Genome-wide association mapping and genomic prediction of stalk rot in two mid-altitude tropical maize populations

Maize stalk rot reduces grain yield and quality.Information about the genetics of resistance to maize stalk rot could help breeders design effective breeding strategies for the trait.Genomic prediction may be a more effective breeding strategy for stalk-rot resistance than marker-assisted selection.We performed a genome-wide association study(GWAS)and genomic prediction of resistance in testcross hybrids of 677 inbred lines from the Tuxpe?o and non-Tuxpe?o heterotic pools grown in three environments and genotyped with 200,681 single-nucleotide polymorphisms(SNPs).Eighteen SNPs associated with stalk rot shared genomic regions with gene families previously associated with plant biotic and abiotic responses.More favorable SNP haplotypes traced to tropical than to temperate progenitors of the inbred lines.Incorporating genotype-by-environment(G×E)interaction increased genomic prediction accuracy.

Exploring differentially expressed genes associated with fertility instability of S-type cytoplasmic male-sterility in maize by RNA-seq

The germplasm resources for the S-type male sterility is rich in maize and it is resistant to Bipolaris maydis race T and CI, but the commercial application of S-type cytoplasmic male sterility （CMS-S） in maize hybrid industry is greatly compromised because of its common fertility instability. Currently, the existence of multiple minor effect loci in specific nuclear genetic backgrounds was considered as the molecular mechanism for this phenomenon. In the present study, we evaluated the fertility segregation of the different populations with the fertility instable material FIL-H in two environments of Beijing and Hainan, China. Our results indicated that the fertility instability of FIL-H was regulated by multiple genes, and the expression of these genes was sensitive to environmental factors. Using RNA sequencing （RNA-seq） technology, transcriptomes of the sterile plants and partially fertile plants resulted from the backcross of FIL-HxJing 724 in Hainan were analyzed and 2 108 genes with different expression were identified, including 1 951 up-regulated and 157 down-regulated genes. The cluster analysis indicated that these differentially expressed genes （DEGs） might play roles in many biological processes, such as the energy production and conversion, carbohydrate metabolism and signal transduction. In addition, the path- way of the starch and sucrose metabolism was emphatically investigated to reveal the DEGs during the process of starch biosynthesis between sterile and partially fertile plants, which were related to the key catalytic enzymes, such as ADP-G pyrophosphorylase, starch synthase and starch branching enzyme. The up-regulation of these genes in the partially fertile plant may promote the starch accumulation in its pollen. Our data provide the important theoretical basis for the further exploration of the molecular mechanism for the fertility instability in CMS-S maize.

Identification of a locus associated with genic male sterility in maize via EMS mutagenesis and bulked-segregant RNA-seq

Genic male sterility(GMS) is one of the most important resources for exploiting heterosis in crop breeding, so that identifying genomic loci regulating GMS is desirable. However, many regulatory genes controlling GMS have not yet been characterized in maize, owing partly to a lack of genetic materials. We generated a recessive male-sterile maize mutant in the Jing 724 genetic background via ethyl methanesulfonate treatment, and found the male sterility to be due to a single gene mutation. Bulk-segregant RNA sequencing of three replicates indicated that one genomic region located at the end of chromosome 4 was associated with the observed mutant phenotype. Among genes with nonsynonymous mutations,Zm00001 d053895(bHLH51) showed abolished expression in the sterile bulks and was annotated as a bHLH transcription factor orthologous to Arabidopsis AMS, suggesting an association with the male sterility of the mutant. Kompetitive Allele-Specific PCR assays further validated the exclusive correlation of male sterility with the single C-to-T mutation in the fifth exon. The new maize mutant and the potential SNP locus provide novel genetic material for investigating the molecular mechanism underlying tapetal development and may facilitate the improvement of hybrid production systems.

