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A wheat integrative regulatory network from large-scale complementary functional datasets enables trait-associated gene discovery for crop improvement

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Molecular Plant 2023年第2期16卷 393-414页

作者： Yongming Chen Yiwen Guo Panfeng Guan Yongfa Wang Xiaobo Wang Zihao Wang Zhen Qin Shengwei Ma Mingming Xin Zhaorong Hu Yingyin Yao zhongfu ni Qixin Sun Weilong Guo Huiru Peng Frontiers Science Center for Molecular Design Breeding Key Laboratory of Crop Heterosis and UtilizationBeijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100193China Hainan Yazhou Bay Seed Laboratory SanyaHainanChina State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina

Gene regulation is central to all aspects of organism growth,and understanding it using large-scale functional datasets can provide a whole view of biological processes controlling complex phenotypic traits in ***,the connection between massive functional datasets and trait-associated gene discovery for crop improvement is still *** this study,we constructed a wheat integrative gene regulatory network(wGRN)by combining an updated genome annotation and diverse complementary functional datasets,including gene expression,sequence motif,transcription factor(TF)binding,chromatin accessibility,and evolutionarily conserved *** contains 7.2 million genome-wide interactions covering 5947 TFs and 127439 target genes,which were further verified using known regulatory relationships,condition-specific expression,gene functional information,and *** used wGRN to assign genome-wide genes to 3891 specific biological pathways and accurately prioritize candidate genes associated with complex phenotypic traits in genome-wide association *** addition,wGRN was used to enhance the interpretation of a spike temporal transcriptome dataset to construct high-resolution *** further unveiled novel regulators that enhance the power of spike phenotypic trait prediction using machine learning and contribute to the spike phenotypic differences among modern wheat ***,we developed an interactive webserver,wGRN(http://***/wGRN),for the community to explore gene regulation and discover trait-associated ***,this community resource establishes the foundation for using large-scale functional datasets to guide trait-associated gene discovery for crop improvement.

关键词： wheat integrative gene regulatory network functional gene discovery phenotype prediction crop improvement

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A highly conserved amino acid in high molecular weight glutenin subunit 1Dy12 contributes to gluten functionality and processing quality in wheat

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Journal of Genetics and Genomics 2023年第11期50卷 909-912页

作者： Changfeng Yang Qian Chen Mingming Xin Zhenqi Su Jinkun Du Weilong Guo Zhaorong Hu Jie Liu Huiru Peng zhongfu ni Qixin Sun Yingyin Yao Frontiers Science Center for Molecular Design Breeding Key Laboratory of Crop Heterosis and Utilization(MOE)Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100193China

Bread wheat(Triticum aestivum L.)is one of the most commonly consumed staples worldwide,with widespread uses in foods such as breads,noodles,cakes,and cookies(Veraverbeke and Delcour,2002).The specific cooking properties of wheat products are mainly conferred by the gluten proteins contained in wheat grains(Delcour et al.,2012).High molecular weight glutenin subunits(HMW-GSs)are important constituents of wheat gluten proteins,largely determining gluten elasticity and processing quality(Branlard and Dardevet,1985;Payne et al.,1988).

关键词： weight wheat gluten

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Natural variations of HvSRN1 modulate the spike rachis node number in barley

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Plant Communications 2024年第1期5卷 148-163页

作者： Chaofeng Fan Dongdong Xu Chunchao Wang Zhaoyan Chen Tingyu Dou Dandan Qin Aikui Guo Meng Zhao Honghong Pei Mengwei Zhao Renxu Zhang Ke Wang Jing Zhang zhongfu ni Ganggang Guo Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization(MARA) The National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural Sciences(ICS-CAAS)Beijing 100081China Hainan Yazhou Bay Seed Laboratory Sanya 572025China Institute of Industrial Crops Shandong Academy of Agricultural SciencesJinan 250100China Key Laboratory of Crop Heterosis and Utilization Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100193China Key Laboratory for Crop Molecular Breeding of Ministry of Agriculture and Rural Affairs Institute of Food CropsHubei Academy of Agricultural SciencesWuhan 430064China

