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A k-mer-based pangenome approach for cataloging seed-storage-protein genes in wheat to facilitate genotype-to-phenotype prediction and improvement of end-use quality

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molecular Plant 2024年第7期17卷 1038-1053页

作者： Zhaoheng Zhang Dan Liu Binyong Li Wenxi Wang Jize Zhang Mingming Xin Zhaorong Hu Jie Liu Jinkun Du Huiru Peng Chenyang Hao Xueyong Zhang Zhongfu Ni Qixin Sun Weilong Guo Yingyin Yao Frontiers Science Center for molecular Design breeding Key Laboratory of Crop Heterosis and Utilization(MOE)and Bejing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing100193China key laboratory of crop Gene Resources and breeding Institute of Crop ScienceChinese Academy of Agricultural SciencesBejingChina

Wheat is a staple foodfor more than 35%of the world's population,with wheatflourused to make hundreds of baked *** end-use quality is a major breeding target;however,improving it is especially time-consuming and ***,genes encoding seed-storage proteins(ssPs)form multigene families and are repetitive,with gaps commonplace in several genome *** overcome these barriers and efficiently identify superior wheat SSP alleles,we developed"PanSK"(Pan-SSP k-mer)for genotype-to-phenotype prediction based on an SsP-based pangenome *** uses 29-mer sequences that represent each ssP gene at the pangenomic level to reveal untapped diversity across landraces and modern ***-wide association studies with k-mers identified 23 Ssp genes associated with end-use quality that represent novel targets for *** evaluated the effect of rye secalin genes on end-use quality and found that removal of w-secalins from 1BL/1RS wheat translocation lines is associated with enhanced end-use ***,using machine-learning-based prediction inspired by PanSK,we predicted the quality phenotypes with high accuracy from genotypes *** study provides an effective approach for genome design based on ssP genes,enabling the breeding of wheat varieties with superior processing capabilities and improved end-use quality.

关键词： wheat seed-storage protein end-use quality k-mer pangenome genomic prediction

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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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The gene encoding flavonol synthase contributes to lesion mimic in wheat

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The crop Journal 2024年第3期12卷 814-825页

作者： Tingting Dong Hongchun Xiong Huijun Guo Yongdun Xie Linshu Zhao Jiayu Gu Huiyuan Li Shirong Zhao Yuping Ding Xiyun Song Luxiang Liu College of Life Sciences Key Laboratory of Major Crop Germplasm Innovation and Application in QingdaoQingdao Agricultural UniversityQingdao 266109ShandongChina State key laboratory of crop Gene Resources and breeding/National Engineering laboratory of crop molecular breeding/CAEA Research and Development Centre on Nuclear Technology Applications for Irradiation Mutation breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Lesion mimic often exhibits leaf disease-like symptoms even in the absence of pathogen infection,and is characterized by a hypersensitive-response(HR)that closely linked to plant disease *** this,only a few lesion mimic genes have been identified in *** this investigation,a lesion mimic wheat mutant named je0297 was discovered,showing no alteration in yield components when compared to the wild type(WT).Segregation ratio analysis of the F_(2)individuals resulting from the cross between the WT and the mutant revealed that the lesion mimic was governed by a single recessive gene in *** Bulked segregant analysis(BSA)and exome capture sequencing,we mapped the lesion mimic gene designated as lm6 to chromosome *** gene fine mapping using 3315 F_(2)individuals delimited the lm6 within a 1.18 Mb *** this region,we identified 16 high-confidence genes,with only two displaying mutations in ***,one of the two genes,responsible for encoding flavonol synthase,exhibited altered expression *** phenotype analysis of TILLING mutants confirmed that the gene encoding flavonol synthase was indeed the causal gene for *** sequencing analysis revealed that the DEGs between the WT and mutant were significantly enriched in KEGG pathways related to flavonoid biosynthesis,including flavone and flavonol biosynthesis,isoflavonoid biosynthesis,and flavonoid biosynthesis ***,more than 30 pathogen infection-related(PR)genes exhibited upregulation in the *** to this expression pattern,the flavonoid content in je0297 showed a significant decrease in the 4^(th)leaf,accompanied by a notable accumulation of reactive oxygen,which likely contributed to the development of lesion mimic in the *** investigation enhances our comprehension of cell death signaling pathways and provides a valuable gene resource for the breeding of disease-resistant wheat.