Simple nonlinear model for the relationship between maize yield and cumulative water amount

Both the additive and multiplicative models of crop yield and water supply are polynomial equations, and the number of parameters increases linearly when the growing period is specified. However, interactions among multiple parameters occasionally lead to unreasonable estimations of certain parameters, which were water sensitivity coefficients but with negative value. Additionally, evapotranspiration must be measured as a model input. To facilitate the application of these models and overcome the aforementioned shortcomings, a simple model with only three parameters was derived in this paper based on certain general quantitative relations of crop yield （Y） and water supply （W）. The new model, Y/Y-W＊/（W＊＋w＊）, fits an S or a saturated curve of crop yield with the cumulative amount of water. Three parameters are related to biological factors： the yield potential （Y＊）, the water requirement to achieve half of the yield potential （half-yield water requirement, wh）, and the water sensitivity coefficient （k）. The model was validated with data from 24 maize lines obtained in the present study and 17 maize hybrids published by other authors. The results showed that the model was well fit to the data, and the normal root of the mean square error （NRMSE） values were 2.8 to 17.8% （average 7.2%） for the 24 maize lines and 2.7 to 12.7% （average 7.4%） for the 17 maize varieties. According to the present model, the maize water-sensitive stages in descending order were pollen shedding and silking, tasselling, jointing, initial grain filling, germination, middle grain filling, late grain filling, and end of grain filling. This sequence was consistent with actual observations in the maize field. The present model may be easily used to analyse the water use efficiency and drought tolerance of maize at specific stages.

Genetic Diversity of Two Important Groups of Maize Landraces with Same Name in China Revealed by M13 Tailed-Primer SSRs

Maize landraces White Dent and Golden Queen played a very important role in the pre-hybrid era of maize production in China. However, dozens of accessions with the same names of White Dent and Golden Queen are preserved in China National Genebank （CNG）. The present study investigated the genetic diversity of these two important groups of maize landraces, as well as the relationships within and among them. Thirty-four landrace accessions with the name of White Dent and 10 with Golden Queen preserved in CNG were fingerprinted with 52 simple sequence repeats with tailed primer M13. Summary statistics including average number of alleles per locus, gene diversity/expected heterozygosity, and observed heterozygosity were carried out using PowerMarker ver. 3.25 software. The test of Hardy-Weinberg equilibrium （HWE） and linkage disequilibrium （LD） of all the 44 maize landrace accessions were also performed by PowerMarker. We observed a significant differentiation in terms of the average number of alleles between White Dent and Golden Queen （6.44 alleles per locus in White Dent, 4.48 in Golden Queen）, while both groups of maize landraces had a relatively high but similar gene diversity （0.61 of White Dent, 0.63 of Golden Queen）. The fixation index （FST） was only 0.0044, while the percentage of loci deviated from Hardy-Weinberg equilibrium within these two groups of White Dent and Golden Queen was 32.69 and 3.92%, respectively. The rather high genetic diversity and average number of alleles per locus confirmed that both groups of landraces had a rather broad germplasm base. The extremely low fixation index showed that there was little genetic variation between White Dent and Golden Queen and the molecular variation within these two groups was remarkably high, indicating no genetic drift between White Dent and Golden Queen and suggesting different improvement approaches to these two important groups of landraces. Hardy-Weinberg equilibrium test revealed that the group of White Dent was deviated from HWE, whereas Golden Queen was under HWE.

Analysis of Genetic Diversity and Population Structure of Maize Landraces from the South Maize Region of China

