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Identification of S-RNase genotype and analysis of its origin and evolutionary patterns in Malus plants

Journal of Integrative Agriculture 2024年第4期23卷 1205-1221页

作者： Zhao Liu Yuan Gao Kun Wang Jianrong Feng Simiao Sun Xiang Lu Lin Wang Wen Tian Guangyi Wang Zichen Li Qingshan Li Lianwen Li Dajiang Wang Research Institute of Pomology Chinese Academy of Agricultural Sciences/Key Laboratory of Horticultural Crops Germplasm Resources UtilizationMinistry of Agriculture and Rural AffairsXingcheng 125100China College of Agriculture Shihezi University/Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization of Xinjiang Production and Construction CorpsShihezi 832000China

Identification of the S genotype of Malus plants will greatly promote the discovery of new genes,the cultivation and production of apple,the breeding of new varieties,and the origin and evolution of self-incompatibility in Malus plants.In this experiment,88 Malus germplasm resources,such as Aihuahong,Xishuhaitang,and Reguanzi,were used as materials.Seven gene-specific primer combinations were used in the genotype identification.PCR amplification using leaf DNA produced a single S-RNase gene fragment in all materials.The results revealed that 70 of the identified materials obtained a complete S-RNase genotype,while only one S-RNase gene was found in 18 of them.Through homology comparison and analysis,13 S-RNase genotypes were obtained:S_(1)S_(2)(Aihuahong,etc.),S_(1)S_(28)(Xixian Haitang,etc.),S_(1)S_(51)(Hebei Pingdinghaitang),S_(1)S_(3)(Xiangyangcun Daguo,etc.),S_(2)S_(3)(Zhaiyehaitang,etc.),S_(3)S_(51)(Xishan 1),S_(3)S_(28)(Huangselihaerde,etc.),S_(2)S_(28)(Honghaitang,etc.),S_(4)S_(28)(Bo 11),S_(7)S_(28)(Jiuquan Shaguo),S_(10)S_e(Dongchengguan 13),S_(10)S_(21)(Dongxiangjiao)and S_(3)S_(51)(Xiongyue Haitang).Simultaneously,the frequency of the S gene in the tested materials was analyzed.The findings revealed that different S genes had varying frequencies in Malus resources,as well as varying frequencies between intraspecific and interspecific.S_(3) had the highest frequency of 68.18%,followed by S_(1)(42.04%).In addition,the phylogenetic tree and origin evolution analysis revealed that the S gene differentiation was completed prior to the formation of various apple species,that cultivated species also evolved new S genes,and that the S_(50) gene is the oldest S allele in Malus plants.The S_(1),S_(29),and S_(33) genes in apple-cultivated species,on the other hand,may have originated in M.sieversii,M.hupehensis,and M.kansuensis,respectively.In addition to M.sieversii,M.kansuensis and M.sikkimensis may have also played a role in the origin and evolution of some Chinese apples.

关键词： Malus S-RNase genotype self-incompatibility origin and evolution

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Uncovering key salt-tolerant regulators through a combined eQTL and GWAS analysis using the super pan-genome in rice

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National science Review 2024年第4期11卷 55-69页

作者： Hua Wei Xianmeng Wang Zhipeng Zhang Longbo Yang Qianqian Zhang Yilin Li Huiying He Dandan Chen Bin Zhang Chongke Zheng Yue Leng Xinglan Cao Yan Cui Chuanlin Shi Yifan Liu Yang Lv Jie Ma Wenchuang He Xiangpei Liu Qiang Xu Qiaoling Yuan Xiaoman Yu Tianyi Wang Hongge Qian Xiaoxia Li Bintao Zhang Hong Zhang Wu Chen Mingliang Guo Xiaofan Dai Yuexing Wang Xiaoming Zheng Longbiao Guo Xianzhi Xie Qian Qian Lianguang Shang Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural Sciences Institute of Wetland Agriculture and Ecology Shandong Academy of Agricultural Sciences State Key Laboratory of Rice Biology China National Rice Research Institute National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Science Chinese Academy of Agricultural Sciences Yazhouwan National Laboratory

