Article
Plant Sciences
Kyu-Won Kim, Bhagwat Nawade, Jungrye Nam, Sang-Ho Chu, Jungmin Ha, Yong-Jin Park
Summary: This study presents an integrated SNP array system for rice breeding research, which combines SNPs from eight different data resources. The developed 580 K Axiom Rice Genotyping Chip demonstrates robust and highly efficient genotyping in various studies, including GWAS and GS. This cost-effective genotyping platform will accelerate rice breeding research.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
Jianmei Chen, Ziyi Wu, Ruxue Chen, Zhihui Huang, Xuelei Han, Ruimin Qiao, Kejun Wang, Feng Yang, Xin-Jian Li, Xiu-Ling Li
Summary: In this study, genome-wide association analyses were performed to explore genes related to sow reproductive traits in French White sows. A notable region and four promising genes were detected, providing a theoretical basis for subsequent molecular breeding. The findings of this study are of great importance for improving the economic benefits of the pig industry.
Article
Biotechnology & Applied Microbiology
Shan Lin, Cuncun Ke, Lin Liu, Yahui Gao, Lingna Xu, Bo Han, Yaofeng Zhao, Shengli Zhang, Dongxiao Sun
Summary: In this study, 14 candidate genes related to immunoglobulin concentrations in colostrum and serum in dairy cattle were identified through genome-wide association studies (GWASs). These findings provide a basis for further investigation into key genes and mutations affecting immunoglobulin concentrations, as well as important information for genetic improvement of immune traits in dairy cattle.
Article
Agriculture, Dairy & Animal Science
Yilong Zhao, Sangang He, Jinfeng Huang, Mingjun Liu
Summary: pH is one of the main factors affecting meat storage/shelf life and overall quality. Through a genome-wide association analysis, candidate genes related to pH were identified, providing new opportunities for genetic improvement and extending the shelf life of meat.
Article
Genetics & Heredity
Kai Wang, Shujie Wang, Xiang Ji, Dong Chen, Qi Shen, Yang Yu, Pingxian Wu, Xuewei Li, Guoqing Tang
Summary: This study aimed to identify CpG sites associated with DNA methylation levels and meat quality traits in Yorkshire pigs. Genome-wide methylation levels were measured using RRBS, and linear mixed-effect models were used to examine associations. Eight CpG sites were associated with drip loss, two CpG sites with yellowness, and five CpG sites with lightness. No significant associations were found with pH levels or meat redness. This study provides new insights into the epigenetic molecular mechanisms of meat quality traits in pigs.
FRONTIERS IN GENETICS
(2023)
Review
Plant Sciences
Muhammad Yasir, Hafiza Hamrah Kanwal, Quaid Hussain, Muhammad Waheed Riaz, Muhammad Sajjad, Junkang Rong, Yurong Jiang
Summary: Over the past two decades, high-density SNP arrays and DNA sequencing technology have been widely used in crop research, particularly in cotton crops. Genome-wide association studies (GWAS) have provided an important tool for uncovering the relationship between crop phenotypes and underlying genetics, helping to advance crop breeding and improvement.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Genetics & Heredity
Hao Li, Cineng Xu, Fanming Meng, Zekai Yao, Zhenfei Fan, Yingshan Yang, Xianglun Meng, Yuexin Zhan, Ying Sun, Fucai Ma, Jifei Yang, Ming Yang, Jie Yang, Zhenfang Wu, Gengyuan Cai, Enqin Zheng
Summary: This study analyzed the scoring results of flesh color and intramuscular fat in different time periods, revealing their genetic structure and identifying related genes and genetic loci, which is of great importance for improving pig meat quality traits.
