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{"title":"Progress on Z genome biosynthetic pathway of bacteriophage.","authors":"Hui-Yu Chen,&nbsp;Su-Wen Zhao","doi":"10.16288/j.yczz.23-059","DOIUrl":"10.16288/j.yczz.23-059","url":null,"abstract":"<p><p>There are abundant base modifications in bacteriophages' genomes, mainly for avoiding the digestion of host endonucleases. More than 40 years ago, researchers discovered that 2-amino-adenine (Z) completely replaced adenine (A) and forms a complementary pairing with three hydrogen bonds with thymine (T) in the DNA of cyanophage S-2L, forming a distinct \"Z-genome\". In recent years, researchers have discovered and validated the biosynthetic pathway of Z-genome in various bacteriophages, constituting a multi-enzyme system. This system includes the phage-encoded enzymes deoxy-2'-aminoadenylosuccinate synthetase (PurZ), deoxyadenosine triphosphate hydrolase (dATPase/DatZ), deoxyadenosine/deoxyguanosine triphosphate pyrophosphatase (DUF550/MazZ) and DNA polymerase (DpoZ). In this review, we provide a concise overview of the historical discovery on diversely modified nucleosides in bacteriophages, then we comprehensively summarize the research progress on multiple enzymes involved in the Z-genome biosynthetic pathway. Finally, the potential applications of the Z-genome and the enzymes in its biosynthetic pathway are discussed in order to provide reference for research in this field.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49692791","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":"Rapid analyzing mixed STR profiles based on the global minimum residual method.","authors":"Xin Li,&nbsp;Hong Fan,&nbsp;Xing-Chun Zhao,&nbsp;Xiao-Nuo Fan,&nbsp;Ruo-Xia Yao","doi":"10.16288/j.yczz.23-101","DOIUrl":"10.16288/j.yczz.23-101","url":null,"abstract":"<p><p>The analysis of mixed short tandem repeat (STR) profiles has been long considered as a difficult challenge in the forensic DNA analysis. In the context of China, the current approach to analyze mixed STR profiles depends mostly on forensic manual method. However, besides the inefficiency, this technique is also susceptible to subjective biases in interpreting analysis results, which can hardly meet up with the growing demand for STR profiles analysis. In response, this study introduces an innovative method known as the global minimum residual method, which not only predicts the proportion of each contributor within a mixture, but also delivers accurate analysis results. The global minimum residual method first gives new definitions to the mixture proportion, then optimizes the allele model. After that, it comprehensively considers all loci present in the STR profile, accumulates and sums the residual values of each locus and selects the mixture proportion with the minimum accumulative sum as the inference result. Furthermore, the grey wolf optimizer is also employed to expedite the search for the optimal value. Notably, for two-person STR profiles, the high accuracy and remarkable efficiency of the global minimum residual method can bring convenience to realize extensive STR profile analysis. The optimization scheme established in this research has exhibited exceptional outcomes in practical applications, boasting significant utility and offering an innovative avenue in the realm of mixed STR profile analysis.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49692792","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":"Genomic prediction of pig growth traits based on machine learning.","authors":"Chen Dong,&nbsp;Wang Shu-Jie,&nbsp;Zhao Zhen-Jian,&nbsp;Ji Xiang,&nbsp;Shen Qi,&nbsp;Yu Yang,&nbsp;Cui Sheng-di,&nbsp;Wang Jun-Ge,&nbsp;Chen Zi-Yang,&nbsp;Wang Jin-Yong,&nbsp;Guo Zong-Yi,&nbsp;Wu Ping-Xian,&nbsp;Tang Guo-Qing","doi":"10.16288/j.yczz.23-120","DOIUrl":"10.16288/j.yczz.23-120","url":null,"abstract":"<p><p>This study aimed to assess and compare the performance of different machine learning models in predicting selected pig growth traits and genomic estimated breeding values (GEBV) using automated machine learning, with the goal of optimizing whole-genome evaluation methods in pig breeding. The research employed genomic information, pedigree matrices, fixed effects, and phenotype data from 9968 pigs across multiple companies to derive four optimal machine learning models: deep learning (DL), random forest (RF), gradient boosting machine (GBM), and extreme gradient boosting (XGB). Through 10-fold cross-validation, predictions were made for GEBV and phenotypes of pigs reaching weight milestones (100 kg and 115 kg) with adjustments for backfat and days to weight. The findings indicated that machine learning models exhibited higher accuracy in predicting GEBV compared to phenotypic traits. Notably, GBM demonstrated superior GEBV prediction accuracy, with values of 0.683, 0.710, 0.866, and 0.871 for B100, B115, D100, and D115, respectively, slightly outperforming other methods. In phenotype prediction, GBM emerged as the best-performing model for pigs with B100, B115, D100, and D115 traits, achieving prediction accuracies of 0.547, followed by DL at 0.547, and then XGB with accuracies of 0.672 and 0.670. In terms of model training time, RF required the most time, while GBM and DL fell in between, and XGB demonstrated the shortest training time. In summary, machine learning models obtained through automated techniques exhibited higher GEBV prediction accuracy compared to phenotypic traits. GBM emerged as the overall top performer in terms of prediction accuracy and training time efficiency, while XGB demonstrated the ability to train accurate prediction models within a short timeframe. RF, on the other hand, had longer training times and insufficient accuracy, rendering it unsuitable for predicting pig growth traits and GEBV.