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

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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Combining QTL Mapping and Multi-Omics Identify Candidate Genes for Nutritional Quality Traits during Grain Filling Stage in Maize

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Phyton-International Journal of Experimental Botany 2024年第7期93卷 1441-1453页

作者： Pengcheng Li Tianze Zhu Yunyun Wang Shuangyi Yin Xinjie Zhu Minggang Ji Wenye Rui Houmiao Wang Zefeng Yang chenwu xu Jiangsu Key Laboratory of Crop Genetics and Physiology Key Laboratory of Plant Functional Genomics of the Ministry of EducationJiangsu Key Laboratory of Crop Genomics and Molecular BreedingAgricultural College of Yangzhou UniversityYangzhou225009China Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops Yangzhou UniversityYangzhou225009China

The nutritional composition and overall quality of maize kernels are largely determined by the key chemical com-ponents:protein,oil,and ***,the genetic basis underlying these nutritional quality traits during grainﬁlling remains poorly *** this study,the concentrations of protein,oil,and starch were studied in 204 recombinant inbred lines resulting from a cross between DH1M and T877 at four different stages *** the traits exhibited considerable phenotypic *** the grain-ﬁlling stage,the levels of protein and starch content generally increased,whereas oil content decreased,with signiﬁcant changes observed between 30 and 40 days after *** trait locus(QTL)mapping was conducted and a total of 32 QTLs,comprising 14,12,and 6 QTLs for grain protein,oil,and starch content were detected,*** QTLs were consistently detectable across different time *** integrating QTL analysis,glo-bal gene expression proﬁling,and comparative genomics,we identiﬁed 157,86,and 54 differentially expressed genes harboring nonsynonymous substitutions between the parental lines for grain protein,oil,and starch con-tent,*** gene function annotation prioritized 15 candidate genes potentially involved in reg-ulating grain quality traits,including those encoding transcription factors(NAC,MADS-box,bZIP,and MYB),cell wall invertase,cellulose-synthase-like protein,cell division cycle protein,trehalase,auxin-responsive factor,and phloem protein *** study offers signiﬁcant insights into the genetic architecture of maize kernel nutritional quality and identiﬁes promising QTLs and candidate genes,which are crucial for the genetic enhance-ment of these traits in maize breeding programs.

关键词： Maize protein oil starch QTL mapping candidate genes

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Rice melatonin deficiency causes premature leaf senescence via DNA methylation regulation

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The Crop Journal 2024年第3期12卷 721-731页

作者： Yue Lu Ahmed Gharib Rujia Chen Hanyao Wang Tianyun Tao Zhihao Zuo Qing Bu Yanze Su Yaoqing Li Yanmo Luo Hamdi F.El-Mowafi Zhichao Wang Qianfeng Huang Shuting Wang Yang xu Pengcheng Li chenwu xu Zefeng Yang Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education Agriculture College of Yangzhou UniversityYangzhou 225009JiangsuChina Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops Jiangsu Key Laboratory of Crop Genetics and PhysiologyYangzhou UniversityYangzhou 225009JiangsuChina National Institute of Laser Enhanced Sciences(NILES) Cairo UniversityGiza 12613Egypt Rice Research Department Field Crops Research InstituteAgricultural Research CenterSakhaKafr El-Sheikh 33717Egypt

In a study of DNA methylation changes in melatonin-deficient rice mutants,mutant plants showed premature leaf senescence during grain-filling and reduced grain *** deficiency led to transcriptional reprogramming,especially of genes involved in chlorophyll and carbon metabolism,redox regulation,and transcriptional regulation,during dark-induced leaf *** of mCG and mCHG in the melatonin-deficient rice mutants was associated with the expression change of both protein-coding genes and transposable element-related *** in gene expression and DNA methylation in the melatonin-deficient mutants were compensated by exogenous application of melatonin.A decreased S-adenosyl-L-methionine level may have contributed to the DNA methylation variations in rice mutants of melatonin deficiency under dark conditions.

关键词： Melatonin Premature leaf senescence Rice DNA methylation Epigenetic regulation

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A new statistical method for mapping QTLs underlying endosperm traits

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Chinese Science Bulletin 2005年第14期50卷 1470-1476页

作者： HU Zhiqiu xu chenwu Jiangsu Provincial Key Lab of Crop Genetics and Physiology Depart-ment of Agronomy Yangzhou University Yangzhou 225009 China

Genetic expression for an endosperm trait in seeds of cereal crops may be controlled simultaneously by the triploid endosperm genotypes and the diploid maternal genotypes. However, current statistical methods for mapping quantitative trait loci (QTLs) underlying endosperm traits have not been effective in dealing with the putative maternal genetic effects. Combining the quantitative genetic model for diploid maternal traits with triploid endosperm traits, here we propose a new statistical method for mapping QTLs con- trolling endosperm traits with maternal genetic effects. This method applies the data set of both DNA molecular marker genotypes of each plant in segregation population and the quantitative observations of single endosperms in each plant to map QTL. The maximum likelihood method implemented via the expectation-maximization algorithm was used to the estimate parameters of a putative QTL. Since this method involves the maternal effect that may contribute to en- dosperm traits, it might be more congruent with the genetics of endosperm traits and more helpful to increasing the preci- sion of QTL mapping. The simulation results show the pro- posed method provides accurate estimates of the QTL effects and locations with high statistical power.