Understanding genetic diversity and population structure of landraces is important in utilization of these germplasm in breeding programs. In the present study, a total of 143 core maize landraces from the South Maize Region （SR） of China, which can represent the general profile of the genetic diversity in the landraces germplasm of SR, were genotyped by 54 DNA microsatellite markers. Totally, 517 alleles （ranging from 4 to 22） were detected among these landraces, with an average of 9.57 alleles per locus. The total gene diversity of these core landraces was 0.61, suggesting a rather higher level of genetic diversity. Analysis of population structure based on Bayesian method obtained the samilar result as the phylogeny neighbor-joining （N J） method. The results indicated that the whole set of 143 core landraces could be clustered into two distinct groups. All landraces from Guangdong, Hainan, and 15 landraces from Jiangxi were clustered into group 1, while those from the other regions of SR formed the group 2. The results from the analysis of genetic diversity showed that both of groups possessed a similar gene diversity, but group 1 possessed relatively lower mean alleles per locus （6.63） and distinct alleles （91） than group 2 （7.94 and 110, respectively）. The relatively high richness of total alleles and distinct alleles preserved in the core landraces from SR suggested that all these germplasm could be useful resources in germplasm enhancement and maize breeding in China.

Genomic prediction of the performance of hybrids and the combining abilities for line by tester trials in maize

The two most important activities in maize breeding are the development of inbred lines with high values of general combining ability(GCA)and specific combining ability(SCA),and the identification of hybrids with high yield potentials.Genomic selection(GS)is a promising genomic tool to perform selection on the untested breeding material based on the genomic estimated breeding values estimated from the genomic prediction(GP).In this study,GP analyses were carried out to estimate the performance of hybrids,GCA,and SCA for grain yield(GY)in three maize line-by-tester trials,where all the material was phenotyped in 10 to 11 multiple-location trials and genotyped with a mid-density molecular marker platform.Results showed that the prediction abilities for the performance of hybrids ranged from 0.59 to0.81 across all trials in the model including the additive effect of lines and testers.In the model including both additive and non-additive effects,the prediction abilities for the performance of hybrids were improved and ranged from 0.64 to 0.86 across all trials.The prediction abilities of the GCA for GY were low,ranging between-0.14 and 0.13 across all trials in the model including only inbred lines;the prediction abilities of the GCA for GY were improved and ranged from 0.49 to 0.55 across all trials in the model including both inbred lines and testers,while the prediction abilities of the SCA for GY were negative across all trials.The prediction abilities for GY between testers varied from-0.66 to 0.82;the performance of hybrids between testers is difficult to predict.GS offers the opportunity to predict the performance of new hybrids and the GCA of new inbred lines based on the molecular marker information,the total breeding cost could be reduced dramatically by phenotyping fewer multiple-location trials.

The priority of management factors for reducing the yield gap of summer maize in the north of Huang-Huai-Hai region, China

Understanding yield potential, yield gap and the priority of management factors for reducing the yield gap in current intensive maize production is essential for meeting future food demand with the limited resources. In this study, we conducted field experiments using different planting modes, which were basic productivity(CK), farmer practice(FP), high yield and high efficiency(HH), and super high yield(SH), to estimate the yield gap. Different factorial experiments(fertilizer, planting density, hybrids, and irrigation) were also conducted to evaluate the priority of individual management factors for reducing the yield gap between the different planting modes. We found significant differences between the maize yields of different planting modes. The treatments of CK, FP, HH, and SH achieved 54.26, 58.76, 65.77, and 71.99% of the yield potential, respectively. The yield gaps between three pairs: CK and FP, FP and HH, and HH and SH, were 0.76, 1.23 and 0.85 t ha^(–1), respectively. By further analyzing the priority of management factors for reducing the yield gap between FP and HH, as well as HH and SH, we found that the priorities of the management factors(contribution rates) were plant density(13.29%)>fertilizer(11.95%)>hybrids(8.19%)>irrigation(4%) for FP to HH, and hybrids(8.94%)>plant density(4.84%)>fertilizer(1.91%) for HH to SH. Therefore, increasing the planting density of FP was the key factor for decreasing the yield gap between FP and HH, while choosing hybrids with density and lodging tolerance was the key factor for decreasing the yield gap between HH and SH.