Article
Biochemistry & Molecular Biology
Maizura Ithnin, Wendy T. Vu, Min-Gyoung Shin, Vasantika Suryawanshi, Katrina Sherbina, Siti Hazirah Zolkafli, Norhalida Mohamed Serdari, Mohd Din Amiruddin, Norziha Abdullah, Suzana Mustaffa, Marhalil Marjuni, Rajanaidu Nookiah, Ahmad Kushairi, Paul Marjoram, Sergey Nuzhdin, Peter L. Chang, Rajinder Singh
Summary: The study reveals genetic similarity between wild American oil palm populations and some cultivated African oil palm populations, potentially originating from the Amazon Basin. Despite genetic bottleneck and inbreeding, there is significant genetic and phenotypic variation for agronomically valuable traits.
Article
Genetics & Heredity
Zheng Chang Wu, Yifu Wang, Xiaoguo Huang, Shenglong Wu, Wenbin Bao
Summary: Improving the reproductive efficiency of sows is a major challenge in the swine industry. This study identified genetic markers associated with reproductive traits in Large White pigs and suggested the use of marker-assisted selection for genetic improvement.
Article
Fisheries
D. S. Liyanage, Sukkyoung Lee, Hyerim Yang, Chaehyeon Lim, W. K. M. Omeka, 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: Selective breeding plays a vital role in the development of disease-resistant traits and high growth rates in flounder aquaculture. This study used a genome-wide association study (GWAS) to analyze viral hemorrhagic septicemia virus (VHSV) resistance in olive flounder. Significant single nucleotide polymorphisms (SNPs) and associated genes were identified, providing valuable information for breeding applications.
FISH & SHELLFISH IMMUNOLOGY
(2022)
Article
Plant Sciences
Jerko Gunjaca, Klaudija Carovic-Stanko, Boris Lazarevic, Monika Vidak, Marko Petek, Zlatko Liber, Zlatko Satovic
Summary: This study identified new genetic sources for improving seed mineral content in common bean through a genome-wide association study (GWAS). Twenty-two quantitative trait nucleotides (QTN) associated with seed nitrogen content, five QTNs with seed phosphorus content, and single QTNs with seed calcium and magnesium content were discovered. The results demonstrate the utility of GWAS for understanding the genetic architecture of seed nutritional traits and its application in genomics-assisted breeding for seed enrichment.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Agriculture, Dairy & Animal Science
Marina Selionova, Magomet Aibazov, Alexander Sermyagin, Anna Belous, Tatiana Deniskova, Tatiana Mamontova, Ekaterina Zharkova, Natalia Zinovieva
Summary: This study aimed to identify candidate genes related to body measurements and body weight of Karachai goats through genome-wide associations. The structural annotation of the identified genomic regions revealed their roles in regulating various biological processes. SNPs that were significant for live weight were selected, and an experimental PCR-RV test system was developed and tested. The study found new DNA markers for genetic improvement in meat goats and provided insights into the genetic mechanisms of complex traits.
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
Anesthesiology
Sirkku Ahlstrom, Paula Bergman, Ritva Jokela, Linda Ottensmann, Ari Ahola-Olli, Matti Pirinen, Klaus T. Olkkola, Mari A. Kaunisto, Eija Kalso
Summary: Genetic variation in the SLCO1A2 gene, accounting for 4% of the variation in rocuronium consumption, was identified as a factor influencing rocuronium dosage. However, the underlying mechanism remains unknown.
BRITISH JOURNAL OF ANAESTHESIA
(2021)
Article
Statistics & Probability
Haoran Xue, Xiaotong Shen, Wei Pan
Summary: Transcriptome-Wide Association Studies (TWAS) have become popular to discover (putative) causal genes by integrating outcome GWAS and eQTL datasets. In the specific application of identifying causal genes for LDL cholesterol, a robust and efficient inferential method is proposed to account for hidden confounding and invalid instrumental variables.
JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION
(2023)
Review
Genetics & Heredity
Guoyu Hu, Duy Ngoc Do, Pourya Davoudi, Younes Miar
Summary: The global population increase has led to higher demand for food and water, particularly meat. This necessitates the search for alternatives to reduce feed consumption and understand the biology of feed efficiency. Non-coding RNAs play a significant role in this area.
