Genome-Wide Association Study and QTL Mapping Reveal Genomic Loci Associated with Fusarium Ear Rot Resistance in Tropical Maize Germplasm

Food Safety Aspects of Breeding Maize to Multi-Resistance against the Major (Fusarium graminearum, F. verticillioides, Aspergillus flavus) and Minor Toxigenic Fungi (Fusarium spp.) as Well as to Toxin Accumulation, Trends, and Solutions-A Review

Maize is the crop which is most commonly exposed to toxigenic fungi that produce many toxins that are harmful to humans and animals alike. Preharvest grain yield loss, preharvest toxin contamination (at harvest), and storage loss are estimated to be between 220 and 265 million metric tons. In the past ten years, the preharvest mycotoxin damage was stable or increased mainly in aflatoxin and fumonisins. The presence of multiple toxins is characteristic. The few breeding programs concentrate on one of the three main toxigenic fungi. About 90% of the experiments except AFB1 rarely test toxin contamination. As disease resistance and resistance to toxin contamination often differ in regard to F. graminearum, F. verticillioides, and A. flavus and their toxins, it is not possible to make a food safety evaluation according to symptom severity alone. The inheritance of the resistance is polygenic, often mixed with epistatic and additive effects, but only a minor part of their phenotypic variation can be explained. All tests are made by a single inoculum (pure isolate or mixture). Genotype ranking differs between isolates and according to aggressiveness level; therefore, the reliability of such resistance data is often problematic. Silk channel inoculation often causes lower ear rot severity than we find in kernel resistance tests. These explain the slow progress and raise skepticism towards resistance breeding. On the other hand, during genetic research, several effective putative resistance genes were identified, and some overlapped with known QTLs. QTLs were identified as securing specific or general resistance to different toxicogenic species. Hybrids were identified with good disease and toxin resistance to the three toxigenic species. Resistance and toxin differences were often tenfold or higher, allowing for the introduction of the resistance and resistance to toxin accumulation tests in the variety testing and the evaluation of the food safety risks of the hybrids within 2-3 years. Beyond this, resistance breeding programs and genetic investigations (QTL-analyses, GWAM tests, etc.) can be improved. All other research may use it with success, where artificial inoculation is necessary. The multi-toxin data reveal more toxins than we can treat now. Their control is not solved. As limits for nonregulated toxins can be introduced, or the existing regulations can be made to be stricter, the research should start. We should mention that a higher resistance to F. verticillioides and A. flavus can be very useful to balance the detrimental effect of hotter and dryer seasons on aflatoxin and fumonisin contamination. This is a new aspect to secure food and feed safety under otherwise damaging climatic conditions. The more resistant hybrids are to the three main agents, the more likely we are to reduce the toxin losses mentioned by about 50% or higher.

Kernel Bioassay Evaluation of Maize Ear Rot and Genome-Wide Association Analysis for Identifying Genetic Loci Associated with Resistance to Fusarium graminearum Infection

Gibberella ear rot (GER) caused by Fusarium graminearum (teleomorph Gibberella zeae) is one of the most destructive diseases in maize, which severely reduces yield and contaminates several potential mycotoxins in the grain. However, few efforts had been devoted to dissecting the genetic basis of maize GER resistance. In the present study, a genome-wide association study (GWAS) was conducted in a maize association panel consisting of 303 diverse inbred lines. The phenotypes of GER severity were evaluated using kernel bioassay across multiple time points in the laboratory. Then, three models, including the fixed and random model circulating probability unification model (FarmCPU), general linear model (GLM), and mixed linear model (MLM), were conducted simultaneously in GWAS to identify single-nucleotide polymorphisms (SNPs) significantly associated with GER resistance. A total of four individual significant association SNPs with the phenotypic variation explained (PVE) ranging from 3.51 to 6.42% were obtained. Interestingly, the peak SNP (PUT-163a-71443302-3341) with the greatest PVE value, was co-localized in all models. Subsequently, 12 putative genes were captured from the peak SNP, and several of these genes were directly or indirectly involved in disease resistance. Overall, these findings contribute to understanding the complex plant-pathogen interactions in maize GER resistance. The regions and genes identified herein provide a list of candidate targets for further investigation, in addition to the kernel bioassay that can be used for evaluating and selecting elite germplasm resources with GER resistance in maize.

Genetic variation in ZmWAX2 confers maize resistance to Fusarium verticillioides

Fusarium verticillioides (F. verticillioides) is a widely distributed phytopathogen that incites multiple destructive diseases in maize, posing a grave threat to corn yields and quality worldwide. However, there are few reports of resistance genes to F. verticillioides. Here, we reveal that a combination of two single nucleotide polymorphisms (SNPs) corresponding to ZmWAX2 gene associates with quantitative resistance variations to F. verticillioides in maize through a genome-wide association study. A lack of ZmWAX2 compromises maize resistance to F. verticillioides-caused seed rot, seedling blight and stalk rot by reducing cuticular wax deposition, while the transgenic plants overexpressing ZmWAX2 show significantly increased immunity to F. verticillioides. A natural occurrence of two 7-bp deletions within the promoter increases ZmWAX2 transcription, thus enhancing maize resistance to F. verticillioides. Upon Fusarium stalk rot, ZmWAX2 greatly promotes the yield and grain quality of maize. Our studies demonstrate that ZmWAX2 confers multiple disease resistances caused by F. verticillioides and can serve as an important gene target for the development of F. verticillioides-resistant maize varieties.

Genome-Wide Association Study Discovers Novel Germplasm Resources and Genetic Loci with Resistance to Gibberella Ear Rot Caused by Fusarium graminearum

Gibberella ear rot (GER) in maize caused by Fusarium graminearum is one of the most devastating maize diseases reducing grain yield and quality worldwide. The genetic bases of maize GER resistance remain largely unknown. Using artificial inoculation across multiple environments, the GER severity of an association panel consisting of 316 diverse inbred lines was observed with wide phenotypic variation. In the association panel, a genome-wide association study using a general linear model identified 69 single-nucleotide polymorphisms (SNPs) significantly associated with GER resistance at the threshold of 2.04 × 10-5, and the average phenotypic variation explained (PVE) of these SNPs was 5.09%. We also conducted a genome-wide association study analysis using a mixed linear model at a threshold of 1.0 × 10-4, and 16 significantly associated SNPs with an average PVE of 4.73% were detected. A combined general linear model and mixed linear model method obtained 10 co-localized significantly associated SNPs linked to GER resistance, including the most significant SNP (PZE-105079915) with the greatest PVE value, 9.07%, at bin 5.05 following 10 candidate genes. These findings are significant for the exploration of the complicated genetic variations in maize GER resistance. The regions and genes identified herein provide a list of candidate targets for further investigation, in addition to the elite germplasm resources that can be used for breeding GER resistance in maize.

