Technological advances in maize breeding: past, present and future

The Effect of Aspergillus flavus on Seedling Development in Maize

Plant growth and its interaction with microorganisms change yearly. High temperature and humidity have characterized recent seasons in the north of Italy and around the world, increasing the parasitic ability of Aspergillus flavus to colonize maize kernels and aflatoxin levels. These molecules have the highest acute and chronic toxicity of all mycotoxins; the maximal concentration in agricultural food and feed products, and their commodities, are regulated worldwide. In this study we suggest a simple methodology to test the susceptibility of candidate maize varieties to A. flavus before their release onto the market. A panel of 92 inbred lines and 14 hybrids were analysed, disease phenotypes were scored on artificially inoculated kernels using a rolled towel assay, and therefore we observed different responses to fungal infection on the kernels, outlining a high variability among the tested lines characterized by a different effect of the pathogen on seedling development. Even the hybrids responded differently on a statistical basis to A. flavus with regard to the development of coleoptile, allowing their categorization into classes of susceptibility to be used for the varietal registration. Interestingly, the hybrid 6a-A was less susceptible to A. flavus compared to its reciprocal in terms of the length of the coleoptile. The comparison of breeding lines released on the market in different years suggested a poor improvement in genetic resistance against A. flavus in maize so far, opening up a possible topic for future research aimed at mitigating the impact of climate change on agriculture.

Tester selection for combining ability estimation of storage root yield and sweetpotato virus disease in sweetpotato breeding

General combining ability (GCA) is the major selection criterion for new sweetpotato (Ipomoea batatas) parents in a reciprocal recurrent selection (RRS) scheme. Here we aimed to estimate GCA and specific combining ability (SCA) by using 16 potential testers involved in an 8 × 8 partial diallel and propose a procedure to identify testers in sweetpotato breeding. Data on storage root yield in tons per hectare (rytha), and sweetpotato virus disease (vir2) from 64 families (1,913 clones) were collected in five trials at two locations in Uganda. The estimates of the female GCA accounted for the largest additive genetic variation for storage root yield compared to the male GCA for both traits. Mid-parent heterosis ranged from - 6.2 to 7% for rytha, and - 1.1 to 1.3% for vir2 in the progeny families. A stepwise procedure to identify testers top-ranked 'NASPOT 7' as a dual tester for both traits. Besides this parent, 'Ejumula' and 'NASPOT 10 O' for rytha, and 'NASPOT 1', 'NK259L', 'SPK004', and 'NASPOT 11' for vir2 are particularly suitable as respective single-trait testers. Testers are important in many plant breeding programs to enhance efficiency of RRS, and thus other crop species might benefit from the strategy and methods applied herein.

A unified VCF dataset from nearly 1,500 diverse maize accessions and resources to explore the genomic landscape of maize

Efforts to capture and analyze maize nucleotide diversity have ranged widely in scope, but differences in reference genome version and software algorithms used in these efforts inhibit comparison, and these data are generally not available in an easy-to-use visualization platform for quick access and analysis. To address these issues, The Maize Genetics and Genomics Database has collaborated with maize researchers to offer variant data from a diverse set of 1,498 inbred lines, traditional varieties, and teosintes through a standardized variant-calling pipeline against version 5 of the B73 reference genome. The output was filtered for mapping quality, completeness, and linkage disequilibrium, and annotated based on variant effects relative to the B73 RefGen_v5 gene annotations. MaizeGDB has also updated a web tool, SNPversity 2.0, to filter, visualize, and download genotype sets based on genomic locations and accessions of interest, and added external datasets to demonstrate SNPversity 2.0's broad usage. MaizeGDB plans to host annual updates of these resources as additional resequencing data become available, with plans to expand to all publicly available sequence data.

Tools and Resources at the Maize Genetics and Genomics Database (MaizeGDB)

The Maize Genetics and Genomics Database (MaizeGDB) is the community resource for maize researchers, offering a suite of tools, informatics resources, and curated data sets to support maize genetics, genomics, and breeding research. Here, we provide an overview of the key resources available at MaizeGDB, including maize genomes, comparative genomics, and pan-genomics tools. This review aims to familiarize users with the range of options available for maize research and highlights the importance of MaizeGDB as a central hub for the maize research community. By providing a detailed snapshot of the database's capabilities, we hope to enable researchers to make use of MaizeGDB's resources, ultimately assisting them to better study the evolution and diversity of maize.

Analytical prediction of genetic contribution across multiple recurrent backcrossing generations

KEY MESSAGE

We derive formulas for the residual donor genome content during trait introgression via recurrent backcrossing and use these formulas to predict (without simulation) residual donor genome content for five future generations. Trait introgression is a common method for introducing valuable genes or alleles into breeding populations and inbred cultivars. The particular breeding scheme is usually designed to maximize the genetic similarity of the converted lines to the recurrent parent while minimizing cost and time to recover the near isogenic lines. Key variables include the number of generations and crosses and how to apply genotyping and selection. One form of trait introgression, which is our focus, involves an initial cross of an elite, homozygous recurrent parent line with a non-recurrent, homozygous donor line. The descendants of this cross are backcrossed with the recurrent parent for several generation before self-pollination in the final generation to recover lines with the alleles of interest. In this paper, we derive analytical formulas that characterize the stochastic nature of residual donor genome content during this form of trait introgression. The development of these formulas expands the mathematical methods one can integrate into breeding design. In particular, we show we can use our formulas in a novel mathematical program to allocate resources to optimize the reduction of residual donor genome content.

