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Integrated linkage mapping and genome-wide association study to dissect the genetic basis of zinc deficiency tolerance in maize at seedling stage

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The Crop Journal 2022年第6期10卷 1807-1818页

作者： Jianqin Xu zhongfu ni Fanjun Chen Xiuyi Fu Futong Yu Key Laboratory of Plant-Soil Interaction(MOE) Centre for ResourcesEnvironment and Food SecurityCollege of Resources and Environmental SciencesChina Agricultural UniversityBeijing 100193China State Key Laboratory for Agrobiotechnology Key Laboratory of Crop Heterosis and Utilization(MOE)Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100193China National Maize Improvement Center of China Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100193China

Zinc(Zn)deficiency is the most widespread micronutrient deficiency,affecting yield and quality of crops *** genes associated with Zn-deficiency tolerance in maize is a basis for elucidating its genetic mechanism.A K22×CI7 recombinant inbred population consisting of 210 lines and an association panel of 508 lines were used to identify genetic loci influencing Zn-deficiency ***-Zn and-Zn/CK conditions,15 quantitative trait loci(QTL)were detected,each explaining 5.7%-12.6%of phenotypic ***-one significant single-nucleotide polymorphisms(SNPs)were identified at Pnificant SNPs,12 were associated with Zn-deficiency *** these candidate genes,four genes associated with hormone signaling in response to Zn-deficiency stress were co-localized with QTL or SNPs,including the genes involved in the auxin(ZmARF7),and ethylene(ZmETR5,ZmESR14,and ZmEIN2)signaling *** candidate genes were identified as being responsible for Zn transport,including ZmNAS3 detected by GWAS,ZmVIT and ZmYSL11 detected by QTL *** of ZmYSL11 was up-regulated in Zn-deficient *** candidate genes that displayed different expression patterns in response to Zn deficiency were detected in the regions overlapping peak GWAS signals,and the haplotypes for each candidate gene were further analyzed.

关键词： Maize(Zea mays L.) Quantitative trait loci(QTL) Genome-wide association study(GWAS) Zinc(Zn)deficiency tolerance Candidate genes

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

Deciphering the evolution and complexity of wheat germplasm from a genomic perspective

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Journal of Genetics and Genomics 2023年第11期50卷 846-860页

作者： Zihao Wang Lingfeng Miao Yongming Chen 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 provides an essential fraction of the daily calorific intake for *** to its huge and complex genome,progress in studying on the wheat genome is substantially trailed behind those of the other two major crops,rice and maize,for at least a *** rapid advances in genome assembling and reduced cost of high-throughput sequencing,emerging de novo genome assemblies of wheat and whole-genome sequencing data are leading to a paradigm shift in wheat ***,we review recent progress in dissecting the complex genome and germplasm evolution of wheat since the release of the first high-quality wheat *** insights have been gained in the evolution of wheat germplasm during domestication and modern breeding progress,genomic variations at multiple scales contributing to the diversity of wheat germplasm,and complex transcriptional and epigenetic regulations of functional genes in polyploid *** databases and bioinformatics tools meeting the urgent needs of wheat ge-nomics research are also *** ever-increasing omics data,along with advanced tools and well-structured databases,are expected to accelerate deciphering the germplasm and gene resources in wheat for future breeding advances.

关键词： Wheat genomics Evolution Wheat germplasm Multi-omics Databases and tools

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.

Genetic improvement of heat tolerance in wheat:Recent progress in understanding the underlying molecular mechanisms

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The Crop Journal 2018年第1期6卷 32-41页

作者： zhongfu ni Hongjian Li Yue Zhao Huiru Peng Zhaorong Hu Mingming Xin Qixin Sun State Key Laboratory for Agrobiotechnology Key Laboratory of Crop Heterosis and Utilization Beijing Key Laboratory of Crop Genetic Improvement China Agricultural University

As a cool season crop, wheat(Triticum aestivum L.) has an optimal daytime growing temperature of 15 ℃ during the reproductive stage. With global climate change, heat stress is becoming an increasingly severe constraint on wheat production. In this review, we summarize recent progress in understanding the molecular mechanisms of heat tolerance in wheat. We firstly describe the impact of heat tolerance on morphology and physiology and its potential effect on agronomic traits. We then review recent discoveries in determining the genetic and molecular factors affecting heat tolerance, including the effects of phytohormone signaling and epigenetic regulation. Finally, we discuss integrative strategies to improve heat tolerance by utilization of existing germplasm including modern cultivars, landraces and related species.