Genome-wide association study and genomic prediction of Fusarium ear rot resistance in tropical maize germplasm

Fusarium ear rot(FER)is a destructive maize fungal disease worldwide.In this study,three tropical maize populations consisting of 874 inbred lines were used to perform genomewide association study(GWAS)and genomic prediction(GP)analyses of FER resistance.Broad phenotypic variation and high heritability for FER were observed,although it was highly influenced by large genotype-by-environment interactions.In the 874 inbred lines,GWAS with general linear model(GLM)identified 3034 single-nucleotide polymorphisms(SNPs)significantly associated with FER resistance at the P-value threshold of 1×10^(-5),the average phenotypic variation explained(PVE)by these associations was 3%with a range from 2.33%to 6.92%,and 49 of these associations had PVE values greater than 5%.The GWAS analysis with mixed linear model(MLM)identified 19 significantly associated SNPs at the P-value threshold of 1×10^(-4),the average PVE of these associations was 1.60%with a range from 1.39%to 2.04%.Within each of the three populations,the number of significantly associated SNPs identified by GLM and MLM ranged from 25 to 41,and from 5 to 22,respectively.Overlapping SNP associations across populations were rare.A few stable genomic regions conferring FER resistance were identified,which located in bins 3.04/05,7.02/04,9.00/01,9.04,9.06/07,and 10.03/04.The genomic regions in bins 9.00/01 and 9.04 are new.GP produced moderate accuracies with genome-wide markers,and relatively high accuracies with SNP associations detected from GWAS.Moderate prediction accuracies were observed when the training and validation sets were closely related.These results implied that FER resistance in maize is controlled by minor QTL with small effects,and highly influenced by the genetic background of the populations studied.Genomic selection(GS)by incorporating SNP associations detected from GWAS is a promising tool for improving FER resistance in maize.

Dynamic changes of root proteome reveal diverse responsive proteins in maize subjected to cadmium stress

Toxic symptoms and tolerance mechanisms of heavy metal in maize are well documented. However, limited information is available regarding the changes in the proteome of maize seedling roots in response to cadmium(Cd) stress. Here, we employed an i TRAQ-based quantitative proteomic approach to characterize the dynamic alterations in the root proteome during early developmental in maize seedling. We conducted our proteomic experiments in three-day seedling subjected to Cd stress, using roots in four time points. We identified a total of 733, 307, 499, and 576 differentially abundant proteins after 12, 24, 48, or 72 h of treatment, respectively. These proteins displayed different functions, such as ribosomal synthesis, reactive oxygen species homeostasis, cell wall organization, cellular metabolism, and carbohydrate and energy metabolism. Of the 166 and 177 proteins with higher and lower abundance identified in at least two time points, 14 were common for three time points. We selected nine proteins to verify their expression using quantitative real-time PCR. Proteins involved in the ribosome pathway were especially responsive to Cd stress. Functional characterization of the proteins and the pathways identified in this study could help our understanding of the complicated molecular mechanism involved in Cd stress responses and create a list of candidate gene responsible for Cd tolerance in maize seeding roots.

Stalk Rot Resistance Analysis and Yield Loss Evaluation on 25 Maize Varieties and Utilization of Resistant Germplasm Jun M9

Stalk rot outbroke in Henan Province in 2014 on maize,and the disease conditions of 25 varieties were investigated.According to national maize variety disease resistance identification standards,Jundan 509 was a resistant variety; Yudan 606,Jinsai 38 and Jundan 3136 were moderately-resistant varieties; and other 21 varieties were all highly susceptible.Based on the yield loss rate of 5% determined as the critical value for division of disease tolerance,disease-tolerant varieties included Jundan 509,Yudan 606,Jinsai 38,Jundan 3136,Huaiyu 5288,Qiaoyu 8,XY046,Zhengyu 10,lile 66,weike 702 and Jundan 29.Varietal disease resistance and tolerance were mainly divided according to incidence and yield loss rate,respectively,and the correlation between them was showed by a Venn diagram.With the male parent Jun M9 of Jundan 509 as a backbone material,multiple maize combinations resistant to stalk rot were formed,and Yongyou 618 among them was approved by Henan Provincial Crop Variety Approval Committee.