Morpho-Phenological, Chemical, and Genetic Characterization of Italian Maize Landraces from the Lazio Region

In the framework of a Collaboration Agreement between CREA and ARSIAL, a morpho-phenological, chemical, and genetic characterization of maize populations native to the Lazio region was carried out. During 2022 and 2023, a set of 50 accessions, belonging both to ARSIAL and CREA maize collections, were multiplied in Bergamo. Morpho-phenological descriptors were recorded in the field: plant height, ear height, and male and female flowering time. The grain chemical composition in terms of protein, lipid, starch, ash and fiber was evaluated by near-infrared spectroscopy (NIRS). A double-digest restriction-site-associated DNA sequencing (ddRADseq) strategy was used to genotype the landraces. The two collections were not significantly different in terms of grain chemical composition. On the other hand, the ARSIAL and CREA germplasm showed a different distribution in the three cluster-based population structure obtained by ddRADseq, which largely corresponded to the distribution map of their collection sites. The materials from the Lazio region maintained by ARSIAL and CREA were revealed to be different. The comparison between the two groups of landraces showed the importance of characterizing germplasm collections to promote the recovery and valorization of local biodiversity.

Regulatory balance between ear rot resistance and grain yield and their breeding applications in maize and other crops

BACKGROUND

Fungi are prevalent pathogens that cause substantial yield losses of major crops. Ear rot (ER), which is primarily induced by Fusarium or Aspergillus species, poses a significant challenge to maize production worldwide. ER resistance is regulated by several small effect quantitative trait loci (QTLs). To date, only a few ER-related genes have been identified that impede molecular breeding efforts to breed ER-resistant maize varieties.

AIM OF REVIEW

Our aim here is to explore the research progress and mine genic resources related to ER resistance, and to propose a regulatory model elucidating the ER-resistant mechanism in maize as well as a trade-off model illustrating how crops balance fungal resistance and grain yield. Key Scientific Concepts of Review: This review presents a comprehensive bibliometric analysis of the research history and current trends in the genetic and molecular regulation underlying ER resistance in maize. Moreover, we analyzed and discovered the genic resources by identifying 162 environmentally stable loci (ESLs) from various independent forward genetics studies as well as 1391 conservatively differentially expressed genes (DEGs) that respond to Fusarium or Aspergillus infection through multi-omics data analysis. Additionally, this review discusses the syntenies found among maize ER, wheat Fusariumhead blight (FHB), and rice Bakanaedisease (RBD) resistance-related loci, along with the significant overlap between fungal resistance loci and reported yield-related loci, thus providing valuable insights into the regulatory mechanisms underlying the trade-offs between yield and defense in crops.

Genetic diversity, relationships among traits and selection of tropical maize inbred lines for low-P tolerance based on root and shoot traits at seedling stage

The tropical maize breeding for low-P tolerance and good performance under low-P stress environments can be achieved through selection based on root morphology traits at seedling stage. Here, we assessed the genotypic variation and genetic diversity of a panel of 151 tropical maize inbred lines for root and shoot seedling traits, investigated the relationship among traits and selected a set of promising inbred lines for low-P tolerance and performance. We evaluated the inbred lines at seedling stage in a greenhouse experiment under two conditions: applied P (AP) and non-applied P (NAP). A mixed model approach was used to estimate variance components and predict the genotypic values of each inbred line. The genetic diversity among inbred lines based on root and shoot traits was assessed, and correlations were estimated between tested traits under AP and NAP. Our panel of inbred lines showed huge genetic variability for all traits and presented large genetic diversity under both P conditions. Variance components due to the inbred line × P condition interaction were also highly significant (P < 0.01) for all traits. Root dry weight (RDW) was positively associated with stalk dimeter (SD), shoot dry weight (SDW) and root length, volume, and area under both P conditions. Also, the SD and SDW were associated with most root traits under AP. Based on low-P tolerance and performance indices, we selected a set of top 20 inbred lines to be used in our maize breeding program. We therefore concluded that there is a significant genetic diversity in the tropical maize inbred lines which have the genetic potential to be use in association mapping studies and also to develop improved low-P tolerant and P-efficient hybrids and maize breeding populations for low-P stress environments.

​Fusarium Protein Toolkit: a web-based resource for structural and variant analysis of Fusarium species

BACKGROUND

​​The genus Fusarium poses significant threats to food security and safety worldwide because numerous species of the fungus cause destructive diseases and/or mycotoxin contamination in crops. The adverse effects of climate change are exacerbating some existing threats and causing new problems. These challenges highlight the need for innovative solutions, including the development of advanced tools to identify targets for control strategies.

DESCRIPTION

In response to these challenges, we developed the Fusarium Protein Toolkit (FPT), a web-based tool that allows users to interrogate the structural and variant landscape within the Fusarium pan-genome. The tool displays both AlphaFold and ESMFold-generated protein structure models from six Fusarium species. The structures are accessible through a user-friendly web portal and facilitate comparative analysis, functional annotation inference, and identification of related protein structures. Using a protein language model, FPT predicts the impact of over 270 million coding variants in two of the most agriculturally important species, Fusarium graminearum and F. verticillioides. To facilitate the assessment of naturally occurring genetic variation, FPT provides variant effect scores for proteins in a Fusarium pan-genome based on 22 diverse species. The scores indicate potential functional consequences of amino acid substitutions and are displayed as intuitive heatmaps using the PanEffect framework.

