Article
Plant Sciences
Maximilian Rembe, Jochen Christoph Reif, Erhard Ebmeyer, Patrick Thorwarth, Viktor Korzun, Johannes Schacht, Philipp H. G. Boeven, Pierrick Varenne, Ebrahim Kazman, Norman Philipp, Sonja Kollers, Nina Pfeiffer, C. Friedrich H. Longin, Niklas Hartwig, Mario Gils, Yusheng Zhao
Summary: This study empirically investigated the potential and limitations of reciprocal recurrent genomic selection in wheat breeding, finding that it can significantly improve hybrid wheat breeding efficiency with a selection gain of 1.0 dt ha(-1) compared to the original 20 parental lines. However, the need to develop robust genome-wide predictive equations was also highlighted for successful implementation.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Genetics & Heredity
Caio Canella Vieira, Reyna Persa, Pengyin Chen, Diego Jarquin
Summary: This research investigates the potential of incorporating soil texture information and its interaction with molecular markers to enhance the predictive ability in plant breeding programs. The study suggests that adding soil texture information and GxS interaction can decrease the variability captured by the environment and residual terms, and outperforms other models. Therefore, obtaining soil texture information before the growing season can optimize the efficiency of a breeding program.
FRONTIERS IN GENETICS
(2022)
Article
Agronomy
Simon Rio, Deniz Akdemir, Tiago Carvalho, Julio Isidro Y. Sanchez
Summary: In this study, new forms of the coefficient of determination (CD) were proposed to forecast the genomic prediction reliability of genotypes, helping to optimize multi-environment trials. These new CD criteria can be used to predict the performance and mean performance of genotypes in multi-environment trials, especially in the presence of complex pedigree relationships between genotypes.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Plant Sciences
Qian Wang, Shan Jiang, Tong Li, Zhixu Qiu, Jun Yan, Ran Fu, Chuang Ma, Xiangfeng Wang, Shuqin Jiang, Qian Cheng
Summary: G2P container is a neutral environment developed for genomic selection-assisted breeding in the seed industry. It contains state-of-the-art GS models and evaluation metrics, and offers auto-ensemble algorithms and training set optimization to improve the prediction precision of genotype-to-phenotype.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
Wenxin Li, Xiaojuan Wang, Xiaoxue Zhang, Fadi Li, Deyin Zhang, Xiaolong Li, Yukun Zhang, Yuan Zhao, Liming Zhao, Dan Xu, Jiangbo Cheng, Jianghui Wang, Bubo Zhou, Changchun Lin, Weimin Wang
Summary: Small ruminants farming is crucial for the livelihood of a significant portion of the population. This study investigates the impact of single nucleotide polymorphisms in the PRKAA2 gene on growth-related traits in Hu sheep and Dorper sheep. Analysis of 1254 sheep's body weight and body type data collected at various time points revealed a significant association between a PRKAA2 gene polymorphism and sheep growth traits. The highest expression of the PRKAA2 gene was observed in the spleen, followed by the kidney. This research suggests that the PRKAA2 gene could be utilized as a marker-assisted selection to enhance growth-related traits in sheep.
ANIMAL BIOTECHNOLOGY
(2023)
Review
Biotechnology & Applied Microbiology
Gopalareddy Krishnappa, Siddanna Savadi, Bhudeva Singh Tyagi, Sanjay Kumar Singh, Harohalli Masthigowda Mamrutha, Satish Kumar, Chandra Nath Mishra, Hanif Khan, Krishnappa Gangadhara, Govindareddy Uday, Gyanendra Singh, Gyanendra Pratap Singh
Summary: Increasing the rate of crop improvement is crucial for sustained food production and meeting the needs of a growing population. Genomic selection offers accelerated breeding cycles through the rapid selection of superior genotypes, with advantages in prediction accuracy and efficiency over other breeding methods. Integrating novel technologies into GS can further enhance efficiency and speed, facilitating the development of new varieties.
Article
Agronomy
Peter K. Wahinya, Gilbert M. Jeyaruban, Andrew A. Swan, Julius H. J. van der Werf
Summary: Genotype by environment interaction affects the effectiveness of dairy cattle breeding programs in developing countries. This study aimed to optimize breeding programs for dairy cattle in different environments within Kenya. Simulation results showed that breeding strategies involving progeny testing bulls within each production system and using both phenotypic and genomic information can maximize genetic responses. Additionally, a joint breeding program with bull testing in all three environments produced the highest response using phenotypes alone.
