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Phylotranscriptomic discordance is best explained by incomplete lineage sorting within Allium subgenus Cyathophora and thus hemiplasy accounts for interspecific trait transition

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Plant Diversity 2024年第1期46卷 28-38页

作者： Zengzhu Zhang Gang Liu Minjie Li state key laboratory of herbage improvement and grassland agro-ecosystems College of EcologyLanzhou UniversityLanzhou 730000GansuPR China

The transition of traits between genetically related lineages is a fascinating topic that provides clues to understanding the drivers of speciation and *** can be learned about this process from phylogeny-based trait ***,such inference is often plagued by genome-wide gene-tree discordance(GTD),mostly due to incomplete lineage sorting(ILS)and/or introgressive hybridization,especially when the genes underlying the traits appear ***,by collecting transcriptomes,whole chloroplast genomes(cpDNA),and population genetic datasets,we used the coalescent model to turn GTD into a source of information for ILS and employed hemiplasy to explain specific cases of apparent“phylogenetic discordance”between different morphological traits and probable species phylogeny in the Allium *** concatenation and coalescence methods consistently showed the same phylogenetic topology for species tree inference based on single-copy genes(SCGs),as supported by the KS ***,GTD was high across the genomes of ***:~27%e38.9%of the SCG trees were in conflict with the species *** and nuclear incongruence was also *** coalescent simulations indicated that such GTD was mainly a product of *** hemiplasy risk factor calculations supported that random fixation of ancient polymorphisms in different populations during successive speciation events along the *** phylogeny may have caused the character transition,as well as the anomalous cpDNA *** study exemplifies how phylogenetic noise can be transformed into evolutionary information for understanding character state transitions along species phylogenies.

关键词： Hemiplasy Multispecies coalescence Lineage sorting Gene tree discordance Phylotranscriptomics Allium subg.Cyathophora

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Effects of formal credit on pastoral household expense: Evidence from the Qinghai-Xizang Plateau of China

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Journal of Integrative Agriculture 2024年第5期23卷 1774-1785页

作者： Yan Zhang Yi Huang Fan Zhang Zeng Tang state key laboratory of herbage improvement and grassland agro-ecosystems College of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhou 730020China

Formal credit is critical in agricultural production,allowing more expenditure and productive input,thereby improving farmers'*** pastoral China,formal financial institutions are gradually ***,a limited understanding remains of how formal credit affects herders'household *** on a survey of 544 herders from the Qinghai-Xizang Plateau of China,this study adopted the propensity score matching approach to identify the effect of formal credit on herders'total household expenses,daily expenses,and productive *** results found that average age,grassland mortgage,and other variables significantly affected herders'participation in formal *** credit could significantly improve household expenses,especially productive expenses.A heterogeneity analysis showed that formal credit had a greater impact on the household total expense for those at higher levels of wealth;however,it significantly affected the productive expense of herders at lower wealth ***,the mediating effect indicated that formal credit could affect herders'household income,thus influencing their household ***,this study suggests that policies should improve herders'accessibility to formal credit.

关键词： formal credit herders expense Qinghai-Xizang Plateau

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Wood of trees:Cellular structure,molecular formation,and genetic engineering

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Journal of Integrative Plant Biology 2024年第3期66卷 443-467页

作者： Yingying Zhu Laigeng Li state key laboratory of herbage improvement and grassland agro-ecosystems and College of Ecology Lanzhou UniversityLanzhou 730000China National key laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200032China

Wood is an invaluable asset to human society due to its renewable nature,making it suitable for both sustainable energy production and material ***,wood derived from forest trees plays a crucial role in sequestering a significant portion of the carbon dioxide fixed during photosynthesis by terrestrial ***,with the expansion of the global population and ongoing industrialization,forest coverage has been substantially decreased,resulting in significant challenges for wood production and *** production practices have changed away from natural forests toward plantation ***,understanding the underlying genetic mechanisms of wood formation is the foundation for developing high-quality,fast-growing plantation *** ideal forest trees for wood production using genetic technologies has attracted the interest of *** studies have been carried out in recent years on the molecular,genetic,and cell-biological mechanisms of wood formation,and considerable progress and findings have been *** studies and findings indicate enormous possibilities and prospects for tree *** review will outline and assess the cellular and molecular mechanisms of wood formation,as well as studies on genetically improving forest trees,and address future development prospects.