CONCLUSION

FPT fills a knowledge gap by providing previously unavailable tools to assess structural and missense variation in proteins produced by Fusarium. FPT has the potential to deepen our understanding of pathogenic mechanisms in Fusarium, and aid the identification of genetic targets for control strategies that reduce crop diseases and mycotoxin contamination. Such targets are vital to solving the agricultural problems incited by Fusarium, particularly evolving threats resulting from climate change. Thus, FPT has the potential to contribute to improving food security and safety worldwide.

Use of simulation to optimize a sweet corn breeding program: implementing genomic selection and doubled haploid technology

Genomic selection and doubled haploids hold significant potential to enhance genetic gains and shorten breeding cycles across various crops. Here, we utilized stochastic simulations to investigate the best strategies for optimize a sweet corn breeding program. We assessed the effects of incorporating varying proportions of old and new parents into the crossing block (3:1, 1:1, 1:3, and 0:1 ratio, representing different degrees of parental substitution), as well as the implementation of genomic selection in two distinct pipelines: one calibrated using the phenotypes of testcross parents (GSTC scenario) and another using F1 individuals (GSF1). Additionally, we examined scenarios with doubled haploids, both with (DH) and without (DHGS) genomic selection. Across 20 years of simulated breeding, we evaluated scenarios considering traits with varying heritabilities, the presence or absence of genotype-by-environment effects, and two program sizes (50 vs 200 crosses per generation). We also assessed parameters such as parental genetic mean, average genetic variance, hybrid mean, and implementation costs for each scenario. Results indicated that within a conventional selection program, a 1:3 parental substitution ratio (replacing 75% of parents each generation with new lines) yielded the highest performance. Furthermore, the GSTC model outperformed the GSF1 model in enhancing genetic gain. The DHGS model emerged as the most effective, reducing cycle time from 5 to 4 years and enhancing hybrid gains despite increased costs. In conclusion, our findings strongly advocate for the integration of genomic selection and doubled haploids into sweet corn breeding programs, offering accelerated genetic gains and efficiency improvements.

Phytochrome B interacts with LIGULELESS1 to control plant architecture and density tolerance in maize

Over the past few decades, significant improvements in maize yield have been largely attributed to increased plant density of upright hybrid varieties rather than increased yield per plant. However, dense planting triggers shade avoidance responses (SARs) that optimize light absorption but impair plant vigor and performance, limiting yield improvement through increasing plant density. In this study, we demonstrated that high-density-induced leaf angle narrowing and stem/stalk elongation are largely dependent on phytochrome B (phyB1/B2), the primary photoreceptor responsible for perceiving red (R) and far-red (FR) light in maize. We found that maize phyB physically interacts with the LIGULELESS1 (LG1), a classical key regulator of leaf angle, to coordinately regulate plant architecture and density tolerance. The abundance of LG1 is significantly increased by phyB under high R:FR light (low density) but rapidly decreases under low R:FR light (high density), correlating with variations in leaf angle and plant height under various densities. In addition, we identified the homeobox transcription factor HB53 as a target co-repressed by both phyB and LG1 but rapidly induced by canopy shade. Genetic and cellular analyses showed that HB53 regulates plant architecture by controlling the elongation and division of ligular adaxial and abaxial cells. Taken together, these findings uncover the phyB-LG1-HB53 regulatory module as a key molecular mechanism governing plant architecture and density tolerance, providing potential genetic targets for breeding maize hybrid varieties suitable for high-density planting.

Association Mapping of Seed Coat Color Characteristics for Near-Isogenic Lines of Colored Waxy Maize Using Simple Sequence Repeat Markers

Waxy maize is mainly cultivated in South Korea for the production of food and snacks, and colored maize with increased anthocyanin content is used in the production of functional foods and medicinal products. Association mapping analysis (AMA) is supported as the preferred method for identifying genetic markers associated with complex traits. Our study aimed to identify molecular markers associated with two anthocyanin content and six seed coat color traits in near-isogenic lines (NILs) of colored waxy maize assessed through AMA. We performed AMA for 285 SSR loci and two anthocyanin content and six seed coat color traits in 10 NILs of colored waxy maize. In the analysis of population structure and cluster formation, the two parental lines (HW3, HW9) of "Mibaek 2ho" variety waxy maize and the 10 NILs were clearly divided into two groups, with each group containing one of the two parental inbred lines. In the AMA, 62 SSR markers were associated with two seed anthocyanin content and six seed coat color traits in the 10 NILs. All the anthocyanin content and seed coat color traits were associated with SSR markers, ranging from 2 to 12 SSR markers per characteristic. The 12 SSR markers were together associated with both of the two anthocyanin content (kuromanin and peonidin) traits. Our current results demonstrate the effectiveness of SSR analysis for the examination of genetic diversity, relationships, and population structure and AMA in 10 NILs of colored waxy maize and the two parental lines of the "Mibaek 2ho" variety waxy maize.

