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Rice gene OsUGT75A regulates seedling emergence under deep-sowing conditions

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The Crop Journal 2024年第1期12卷 133-141页

作者： Jia Zhao Siyu Liu Xiaoqian Zhao Zhibo Huang Shan Sun Zixuan Zeng Yongqi He Zhoufei Wang The laboratory of Seed Science and Technology Guangdong Key Laboratory of Plant Molecular BreedingNational Engineering Research Center of Plant Space BreedingSouth China Agricultural UniversityGuangzhou 510642GuangdongChina

Poor seedling emergence is a challenge for direct seeding of rice under deep-sowing field conditions.Here we reveal that UDP-glucosyltransferase OsUGT75A promotes rice seedling emergence under deepsowing conditions by increasing shoot length.Expression of OsUGT75A was higher in the middle regions of the shoot and in shoots under deep-sowing conditions.Levels of free abscisic acid(ABA)and jasmonates(JA)were higher in shoots of OsUGT75A mutants than in those of wild-type plants,and OsUGT75A mutants were more sensitive to ABA and JA treatments.Reduced shoot length was attributed to higher ABA INSENSITIVE 3(OsABI3)expression and lower JASMONATE-ZIM domain protein(OsJAZ)expression in shoots.Shoot extension by OsUGT75A is achieved mainly by promotion of cell elongation.An elite haplotype of OsUGT75A associated with increased shoot length was identified among indica rice accessions.OsUGT75A acts to increase seedling emergence under deep-sowing conditions.

关键词： Abscisic acid Deep-sowing Jasmonic acid Rice Shoot length

Structural insights into the Oryza sativa cation transporters HKTs in salt tolerance

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Journal of Integrative Plant Biology 2024年第4期66卷 700-708页

作者： Ran Gao Yutian Jia Xia Xu Peng Fu Jiaqi Zhou Guanghui Yang State Key laboratory of Plant Environmental Resilience Frontiers Science Center for Molecular Design BreedingCollege of Biological SciencesChina Agricultural UniversityBeijing 100193China

The high-affinity potassium transporters(HKTs),selectively permeable to either Na^(+)alone or Na^(+)/K^(+),play pivotal roles in maintaining plant Na^(+)/K^(+)homeostasis.Although their involvement in salt tolerance is widely reported,the molecular underpinnings of Oryza sativa HKTs remain elusive.In this study,we elucidate the structures of OsHKT1;1 and OsHKT2;1,representing two distinct classes of rice HKTs.The dimeric assembled OsHKTs can be structurally divided into four domains.At the dimer interface,a half-helix or a loop in the third domain is coordinated by the C-terminal region of the opposite subunit.Additionally,we present the structures of OsHKT1;5 salt-tolerant and salt-sensitive variants,a key quantitative trait locus associated with salt tolerance.The salt-tolerant variant of OsHKT1;5 exhibits enhanced Na^(+)transport capability and displays a more flexible conformation.These findings shed light on the molecular basis of rice HKTs and provide insights into their role in salt tolerance.

关键词： HKT salt-tolerant structure

DNA methylation in poultry:a review

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Journal of Animal Science and Biotechnology 2024年第2期15卷 509-518页

作者： Xing Ju Zhijun Wang Danfeng Cai Semiu Folaniyi Bello Qinghua Nie State Key laboratory for Conservation and Utilization of Subtropical Agro‑Bioresources Lingnan Guangdong Laboratory of AgricultureCollege of Animal ScienceSouth China Agricultural UniversityGuangzhouGuangdong 510642China Guangdong Provincial Key lab of Agro‑Animal Genomics and molecular breeding and Key lab of Chicken Genetics Breeding and ReproductionMinistry of AgricultureGuangzhouGuangdong 510642China College of Animal Science and Technology Zhejiang Agriculture and Forestry University666 Wusu RoadLin’an 311300China

As an important epigenetic modification,DNA methylation is involved in many biological processes such as animal cell differentiation,embryonic development,genomic imprinting and sex chromosome inactivation.As DNA methylation sequencing becomes more sophisticated,it becomes possible to use it to solve more zoological problems.This paper reviews the characteristics of DNA methylation,with emphasis on the research and application of DNA methylation in poultry.

