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

Genomic selection in plant breeding: Key factors shaping two decades of progress

Genomic selection, the application of genomic prediction (GP) models to select candidate individuals, has significantly advanced in the past two decades, effectively accelerating genetic gains in plant breeding. This article provides a holistic overview of key factors that have influenced GP in plant breeding during this period. We delved into the pivotal roles of training population size and genetic diversity, and their relationship with the breeding population, in determining GP accuracy. Special emphasis was placed on optimizing training population size. We explored its benefits and the associated diminishing returns beyond an optimum size. This was done while considering the balance between resource allocation and maximizing prediction accuracy through current optimization algorithms. The density and distribution of single-nucleotide polymorphisms, level of linkage disequilibrium, genetic complexity, trait heritability, statistical machine-learning methods, and non-additive effects are the other vital factors. Using wheat, maize, and potato as examples, we summarize the effect of these factors on the accuracy of GP for various traits. The search for high accuracy in GP-theoretically reaching one when using the Pearson's correlation as a metric-is an active research area as yet far from optimal for various traits. We hypothesize that with ultra-high sizes of genotypic and phenotypic datasets, effective training population optimization methods and support from other omics approaches (transcriptomics, metabolomics and proteomics) coupled with deep-learning algorithms could overcome the boundaries of current limitations to achieve the highest possible prediction accuracy, making genomic selection an effective tool in plant breeding.

Genome-Wide Association Study and Prediction of Tassel Weight of Tropical Maize Germplasm in Multi-Parent Population

Tassel weight (TW) is a crucial agronomic trait that significantly affects pollen supply and grain yield development in maize breeding. To improve maize yield and develop new varieties, a comprehensive understanding of the genetic mechanisms underlying tassel weight is essential. In this study, tropical maize inbred lines, namely CML312, CML373, CML444, and YML46, were selected as female parents and crossed with the elite maize inbred line Ye107, which served as the common male parent, to develop a multi-parent population comprising four F8 recombinant inbred line (RIL) subpopulations. Using 6616 high-quality single nucleotide polymorphism (SNP) markers, we conducted genome-wide association analysis (GWAS) and genomic selection (GS) on 642 F8 RILs in four subpopulations across three different environments. Through GWAS, we identified 16 SNPs that were significantly associated with TW, encompassing two stable loci expressed across multiple environments. Furthermore, within the candidate regions of these SNPs, we discovered four novel candidate genes related to TW, namely Zm00001d044362, Zm00001d011048, Zm00001d011049, and Zm00001d031173 distributed on chromosomes 1, 3, and 8, which have not been previously reported. These genes are involved in processes such as signal transduction, growth and development, protein splicing, and pollen development, all of which play crucial roles in inflorescence meristem development, directly affecting TW. The co-localized SNP, S8_137379725, on chromosome 8 was situated within a 16.569 kb long terminal repeat retrotransposon (LTR-RT), located 22.819 kb upstream and 26.428 kb downstream of the candidate genes (Zm00001d011048 and Zm00001d011049). When comparing three distinct GS models, the BayesB model demonstrated the highest accuracy in predicting TW. This study establishes the theoretical foundation for future research into the genetic mechanisms underlying maize TW and the efficient breeding of high-yielding varieties with desired tassel weight through GS.

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.

Genome-wide association study and pathway analysis to decipher loci associated with Fusarium ear rot resistance in tropical maize germplasm

Breeding for host resistance is the most efficient and environmentally safe method to curb the spread of fusarium ear rot (FER). However, conventional breeding for resistance to FER is hampered by the complex polygenic nature of this trait, which is highly influenced by environmental conditions. This study aimed to identify genomic regions, single nucleotide polymorphisms (SNPs), and putative candidate genes associated with FER resistance as well as candidate metabolic pathways and pathway genes involved in it. A panel of 151 tropical inbred maize lines were used to assess the genetic architecture of FER resistance over two seasons. During the study period, seven SNPs associated with FER resistance were identified on chromosomes 1, 2, 4, 5, and 9, accounting for 4-11% of the phenotypic variance. These significant markers were annotated into four genes. Seven significant metabolic pathways involved in FER resistance were identified using the Pathway Association Study Tool, the most significant being the superpathway of the glyoxylate cycle. Overall, this study confirmed that resistance to FER is indeed a complex mechanism controlled by several small to medium-effect loci. Our findings may contribute to fast-tracking the efforts to develop disease-resistant maize lines through marker-assisted selection.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10722-023-01793-4.

