{"title":"Using Bayesian threshold model and machine learning method to improve the accuracy of genomic prediction for ordered categorical traits in fish","authors":"Hailiang Song, Tian Dong, Xiaoyu Yan, Wei Wang, Zhaohui Tian, Hongxia Hu","doi":"10.1016/j.agrcom.2023.100005","DOIUrl":"https://doi.org/10.1016/j.agrcom.2023.100005","url":null,"abstract":"<div><p>Ordered categorical traits are commonly used in fish breeding programs as they are easier to obtain than continuous observations. However, most studies treat ordered categorical traits as linear traits and analyze them using linear models, which can lead to a serious reduction in prediction accuracy by violating the basic assumptions of linear models. The aim of this study was to evaluate the advantages of Bayesian threshold model and machine learning method in genomic prediction of ordered categorical traits in fish. The study was based on the analyses of simulated data and real data of Atlantic salmon. Ordinal categorical traits were simulated with varying numbers of categories (2, 3 and 4) and levels of heritabilities (0.1, 0.3 and 0.5). Linear and threshold models with BayesA and BayesCπ methods, as well as a machine learning method, support vector regression with default (SVRdef) and tuning (SVRtuning) hyperparameters were used to investigate their prediction abilities. The results showed that Bayesian threshold models yielded 2.1%, 2.6% and 2.9% higher prediction accuracies on average for 2-, 3- and 4-category traits, respectively, than Bayesian linear models. Furthermore, SVRtuning produced higher prediction accuracy compared with SVRdef and Bayesian threshold models in all scenarios. For real data, Bayesian threshold models yielded 1.2% higher prediction accuracy than Bayesian linear models, and SVRdef and SVRtuning yielded 3.3% and 6.6% higher prediction accuracies than Bayesian methods, respectively. In conclusion, the use of Bayesian threshold model and machine learning method was beneficial for genomic prediction of ordered categorical traits in fish.</p></div>","PeriodicalId":100065,"journal":{"name":"Agriculture Communications","volume":"1 1","pages":"Article 100005"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49720528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Superoxide dismutase promotes early flowering in Triticum aestivum L.","authors":"Hao-yu Guo , Yong-jie Liu , Shao-hua Yuan , Jie-ru Yue, Yan-mei Li, Xiang-zheng Liao, Sheng-kai Ying, Zi-han Liu, Jian-fang Bai, Li-ping Zhang","doi":"10.1016/j.agrcom.2023.100007","DOIUrl":"https://doi.org/10.1016/j.agrcom.2023.100007","url":null,"abstract":"<div><p>Superoxide dismutase (SOD) is a first-line-defense antioxidant enzyme that plays a crucial role in scavenging reactive oxygen species (ROS) to maintain homeostasis in plants. SOD catalyzes the conversion of superoxide (O<sub>2</sub><sup>-</sup>) into oxygen (O<sub>2</sub>) and hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>), and besides its role in stress resistance, SOD also impacts plant growth and development. Here, we cloned and characterized a <em>TaCSOD</em> gene from the wheat photo-thermosensitive genic male sterile line BS366. Phylogenetic and motif analyses identified <em>TaCSOD</em> as a Cu/Zn-dependent SOD due to the presence of conserved Cu<sup>2+</sup> and Zn<sup>2+</sup> binding sites. Overexpression of <em>TaCSOD</em> enhanced drought and salt tolerance in both <em>Arabidopsis thaliana</em> and yeast. In addition, seed germination rate, primary root length, and fresh weight of the transgenic plants were higher than those of the wild-type under drought- and salt-stressed conditions. The <em>Arabidopsis TaCSOD</em> overexpression lines also exhibited an early flowering phenotype, with fewer leaves and shorter flowering period. Nitroblue tetrazolium (NBT) and 3, 3-diaminobenzidine (DAB) staining, along with transcriptome analysis, demonstrated that <em>TaCSOD</em> regulates ROS homeostasis and flowering time through carbohydrate signaling, aging, vernalization, and gibberellic acid pathways. Our study provides valuable insights into the functions of <em>SOD</em> genes in regulating flowering through the regulation of ROS homeostasis in plants.</p></div>","PeriodicalId":100065,"journal":{"name":"Agriculture Communications","volume":"1 1","pages":"Article 100007"},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49720464","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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