Forestry researchPub Date : 2022-03-31eCollection Date: 2022-01-01DOI: 10.48130/FR-2022-0004
Xiangyang Kang, Hairong Wei
{"title":"Breeding polyploid <i>Populus</i>: progress and perspective.","authors":"Xiangyang Kang, Hairong Wei","doi":"10.48130/FR-2022-0004","DOIUrl":"https://doi.org/10.48130/FR-2022-0004","url":null,"abstract":"<p><p><i>Populus</i> is a genus of 25-30 species of deciduous flowering plants in the family Salicaceae, which are primarily planted in short-rotation planations for producing timber, pulpwood, wooden products as well as bioenergy feedstock; they are also widely planted in agricultural fields and along roadsides as shelter forest belts for windbreak, decoration, and reduction of pollutants and noise. Moreover, their fast-growth and good adaptation to marginal lands enable them to provide some critical ecosystem services at various phytoremediation sites for land restoration and reclaimation. Thanks to their important roles, breeding for fast growing poplar trees has been one of the most important objectives for nearly a century. One of the most demonstrated, documented achievements in this aspect is polyploid breeding, especially triploid breeding. This paper critically reviews the various techniques used in inducing triploid plants, including natural 2n formation, artificial induction of 2n male and female gemmates through chemical or physical treatments, trait characterization of the triploid and tetraploid breeding populations, unveiling the molecular mechanisms underpinning the significantly improved traits, and identification and selection of the best triploid progenies. This review also recapitulated the challenges and strategies facing the future of triploid breeding in <i>Populus</i>, including amelioration of 2n gamete induction techniques and efficiency, selection of the best parents and identification of the best progrenies, utilization of the huge amount of genomic, transcriptomic, proteomic, metabolomic, and other omics data for selecting parents for improving target traits.</p>","PeriodicalId":520285,"journal":{"name":"Forestry research","volume":"2 ","pages":"4"},"PeriodicalIF":0.0,"publicationDate":"2022-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11524227/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142635528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Forestry researchPub Date : 2021-06-24eCollection Date: 2021-01-01DOI: 10.48130/FR-2021-0010
Fuqiang Cui, Yifan Yang, Mengyuan Ye, Wei Wei, Wenqian Huang, Ying Wu, Xi Jiao, Xiaoxue Ye, Shutong Zhou, Zhubing Hu, Yinhai Zhang, Renyi Gui, Wenwu Wu, Kim Yrjälä, Kirk Overmyer, Shenkui Liu
{"title":"Case study of a rhizosphere microbiome assay on a bamboo rhizome with excessive shoots.","authors":"Fuqiang Cui, Yifan Yang, Mengyuan Ye, Wei Wei, Wenqian Huang, Ying Wu, Xi Jiao, Xiaoxue Ye, Shutong Zhou, Zhubing Hu, Yinhai Zhang, Renyi Gui, Wenwu Wu, Kim Yrjälä, Kirk Overmyer, Shenkui Liu","doi":"10.48130/FR-2021-0010","DOIUrl":"https://doi.org/10.48130/FR-2021-0010","url":null,"abstract":"<p><p>Young moso bamboo shoots are a popular seasonal food and an important source of income for farmers, with value for cultivation estimated at $30,000 per hectare. Bamboo also has great environmental importance and its unique physiology is of scientific interest. A rare and valuable phenomenon has recently appeared where a large number of adjacent buds within a single moso bamboo rhizome have grown into shoots. Although of practical importance for the production of edible shoots, such occurrences have not been scientifically studied, due to their rarity. Analysis of collected reports from enhanced shoot production events in China showed no evidence that enhanced shoot development was heritable. We report the analysis of the rhizosphere microbiome from a rhizome with 18 shoots, compared to rhizomes having one or no shoots as controls. The community of prokaryotes, but not fungi, correlated with the shoot number. <i>Burkholderia</i> was the most abundant genus, which was negatively correlated with rhizome shoot number, while <i>Clostridia</i> and <i>Ktedonobacteria</i> were positively correlated. Two <i>Burkholderia</i> strains were isolated and their plant-growth promoting activity was tested. The isolated <i>Burkholderia</i> strains attenuated the growth of bamboo seedlings. These data provide the first study on excessive shoot development in bamboo, which will facilitate hypothesis building for future studies.</p>","PeriodicalId":520285,"journal":{"name":"Forestry research","volume":"1 ","pages":"10"},"PeriodicalIF":0.0,"publicationDate":"2021-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11524271/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142635519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Forestry researchPub Date : 2021-03-30eCollection Date: 2021-01-01DOI: 10.48130/FR-2021-0006
Wenping Deng, Kui Zhang, Cheng He, Sanzhen Liu, Hairong Wei
{"title":"HB-PLS: A statistical method for identifying biological process or pathway regulators by integrating Huber loss and Berhu penalty with partial least squares regression.","authors":"Wenping Deng, Kui Zhang, Cheng He, Sanzhen Liu, Hairong Wei","doi":"10.48130/FR-2021-0006","DOIUrl":"https://doi.org/10.48130/FR-2021-0006","url":null,"abstract":"<p><p>Gene expression data features high dimensionality, multicollinearity, and non-Gaussian distribution noise, posing hurdles for identification of true regulatory genes controlling a biological process or pathway. In this study, we integrated the Huber loss function and the Berhu penalty (HB) into partial least squares (PLS) framework to deal with the high dimension and multicollinearity property of gene expression data, and developed a new method called HB-PLS regression to model the relationships between regulatory genes and pathway genes. To solve the Huber-Berhu optimization problem, an accelerated proximal gradient descent algorithm with at least 10 times faster than the general convex optimization solver (CVX), was developed. Application of HB-PLS to recognize pathway regulators of lignin biosynthesis and photosynthesis in <i>Arabidopsis thaliana</i> led to the identification of many known positive pathway regulators that had previously been experimentally validated. As compared to sparse partial least squares (SPLS) regression, an efficient method for variable selection and dimension reduction in handling multicollinearity, HB-PLS has higher efficacy in identifying more positive known regulators, a much higher but slightly less sensitivity/(1-specificity) in ranking the true positive known regulators to the top of the output regulatory gene lists for the two aforementioned pathways. In addition, each method could identify some unique regulators that cannot be identified by the other methods. Our results showed that the overall performance of HB-PLS slightly exceeds that of SPLS but both methods are instrumental for identifying real pathway regulators from high-throughput gene expression data, suggesting that integration of statistics, machine leaning and convex optimization can result in a method with high efficacy and is worth further exploration.</p>","PeriodicalId":520285,"journal":{"name":"Forestry research","volume":"1 ","pages":"6"},"PeriodicalIF":0.0,"publicationDate":"2021-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11524267/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142635523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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