关键词：胚乳特性遗传因子遗传模型染色体

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Genetic mapping of quantitative trait loci in crops

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The Crop Journal 2017年第2期5卷 175-184页

作者： Yang xu Pengcheng Li Zefeng Yang chenwu xu Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops Key Laboratory of Plant Functional Genomics of Ministry of Education Yangzhou University Yangzhou 225009 China

Dissecting the genetic architecture of complex traits is an ongoing challenge for *** complementary approaches for genetic mapping,linkage mapping and association mapping have led to successful dissection of complex traits in many crop *** of these methods detect quantitative trait loci(QTL) by identifying marker–trait associations,and the only fundamental difference between them is that between mapping populations,which directly determine mapping resolution and *** on this difference,we first summarize in this review the advances and limitations of family-based mapping and natural population-based mapping instead of linkage mapping and association *** then describe statistical methods used for improving detection power and computational speed and outline emerging areas such as large-scale meta-analysis for genetic mapping in *** the era of next-generation sequencing,there has arisen an urgent need for proper population design,advanced statistical strategies,and precision phenotyping to fully exploit high-throughput genotyping.

关键词： Family-based mapping Natural population-based mapping Mixed linear model MAGIC population Meta-analysis Genotyping by sequencing

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A multivariate partial least squares approach to joint association analysis for multiple correlated traits

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The Crop Journal 2016年第1期4卷 21-29页

作者： Yang xu Wenming Hu Zefeng Yang chenwu xu Jiangsu Key Laboratory of Crop Genetics and Physiology Co-Innovation Center for Modern Production Technology of Grain CropsKey Laboratory of Plant Functional Genomics of the Ministry of Education Yangzhou University

Many complex traits are highly correlated rather than independent. By taking the correlation structure of multiple traits into account, joint association analyses can achieve both higher statistical power and more accurate estimation. To develop a statistical approach to joint association analysis that includes allele detection and genetic effect estimation, we combined multivariate partial least squares regression with variable selection strategies and selected the optimal model using the Bayesian Information Criterion(BIC). We then performed extensive simulations under varying heritabilities and sample sizes to compare the performance achieved using our method with those obtained by single-trait multilocus methods. Joint association analysis has measurable advantages over single-trait methods, as it exhibits superior gene detection power, especially for pleiotropic genes. Sample size, heritability,polymorphic information content(PIC), and magnitude of gene effects influence the statistical power, accuracy and precision of effect estimation by the joint association analysis.

关键词： Association analysis Multiple correlated traits Supersaturated model Multilocus Multivariate partial least squares

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Genomic selection methods for crop improvement:Current status and prospects

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The Crop Journal 2018年第4期6卷 330-340页

作者： Xin Wang Yang xu Zhongli Hu chenwu xu Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops/Key Laboratory of Plant Functional Genomics of Ministry of Education Yangzhou University Yangzhou 225009 Jiangsu China College of Information Engineering Yangzhou University Yangzhou 225009 Jiangsu China State Key Laboratory of Hybrid Rice College of Life Sciences Wuhan University Wuhan 430072 Hubei China

With marker and phenotype information from observed populations, genomic selection （GS） can be used to establish associations between markers and phenotypes. It aims to use genome-wide markers to estimate the effects of all loci and thereby predict the genetic values of untested populations, so as to achieve more comprehensive and reliable selection and to accelerate genetic progress in crop breeding. GS models usually face the problem that the number of markers is much higher than the number of phenotypic observations. To overcome this issue and improve prediction accuracy, many models and algorithms, including GBLUP, Bayes, and machine learning have been employed for GS. As hot issues in GS research, the estimation of non-additive genetic effects and the combined analysis of multiple traits or multiple environments are also important for improving the accuracy of prediction. In recent years, crop breeding has taken advantage of the development of GS. The principles and characteristics of current popular GS methods and research progress in hese methods for crop improvement are reviewed in this paper.