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49692787","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":"Progress on lysosomal PPT1-mediated regulation of cellular homeostasis and pathogenesis.","authors":"Xin-Yi Zhou,&nbsp;Dong Chang,&nbsp;Huang-Ying Xu,&nbsp;Rui-Qi Guan,&nbsp;Cheng-Hao Yan,&nbsp;Qiu-Yuan Yin,&nbsp;Jian-Wei Sun","doi":"10.16288/j.yczz.23-186","DOIUrl":"10.16288/j.yczz.23-186","url":null,"abstract":"<p><p>Palmitoyl protein thioesterase 1(PPT1) is a lysosomal enzyme that catalyzes the protein depalmitoylation. It is considered to play a crucial role in regulating lysosomes, mitochondria and lipid metabolism. PPT1 has been reported to play an important role in the occurrence and progression of diseases, such as neurological diseases and cancers. However, the regulatory mechanisms remain unknown. In this review, we summarize the progress of PPT1 function and mechanisms in neurological disorders and cancers, which will provide as reference and guidance for exploring the regulatory mechanisms of PPT1 and developing new drugs for treating related diseases in the future.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49692790","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":"Autotetraploid rice: challenges and opportunities.","authors":"Xiang-Dong Liu,&nbsp;Jin-Wen Wu,&nbsp;Zi-Jun Lu,&nbsp;Muhammad Qasim Shahid","doi":"10.16288/j.yczz.23-074","DOIUrl":"https://doi.org/10.16288/j.yczz.23-074","url":null,"abstract":"<p><p>Autotetraploid rice is a type of germplasm developed from the whole genome duplication of diploid rice, leading to large grains, high nutrient content, and resistance. However, its low fertility has reduced yield and hampered commercialization. To address this issue, a new type of high fertility tetraploid rice was developed, which may serve as a useful germplasm for polyploid rice breeding. In this review, we summarize the progress made in understanding the cellular and molecular genetic mechanisms underlying the low fertility of autotetraploid rice and its F₁ hybrid, as well as the main types of new tetraploid rice with high fertility. Lastly, the idea of utilizing the multi-generation heterosis of neo-tetraploid rice in the future is proposed as a reference for polyploid rice breeding.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41131512","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":"<i>De novo</i> domestication: a new way for crop design and breeding.","authors":"Liu-Mei Jian,&nbsp;Ying-Jie Xiao,&nbsp;Jian-Bing Yan","doi":"10.16288/j.yczz.23-194","DOIUrl":"https://doi.org/10.16288/j.yczz.23-194","url":null,"abstract":"<p><p>The impending global climate change presents significant challenges to agricultural production. It is imperative to find approaches to ensure sustained growth in food production while reducing agricultural input, in order to meet the needs of worldwide people for nutritious food supply. One of the effective strategies to address this challenge is still the development of new crop varieties with high yield, stable yield, environmental friendliness and rich nutrition. The creation of new crop cultivars depends largely on the expansion of genetic resources and the innovation of breeding techniques. <i>De novo</i> domestication is an innovative breeding strategy for developing new crop varieties. It involves utilizing undomesticated or semi-domesticated plants with desirable traits as founder species for breeding. The process involves rapid domestication of wild plants through the redesign of agronomic traits and the introduction of domestication genes to meet diverse human needs. In this review, we overview the history of crop domestication and genetic improvement, clarify the necessity of enriching crop diversity, and emphasize the significance of wild plants' genetic diversity in expanding the scope for crop redesign. Breeding strategy innovation is the key to accelerate crop breeding. We also discuss the feasibility and prospects of rapid developing new crops through <i>de novo</i> domestication.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41159576","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":"The biological functions of peptide signaling in plant and the advances on its utilization for crop improvement.","authors":"Qian-Wen Lv,&nbsp;Yong-Fang Yang","doi":"10.16288/j.yczz.23-169","DOIUrl":"https://doi.org/10.16288/j.yczz.23-169","url":null,"abstract":"As the important signaling molecules in plants, peptides at femtomolar levels are recognized and bound by the corresponding plasma membrane-localized receptor-like kinases. This triggers the peptide-receptor-mediated intercellular signal transduction for regulation of the stem cell growth and proliferation, modulation of the development of plant organs (such as roots, stems, leaves, flowers, and fruits) as well as coordinating plant responses to biotic and abiotic stresses. With the advancement of in-depth research, an increasing number of studies have revealed the crucial role of peptides in regulating agronomic traits of various crops, including rice (Oryza sativa), maize (Zea mays), potato (Solanum tuberosum) and tomato (Solanum lycopersicum). These findings suggest the great potentials of utilizing the peptide signaling for genetic improvement of crops. In this review, we provide a comprehensive overview of the biological function and molecular mechanism of peptide-receptor signaling in plants, and highlight the advances in research of peptides in regulating crop yield, quality and resistance. Then, we discuss the strategies for the