For sessile plants, gene expression plays a pivotal role in responding to salinity stress by activating or suppressing specific genes. However, our knowledge of genetic variations governing gene expression in response to salt stress remains limited in natural germplasm. Through transcriptome analysis of the Global Mini-Core Rice Collection consisting of a panel of 202 accessions, we identified 22 345 and 27 610expression quantitative trait loci associated with the expression of 7787 and 9361 e Genes under normal and salt-stress conditions, respectively, leveraging the super pan-genome map. Notably, combined with genome-wide association studies, we swiftly pinpointed the potential candidate gene STG5—a major salt-tolerant locus known as q STS5. Intriguingly, STG5 is required for maintaining Na+/K+homeostasis by directly regulating the transcription of multiple members of the Os HKT gene family. Our study sheds light on how genetic variants influence the dynamic changes in gene expression responding to salinity stress and provides a valuable resource for the mining of salt-tolerant genes in the future.

关键词： super pan-genome expression quantitative trait loci GWAS salt tolerance rice

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Characterization of the pheromone receptors in Mythimna loreyi reveals the differentiation of sex pheromone recognition in Mythimna species

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Insect science 2024年第1期31卷 173-185页

作者： Chan Wang Lei Liu Tian-Yu Huang Yu Zhang Yang Liu Gui-Rong Wang State Key Laboratory for Biology of Plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijingChina Guangdong Laboratory of Lingnan Modern Agriculture ShenzhenGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina School of Forestry Northeast Forestry UniversityHarbinChina Key Laboratory of Biohazard Monitoring Green Prevention and Control for Artificial GrasslandMinistry of Agriculture and Rural AffairsInstitute of Grassland Research of Chinese Academy of Agricultural SciencesInner Mongolia HohhotChina

Pheromone receptors(PRs)are key proteins in the molecular mechanism of pheromone recognition,and exploring the functional differentiation of PRs between closely related species helps to understand the evolution of moth mating systems.Pheromone components of the agricultural pest Mythimna loreyi have turned into(Z)-9-tetradecen-1-yl acetate(Z9-14:OAc),(Z)-7-dodecen-1-yl acetate(Z7-12:OAc),and(Z)-11-hexadecen-1-yl acetate,while the composition differs from that of M.separata in the genus Mythimna.To understand the molecular mechanism of pheromone recognition,we sequenced and analyzed antennal transcriptomes to identify 62 odorant receptor(OR)genes.The expression levels of all putative ORs were analyzed using differentially expressed gene analysis.Six candidate PRs were quantified and functionally characterized in the Xenopus oocytes system.MlorPR6 and MlorPR3 were determined to be the receptors of major and minor components Z9-14:OAc and Z7-12:OAc.MlorPR1 and female antennae(FA)-biased MlorPR5 both possessed the ability to detect pheromones of sympatric species,including(Z,E)-9,12-tetradecadien-1-ol,(Z)-9-tetradecen-1-ol,and(Z)-9-tetradecenal.Based on the comparison of PR functions between M.loreyi and M.separata,we analyzed the differentiation of pheromone recognition mechanisms during the evolution of the mating systems of 2 Mythimna species.

关键词： antennal transcriptome Mythimna loreyi pheromone receptor sex pheromone Xenopus oocyte

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Natural sources,refined extraction,biosynthesis,metabolism,and bioactivities of dietary polymethoxyflavones(PMFs)

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Food science and Human Wellness 2024年第1期13卷 27-49页

作者： Renyou Gan Yi Liu Hang Li Yu Xia Huan Guo Fang Geng Qiguo Zhuang Huabin Li Dingtao Wu Research Center for Plants and Human Health Institute of Urban AgricultureChinese Academy of Agricultural SciencesChengdu National Agricultural Science and Technology CenterChengdu 610213China Key Laboratory of Coarse Cereal Processing Ministry of Agriculture and Rural AffairsSichuan Engineering and Technology Research Centre of Coarse Cereal IndustralizationSchool of Food and Biological EngineeringChengdu UniversityChengdu 610106China China-New Zealand Belt and Road Joint Laboratory on Kiwifruit Sichuan Provincial Academy of Natural Resource SciencesChengdu 610213China Guangdong Provincial Key Laboratory of Food Nutrition and HealthSchool of Public HealthSun Yat-sen UniversityGuangzhou 510080China