关键词： Lesion mimic mutant Wheat Gene mapping Flavonol synthase gene Flavonoid

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Integrating machine learning and genome editing for crop improvement

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aBIOTECH 2024年第2期5卷 262-277页

作者： Long Chen Guanqing Liu Tao Zhang Jiangsu key laboratory of crop Genomics and molecular breeding/Zhongshan Biological breeding laboratory/key laboratory of Plant Functional Genomics of the Ministry of Education Agricultural College of Yangzhou UniversityYangzhou 225009China Jiangsu Co-Innovation Center for Modern Production Technology of Grain crops/Jiangsu key laboratory of crop Genetics and Physiology Yangzhou UniversityYangzhou 225009China

Genome editing is a promising technique that has been broadly utilized for basic gene function studies and trait ***,the exponential growth of computational power and big data now promote the application of machine learning for biological *** this regard,machine learning shows great potential in the refinement of genome editing systems and crop ***,we review the advances of machine learning to genome editing optimization,with emphasis placed on editing efficiency and specificity ***,we demonstrate how machine learning bridges genome editing and crop breeding,by accurate key site detection and guide RNA ***,we discuss the current challenges and prospects of these two techniques in crop *** integrating advanced genome editing techniques with machine learning,progress in crop breeding will be further accelerated in the future.

关键词： Machine learning Genome editing crop improvement molecular design breeding

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Fine mapping of two recessive genes TaFLA1 and TaSPL8 controlling flag leaf angle in bread wheat

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The crop Journal 2024年第4期12卷 1159-1167页

作者： Qiushi Wang Jiaxing Bai Hongchun Xiong Yongdun Xie Chaojie Wang Jiayu Gu Linshu Zhao Huiyuan Li Jinfeng Zhang Shirong Zhao Yuping Ding Zhengwu Fang Huijun Guo Luxiang Liu College of Agriculture Yangtze University/MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River(Co-Construction by Ministry and Province)Jingzhou 434000HubeiChina State key laboratory of crop Gene Resources and breeding/National Engineering laboratory of crop molecular breeding/CAEA Research and Development Centre on Nuclear Technology Applications for Irradiation Mutation breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Flag leaf angle is one of the key target traits in high yield wheat breeding.A smaller flag leaf angle reduces shading and enables plants to grow at a higher density,which increases *** we identified a mutant,je0407,with an 84.34%-89.35%smaller flag leaf angle compared with the wild *** mutant also had an abnormal lamina joint and no ligule or *** analysis indicated that the ligule was controlled by two recessive genes,which were mapped to chromosomes 2AS and *** mutant allele on chromosome 2AS was named Tafla1b,and it was fine mapped to a 1 Mb physical *** mutant allele on chr.2DL was identified as Taspl8b,a novel allele of TaSPL8 with a missense mutation in the second exon,which was used to develop a cleaved amplified polymorphic sequence marker.F3 and F4 lines derived from crosses between Jing411 and je0407 were genotyped to investigate interactions between the Tafla1b and Taspl8b *** with the Tafla1b/Taspl8a genotype had 58.41%-82.76%smaller flag leaf angles,6.4%-24.9%shorter spikes,and a greater spikelet density(0.382 more spikelets per cm)compared with the wild *** with the Tafla1a/Taspl8b genotype had 52.62%-82.24%smaller flag leaf angles and no differences in plant height or spikelet density compared with the wild ***1b/Taspl8b plants produced erect leaves with an abnormal lamina *** two alleles had dosage effects on ligule formation and flag leaf angle,but no significant effect on thousand-grain *** mutant alleles provide novel resources for improvement of wheat plant architecture.

