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Opportunities and challenges in studies of mammalian hybrid speciation

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Science China(Life Sciences) 2024年第3期67卷 614-617页

作者： Hong Wu Yuxing Zhang Li Yu State key laboratory for conservation and utilization of Bio-Resource in Yunnan School of Life SciencesYunnan UniversityKunming 650091China

Revealing the mechanisms of speciation remains one of the most attractive and challenging issues in the field of evolutionary biology, and is also key to understanding the biodiversity present in nature.

关键词： biodiversity attractive evolutionary

Soil conditioners improve Cd-contaminated farmland soil microbial communities to inhibit Cd accumulation in rice

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Journal of Integrative Agriculture 2023年第8期22卷 2521-2535页

作者： ZHAO Jun-yang LU Hua-ming QIN Shu-tao PAN Peng TANG Shi-de CHEN Li-hong WANG Xue-li TANG Fang-yu TAN Zheng-long WEN Rong-hui HE Bing State key laboratory for conservation and utilization of Subtropical Agro-Bioresources/guangxi key laboratory of Agro-Environment and Agric-Products Safety College of AgricultureGuangxi UniversityNanning 530004P.R.China College of Life Science and Technolegy Guangxi UniversityNanning 530004P.R.China guangxi Liyuanbao Science and Technology Co. Ltd.Guangxi Zhuang Autonomous RegionNanning 530004P.R.China

The addition of silicon(Si)and organic fertilizers to soil conditioners can inhibit the transfer of heavy metal ions from soil to ***,it is not clear how Si and organic fertilizers affect soil properties and the micro-ecological environment and thereby reduce cadmium(Cd)accumulation in *** this study,the effects of L-type soil conditioners containing Si and organic fertilizers on bacterial and fungal community diversity,soil pH,organic matter,and available Si were analyzed with field experiments at two sites in Liuzhou City and Hezhou City,respectively,in guangxi,*** the increase of Si and organic fertilizer content in soil conditioner,rice yield respectively increased by 16.8–25.8 and 6.8–13.1%,and rice Cd content decreased significantly by 8.2–21.1 and 10.8–40.6%,respectively,at the two experimental *** microbiome analysis showed that the increase in abundance of Firmicutes and Actinobacteriota bacteria associated with Cd adsorption and sequestration,and Basidiomycota fungal populations associated with degradation of macromolecules favored the inhibition of soil Cd activity(soil exchangeable Cd decreased by 14.4–14.8 and 18.1–20.6%).This was associated with an increase in organic matter and Si content caused by applying soil *** conclusion,L-type soil conditioners,rich in Si and organic fertilizer,can reduce soil Cd bioavailability by regulating the dominant Cd passivating flora in the soil and ultimately reduce Cd accumulation in rice.

关键词： soil conditioner silicon organic matter microbial community Cd accumulation in rice

Target chromosome-segment substitution: A way to breeding by design in rice

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The Crop Journal 2021年第3期9卷 658-668页

作者： Guiquan Zhang Guangdong Provincial key laboratory of Plant Molecular Breeding State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesSouth China Agricultural UniversityGuangzhou 510642GuangdongChina

Progress in plant breeding depends on the development of genetic resources,genetic knowledge,and breeding *** core of plant breeding is the use of naturally occurring *** the beginning of the post-genomic era,a new concept of"breeding by design"was proposed,which aims to control all allelic variation for all genes of agronomic *** the past two decades,we have applied a three-step strategy for research on rice breeding by *** the first step,we constructed a singlesegment substitution line(SSSL)library using Huajingxian 74(HJX74),an elite xian(indica)rice cultivar,as the recipient in which to assemble genes from the rice AA *** the second step,we identified a series of desirable genes in the SSSL *** the third step,we designed new rice lines,and achieved the breeding goals by pyramiding target genes in the HJX74-SSSL *** review introduces the background,concept,and strategy of breeding by design,as well as our achievements in rice breeding by design using the HJX74-SSSL *** practice shows that target chromosome-segment substitution is a way to breeding by design.