关键词： CpG islands Differentially methylated genes Differentially methylated regions DNA methylation Poultry

Two H3K36 methyltransferases differentially associate with transcriptional activity and enrichment of facultative heterochromatin in rice blast fungus

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aBIOTECH 2024年第1期5卷 1-16页

作者： Mengting Xu Ziyue Sun Huanbin Shi Jiangnan Yue Xiaohui Xiong Zhongling Wu Yanjun Kou Zeng Tao Ministry of Agriculture Key laboratory of molecular Biology of Crop Pathogens and Insects Institute of BiotechnologyZhejiang UniversityHangzhou 310058China State Key lab of Rice Biology and breeding China National Rice Research InstituteHangzhou 310021China

Di-and tri-methylation of lysine 36 on histone H3(H3K36me2/3)is catalysed by histone methyltransferase Set2,which plays an essential role in transcriptional regulation.Although there is a single H3K36 methyltransferase in yeast and higher eukaryotes,two H3K36 methyltransferases,Ash1 and Set2,were present in many filamentous fungi.However,their roles in H3K36 methylation and transcriptional regulation remained unclear.Combined with methods of RNA-seq and ChIP-seq,we revealed that both Ash1 and Set2 are redundantly required for the full H3K36me2/3 activity in Magnaporthe oryzae,which causes the devastating worldwide rice blast disease.Ash1 and Set2 distinguish genomic H3K36me2/3-marked regions and are differentially associated with repressed and activated transcription,respectively.Furthermore,Ash1-catalysed H3K36me2 was co-localized with H3K27me3 at the chromatin,and Ash1 was required for the enrichment and transcriptional silencing of H3K27me3-occupied genes.With the different roles of Ash1 and Set2,in H3K36me2/3 enrichment and transcriptional regulation on the stress-responsive genes,they differentially respond to various stresses in M.oryzae.Overall,we reveal a novel mechanism by which two H3K36 methyltransferases catalyze H3K36me2/3 that differentially associate with transcriptional activities and contribute to enrichment of facultative heterochromatin in eukaryotes.

关键词： Ash1 Facultative heterochromatin H3K36me2/3 Magnaporthe oryzae Set2 Transcriptional regulation

Expansion and improvement of ChinaMu by MuT-seq and chromosome-level assembly of the Mu-starter genome

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Journal of Integrative Plant Biology 2024年第4期66卷 645-659页

作者： Lei Liang Yuancong Wang Yanbin Han Yicong Chen Mengfei Li Yibo Wu Zeyang Ma Han Zhao Rentao Song State Key laboratory of Maize Bio-breeding Frontiers Science Center for Molecular Design BreedingJoint International Research Laboratory of Crop Molecular BreedingNational Maize Improvement CenterCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijing 100091China Institute of Crop Germplasm and Biotechnology Jiangsu Provincial Key Laboratory of AgrobiologyJiangsu Academy of Agricultural SciencesNanjing 210014China Sanya Institute of China Agricultural University Sanya 572025China Hainan Yazhou Bay Seed laboratory Sanya 572025China

ChinaMu is the largest sequence-indexed Mutator(Mu)transposon insertional library in maize(Zea mays).In this study,we made significant improvements to the size and quality of the ChinaMu library.We developed a new Mu-tag isolation method Mu-Tn5-seq(MuT-seq).Compared to the previous method used by ChinaMu,MuT-seq recovered 1/3 more germinal insertions,while requiring only about 1/14 of the sequencing volume and 1/5 of the experimental time.Using MuT-seq,we identified 113,879 germinal insertions from 3,168 Mu-active F1 families.We also assembled a high-quality genome for the Mu-active line Mu-starter,which harbors the initial active MuDR element and was used as the pollen donor for the mutation population.Using the Mu-starter genome,we recovered 33,662(15.6%)additional germinal insertions in 3,244(7.4%)genes in the Mu-starter line.The Mu-starter genome also improved the assignment of 117,689(54.5%)germinal insertions.The newly upgraded ChinaMu dataset currently contains 215,889 high-quality germinal insertions.These insertions cover 32,224 pan-genes in the Mu-starter and B73Ref5 genomes,including 23,006(80.4%)core genes shared by the two genomes.As a test model,we investigated Mu insertions in the pentatricopeptide repeat(PPR)superfamily,discovering insertions for 92%(449/487)of PPR genes in ChinaMu,demonstrating the usefulness of ChinaMu as a functional genomics resource for maize.

关键词： ChinaMu Mutator MuT-seq PPR gene Zea mays

LociScan,a tool for screening genetic marker combinations for plant variety discrimination

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The Crop Journal 2024年第2期12卷 583-593页

作者： Yang Yang Hongli Tian Hongmei Yi Zi Shi Lu Wang Yaming Fan Fengge Wang Jiuran Zhao Beijing Key laboratory of Maize DNA Fingerprinting and molecular breeding Maize Research InstituteBeijing Academy of Agriculture and Forestry SciencesBeijing 100097China

To reduce the cost and increase the efficiency of plant genetic marker fingerprinting for variety discrimination,it is desirable to identify the optimal marker combinations.We describe a marker combination screening model based on the genetic algorithm(GA)and implemented in a software tool,Loci Scan.Ratio-based variety discrimination power provided the largest optimization space among multiple fitness functions.Among GA parameters,an increase in population size and generation number enlarged optimization depth but also calculation workload.Exhaustive algorithm afforded the same optimization depth as GA but vastly increased calculation time.In comparison with two other software tools,Loci Scan accommodated missing data,reduced calculation time,and offered more fitness functions.In large datasets,the sample size of training data exerted the strongest influence on calculation time,whereas the marker size of training data showed no effect,and target marker number had limited effect on analysis speed.