Grain number,one of the major determinants of yield in Triticeae crops,is largely determined by spikelet number and spike rachis node number(SRN).Here,we identified three quantitative trait loci(QTLs)for SRN using 145 recombinant inbred lines derived from a barley R90/1815D ***1,the major-effect QTL,was mapped to chromosome 2H and explained up to 38.77%of SRN ***-based cloning revealed that qSRN1 encodes the RAWUL domain-containing protein *** analysis revealed that two key SNPs in the HvSRN1 promoter region(-2 kb upstream of the transcription start site)affect the transcript level of HvSRN1 and contribute to variation in *** to its orthologous proteins OsLAX2 and ZmBA2,HvSRN1 showed protein–protein interactions with HvLAX1,suggesting that the LAX2–LAX1 model for spike morphology regulation may be conserved in Poaceae ***-Cas9-induced HvSRN1 mutants showed reduced SRN but increased grain size and weight,demonstrating a trade-off *** results shed light on the role of HvSRN1 variation in regulating the balance between grain number and weight in barley.

关键词： barley fine-mapping grain number kernel weight

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On the evolution and genetic diversity of the bread wheat D genome

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Molecular Plant 2024年第11期17卷 1672-1686页

作者： Zihao Wang Wenxi Wang Yachao He Xiaoming Xie Zhengzhao Yang Xiaoyu Zhang Jianxia niu Huiru Peng Yingyin Yao Chaojie Xie Mingming Xin Zhaorong Hu Qixin Sun zhongfu ni 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 Sanya Institute of China Agricultural University Sanya 572025China

Bread wheat(Triticum aestivum)became a globally dominant crop after incorporating the D genome from the donor species Aegilops tauschii,but the evolutionary history that shaped the D genome during this process remains to be ***,we propose a renewed evolutionary model linking *** and the hexaploid wheat D genome by constructing an ancestral haplotype map covering 762 *** and hexaploid wheat *** dissected the evolutionary trajectories of *** lineages and reported a few independent intermediate accessions,demonstrating that low-frequency intersublineage gene flow had enriched the diversity of *** discovered that the D genome of hexaploid wheat was inherited from a unified ancestral template,but with a mosaic composition that was highly mixed and derived mainly from three *** L2 sublineages located in the Caspian coastal *** result suggests that early agricultural activities facilitated innovations in D-genome composition and finalized the success of *** found that the majority(51.4%)of genetic diversity was attributed to novel mutations absent in ***,and we identified large *** introgressions from various lineages,which expanded the diversity of the wheat D genome and introduced beneficial *** work sheds light on the process of wheat hexaploidization and highlights the evolutionary significance of the multi-layered genetic diversity of the bread wheat D genome.

关键词： wheat Aegilops tauschii D genome genetic diversity evolution

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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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TaACTIN7-D regulates plant height and grain shape in bread wheat

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Journal of Genetics and Genomics 2023年第11期50卷 895-908页

作者： Xiongtao Li Beilu Cao Dejie Du Long Song Lulu Tian Xiaoming Xie Zhaoyan Chen Yanpeng Ding Xuejiao Cheng Yingyin Yao Weilong Guo Zhenqi Su Qixin Sun zhongfu ni Lingling Chai Jie Liu Frontiers Science Center for Molecular Design Breeding China Agricultural UniversityBeijing 100193China State Key Laboratory for Crop Genetics and Germplasm Enhancement Nanjing Agricultural UniversityNanjingJiangsu 210095China