关键词： Gene pool Chromosome-segment substitution Breeding by design Breeding platform Rice

Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape

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Journal of Integrative Plant Biology 2024年第7期66卷 1408-1426页

作者： Tianhao Zhang Wenjing Peng Hua Xiao Shuo Cao Zhuyifu Chen Xiangnian Su Yuanyuan Luo Zhongjie Liu Yanling Peng Xiping Yang Guo-Feng Jiang Xiaodong Xu Zhiyao Ma Yongfeng Zhou National key laboratory of Tropical Crop Breeding Shenzhen BranchGuangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Synthetic BiologyMinistry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518000China State key laboratory for conservation and utilization of Subtropical Agro‐Bioresources Guangxi UniversityNanning 530004China guangxi key laboratory of Forest Ecology and conservation Guangxi Colleges and Universities Key Laboratory for Cultivation and Utilization of Subtropical Forest PlantationCollege of ForestryGuangxi UniversityNanning 530004China College of Informatics Huazhong Agricultural UniversityWuhan 430070China guangxi key laboratory of Sugarcane Biology College of AgricultureGuangxi UniversityNanning 530004China key laboratory of Horticultural Plant Biology Ministry of Education Huazhong Agricultural UniversityWuhan 430070China Zhengzhou Fruit Research Institute Chinese Academy of Agricultural SciencesZhengzhou 450009China National key laboratory of Tropical Crop Breeding Tropical Crops Genetic Resources InstituteChinese Academy of Tropical Agricultural SciencesHaikou 571101China

Structural variations(SVs)are a feature of plant genomes that has been largely unexplored despite their significant impact on plant phenotypic traits and local adaptation to abiotic and biotic *** this study,we employed woolly grape(Vitis retordii),a species native to the tropical and subtropical regions of East Asia with both coastal and inland habitats,as a valuable model for examining the impact of SVs on local *** assembled a haplotype-resolved chromosomal reference genome for woolly grape,and conducted population genetic analyses based on whole-genome sequencing(WGS)data from coastal and inland *** demographic analyses revealed recent bottlenecks in all populations and asymmetric gene flow from the inland to the coastal *** total,1,035 genes associated with plant adaptive regulation for salt stress,radiation,and environmental adaptation were detected underlying local selection by SVs and SNPs in the coastal population,of which 37.29% and 65.26% were detected by SVs and SNPs,*** genes such as FSD2,RGA1,and AAP8 associated with salt tolerance were found to be highly differentiated and selected during the process of local adaptation to coastal habitats in SV *** study highlights the importance of SVs in local adaptation;candidate genes related to salt stress and climatic adaptation to tropical and subtropical environments are important genomic resources for future breeding programs of grapevine and its rootstocks.

关键词： climate change grape breeding local adaptation with gene flow salt tolerance viticulture Vitis

Safety assessment of a novel marine multi-stress-tolerant yeast Meyerozyma guilliermondii GXDK6 according to phenotype and whole genome-sequencing analysis

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Food Science and Human Wellness 2024年第4期13卷 2048-2059页

作者： Xueyan Mo Mengcheng Zhou Yanmei Li Lili Yu Huashang Bai Peihong Shen Xing Zhou Haojun Zhu Huijie Sun Ru Bu Chengjian Jiang State key laboratory for conservation and utilization of Subtropical Agro-Bioresources Guangxi Research Center for Microbial and Enzyme Engineering TechnologyCollege of Life Science and TechnologyGuangxi UniversityNanning 530004China National Engineering Research Center for Non-Food Biorefinery State Key Laboratory of Non-Food Biomass and Enzyme TechnologyGuangxi Research Center for Biological Science and TechnologyGuangxi Academy of SciencesNanning 530007China guangxi key laboratory for Green Processing of Sugar Resources College of Biological and Chemical EngineeringGuangxi University of Science and TechnologyLiuzhou 545006China

The application of microorganisms as probiotics is limited due to lack of safety ***,a novel multi-stress-tolerant yeast Meyerozyma guilliermondii GXDK6 with aroma-producing properties was identified from marine mangrove *** safety and probiotic properties were assessed in accordance with phenotype and whole-genome sequencing *** showed that the genes and phenotypic expression of related virulence,antibiotic resistance and retroelement were rarely *** morphogenesis genes(SIT4,HOG1,SPA2,ERK1,ICL1,CST20,HSP104,TPS1,and RHO1)and phospholipase secretion gene(VPS4)were *** hyphae and phospholipase were *** one retroelement(Tad1-65_BG)was *** biogenic amines(BAs)encoding genes were absent,except for spermidine synthase(JA9_002594),spermine synthase(JA9_004690),and tyrosine decarboxylase(inx).The production of single BAs and total BAs was far below the food-defined ***6 had no resistance to common antifungal *** enzymes,such as gelatinase,DNase,hemolytic,lecithinase,and thrombin were *** toxicity test with mice demonstrated that GXDK6 is ***6 has a good reproduction ability in the simulation gastrointestinal ***6 also has a strong antioxidant ability,β-glucosidase,and inulinase *** sum up,GXDK6 is considered as a safe probiotic for human consumption and food fermentation.