ZmSIZ1a and ZmSIZ1b play an indispensable role in resistance against Fusarium ear rot in maize

Fusarium ear rot (FER) is a destructive fungal disease of maize caused by Fusarium verticillioides. FER resistance is a typical complex quantitative trait controlled by micro-effect genes, leading to difficulty in identifying the host resistance genes. SIZ1 encodes a SUMO E3 ligase regulating a wide range of plant developmental processes and stress responses. However, the function of ZmSIZ1 remains poorly understood. In this study, we demonstrate that ZmSIZ1a and ZmSIZ1b possess SUMO E3 ligase activity, and that the Zmsiz1a/1b double mutant, but not the Zmsiz1a or Zmsiz1b single mutants, exhibits severely impaired resistance to FER. Transcriptome analysis showed that differentially expressed genes were significantly enriched in plant disease resistance-related pathways, especially in plant-pathogen interaction, MAPK signalling, and plant hormone signal transduction. Thirty-five candidate genes were identified in these pathways. Furthermore, the integration of the transcriptome and metabolome data revealed that the flavonoid biosynthesis pathway was induced by F. verticillioides infection, and that accumulation of flavone and flavonol was significantly reduced in the Zmsiz1a/1b double mutant. Collectively, our findings demonstrate that ZmSIZ1a and ZmSIZ1b play a redundant, but indispensable role against FER, and provide potential new gene resources for molecular breeding of FER-resistant maize cultivars.

Meta-analysis and co-expression analysis revealed stable QTL and candidate genes conferring resistances to Fusarium and Gibberella ear rots while reducing mycotoxin contamination in maize

Fusarium (FER) and Gibberella ear rots (GER) are the two most devastating diseases of maize (Zea mays L.) which reduce yield and affect grain quality worldwide, especially by contamination with mycotoxins. Genetic improvement of host resistance to effectively tackle FER and GER diseases requires the identification of stable quantitative trait loci (QTL) to facilitate the application of genomics-assisted breeding for improving selection efficiency in breeding programs. We applied improved meta-analysis algorithms to re-analyze 224 QTL identified in 15 studies based on dense genome-wide single nucleotide polymorphisms (SNP) in order to identify meta-QTL (MQTL) and colocalized genomic loci for fumonisin (FUM) and deoxynivalenol (DON) accumulation, silk (SR) and kernel (KR) resistances of both FER and GER, kernel dry-down rate (KDD) and husk coverage (HC). A high-resolution genetic consensus map with 36,243 loci was constructed and enabled the projection of 164 of the 224 collected QTL. Candidate genes (CG) mining was performed within the most refined MQTL, and identified CG were cross-validated using publicly available transcriptomic data of maize under Fusarium graminearum infection. The meta-analysis revealed 40 MQTL, of which 29 were associated each with 2-5 FER- and/or GER-related traits. Twenty-eight of the 40 MQTL were common to both FER and GER resistances and 19 MQTL were common to silk and kernel resistances. Fourteen most refined MQTL on chromosomes 1, 2, 3, 4, 7 and 9 harbored a total of 2,272 CG. Cross-validation identified 59 of these CG as responsive to FER and/or GER diseases. MQTL ZmMQTL2.2, ZmMQTL9.2 and ZmMQTL9.4 harbored promising resistance genes, of which GRMZM2G011151 and GRMZM2G093092 were specific to the resistant line for both diseases and encoded "terpene synthase21 (tps21)" and "flavonoid O-methyltransferase2 (fomt2)", respectively. Our findings revealed stable refined MQTL harboring promising candidate genes for use in breeding programs for improving FER and GER resistances with reduced mycotoxin accumulation. These candidate genes can be transferred into elite cultivars by integrating refined MQTL into genomics-assisted backcross breeding strategies.

A novel maize microRNA negatively regulates resistance to Fusarium verticillioides

Although microRNAs (miRNAs) regulate the defence response against multiple pathogenic fungi in diverse plant species, few efforts have been devoted to deciphering the involvement of miRNA in resistance to Fusarium verticillioides, a major pathogenic fungus affecting maize production. In this study, we discovered a novel F. verticillioides-responsive miRNA designated zma-unmiR4 in maize kernels. The expression of zma-unmiR4 was significantly repressed in the resistant maize line but induced in the susceptible lines upon exposure to F. verticillioides exposure, whereas its target gene ZmGA2ox4 exhibited the opposite pattern of expression. Heterologous overexpression of zma-unmiR4 in Arabidopsis resulted in enhanced growth and compromised resistance to F. verticillioides. By contrast, transgenic plants overexpressing ZmGA2ox4 or the homologue AtGA2ox7 showed impaired growth and enhanced resistance to F. verticillioides. Moreover, zma-unmiR4-mediated suppression of AtGA2ox7 disturbed the accumulation of bioactive gibberellin (GA) in transgenic plants and perturbed the expression of a set of defence-related genes in response to F. verticillioides. Exogenous application of GA or a GA biosynthesis inhibitor modulated F. verticillioides resistance in different plants. Taken together, our results suggest that the zma-unmiR4-ZmGA2ox4 module might act as a major player in balancing growth and resistance to F. verticillioides in maize.

Identification of a Fusarium ear rot resistance gene in maize by QTL mapping and RNA sequencing

Fusarium ear rot (FER) caused by Fusarium verticillioides is a prevalent maize disease. To comprehensively characterize the genetic basis of the natural variation in FER resistance, a recombinant inbred line (RIL) population was used to map quantitative trait loci (QTL) for FER resistance. A total of 17 QTL were identified by linkage mapping in eight environments. These QTL were located on six chromosomes and explained 3.88-15.62% of the total phenotypic variation. Moreover, qFER1.03 had the strongest effect and accounted for 4.98-15.62% of the phenotypic variation according to analyses of multiple environments involving best linear unbiased predictions. The chromosome segment substitution lines (CSSLs) derived from a cross between Qi319 (donor parent) and Ye478 (recurrent parent) were used to verify the contribution of qFER1.03 to FER resistance. The line CL171, which harbored an introgressed qFER1.03, was significantly resistant to FER. Further fine mapping of qFER1.03 revealed that the resistance QTL was linked to insertion/deletion markers InDel 8 and InDel 2, with physical distances of 43.55 Mb and 43.76 Mb, respectively. Additionally, qFER1.03 differed from the previous resistance QTL on chromosome 1. There were three annotated genes in this region. On the basis of the RNA-seq data, which revealed the genes differentially expressed between the FER-resistant Qi319 and susceptible Ye478, GRMZM2G017792 (MPK3) was preliminarily identified as a candidate gene in the qFER1.03 region. The Pr-CMV-VIGS system was used to decrease the GRMZM2G017792 expression level in CL171 by 34-57%, which led to a significant decrease in FER resistance. Using RIL and CSSL populations combined with RNA-seq and Pr-CMV-VIGS, the candidate gene can be dissected effectively, which provided important gene resource for breeding FER-resistant varieties.