关键词： Wheat Ligule Flag leaf angle Fine mapping Tafla1 Taspl8

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OsbZIP53 Negatively Regulates Immunity Response by Involving in Reactive Oxygen Species and Salicylic Acid Metabolism in Rice

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Rice science 2024年第2期31卷 190-202,I0022-I0028页

作者： WU Lijuan HAN Cong WANG Huimei HE Yuchang LIN Hai WANG Lei CHEN Chen E Zhiguo State key laboratory of Rice Biology and breeding China National Rice Research InstituteHangzhou 310006China Jiangsu key laboratory of crop Genetics and Physiology/key laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu key laboratory of crop Genomics and molecular breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain crops Agricultural College of Yangzhou UniversityYangzhou 225009China

The basic region/leucine zipper(bZIP)transcription factors play important roles in plant development and responses to abiotic and biotic ***53 regulates resistance to Magnaporthe oryzae in rice by analyzing APIP5-RNAi transgenic *** further investigate the biological functions of OsbZIP53,we generated osbzip53 mutants using CRISPR/Cas9 editing and also constructed OsbZIP53 over-expression transgenic *** analysis of phenotypical,physiological,and transcriptional data showed that knocking-out OsbZIP53 not only improved disease resistance by inducing a hypersensitivity response in plants,but also regulated the immune response through the salicylic acid ***,disrupting OsbZIP53 increased H2O2 accumulation by promoting reactive oxygen species generation through up-regulation of several respiratory burst oxidase homologs(Osrboh genes)and weakened H2O2 degradation by directly targeting *** addition,the growth of osbzip53 mutants was seriously impaired,while OsbZIP53 over-expression lines displayed a similar phenotype to the wild type,suggesting that OsbZIP53 has a balancing effect on rice immune response and growth.

关键词： OsbZIP53 hypersensitive response reactive oxygen species metabolism rice immunity salicylic acid transcription factor

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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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lcQTH:Rapid quantitative trait mapping by tracing parental haplotypes with ultra-low-coverage sequencing

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Plant Communications 2024年第10期5卷 5-7页

作者： Wenxi Wang Zhe Chen Zhengzhao Yang Zihao Wang Jilu Liu Jie Liu Huiru Peng Zhenqi Su 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

Dear Editor,Gene cloning has a fundamental role in crop research but has long been hindered by high costs and labor requirements,which have limited the numbers of genes that have been functionally characterized,especially in wheat(Liang et al.,2021).Quantitative trait locus(QTL)mapping is the first step in gene cloning,enabling the localization of genomic loci that show significant associations with quantitative *** commonly used strategy is based on single-nucleotide polymorphism(SNP)arrays(Sun et al.,2020).

关键词： trait mapping parental

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The RNA binding protein EHD6 recruits the m^(6)A reader YTH07 and sequesters OsCOL4 mRNA into phase-separated ribonucleoprotein condensates to promote rice flowering

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molecular Plant 2024年第6期17卷 935-954页

作者： Song Cui Peizhe Song Chaolong Wang Saihua Chen Benyuan Hao Zhuang Xu Liang Cai Xu Chen Shanshan Zhu Xiangchao Gan Hui Dong Yuan Hu Liang Zhou Haigang Hou Yunlu Tian Xi Liu Liangming Chen Shijia Liu Ling Jiang Haiyang Wang Guifang Jia Shirong Zhou Jianmin Wan State key laboratory for crop Genetics&Germplasm Enhancement and Utilization Zhongshan Biological Breeding LaboratoryNational Observation and Research Station of Rice Germplasm ResourcesNanjing Agricultural UniversityNanjing 210095China State key laboratory for crop Gene Resources and breeding Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular SciencesKey Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of EducationCollege of Chemistry and Molecular EngineeringPeking-Tsinghua Center for Life SciencesBeijing Advanced Center of RNA BiologyPeking UniversityBeijingChina Jiangsu key laboratory of crop Genomics and molecular breeding Agricultural College of Yangzhou UniversityYangzhou 225009China Max Planck Institute for Plant breeding Research Carl-von-Linne´-Weg 1050829 KolnGermany