Exploitation of new gene resources and genetic networks contributing to the control of crop yield-related traits,such as plant height,grain size,and shape,may enable us to breed modern high-yielding wheat varieties through molecular *** this study,via ethylmethanesulfonate mutagenesis,we identify a wheat mutant plant,mu-597,that shows semi-dwarf plant architecture and round grain *** bulked segregant RNA-seq and map-based cloning,the causal gene for the semi-dwarf phenotype of mu-597 is *** find that a single-base mutation in the coding region of TaACTIN7-D(TaACT7-D),leading to a Gly-to-Ser(G65S)amino acid mutation at the 65th residue of the deduced TaACT7-D protein,can explain the semi-dwarfism and round grain shape of *** evidence shows that the G65S mutation in TaACT7-D hinders the polymerization of actin from monomeric(G-actin)to filamentous(F-actin)status while attenuates wheat responses to multiple phytohormones,including brassinosteroids,auxin,and ***,these findings not only define a new semi-dwarfing gene resource that can be potentially used to design plant height and grain shape of bread wheat but also establish a direct link between actin structure modulation and phytohormone signal transduction.

关键词： Wheat(Triticum aestivum L.) Plant height Grain shape TaACT7-D Phytohormone signaling

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Paternally imprinted LATE-FLOWERING2 transcription factor contributes to paternal-excess interploidy hybridization barriers in wheat∞

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Journal of Integrative Plant Biology 2023年第12期65卷 2587-2603页

作者： Guanghui Yang Man Feng Kuohai Yu Guangxian Cui Yan Zhou Lv Sun Lulu Gao Yumei Zhang Huiru Peng Yingyin Yao Zhaorong Hu Vincenzo Rossi Ive De Smet zhongfu ni Qixin Sun Mingming Xin State Key Laboratory for Agrobiotechnology Key Laboratory of Crop Heterosis Utilization(MOE)Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100193China Qingdao Agricultural University Qingdao 266109China Council for Agricultural Research and Economics Research Centre for Cereal and Industrial CropsBergamo 24126Italy Department of Plant Biotechnology and Bioinformatics Ghent UniversityGhent B‐9052Belgium VIB Center for Plant Systems Biology Ghent B‐9052Belgium

Interploidy hybridization between hexaploid and tetraploid genotypes occurred repeatedly during genomic introgression events throughout wheat evolution,and is commonly employed in wheat breeding *** wheat usually serves as maternal parent because the reciprocal cross generates progeny with severe defects and poor seed germination,but the underlying mechanism is poorly ***,we performed detailed analysis of phenotypic variation in endosperm between two interploidy reciprocal crosses arising from tetraploid(Triticum durum,AABB)and hexaploid wheat(Triticum aestivum,AABBDD).In the paternal‐versus the maternal‐excess cross,the timing of endosperm cellularization was delayed and starch granule accumulation in the endosperm was repressed,causing reduced germination *** expression profiles of genes involved in nutrient metabolism differed strongly between these endosperm ***,expression patterns of parental alleles were dramatically disturbed in interploidy versus intraploidy crosses,leading to increased number of imprinted *** endosperm‐specific TaLFL2 showed a paternally imprinted expression pattern in interploidy crosses partially due to allele‐specific DNA *** TaLFL2 binds to and represses a nutrient accumulation regulator TaNAC019,leading to reduced storage protein and starch accumulation during endosperm development in paternal‐excess cross,as confirmed by interploidy crosses between tetraploid wild‐type and clustered regularly interspaced palindromic repeats(CRISPR)–CRISPR‐associated protein 9 generated hexaploid *** findings reveal a contribution of genomic imprinting to paternal‐excess interploidy hybridization barriers during wheat evolution history and explains why experienced breeders preferentially exploit maternal‐excess interploidy crosses in wheat breeding programs.

关键词： imprinting interploidy cross wheat

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Clone and characterization of differentially expressed ZmRR7 gene between maize(Zea mays L.) hybrids and its parental inbreds

Clone and characterization of differentially expressed ZmRR7...

