Article
Biotechnology & Applied Microbiology
Marie-Pierre Sanchez, Clementine Escouflaire, Aurelia Baur, Fiona Bottin, Chris Hoze, Mekki Boussaha, Sebastien Fritz, Aurelien Capitan, Didier Boichard
Summary: This study aimed to assess the importance of the X chromosome in the genetic determinism of complex traits in dairy cattle. The results showed that the X chromosome explained about 3.5% of the genetic variance in these traits and revealed many new functional candidate genes. This study highlights the importance of the X chromosome in the genetic determinism of complex traits in dairy cattle and identifies new functional candidate genes for these traits.
Article
Genetics & Heredity
Dzianis Prakapenka, Zuoxiang Liang, Jicai Jiang, Li Ma, Yang Da
Summary: Epistasis studies for production and fertility traits in Holstein cattle revealed that majority of epistasis effects are within chromosome regions while a small percentage involve interactions between different chromosomes. This suggests a complex genetic mechanism underlying quantitative traits in cattle.
Article
Biology
Siqian Chen, Shuli Liu, Shaolei Shi, Yifan Jiang, Mingyue Cao, Yongjie Tang, Wenlong Li, Jianfeng Liu, Lingzhao Fang, Ying Yu, Shengli Zhang
Summary: In this study, the researchers systematically analyzed functional genomic regulatory elements (REs) in the liver across six mammals and demonstrated their associations with gene expression, evolutionary conservation, and complex traits. By integrating large-scale GWAS and eQTLs data, they found that REs with different degrees of evolutionary conservation showed enrichment for GWAS signals of complex traits. This study is of great importance for understanding the genetic basis of complex traits in livestock and humans.
Article
Agriculture, Dairy & Animal Science
Helen Schneider, Dierck Segelke, Jens Tetens, Georg Thaller, Jorn Bennewitz
Summary: This study conducted a detailed analysis of milk production and disease traits in dairy cattle and their genetic correlations. By analyzing the genotypes of 34,497 German Holstein cows, the study found shared genetic effects between milk production and disease traits on a genetic level, as well as identified specific genomic regions affecting these trait combinations. These findings provide important insights into the underlying biological pathways and can be utilized in breeding schemes for more precise designs.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Jessica Powell, Andrea Talenti, Andressa Fisch, Johanneke D. Hemmink, Edith Paxton, Philip Toye, Isabel Santos, Beatriz R. Ferreira, Tim K. Connelley, Liam J. Morrison, James G. D. Prendergast
Summary: This study generates over 150 libraries at base-pair resolution to investigate the dynamics of DNA methylation and chromatin accessibility of the bovine immune system. The research reveals extensive epigenetic divergence between different cattle breeds across immune cell types, which is related to the levels of DNA sequence divergence between sub-species. Additionally, distinct sub-categories of CpG islands based on their chromatin and methylation profiles are identified, discriminating between different transcriptional states.
Article
Agriculture, Dairy & Animal Science
Hengwei Yu, Shengchen Yu, Juntao Guo, Gong Cheng, Chugang Mei, Linsen Zan
Summary: A genome-wide association study was conducted to identify the dominant genes of body conformation traits in Qinchuan cattle. A total of 250 suggestive SNPs were identified and 37 candidate genes were annotated. Eight genes were found to be involved in growth traits, providing new insights into the regulatory mechanisms of bovine body size development.
Review
Agronomy
Yulin Ma, Muhammad Zahoor Khan, Jianxin Xiao, Gibson Maswayi Alugongo, Xu Chen, Tianyu Chen, Shuai Liu, Zhiyuan He, Jingjun Wang, Muhammad Kamal Shah, Zhijun Cao
Summary: Increasing milk production is a key concern in animal production, but traditional breeding has limited achievements in this area. Identifying candidate genes associated with milk production traits can improve the accuracy of animal selection.
Article
Cell Biology
Laura Bernhardt, Marcus Dittrich, Andreas Prell, Ramya Potabattula, Charis Drummer, Ruediger Behr, Thomas Hahn, Martin Schorsch, Tobias Mueller, Thomas Haaf
Summary: Advanced paternal age is associated with increased risks for reproductive and offspring medical problems, possibly due to age-related changes in the sperm epigenome.