关键词： Meyerozyma guilliermondii Safety assessment Probiotics Marine mangrove microorganisms Whole-genome sequencing analysis

SsRSS1 mediates salicylic acid tolerance and contributes to virulence in sugarcane smut fungus

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Journal of Integrative Agriculture 2023年第7期22卷 2126-2137页

作者： ZHANG Hao-yang YANG Yan-fang GUO Feng SHEN Xiao-rui LU Shan CHEN Bao-shan College of Agriculture/guangxi key laboratory of Sugarcane Biology Guangxi UniversityNanning 530004P.R.China State key laboratory for conservation and utilization of Subtropical Agro-Bioresources/College of Life Science and Technology Guangxi UniversityNanning 530004P.R.China Ministry and Province Co-sponsored Collaborative Innovation Center for Sugarcane and Sugar Industry Guangxi UniversityNanning 530004P.R.China

Sugarcane smut caused by Sporisorium scitamineum is a destructive disease responsible for significant losses in sugarcane production ***,the mechanisms underlying the pathogenicity of this fungus remain largely *** this study,we found that the disruption of the SsRSS1 gene,which encodes a salicylic acid(SA)sensing regulator,does not affect phenotypic traits such as the morphology,growth rate,and sexual mating ability of haploid basidiospores,but rather reduces the tolerance of basidiospores to SA stress by blocking the induction of SsSRG1,a gene encoding a SA response protein in ***1 deletion resulted in the attenuation of the virulence of the *** addition to a significant reduction in whip formation,a portion of plantlets(18.3%)inoculated with theΔSsRSS1 strains were found to be infected but failed to produce whips for up to 90 days ***,the development of hyphae and teliospore from theΔSsRSS1-infected plants that formed whips seemed indistinguishable from that in the wild-type-infected ***,our findings suggested that SsRss1 is required for maintaining fungal fitness in planta by counteracting SA stress.

关键词： Sporisorium scitamineum SsRSS1 pathogenicity salicylic acid response

Directed message passing neural network (D-MPNN) with graph edge attention (GEA) for property prediction of biofuel-relevant species

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Energy and AI 2022年第4期10卷 115-125页

作者： Xu Han Ming Jia Yachao Chang Yaopeng Li Shaohua Wu key laboratory of Ocean Energy utilization and Energy conservation of Ministry of Education Dalian University of TechnologyDalian 116024China

Predictive models based on graph neural network (GNN) have attracted increasing interest in quantitative structure-property relation (QSPR) modeling of organic species including biofuel components in recent years. For the task of property prediction of biofuel-relevant species, the present work applies the Directed Message Passing Neural Network (D-MPNN) framework, an emerging type of GNN, and incorporates graph attention on the DMPNN architecture to improve its capability. modeling using other common machine learning methods is also conducted, confirming the advantage of D-MPNN in comparison. Graph Edge Attention (GEA) is proposed for the D-MPNN layers and shows success in increasing model accuracy after implementation. A relatively sizable subset from the QM9 data and 4 other datasets forming a wide scope of target properties (e.g., thermodynamic properties, ignition properties, surface tension, etc.) are selected for the models. A breakdown analysis of the species distribution of these datasets is conducted for more informed modeling. As the data availability of biofuel species is often a main obstacle for related modeling tasks, this study shows that the performance of D-MPNN with the proposed GEA attention mechanism is most enhanced when using a medium data size of 2000~5000. Some discussions are made regarding data issues and the use of machine learning methods and graph attention for the predictive modeling of biofuel properties, pointing out the need for more data with better species distribution that is representative of biofuels.

