Article
Plant Sciences
Xiongwei Li, Jiabo Wang, Mingshen Su, Minghao Zhang, Yang Hu, Jihong Du, Huijuan Zhou, Xiaofeng Yang, Xianan Zhang, Huijuan Jia, Zhongshan Gao, Zhengwen Ye
Summary: This study identified candidate genes associated with several agronomic traits and key volatile odor compounds in peaches using genome-wide association studies and genomic selection. A diagnostic marker for predicting aroma substances was also found to be valuable for breeders in developing strong-aroma cultivars.
HORTICULTURE RESEARCH
(2023)
Article
Fisheries
W. K. M. Omeka, D. S. Liyanage, Sukkyoung Lee, Chaehyeon Lim, Hyerim Yang, W. M. Gayashani Sandamalika, H. M. V. Udayantha, Gaeun Kim, Subothini Ganeshalingam, Taehyug Jeong, Seong-Rip Oh, Seung-Hwan Won, Hyoung-Bum Koh, Mun-Kwan Kim, David B. Jones, Cecile Massault, Dean R. Jerry, Jehee Lee
Summary: Traits linked to growth performance in farmed fish are important for profitability in aquaculture. A genome-wide association study (GWAS) on olive flounder identified several single nucleotide polymorphisms (SNPs) associated with growth traits. These findings contribute to understanding the molecular basis of growth regulation and promote the use of SNP-based genomic selection in flounder culture.
Article
Biochemistry & Molecular Biology
Haonan Zeng, Wenjing Zhang, Qing Lin, Yahui Gao, Jinyan Teng, Zhiting Xu, Xiaodian Cai, Zhanming Zhong, Jun Wu, Yuqiang Liu, Shuqi Diao, Chen Wei, Wentao Gong, Xiangchun Pan, Zedong Li, Xiaoyu Huang, Xifan Chen, Jinshi Du, Fuping PigGTEx Consortium, Fuping Zhao, Yunxiang Zhao, Maria Ballester, Daniel Crespo-Piazuelo, Marcel Amills, Alex Clop, Peter Karlskov-Mortensen, Merete Fredholm, Pinghua Li, Ruihua Huang, Guoqing Tang, Mingzhou Li, Xiaohong Liu, Yaosheng Chen, Qin Zhang, Jiaqi Li, Xiaolong Yuan, Xiangdong Ding, Lingzhao Fang, Zhe Zhang
Summary: To unlock the potential of pigs in agriculture and biomedical research, the PigBiobank was created to investigate the molecular and cellular mechanisms underlying complex traits in pigs and translate the findings to other species.
NUCLEIC ACIDS RESEARCH
(2023)
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
Multidisciplinary Sciences
Bingxin Zhao, Yue Shan, Yue Yang, Zhaolong Yu, Tengfei Li, Xifeng Wang, Tianyou Luo, Ziliang Zhu, Patrick Sullivan, Hongyu Zhao, Yun Li, Hongtu Zhu
Summary: The study found that structural variations of the human brain are highly heritable and have been linked to various complex traits. By performing cross-tissue TWAS analysis on 211 structural neuroimaging, the researchers identified 278 associated genes. Furthermore, TWAS gene-based polygenic risk scores showed significant improvement in association analysis compared to conventional variant-based GWAS PRS, explaining up to 6.97% of phenotypic variance.
NATURE COMMUNICATIONS
(2021)
Article
Agronomy
Joyce N. Njuguna, Lindsay V. Clark, Alexander E. Lipka, Kossonou G. Anzoua, Larisa Bagmet, Pavel Chebukin, Maria S. Dwiyanti, Elena Dzyubenko, Nicolay Dzyubenko, Bimal Kumar Ghimire, Xiaoli Jin, Douglas A. Johnson, Hironori Nagano, Junhua Peng, Karen Koefoed Petersen, Andrey Sabitov, Eun Soo Seong, Toshihiko Yamada, Ji Hye Yoo, Chang Yeon Yu, Hua Zhao, Stephen P. Long, Erik J. Sacks
Summary: Accelerating biomass improvement is a major goal of Miscanthus breeding, and genomic-enabled breeding tools like MAS and genomic selection can effectively improve the efficiency of Miscanthus breeding. This study conducted GWA and genomic prediction in Miscanthus sacchariflorus, identifying significant SNPs and candidate genes related to biomass yield. The study also showed that with adequate sample sizes, genomic selection can be beneficial for improving the population of M. sacchariflorus.