Article
Genetics & Heredity
Partha S. Biswas, M. M. Emam Ahmed, Wazifa Afrin, Anisar Rahman, A. K. M. Shalahuddin, Rafiqul Islam, Fahamida Akter, Md Abu Syed, Md Ruhul Amin Sarker, K. M. Ifterkharuddaula, Mohammad Rafiqul Islam
Summary: Increasing selection differential and decreasing cycle time can accelerate the rate of genetic improvement. Creating and capturing higher genetic with higher accuracy within the shortest possible time is crucial for enhancing genetic gain. Comprehensive yield testing at multi-locations at early generations together with shorter line fixation time can expedite the rapid recycling of parents in the breeding program through recurrent selection. Genomic selection is efficient in capturing high breeding value individuals, considering additive genetic effects of all genes, and reducing breeding cycle time, thereby enhancing genetic gain.
FRONTIERS IN GENETICS
(2023)
Article
Multidisciplinary Sciences
Elaheh Vojgani, Armin C. Hoelker, Manfred Mayer, Chris-Carolin Schoen, Henner Simianer, Torsten Pook
Summary: This study compared the predictive ability of using haplotype blocks and pruned sets of SNPs in genomic prediction for plant breeding. The results showed that utilizing haplotype blocks significantly reduces computational load while maintaining similar prediction accuracy compared to pruned SNP sets. Additionally, genomic correlation was identified as the most influential factor affecting the prediction accuracy of bivariate models.
Article
Horticulture
Amparo Rosero, William Burgos-Paz, Hernando Araujo, Ivan Javier Pastrana-Vargas, Remberto Martinez, Jose-Luis Perez, Laura Espitia
Summary: Adapting to different environmental conditions is a challenge for breeders, who select genotypes with better performance to develop new varieties. This study used the CropInd tool to evaluate the agronomic performance of 19 sweet potato genotypes and selected the new variety 0113-672COR for the Colombian Caribbean region based on its multi-trait performance and stability. The use of multi-trait selection index, stability analysis, and genetic gain analysis assisted breeders in phenotypic selection.
Article
Agriculture, Dairy & Animal Science
Xufang Ren, Zi Guan, Haiying Li, Junhui Wen, Xiurong Zhao, Gang Wang, Xinye Zhang, Huie Wang, Li Zhang, Fuqing Yu, Lujiang Qu
Summary: This study investigated the population genetic structure and admixture of 5 Chinese gamecock breeds and their admixture with 9 other indigenous Chinese chicken breeds. The results showed that different gamecock breeds were grouped into different clusters. Gene flow was observed between gamecocks and indigenous chickens. Ancestral component analysis revealed the important role of modern domestic chickens in the history of Chinese gamecock domestication and evolution.
Article
Plant Sciences
Guilherme Ferreira Simiqueli, Rafael Tassinari Resende, Elizabete Keiko Takahashi, Joao Edesio de Sousa, Dario Grattapaglia
Summary: This study assessed the realized predictive ability for volume growth at harvest age by genomic selection (GS) in hybrid Eucalyptus. It found that the predictive ability of GS improved when the direct parents of selection candidates were used in training, and that pure species data resulted in higher predictive abilities than hybrid data.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Damiano Puglisi, Stefano Delbono, Andrea Visioni, Hakan Ozkan, Ibrahim Kara, Ana M. Casas, Ernesto Igartua, Giampiero Vale, Angela Roberta Lo Piero, Luigi Cattivelli, Alessandro Tondelli, Agostino Fricano
Summary: MAGIC lines have mosaic genomes generated by shuffling genetic material of founder parents, used for investigating genetic bases of traits in cereal crops. Genomic prediction models are usually fitted using unrelated accessions or individuals of biparental families. Empirical analyses showed that limited number of MAGIC lines can predict grain yield with values varying from 0.25 to 0.60, suggesting that the population can be used for training genomic prediction models.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Plant Sciences
Gayle M. Volk, Patrick F. Byrne, Clarice J. Coyne, Sherry Flint-Garcia, Patrick A. Reeves, Chris Richards
Summary: Plant genebanks provide genetic resources for breeding and research programs, with access to high-quality, standardized data being crucial. Advances in technology allow for collection of phenomic and genomic data, which can directly inform breeding programs. Consideration of homogeneity and heterogeneity in genebank collections during data collection and documentation is important for meeting the needs of plant genetic resource managers and users.
