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

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.

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

The nutritional composition and overall quality of maize kernels are largely determined by the key chemical com-ponents:protein,oil,and starch.Nevertheless,the genetic basis underlying these nutritional quality traits during grainfilling remains poorly understood.In 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 post-pollination.All the traits exhibited considerable phenotypic variation.During 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 pollination.Quantitative 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,respectively.Few QTLs were consistently detectable across different time points.By 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,respectively.Subsequent 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 2-A13.Our 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.

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

Stalk strength increases resistance to stalk lodging,which causes maize(Zea mays L.)production losses worldwide.The genetic mechanisms regulating stalk strength remain unclear.In 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 trials.Substantial 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 detected.By 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 RPR.Comparison of the RPR of the zmnr2EMS mutant and the wild-type plant under high-and low-nitrogen conditions verified the GRMZM5G878558 function.These findings may be useful for clarifying the genetic basis of stalk strength.The identified candidate genes and variants may be useful for the genetic improvement of maize lodging resistance.

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

Crown root traits,including crown root angle(CRA),diameter(CRD),and number(CRN),are major determining factors of root system architecture,which influences crop production.In maize,the genetic mechanisms determining crown root traits in the field are largely unknown.CRA,CRD,and CRN were evaluated in a recombinant inbred line population in three field trials.High phenotypic variation was observed for crown root traits,and all measured traits showed significant genotype–environment interactions.Singleenvironment(SEA)and multi-environment(MEA)quantitative trait locus(QTL)analyses were conducted for CRA,CRD,and CRN.Of 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 traits.MEA 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 environment.These findings contribute to our understanding of the phenotypic and genotypic patterns of crown root traits in different environments.The identified environment-specific QTL and stable QTL may be used to improve root traits in maize breeding.

Development and validation of simple sequence repeat markers from Arachis hypogaea transcript sequences

Simple sequence repeats(SSRs) are important molecular markers for assessing genetic diversity in Arachis hypogaea L. and many other crops and constructing genetic linkage maps for important agricultural traits. In this study, 29,357 potential SSRs were identified in 22,806 unigenes assembled from A. hypogaea transcript sequences. Of these unigenes, 1883 and 4103 were annotated and assigned in Kyoto Encyclopedia of Genes and Genomes Orthology and Eukaryotic Orthologous Groups databases, respectively. Among the SSR motifs, mono-(19,065; 64.94%) and trinucleotide(5033; 17.14%) repeats were the most common, and the three most dominant motifs were A/T(18,358; 62.54%), AG/CT(2804;9.55%), and AAG/CTT(1396; 4.76%). Polymerase chain reaction(PCR) primer pairs were designed for 4340 novel SSR markers and 210 new SSRs were validated using 24 A. hypogaea varieties. Of the 210, 191(91%) yielded PCR products, with 37(18%) identifying polymorphisms. The 37 polymorphic SSR markers detected 146 alleles(2–10 alleles per locus), and the average polymorphic information content was 0.403(with a range of 0.077 to0.819). The new SSRs enrich the current marker resources for A. hypogaea and may also be useful for genetic diversity analysis, functional genomics research, and molecular breeding.