Breeding for improved digestibility and processing of lignocellulosic biomass in Zea mays

Forage maize is a versatile crop extensively utilized for animal nutrition in agriculture and holds promise as a valuable resource for the production of fermentable sugars in the biorefinery sector. Within this context, the carbohydrate fraction of the lignocellulosic biomass undergoes deconstruction during ruminal digestion and the saccharification process. However, the cell wall's natural resistance towards enzymatic degradation poses a significant challenge during both processes. This so-called biomass recalcitrance is primarily attributed to the presence of lignin and ferulates in the cell walls. Consequently, maize varieties with a reduced lignin or ferulate content or an altered lignin composition can have important beneficial effects on cell wall digestibility. Considerable efforts in genetic improvement have been dedicated towards enhancing cell wall digestibility, benefiting agriculture, the biorefinery sector and the environment. In part I of this paper, we review conventional and advanced breeding methods used in the genetic improvement of maize germplasm. In part II, we zoom in on maize mutants with altered lignin for improved digestibility and biomass processing.

Leveraging Multiomics Insights and Exploiting Wild Relatives' Potential for Drought and Heat Tolerance in Maize

Climate change, particularly drought and heat stress, may slash agricultural productivity by 25.7% by 2080, with maize being the hardest hit. Therefore, unraveling the molecular nature of plant responses to these stressors is vital for the development of climate-smart maize. This manuscript's primary objective was to examine how maize plants respond to these stresses, both individually and in combination. Additionally, the paper delved into harnessing the potential of maize wild relatives as a valuable genetic resource and leveraging AI-based technologies to boost maize resilience. The role of multiomics approaches particularly genomics and transcriptomics in dissecting the genetic basis of stress tolerance was also highlighted. The way forward was proposed to utilize a bunch of information obtained through omics technologies by an interdisciplinary state-of-the-art forward-looking big-data, cyberagriculture system, and AI-based approach to orchestrate the development of climate resilient maize genotypes.

Maternal effects, reciprocal differences and combining ability study for yield and its component traits in maize (Zea mays L.) through modified diallel analysis

Combining ability status of the inbred lines is crucial information for hybrid breeding program. Diallel or line × tester mating designs are frequently used to evaluate the combining ability. In the current study a modified diallel model was used, wherein the Griffing's combining ability effects were further partitioned to understand the effects due to maternal and reciprocal. To do this, eight parental lines of maize were crossed in full diallel method and the generated hybrids along with parents were phenotyped. The field data on the quantitative traits was analyzed using both Griffing's and the modified model to determine how well the parents' and the F1 hybrids combined. For each of the traits, a sizable reciprocal and maternal variance was observed. The number of kernel rows per cob variable had a ratio of additive variance to dominance variance greater than one. All other traits including grain yield had a ratio close to zero, suggesting that non-additive gene action was primarily responsible for the genetic control of most of the traits. The narrow sense heritability was low to moderate for majority of the variables, except for number of kernel rows per cob. With the help of the improved model, it was possible to choose superior parents and cross-parent pairings with accuracy. Based on the modified general combining ability effects and maternal effects, the parental line P5 was recognized as a potential female parent and P7 as a good male parent for grain yield and yield-attributing characteristics. The cross combination of P8×P1 had the highest specific combining ability effect on grain yield. P5×P6 cross had the highest reciprocal effect. The correlation analysis implies that the Griffing's general combining ability effects and specific combining ability effects were found to be less efficient in predicting F1 performance as compared to the modified model.

Enhanced pan-genomic resources at the maize genetics and genomics database

Pan-genomes, encompassing the entirety of genetic sequences found in a collection of genomes within a clade, are more useful than single reference genomes for studying species diversity. This is especially true for a species like Zea mays, which has a particularly diverse and complex genome. Presenting pan-genome data, analyses, and visualization is challenging, especially for a diverse species, but more so when pan-genomic data is linked to extensive gene model and gene data, including classical gene information, markers, insertions, expression and proteomic data, and protein structures as is the case at MaizeGDB. Here, we describe MaizeGDB's expansion to include the genic subset of the Zea pan-genome in a pan-gene data center featuring the maize genomes hosted at MaizeGDB, and the outgroup teosinte Zea genomes from the Pan-Andropoganeae project. The new data center offers a variety of browsing and visualization tools, including sequence alignment visualization, gene trees and other tools, to explore pan-genes in Zea that were calculated by the pipeline Pandagma. Combined, these data will help maize researchers study the complexity and diversity of Zea, and to use the comparative functions to validate pan-gene relationships for a selected gene model.

Cytoplasmic genome contributions to domestication and improvement of modern maize

BACKGROUND

Studies on maize evolution and domestication are largely limited to the nuclear genomes, and the contribution of cytoplasmic genomes to selection and domestication of modern maize remains elusive. Maize cytoplasmic genomes have been classified into fertile (NA and NB) and cytoplasmic-nuclear male-sterility (CMS-S, CMS-C, and CMS-T) groups, but their contributions to modern maize breeding have not been systematically investigated.

