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IbNIEL-mediated degradation of IbNAC087 regulates jasmonic acid-dependent salt and drought tolerance in sweet potato

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Journal of Integrative Plant Biology 2024年第2期66卷 176-195页

作者： Xu Li Zhen Wang Sifan Sun Zhuoru Dai Jun Zhang Wenbin Wang Kui Peng Wenhao Geng Shuanghong Xia Qingchang Liu Hong Zhai Shaopei Gao Ning Zhao Feng Tian Huan Zhang Shaozhen He key laboratory of Sweet Potato Biology and Biotechnology Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis&Utilization and Joint Laboratory for International Cooperation in Crop Molecular BreedingMinistry of EducationCollege of Agronomy&BiotechnologyChina Agricultural UniversityBeijing 100193China Sanya Institute of China Agricultural University Sanya 572025China State key laboratory of Plant Physiology and Biochemistry National Maize Improvement CenterKey Laboratory of Biology and Genetic Improvement of MaizeBeijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100193China

Sweet potato(Ipomoea batatas[L.]Lam.)is a crucial staple and bioenergy *** abiotic stress tolerance holds significant importance in fully utilizing marginal *** processes regulate abiotic stress responses,yet the molecular regulatory mechanisms in sweet potato remain *** this study,a NAC(NAM,ATAF1/2,and CUC2)transcription factor,IbNAC087,was identified,which is commonly upregulated in salt-and drought-tolerant *** of IbNAC087 increased salt and drought tolerance by increasing jasmonic acid(JA)accumulation and activating reactive oxygen species(ROS)scavenging,whereas silencing this gene resulted in opposite ***-rich IbNAC087-OE(overexpression)plants exhibited more stomatal closure than wild-type(WT)and IbNAC087-Ri plants under NaCl,polyethylene glycol,and methyl jasmonate ***087 functions as a nuclear transcriptional activator and directly activates the expression of the key JA biosynthesisrelated genes lipoxygenase(IbLOX)and allene oxide synthase(IbAOS).Moreover,IbNAC087 physically interacted with a RING-type E3 ubiquitin ligase NAC087-INTERACTING E3 LIGASE(IbNIEL),negatively regulating salt and drought tolerance in sweet *** ubiquitinated IbNAC087 to promote 26S proteasome degradation,which weakened its activation on IbLOX and *** findings provide insights into the mechanism underlying the IbNIEL-IbNAC087 module regulation of JA-dependent salt and drought response in sweet potato and provide candidate genes for improving abiotic stress tolerance in crops.

关键词： abiotic tolerance IbNAC087 IbNIEL JA sweet potato

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OcBSA:An NGS-based bulk segregant analysis tool for outcross populations

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Molecular Plant 2024年第4期17卷 648-657页

作者： Lingkui Zhang Yanfeng Duan Zewei Zhang Lei Zhang Shumin Chen Chengcheng Cai Shaoguang Duan Kang Zhang Guangcun Li Feng Cheng State key laboratory of Vegetable Biobreeding Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural AffairsKey Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural AffairsSino-Dutch Joint Laboratory of Horticultural GenomicsInstitute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijing 100081China

Constructing inbred lines for self-incompatible species and species with long generation times is challenging,making the use of F1 outcross/segregating populations the main strategy for genetic studies of such ***,there is a lack of dedicated algorithms/tools for rapid quantitative trait locus(QTL)mapping using the F1 *** this end,we have designed and developed an algorithm/tool called OcBSA specifically for QTL mapping of F1 *** transforms the four-haplotype inheritance problem from the two heterozygous diploid parents of the F1 population into the two-haplotype inheritance problem common in current genetic studies by removing the two haplotypes from the heterozygous parent that do not contribute to phenotype segregation in the F1 *** of OcBSA on 1800 simulated F1 populations demonstrated its advantages over other currently available tools in terms of sensitivity and *** addition,the broad applicability of OcBSA was validated by QTL mapping using seven reported F1 populations of apple,pear,peach,citrus,grape,tea,and *** also used OcBSA to map the QTL for flower color in a newly constructed F1 population of potato generated in this *** OcBSA mapping result was verified by the insertion or deletion markers to be consistent with a previously reported locus harboring the ANTHOCYANIN 2 gene,which regulates potato flower *** together,these results highlight the power and broad utility of OcBSA for QTL mapping using F1 populations and thus a great potential for functional gene mining in outcrossing *** ease of use,we have developed both Windows and Linux versions of OcBSA,which are freely available at:https://***/Bioinformaticslab/OcBSA.