关键词： Plant variety discrimination Genetic marker combination Variety discrimination power Genetic algorithm

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Designing salt stress-resilient crops:Current progress and future challenges

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Journal of Integrative Plant Biology 2024年第3期66卷 303-329页

作者： Xiaoyan Liang Jianfang Li Yongqing Yang Caifu Jiang Yan Guo State Key laboratory of Plant Environmental Resilience College of Biological SciencesChina Agricultural UniversityBeijing 100094China State Key laboratory of Nutrient Use and Management College of Resources and Environmental SciencesChina Agricultural UniversityBeijing 100194China Center for Crop Functional Genomics and molecular breeding China Agricultural UniversityBeijing 100094China Frontiers Science Center for molecular Design breeding China Agricultural UniversityBeijing 100193China

Excess soil salinity affects large regions of land and is a major hindrance to crop production worldwide.Therefore,understanding the molecular mechanisms of plant salt tolerance has scientific importance and practical significance.In recent decades,studies have characterized hundreds of genes associated with plant responses to salt stress in different plant species.These studies have substantially advanced our molecular and genetic understanding of salt tolerance in plants and have introduced an era of molecular design breeding of salt-tolerant crops.This review summarizes our current knowledge of plant salt tolerance,emphasizing advances in elucidating the molecular mechanisms of osmotic stress tolerance,salt-ion transport and compartmentalization,oxidative stress tolerance,alkaline stress tolerance,and the trade-off between growth and salt tolerance.We also examine recent advances in understanding natural variation in the salt tolerance of crops and discuss possible strategies and challenges for designing salt stress-resilient crops.We focus on the model plant Arabidopsis(Arabidopsis thaliana)and the four most-studied crops:rice(Oryza sativa),wheat(Triticum aestivum),maize(Zea mays),and soybean(Glycine max).

关键词： molecular design breeding salt stress-resilient crop salt tolerance

Innovative computational tools provide new insights into the polyploid wheat genome

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aBIOTECH 2024年第1期5卷 52-70页

作者： Yongming Chen Wenxi Wang Zhengzhao Yang Huiru Peng Zhongfu Ni Qixin Sun Weilong Guo Frontiers Science Center for molecular Design breeding Key Laboratory of Crop Heterosis and UtilizationBeijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100193China

Bread wheat(Triticum aestivum)is an important crop and serves as a significant source of protein and calories for humans,worldwide.Nevertheless,its large and allopolyploid genome poses constraints on genetic improvement.The complex reticulate evolutionary history and the intricacy of genomic resources make the deciphering of the functional genome considerably more challenging.Recently,we have developed a comprehensive list of versatile computational tools with the integration of statistical models for dissecting the polyploid wheat genome.Here,we summarize the methodological innovations and applications of these tools and databases.A series of step-by-step examples illustrates how these tools can be utilized for dissecting wheat germplasm resources and unveiling functional genes associated with important agronomic traits.Furthermore,we outline future perspectives on new advanced tools and databases,taking into consideration the unique features of bread wheat,to accelerate genomic-assisted wheat breeding.

关键词： Polyploid wheat Genome complexity Functional genomics Tool development

Hi-Tag:a simple and efficient method for identifying protein-mediated long-range chromatin interactions with low cell numbers

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Science China(Life Sciences) 2024年第5期67卷 1027-1034页

作者： Xiaolong Qi Lu Zhang Qiulin Zhao Peng Zhou Sai Xian Zhang Jingjin Li Zhuqing Zheng Yue Xiang Xueting Dai Zhe Jin Yaobang Jian Xinyun Li Liangliang Fu Shuhong Zhao Key lab of Agricultural Animal Genetics Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of AgricultureCollege of Animal Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China The Cooperative Innovation Center for Sustainable Pig Production Wuhan 430070China Hubei Hongshan laboratory Frontiers Science Center for Animal Breeding and Sustainable ProductionWuhan 430070China

Protein-mediated chromatin interactions can be revealed by coupling proximity-based ligation with chromatin immunoprecipitation.However,these techniques require complex experimental procedures and millions of cells per experiment,which limits their widespread application in life science research.Here,we develop a novel method,Hi-Tag,that identifies high-resolution,long-range chromatin interactions through transposase tagmentation and chromatin proximity ligation(with a phosphorothioate-modified linker).Hi-Tag can be implemented using as few as 100,000 cells,involving simple experimental procedures that can be completed within 1.5 days.Meanwhile,Hi-Tag is capable of using its own data to identify the binding sites of specific proteins,based on which,it can acquire accurate interaction information.Our results suggest that Hi-Tag has great potential for advancing chromatin interaction studies,particularly in the context of limited cell availability.

关键词： Hi-Tag chromatin interactions transposase tagmentation chromatin proximity ligation low cell numbers