GLOBAL CHANGE BIOLOGY BIOENERGY
(2023)
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
Agriculture, Dairy & Animal Science
Lijun Shi, Huihui Li, Xuefeng Gao, Lixian Wang
Summary: This study identified significant SNPs and candidate genes associated with litter traits in Yorkshire pigs using genome-wide association studies.
Review
Biochemical Research Methods
Denis Awany, Emile R. Chimusa
Summary: Geneticists are puzzled by the problem of missing/hidden heritability, and propose that incorporating host microbiota information into GWAS models could offer a solution. Current GWAS models do not take into account the contributory role of the microbiome in heritability estimate, despite empirical observations indicating its relevance in complex human phenotypes.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Agriculture, Dairy & Animal Science
Ruifeng Zhang, Yi Zhang, Tongni Liu, Bo Jiang, Zhenyang Li, Youping Qu, Yaosheng Chen, Zhengcao Li
Summary: This study utilized three genome-wide association study methods to identify variants related to growth traits in pigs and performed genomic selection. The results showed that genomic best linear unbiased prediction (GBLUP) models with pre-selected variants significantly improved prediction accuracies compared to using 60K SNP-chip data, with improvements ranging from 4% to 46% for the four traits; and a two-kernel based GBLUP model showed improvements ranging from 5% to 27%.
Article
Biology
Sumeet K. Tiwari, Boas C. L. van der Putten, Thilo M. Fuchs, Trung N. Vinh, Martin Bootsma, Rik Oldenkamp, Roberto La Ragione, Sebastien Matamoros, Ngo T. Hoa, Christian Berens, Joy Leng, Julio Alvarez, Marta Ferrandis-Vila, Jenny M. Ritchie, Angelika Fruth, Stefan Schwarz, Lucas Dominguez, Maria Ugarte-Ruiz, Astrid Bethe, Charlotte Huber, Vanessa Johanns, Ivonne Stamm, Lothar H. Wieler, Christa Ewers, Amanda Fivian-Hughes, Herbert Schmidt, Christian Menge, Torsten Semmler, Constance Schultsz
Summary: This study analyzes the genetic determinants of host specificity in E. coli and identifies specific genes associated with different hosts. The nan-9 gene cluster shows a strong association with the human host, while previously known sialic acid regulon genes show no significant association with any host.
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.
Article
Plant Sciences
Dongdong Dang, Yuan Guan, Hongjian Zheng, Xuecai Zhang, Ao Zhang, Hui Wang, Yanye Ruan, Li Qin
Summary: Sweet corn and waxy corn have better taste and higher nutritional value than regular maize. A genome-wide association study (GWAS) and genomic prediction analysis were conducted on plant architecture traits in sweet corn and waxy corn. Significant differences were observed between sweet corn and waxy corn for plant height, ear height, and tassel branch number.
Review
Gastroenterology & Hepatology
Lusheng Huang, Congying Chen
Summary: The gut microbiota, composed of trillions of microbes, plays a crucial role in the host's immunity, metabolism, and behavior. Both environmental and host factors contribute to the variation in gut microbial compositions among individuals. Research has shown that certain bacterial taxa are heritable, and genomic variants associated with the gut microbiome have been identified in humans and pigs. Pig models offer advantages and challenges in studying the host genetic effect on gut microbial composition.
Article
Genetics & Heredity
Jingchun Sun, Jinhong Xiao, Yifan Jiang, Yaxin Wang, Minghao Cao, Jialin Wei, Taiyong Yu, Xiangdong Ding, Gongshe Yang
Summary: In this study, a genome-wide association study (GWAS) was conducted to identify genetic structure and potential genes influencing reproductive traits in Yorkshire pigs. Through analysis of chip and imputed data, 71 significant SNPs and 25 potential candidate genes were discovered. Functional enrichment analysis showed that these genes are mainly related to calcium signaling pathway, ovarian steroidogenesis, and GnRH signaling pathways. This research provides valuable insights into the genetic basis of porcine reproductive traits and offers molecular markers for genomic selection in pig breeding.