Article
Biochemistry & Molecular Biology
Siyu Pan, Hongen Kang, Xinxuan Liu, Shuhua Li, Peng Yang, Mingqiu Wu, Na Yuan, Shiqi Lin, Qiwen Zheng, Peilin Jia
Summary: COLOCdb is a comprehensive genetic colocalization database that integrates over 3000 GWAS summary statistics and 13 types of xQTL. By employing two representative approaches for colocalization analysis, COLOCdb provides the most comprehensive colocalization analysis results, which can aid in advancing the discovery of new biological mechanisms and benefiting future functional studies.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Endocrinology & Metabolism
Nicole Lafontaine, Purdey J. Campbell, Juan E. Castillo-Fernandez, Shelby Mullin, Ee Mun Lim, Phillip Kendrew, Michelle Lewer, Suzanne J. Brown, Rae-Chi Huang, Phillip E. Melton, Trevor A. Mori, Lawrence J. Beilin, Frank Dudbridge, Tim D. Spector, Margaret J. Wright, Nicholas G. Martin, Allan F. McRae, Vijay Panicker, Gu Zhu, John P. Walsh, Jordana T. Bell, Scott G. Wilson
Summary: This study identified associations between blood-based DNAm and both fT3 and TSH, shedding light on the mechanisms underlying thyroid hormone action and/or pituitary-thyroid axis function.
JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM
(2021)
Article
Biochemistry & Molecular Biology
E. Capra, B. Lazzari, M. Milanesi, G. P. Nogueira, J. F. Garcia, Y. T. Utsunomiya, P. Ajmone-Marsan, A. Stella
Summary: In this study, methylation differences between taurine Angus and indicine Nellore cattle breeds were identified using RRBS profiling. Most differentially methylated sites clustered around genes involved in cellular and anatomical structure morphogenesis. Furthermore, sequences flanking differentially methylated sites were enriched with SNPs compared to other CpG sites. These findings suggest that epigenetics contributes to the regulation and divergence of anatomical morphogenesis in cattle evolution and sub-species differentiation and adaptation.
Article
Food Science & Technology
N. A. Marin-Garzon, A. F. B. Magalhaes, L. F. M. Mota, L. F. S. Fonseca, L. A. L. Chardulo, L. G. Albuquerque
Summary: This study in Nellore cattle identified candidate genes and genomic regions associated with meat color traits through single and multiple-trait GWAS, explaining genetic variance rates and confirming pleiotropic effects in certain regions. The research was conducted using the single-step GWAS method and the BLUPF90 family programs.
Article
Biochemistry & Molecular Biology
Tianzhen Wang, Qunhao Niu, Tianliu Zhang, Xu Zheng, Haipeng Li, Xue Gao, Yan Chen, Huijiang Gao, Lupei Zhang, George E. Liu, Junya Li, Lingyang Xu
Summary: This study conducted an integrative analysis of gene-based GWAS and eQTL analysis to identify candidate genes for carcass yield traits in beef cattle. The results revealed shared genes that may play important roles in carcass yield traits and further demonstrated the effects of two genes, PON3 and PRIM2, on the proliferation and differentiation of bovine skeletal muscle satellite cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Lucio F. M. Mota, Samuel W. B. Santos, Gerardo A. Fernandes Junior, Tiago Bresolin, Maria E. Z. Mercadante, Josineudson A. V. Silva, Joslaine N. S. G. Cyrillo, Fabio M. Monteiro, Roberto Carvalheiro, Lucia G. Albuquerque
Summary: Multi-trait weighted GWAS and meta-analysis identified genomic regions associated with feed efficiency-related traits in beef cattle, highlighting the importance of physiological mechanisms related to energy metabolism and hypothalamus signaling.