Evaluation and Identification of Resistance Lines and QTLs of Maize to Seedborne Fusarium verticillioides

Internal fungal contamination in cereal grains may affect plant growth and result in health concerns for humans and animals. Fusarium verticillioides is a seedborne fungus that can systemically infect maize. However, few efforts had been devoted to studying the genetics of maize resistance to seedborne F. verticillioides. In this study, we developed a disease evaluation method to identify resistance to seedborne F. verticillioides in maize, by which a set of 121 diverse maize inbred lines were evaluated. A 160 F₁₀-generation recombinant inbred line (RIL) population derived from a cross of the resistant (BT-1) and susceptible (N6) inbred line was further used to identify major quantitative trait loci (QTLs) for seedborne F. verticillioides resistance. Eighteen inbred lines with a high resistance to seedborne F. verticillioides were characterized and could be used as potential germplasm resources for genetic improvement of maize resistance. Six QTLs with high heritability across multiple environments were detected on chromosomes 3, 4, 6, and 10, among which was a major QTL, qISFR4-1. Located on chromosome 4 at the interval of 12922609-13418025, qISFR4-1 could explain 16.63% of the total phenotypic variance. Distinct expression profiles of eight candidate genes in qISFR4-1 between BT-1 and N6 inbred lines suggested their pivotal regulatory roles in seedborne F. verticillioides resistance. Taken together, these results will improve our understanding of the resistant mechanisms of seedborne F. verticillioides and would provide valuable germplasm resources for disease resistance breeding in maize.

Identification of Fusarium verticillioides Resistance Alleles in Three Maize Populations With Teosinte Gene Introgression

Fusarium ear rot (FER) is a common fungal disease in maize (Zea mays L.) caused by Fusarium verticillioides. Resistant germplasm resources for FER are rare in cultivated maize; however, teosintes (Z. mays ssp. parviglumis and Z. mays ssp. diploperennis), which are wild-type species of maize, have the potential to offer a novel source of resistance alleles to enhance pathogen resistance in modern maize. Therefore, the aim of this study was to identify favorable alleles that confer significant levels of resistance toward FER. Three populations of BC₂F₈ recombinant inbred lines (RILs) were developed by crossing two different teosintes, Z. diploperennis and Z. parviglumis, with maize inbred lines B73 and Zheng58, and were screened for FER resistance. We found that Z. diploperennis and Z. parviglumis had higher resistance toward F. verticillioides in the leaves than B73 and Zheng58. However, the resistance toward F. verticillioides in the leaf and ear was unrelated among RILs. FER resistance was positively correlated with grain yield in the B73 × diploperennis (BD) and Zheng58 × parviglumis (ZP) populations, partly because the quantitative trait loci (QTLs) of FER resistance and yield traits were located close together. Four coincident QTLs (qFERbd5.177, qFERbd10.140, qFERzp4.066, and qFERzp5.116) and two highly reliable resistance-yield synergistic QTLs (qFERbd10.140 and qFERzp4.066) were identified in the BD and ZP populations, opening up the possibility of breeding for FER resistance without reducing yield.

Genome-Wide Association Analysis Reveals Genetic Architecture and Candidate Genes Associated with Grain Yield and Other Traits under Low Soil Nitrogen in Early-Maturing White Quality Protein Maize Inbred Lines

Maize production in the savannas of sub-Saharan Africa (SSA) is constrained by the low nitrogen in the soils. The identification of quantitative trait loci (QTL) conferring tolerance to low soil nitrogen (low-N) is crucial for the successful breeding of high-yielding QPM maize genotypes under low-N conditions. The objective of this study was to identify QTLs significantly associated with grain yield and other low-N tolerance-related traits under low-N. The phenotypic data of 140 early-maturing white quality protein maize (QPM) inbred lines were evaluated under low-N. The inbred lines were genotyped using 49,185 DArTseq markers, from which 7599 markers were filtered for population structure analysis and genome-wide association study (GWAS). The inbred lines were grouped into two major clusters based on the population structure analysis. The GWAS identified 24, 3, 10, and 3 significant SNPs respectively associated with grain yield, stay-green characteristic, and plant and ear aspects, under low-N. Sixteen SNP markers were physically located in proximity to 32 putative genes associated with grain yield, stay-green characteristic, and plant and ear aspects. The putative genes GRMZM2G127139, GRMZM5G848945, GRMZM2G031331, GRMZM2G003493, GRMZM2G067964, GRMZM2G180254, on chromosomes 1, 2, 8, and 10 were involved in cellular nitrogen assimilation and biosynthesis, normal plant growth and development, nitrogen assimilation, and disease resistance. Following the validation of the markers, the putative candidate genes and SNPs could be used as genomic markers for marker-assisted selection, to facilitate genetic gains for low-N tolerance in maize production.

Genomics and Pathways Involved in Maize Resistance to Fusarium Ear Rot and Kernel Contamination With Fumonisins

Fusarium verticillioides is a causal agent of maize ear rot and produces fumonisins, which are mycotoxins that are toxic to animals and humans. In this study, quantitative trait loci (QTLs) and bulk-segregant RNA-seq approaches were used to uncover genomic regions and pathways involved in resistance to Fusarium ear rot (FER) and to fumonisin accumulation in maize kernels. Genomic regions at bins 4.07-4.1, 6-6.01, 6.04-6.05, and 8.05-8.08 were related to FER resistance and/or reduced fumonisin levels in kernels. A comparison of transcriptomes between resistant and susceptible inbred bulks 10 days after inoculation with F. verticillioides revealed 364 differentially expressed genes (DEGs). In the resistant inbred bulks, genes involved in sink metabolic processes such as fatty acid and starch biosynthesis were downregulated, as well as those involved in phytosulfokine signaling and many other genes involved in cell division; while genes involved in secondary metabolism and compounds/processes related to resistance were upregulated, especially those related to cell wall biosynthesis/rearrangement and flavonoid biosynthesis. These trends are indicative of a growth-defense trade-off. Among the DEGs, Zm00001d053603, Zm00001d035562, Zm00001d037810, Zm00001d037921, and Zm00001d010840 were polymorphic between resistant and susceptible bulks, were located in the confidence intervals of detected QTLs, and showed large differences in transcript levels between the resistant and susceptible bulks. Thus, they were identified as candidate genes involved in resistance to FER and/or reduced fumonisin accumulation.

