA methylation pattern was found, with hypo-methylated regions up- and down-stream of gene body. Genes related to lipogenesis and oxygenolysis showed up-regulated expression associated with down-regulated DNA methylation, while genes related to cellular junction and communication pathways exhibited inhibition with associated up-regulation of DNA methylation. These findings suggest that increased lipid accumulation and hepatocyte rupture are central pathways regulated by DNA methylation in FLHS chickens.
Article
Agriculture, Dairy & Animal Science
Mohamed Shafey Elsharkawy, Ying Chen, Ranran Liu, Xiaodong Tan, Wei Li, Ibrahim El-Wardany, Dongqin Zhao, Maiqing Zheng, Jie Wen, Guiping Zhao
Summary: The study shows that paternal dietary supplementation with 0.1% methionine can enhance offspring carcass traits and meat quality, such as increasing thigh muscle yield, reducing abdominal fat, and affecting meat quality indicators like pH value and color. Genes associated with meat quality also support these results. The findings suggest that the addition of 0.1% methionine to rooster diets can improve the carcass characteristics and meat quality of progeny.
Article
Biotechnology & Applied Microbiology
Zheng Ma, Na Luo, Lu Liu, Huanxian Cui, Jing Li, Hai Xiang, Huimin Kang, Hua Li, Guiping Zhao
Summary: The study observed a significant decrease in lipid content in DIMFPs compared to DAFPs, with 72 differentially expressed genes involved in lipid metabolism. Among them, 19 genes enriched in the PPAR signaling pathway were identified, providing insights into the molecular mechanisms underlying the differences in lipid deposition between DAFPs and DIMFPs.
Article
Microbiology
Hai Xiang, Jiankang Gan, Daoshu Zeng, Jing Li, Hui Yu, Haiquan Zhao, Ying Yang, Shuwen Tan, Gen Li, Chaowei Luo, Zhuojun Xie, Guiping Zhao, Hua Li
Summary: Genetically selected chickens with better growth and early maturation that show increased abdominal fat deposition (AFD) have been found to have a decrease in gut microbiota richness and diversity, with a decrease in Bacteroidetes and an increase in Firmicutes associated with AFD accumulation. The specific microbial taxa such as Bacteroidetes genera and Firmicutes genera were identified to play a role in alleviating obesity or contributing to fat accumulation in chickens. These findings provide insights into the complex relationship between gut microbiota and chicken fat accumulation, which could contribute to the development of effective therapies for reducing chicken fat deposition.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Genetics & Heredity
Xiaodong Tan, Lu Liu, Xiaojing Liu, Huanxian Cui, Ranran Liu, Guiping Zhao, Jie Wen
Summary: This study investigated the genetic architecture and key variants associated with breast muscle weight (BrW) in Jingxing yellow chickens. The researchers identified high-impact single nucleotide polymorphisms (SNPs) and muscle-related genes through genome-wide association study and integrated analysis. They also discovered a major haplotype and a crucial gene, IGF2BP1, associated with BrW.
Article
Genetics & Heredity
Yuxi Jin, Xiaoya Yuan, Wenjuan Zhao, Hua Li, Guiping Zhao, Jianfeng Liu
Summary: This study identifies key genes and pathways related to the formation of hexanal using gene expression analysis and co-expression network analysis. The results show that differentially expressed genes and hub genes are enriched in various signaling pathways, including the PPAR signaling pathway and the MAPK signaling pathway. These findings are important for understanding and further researching genes related to hexanal content.
Article
Genetics & Heredity
Jiahong Sun, Xiaodong Tan, Xinting Yang, Lu Bai, Fuli Kong, Guiping Zhao, Jie Wen, Ranran Liu
Summary: This study identifies candidate genes associated with chicken meat color by comparing fast-growing, white-feathered chickens and slow-growing, yellow-feathered chickens. The findings contribute to the understanding of the molecular mechanisms regulating meat color and the development of molecular markers for chicken meat color selection.