application of peptide signaling in crop improvement. Finally, we point out some future directions for peptide research in plant.","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41164609","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":"Revelation of rice molecular design breeding: the blend of tradition and modernity.","authors":"Zhong Bian,&nbsp;Dong-Ping Cao,&nbsp;Wen-Shu Zhuang,&nbsp;Shu-Wei Zhang,&nbsp;Qiao-Quan Liu,&nbsp;Lin Zhang","doi":"10.16288/j.yczz.23-092","DOIUrl":"https://doi.org/10.16288/j.yczz.23-092","url":null,"abstract":"<p><p>As one of the major staple crops, rice feeds more than one half of the world population. Due to increasing population and dramatic climate change, the rice varieties with higher yield performance and excellent overall agronomic performance should be developed. The raise of molecular design breeding concept provides opportunity to get new breakthrough for variety development, and it is important to clarify the efficient gene combination during actual breeding. In this review, we summarize the recent advances about rice variety improvement either by marker assisted selection (MAS) breeding or popular gene editing technique, which will be beneficial to understand different aspects of the molecular design breeding. We provide genetic views for the classical MAS application, including the genetic effect of key genes and their combinations, the recurrent genome recovery rate at different backcross generations, linkage drag and recombination selection. Moreover, we compare the breeding value of recently-developed molecular techniques, including the advantage of high-throughput genotyping and the way and effect of gene editing in creating useful traits. Considering the current status and actual demands of rice breeding, we raise the strategy to take advantages of both traditional breeding resources and popular molecular techniques, which might pave the way to optimize the process of molecular design breeding in future.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41177104","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":"Application value of protein phase separation mechanism of flowering regulation in <i>de novo</i> domestication.","authors":"Lu-Yan Tian,&nbsp;Xiao-Zhen Huang","doi":"10.16288/j.yczz.23-165","DOIUrl":"https://doi.org/10.16288/j.yczz.23-165","url":null,"abstract":"<p><p>Global climate change and population growth pose a serious threat to world food security. The current crops varieties will be insufficient to meet food needs in the future, and there is an urgent need for high yielding and quality crops varieties with strong environmental adaptability. The rapid <i>de novo</i> domestication of wild species to create new germplasm that can be applied to crop breeding is a new strategy for ensuring food security. The flowering time is an important factor in determining the crop planting area and yield, and is a trait that is often selected in crop domestication. At present, the modification of flowering traits by <i>de novo</i> domestication is usually achieved by direct editing of the major genes that control flowering in crop, which are very limited in number and relatively homogeneous in function. Floral transition is regulated by the complex network of environmental and endogenous signals. Here, we propose a new strategy that using genome editing to precisely modify protein function by changing protein phase separation capacity of important proteins that regulate expression of flowering genes, which may provide new options for the design of flowering traits in <i>de novo</i> domestication.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41180126","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":"<i>qGL3.4</i> controls kernel size and plant architecture in rice.","authors":"Zhen-Wu Zheng,&nbsp;Hong-Yuan Zhao,&nbsp;Xiao-Ya Liang,&nbsp;Yi-Jun Wang,&nbsp;Chi-Hang Wang,&nbsp;Gao-Yan Gong,&nbsp;Jin-Yan Huang,&nbsp;Gui-Quan Zhang,&nbsp;Shao-Kui Wang,&nbsp;Zu-Pei Liu","doi":"10.16288/j.yczz.23-064","DOIUrl":"https://doi.org/10.16288/j.yczz.23-064","url":null,"abstract":"<p><p>Kernel size and plant architecture play important roles in kernel yield in rice. Cloning and functional study of genes related to kernel size and plant architecture are of great significance for breeding high-yield rice. Using the single-segment substitution lines which developed with <i>Oryza barthii</i> as a donor parent and an elite <i>indica</i> cultivar Huajingxian74 (HJX74) as a recipient parent, we identified a novel QTL (quantitative trait locus), named <i>qGL3.4</i>, which controls kernel size and plant architecture. Compared with HJX74, the kernel length, kernel width, 1000-kernel weight, panicle length, kernels per plant, primary branches, yield per plant, and plant height of near isogenic line-<i>qGL3.4</i> (NIL-<i>qGL3.4</i>) are increased, whereas the panicles per plant and secondary branches per panicle of NIL-<i>qGL3.4</i> are comparable to those of HJX74. <i>qGL3.4</i> was narrowed to a 239.18 kb interval on chromosome 3. Cell analysis showed that NIL-<i>qGL3.4</i> controlled kernel size by regulating cell growth. <i>qGL3.4</i> controls kernel size at least in part through regulating the transcription levels of <i>EXPANSINS</i>, <i>GS3</i>, <i>GL3.1</i>, <i>PGL1</i>, <i>GL7</i>, <i>OsSPL13</i> and <i>GS5</i>. These results indicate that <i>qGL3.4</i> might be beneficial for improving kernel yield and plant architecture in rice breeding.</p>","PeriodicalId":35536,"journal":{"name":"Yi chuan = Hereditas / Zhongguo yi chuan xue hui bian ji","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41131511","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}