Article
Multidisciplinary Sciences
Zhaoli Song, Wen-Dong Li, Xuye Jin, Junbiao Ying, Xin Zhang, Ying Song, Hengtong Li, Qiao Fan
Summary: Twin studies have shown that the occupation of leadership roles is a heritable trait, but previous studies have lacked power in identifying specific genes associated with this trait. In this study using data from the UK Biobank, a genome-wide association study was conducted on individuals' leadership phenotypes. Several significant loci were identified, some of which were previously linked to bipolar disorder and schizophrenia. Genetic correlations were found between leadership positions and both positive and negative indicators of well-being and health. This study provides insights into the polygenic nature of leadership and its genetic relationship with individuals' well-being and health.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Agriculture, Dairy & Animal Science
Mei Liu, Jie Cheng, Yuhan Chen, Long Yang, Sayed Haidar Abbas Raza, Yongzhen Huang, Chuzhao Lei, George E. Liu, Xianyong Lan, Hong Chen
Summary: This study revealed the distribution of DGAT1 CNV in Chinese goats for the first time and found significant differences among dairy, meat, and fiber goats. The study also showed significant associations between DGAT1 CNV and milk production traits, indicating its potential role in marker-assisted selection of dairy goat breeding.
ANIMAL BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Tianliu Zhang, Tianzhen Wang, Qunhao Niu, Xu Zheng, Haipeng Li, Xue Gao, Yan Chen, Huijiang Gao, Lupei Zhang, George E. Liu, Junya Li, Lingyang Xu
Summary: This study characterized the expression differences of genes in different beef cuts and identified candidate genes related to meat quality. The findings provide valuable insights into the regulation of transcriptome and could contribute to the improvement of health-beneficial meat selection in beef cattle.
Article
Veterinary Sciences
Matthew Barden, Alkiviadis Anagnostopoulos, Bethany E. Griffiths, Cherril Bedford, Marco Winters, Bingjie Li, Mike Coffey, Androniki Psifidi, Georgios Banos, Georgios Oikonomou
Summary: This study found an association between the lameness advantage genetic index and sole haemorrhage, sole ulcers, and lameness. Selection on the lameness advantage index could be considered in herds aiming to reduce lameness.
Article
Agriculture, Dairy & Animal Science
Matthew Barden, Alkiviadis Anagnostopoulos, Bethany E. Griffiths, Bingjie Li, Cherry Bedford, Chris Watson, Androniki Psifidi, Georgios Banos, Georgios Oikonomou
Summary: This study aimed to estimate the genetic parameters of recovery from sole lesions in dairy cows and evaluate its genetic correlation with overall susceptibility. The findings showed that recovery from sole lesions is heritable and negatively correlated with susceptibility. If confirmed in further research, selective breeding could be used to reduce the frequency of chronically lame cows.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
F. L. Guinan, G. R. Wiggans, H. D. Norman, J. W. Durr, J. B. Cole, C. P. Van Tassell, I. Misztal, D. Lourenco
Summary: Genomic selection accelerates genetic changes in populations by increasing accuracy and decreasing generation interval. The genetic gain and inbreeding levels of US dairy cattle breeds since the implementation of genomic evaluations in 2009 were examined. The Holstein and Jersey breeds have seen the most significant increase in genetic gain since then.
JOURNAL OF DAIRY SCIENCE
(2023)
Review
Agriculture, Dairy & Animal Science
Hafedh Ben Zaabza, Curtis P. Van Tassell, Jeremie Vandenplas, Paul VanRaden, Zengting Liu, Herwin Eding, Stephanie McKay, Katrine Haugaard, Martin H. Lidauer, Esa A. Mantysaari, Ismo Stranden
Summary: This paper provides an overview of different methods and computational approaches for calculating reliability, from the animal model era to the single-step genomic model era. It also discusses the challenges faced in reliability computation and presents efficient and accurate algorithms developed recently for large-scale genomic evaluations.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Multidisciplinary Sciences
Yi Zhang, Andrew Liu, Shao Kang Huang, Jay D. Evans, Steve C. Cook, Evan Palmer-Young, Miguel Corona, Mohamed Alburaki, Ge Liu, Ri Chou Han, Wen Feng Li, Yue Hao, Ji Lian Li, Todd M. Gilligan, Allan H. Smith-Pardo, Olubukola Banmeke, Francisco J. Posada-Florez, Ya Hui Gao, Gloria DeGrandi-Hoffman, Hui Chun Xie, Alex M. Sadzewicz, Michele Hamilton, Yan Ping Chen
Summary: Honey bees are important for pollination and carbon dioxide removal, but their population has been declining. This study reveals that winter colony losses are mainly due to weakened immune function leading to disease infections. Activation of the SIRT1 gene expression improves bee physiology and extends lifespan.