RESULTS

Here we report co-selection and convergent evolution between nuclear and cytoplasmic genomes by analyzing whole genome sequencing data of 630 maize accessions modern maize and its relatives, including 24 fully assembled mitochondrial and chloroplast genomes. We show that the NB cytotype is associated with the expansion of modern maize to North America, gradually replaces the fertile NA cytotype probably through unequal division, and predominates in over 90% of modern elite inbred lines. The mode of cytoplasmic evolution is increased nucleotypic diversity among the genes involved in photosynthesis and energy metabolism, which are driven by selection and domestication. Furthermore, genome-wide association study reveals correlation of cytoplasmic nucleotypic variation with key agronomic and reproductive traits accompanied with the diversification of the nuclear genomes.

CONCLUSIONS

Our results indicate convergent evolution between cytoplasmic and nuclear genomes during maize domestication and breeding. These new insights into the important roles of mitochondrial and chloroplast genomes in maize domestication and improvement should help select elite inbred lines to improve yield stability and crop resilience of maize hybrids.

The Combining Ability and Heterosis Analysis of Sweet-Waxy Corn Hybrids for Yield-Related Traits and Carotenoids

Improving sweet-waxy corn hybrids enriched in carotenoids via a hybrid breeding approach may provide an alternative cash crop for growers and provide health benefits for consumers. This study estimates the combining ability and heterosis of sweet-waxy corn hybrids for yield-related traits and carotenoids. Eight super sweet corn and three waxy corn lines were crossed to generate 24 F1 hybrids according to the North Carolina Design II scheme, and these hybrids were evaluated across two seasons of 2021/22. The results showed that both additive and non-additive genetic effects were involved in expressing the traits, but the additive genetic effect was more predominant. Most observed traits exhibited moderate to high narrow-sense heritability. Three parental lines, namely the ILS2 and ILS7 females and the ILW1 male, showed the highest positive GCA effects on yield-related traits, making them desirable for developing high-yielding hybrids. Meanwhile, five parental lines, namely the ILS3, ILS5, and ILS7 females and the ILW1 and ILW2 males, were favorable general combiners for high carotenoids. A tested hybrid, ILS2 × ILW1, was a candidate biofortified sweet-waxy corn hybrid possessing high yields and carotenoids. Heterosis and per se performance were more positively correlated with GCAsum than SCA, indicating that GCAsum can predict heterosis for improving biofortified sweet-waxy corn hybrid enriched in carotenoids. The breeding strategies of biofortified sweet-waxy corn hybrids with high yield and carotenoid content are discussed.

Enabling genome editing in tropical maize lines through an improved, morphogenic regulator-assisted transformation protocol

The recalcitrance exhibited by many maize (Zea mays) genotypes to traditional genetic transformation protocols poses a significant challenge to the large-scale application of genome editing (GE) in this major crop species. Although a few maize genotypes are widely used for genetic transformation, they prove unsuitable for agronomic tests in field trials or commercial applications. This challenge is exacerbated by the predominance of transformable maize lines adapted to temperate geographies, despite a considerable proportion of maize production occurring in the tropics. Ectopic expression of morphogenic regulators (MRs) stands out as a promising approach to overcome low efficiency and genotype dependency, aiming to achieve 'universal' transformation and GE capabilities in maize. Here, we report the successful GE of agronomically relevant tropical maize lines using a MR-based, Agrobacterium-mediated transformation protocol previously optimized for the B104 temperate inbred line. To this end, we used a CRISPR/Cas9-based construct aiming at the knockout of the VIRESCENT YELLOW-LIKE (VYL) gene, which results in an easily recognizable phenotype. Mutations at VYL were verified in protoplasts prepared from B104 and three tropical lines, regardless of the presence of a single nucleotide polymorphism (SNP) at the seed region of the VYL target site in two of the tropical lines. Three out of five tropical lines were amenable to transformation, with efficiencies reaching up to 6.63%. Remarkably, 97% of the recovered events presented indels at the target site, which were inherited by the next generation. We observed off-target activity of the CRISPR/Cas9-based construct towards the VYL paralog VYL-MODIFIER, which could be partly due to the expression of the WUSCHEL (WUS) MR. Our results demonstrate efficient GE of relevant tropical maize lines, expanding the current availability of GE-amenable genotypes of this major crop.

Genome-wide association analysis of plant architecture traits using doubled haploid lines derived from different cycles of the Iowa Stiff Stalk Synthetic maize population

Selection in the Iowa Stiff Stalk Synthetic (BSSS) maize population for high yield, grain moisture, and root and stalk lodging has indirectly modified plant architecture traits that are important for adaptation to high plant density. In this study, we developed doubled haploid (DH) lines from the BSSS maize population in the earliest cycle of recurrent selection (BSSS), cycle 17 of reciprocal recurrent selection, [BSSS(R)17] and the cross between the two cycles [BSSS/BSSS(R)C17]. We aimed to determine the phenotypic variation and changes in agronomic traits that have occurred through the recurrent selection program in this population and to identify genes or regions in the genome associated with the plant architecture changes observed in the different cycles of selection. We conducted a per se evaluation of DH lines focusing on high heritability traits important for adaptation to high planting density and grain yield. Trends for reducing flowering time, anthesis-silking interval, ear height, and the number of primary tassel branches in BSSS(R)17 DH lines compared to BSSS and BSSS/BSSS(R)C17 DH lines were observed. Additionally, the BSSS(R)C17 DH lines showed more upright flag leaf angles. Using the entire panel of DH lines increased the number of SNP markers identified within candidate genes associated with plant architecture traits. The genomic regions identified for plant architecture traits in this study may help to elucidate the genetic basis of these traits and facilitate future work about marker-assisted selection or map-based cloning in maize breeding programs.