Maize grain yield and water use efficiency in relation to climatic factors and plant population in northern China

Water scarcity has become a limiting factor for increasing crop production.Finding ways to improve water use efficiency(WUE)has become an urgent task for Chinese agriculture.To understand the response of different maize populations to changes in precipitation and the effects of changes in maize populations on WUE,this study conducted maize population experiments using maize hybrids with different plant types(compact and semi compact)and different planting densities at 25 locations across China.It was found that,as precipitation increased across different locations,maize grain yield first increased and then decreased,while WUE decreased significantly.Analyzing the relationship between WUE and the main climatic factors,this study found that WUE was significantly and negatively correlated with precipitation(R(daily mean precipitation)and R(accumulated precipitation))and was positively correlated with temperature(TM(daily mean maximum temperature),T_(M-m)(T_(m),daily mean minimum temperature)and GDD(growing degree days))and solar radiation(Ra(daily mean solar radiation)and Ra(accumulated solar radiation))over different growth periods.Significant differences in maize grain yield,WUE and precipitation were found at different planting densities.The population densities were ranked as follows according to maize grain yield and WUE based on the multi-site experiment data:60000 plants ha^(-1)(P_(2))>90000 plants ha^(-1)(P_(3))>30000 plants ha^(-1)(P_(1)).Further analysis showed that,as maize population increased,water consumption increased significantly while soil evaporation decreased significantly.Significant differences were found between the WUE of ZD958(compact type)and that of LD981(semi-compact type),as well as among the WUE values at different planting densities.In addition,choosing the optimum hybrid and planting density increased WUE by 21.70 and 14.92%,respectively,which showed that the hybrid played a more significant role than the planting density in improving WUE.Therefore,choosing drought-resistant hybrids could be more effective than increasing the planting density to increase maize grain yield and WUE in northern China.Comprehensive consideration of climatic impacts,drought-resistant hybrids(e.g.,ZD958)and planting density(e.g.,60000 plants ha^(-1))is an effective way to increase maize grain yield and WUE across different regions of China.

Application of Mechanical Grain Harvest of Maize by Combiners in Anhui Province

Eight summer maize varieties were evaluated in Funan County,Anhui Province,for yield and grain quality under mechanical grain harvest conditions in2019 growth season.ZY432,LY35 and JNK728 had higher grain yield potentials than FDC10,LX98,LD575,YD9953 and TT619.Postponed harvest from 28th Sept.to 11 thOct.was positively linked to the grain yield at roughly 1% of daily yield increase.Early harvest gave higher grain water content which was positively related to the percentage of broken grain as y=0.422 x-2.984(R^2=0.445),and to the percentage of foreign substance as y=0.248 x-3.245(R2=0.698).The relationship between grain water content and the rate of grain loss was negative as y=-0.052x+2.450(R^2=0.089).There was about 0.89% of grain water content decrease daily between harvests from 28^th Sept.to 4^th Oct.,and then was a‘slow-down’rate of dehydration.Grain weight was increasing for each variety when the harvest was postponed.JNK728 had the highest hundred-grain weight(HGW) and YD9953 had the lowest HGW.To make the mechanical grain harvest of summer maize feasible and acceptable,farmers need to pay attention to the adoption of proper varieties,following the suitable cultivation procedure and the improvement of mechanical facilities and operation.