N6-Methyladenosine(m^(6)A)is one of the most abundant modifications of eukaryotic mRNA,but its comprehensive biological functionality remains further *** this study,we identified and characterized a new flowering-promoting gene,EARLY HEADING DATE6(EHD6),in ***6 encodes an RNA recognition motif(RRM)-containing RNA binding protein that is localized in the non-membranous cytoplasm ribonucleoprotein(RNP)granules and can bind both m^(6)A-modified RNA and unmodified RNA *** found that EHD6 can physically interact with YTH07,a YTH(YT521-B homology)domain-containing m^(6)A *** showed that their interaction enhances the binding of an m^(6)A-modified RNA and triggers relocation of a portion of YTH07 from the cytoplasm into RNP granules through phase-separated *** these condensates,the mRNA of a rice flowering repressor,CONSTANS-like 4(OsCOL4),becomes sequestered,leading to a reduction in its protein abundance and thus accelerated flowering through the Early heading date 1 *** together,these results not only shed new light on the molecular mechanism of efficient m^(6)A recognition by the collaboration between an RNA binding protein and YTH family m^(6)A reader,but also uncover the potential for m^(6)A-mediated translation regulation through phaseseparated ribonucleoprotein condensation in rice.

关键词： N6-methyladenosine m^(6)A EHD6 YTH domain-containing protein phase separation heading date

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Dynamics and genetic regulation of macronutrient concentrations during grain development in maize

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Journal of Integrative Agriculture 2024年第3期23卷 781-794页

作者： Pengcheng Li Shuangyi Yin Yunyun Wang Tianze Zhu Xinjie Zhu Minggang Ji Wenye Rui Houmiao Wang Chenwu Xu Zefeng Yang Jiangsu key laboratory of crop Genetics and Physiology/key laboratory of Plant Functional Genomics Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Agricultural CollegeYangzhou UniversityYangzhou 225009China Jiangsu Co-lnnovation Center for Modern Production Technology of Grain crops Yangzhou UniversityYangzhou 225009China

Nitrogen(N), phosphorus(P), and potassium(K) are essential macronutrients that are crucial not only for maize growth and development, but also for crop yield and quality. The genetic basis of macronutrient dynamics and accumulation during grain filling in maize remains largely unknown. In this study, we evaluated grain N, P, and K concentrations in 206 recombinant inbred lines generated from a cross of DH1M and T877 at six time points after pollination. We then calculated conditional phenotypic values at different time intervals to explore the dynamic characteristics of the N, P, and K concentrations. Abundant phenotypic variations were observed in the concentrations and net changes of these nutrients. Unconditional quantitative trait locus(QTL) mapping revealed 41 non-redundant QTLs, including 17, 16, and 14 for the N, P, and K concentrations, respectively. Conditional QTL mapping uncovered 39 non-redundant QTLs related to net changes in the N, P, and K concentrations. By combining QTL, gene expression, co-expression analysis, and comparative genomic data, we identified 44, 36, and 44 candidate genes for the N, P, and K concentrations, respectively, including GRMZM2G371058 encoding a Doftype zinc finger DNA-binding family protein, which was associated with the N concentration, and GRMZM2G113967encoding a CBL-interacting protein kinase, which was related to the K concentration. The results deepen our understanding of the genetic factors controlling N, P, and K accumulation during maize grain development and provide valuable genes for the genetic improvement of nutrient concentrations in maize.

关键词： maize nutrient concentration unconditional QTL mapping conditional QTL mapping dynamic trait

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