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第十四届全国植物基因组学大会

作者： Chuan Li Lingxue Meng Qixin Sun zhongfu ni State Key Laboratory for Agrobiotechnology China Agricultural UniversityNational Plant Gene Research Centre(Beijing)Key Laboratory of Crop Heterosis and UtilizationMinistry of EducationBeijing Key Laboratory of Crop Genetic Improvement

Plant organ size is a very important trait and often shows obvious ***, which has occupied the largest sown area in China,is used as a model plant for heterosis *** length,width and area of the third leaf maize hybrid... 详细信息

关键词： maize heterosis differential expression leaf area cell number

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TaANR1-TaMADS25 module regulates lignin biosynthesis and root development in wheat(Triticum aestivum L.)

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Journal of Genetics and Genomics 2023年第11期50卷 917-920页

作者： Weiya Xu Yongming Chen Bin Liu Qiuyuan Li Yilan Zhou Xuanshuang Li Weilong Guo Zhaorong Hu Zhenshan Liu Mingming Xin Yingyin Yao Mingshan You Huiru Peng zhongfu ni Jiewen Xing Key Laboratory of Crop Heterosis and Utilization(MOE) Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100193China State Key Laboratory of Crop Stress Biology for Arid Areas College of AgronomyNorthwest A&F UniversityYanglingShaanxi 712100China

Common wheat is a staple food for 35%of the global population,therefore increasing wheat yield in an ever-changing environment is essential for food security in the present day(Peng et al.,2011).Root system is responsible for water and nutrient acquisition,thus crucial for competitive fitness and crop yield in challenging environments(Karlova et al.,2021;Liu et al.,2022).Over the past decades,extensive research has focused on identifying genes accountable for root growth and development in plants(Rogers and Benfey,2015).However,only a limited number of genes have been cloned in wheat(Li et al.,2021).

关键词： wheat environments Root

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Phosphorylation of KAT-2B by WKS1/Yr36 redirects the lipid flux to jasmonates to enhance resistance against wheat stripe rust

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Journal of Genetics and Genomics 2023年第11期50卷 872-882页

作者： Yan Yan Xiao-Ming Li Yun Chen Tian-Tian Wu Ci-Hang Ding Mei-Qi Zhang Yue-Ting Guo Chu-Yang Wang Junli Zhang Xuebin Zhang Awais Rasheed Shengchun Xu Meng-Lu Wang zhongfu ni Qixin Sun 缑金营 Frontiers Science Center for Molecular Design Breeding(MOE) China Agricultural UniversityBeijing 100193China Xianghu Laboratory HangzhouZhejiang 311231China School of Life Sciences Fudan UniversityShanghai 200438China Institute of Metabolism and Integrative Biology Fudan UniversityShanghai 200438China State Key Laboratory of Crop Stress Adaptation and Improvement Henan Joint International Laboratory for Crop Multi-Omics ResearchSchool of Life SciencesHenan UniversityKaifengHenan 475004China International Maize and Wheat Improvement Center(CIMMYT) Chinese Academy of Agricultural SciencesBeijing 100081China

Wheat(Triticum aestivum)is one of the most essential human energy and protein ***,wheat production is threatened by devastating fungal diseases such as stripe rust,caused by Puccinia striiformis ***(Pst).Here,we reveal that the alternations in chloroplast lipid profiles and the accumulation of jasmonate(JA)in the necrosis region activate JA signaling and trigger the host *** collapse of chloroplasts in the necrosis region results in accumulations of polyunsaturated membrane lipids and the lipid-derived phytohormone JA in transgenic lines of Yr36 that encodes Wheat Kinase START 1(WKS1),a high-temperature-dependent adult plant resistance ***1.1,a protein encoded by a full-length splicing variant of WKS1,phosphorylates and enhances the activity of keto-acyl thiolase(KAT-2B),a critical enzyme catalyzing theβ-oxidation reaction in JA *** premature stop mutant,kat-2b,accumulates less JA and shows defects in the host defense against ***,overexpression of KAT-2B results in a higher level of JA and limits the growth of ***,JA inhibits the growth and reduces pustule densities of *** study illustrates the WKS1.1-KAT-2B-JA pathway for enhancing wheat defense against fungal pathogens to attenuate yield loss.

关键词： Wheat Stripe rust Cell death Jasmonate Hostdefense

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