Identification of the candidate gene controlling tiller angle in common wheat through genome-wide association study and linkage analysis

Wheat tiller angle(TA)is an important agronomic trait that contributes to grain production by affecting plant architecture.It also plays a crucial role in high-yield wheat breeding.An association panel and a recombinant inbred line(RIL)population were used to map quantitative trait loci(QTL)for TA.Results showed that 470 significant SNPs with 10.4%–28.8%phenotypic variance explained(PVE)were detected in four replicates by a genome-wide association study(GWAS).Haplotype analysis showed that the TA_Hap_4B1 locus on chromosome 4B was a major QTL to regulate wheat TA.Ten QTL were totally detected by linkage mapping with the RIL population,and QTA.hau-4B.1 identified in six environments with the PVE of 7.88%–18.82%was a major and stable QTL.A combined analysis demonstrated that both TA_Hap_4B1 and QTA.hau-4B.1 were co-located on the same region.Moreover,QTA.hau-4B.1 was confirmed by bulked segregant RNA-Seq(BSR-Seq)analysis.Phenotypic analysis showed that QTA.hau-4B.1was also closely related to yield traits.Furthermore,Traes CS4B02G049700 was considered as a candidate gene through analysis of gene sequence and expression.This study can be potentially used in cloning key genes modulating wheat tillering and provides valuable genetic resources for improvement of wheat plant architecture.

Abiotic stress tolerance:Genetics,genomics,and breeding

1.Tenth anniversary of The Crop Journal The Crop Journal will be 10 years old in October 2023.The journal is sponsored by the Crop Science Society of China,the Institute of Crop Sciences,Chinese Academy of Agricultural Sciences,and China Science Publishing&Media Group Ltd.(Science Press).It is published by Science Press and Ke Ai (founded by China Science Publishing&Media Ltd.and Elsevier).

Impact of Fungicide Treatments on the Constitution of Unsound Wheat Kernels

Nine fungicides were applied,either through seed-dressing or post-anthesis foliar-spray,to eight winter wheat varieties to understand their influences on the constitution of unsound kernels during the 2017-2018 growth season in Funan Experimental Station,Anhui,P.R.China.Three unsound kernel items,i.e.Fusarium-damaged kernels( FDKs),black-germ kernels( BGKs) and pre-harvest sprouted kernels( PHSKs),were measured from the harvested grains.A high percentage of unsound kernels was noticed as 6.00% for FDKs,8.43% for BGKs,and 38.19% for PHSKs due to excessive precipitation during the filling and maturation stages within the season.Fungicide treatments showed positive impacts on the formation of FDKs and BGKs.No significant differences were noticed on the percentage of PHSKs among treatments.The best control efficiency on FDKs,24.63%,was observed in the treatment of‘tebuconazole + prochloraz-manganese chloride complex'.The highest control efficiency on BGKs,31.54%,was achieved by the treatment of‘phenazino-1-carboxylic acid'.Significant differences were noticed among varieties with respect to the constitution of unsound kernels.Under the specific ecological conditions,70%-75% of the final grain quality of wheat was determined by the genotype itself.It was concluded that the genetic resistance or tolerance to relevant fungal pathogens and pre-harvest sprouting was the key factor determining the constitution of unsound wheat kernels,whilst chemical control might function with limited effects when crop was grown under high-pressure or stress conditions.

Comparison of algorithms for monitoring wheat powdery mildew using multi-angular remote sensing data

Powdery mildew is a disease that threatens wheat production and causes severe economic losses worldwide. Its timely diagnosis is imperative for preventing and controlling its spread. In this study, the multiangle canopy spectra and disease severity of wheat were investigated at several developmental stages and degrees of disease severity. Four wavelength variable-selected algorithms: successive projection(SPA), competitive adaptive reweighted sampling(CARS), feature selection learning(Relief-F), and genetic algorithm(GA), were used to identify bands sensitive to powdery mildew. The wavelength variables selected were used as input variables for partial least squares(PLS), extreme learning machine(ELM), random forest(RF), and support vector machine(SVM) algorithms, to construct a suitable prediction model for powdery mildew. Spectral reflectance and conventional vegetation indices(VIs) displayed angle effects under several disease severity indices(DIs). The CARS method selected relatively few wavelength variables and showed a relatively homogeneous distribution across the 13 viewing zenith angles.Overall accuracies of the four modeling algorithms were ranked as follows: ELM(0.70–0.82) > PLS(0.63–0.79) > SVM(0.49–0.69) > RF(0.43–0.69). Combinations of features and algorithms generated varied accuracies, with coefficients of determination(R^(2)) single-peaked at different observation angles. The constructed CARS-ELM model extracted a predictable bivariate relationship between the multi-angle canopy spectrum and disease severity, yielding an R^(2)> 0.8 at each measured angle. Especially for larger angles,monitoring accuracies were increased relative to the optimal VI model(40% at-60°, 33% at +60°), indicating that the CARS-ELM model is suitable for extreme angles of-60° and +60°. The results are proposed to provide a technical basis for rapid and large-scale monitoring of wheat powdery mildew.