关键词： outcross BSA self-incompatible F1 population QTL mapping potato

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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,***,its large and allopolyploid genome poses constraints on genetic *** complex reticulate evolutionary history and the intricacy of genomic resources make the deciphering of the functional genome considerably more ***,we have developed a comprehensive list of versatile computational tools with the integration of statistical models for dissecting the polyploid wheat ***,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 ***,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

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Improved genome annotation of Brassica oleracea highlights the importance of alternative splicing

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Horticultural Plant Journal 2024年第4期10卷 961-970页

作者： Yinqing Yang Lei Zhang Qi Tang Lingkui Zhang Xing Li Shumin Chen Kang Zhang Ying Li Xilin Hou Feng Cheng State key laboratory of crop genetics and Germplasm Enhancement College of HorticultureNanjing Agricultural UniversityNanjing 210095China State key laboratory of Vegetable Biobreeding Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesKey Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural AffairsSino-Dutch Joint Laboratory of Horticultural GenomicsBeijing 100081China

Brassica oleracea has been developed into many important crops,including cabbage,kale,cauliflower,broccoli and so *** genome and gene annotation of cabbage(cultivar JZS),a representative morphotype of ***,has been widely used as a common reference in biological *** its genome assembly has been updated twice,the current gene annotation still lacks information on untranslated regions(UTRs)and alternative splicing(AS).Here,we constructed a high-quality gene annotation(JZSv3)using a full-length transcriptome acquired by nanopore sequencing,yielding a total of 59452 genes and 75684 ***,we re-analyzed the previously reported transcriptome data related to the development of different tissues and cold response using JZSv3 as a reference,and found that 3843 out of 11908 differentially expressed genes(DEGs)underwent AS during the development of different tissues and 309 out of 903 cold-related genes underwent AS in response to cold ***,we also identified many AS genes,including BolLHCB5 and BolHSP70,that displayed distinct expression patterns within variant transcripts of the same gene,highlighting the importance of JZSv3 as a pivotal reference for AS ***,JZSv3 provides a valuable resource for exploring gene function,especially for obtaining a deeper understanding of AS regulation mechanisms.

关键词： Brassica oleracea Oxford nanopore technologies Gene annotation Alternative splicing

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A centromere map based on super pan-genome highlights the structure and function of rice centromeres

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Journal of Integrative Plant Biology 2024年第2期66卷 196-207页

作者： Yang Lv Congcong Liu Xiaoxia Li Yueying Wang Huiying He Wenchuang He Wu Chen Longbo Yang Xiaofan Dai Xinglan Cao Xiaoman Yu Jiajia Liu Bin Zhang Hua Wei Hong Zhang Hongge Qian Chuanlin Shi Yue Leng Xiangpei Liu Mingliang Guo Xianmeng Wang Zhipeng Zhang Tianyi Wang Bintao Zhang Qiang Xu Yan Cui Qianqian Zhang Qiaoling Yuan Noushin Jahan Jie Ma Xiaoming Zheng Yongfeng Zhou Qian Qian Longbiao Guo Lianguang Shang State key laboratory of Rice Biology China National Rice Research InstituteHangzhou 310006China 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 SciencesShenzhen 518120China Yazhouwan National laboratory No.8 Huanjin RoadYazhou DistrictSanya City 572024China National key Facility for crop Gene Resources and genetic improvement Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China

Rice(Oryza sativa)is a significant crop worldwide with a genome shaped by various evolutionary *** centromeres are crucial for chromosome segregation,and contain some unreported *** to the diverse and complex centromere region,a comprehensive understanding of rice centromere structure and function at the population level is *** constructed a high-quality centromere map based on the rice super pangenome consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African *** showed that rice centromeres have diverse satellite repeat CentO,which vary across chromosomes and subpopulations,reflecting their distinct evolutionary *** also revealed that long terminal repeats(LTRs),especially young Gypsy-type LTRs,are abundant in the peripheral CentO-enriched regions and drive rice centromere expansion and ***,high-quality genome assembly and complete telomere-to-telomere(T2T)reference genome enable us to obtain more centromeric genome information despite mapping and cloning of centromere genes being *** investigated the association between structural variations and gene expression in the rice centromere.A centromere gene,OsMAB,which positively regulates rice tiller number,was further confirmed by expression quantitative trait loci,haplotype analysis and clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated protein9 *** revealing the new insights into the evolutionary patterns and biological roles of rice centromeres,our finding will facilitate future research on centromere biology and crop improvement.