关键词： cambium cell wall Populus wood formation xylem

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The jasmonate pathway promotes nodule symbiosis and suppresses host plant defense in Medicago truncatula

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Molecular Plant 2024年第8期17卷 1183-1203页

作者： Da Guo Jingrui Li Peng Liu Yuzhan Wang Na Cao Xiangling Fang Tao Wang Jiangli Dong College of Biological Sciences China Agricultural UniversityBejing 100193China state key laboratory of Plant Environmental Resilience College of Biological SciencesChina Agricultural UniversityBejing 100193China state key laboratory of herbage improvement and grassland agro-ecosystems College of Pastoral Agricuture Science and TechnologyLanzhou UniversityLanzhou730020China

Root nodule symbiosis(RNs)between legumes and rhizobia is a major source of nitrogen in agricultural *** symbiosis requires precise regulation of plant defense *** role of the defense hormone jasmonic acid(JA)in the immune response has been extensively *** research shows that JA can play either a positive or negative regulatory role in RNS depending on its concentration,but the molecular mechanisms remain to be *** this study,we found that inoculation with the rhizobia Sm1021 induces the JA pathway in Medicago truncatula,and blocking the JA pathway significantly reduces the number of infection *** in the MtMYc2 gene,which encodes a JA signaling master transcription factor,significantly inhibited rhizobia infection,terminal differentiation,and symbiotic cell *** RNA sequencing and chromatin immunoprecipitation sequencing,we discovered that MtMYc2 regulates the expression of nodule-specific MtDNF2,MtNAD1,and MtSymCRK to suppress host defense,while it activates MtDNF1 expression to regulate the maturation of MtNCRs,which in turn promotes bacteroid *** importantly,MtMYC2 participates in symbiotic signal transduction by promoting the expression of ***,the MtMYC2-MtiPD3 transcriptional regulatory module is specifically present in legumes,and the Mtmyc2 mutants are susceptible to the infection by the pathogen Rhizoctonia ***,these findings reveal the molecular mechanisms of how the JA pathway regulates RNS,broadening our understanding of the roles of JA in plant-microbe interactions.

关键词： jasmonic acid MYC2 symbiosis defense Medicago truncatula

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The Combination of Achnatherum inebrians Extracts and Soil Microorganisms Inhibited Seed Germination and Seedling Growth in Elymus nutans

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Phyton-International Journal of Experimental Botany 2024年第3期93卷 567-580页

作者： Rui Zhang Taixiang Chen Zhenjiang Chen Hao Chen Xuekai Wei Malik Kamran Chunjie Li state key laboratory of herbage improvement and grassland agro-ecosystems Key Laboratory of Animal Husbandry InnovationMinistry of Agriculture and Rural AffairsEngineering Research Center of Grassland AgricultureMinistry of EducationWest Gansu Province Prataculture Technology Innovation CenterCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhou730020China Center for grassland Research National Forestry and Grassland AdministrationCaFBeijing100091China