Article
Genetics & Heredity
Ibrahim Abousoliman, Henry Reyer, Michael Oster, Eduard Murani, Ismail Mohamed, Klaus Wimmers
Summary: Sheep play a critical role in Egypt's agricultural and livestock sectors. The Barki sheep breed, known for its adaptation to harsh environmental conditions, contributes significantly to meat production in semi-arid regions. A study using a genome-wide SNP panel identified genetic regions diversified between Egyptian Barki sheep with high and low growth performance traits, highlighting potential for improving growth traits in this breed.
Article
Genetics & Heredity
Lidia De los Rios-Perez, Tom Druet, Tom Goldammer, Doerte Wittenburg
Summary: This study identified and characterized autozygosity in European pikeperch, assessed relatedness among parental individuals, and determined the effective population size. The results highlight the potential risks of inbreeding in pikeperch aquaculture without selective breeding programs. This study emphasizes the importance of utilizing genomic information in the aquaculture industry.
FRONTIERS IN GENETICS
(2022)
Article
Agronomy
Dario Fornara, Elizabeth M. E. Ball, Christina Mulvenna, Henry Reyer, Michael Oster, Klaus Wimmers, Hanne Damgaard Poulsen, Arno Rosemarin
Summary: The over-supplementation of animal feeds with phosphorus leads to high rates of P excretion and negative environmental impacts. Adding phytase to pig and poultry diets can reduce P excretion, but the effects on plant-soil systems are poorly understood. This study found that phytase supplementation significantly influenced P content of animal waste and plant P dynamics, with intermediate phytase levels contributing to higher P use efficiency and lower soil P availability. The effects of dietary P content on P losses from soils varied depending on the type of organic amendment.
Article
Agriculture, Dairy & Animal Science
Saber Qanbari, Robert D. Schnabel, Dorte Wittenburg
Summary: By evaluating the map coordinates of SNP markers using population genetic metrics, this study identified a panel of misplaced markers in cattle. These misplaced markers account for a small proportion of the SNP genotyping array and it is recommended to remove them in association mapping studies.
Article
Agriculture, Dairy & Animal Science
Christina C. Mulvenna, Ursula M. McCormack, Elizabeth Magowan, John McKillen, Mike R. Bedford, Carrie L. Walk, Michael Oster, Henry Reyer, Klaus Wimmers, Dario A. Fornara, M. Elizabeth E. Ball
Summary: Phytase has been a common addition to poultry diets for over 20 years, showing benefits in growth performance, nutrient digestibility, and bone parameters. This study found that superdosing phytase in rapeseed meal and maize dried distiller grains with solubles diets can improve performance, increase digestibility, and reduce P excretion by 15% compared to birds without phytase.
Article
Biochemistry & Molecular Biology
Maruf Hasan, Michael Oster, Henry Reyer, Siriluck Ponsuksili, Eduard Murani, Petra Wolf, Dagmar-Christiane Fischer, Klaus Wimmers
Summary: This study investigated the tissue-wide expression patterns of key genes related to vitamin D metabolism and FGF23 signaling in pigs fed different phosphorus diets. The results showed that non-renal tissues and cells have specific requirements for active vitamin D formation. Low phosphorus diet suppressed vitamin D signaling locally, while high phosphorus diet stimulated local vitamin D synthesis and regulation of FGF23 signaling in bone.
Article
Agriculture, Dairy & Animal Science
Adewunmi O. Omotoso, Henry Reyer, Michael Oster, Steffen Maak, Siriluck Ponsuksili, Klaus Wimmers
Summary: Phosphorus inclusion in broiler diets needs to be tailored to their physiological demands at different developmental stages. A timed nutritional conditioning strategy, such as P depletion, may enhance mineral homeostasis mechanisms and reduce dietary P supply. This study investigated the effects of dietary P depletion on broiler chickens at different developmental stages, revealing marked responses early on, but indications of compensatory mechanisms later. Endocrine control mediated by calcitriol, intestinal P uptake, and mineral mobilization from bones were identified as potential mechanisms for maintaining mineral homeostasis. Precise timing, duration, and extent of P depletion should be considered for optimized nutrient utilization in broiler husbandry.