Review
Agronomy
Leon Muntean, Andreea Ona, Ioana Berindean, Ionut Racz, Sorin Muntean
Summary: Maize will continue to expand and diversify as an industrial resource and a feed and fuel crop, and genomics tools are essential for precise, fast, and efficient crop breeding in the face of climate challenges. Furthermore, genomic tools have the potential to accelerate the process of de novo domestication of maize.
Article
Fisheries
Cecile Massault, Cara Jeffrey, David B. Jones, Roger Barnard, Jan M. Strugnell, Kyall R. Zenger, Dean R. Jerry
Summary: This study validated the efficiency of using the swab technique to collect DNA for breeding programs of pearl oysters, and demonstrated that this method reliably collects sufficient quantity and quality of DNA for accurate pedigree reconstruction.
Article
Fisheries
P. McIntosh, L. T. Barrett, F. Warren-Myers, A. Coates, G. Macaulay, A. Szetey, N. Robinson, C. White, F. Samsing, F. Oppedal, O. Folkedal, P. Klebert, T. Dempster
Summary: Salmonid aquaculture has expanded globally in recent decades, with changes in cage technologies and locations. This study used satellite images to analyze the changes in cage size, location, and proximity to neighboring farms. The results showed that cage diameters have increased, leading to larger farms, while the distance to neighboring farms varied across regions. These changes have environmental and production consequences, emphasizing the importance of analyzing and improving management practices in salmon farming.
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
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)
Correction
Multidisciplinary Sciences
Roger Huerlimann, Nicholas M. Wade, Lavinia Gordon, Juan D. Montenegro, Jake Goodall, Sean McWilliam, Matthew Tinning, Kirby Siemering, Erika Giardina, Dallas Donovan, Melony J. Sellars, Jeff A. Cowley, Kelly Condon, Greg J. Coman, Mehar S. Khatkar, Herman W. Raadsma, Gregory E. Maes, Kyall R. Zenger, Dean R. Jerry
SCIENTIFIC REPORTS
(2022)
Article
Ecology
Donald T. McKnight, Roger Huerlimann, Deborah S. Bower, Lin Schwarzkopf, Ross A. Alford, Kyall R. Zenger
Summary: The bacterial and fungal microbiomes of four Australian frog species were examined to understand their role in infection dynamics. Both microbial communities were correlated, suggesting mutual influences. There was mixed evidence of associations between richness and the fungal disease, with high richness potentially providing protection.
Review
Fisheries
Nicholas A. Robinson, Diego Robledo, Lene Sveen, Rose Ruiz Daniels, Aleksei Krasnov, Andrew Coates, Ye Hwa Jin, Luke T. Barrett, Marie Lillehammer, Anne H. Kettunen, Ben L. Phillips, Tim Dempster, Andrea Doeschl-Wilson, Francisca Samsing, Gareth Difford, Sarah Salisbury, Bjarne Gjerde, John-Erik Haugen, Erik Burgerhout, Binyam S. Dagnachew, Dominic Kurian, Mark D. Fast, Morten Rye, Marcela Salazar, James E. Bron, Sean J. Monaghan, Celeste Jacq, Mike Birkett, Howard I. Browman, Anne Berit Skiftesvik, David M. Fields, Erik Selander, Samantha Bui, Anna Sonesson, Stanko Skugor, Tone-Kari Knutsdatter Ostbye, Ross D. Houston
Summary: Disease and parasitism pose significant challenges to global aquaculture, and genetic technologies offer potential solutions. Understanding genetic mechanisms, developing tools for boosting host resistance, and applying genetic technologies can improve disease resistance and transform aquaculture.
REVIEWS IN AQUACULTURE
(2023)
Article
Fisheries
Nga T. T. Vu, Dean R. Jerry, Richard C. Edmunds, David B. Jones, Kyall R. Zenger
Summary: This study introduces five low-density SNP panels for the giant black tiger shrimp, which can improve aquaculture practices and fishery management strategies by enhancing diversity, provenance, and pedigree determination.