Phenotypic and genome-wide association analyses for nitrogen use efficiency related traits in maize (Zea mays L.) exotic introgression lines

Nitrogen (N) limits crop production, yet more than half of N fertilizer inputs are lost to the environment. Developing maize hybrids with improved N use efficiency can help minimize N losses and in turn reduce adverse ecological, economical, and health consequences. This study aimed to identify single nucleotide polymorphisms (SNPs) associated with agronomic traits (plant height, grain yield, and anthesis to silking interval) under high and low N conditions. A genome-wide association study (GWAS) was conducted using 181 doubled haploid (DH) lines derived from crosses between landraces from the Germplasm Enhancement of Maize (BGEM lines) project and two inbreds, PHB47 and PHZ51. These DH lines were genotyped using 62,077 SNP markers. The same lines from the per se trials were used as parental lines for the testcross field trials. Plant height, anthesis to silking interval, and grain yield were collected from high and low N conditions in three environments for both per se and testcross trials. We used three GWAS models, namely, general linear model (GLM), mixed linear model (MLM), and Fixed and Random model Circulating Probability Unification (FarmCPU) model. We observed significant genetic variation among the DH lines and their derived testcrosses. Interestingly, some testcrosses of exotic introgression lines were superior under high and low N conditions compared to the check hybrid, PHB47/PHZ51. We detected multiple SNPs associated with agronomic traits under high and low N, some of which co-localized with gene models associated with stress response and N metabolism. The BGEM panel is, thus, a promising source of allelic diversity for genes controlling agronomic traits under different N conditions.

Enhancing Maize Transformation and Targeted Mutagenesis through the Assistance of Non-Integrating Wus2 Vector

Efficient genetic transformation is a prerequisite for rapid gene functional analyses and crop trait improvements. We recently demonstrated that new T-DNA binary vectors with NptII/G418 selection and a compatible helper plasmid can efficiently transform maize inbred B104 using our rapid Agrobacterium-mediated transformation method. In this work, we implemented the non-integrating Wuschel2 (Wus2) T-DNA vector method for Agrobacterium-mediated B104 transformation and tested its potential for recalcitrant inbred B73 transformation and gene editing. The non-integrating Wus2 (NIW) T-DNA vector-assisted transformation method uses two Agrobacterium strains: one carrying a gene-of-interest (GOI) construct and the other providing an NIW construct. To monitor Wus2 co-integration into the maize genome, we combined the maize Wus2 expression cassette driven by a strong constitutive promoter with a new visible marker RUBY, which produces the purple pigment betalain. As a GOI construct, we used a previously tested CRISPR-Cas9 construct pKL2359 for Glossy2 gene mutagenesis. When both GOI and NIW constructs were delivered by LBA4404Thy- strain, B104 transformation frequency was significantly enhanced by about two-fold (10% vs. 18.8%). Importantly, we were able to transform a recalcitrant inbred B73 using the NIW-assisted transformation method and obtained three transgene-free edited plants by omitting the selection agent G418. These results suggest that NIW-assisted transformation can improve maize B104 transformation frequency and provide a novel option for CRISPR technology for transgene-free genome editing.

Molecular characterization of doubled haploid lines derived from different cycles of the Iowa Stiff Stalk Synthetic (BSSS) maize population

Molecular characterization of a given set of maize germplasm could be useful for understanding the use of the assembled germplasm for further improvement in a breeding program, such as analyzing genetic diversity, selecting a parental line, assigning heterotic groups, creating a core set of germplasm and/or performing association analysis for traits of interest. In this study, we used single nucleotide polymorphism (SNP) markers to assess the genetic variability in a set of doubled haploid (DH) lines derived from the unselected Iowa Stiff Stalk Synthetic (BSSS) maize population, denoted as C0 (BSSS(R)C0), the seventeenth cycle of reciprocal recurrent selection in BSSS (BSSS(R)C17), denoted as C17 and the cross between BSSS(R)C0 and BSSS(R)C17 denoted as C0/C17. With the aim to explore if we have potentially lost diversity from C0 to C17 derived DH lines and observe whether useful genetic variation in C0 was left behind during the selection process since C0 could be a reservoir of genetic diversity that could be untapped using DH technology. Additionally, we quantify the contribution of the BSSS progenitors in each set of DH lines. The molecular characterization analysis confirmed the apparent separation and the loss of genetic variability from C0 to C17 through the recurrent selection process. Which was observed by the degree of differentiation between the C0_DHL versus C17_DHL groups by Wright's F-statistics (FST). Similarly for the population structure based on principal component analysis (PCA) revealed a clear separation among groups of DH lines. Some of the progenitors had a higher genetic contribution in C0 compared with C0/C17 and C17 derived DH lines. Although genetic drift can explain most of the genetic structure genome-wide, phenotypic data provide evidence that selection has altered favorable allele frequencies in the BSSS maize population through the reciprocal recurrent selection program.