关键词： Genomic selection Prediction Accuracy Crop

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Using genomic data to improve the estimation of general combining ability based on sparse partial diallel cross designs in maize

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The Crop Journal 2020年第5期8卷 819-829页

作者： Xin Wang Zhenliang Zhang Yang xu Pengchen Li xuecai Zhang chenwu xu College of Information Engineering Yangzhou UniversityYangzhou 225009JiangsuChina 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 College of AgricultureYangzhou UniversityYangzhou 225009JiangsuChina International Maize and Wheat Improvement Center(CIMMYT) Mexico D.F.06600Mexico

Evaluation of general combining ability(GCA)is crucial to hybrid breeding in *** the complete diallel cross design can provide an efficient estimation,sparse partial diallel cross(SPDC)is more flexible in breeding *** real and simulated data sets of partial diallel crosses between 266 maize inbred lines,this study investigated the performance of SPDC designs for estimating the *** different distributions of parental lines involved in crossing(called random,balanced and unbalanced samplings),different numbers of hybrids were sampled as the training sets to estimate the GCA of the 266 inbred *** this process,three statistical approaches were *** obtained estimations through the ordinary least square(OLS)method,and the other two utilized genomic prediction(GP)to estimate the *** was found that the coefficient of determination of each approach was always higher than the heritability of a target trait,showing that the GCA for maize inbred lines could be accurately predicted with SPDC *** the GP approaches were more accurate than the OLS,particularly in the scenario for a low-heritability trait with a small sample ***,prediction results demonstrated that a big sample of hybrids could greatly help improve the *** random sampling of parental lines had little influence on the average ***,the prediction for lines that never or seldom involved in crossing might suffer from much lower accuracy.

关键词： breeding estimation prediction

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Genome-wide association study identifies novel candidate loci or genes affecting stalk strength in maize

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The Crop Journal 2023年第1期11卷 220-227页

作者： Shuhui xu Xiao Tang Xiaomin Zhang Houmiao Wang Weidong Ji chenwu xu Zefeng Yang Pengcheng Li 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 Yangzhou UniversityYangzhou 225009JiangsuChina Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops Yangzhou UniversityYangzhou 225009JiangsuChina National Maize Improvement Center of China China Agricultural UniversityBeijing 100193China State Key Laboratory of Crop Stress Adaptation and Improvement Key Laboratory of Plant Stress BiologySchool of Life SciencesHenan UniversityKaifeng 475001HenanChina

Stalk strength increases resistance to stalk lodging,which causes maize(Zea mays L.)production losses *** genetic mechanisms regulating stalk strength remain *** this study,three stalk strength-related traits(rind penetrometer resistance,stalk crushing strength,and stalk bending strength)and four plant architecture traits(plant height,ear height,stem diameter,stem length)were measured in three field *** phenotypic variation was detected for these traits.A genome-wide association study(GWAS)was conducted using general and mixed linear models and 372,331 single-nucleotide polymorphisms(SNPs).A total of 94 quantitative trait loci including 241 SNPs were *** combining the GWAS data with public gene expression data,56 candidate genes within 50 kb of the significant SNPs were identified,including genes encoding flavonol synthase(GRMZM2G069298,ZmFLS2),nitrate reductase(GRMZM5G878558,ZmNR2),glucose-1-phosphate adenylyltransferase(GRMZM2G027955),and laccase(GRMZM2G447271).Resequencing GRMZM2G069298 and GRMZM5G878558 in all tested lines revealed respectively 47 and 2 variants associated with *** of the RPR of the zmnr2EMS mutant and the wild-type plant under high-and low-nitrogen conditions verified the GRMZM5G878558 *** findings may be useful for clarifying the genetic basis of stalk *** identified candidate genes and variants may be useful for the genetic improvement of maize lodging resistance.

关键词： Stalk strength Maize GWAS Candidate genes Lodging resistance

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Multi-environment QTL mapping of crown root traits in a maize RIL population

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The Crop Journal 2020年第4期8卷 645-654页

作者： Pengcheng Li Yingying Fana Shuangyi Yina Yunyun Wanga Houmiao Wang Yang xu Zefeng Yang chenwu xu 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 Agricultural College of Yangzhou UniversityYangzhou 225009JiangsuChina Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops Yangzhou UniversityYangzhou 225009JiangsuChina Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China Yangzhou UniversityYangzhou 225009JiangsuChina

Crown root traits,including crown root angle(CRA),diameter(CRD),and number(CRN),are major determining factors of root system architecture,which influences crop *** maize,the genetic mechanisms determining crown root traits in the field are largely ***,CRD,and CRN were evaluated in a recombinant inbred line population in three field *** phenotypic variation was observed for crown root traits,and all measured traits showed significant genotype–environment ***(SEA)and multi-environment(MEA)quantitative trait locus(QTL)analyses were conducted for CRA,CRD,and *** 46 QTL detected by SEA,most explained less than 10%of the phenotypic variation,indicating that a large number of minor-effect QTL contributed to the genetic component of these *** detected 25 QTL associated with CRA,CRD,and CRN,and 2 and 1 QTL were identified with significant QTL-by-environment interaction effects for CRA and CRD,respectively.A total of 26.1%(12/46)of the QTL identified by SEA were also detected by MEA,with many being detected in more than one *** findings contribute to our understanding of the phenotypic and genotypic patterns of crown root traits in different *** identified environment-specific QTL and stable QTL may be used to improve root traits in maize breeding.

关键词： crown traits maize

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