In a greenhouse experiment,the effects of soil microorganisms and extracts of Achnatherum inebrians on the seed germination and seedling growth of Elymus nutans were *** results showed that both the extracts from aboveground and belowground parts of *** signiﬁcantly inhibited the germination rate,germination potential,germination index,vigor index,seedling height,root length,and fresh weight of ***,but increased malondialdehyde content,catalase,peroxidase and superoxide dismutase activity of *** seedlings(p<0.05).The allelopathy of aqueous extracts of the aboveground parts of *** was stronger than that of the *** extracts of the aboveground parts of *** decreased seed germination rate,germination potential,germination index,vigor index,seedling length,root length,and seedling fresh weight by 10.45%-74.63%,24.18%-32.50%,19.03%-73.36%,37.83%-88.41%,21.42%-53.14%,2.65%-40.21%,and 20.45%-61.36%,respectively,and malondialdehyde content,peroxidase,catalase,and superoxide dismutase activity increased by 8.09%-62.24%,27.83%-86.47%,22.90%-93.17%,and 11.15%-75.91%,*** above indexes were higher in live soil than in sterilized *** microorganisms increased the allelopathy of *** seed germination rate,germination potential,germination index,vigor index,seedling length,and seedling fresh weight of *** planted in live soil decreased by 8.22%-48.48%,10.00%-51.85%,8.19%-53.26%,16.43%-60.03%,12.91%-28.81%,and 9.09%-22.86%compared with sterilized soil,*** content,peroxidase,catalase,and superoxide dismutase activity of *** planted in live soil increased by 53.91%-81.06%,15.71%-57.34%,33.33%-86.31%,and 9.78%-52.51%compared with sterilized soil,*** existence of soil microorganisms enhanced the allelopathy of the secondary metabolites of ***.A combination of microorganisms and aqueous extracts from the aboveground parts of *** had the s

关键词： Achnatherum inebrians water immersion liquid aqueous leachate precipitate allelopathy Elymus nutans soil microorganisms

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Whole-genome resequencing of Hu sheep identifies candidate genes associated with agronomic traits

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Journal of Genetics and Genomics 2024年第8期51卷 866-876页

作者： Liming Zhao Lvfeng Yuan Fadi Li Xiaoxue Zhang Huibin Tian Zongwu Ma Deyin Zhang Yukun Zhang Yuan Zhao Kai Huang Xiaolong Li Jiangbo Cheng Dan Xu Xiaobin Yang Kunchao Han Xiuxiu Weng Weimin Wang state key laboratory of herbage improvement and grassland agro-ecosystems Key Laboratory of Grassland Livestock Industry InnovationMinistry of Agriculture and Rural AffairsEngineering Research Center of Grassland IndustryMinistry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouGansu 730020China Lanzhou Veterinary Research Institute Chinese Academy of Agricultural SciencesLanzhouGansu 730046China College of Animal Science and Technology Gansu Agricultural UniversityLanzhouGansu 730070China

The phenotypic diversity resulting from artificial or natural selection of sheep has made a significant contribution to human *** sheep are a local sheep breed unique to China with high reproductive rates and rapid *** selection signatures have been widely used to investigate the genetic mechanisms underlying phenotypic variation in ***,we conduct whole-genome sequencing of 207 Hu sheep and compare them with the wild ancestors of domestic sheep(Asiatic mouflon)to investigate the genetic characteristics and selection signatures of Hu *** on six signatures of selection approaches,we detect genomic regions containing genes related to reproduction(BMPR1B,BMP2,PGFS,CYP19,CAMK4,GGT5,and GNAQ),vision(ALDH1A2,SAG,and PDE6B),nervous system(NAV1),and immune response(GPR35,SH2B2,PIK3R3,and HRAS).Association analysis with a population of 1299 Hu sheep reveals that those missense mutations in the GPR35(GPR35 g.952651 A>G;GPR35 g.952496 C>T)and NAV1(NAV1 g.84216190 C>T;NAV1 g.84227412 G>A)genes are significantly associated(Pimprovement and molecular investigations.

关键词： Hu sheep Whole-genome resequencing Selection signature GPR35 NAV1 Single nucleotide polymorphism

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Responses of arbuscular mycorrhizal fungi to straw return and nitrogen fertilizer reduction in a rainfed maize field

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Pedosphere 2024年第2期34卷 351-360页

作者： Zhenling PENG Hao XI Lin MAO Huyuan FENG Jianjun ZHANG Yongjun LIU state key laboratory of herbage improvement and grassland agro-ecosystems College of EcologyLanzhou UniversityLanzhou 730000China College of Life Sciences Northwest Normal UniversityLanzhou 730070China School of Life Sciences Lanzhou UniversityLanzhou 730000China Dryland Agriculture Institute Gansu Academy of Agricultural SciencesLanzhou 730070China