关键词： centromere super pan-genome CentoO satellite repeat rice

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The light and hypoxia induced gene ZmPORB1 determines tocopherol content in the maize kernel

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Science China(Life Sciences) 2024年第3期67卷 435-448页

作者： Nannan Liu Yuanhao Du Shijuan Yan Wei Chen Min Deng Shutu Xu Hong Wang Wei Zhan Wenjie Huang Yan Yin Xiaohong Yang Qiao Zhao Alisdair R.Fernie Jianbing Yan National key laboratory of crop genetic improvement Huazhong Agricultural UniversityWuhan 430070China Hubei Hongshan laboratory Wuhan 430070China Agro-biological Gene Research Center Guangdong Academy of Agricultural SciencesGuangzhou 510640China College of Agronomy Hunan Agricultural UniversityChangsha 410128China College of Agronomy Northwest A&F UniversityXi'an 710000China State key laboratory of North China crop improvement and Regulation Hebei Sub-center of National Maize Improvement Center of ChinaCollege of AgronomyHebei Agricultural UniversityBaoding 071001China College of Life Sciences South-Central Minzu UniversityWuhan 430070China Plant Science Facility of the Institute of Botany Chinese Academy of SciencesBeijing 100093China National Maize improvement Center of China Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100093China Shenzhen key laboratory of Synthetic genomics Guangdong Provincial Key Laboratory of Synthetic GenomicsShenzhen Institute of Synthetic BiologyShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China Max Planck Institute of Molecular Plant Physiology Potsdam-Golm 14476Germany

Tocopherol is an important lipid-soluble antioxidant beneficial for both human health and plant growth. Here, we fine mapped a major QTLqVE1 affecting γ-tocopherol content in maize kernel, positionally cloned and confirmed the underlying gene ZmPORB1(por1), as a protochlorophyllide oxidoreductase. A 13.7 kb insertion reduced the tocopherol and chlorophyll content, and the photosynthetic activity by repressing ZmPORB1 expression in embryos of NIL-K22, but did not affect the levels of the tocopherol precursors HGA(homogentisic acid)and PMP(phytyl monophosphate). Furthermore, ZmPORB1 is inducible by low oxygen and light, thereby involved in the hypoxia response in developing embryos. Concurrent with natural hypoxia in embryos, the redox state has been changed with NO increasing and H_(2)O_(2) decreasing, which lowered γ-tocopherol content via scavenging reactive nitrogen species. In conclusion, we proposed that the lower lightharvesting chlorophyll content weakened embryo photosynthesis, leading to fewer oxygen supplies and consequently diverse hypoxic responses including an elevated γ-tocopherol consumption. Our findings shed light on the mechanism for fine-tuning endogenous oxygen concentration in the maize embryo through a novel feedback pathway involving the light and low oxygen regulation of ZmPORB1 expression and chlorophyll content.

关键词： maize tocopherol hypoxia photosynthesis ZmPORB1

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The cropGPT project:Call for a global,coordinated effort in precision design breeding driven by Al using biological big data

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Molecular Plant 2024年第2期17卷 215-218页

作者： Wanchao Zhu Rui Han Xiaoyang Shang Tao Zhou Chengyong Liang Xiaomeng Qin Hong Chen Zaiwen Feng Hongwei Zhang Xingming Fan Weifu Li Lin Li National key laboratory of crop genetic improvement Huazhong Agricultural UniversityWuhan 430070China key laboratory of Biology and genetic improvement of Maize in Arid Area of Northwest Region College of AgronomyNorthwest A&F UniversityYanglingShaanxi712100China College of Informatics Huazhong Agricultural UniversityWuhan 430070China State key laboratory of crop Gene Resources and Breeding Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China institute of Food crops Sciences Yunnan Academy of Agricultural Sciences2238 Beijing RoadKunmingYunnan 650200China Hubei Hongshan laboratory Wuhan 430070China Shenzhen Institute of Nutrition and Health Huazhong Agricultural UniversityWuhan 430070China Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China

Since the beginning of humanity,people have been seeking practical solutions to meet their most basic need:*** advent of agriculture greatly increased the food supply and led to a rapid increase in the human *** food production via agriculture can be attributed to both improved crop management practices and crop breeding through ***(crop)breeding has been categorized into four major stages based on the techniques employed(Wallace et al.,2018).

关键词： breeding seeking Wallace

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Wide hybridizations reveal the robustness of functional centromeres in Triticum-Aegilops species complex lines

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Journal of genetics and genomics 2024年第5期51卷 570-573页

作者： Yuhong Huang Qinghua Shi Chen Zhou Chunhui Wang Yang Liu Congyang Yi Handong Su Fangpu Han State key laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Bejing 100049China National key laboratory of crop genetic improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhanHubei430070China

The Triticum-Aegilops complex groups demonstrated high cross-affinity with each other to overcome the barriers of distant hybridization(Loureiro et al.,2023).Distant hybridization involves two distinct yet closely related events:hybridization and genome *** studies have indicated that bursts of transposable elements(TEs)can occur as a consequence or concomitant to hybridization or genome duplication(Parisod et al.,2010).This raises an important scientific question regarding how the TEs-rich centromere region copes with genomic shock(McClintock,1984).The Triticum-Aegilops species complexes,particularly in the F1,So,and subsequent early generations resulting from successive selfcrossing,offer an opportunity to investigate whether the centromere environment undergoes reconstruction and the associated mechanisms that maintain genomic stability.