Polymethoxyflavones(PMFs)are a type of uncommon dietary flavonoids,characterized by more than one methoxy group,which exist in limited plant species,like Citrus species and Kaempferia parviflora.In addition,different PMFs,such as nobiletin,sinensetin,tangeretin,and casticin,have been isolated from these natural sources.PMFs have received increasing attention due to their multiple bioactivities,such as antioxidant,anti-inflammatory,anti-cancer,metabolic regulatory,immunoregulatory,neuroprotective,and skin protective effects.These bioactivities of PMFs should be associated with the regulation of critical molecular targets and the interaction with gut microbiota.In order to provide a comprehensive and updated review of PMFs,their natural sources,refined extraction,biosynthesis,metabolism,and bioactivities are summarised and discussed,with the emphasis on the molecular mechanisms of PMFs on regulating different chronic diseases.Overall,PMFs may be promising flavonoids to the forefront of nutraceuticals for the prevention and/or treatment of certain human chronic diseases.

关键词： Nobiletin O-Methyltransferases Gut microbiota Bioactivities Molecular mechanism

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Decreased eggshell strength caused by impairment of uterine calcium transport coincide with higher bone minerals and quality in aged laying hens

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Journal of Animal science and Biotechnology 2024年第3期15卷 1258-1277页

作者： Yu Fu Jianmin Zhou Martine Schroyen Haijun Zhang Shugeng Wu Guanghai Qi Jing Wang Key Laboratory of Feed Biotechnology Ministry of Agriculture and Rural AffairsInstitute of Feed ResearchChinese Academy of Agricultural SciencesBeijing 100081China Precision Livestock and Nutrition Laboratory Gembloux Agro‑Bio TechTERRA Teaching and Research CentreUniversity of LiegeGembloux B‑5030Belgium

Background Deteriorations in eggshell and bone quality are major challenges in aged laying hens.This study compared the differences of eggshell quality,bone parameters and their correlations as well as uterine physiologi-cal characteristics and the bone remodeling processes of hens laying eggs of different eggshell breaking strength to explore the mechanism of eggshell and bone quality reduction and their interaction.A total of 24074-week-old Hy-line Brown laying hens were selected and allocated to a high(HBS,44.83±1.31 N)or low(LBS,24.43±0.57 N)eggshell breaking strength group.Results A decreased thickness,weight and weight ratio of eggshells were observed in the LBS,accompanied with ultrastructural deterioration and total Ca reduction.Bone quality was negatively correlated with eggshell quality,marked with enhanced structures and increased components in the LBS.In the LBS,the mammillary knobs and effective layer grew slowly.At the initiation stage of eggshell calcification,a total of 130 differentially expressed genes(DEGs,122 upregulated and 8 downregulated)were identified in the uterus of hens in the LBS relative to those in the HBS.These DEGs were relevant to apoptosis due to the cellular Ca overload.Higher values of p62 protein level,caspase-8 activity,Bax protein expression and lower values of Bcl protein expression and Bcl/Bax ratio were seen in the LBS.TUNEL assay and hematoxylin-eosin staining showed a significant increase in TUNEL-positive cells and tissue damages in the uterus of the LBS.Although few DEGs were identified at the growth stage,similar uterine tissue damages were also observed in the LBS.The expressions of runt-related transcription factor 2 and osteocal-cin were upregulated in humeri of the LBS.Enlarged diameter and more structural damages of endocortical bones and decreased ash were observed in femurs of the HBS.Conclusion The lower eggshell breaking strength may be attributed to a declined Ca transport due to uterine tissue damages,which could affect eggshell calcification and lead to