Proteomic profiling of royal jelly produced by Apis mellifera L. exposed to food containing herbicide-based glyphosate

Royal jelly (RJ) is rich in protective elements associated with collective immune defenses in the hive of Apis mellifera. Exposure of bees to glyphosate-based herbicides causes ultrastructural changes in the hypopharyngeal glands and a reduction in the production of RJ. However, the effects of glyphosate-based herbicides on the protein composition of RJ and consequences for the hive are unknown. Thus, we performed proteomic profiling of royal jelly produced in hives of A. mellifera exposed to food containing 1,5 μL of Roundup® (2.16 mg. g-1 of glyphosate). The production of RJ was carried out in six hives, following the method of artificial production of queens. The combs containing 80 grafting cells were introduced into the hives, and the collection of royal jelly was performed after 72 h. Two treatments were determined based on hive feeding and the hive as the experimental unit: Control and "Roundup®". Royal jelly from the Roundup® treatment hives was compared to the Control hives. Proteins with differences in expression were identified by mass spectrometry. Only the proteins present in all three biological replicates were considered in the differential abundance analysis, using Student's t-test (p-value < 0.05, two-tailed). Hives that received food containing Roundup®, analysis showed alterations in protein profile in the RJ produced therein. In total, 24 proteins were identified, and the accumulation of Major royal jelly protein 3 (MRJP3) was downregulated, showing a significant reduction in hives exposed to food containing Roundup® in relation to control hives (t = 0.0017). MRJP3 acts analogously to polyclonal antigen-antibody reactions, performing functions related to immunity in bees of different ages and castes. To the best of our knowledge, this is the first study to demonstrate changes in the proteomic profile of RJ caused by glyphosate-based herbicides, indicating its negative effects on the nutrition and social immunity of bees.

Discovery of Single Nucleotide Polymorphisms for Resistance to Abnormal Vertical Growth in Macadamia

Abnormal vertical growth (AVG) syndrome is a serious threat to the Australian macadamia industry as it decreases the yield of nuts by as much as 70% per annum. A lack of information on the cause of AVG has hindered the development of an effective disease management strategy. Discovery of genetic markers associated with disease resistance can be used as tool for rapid selection of elite cultivars, hence helps in efficient disease management. Differences in field susceptibility of macadamia cultivars provide an opportunity for discovery of genetic markers that are associated with host resistance. REML mixed model analysis was performed to estimate the AVG rating of 51 cultivars from multiple origins using phenotypic data from 359 trees planted in four sites. Most of the Hawaiian cultivars were found as susceptible, while selections from the Australian macadamia industry breeding program were predominantly resistant. All the cultivars were genotyped for 13,221 DArTseq-based single nucleotide polymorphism (SNP) markers. A bulked sample analysis was performed using 20 genotypes each at the extremes of AVG phenotypic ratings. Ten SNP markers were predicted to be associated with AVG resistance and two arbitrarily selected SNP markers were validated using PCR and Sanger sequencing. Our findings suggest that AVG resistance in the commercial cultivars may be derived from the genomic introgression of Macadamia tetraphylla through interspecific hybridization. The results may support marker-assisted selection for macadamia germplasm with AVG resistance.

Mapping and Validation of a Stable Quantitative Trait Locus Conferring Maize Resistance to Gibberella Ear Rot

Gibberella ear rot (GER), a prevalent disease caused by Fusarium graminearum, can result in significant yield loss and carcinogenic mycotoxin contamination in maize worldwide. However, only a few quantitative trait loci (QTLs) for GER resistance have been reported. In this study, we evaluated a Chinese recombinant inbred line (RIL) population comprising 204 lines, developed from a cross between a resistant parent DH4866 and a susceptible line T877, in three field trials under artificial inoculation with F. graminearum. The RIL population and their parents were genotyped with an Affymetrix microarray CGMB56K SNP Array. Based on the genetic linkage map constructed using 1,868 bins as markers, 11 QTLs, including five stable QTLs, were identified by individual environment analysis. Joint multiple environments analysis and epistatic interaction analysis revealed six additive and six epistatic (additive × additive) QTLs, respectively. None of the QTLs could explain more than 10% of phenotypic variation, suggesting that multiple minor-effect QTLs contributed to the genetic component of resistance to GER, and both additive and epistatic effects contributed to the genetic architecture of resistance to GER. A novel QTL, qGER4.09, with the largest effect, identified and validated using 588 F₂ individuals, was colocalized with genomic regions for Fusarium ear rot and Aspergillus ear rot, indicating that this genetic locus likely confers resistance to multiple pathogens and can potentially be utilized in breeding maize varieties aimed at improving the resistance not only to GER but also other ear rot diseases.

Genome-wide association mapping in maize: status and prospects

Genome-wide association study (GWAS) provides a robust and potent tool to retrieve complex phenotypic traits back to their underlying genetics. Maize is an excellent crop for performing GWAS due to diverse genetic variability, rapid decay of linkage disequilibrium, availability of distinct sub-populations and abundant SNP information. The application of GWAS in maize has resulted in successful identification of thousands of genomic regions associated with many abiotic and biotic stresses. Many agronomic and quality traits of maize are severely affected by such stresses and, significantly affecting its growth and productivity. To improve productivity of maize crop in countries like India which contribute only 2% to the world's total production in 2019-2020, it is essential to understand genetic complexity of underlying traits. Various DNA markers and trait associations have been revealed using conventional linkage mapping methods. However, it has achieved limited success in improving polygenic complex traits due to lower resolution of trait mapping. The present review explores the prospects of GWAS in improving yield, quality and stress tolerance in maize besides, strengths and challenges of using GWAS for molecular breeding and genomic selection. The information gathered will facilitate elucidation of genetic mechanisms of complex traits and improve efficiency of marker-assisted selection in maize breeding.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02799-4.