Research Progress on the Mechanism of Salt Tolerance in Maize: A Classic Field That Needs New Efforts

Maize is the most important cereal crop globally. However, in recent years, maize production faced numerous challenges from environmental factors due to the changing climate. Salt stress is among the major environmental factors that negatively impact crop productivity worldwide. To cope with salt stress, plants developed various strategies, such as producing osmolytes, increasing antioxidant enzyme activity, maintaining reactive oxygen species homeostasis, and regulating ion transport. This review provides an overview of the intricate relationships between salt stress and several plant defense mechanisms, including osmolytes, antioxidant enzymes, reactive oxygen species, plant hormones, and ions (Na⁺, K⁺, Cl^-), which are critical for salt tolerance in maize. It addresses the regulatory strategies and key factors involved in salt tolerance, aiming to foster a comprehensive understanding of the salt tolerance regulatory networks in maize. These new insights will also pave the way for further investigations into the significance of these regulations in elucidating how maize coordinates its defense system to resist salt stress.

Leaf Proteomic Analysis in Seedlings of Two Maize Landraces with Different Tolerance to Boron Toxicity

Boron (B) toxicity is an important stressor that negatively affects maize yield and the quality of the produce. The excessive B content in agricultural lands is a growing problem due to the increase in arid and semi-arid areas because of climate change. Recently, two Peruvian maize landraces, Sama and Pachía, were physiologically characterized based on their tolerance to B toxicity, the former being more tolerant to B excess than Pachía. However, many aspects regarding the molecular mechanisms of these two maize landraces against B toxicity are still unknown. In this study, a leaf proteomic analysis of Sama and Pachía was performed. Out of a total of 2793 proteins identified, only 303 proteins were differentially accumulated. Functional analysis indicated that many of these proteins are involved in transcription and translation processes, amino acid metabolism, photosynthesis, carbohydrate metabolism, protein degradation, and protein stabilization and folding. Compared to Sama, Pachía had a higher number of differentially expressed proteins related to protein degradation, and transcription and translation processes under B toxicity conditions, which might reflect the greater protein damage caused by B toxicity in Pachía. Our results suggest that the higher tolerance to B toxicity of Sama can be attributed to more stable photosynthesis, which can prevent damage caused by stromal over-reduction under this stress condition.

INDETERMINATE1 autonomously regulates phosphate homeostasis upstream of the miR399-ZmPHO2 signaling module in maize

The macronutrient phosphorus is essential for plant growth and development. Plants have evolved multiple strategies to increase the efficiency of phosphate (Pi) acquisition to protect themselves from Pi starvation. However, the crosstalk between Pi homeostasis and plant development remains to be explored. Here, we report that overexpressing microRNA399 (miR399) in maize (Zea mays) is associated with premature senescence after pollination. Knockout of ZmPHO2 (Phosphate 2), a miR399 target, resulted in a similar premature senescence phenotype. Strikingly, we discovered that INDETERMINATE1 (ID1), a floral transition regulator, inhibits the transcription of ZmMIR399 genes by directly binding to their promoters, alleviating the repression of ZmPHO2 by miR399 and ultimately contributing to the maintenance of Pi homeostasis in maize. Unlike ZmMIR399 genes, whose expression is induced by Pi deficiency, ID1 expression was independent of the external inorganic orthophosphate status, indicating that ID1 is an autonomous regulator of Pi homeostasis. Furthermore, we show that ZmPHO2 was under selection during maize domestication and cultivation, resulting in a more sensitive response to Pi starvation in temperate maize than in tropical maize. Our study reveals a direct functional link between Pi-deprivation sensing by the miR399-ZmPHO2 regulatory module and plant developmental regulation by ID1.

Bacillus strains exhibit various plant growth promoting traits and their biofilm-forming capability correlates to their salt stress alleviation effect on maize seedlings

Soil salinity interferes with plant growth and development. Bacillus genus has been used to increase the growth and productivity of a wide variety of crops by alleviating the effects of salt stress. A total of thirty two Bacillus isolates were obtained from maize rhizosphere, and their plant growth-promoting (PGP) traits and biocontrol activities were tested. Bacillus isolates displayed varying degrees of PGP properties-the production of extracellular enzymes, indole acetic acid, hydrogen cyanide, phosphate solubilization, biofilm formation, and antifungal potential against several fungal pathogens. The phosphate-solubilizing isolates belong to B. safensis, B. thuringiensis, B. cereus, and B. megaterium species. Each Bacillus isolate demonstrated different levels of antifungal activity against the fungal pathogens tested. Biofilm production by some salt-tolerant isolates significantly increased at elevated levels of NaCl (p<0.05). The strains B. safensis B24, B. halotolerans B7/B18, B. subtilis B26, and B. thuringiensis B10 significantly increased the length of root (by 32.7-38.2%) and shoot (by 19.5-29.8%) of maize (p<0.05). Maize plants treated with some Bacillus strains displayed significantly greater chlorophyll content with an increase of 26.7-32.1% (p <0.05). Among PGP properties, enhanced biofilm formation played a more important role in maize growth under higher salinity. These salt-tolerant biofilm-forming strains could be efficiently used as bio-inoculant for maize under salinity stress.