Straw return can be used to reduce fertilizer input and improve agricultural sustainability and soil ***,how straw return and reduced fertilizer application affect beneficial soil microbes,particularly arbuscular mycorrhizal fungi(AMF),remains poorly ***,we conducted a five-year field experiment in a rainfed maize field on the Loess Plateau of northwestern *** tested four treatments with straw return combined with four nitrogen(N)application rates,i.e.,100%,80%,60%,and 0%of the common N application rate(225 kg N ha^(-1)year^(-1))in this region,and two reference treatments(full or no N application),with three replicates for each *** colonization was quantified and AMF communities colonizing maize roots were characterized using Illumina *** virtual taxa(VTs)of AMF were identified in root samples,among which VT113(related to Rhizophagus fasciculatus)and VT156(related to Dominikia gansuensis)were the predominant *** root length colonization and AMF VT richness were sensitive to N fertilization,but not to straw return;furthermore,both gradually increased with decreasing N application *** VT composition of the AMF community was also affected by N fertilization,but not by straw return,and the community variation could be well explained by soil available N and phosphorus ***,60%,80%,and full N fertilization produced similar maize ***,our study revealed the response patterns of AMF to straw return and N fertilizer reduction and showed that straw return combined with N fertilizer reduction may be a promising practice to maintain mycorrhizal symbiosis concomitantly with crop productivity.

关键词： agricultural sustainability crop productivity mycorrhizal colonization mycorrhizal symbiosis root length colonization virtual taxon

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Neighbour effects on plant biomass and its allocation for forbs growing in heterogeneous soils

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Journal of Plant Ecology 2024年第4期17卷 90-99页

作者： Yongjie Liu Chunyan Ma Shiting Liu Mingrui Liu Hui Li Mingxia Wang Guoe Li Hans J.De Boeck Fujiang Hou Zhanhui Tang Zhenxin Li state key laboratory of herbage improvement and grassland agro-ecosystems Key Laboratory of Grassland Livestock Industry InnovationMinistry of Agriculture and Rural AffairsCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhou 730020China School of Ecology and Environmental Sciences Yunnan UniversityKunming 650091China Plant and ecosystems(PLECO) Department of BiologyUniversity of AntwerpWilrijk B-2610Belgium state Environmental Protection key laboratory of Wetland Ecology and Vegetation Restoration School of EnvironmentNortheast Normal UniversityChangchun 130117China key laboratory of Biodiversity and Environment on the Qinghai-Tibet Plateau Ministry of EducationLhasa 850011China

Focal plants are considerably affected by their neighbouring plants,especially when growing in heterogeneous soils.A previous study on grasses demonstrated that soil heterogeneity and species composition affected plant biomass and above-and belowground allocation *** now tested whether these findings were similar for *** forb species(*** anglica,Limonium bicolor and Suaeda glauca)were grown in pots with three levels of soil heterogeneity,created by alternatively filling resource-rich and resource-poor substrates using small,medium or large patch *** compositions were created by growing these forbs either in monocultures or in *** showed that patch size×species composition significantly impacted shoot biomass,root biomass and total biomass of forbs at different ***,at the pot scale,shoot biomass,root biomass and total biomass increased with increasing patch *** the substrate scale,shoot biomass and total biomass were higher at the large patch size than at the medium patch size,both in resource-rich and resource-poor ***,at the community scale,monocultures had more shoot biomass,root biomass and total biomass than those in the two-or three-species *** results differ from earlier findings on the responses of grasses,where shoot biomass and total biomass decreased with patch size,and more shoot biomass and total biomass were found in resource-rich than resource-poor *** further elucidate the effects of soil heterogeneity on the interactions between neighbour plants,we advise to conduct longer-term experiments featuring a variety of functional groups.