New genomic approaches for enhancing maize genetic improvement

Maize (Zea mays) is one of the most widely grown crops in the world, with an annual global production of over 1147 million tons. Genomics approaches are thought to be the best solution for accelerating yield improvement to meet the challenges of a growing population and global climate change. Here, we review current approaches to the exploration of novel genetic variation in genomes, DNA modifications, and transcription levels of cultivated maize, landraces, and wild relatives. We discuss applications of genetic engineering to maize yield improvement and highlight future directions for maize genomics studies.

QTL Mapping of Fusarium Ear Rot Resistance in Maize

Ear rot is a globally prevalent class of disease in maize, of which Fusarium ear rot (FER), caused by the fungal pathogen Fusarium verticillioides, is the most commonly reported. In this study, three F₂ populations, namely F₂-C, F₂-D, and F₂-J, and their corresponding F_2:3 families were produced by crossing three highly FER-resistant inbred lines, Cheng351, Dan598, and JiV203, with the same susceptible line, ZW18, for quantitative trait locus (QTL) mapping of FER resistance. The individual crop plants were inoculated with a spore suspension of the pathogen injected into the kernels of the maize ears. The broad-sense heritability (H²) for FER resistance was estimated to be as high as 0.76, 0.81, and 0.78 in F₂-C, F₂-D, and F₂-J, respectively, indicating that genetic factors played a key role in the phenotypic variation. We detected a total of 20 FER-resistant QTLs in the three F₂ populations, among which QTLs derived from the resistant parent Cheng351, Dan598, and JiV203 explained 62.89 to 82.25%, 43.19 to 61.51%, and 54.70 to 75.77% of the phenotypic variation, respectively. Among all FER-resistant QTLs detected, qRfer1, qRfer10, and qRfer17 accounted for the phenotypic variation as high as 26.58 to 43.36%, 11.76 to 18.02%, and 12.02 to 21.81%, respectively. Furthermore, QTLs mapped in different F₂ populations showed some extent of overlaps indicating potential resistance hotspots. The FER-resistant QTLs detected in this study can be explored as useful candidates to improve FER resistance in maize by introducing these QTLs into susceptible maize inbred lines via molecular marker-assisted selection.

Application of Genomic Big Data in Plant Breeding:Past, Present, and Future

Plant breeding has a long history of developing new varieties that have ensured the food security of the human population. During this long journey together with humanity, plant breeders have successfully integrated the latest innovations in science and technologies to accelerate the increase in crop production and quality. For the past two decades, since the completion of human genome sequencing, genomic tools and sequencing technologies have advanced remarkably, and adopting these innovations has enabled us to cost down and/or speed up the plant breeding process. Currently, with the growing mass of genomic data and digitalized biological data, interdisciplinary approaches using new technologies could lead to a new paradigm of plant breeding. In this review, we summarize the overall history and advances of plant breeding, which have been aided by plant genomic research. We highlight the key advances in the field of plant genomics that have impacted plant breeding over the past decades and introduce the current status of innovative approaches such as genomic selection, which could overcome limitations of conventional breeding and enhance the rate of genetic gain.

It takes three to tango: the importance of microbes, host plant, and soil management to elucidate manipulation strategies for the plant microbiome

The world’s population is expected to grow to almost 10 billion by 2050, placing unprecedented demands on agriculture and natural resources. The risk in food security is also aggravated by climate change and land degradation, which compromise agricultural productivity. In recent years, our understanding of the role of microbial communities on ecosystem functioning, including plant-associated microbes, has advanced considerably. Yet, translating this knowledge into practical agricultural technologies is challenged by the intrinsic complexity of agroecosystems. Here, we review current strategies for plant microbiome manipulation, classifying them into three main pillars: (i) introducing and engineering microbiomes, (ii) breeding and engineering the host plant, and (iii) selecting agricultural practices that enhance resident soil and plant-associated microbial communities. In each of these areas, we analyze current trends in research, as well as research priorities and future perspectives.

Genomics of Maize Resistance to Fusarium Ear Rot and Fumonisin Contamination

Food contamination with mycotoxins is a worldwide concern, because these toxins produced by several fungal species have detrimental effects on animal and/or human health. In maize, fumonisins are among the toxins with the highest threatening potential because they are mainly produced by Fusarium verticillioides, which is distributed worldwide. Plant breeding has emerged as an effective and environmentally safe method to reduce fumonisin levels in maize kernels, but although phenotypic selection has proved effective for improving resistance to fumonisin contamination, further resources should be mobilized to meet farmers' needs. Selection based on molecular markers linked to quantitative trait loci (QTL) for resistance to fumonisin contamination or/and genotype values obtained using prediction models with markers distributed across the whole genome could speed up breeding progress. Therefore, in the current paper, previously identified genomic regions, genes, and/or pathways implicated in resistance to fumonisin accumulation will be reviewed. Studies done until now have provide many markers to be used by breeders, but to get further insight on plant mechanisms to defend against fungal infection and to limit fumonisin contamination, the genes behind those QTLs should be identified.

Complex Genetic System Involved in Fusarium Ear Rot Resistance in Maize as Revealed by GWAS, Bulked Sample Analysis, and Genomic Prediction

Fusarium ear rot (FER) caused by Fusarium verticillioides is one of the most prevalent maize diseases in China and worldwide. Resistance to FER is a complex trait controlled by multiple genes highly affected by environment. In this paper, genome-wide association study (GWAS), bulked sample analysis (BSA), and genomic prediction were performed for understanding FER resistance using 509 diverse inbred lines, which were genotyped by 37,801 high-quality single-nucleotide polymorphisms (SNPs). Ear rot evaluation was performed using artificial inoculation in four environments in China: Xinxiang, Henan, and Shunyi, Beijing, during 2017 and 2018. Significant phenotypic and genetic variation for FER severity was observed, and FER resistance was significantly correlated among the four environments with a generalized heritability of 0.78. GWAS identified 23 SNPs that were associated with FER resistance, 2 of which (1_226233417 on chromosome 1 and 10_14501044 on chromosome 10) were associated at threshold of 2.65 × 10^-7 [-log(0.01/37,801)]. Using BSA, resistance quantitative trait loci were identified on chromosomes 3, 4, 7, 9, and 10 at the 90% confidence level and on chromosomes 3 and 10 at the 95% confidence level. A key region, bin 10.03, was detected by both GWAS and BSA. Genomic prediction for FER resistance showed that the prediction accuracy by trait-related markers was higher than that by randomly selected markers under different levels of marker density. Marker-assisted selection using genomic prediction could be an efficient strategy for genetic improvement for complex traits like FER resistance.