Article
Agriculture, Dairy & Animal Science
Pourya Davoudi, Duy Do, Stefanie M. Colombo, Bruce Rathgeber, Guoyu Hu, Mehdi Sargolzaei, Zhiquan Wang, Graham Plastow, Younes Miar
Summary: The improvement of feed efficiency in American mink is crucial for reducing the cost of production. This study estimated the heritability and genetic correlations of different feed efficiency measures and component traits. The residual intake and gain were found to be a favorable trait for selecting faster-growing mink with reduced feed intake. The Kleiber ratio was also identified as a promising indirect measure of feed efficiency. Overall, including feed efficiency traits in breeding programs can effectively select feed-efficient mink.
JOURNAL OF ANIMAL SCIENCE
(2022)
Article
Multidisciplinary Sciences
Seyed Ali Goldansaz, Susan Markus, Graham Plastow, David S. Wishart
Summary: This study identified and validated predictive serum biomarkers of sheep pregnancy and litter size (PLS) using metabolomics. Three panels of serum metabolite biomarkers were identified that can predict ewe PLS as early as 50 days after breeding. These biomarkers could lead to the development of a simple, low-cost blood test to measure PLS at an early stage of pregnancy, optimizing reproductive management on sheep farms.
SCIENTIFIC REPORTS
(2022)
Article
Genetics & Heredity
Xingjie Hao, Aixin Liang, Graham Plastow, Chunyan Zhang, Zhiquan Wang, Jiajia Liu, Angela Salzano, Bianca Gasparrini, Giuseppe Campanile, Shujun Zhang, Liguo Yang
Summary: In this study, a new approach (pGBLUP) was introduced to improve genomic prediction in buffalo by incorporating QTL information from cattle milk traits. The results showed that the pGBLUP performed slightly better or equal to other approaches. The heritability of the buffalo genomic region corresponding to cattle milk trait QTLs was enriched in four buffalo milk traits when using DEBV as the response variable. The study suggests that a larger sample size, higher-density SNP chips, and more precise prior biological information can further improve genomic prediction in buffalo.
Article
Immunology
Sean Lipsit, Antonio Facciuolo, Erin Scruten, James Wilkinson, Graham Plastow, Anthony Kusalik, Scott Napper
Summary: Individual variability in vaccine responses can result in subjects failing to develop protective immunity. Biomarkers of vaccine unresponsiveness can aid in vaccine research and development, as well as improving vaccine administration programs. This study identifies phosphorylation biomarkers as robust predictors of vaccine responsiveness and suggests their potential use in evaluating vaccine efficacy.
Article
Agriculture, Dairy & Animal Science
J. L. Moroni, S. Tsoi, I. I. Wenger, C. Tran, G. S. Plastow, P. Charagu, M. K. Dyck
Summary: This study found that poor placental development in sows with low litter birth weight phenotype may lead to lower birth weights for the entire litter.
ANIMAL REPRODUCTION SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Pourya Davoudi, Duy Ngoc Do, Bruce Rathgeber, Stefanie M. Colombo, Mehdi Sargolzaei, Graham Plastow, Zhiquan Wang, Karim Karimi, Guoyu Hu, Shafagh Valipour, Younes Miar
Summary: This study presents the first genome-wide CNV analysis of American mink, using whole-genome sequence data from 100 individuals. The results suggest potential links between CNVs and mink behavior, fur quality, and immune response.
Article
Agriculture, Dairy & Animal Science
Guoyu Hu, Duy Ngoc Do, Pourya Davoudi, Ghader Manafiazar, Alyson A. Kelvin, Graham Plastow, Zhiquan Wang, Mehdi Sargolzaei, Younes Miar
Summary: This study estimated the genetic and phenotypic correlations between Aleutian disease (AD) tests and various traits in mink, including body weight, growth, and feed-related traits. The findings suggest that selecting AD tests does not have adverse effects on the growth, feed efficiency, and feed intake of mink. Additionally, the antigen-based enzyme-linked immunosorbent assay test could be considered a reliable and practical indicator trait for selecting AD-resilient mink on AD-positive farms.