关键词： Deep learning Biofuel Quantitative structure-property relation Machine learning Molecules Graph neural network

Conversion of pure Chinese fir plantation to multi-layered mixed plantation enhances the soil aggregate stability by regulating microbial communities in subtropical China

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Forest Ecosystems 2022年第6期9卷 823-837页

作者： Guannv Gao Xueman Huang Haocheng Xu Yi Wang Weijun Shen Wen Zhang Jinliu Yan Xiaoyan Su Shushou Liao Yeming You guangxi key laboratory of Forest Ecology and conservation State Key Laboratory for Conservation and Utilization of Subtropical Agro-BioresourcesCollege of ForestryGuangxi UniversityNanning530004China guangxi Youyiguan Forest Ecosystem Research Station Pingxiang532600GuangxiChina School of Agriculture Shenzhen Campus of Sun Yat-sen UniversityShenzhen518107GuangdongChina Institute of Resources and Environment Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo&Rattan Science and TechnologyInternational Centre for Bamboo and RattanBeijing100102China Experimental Centre of Tropical Forestry Chinese Academy of ForestryPingxiang532600GuangxiChina

Background:Soil aggregates are the basic units of soil structure,and their stability is a key indicator of soil quality and capacity to support ecosystem *** impacts of various environmental factors on soil aggregates have been widely ***,there remains elusive knowledge on the synergistic effects of changing forest stand structure on soil aggregate stability(SAS),particularly in subtropical China where soil erosion remains a critical ***:We investigated variations in the components of soil humus(HS),including humic acids(HAs),fulvic acids(FAs),and humins(HMs),under pure Chinese fir(Cunninghamia lanceolata)plantation(PP)and multilayered mixed plantation(MP)comprising ***,Castanopsis hystrix,and Michelia *** state of soil aggregate stability,was determined by three separate methods,i.e.,dry-sieving,wet-sieving,and the Le ***-throughput sequencing was used to determine the diversity and composition of microbial communities under PP and *** then built partial least squares path models(PLS-PM)for assessing the responses of SAS to the variations in soil microorganisms and HS ***:The MP stands had significantly greater SAS(P<0.05),higher content of HAs and more rapid organic matter humification within aggregates,than the PP ***-throughput sequencing confirmed that the Pielou andα-diversity index values(Chao1 and Shannon)for fungi were all significantly higher under MP than under PP,while no marked difference was found in bacterialα-diversity between the two plantation ***,there were markedly greater abundance of three bacterial phyla(Verrucomicrobia,Chloroflexi,and Gemmatimonadetes)and three fungal phyla(Ascomycota,Kickxellomycota,and Glomeromycota),and significantly less abundance of two bacterial phyla(Planctomycetes and Firmicutes)and four fungal phyla(Basidiomycota,Mortierellomycota,Mucoromycota,and Rozellomycota)under MP than under *** Chloroflexi and Ascomycota phy

关键词： Broadleaved tree species Chinese fir plantation Soil aggregate stability Humus Bacterial and fungal communities High-throughput sequencing

A New Species of the Asian Toad Genus Megophrys sensu lato(Amphibia: Anura: Megophryidae) from Guizhou Province, China

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Asian Herpetological Research 2018年第4期9卷 224-239页

作者： Shize LI Ning XU Jing LIU Jianping JIANG Gang WEI Bin WANG Department of Food Science and Engineering Maotai University CAS key laboratory of Mountain Ecological Restoration and Bioresource utilization and Ecological Restoration Biodiversity conservation key laboratory of Sichuan Province Chengdu Institute of Biology (CIB) Chinese Academy of Sciences (CAS) Biodiversity conservation key laboratory Guiyang College

We describe a new species of the genus Megophrys sensu lato from Guizhou Province, China. Molecular phylogenetic analyses based on mitochondrial DNA and nuclear DNA sequences all strongly supported the new species as an independent lineage in Megophrys(Panophrys) clade. The new species is distinguished from its congeners by a combination of the following morphological characteristics:(1) small body size with SVL < 38.8 mm in male and SVL < 42.3 mm in female;(2) vomerine teeth absent;(3) tongue not notched behind;(4) a small horn-like tubercle at the edge of each upper eyelid;(5) tympanum distinctly visible, rounded;(6) two metacarpal tubercles in hand;(7) relative finger lengths: II < I < V < III;(8) toes with rudimentary webbing at bases;(9) heels overlapping when thighs are positioned at right angles to the body;(10) tibiotarsal articulation reaching the level between tympanum to eye when leg stretched forward;(11) an internal single subgular vocal sac in male;(12) in breeding male, the nuptial pads with black nuptial spines on the dorsal bases of the first and second fingers.

关键词： Megophrys sensu lato new species taxonomy phylogenetic analysis Guizhou Province China