Linkage mapping and genome-wide association study reveals conservative QTL and candidate genes for Fusarium rot resistance in maize

BACKGROUND

Fusarium ear rot (FER) caused by Fusarium verticillioides is a major disease of maize that reduces grain yield and quality globally. However, there have been few reports of major loci for FER were verified and cloned.

RESULT

To gain a comprehensive understanding of the genetic basis of natural variation in FER resistance, a recombinant inbred lines (RIL) population and one panel of inbred lines were used to map quantitative trait loci (QTL) for resistance. As a result, a total of 10 QTL were identified by linkage mapping under four environments, which were located on six chromosomes and explained 1.0-7.1% of the phenotypic variation. Epistatic mapping detected four pairs of QTL that showed significant epistasis effects, explaining 2.1-3.0% of the phenotypic variation. Additionally, 18 single nucleotide polymorphisms (SNPs) were identified across the whole genome by genome-wide association study (GWAS) under five environments. Compared linkage and association mapping revealed five common intervals located on chromosomes 3, 4, and 5 associated with FER resistance, four of which were verified in different near-isogenic lines (NILs) populations. GWAS identified three candidate genes in these consistent intervals, which belonged to the Glutaredoxin protein family, actin-depolymerizing factors (ADFs), and AMP-binding proteins. In addition, two verified FER QTL regions were found consistent with Fusarium cob rot (FCR) and Fusarium seed rot (FSR).

CONCLUSIONS

These results revealed that multi pathways were involved in FER resistance, which was a complex trait that was controlled by multiple genes with minor effects, and provided important QTL and genes, which could be used in molecular breeding for resistance.

Genomics-assisted breeding for ear rot resistances and reduced mycotoxin contamination in maize: methods, advances and prospects

Genetic mapping, genomic profiling and bioinformatic approaches were used to identify putative resistance genes for ear rots and low mycotoxin contamination in maize. Genomic selection seems to have good perspectives. Maize is globally an indispensable crop for humans and livestock. About 30% of yield is lost by fungal diseases with Gibberella, Fusarium and Aspergillus ear rots (ERs) having a high economic impact in most maize-growing regions of the world. They reduce not only yield, but also contaminate grains with mycotoxins like deoxynivalenol, zearalenone, fumonisins and aflatoxins, respectively. These mycotoxins pose serious health problems to humans and animals. A number of studies have been conducted to dissect the genetic architecture of resistance to these three major ear rots over the past decade. The review concentrates on studies carried out to locate quantitative trait loci (QTL) and candidate genes (CG) on the maize genome as well as the application of genomic selection in maize for resistance against Fusarium graminearum, Fusarium verticillioides and Aspergillus flavus. QTL studies by linkage or genome-wide association mapping, omic technologies (genomics, proteomics, transcriptomics and metabolomics) and bioinformatics are the methods used in the current studies to propose resistance genes against ear rot pathogens. Though a number of QTL and CG are reported, only a few specific genes were found to directly confer ER resistance in maize. A combination of two or more gene identification methods would provide a more powerful and reliable tool. Genomic selection seems to be promising for ER resistance breeding, but there are only a limited number of studies in this area. A strategy that can accurately validate and predict genotypes with major effect QTL and CG for selection will be worthwhile for practical breeding against ERs and mycotoxin contamination in maize.

Genetic architecture of maize chlorotic mottle virus and maize lethal necrosis through GWAS, linkage analysis and genomic prediction in tropical maize germplasm

KEY MESSAGE

Analysis of the genetic architecture of MCMV and MLN resistance in maize doubled-haploid populations revealed QTLs with major effects on chromosomes 3 and 6 that were consistent across genetic backgrounds and environments. Two major-effect QTLs, qMCMV3-108/qMLN3-108 and qMCMV6-17/qMLN6-17, were identified as conferring resistance to both MCMV and MLN. Maize lethal necrosis (MLN) is a serious threat to the food security of maize-growing smallholders in sub-Saharan Africa. The ability of the maize chlorotic mottle virus (MCMV) to interact with other members of the Potyviridae causes severe yield losses in the form of MLN. The objective of the present study was to gain insights and validate the genetic architecture of resistance to MCMV and MLN in maize. We applied linkage mapping to three doubled-haploid populations and a genome-wide association study (GWAS) on 380 diverse maize lines. For all the populations, phenotypic variation for MCMV and MLN was significant, and heritability was moderate to high. Linkage mapping revealed 13 quantitative trait loci (QTLs) for MCMV resistance and 12 QTLs conferring MLN resistance. One major-effect QTL, qMCMV3-108/qMLN3-108, was consistent across populations for both MCMV and MLN resistance. Joint linkage association mapping (JLAM) revealed 18 and 21 main-effect QTLs for MCMV and MLN resistance, respectively. Another major-effect QTL, qMCMV6-17/qMLN6-17, was detected for both MCMV and MLN resistance. The GWAS revealed a total of 54 SNPs (MCMV-13 and MLN-41) significantly associated (P ≤ 5.60 × 10-05) with MCMV and MLN resistance. Most of the GWAS-identified SNPs were within or adjacent to the QTLs detected through linkage mapping. The prediction accuracy for within populations as well as the combined populations is promising; however, the accuracy was low across populations. Overall, MCMV resistance is controlled by a few major and many minor-effect loci and seems more complex than the genetic architecture for MLN resistance.

Genome-wide association study and quantitative trait loci mapping of seed dormancy in common wheat (Triticum aestivum L.)

Totally, 23 and 26 loci for the first count germination ratio and the final germination ratio were detected by quantitative trait loci (QTL) mapping and association mapping, respectively, which could be used to facilitate wheat pre-harvest sprouting breeding. Weak dormancy can cause pre-harvest sprouting in seeds of common wheat which significantly reduces grain yield. In this study, both quantitative trait loci (QTL) mapping and genome-wide association study (GWAS) were used to identify loci controlling seed dormancy. The analyses were based on a recombinant inbred line population derived from Zhou 8425B/Chinese Spring cross and 166 common wheat accessions. Inclusive composite interval mapping detected 8 QTL, while 45 loci were identified in the 166 wheat accessions by GWAS. Among these, four loci (Q_bifcgr.cas-3AS/Qfcgr.cas-3AS, Q_bifcgr.cas-6AL.1/Qfcgr.cas-6AL.1, Q_bifcgr.cas-7BL.2/Qfcgr.cas-7BL.2, and Q_bigr.cas-3DL/Qgr.cas-3DL) were detected in both QTL mapping and GWAS. In addition, 41 loci co-located with QTL reported previously, whereas 8 loci (Qfcgr.cas-5AL, Qfcgr.cas-6DS, Qfcgr.cas-7AS, Qgr.cas-3DS.1, Qgr.cas-3DS.2, Q_bigr.cas-3DL/Qgr.cas-3DL, Qgr.cas-4B, and Qgr.cas-5A) were likely to be new. Linear regression showed the first count germination ratio or the final germination ratio reduced while multiple favorable alleles increased. It is suggested that QTL pyramiding was effective to reduce pre-harvest sprouting risk. This study could enrich the research on pre-harvest sprouting and provide valuable information of marker exploration for wheat breeding programs.

