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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

Shaping polyploid wheat for success:Origins,domestication,and the genetic improvement of agronomic traits

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Journal of Integrative Plant Biology 2022年第2期64卷 536-563页

作者： Jie Liu yingyin yao Mingming Xin Huiru Peng zhongfu ni qixin sun State Key Laboratory for Agrobiotechnology Key Laboratory of Crop Heterosis and Utilizationthe Ministry of EducationKey Laboratory of Crop Genetic ImprovementNational Plant Gene Research CentreChina Agricultural UniversityBeijing100193 China

Bread wheat(Triticum aestivum L.,AABBDD,2 n=6 x=42),which accounts for most of the cultivated wheat crop worldwide,is a typical allohexaploid with a genome derived from three diploid wild *** wheat arose and evolved via two sequential allopolyploidization events and was further polished through multiple steps of ***,cultivated allohexaploid bread wheat has numerous advantageous traits,including adaptive plasticity,favorable yield traits,and extended end-use quality,which have enabled its cultivation well beyond the ranges of its tetraploid and diploid progenitors to become a global staple food *** the past decade,rapid advances in wheat genomic research have considerably accelerated our understanding of the bases for the shaping of complex agronomic traits in this polyploid ***,we summarize recent advances in characterizing major genetic factors underlying the origin,evolution,and improvement of polyploid *** end with a brief discussion of the future prospects for the design of gene cloning strategies and modern wheat breeding.

关键词： adaptation bread wheat domestication end-use quality photoperiod response polyploid semi-dwarfing breeding vernalization

Ectopic Overexpression of Wheat Adenosine Diphosphate-ribosylation Factor,TaARF,Increases Growth Rate in Arabidopsis

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Journal of Integrative Plant Biology 2009年第1期51卷 35-44页

作者： yingyin yao zhongfu ni Jinkun Du Zongfu Han Yan chen Qingbo Zhang qixin sun Department of Plant Genetics & Breeding and State Key Laboratory for Agrobiotechnology Key Laboratory of Crop Heterosis and UtilizationMinistry of Education Key Laboratory of Crop Genomics and Genetic Improvement Ministry of Agdculture Beijing Key Laboratory of Crop Genetic Improvement China Agricultural University Beijing 100094 China

Differential gene expression between hybrids and their parents is considered to be associated with heterosis. However, the physiological functions and possible contribution to heterosis of these differentially expressed genes are unknown. We have isolated one hybrid upregulated gene encoding putative wheat ADP-ribosylation factor, designated TaARF. In this study, real-time quantitative reverse transcription-polymerase chain reaction analysis indicated that the TaARF transcript was preferentially expressed in root, node and crown, and the accumulation of TaARF mRNA in hybrid was more than 1.5-fold higher than that in two parents. In order to understand possible roles of the putative wheat ARF gene, TaARF was overexpressed in Arabidopsis, and the transgenic plants were characterized. We show that ectopic overexpression of TaARF in Arabidopsis leads to increased leaf area, increased growth rate and earlier transition to flowering, suggesting that TaARF plays significant roles in growth and development. This study provides evidence demonstrating that TaARF plays important roles in growth and development and we speculate that the upregulated expression of this gene might contribute to the heterosis observed in wheat root and leaf growth.

关键词： adenosine diphosphate-ribosylation factor Arabidopsis ectopic heterosis overexpression wheat.

The genetic and molecular basis for improving heat stress tolerance in wheat

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aBIOTECH 2022年第1期3卷 25-39页

作者： Lv sun Jingjing Wen Huiru Peng yingyin yao Zhaorong Hu zhongfu ni qixin sun Mingming Xin Key Laboratory of Crop Heterosis Utilization(MOE) China Agricultural UniversityBeijing 100193China

Wheat production requires at least-2.4%increase per year rate by 2050 globally to meet food ***,heat stress results in serious yield loss of wheat ***,wheat has evolved genetic basis and molecular mechanisms to protect themselves from heat-induced ***,it is very urgent to understand the underlying genetic basis and molecular mechanisms responsive to elevated temperatures to provide important strategies for heat-tolerant varieties *** this review,we focused on the impact of heat stress on morphology variation at adult stage in wheat breeding *** also summarize the recent studies of genetic and molecular factors regulating heat tolerance,including identification of heat stress tolerance related QTLs/genes,and the regulation pathway in response to heat *** addition,we discuss the potential ways to improve heat tolerance by developing new technologies such as genome *** review of wheat responses to heat stress may shed light on the understanding heat-responsive mechanisms,although the regu-latory network of heat tolerance is still ambiguous in wheat.

关键词： Wheat Heat stress Genetic basis Molecular mechanisms

Characterization of a new hexaploid triticale 6D(6A) substitution line with increased grain weight and decreased spikelet number

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The Crop Journal 2019年第5期7卷 598-607页

作者： Zhiyu Feng Zhongqi Qi Dejie Du Mingyi Zhang Aiju Zhao Zhaorong Hu Mingming Xin yingyin yao Huiru Peng qixin sun zhongfu ni Key Laboratory of Crop Heterosis and Utilization State Key Laboratory for AgrobiotechnologyBeijing Key Laboratory of Crop Genetic ImprovementCollege of Agronomy and BiotechnologyChina Agricultural UniversityBeijing 100193China Institute of Wheat Research Shanxi Academy of Agricultural SciencesLinfen 041000ShanxiChina Hebei Crop Genetic Breeding Laboratory Institute of Cereal and Oil CropsHebei Academy of Agriculture and Forestry SciencesShijiazhuang 050035HebeiChina

Hexaploid triticale(×Triticosecale,AABBRR)is an important forage crop and a promising energy *** D-genome chromosomes or segments from common wheat(Triticum aestivum)into hexaploid triticale is attractive in improving its economically important ***,a hexaploid triticale 6D(6A)substitution line Lin 456 derived from the cross between the octoploid triticale line H400 and the hexaploid wheat Lin 56 was identified and analyzed by genomic in situ hybridization(GISH),fluorescence in situ hybridization(FISH),and molecular *** GISH analysis showed that Lin 456 is a hexaploid triticalewith 14 rye(Secale cereale)chromosomes and 28 wheat chromosomes,whereas non-denaturing fluorescence in situ hybridization(ND-FISH)and molecular marker analysis revealed that it is a 6D(6A)substitution *** contrast to previous studies,the signal of Oligo-pSc119.2 was observed at the distal end of 6DL in Lin *** wheat chromosome 6D was associatedwith increased grain weight and decreased spikelet number using the genotypic data combined with the phenotypes of the F2 population in the three *** thousand-grain weight and grain width in the substitution individuals were significantly higher than those in the non-substitution individuals in the F2 population across the three *** propose that the hexaploid triticale 6D(6A)substitution line Lin 456 can be a valuable and promising donor stock for genetic improvement during triticale breeding.

关键词： In situ hybridization Spikelet number Substitution line Thousand-grain weight Triticale

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

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

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

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