关键词： Bone parameter Calcium transport Eggshell quality Laying hen Tissue damage

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Nitrogen deposition mediates more stochastic processes in structuring plant community than soil microbial community in the Eurasian steppe

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science China(Life sciences) 2024年第4期67卷 778-788页

作者： Wei Yang Shuhan Zhang Ang Li Junjie Yang Shuang Pang Zonghao Hu Zhiping Wang Xingguo Han Ximei Zhang Key Laboratory of Dryland Agriculture Ministry of AgricultureInstitute of Environment and Sustainable Development in AgricultureChinese Academy of Agricultural SciencesBeijing 100081China State Key Laboratory of Vegetation and Environmental Change Institute of BotanyChinese Academy of SciencesBeijing 100093China

Anthropogenic environmental changes may affect community assembly through mediating both deterministic(e.g.,competitive exclusion and environmental filtering)and stochastic processes(e.g.,birth/death and dispersal/colonization).It is traditionally thought that environmental changes have a larger mediation effect on stochastic processes in structuring soil microbial community than aboveground plant community;however,this hypothesis remains largely untested.Here we report an unexpected pattern that nitrogen(N)deposition has a larger mediation effect on stochastic processes in structuring plant community than soil microbial community(those<2 mm in diameter,including archaea,bacteria,fungi,and protists)in the Eurasian steppe.We performed a ten-year nitrogen deposition experiment in a semiarid grassland ecosystem in Inner Mongolia,manipulating nine rates(0–50 g N m^(-2)per year)at two frequencies(nitrogen added twice or 12 times per year)under two grassland management strategies(fencing or mowing).We separated the compositional variation of plant and soil microbial communities caused by each treatment into the deterministic and stochastic components with a recently-developed method.As nitrogen addition rate increased,the relative importance of stochastic component of plant community first increased and then decreased,while that of soil microbial community first decreased and then increased.On the whole,the relative importance of stochastic component was significantly larger in plant community(0.552±0.035;mean±standard error)than in microbial community(0.427±0.035).Consistently,the proportion of compositional variation explained by the deterministic soil and community indices was smaller for plant community(0.172–0.186)than microbial community(0.240–0.767).Meanwhile,as nitrogen addition rate increased,the linkage between plant and microbial community composition first became weaker and then became stronger.The larger stochasticity in plant community relative to microbial community assembly suggested that more stochasti

关键词： deterministic process environmental change grassland restoration nitrogen deposition stochastic process

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Green manuring relocates microbiomes in driving the soil functionality of nitrogen cycling to obtain preferable grain yields in thirty years

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science China(Life sciences) 2024年第3期67卷 596-610页

作者： Guopeng Zhou Kunkun Fan Songjuan Gao Danna Chang Guilong Li Ting Liang Hai Liang Shun Li Jiudong Zhang Zongxian Che Weidong Cao State Key Laboratory of Efficient Utilization of Arid and Semi-arid Arable Land in Northern China/Institute of agricultural Resources and Regional Planning Chinese Academy of Agricultural SciencesBeijing 100081China State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil ScienceChinese Academy of SciencesNanjing 210008China College of Resources and Environmental sciences Nanjing Agricultural UniversityNanjing 210095China Institute of Soil&Fertilizer and Resource&Environment Jiangxi Academy of Agricultural SciencesNanchang 330200China Institute of Soil and Fertilizer and Water-saving Agriculture Gansu Academy of Agricultural SciencesLanzhou 730070China