QTLs for Resistance to Fusarium Ear Rot in a Multiparent Advanced Generation Intercross (MAGIC) Maize Population

Alternative approaches to linkage and association mapping using inbred panels may allow further insights into loci involved in resistance to Fusarium ear rot and lead to the discovery of suitable markers for breeding programs. Here, the suitability of a maize multiparent advanced-generation intercross population for detecting quantitative trait loci (QTLs) associated with Fusarium ear rot resistance was evaluated and found to be valuable in uncovering genomic regions containing resistance-associated loci in temperate materials. In total, 13 putative minor QTLs were located over all of the chromosomes, except chromosome 5, and frequencies of favorable alleles for resistance to Fusarium ear rot were, in general, high. These findings corroborated the quantitative characteristic of resistance to Fusarium ear rot in which many loci have small additive effects. Present and previous results indicate that crucial regions such as 210 to 220 Mb in chromosome 3 and 166 to 173 Mb in chromosome 7 (B73-RefGen-v2) contain QTLs for Fusarium ear rot resistance and fumonisin content.

Genome-wide association analysis for fumonisin content in maize kernels

BACKGROUND

Plant breeding has been proposed as one of the most effective and environmentally safe methods to control fungal infection and to reduce fumonisin accumulation. However, conventional breeding can be hampered by the complex genetic architecture of resistance to fumonisin accumulation and marker-assisted selection is proposed as an efficient alternative. In the current study, GWAS has been performed for the first time for detecting high-resolution QTL for resistance to fumonisin accumulation in maize kernels complementing published GWAS results for Fusarium ear rot.

RESULTS

Thirty-nine SNPs significantly associated with resistance to fumonisin accumulation in maize kernels were found and clustered into 17 QTL. Novel QTLs for fumonisin content would be at bins 3.02, 5.02, 7.05 and 8.07. Genes with annotated functions probably implicated in resistance to pathogens based on previous studies have been highlighted.

CONCLUSIONS

Breeding approaches to fix favorable functional variants for genes implicated in maize immune response signaling may be especially useful to reduce kernel contamination with fumonisins without significantly interfering in mycelia development and growth and, consequently, in the beneficial endophytic behavior of Fusarium verticillioides.

Unravelling the genetic basis of Fusarium seedling rot resistance in the MAGIC maize population: novel targets for breeding

Fungal infection by Fusarium verticillioides is cause of prevalent maize disease leading to substantial reductions in yield and grain quality worldwide. Maize resistance to the fungus may occur at different developmental stages, from seedling to maturity. The breeding of resistant maize genotypes may take advantage of the identification of quantitative trait loci (QTL) responsible for disease resistance already commenced at seedling level. The Multi-parent Advance Generation Intercross (MAGIC) population was used to conduct high-definition QTL mapping for Fusarium seedling rot (FSR) resistance using rolled towel assay. Infection severity level, seedling weight and length were measured on 401 MAGIC maize recombinant inbred lines (RILs). QTL mapping was performed on reconstructed RIL haplotypes. One-fifth of the MAGIC RILs were resistant to FSR and 10 QTL were identified. For FSR, two QTL were detected at 2.8 Mb and 241.8 Mb on chromosome 4, and one QTL at 169.6 Mb on chromosome 5. Transcriptomic and sequencing information generated on the MAGIC founder lines was used to guide the identification of eight candidate genes within the identified FSR QTL. We conclude that the rolled towel assay applied to the MAGIC maize population provides a fast and cost-effective method to identify QTL and candidate genes for early resistance to F. verticillioides in maize.

Genetic analysis of cob resistance to F. verticillioides: another step towards the protection of maize from ear rot

We lay the foundation for further research on maize resistance to Fusarium verticillioides cob rot by identifying a candidate resistance gene. Fusarium verticillioides ear rot is the most common type of maize ear rot in the Huanghuaihai Plain of China. Ear rot resistance includes cob and kernel resistance. Most of the current literature concentrates on kernel resistance, and genetic studies on cob resistance are scarce. We aimed on identifying the QTLs responsible for F. verticillioides cob rot (FCR) resistance. Twenty-eight genes associated with 48 single nucleotide polymorphisms (SNPs) were identified (P < 10^-4) to correlate with FCR resistance using a whole-genome association study. The major quantitative trait locus, qRcfv2, for FCR resistance was identified on chromosome 2 through linkage mapping and was validated in near-isogenic line populations. Two candidate genes associated with two SNPs were detected in the qRcfv2 region with a lower threshold (P < 10^-3). Through real-time fluorescence quantitative PCR, one candidate gene was found to have no expression in the cob but the other was expressed in response to F. verticillioides. These results lay a foundation for research on the resistance mechanisms of cob and provide resources for marker-assisted selection.

Assessing the genetic diversity and characterizing genomic regions conferring Tan Spot resistance in cultivated rye

Rye (Secale cereale L.) is known for its wide adaptation due to its ability to tolerate harsh environments in semiarid areas. To assess the diversity in rye we genotyped a panel of 178 geographically diverse accessions of four Secale sp. from U.S. National Small Grains Collection using 4,037 high-quality SNPs (single nucleotide polymorphisms) developed by genotyping-by-sequencing (GBS). PCA and STRUCTURE analysis revealed three major clusters that separate S. cereale L. from S. strictum and S. sylvestre, however, genetic clusters did not correlate with geographic origins and growth habit (spring/winter). The panel was evaluated for response to Pyrenophora tritici-repentis race 5 (PTR race 5) and nearly 59% accessions showed resistance or moderate resistance. Genome-wide association study (GWAS) was performed on S. cereale subsp. cereale using the 4,037 high-quality SNPs. Two QTLs (QTs.sdsu-5R and QTs.sdsu-2R) on chromosomes 5R and 2R were identified conferring resistance to PTR race 5 (p < 0.001) that explained 13.1% and 11.6% of the phenotypic variation, respectively. Comparative analysis showed a high degree of synteny between rye and wheat with known rearrangements as expected. QTs.sdsu-2R was mapped in the genomic region corresponding to wheat chromosome group 2 and QTs.sdsu-5R was mapped to a small terminal region on chromosome 4BL. Based on the genetic diversity, a set of 32 accessions was identified to represents more than 99% of the allelic diversity with polymorphic information content (PIC) of 0.25. This set can be utilized for genetic characterization of useful traits and genetic improvement of rye, triticale, and wheat.