Selection and development of representative simple sequence repeat primers and multiplex SSR sets for high throughput automated genotyping in maize

In the current study, 1900 maize simple sequence repeat (SSR) primers published in MaizeGDB were screened utilizing reference literature, 15 representative Chinese maize inbred lines and 15 Chinese maize hybrids from national regional testing. In total, 500 highly polymorphic primers were identified and used to construct a genetic map. 100 evenly distributed primers, 10 primers per chromosome, were further selected as a set of universal SSR core primers, recommended as preferred primers for general studies. These core primers were then redesigned and used to construct a high throughput multiplex PCR system based on a five-color fluorescence capillary detection system. We report here that two sets of ten-plex PCR combinations have been constructed, each consisting of 10 primers, with one primer per chromosome.

The HuangZaoSi Maize Genome Provides Insights into Genomic Variation and Improvement History of Maize

Maize is a globally important crop that was a classic model plant for genetic studies. Here, we report a 2.2 Gb draft genome sequence of an elite maize line, HuangZaoSi (HZS). Hybrids bred from HZS-improved lines (HILs) are planted in more than 60% of maize fields in China. Proteome clustering of six completed sequeneed maize genomes show that 638 proteins fall into 264 HZS-specific gene families with the majority of contributions from tandem duplication events. Resequencing and comparative analysis of 40 HZSrelated lines reveals the breeding history of HILs. More than 60% of identified selective sweeps were clustered in identity.by.descent conserved regions, and yield-related genes/QTLs were enriched in HZS characteristic selected regions. Furthermore, we dem on strated that HZS-specific family genes were not uniformly distributed in the genome but enriched in improvement/function.related genomic regions. This study provides an important and novel resource for maize genome research and expands our knowledge on the breadth of genomic variation and improvement history of maize.

Gene-lndexed Mutations in Maize

The availability of the B73 inbred reference genome sets the stage for high-throughput functional charac- terization of maize genes on a whole-genome scale. Among the 39 324 protein-coding genes predicted, the vast majority are untapped due to the lack of suitable high-throughput reverse genetic resources. We have generated a gene-indexed maize mutant collection through ethyl methanesulfonate mutagenesis and de- tected the mutations by combining exome capture and next-generation sequencing. A total of 1086 mutated MI plants were sequenced, and 195 268 CG〉TA-type point mutations, including stop gain/loss, missplice, start gain/loss, and various non-synonymous protein mutations as well as 4610 InDel mutations, were identified. These mutations were distributed on 32 069 genes, representing 82% of the predicted protein-coding genes in the maize genome. We detected an average of 180 mutations per mutant line and 6.1 mutations per gene. As many as 27 214 mutations of start codons, stop codons, or missplice sites were identified in 14 101 genes, among which 6232 individual genes harbored more than two such muta- tions. Application of this mutant collection is exemplified by the identification of the ent-kaurene synthase gene, which encodes a key enzyme in the gibberellin biosynthesis pathway. This gene-indexed genome- wide mutation collection provides an important resource for functional analysis of maize genes and may bring desirable allelic variants for genetic breeding in maize.