Fertilizers are widely used to produce more food, inevitably altering the diversity and composition of soil organisms. The role of soil biodiversity in controlling multiple ecosystem services remains unclear, especially after decades of fertilization. Here, we assess the contribution of the soil functionalities of carbon(C), nitrogen(N), and phosphorus(P) cycling to crop production and explore how soil organisms control these functionalities in a 33-year field fertilization experiment. The long-term application of green manure or cow manure produced wheat yields equivalent to those obtained with chemical N, with the former providing higher soil functions and allowing the functionality of N cycling(especially soil N mineralization and biological N fixation) to control wheat production. The keystone phylotypes within the global network rather than the overall microbial community dominated the soil multifunctionality and functionality of C,N, and P cycling across the soil profile(0–100 cm). We further confirmed that these keystone phylotypes consisted of many metabolic pathways of nutrient cycling and essential microbes involved in organic C mineralization, N_(2)O release, and biological N fixation. The chemical N, green manure, and cow manure resulted in the highest abundances of amoB, nifH, and GH48 genes and Nitrosomonadaceae,Azospirillaceae, and Sphingomonadaceae within the keystone phylotypes, and these microbes were significantly and positively correlated with N_(2)O release, N fixation, and organic C mineralization, respectively. Moreover, our results demonstrated that organic fertilization increased the effects of the network size and keystone phylotypes on the subsoil functions by facilitating the migration of soil microorganisms across the soil profiles and green manure with the highest migration rates. This study highlights the importance of the functionality of N cycling in controlling crop production and keystone phylotypes in regulating soil functions, and provides selectable fertilization strategies f

关键词： soil biodiversity soil multifunctionality element cycling keystone phylotypes

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Associations of genome-wide structural variations with phenotypic differences in cross-bred Eurasian pigs

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Journal of Animal science and Biotechnology 2024年第1期15卷 68-87页

作者： Wencheng Zong Jinbu Wang Runze Zhao Naiqi Niu Yanfang Su Ziping Hu Xin Liu Xinhua Hou Ligang Wang Lixian Wang Longchao Zhang State Key Laboratory of Animal Biotech Breeding Institute of Animal SciencesChinese Academy of Agricultural SciencesBeijing 100193China College of Animal science Shanxi Agricultural UniversityJinzhong 030801China College of Animal science and technology Qingdao Agricultural UniversityQingdao 266109China

Background During approximately 10,000 years of domestication and selection,a large number of structural variations(SVs)have emerged in the genome of pig breeds,profoundly influencing their phenotypes and the ability to adapt to the local environment.SVs(≥50 bp)are widely distributed in the genome,mainly in the form of insertion(INS),mobile element insertion(MEI),deletion(DEL),duplication(DUP),inversion(INV),and translocation(TRA).While studies have investigated the SVs in pig genomes,genome-wide association studies(GWAS)-based on SVs have been rarely conducted.Results Here,we obtained a high-quality SV map containing 123,151 SVs from 15 Large White and 15 Min pigs through integrating the power of several SV tools,with 53.95%of the SVs being reported for the first time.These high-quality SVs were used to recover the population genetic structure,confirming the accuracy of genotyping.Potential functional SV loci were then identified based on positional effects and breed stratification.Finally,GWAS were performed for 36 traits by genotyping the screened potential causal loci in the F2 population according to their corresponding genomic positions.We identified a large number of loci involved in 8 carcass traits and 6 skeletal traits on chromosome 7,with FKBP5 containing the most significant SV locus for almost all traits.In addition,we found several significant loci in intramuscular fat,abdominal circumference,heart weight,and liver weight,etc.Conclusions We constructed a high-quality SV map using high-coverage sequencing data and then analyzed them by performing GWAS for 25 carcass traits,7 skeletal traits,and 4 meat quality traits to determine that SVs may affect body size between European and Chinese pig breeds.

关键词： Body size GWAS Pig Skeleton Structural variations

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The virulence regulator AbsR in avian pathogenic Escherichia coli has pleiotropic effects on bacterial physiology

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Journal of Integrative Agriculture 2024年第2期23卷 649-668页

作者： Dongfang Zhao Haobo Zhang Xinyang Zhang Fengwei Jiang Yijing Li Wentong Cai Ganwu Li State Key Laboratory for Animal Disease Control and Prevention Harbin Veterinary Research InstituteChinese Academy of Agricultural SciencesHarbin 150069China College of Veterinary Medicine Northeast Agricultural UniversityHarbin 150038China National Animal Tuberculosis Reference Laboratory Division of Zoonoses SurveillanceChina Animal Health and Epidemiology CenterQingdao 266032China Department of Veterinary Diagnostic and Production Animal Medicine College of Veterinary MedicineIowa State UniversityAmesIowa 50011-1134the United States