Genome-wide haplotype-based association analysis of key traits of plant lodging and architecture of maize identifies major determinants for leaf angle: hapLA4

Traits related to plant lodging and architecture are important determinants of plant productivity in intensive maize cultivation systems. Motivated by the identification of genomic associations with the leaf angle, plant height (PH), ear height (EH) and the EH/PH ratio, we characterized approximately 7,800 haplotypes from a set of high-quality single nucleotide polymorphisms (SNPs), in an association panel consisting of tropical maize inbred lines. The proportion of the phenotypic variations explained by the individual SNPs varied between 7%, for the SNP S1_285330124 (located on chromosome 9 and associated with the EH/PH ratio), and 22%, for the SNP S1_317085830 (located on chromosome 6 and associated with the leaf angle). A total of 40 haplotype blocks were significantly associated with the traits of interest, explaining up to 29% of the phenotypic variation for the leaf angle, corresponding to the haplotype hapLA4.04, which was stable over two growing seasons. Overall, the associations for PH, EH and the EH/PH ratio were environment-specific, which was confirmed by performing a model comparison analysis using the information criteria of Akaike and Schwarz. In addition, five stable haplotypes (83%) and 15 SNPs (75%) were identified for the leaf angle. Finally, approximately 62% of the associated haplotypes (25/40) did not contain SNPs detected in the association study using individual SNP markers. This result confirms the advantage of haplotype-based genome-wide association studies for examining genomic regions that control the determining traits for architecture and lodging in maize plants.

Diverse Components of Resistance to Fusarium verticillioides Infection and Fumonisin Contamination in Four Maize Recombinant Inbred Families

The fungus Fusarium verticillioides can infect maize ears, causing Fusarium ear rot (FER) and contaminating the grain with fumonisins (FUM), which are harmful to humans and animals. Breeding for resistance to FER and FUM and post-harvest sorting of grain are two strategies for reducing FUM in the food system. Kernel and cob tissues have been previously associated with differential FER and FUM. Four recombinant inbred line families from the maize nested associated mapping population were grown and inoculated with F. verticillioides across four environments, and we evaluated the kernels for external and internal infection severity as well as FUM contamination. We also employed publicly available phenotypes on innate ear morphology to explore genetic relationships between ear architecture and resistance to FER and FUM. The four families revealed wide variation in external symptomatology at the phenotypic level. Kernel bulk density under inoculation was an accurate indicator of FUM levels. Genotypes with lower kernel density-under both inoculated and uninoculated conditions-and larger cobs were more susceptible to infection and FUM contamination. Quantitative trait locus (QTL) intervals could be classified as putatively resistance-specific and putatively shared for ear and resistance traits. Both types of QTL mapped in this study had substantial overlap with previously reported loci for resistance to FER and FUM. Ear morphology may be a component of resistance to F. verticillioides infection and FUM accumulation.

Combining Three Mapping Strategies to Reveal Quantitative Trait Loci and Candidate Genes for Maize Ear Length

Ear length (EL) is an important trait in maize ( L.) because it is positively correlated with grain yield. To understand the genetic basis of natural EL variation, a F, a four-way cross and a genome-wide association study (GWAS) population were used to identify the quantitative trait loci (QTLs) and candidate EL genes. Linkage mapping identified 14 QTLs in two types of populations from multiple environments. Six of them were located in three common genomic regions considered "stable QTLs". Candidate genes for the three stable QTLs were identified by the GWAS results. These were related to auxin transport, cell proliferation, and developmental regulation. These results confirm that maize EL is under strong genetic control by many small-effect genes. They also improve our understanding of the genetic basis of maize EL.

Genomic-based-breeding tools for tropical maize improvement

Maize has traditionally been the main staple diet in the Southern Asia and Sub-Saharan Africa and widely grown by millions of resource poor small scale farmers. Approximately, 35.4 million hectares are sown to tropical maize, constituting around 59% of the developing worlds. Tropical maize encounters tremendous challenges besides poor agro-climatic situations with average yields recorded <3 tones/hectare that is far less than the average of developed countries. On the contrary to poor yields, the demand for maize as food, feed, and fuel is continuously increasing in these regions. Heterosis breeding introduced in early 90 s improved maize yields significantly, but genetic gains is still a mirage, particularly for crop growing under marginal environments. Application of molecular markers has accelerated the pace of maize breeding to some extent. The availability of array of sequencing and genotyping technologies offers unrivalled service to improve precision in maize-breeding programs through modern approaches such as genomic selection, genome-wide association studies, bulk segregant analysis-based sequencing approaches, etc. Superior alleles underlying complex traits can easily be identified and introgressed efficiently using these sequence-based approaches. Integration of genomic tools and techniques with advanced genetic resources such as nested association mapping and backcross nested association mapping could certainly address the genetic issues in maize improvement programs in developing countries. Huge diversity in tropical maize and its inherent capacity for doubled haploid technology offers advantage to apply the next generation genomic tools for accelerating production in marginal environments of tropical and subtropical world. Precision in phenotyping is the key for success of any molecular-breeding approach. This article reviews genomic technologies and their application to improve agronomic traits in tropical maize breeding has been reviewed in detail.

Genome-wide Association Studies in Maize: Praise and Stargaze

Genome-wide association study (GWAS) has become a widely accepted strategy for decoding genotype-phenotype associations in many species thanks to advances in next-generation sequencing (NGS) technologies. Maize is an ideal crop for GWAS and significant progress has been made in the last decade. This review summarizes current GWAS efforts in maize functional genomics research and discusses future prospects in the omics era. The general goal of GWAS is to link genotypic variations to corresponding differences in phenotype using the most appropriate statistical model in a given population. The current review also presents perspectives for optimizing GWAS design and analysis. GWAS analysis of data from RNA, protein, and metabolite-based omics studies is discussed, along with new models and new population designs that will identify causes of phenotypic variation that have been hidden to date. The joint and continuous efforts of the whole community will enhance our understanding of maize quantitative traits and boost crop molecular breeding designs.