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.

Genome-wide association and genomic prediction for resistance to southern corn rust in DH and testcross populations

Southern corn rust (SCR), caused by Puccinia polysora Underw, is a destructive disease that can severely reduce grain yield in maize (Zea mays L.). Owing to P. polysora being multi-racial, it is very important to explore more resistance genes and develop more efficient selection approaches in maize breeding programs. Here, four Doubled Haploid (DH) populations with 384 accessions originated from selected parents and their 903 testcross hybrids were used to perform genome-wide association (GWAS). Three GWAS processes included the additive model in the DH panel, additive and dominant models in the hybrid panel. As a result, five loci were detected on chromosomes 1, 7, 8, 8, and 10, with P-values ranging from 4.83×10^-7 to 2.46×10^-41. In all association analyses, a highly significant locus on chromosome 10 was detected, which was tight chained with the known SCR resistance gene RPPC and RPPK. Genomic prediction (GP), has been proven to be effective in plant breeding. In our study, several models were performed to explore predictive ability in hybrid populations for SCR resistance, including extended GBLUP with different genetic matrices, maker based prediction models, and mixed models with QTL as fixed factors. For GBLUP models, the prediction accuracies ranged from 0.56-0.60. Compared with traditional prediction only with additive effect, prediction ability was significantly improved by adding additive-by-additive effect (P-value< 0.05). For maker based models, the accuracy of BayesA and BayesB was 0.65, 8% higher than other models (i.e., RRBLUP, BRR, BL, BayesC). Finally, by adding QTL into the mixed linear prediction model, the accuracy can be further improved to 0.67, especially for the G_A model, the prediction performance can be increased by 11.67%. The prediction accuracy of the BayesB model can be further improved significantly by adding QTL information (P-value< 0.05). This study will provide important valuable information for understanding the genetic architecture and the application of GP for SCR in maize breeding.

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.