Article
Biodiversity Conservation
Brooke L. L. Whitelaw, David B. B. Jones, Jarrod Guppy, Peter Morse, Jan M. M. Strugnell, Ira R. R. Cooke, Kyall Zenger
Summary: The study presents the first linkage map of a cephalopod species, H. maculosa, providing valuable insights into the evolution of cephalopod genomes.
Article
Fisheries
Susannah M. Leahy, Dean R. Jerry, Brett B. C. Wedding, Julie B. Robins, Carole L. Wright, Aleksey Sadekov, Stephen Boyle, David B. Jones, Samuel M. Williams, Steve Grauf, Luke Pavich, Mark McLennan, Michelle J. Sellin, Julie A. Goldsbury, Richard J. Saunders
Summary: Fish stocking is important for conservation, recreational fishing, and commercial fisheries. This study compared three methods, otolith microchemistry, genetic parentage analysis, and near-infrared spectroscopy (NIRS), for determining the provenance of barramundi in northern Australia. Otolith microchemistry had the highest accuracy (>99%), while genetic parentage analysis had a slightly lower accuracy (95%) due to genetic introgression. NIRS had the lowest overall accuracy (76%), but shows potential for cost-effective provenance determination with improvements.
CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES
(2023)
Article
Fisheries
Hunter S. Bailey, Ashley N. Fincannon, Lee A. Fuiman
Summary: This study investigated the transfer of fatty acids from broodstock diets to eggs and the time needed for the eggs to equilibrate to the diet in Southern flounder. The findings indicate that different diet treatments significantly affect the fatty acid composition of eggs, and it takes 8-16 weeks for the eggs to adapt to changes in the adult diet. These results are important for improving broodstock diets and feeding protocols in stock-enhancement programs.
Article
Fisheries
Yu Liu, Mingtao Lei, Hector Victor, Yan Wang
Summary: This study confirms the feasibility of replacing raw fish diet with a formulated diet in commercial farming of large yellow croaker, which can increase fish survival and yield, and reduce feed cost and body lipid deposition.
Article
Fisheries
Xiaoyan Zhang, Lize San, Yucong Yang, Yuehong Tao, Jiangong Ren, Yufeng Liu, Zhongwei He, Jiashuo Di, Ziteng Pei, Guixing Wang, Jilun Hou
Summary: Gynogenesis is an effective technique for establishing homogeneous lines and confirming potential chromosomal mechanisms of sex determination in fish. This study successfully induced gynogenetic families in Thamnaconus modestus and established a complete method for gynogenesis induction.
Article
Fisheries
Julieta C. Martinelli, Megan Considine, Helen R. Casendino, Carolyn M. Tarpey, Isadora Jimenez-Hidalgo, Jacqueline L. Padilla-Gamino, Teri L. King, Lorenz Hauser, Steven Rumrill, Chelsea L. Wood
Summary: Shell-boring polychaetes have caused significant damage to mariculture operations worldwide, particularly in the US Pacific region. This study provides a comprehensive dataset on the prevalence, species distribution, and environmental associations of these parasites, highlighting the impact of season, culturing methods, and environmental factors on infestation.
Article
Fisheries
Juan Gao, Xueshan Li, Kangle Lu, Kai Song, Jian Zhang, Ling Wang, Chunxiao Zhang
Summary: This study investigated the effects of dietary protein levels on growth performance, antioxidant capacity, digestive enzyme activity, and metamorphosis rate of bullfrog tadpoles. The optimal dietary protein level for bullfrog tadpoles was estimated to be 42.49%-46.50% of the diet.
Article
Fisheries
Qiang Li, Lijun Duan, Dongsheng Jin, Yuxin Chen, Yirong Lou, Qianjin Zhou, Zhongjie Xu, Fangjie Chen, Hongxian Chen, Guizong Xu, Maocang Yan, Guanjun Yang, Jianfei Lu, Yanjun Zhang, Jiong Chen
Summary: This study developed a centrifugal microfluidic chip with on-chip RPA to detect five pathogenic microorganisms. The chip enabled the parallel analysis of six genetic markers from a single sample and allowed for the highly automated detection of multiple samples. Compared with PCR and DNA sequencing, the on-chip RPA assay showed high sensitivity and specificity for detecting multiple pathogens in shrimp aquaculture.