Avian pathogenic Escherichia coli(APEC)belonging to extraintestinal pathogenic E.coli(ExPEC)can cause severe infections in extraintestinal tissues in birds and humans,such as the lungs and blood.MprA(microcin production regulation,locus A,herein renamed AbsR,a blood survival regulator),a member of the MarR(multiple antibiotic resistance regulator)transcriptional regulator family,governs the expression of capsule biosynthetic genes in human ExPEC and represents a promising druggable target for antimicrobials.However,a deep understanding of the AbsR regulatory mechanism as well as its regulon is lacking.In this study,we present a systems-level analysis of the APEC AbsR regulon using ChIP-Seq(chromatin immunoprecipitation sequencing)and RNA-Seq(RNA sequencing)methods.We found that AbsR directly regulates 99 genes and indirectly regulates 667 genes.Furthermore,we showed that:1)AbsR contributes to antiphagocytotic effects by macrophages and virulence in a mouse model for systemic infection by directly activating the capsular gene cluster;2)AbsR positively impacts biofilm formation via direct regulation of the T2SS(type II secretion system)but plays a marginal role in virulence;and 3)AbsR directly upregulates the acid tolerance signaling system EvgAS to withstand acid stress but is dispensable in ExPEC virulence.Finally,our data indicate that the role of AbsR in virulence gene regulation is relatively conserved in ExPEC strains.Altogether,this study provides a comprehensive analysis of the AbsR regulon and regulatory mechanism,and our data suggest that AbsR likely influences virulence primarily through the control of capsule production.Interestingly,we found that AbsR severely represses the expression of the type I-F CRISPR(clustered regularly interspaced short palindromic repeats)-Cas(CRISPR associated)systems,which could have implications in CRISPR biology and application.

关键词： avian pathogenic Escherichia coli(APEC) extraintestinal pathogenic Escherichia coli(ExPEC) AbsR RNA-Seq ChIP-Seq gene regulation

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Preweaning period is a critical window for rumen microbial regulation of average daily gain in Holstein heifer calves

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Journal of Animal science and Biotechnology 2024年第1期15卷 396-411页

作者： Shengyang Xu Chong Jiao Qiyu Diao Yan Tu Beijing Key Laboratory for Dairy Cow Nutrition Institute of Feed ResearchChinese Academy of Agricultural SciencesBeijing 100081People’s Republic of China

Background Rumen bacterial groups can affect growth performance,such as average daily gain(ADG),feed intake,and efficiency.The study aimed to investigate the inter-relationship of rumen bacterial composition,rumen fermentation indicators,serum indicators,and growth performance of Holstein heifer calves with different ADG.Twelve calves were chosen from a trail with 60 calves and divided into higher ADG(HADG,high pre-and post-weaning ADG,n=6)and lower ADG(LADG,low pre-and post-weaning ADG,n=6)groups to investigate differences in bacterial composition and functions and host phenotype.Results During the preweaning period,the relative abundances of propionate producers,including g_norank_f_Butyricicoccaceae,g_Pyramidobacter,and g_norank_f_norank_o_Clostridia_vadin BB60_group,were higher in HADG calves(LDA>2,P<0.05).Enrichment of these bacteria resulted in increased levels of propionate,a gluconeogenic precursor,in preweaning HADG calves(adjusted P<0.05),which consequently raised serum glucose concentrations(adjusted P<0.05).In contrast,the relative abundances of rumen bacteria in post-weaning HADG calves did not exert this effect.Moreover,no significant differences were observed in rumen fermentation parameters and serum indices between the two groups.Conclusions The findings of this study revealed that the preweaning period is the window of opportunity for rumen bacteria to regulate the ADG of calves.

关键词： Average daily gain Calves Preweaning period Rumen microbiota

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