JOURNAL OF ADVANCED RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Zuoxiang Liang, Dzianis Prakapenka, Paul M. VanRaden, Jicai Jiang, Li Ma, Yang Da
Summary: A genome-wide association study identified new effects and confirmed effects on daughter pregnancy rate (DPR), cow conception rate (CCR), and heifer conception rate (HCR) in U.S. Holstein cows, with several effects located near known reproduction-related genes. Specific SNPs were recommended for heifer culling based on their negative effects on fertility traits. The study provided valuable insights into the genetic variants and genomic regions influencing fertility traits in Holstein cows.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Agriculture, Dairy & Animal Science
Badjibassa Akounda, Dominique Ouedraogo, Albert Soudre, Pamela A. Burger, Benjamin D. Rosen, Curtis P. Van Tassell, Johann Soelkner
Summary: This study explores the morphological differences between different goat populations in Burkina Faso using morphometric traits. The results show that there is no strict distinction between the two populations, indicating a close genetic relationship. Four groups were identified based on body size, representing the main breeds and their crosses. These different goat morphotypes are the result of farmers breeding practices. The study highlights the need for sustainable genetic improvement approaches for the use of these adapted local goat genetic resources.
Article
Biotechnology & Applied Microbiology
Yahui Gao, Alexis Marceau, Victoria Iqbal, Jose Antonio Torres-Vazquez, Mahesh Neupane, Jicai Jiang, George E. Liu, Li Ma
Summary: Our large-scale GWAS analyses identified a major QTL in the bovine MHC region for early first calving in heifers. Additional functional enrichment and TWAS analyses confirmed the MHC QTL with relevant biological evidence. Our results revealed the complex genetic basis of heifer health and fertility traits and indicated a potential connection between the immune system and reproduction in cattle.
Article
Genetics & Heredity
Alexis Marceau, Junjian Wang, Victoria Iqbal, Jicai Jiang, George E. Liu, Li Ma
Summary: This study aims to identify and analyze lncRNA transcripts in Bos taurus mammary tissue samples to understand their features and functions, particularly their connection to lactation. The findings reveal that the lncRNAs in mammary tissue have distinct characteristics and functional annotations, and are associated with both mammary tissue development and genes/proteins related to pregnancy.
Article
Biochemical Research Methods
Jian Cheng, Christian Maltecca, Paul M. VanRaden, Jeffrey R. O'Connell, Li Ma, Jicai Jiang
Summary: SLEMM is a new software tool for large-scale genomic prediction, which can improve prediction accuracy through SNP weighting. Extensive analyses on multiple datasets showed that SLEMM had the best predictive ability and computational performance compared to other genomic prediction methods. Simulation analyses also demonstrated that SLEMM had comparable accuracy to BayesR.
Article
Agriculture, Dairy & Animal Science
Bingjie Li, Matthew Barden, Vanessa Kapsona, Enrique Sanchez-Molano, Alkiviadis Anagnostopoulos, Bethany Eloise Griffiths, Cherril Bedford, Xiaoxia Dai, Mike Coffey, Androniki Psifidi, Georgios Oikonomou, Georgios Banos
Summary: This study examined the genetic architecture of foot lesions in dairy cattle and found that they are under genetic control. The traits showed genetic variation and can be improved through breeding.
GENETICS SELECTION EVOLUTION
(2023)
Meeting Abstract
Agriculture, Dairy & Animal Science
Junjian Wang, Christian Maltecca, Francesco Tiezzi, Yijian Huang, Jicai Jiang
JOURNAL OF ANIMAL SCIENCE
(2023)