First report of Corn Ear Rot Caused by Fusarium asiaticum in China

Corn (Zea mays L.) ear rot, caused by various pathogens, is one of the most significant diseases of corn worldwide. In September 2020, a survey was undertaken to identify pathogenic fungi associated with corn ear rot in Suihua city (46.63°N 126.98°E), Heilongjiang Province, China. The average disease incidence was 14.2% and 15.6% in each of two fields sampled (~5 ha) using a five-point method (100 plants/each point). Twenty tissue samples from 20 diseased ears, showing white or pink mold on the surface of corn ears, were surface disinfected in 0.5% NaOCl for 5 min, rinsed 3 times in autoclaved distilled water. After drying, four treated corn kernels (one kernel/each ear) were placed onto potato dextrose agar (PDA) amended with 50 µg/mL streptomycin. The plates were sealed with parafilm sealing film and cultured in the dark at 26℃ with 80% RH for 3 days in an incubator. A total of 12 morphologically similar fungal isolates were obtained and subcultured by transferring hyphal tips for 3-5 days. Single-conidium isolates were generated with methods reported previously (Leslie and Summerell 2006). Colonies on PDA, reaching 20.3-20.9 mm·d-1 at 26℃, consisted of white to pale yellow, locculent, lush and dense aerial mycelium with red to apricot color. Macroconidia of six isolates randomly selected on carnation leaf agar (CLA) were falciform with a foot cell, three- to six-septate, measuring 12.6-67.2 × 2.6-5.4 µm (n = 100) in the dark at 26℃ with 80% RH for 5 days. No microconidia were observed. Based on these characteristics, the isolates were preliminarily identified as Fusarium asiaticum (Chang et al. 2020; Leslie and Summerell 2006). Genomic DNA of three representative isolates YSF2, YSF4 and YSF7 were extracted and the translation elongation factor 1-α (TEF-1ɑ) gene was amplified and sequenced using the primers EF1-728F/EF1-986R (Carbone and Kohn 1999). The DNA sequences of YSF2, YSF4 and YSF7 were deposited in GenBank (OL631287.1, OP272129 and OP272130). Analysis of TEF-1ɑ sequences of YSF2, YSF4 and YSF7 showed that they were 100% identical to F. asiaticum isolates NRRL 26156 (AF212452.1) in NCBI and NRRL 13818 (AF212451.1) in Fusarium MLST. A pathogenicity test was performed on corn cv. Xinxin 1. Four days after silk emergence, 3 mL conidial suspension (106 macroconidia/ml) of each 12 isolates was individually injected into the center of the ear through the husk sideways, penetrating the kernels to a depth of about 5 mm (6 ears/each isolate) in the field (Guo et al. 2020). Six corn ears treated with sterile distilled water were used as the control. After inoculation, normal field management was carried out. All inoculated ears showed symptoms similar to those observed in the field 50 days after inoculation, while no symptoms were observed on the blank control ears. Five fungal isolates with the same colony morphology as the naturally occurring ear rot in the field were re-isolated from the inoculated corn kernels and confirmed to be F. asiaticum according to morphological characteristics and sequence analysis of five fungal isolates. F. asiaticum has previously been reported to cause corn ear rots in Japan (Kawakami et al. 2015). To our knowledge, this is the first report of F. asiaticum causing corn ear rot in Northeast China. Corn ear rot poses a threat to significantly reduce the quality of corn in a major production zone of maize in China. Therefore, its distribution needs to be investigated and effective disease management strategies developed.

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.

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.

Identification and fine mapping of a major QTL (qRtsc8-1) conferring resistance to maize tar spot complex and validation of production markers in breeding lines

A major QTL of qRtsc8-1 conferring TSC resistance was identified and fine mapped to a 721 kb region on chromosome 8 at 81 Mb, and production markers were validated in breeding lines. Tar spot complex (TSC) is a major foliar disease of maize in many Central and Latin American countries and leads to severe yield loss. To dissect the genetic architecture of TSC resistance, a genome-wide association study (GWAS) panel and a bi-parental doubled haploid population were used for GWAS and selective genotyping analysis, respectively. A total of 115 SNPs in bin 8.03 were detected by GWAS and three QTL in bins 6.05, 6.07, and 8.03 were detected by selective genotyping. The major QTL qRtsc8-1 located in bin 8.03 was detected by both analyses, and it explained 14.97% of the phenotypic variance. To fine map qRtsc8-1, the recombinant-derived progeny test was implemented. Recombinations in each generation were backcrossed, and the backcross progenies were genotyped with Kompetitive Allele Specific PCR (KASP) markers and phenotyped for TSC resistance individually. The significant tests for comparing the TSC resistance between the two classes of progenies with and without resistant alleles were used for fine mapping. In BC₅ generation, qRtsc8-1 was fine mapped in an interval of  ~ 721 kb flanked by markers of KASP81160138 and KASP81881276. In this interval, the candidate genes GRMZM2G063511 and GRMZM2G073884 were identified, which encode an integral membrane protein-like and a leucine-rich repeat receptor-like protein kinase, respectively. Both genes are involved in maize disease resistance responses. Two production markers KASP81160138 and KASP81160155 were verified in 471 breeding lines. This study provides valuable information for cloning the resistance gene, and it will also facilitate the routine implementation of marker-assisted selection in the breeding pipeline for improving TSC 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.