JOURNAL OF ANIMAL SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
Saeed Shadpour, Tatiane C. S. Chud, Dagnachew Hailemariam, Graham Plastow, Hinayah R. Oliveira, Paul Stothard, Jan Lassen, Filippo Miglior, Christine F. Baes, Dan Tulpan, Flavio S. Schenkel
Summary: This study investigated the effectiveness of milk mid-infrared spectroscopy (MIRS) data in predicting CH4 emissions in lactating cows. The results showed that using only milk yield (MY) for prediction had low accuracy, while adding other factors such as fat yield (FY) and protein yield (PY) improved the accuracy. However, using only MIRS data yielded the highest accuracy compared to other combinations.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
Saeed Shadpour, Tatiane C. S. Chud, Dagnachew Hailemariam, Hinayah R. Oliveira, Graham Plastow, Paul Stothard, Jan Lassen, Ransom Baldwin, Filippo Miglior, Christine F. Baes, Dan Tulpan, Flavio S. Schenkel
Summary: This study aimed to improve DMI predictions of Canadian Holstein cows using milk MIRS data with the help of artificial neural networks (ANN). Different ANN architectures were explored to predict unobserved DMI, and the robustness of developed prediction models was validated by analyzing data from dairy cows in Canada, Denmark, and the United States.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
Elda Dervishi, Xuechun Bai, Jian Cheng, Frederic Fortin, Mike K. Dyck, John C. S. Harding, Yolande M. Seddon, Jack C. M. Dekkers, PigGen Canada, Graham Plastow
Summary: This study identifies L-alpha-aminobutyric acid as a potential genetic marker for lymphocyte response after pathogen exposure. It also contributes to understanding the impact of environmental enrichment on plasma metabolite concentration.
JOURNAL OF ANIMAL SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
Yulu Chen, Steven Lonergan, Kyu-Sang Lim, Jian Cheng, Austin M. Putz, Michael K. Dyck, PigGen Canada, Frederic Fortin, John C. S. Harding, Graham S. Plastow, Jack C. M. Dekkers
Summary: This study found that plasma protein levels can be used as an indicator to select pigs with disease resilience, as they are genetically correlated with disease resilience. Therefore, plasma protein levels have the potential to be used as a tool for pig breeding and management.
JOURNAL OF ANIMAL SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
Stephanie Kamalanathan, Kerry Houlahan, Filippo Miglior, Tatiane C. S. Chud, Dave J. Seymour, Dagnachew Hailemariam, Graham Plastow, Hinayah R. de Oliveira, Christine F. Baes, Flavio S. Schenkel
Summary: Dairy cows contribute to greenhouse gas emissions from livestock, and strategies involving genetics and breeding can be used to reduce methane emissions. This study assessed three definitions for methane emission traits and their genetic parameters in Holstein cattle. The heritability of daily methane production, methane yield, and methane intensity was estimated, and a high genetic correlation was found between daily methane production and methane intensity. This study suggests that genetic selection can potentially mitigate methane emissions in Holstein cattle.
Article
Chemistry, Applied
Guangyu Wu, Chuan Yang, Heather L. Bruce, Bimol C. Roy, Xia Li, Chunhui Zhang
Summary: AEF technology was used during freezing-thawing-aging process of beef. Comparisons were made between beef aged with AEF (AEF + FA), beef aged without AEF (FA), and aged only (OA) controls. FA increased purge loss, cooking loss, shear force values, and lipid oxidation, while decreasing a* values compared to AEF + FA treatment. AEF helped to maintain meat quality by reducing purge loss, cooking loss, increasing tenderness, and maintaining color and lipid oxidation only in frozen aged steak.