关键词： centromere Triticum complex

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Evolutionary genomics of climatic adaptation and resilience to climate change in alfalfa

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Molecular Plant 2024年第6期17卷 867-883页

作者： Fan Zhang Ruicai Long Zhiyao Ma Hua Xiao Xiaodong Xu Zhongjie Liu Chunxue Wei Yiwen Wang Yanling Peng Xuanwen Yang Xiaoya Shi Shuo Cao Mingna Li Ming Xu Fei He Xueqian Jiang Tiejun Zhang Zhen Wang Xianran Li Long-Xi Yu Junmei Kang Zhiwu Zhang Yongfeng Zhou Qingchuan Yang Institute of Animal Science Chinese Academy of Agricultural SciencesBeijing 100193China 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 School of Grassland Science Beijing Forestry UniversityBeijing 100083China Department of Agronomy and Horticulture University of Nebraska-LincolnLincolnNE 68583USA Department of crop and Soil Sciences Washington State UniversityPullmanWA 99163USA U.S.Department of agriculture-Agricultural Research Service Plant Germplasm Introduction and Testing ResearchProsserWA 99350USA National key laboratory of Tropical crop Breeding Tropical Crops Genetic Resources InstituteChinese Academy of Tropical Agricultural SciencesHaikou 571101China

Given the escalating impact of climate change on agriculture and food security,gaining insights into the evolutionary dynamics of climatic adaptation and uncovering climate-adapted variation can empower the breeding of climate-resilient crops to face future climate ***(Medicago sativa ***),the queen of forages,shows remarkable adaptability across diverse global environments,making it an excellent model for investigating species responses to climate *** this study,we performed population genomic analyses using genome resequencing data from 702 accessions of 24 Medicago species to unravel alfalfa’s climatic adaptation and genetic susceptibility to future climate *** found that interspecific genetic exchange has contributed to the gene pool of alfalfa,particularly enriching defense and stress-response *** introgression between *** ***(***)and alfalfa not only aids alfalfa’s climatic adaptation but also introduces genetic burden.A total of 1671 genes were associated with climatic adaptation,and 5.7%of them were introgressions from *** integrating climate-associated variants and climate data,we identified populations that are vulnerable to future climate change,particularly in higher latitudes of the Northern *** findings serve as a clarion call for targeted conservation initiatives and breeding *** also identified preadaptive populations that demonstrate heightened resilience to climate fluctuations,illuminating a pathway for future breeding ***,this study enhances our understanding about the local adaptation mechanisms of alfalfa and facilitates the breeding of climate-resilient alfalfa cultivars,contributing to effective agricultural strategies for facing future climate change.

关键词： Medicago local adaptation population genetics adaptive introgression genetic vulnerability alfalfa breeding

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genetic and molecular mechanisms of reproductive isolation in the utilization of heterosis for breeding hybrid rice

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Journal of genetics and genomics 2024年第6期51卷 583-593页

作者： Chaolong Wang Xiaowen Yu Jian Wang Zhigang Zhao Jianmin Wan State key laboratory for crop genetics&Germplasm Enhancement and Utlization Nanjing Agricultural UniversityZhongshan Biological Breeding LaboratoryNanjingJiangsu210095China State key laboratory of crop Gene Resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Heterosis,also known as hybrid vigor,is commonly observed in rice *** hybridization of rice species or subspecies exhibits robust hybrid vigor,however,the direct harnessing of this vigor is hindered by reproductive ***,we review recent advances in the understanding of the molecular mechanisms governing reproductive isolation in inter-subspecific and inter-specific *** review encompasses the genetic model of reproductive isolation within and among Oryza sativa species,emphasizing the essential role of mitochondria in this ***,we delve into the molecular intricacies governing the interaction between mitochondria and autophagosomes,elucidating their significant contribution to reproductive ***,our exploration extends to comprehending the evolutionary dynamics of reproductive isolation and speciation in *** on these advances,we offer a forward-looking perspective on how to overcome the challenges of reproductive isolation and facilitate the utilization of heterosis in future hybrid rice breeding endeavors.

关键词： Hybrid vigor Reproductive isolation Hybrid ricebreeding

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