关键词： biomass allocation neighbour effect patch size soil heterogeneity shoot biomass

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The δ^(15)N values of foxtail millet(Setaria italica)and common millet(Panicum miliaceum)are reliable indicators of manuring practices

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Science China Earth Sciences 2024年第9期67卷 2910-2923页

作者： Jishuai YANG Xiaoyan YANG Ting YOU Fahu CHEN key Scientific Research Base of Bioarchaeology in Cold and Arid Regions(National Cultural Heritage Administration) Key Laboratory of Western China’s Environmental Systems(Ministry of Education)College of Earth and Environmental SciencesLanzhou UniversityLanzhou 730000China Group of Alpine Paleoecology and Human Adaptation(ALPHA) State Key Laboratory of Tibetan Plateau Earth SystemResources and Environment(TPESRE)Institute of Tibetan Plateau ResearchChinese Academy of SciencesBeijing 100101China state key laboratory of herbage improvement and grassland agro-ecosystems College of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhou 730000China

Millet agriculture,which originated in northern China,alongside rice agriculture,have nurtured the Chinese *** manuring practices likely promoted and maintained sustainable millet agricultural production in the loess area of northern ***,ongoing controversy exists regarding the indicators of prehistoric manuring intensity of foxtail millet(Setaria italica)and common millet(Panicum miliaceum).Here,we present the results of pot and field fertilization experiments on two millet *** findings suggest that manuring can significantly increase the δ^(15)N values of foxtail millet,and its δ^(15)N values increase with increasing manuring *** δ^(15)N values of foxtail millet leaves are systematically greater than those of grains by approximately 1.6‰.Manuring could have a long-term residual impact on increasing the δ^(15)N values of soil and millet *** with previous crop fertilization experiment results,we propose that the impact of manuring on the δ^(15)N values of non-nitrogen-fixing crops is roughly *** δ^(15)N value and amount of manure are key factors determining the extent of change in plant δ^(15)N *** millet grain δ^(15)N values can serve as reliable indicators of manuring ***,we provide an interpretive framework for assessing the correlation between manuring levels and the δ^(15)N values of archaeological millet *** δ^(15)N values of ancient millet grains suggest widespread and intensive manuring practices in prehistoric millet agriculture in northern China,spanning from the early Yangshao period to the Longshan period.

关键词： Millet farming Manuring experiment Farming system Archaeobotany North China

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Habitat-specific changes of plant and soil microbial community composition in response to fairy ring fungus Agaricus xanthodermus on the Qinghai-Tibet Plateau

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SOIL ECOLOGY LETTERS 2024年第3期6卷 230214-230214页

作者： Du, Juan He, Cong Wang, Fuxin Ling, Ning Jiang, Shengjing Lanzhou Univ Coll Pastoral Agr Sci & Technol State Key Lab Herbage Improvement & Grassland Agro Lanzhou 730000 Peoples R China Lanzhou Univ Coll Ecol Lanzhou 730000 Peoples R China

A new fairy ring fungus was reported in this study. Fairy ring fungi influence plants and soil microbes by promoting soil nutrients. The effect of fairy ring fungi on plants and soil microbes depends on the habitat type. Fairy rings are common in diverse global biomes and often appear as lush vegetation in one to three concentric zones caused by the spread of mycelia in grassland ecosystems. However, the underlying mechanisms and environmental adaptation of fairy rings remain largely unclear. In this study, two fairy rings (A and B) caused by Agaricus xanthodermus were sampled on the Qinghai-Tibet Plateau during a time when fairy rings are most obvious. By conducting a vegetation survey and high-throughput sequencing, the changes of plants and soil microorganisms to fairy ring fungi were examined. Plant above-ground biomass at both fairy rings was greatly increased by fairy ring fungi, but the response of dominant plant species is different at two fairy ring sites. In addition, bacterial and fungal communities significantly varied within distinct sampling zones across the fairy rings, and showed variable genus-specific responses at two fairy ring sites. At fairy ring A, soil available N:P ratio was essential in shaping the structure of plant and microbial community, while soil available N concentration was the most important predictor at fairy ring B. Taken together, our results indicated Agaricus xanthodermus fairy rings have variable effects on alpine meadow plants and soil microbes at different habitats. We propose that the impacts of fairy ring fungi on plants and microbes are determined by the level of soil available N concentration and available N:P ratio. These results contribute to a better understanding of the mechanisms through which fairy rings affect the vegetation of alpine meadows.

关键词： Fairy rings alpine meadow soil microbes plant-soil relationships PRODUCTIVITY DIVERSITY

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