Article
Chemistry, Analytical
Mohd. Rahil Hasan, Pradakshina Sharma, Shifa Shaikh, Saumitra Singh, Roberto Pilloton, Jagriti Narang
Summary: We have developed a paper-based experimental platform for analyzing dengue virus, which incorporates screen-printing technology and black carbon conductive ink. The platform utilizes both two-electrode and three-electrode systems, with an LOD of 0.1 μg/mL for detecting the virus. The three-electrode system exhibits a significantly higher current range and amplification compared to the two-electrode system, making it a viable option for sensitive detection of dengue virus and other diseases.
Article
Nutrition & Dietetics
Maruf Hasan, Michael Oster, Henry Reyer, Klaus Wimmers, Dagmar-Christiane Fischer
Summary: Vitamin D-3 (Vit D-3) and 25(OH)D-3 are used as dietary sources of active vitamin D in pig husbandry, and while their primary effects are on the intestine, kidney, and bone, they also have wide-ranging effects on peripheral tissues. The use of Vit D-3 and 25(OH)D-3 in pig nutrition has been shown to have different outcomes in terms of reproductive capacities, growth performance, immunity, and bone development.
BRITISH JOURNAL OF NUTRITION
(2023)
Correction
Nutrition & Dietetics
Maruf Hasan, Michael Oster, Henry Reyer, Klaus Wimmers, Dagmar-Christiane Fischer
BRITISH JOURNAL OF NUTRITION
(2023)
Article
Agriculture, Dairy & Animal Science
Hanne Honerlagen, Henry Reyer, Ibrahim Abou-Soliman, Dierck Segelke, Siriluck Ponsuksili, Nares Trakooljul, Norbert Reinsch, Bjoern Kuhla, Klaus Wimmers
Summary: Improving the nitrogen-utilization efficiency (NUE) of dairy cows through breeding selection has benefits in terms of nutrition, environment, and economics. The individual milk urea concentration (MU) of cows has been proposed as an indicator trait for NUE. This study aimed to identify different microbial genera in the rumen of Holstein cows with divergent genomic breeding values for MU (GBVMU). The identified microbial genera were further investigated for their correlations with MU and other NUE-associated traits, providing insight into genetically determined N-utilization in Holstein cows.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Cell Biology
Julia Brenmoehl, Elli Brosig, Nares Trakooljul, Christina Walz, Daniela Ohde, Antonia Noce, Michael Walz, Martina Langhammer, Stefan Petkov, Monika Roentgen, Steffen Maak, Christina E. E. Galuska, Beate Fuchs, Bjoern Kuhla, Siriluck Ponsuksili, Klaus Wimmers, Andreas Hoeflich
Summary: This study investigated the contribution of non-mitochondrial and mitochondrial metabolic pathways in contracting muscles during repeated training. The results showed that marathon mice displayed increased glucose and fatty acid oxidation, reduced lactate dehydrogenase activity, and inhibited lactate formation compared to trained control mice. This suggests that marathon mice have enhanced metabolic flexibility towards lipid catabolism regulated by lactate dehydrogenase.
Article
Biochemical Research Methods
Jan Klosa, Noah Simon, Volkmar Liebscher, Doerte Wittenburg
Summary: In life sciences, high-throughput techniques often result in high-dimensional data with a large number of covariates compared to observations, leading to multicollinearity challenges in linear regression analysis. Penalization methods, such as lasso, ridge regression, and group lasso, have been effective in addressing this issue. This study introduces a novel approach that combines lasso and standardized group lasso to achieve meaningful weighting of predicted outcomes, which is particularly important in breeding populations. The method was evaluated through extensive simulation studies and demonstrated improved prediction abilities and accurate localization of simulated features compared to other penalization approaches.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Review
Agriculture, Dairy & Animal Science
Benjamin Diehl, Michael Oster, Andreas Vernunft, Klaus Wimmers, Hartwig Bostedt
Summary: The losses of piglets in commercial pig farming remain a concern and sustainable breeding and management strategies are needed. This review systematically presents the three phases of neonatal adaptation in piglets and highlights the key developments and influencing factors in each phase.
ARCHIVES ANIMAL BREEDING
(2022)
Review
Biochemistry & Molecular Biology
Fabio Sarais, Alvaro Perdomo-Sabogal, Klaus Wimmers, Siriluck Ponsuksili
Summary: This review focuses on the latest discoveries of tsRNAs, with special attention to molecules initially thought to be associated with tiRNAs. The paper outlines their biological functions, provides a collection of useful databases, and discusses future research perspectives and applications in livestock basic and applied research.