Article
Fisheries
Xingchen Huo, Pengxu Wang, Fengxia Zhao, Qian Liu, Qingqing Tian, Lingjie Tang, Maolin Lv, Zhaohui Wei, Chunrong Yang, Jianguo Su
Summary: Bacterial diseases in aquaculture ponds have negative effects on sustainable development. The use of composite I20 biotherapy has been shown to effectively treat bacterial diseases in bullfrog ponds, providing a new strategy for controlling bacterial diseases in aquaculture.
Article
Fisheries
Peng Yin, Takaya Saito, Per Gunnar Fjelldal, Bjorn Tharandur Bjornsson, Sofie Charlotte Remo, Sandeep Sharma, Rolf Erik Olsen, Kristin Hamre
Summary: This study aims to investigate the effect of seasonal changes in temperature and photoperiod on the redox metabolism of Atlantic salmon at the molecular level. The research findings suggest that the changing photoperiod and temperature influenced the redox metabolism of Atlantic salmon, highlighting the importance of oxidative status in the ecological implications.
Article
Fisheries
Nicholas Oppong Mensah, Jeffery Kofi Asare, Emmanuel Tetteh-Doku Mensah, Ernest Christlieb Amrago, Frank Osei Tutu, Anthony Donkor
Summary: This study investigates aquaculture farmers' preference for climate-smart aquaculture insurance products, the challenges they face, and their preferred insurance coverage. The results show that farmers prefer Climate-Induced Aquaculture Stock Mortality Insurance and the most significant constraint is the delay in claim settlement.
Article
Fisheries
Qiu-Ping Chai, Pei Wu, Wei-Dan Jiang, Yang Liu, Hong-Mei Ren, Xiao-Wan Jin, Lin Feng, Xiao-Qiu Zhou
Summary: The study found that appropriate levels of potassium diformate (KDF) can enhance the immune defense and mediate the inflammatory process in fish, possibly through the regulation of T cell differentiation via JAK-STAT and NF-kappa B signaling pathways.
Article
Fisheries
Tian Zhu, Haomin Jia, Haopeng Zhang, Yujing Xiao, Cui Han, Jiaxin Yang
Summary: Chicken manure has significant effects on the cultivation of Chlorella and rotifers. The optimal amount of chicken manure extract for continuous cultivation is 10 mLL-1. Chicken manure can promote the growth of Chlorella and improve the fatty acid composition, indirectly enhancing the growth condition and fatty acid content of rotifers.
Article
Fisheries
Zheng Luo, Yang Yu, Zhenning Bao, Fuhua Li
Summary: This study analyzed the heritability and genetic correlation of two growth traits in Pacific white shrimp and evaluated the genomic prediction using different genomic selection models. The results showed that the NeuralNet model had the highest prediction accuracy and better prospects for predicting shrimp growth traits.
Article
Fisheries
Alberto Ruiz, Ignasi Sanahuja, Karl B. Andree, Dolors Furones, Paul G. Holhorea, Josep A. Calduch-Giner, Jose J. Pastor, Marc Vinas, Jaume Perez-Sanchez, Sofia Morais, Enric Gisbert
Summary: Supplementing diets with a combination of spice oleoresins can reduce lipid accumulation and inflammation in farmed fish. The combination of spice oleoresins also has an immunomodulatory effect on the fish's intestinal immune system, potentially offering anti-inflammatory benefits.
Article
Fisheries
Beibei Zhao, Renhui Mei, Le Li, Di Hu, Lei Li
Summary: This study reveals that JfCXCL8_L1a and JfCXCL8_L1b have different immune pathways, and JfCXCL8_L1b plays a significant role in enhancing the adaptive immunity of T cell-dependent antigen.
Article
Fisheries
Yuhang Liu, Danying Cao, Nan Wu, Xuyang Zhao, Qingsong Zhu, Lian Su, Fatima Altaf, Qianqian Zhang, Haokun Liu, Yongming Li, Bruno Hamish Unger, Yingyin Cheng, Wanting Zhang, Aihua Li, Yaping Wang, Xiao-Qin Xia
Summary: Based on previous research, sinomenine has been found to protect mucosal immunity in farmed fish species by preventing intestinal pathological changes and regulating gene expression related to inflammation. It also enhances immune homeostasis and controls the growth of pathogenic bacteria.