关键词： Heat stress Phytohormone signaling Epigenetic regulation Triticum aestiuum

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

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

A Collinearity-Incorporating Homology Inference Strategy for Connecting Emerging Assemblies in the Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era

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Molecular Plant 2020年第12期13卷 1694-1708页

作者： Yongming Chen Wanjun Song Xiaoming Xie Zihao Wang Panfeng Guan Huiru Peng Yuannian Jiao zhongfu ni Qixin Sun Weilong Guo Key Laboratory of Crop Heterosis and Utilization State Key Laboratory for AgrobiotechnologyBeijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100193China Beijing Geek Gene Technology Co Ltd Beijing 100193China State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of SciencesBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China

Plant genome sequencing has dramatically increased,and some species even have multiple high-quality reference *** for clade-specific homology inference and analysis have increased in the pangenomic *** we present a novel method,GeneTribe(https://***/genetribe/),for homology inference among genetically similar genomes that incorporates gene collinearity and shows bet-ter performance than traditional sequence-similarity-based methods in terms of accuracy and *** Triticeae tribe is a typical allopolyploid-rich clade with complex species relationships that includes many important crops,such as wheat,barley,and *** built Triticeae-GeneTribe(http://***/TGT/),a homology database,by integrating 12 Triticeae genomes and 3 outgroup model genomes and implemented versatile analysis and visualization *** macrocollinearity analysis,we were able to construct a refined model illustrating the structural rearrangements of the 4A-5A-7B chromosomes in wheat as two major translocation *** collinearity analysis at both the macro-and microscale,we illustrated the complex evolutionary history of homologs of the wheat vernalization gene Vm2,which evolved as a combined result of genome translocation,duplication,and polyploidization and gene loss *** work provides a useful practice for connecting emerging genome assemblies,with awareness of the extensive polyploidy in plants,and will help researchers efficiently exploit genome sequence re-sources.

关键词： homology inference collinearity database pangenome Triticeae tribe polyploid

Genome-wide linkage mapping of QTL for root hair length in a Chinese common wheat population

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The Crop Journal 2020年第6期8卷 1049-1056页

作者： Feng Huang Zhaoyan Chen Dejie Du Panfeng Guan Lingling Chai Weilong Guo Zhaorong Hu Mingming Xin Huiru Peng Yingyin Yao zhongfu ni Key Laboratory of Crop Heterosis and Utilization(MOE)/State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Genetic Improvement China Agricultural UniversityBeijing 100193China National Plant Gene Research Center Beijing 100193China Zhoukou Academy of Agriculture Sciences Zhoukou 466001HenanChina

Root hairs are fast growing,ephemeral tubular extensions of the root epidermis that aid nutrient and water *** aim of the present study was to identify QTL for root hair length(RHL)using 227 F8 recombinant inbred lines(RILs)derived from a cross of Zhou 8425 B(Z8425 B)and Chinese Spring(CS),and to develop convenient molecular markers for markerassisted breeding in *** of variance of root hair length showed significant differences(Pnique SNP *** composite interval mapping,four major QTL(LOD>2.5)for RHL were identified on chromosomes 1 B(2),2 D and 6 D and four putative QTL(2≤LOD≤2.5)were detected on chromosomes 1 A,3 A,6 B,and 7 B,explaining 3.32%–6.52%of the phenotypic *** positive alleles for increased RHL of QTL on chromosomes 2 D,6 B and 6 D(***-2 D,q ***-6 B,and ***-6 D)were contributed by Z8425 B,and CS contributed positive QTL alleles on chromosomes 1 A(q ***-1 A),1 B(***-1 B.1 and ***-1 B.2),3 A(q ***-3 A)and 7 B(q ***-7 B).STARP markers were developed for ***-1 B.1,***-2 D,***-6 D,and q ***-7 *** and association analysis indicated that the positive allele of ***-6 D had been strongly selected in Chinese wheat breeding ***,the identified QTL for root hair length are likely to be useful for marker-assisted selection.

关键词： GWAS QTL mapping STARP marker Triticum aestivum