Article
Microbiology
Mamadou Thiam, Astrid Lissette Barreto Sanchez, Jin Zhang, Jie Wen, Guiping Zhao, Qiao Wang
Summary: This study revealed the association between H/L ratio and Salmonella resistance, and proposed a method for selecting and breeding Salmonella-resistant chickens.
Article
Agriculture, Dairy & Animal Science
Zhengxiao He, Sen Li, Wei Li, Jiqiang Ding, Maiqing Zheng, Qinghe Li, Alan G. Fahey, Jie Wen, Ranran Liu, Guiping Zhao
Summary: This study compared the GBLUP model and GA-BLUP model with previously identified associated SNPs. The GA-BLUP model with nine RFI-associated SNPs showed improved prediction accuracy compared to the GBLUP model.
Article
Biotechnology & Applied Microbiology
Na Luo, Jingting Shu, Xiaoya Yuan, Yuxi Jin, Huanxian Cui, Guiping Zhao, Jie Wen
Summary: By studying the deposition of IMF and AF in chicken meat, the study revealed the regulatory mechanisms of crucial genes and signaling pathways in their deposition, providing a theoretical basis for producing high-quality broilers.
Article
Agriculture, Dairy & Animal Science
Xiaodong Tan, Ranran Liu, Wei Li, Maiqing Zheng, Dan Zhu, Dawei Liu, Furong Feng, Qinghe Li, Li Liu, Jie Wen, Guiping Zhao
Summary: This study demonstrates the effective use of genomic selection (GS) for improvements in body weight and meat production in a chicken line. The study also identifies genomic regions and genes that are influenced by intensive genetic selection.
Article
Genetics & Heredity
Astrid Lissette Barreto Sanchez, Qiao Wang, Mamadou Thiam, Zixuan Wang, Jin Zhang, Qi Zhang, Na Zhang, Qinghe Li, Jie Wen, Guiping Zhao
Summary: This study evaluated the heat tolerance and identified potential driver and hub genes related to heat stress in native and commercial chicken breeds through phenotypical, physiological, liver transcriptome comparative analysis and WGCNA. The results showed that native chickens were less affected by heat stress and had fewer differentially expressed genes (DEGs) related to metabolism activity, while commercial chickens had pathways related to inflammatory reactions. CPT1A and ANGPTL4 were identified as candidate genes associated with heat stress in native chickens, while HSP90B1 and HSPA5 were identified in commercial chickens. TLR7, AR, and BAG3 genes were revealed as hub genes playing an important role in heat stress.
Article
Agriculture, Dairy & Animal Science
Jiqiang Ding, Fan Ying, Qinghe Li, Gaomeng Zhang, Jin Zhang, Ranran Liu, Maiqing Zheng, Jie Wen, Guiping Zhao
Summary: Genetic analyses on 11,279 chickens from seven material lines identified a genomic region associated with egg number in meat-type chickens, as well as 29 SNPs and 9 candidate genes potentially affecting egg production traits.
JOURNAL OF ANIMAL SCIENCE AND BIOTECHNOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Qiao Wang, Jin Zhang, Hailong Wang, Zixuan Wang, Qinghe Li, Guiping Zhao, Maiqing Zheng, Jie Wen
Summary: Runs of homozygosity (ROHs) are effective for assessing inbreeding and detecting selection in livestock populations. This study investigated the occurrence and distribution of ROHs, compared genomic inbreeding coefficients, and identified genomic regions with high ROH frequencies in different Beijing-You chicken populations. The findings contribute to understanding genetic diversity and population demography.
Article
Agriculture, Dairy & Animal Science
G. M. Zhang, P. H. Liu, L. Chen, J. M. Zheng, G. P. Zhao, W. H. Xing, J. Wen, Q. H. Li
Summary: Researchers identified genome-wide significant markers on chromosome 7 related to semen volume in white-feathered broilers, and four candidate genes (FAPP1, OSBPL6, SESTD1, and SSFA2) potentially involved in semen volume were identified. These findings may contribute to further research on the genetic mechanism and marker-assisted selection of semen volume in white-feathered broilers.