Genome editing in maize: Toward improving complex traits in a global crop

Recent advances in genome editing have enormously enhanced the effort to develop biotechnology crops for more sustainable food production. CRISPR/Cas, the most versatile genome-editing tool, has shown the potential to create genome modifications that range from gene knockout and gene expression pattern modulations to allele-specific changes in order to design superior genotypes harboring multiple improved agronomic traits. However, a frequent bottleneck is the delivery of CRISPR/Cas to crops that are less amenable to transformation and regeneration. Several technologies have recently been proposed to overcome transformation recalcitrance, including HI-Edit/IMGE and ectopic/transient expression of genes encoding morphogenic regulators. These technologies allow the eroding of the barriers that make crops inaccessible for genome editing. In this review, we discuss the advances in genome editing in crops with a particular focus on the use of technologies to improve complex traits such as water use efficiency, drought stress, and yield in maize.

Large haplotypes highlight a complex age structure within the maize pan-genome

The genomes of maize and other eukaryotes contain stable haplotypes in regions of low recombination. These regions, including centromeres, long heterochromatic blocks, and rDNA arrays, have been difficult to analyze with respect to their diversity and origin. Greatly improved genome assemblies are now available that enable comparative genomics over these and other nongenic spaces. Using 26 complete maize genomes, we developed methods to align intergenic sequences while excluding genes and regulatory regions. The centromere haplotypes (cenhaps) extend for megabases on either side of the functional centromere regions and appear as evolutionary strata, with haplotype divergence/coalescence times dating as far back as 450 thousand years ago (kya). Application of the same methods to other low recombination regions (heterochromatic knobs and rDNA) and all intergenic spaces revealed that deep coalescence times are ubiquitous across the maize pan-genome. Divergence estimates vary over a broad timescale with peaks at ∼16 and 300 kya, reflecting a complex history of gene flow among diverging populations and changes in population size associated with domestication. Cenhaps and other long haplotypes provide vivid displays of this ancient diversity.

TasselLFANet: a novel lightweight multi-branch feature aggregation neural network for high-throughput image-based maize tassels detection and counting

Accurately and rapidly counting the number of maize tassels is critical for maize breeding, management, and monitoring the growth stage of maize plants. With the advent of high-throughput phenotyping platforms and the availability of large-scale datasets, there is a pressing need to automate this task for genotype and phenotype analysis. Computer vision technology has been increasingly applied in plant science, offering a promising solution for automated monitoring of a large number of plants. However, the current state-of-the-art image algorithms are hindered by hardware limitations, which compromise the balance between algorithmic capacity, running speed, and overall performance, making it difficult to apply them in real-time sensing field environments. Thus, we propose a novel lightweight neural network, named TasselLFANet, with an efficient and powerful structure for accurately and efficiently detecting and counting maize tassels in high spatiotemporal image sequences. Our proposed approach improves the feature-learning ability of TasselLFANet by adopting a cross-stage fusion strategy that balances the variability of different layers. Additionally, TasselLFANet utilizes multiple receptive fields to capture diverse feature representations, and incorporates an innovative visual channel attention module to detect and capture features more flexibly and precisely. We conducted a series of comparative experiments on a new, highly informative dataset called MrMT, which demonstrate that TasselLFANet outperforms the latest batch of lightweight networks in terms of performance, flexibility, and adaptability, achieving an F1 measure value of 94.4%, a mAP.@5 value of 96.8%, and having only 6.0M parameters. Moreover, compared with the regression-based TasselNetV3-Seg† model, our proposed model achieves superior counting performance, with a mean absolute error (MAE) of 1.80, a root mean square error (RMSE) of 2.68, and a R² of 0.99. The proposed model meets the accuracy and speed requirements of the vision system in maize tassel detection. Furthermore, our proposed method is reliable and unaffected by geographical changes, providing essential technical support for computerized counting in the field.

Effectiveness of vegetation indices and UAV-multispectral imageries in assessing the response of hybrid maize (Zea mays L.) to water deficit stress under field environment

Unmanned aerial vehicles (UAVs) equipped with multi-sensors are one of the most innovative technologies for measuring plant health and predicting final yield in field conditions, especially in the water deficit situation in rain-deprived regions. The objective of this investigation was to evaluate the individual plant and canopy-level measurements using UAV imageries in three different genotypes, Suwan4452 (drought-tolerant), Pac339, and S7328 (drought-sensitive) of maize (Zea mays L.) at vegetative and reproductive stages under WW (well-watered) and WD (water deficit) conditions. At the vegetative stage, only CWSI (crop water stress index) of Pac339 and S7328 under WD increased significantly by 1.86- and 1.69-fold over WW, whereas the vegetation indices (EVI2 (Enhanced Vegetation Index 2), OSAVI (Optimized Soil-Adjusted Vegetation Index), GNDVI (Green Normalized Difference Vegetation Index), NDRE (Normalized Difference Red Edge Index), and NDVI (Normalized Difference Vegetation Index)) derived from UAV multi-sensors did not vary. At the reproductive stage, CWSI in drought-sensitive genotype (S7328) under WD increased by 1.92-fold over WW. All the vegetation indices (EVI2, OSAVI, GNDVI, NDRE, and NDVI) of Pac339 and S7328 under WD decreased when compared with those of Suwan4452. NDVI derived from GreenSeeker^® handheld and NDVI from UAV data was closely related (R² = 0.5924). An increase in leaf temperature (T_leaf) and reduction in NDVI of WD stressed maize plants was observed (R² = 0.5829) leading to yield loss (R² = 0.5198). In summary, a close correlation was observed between the physiological data of individual plants and vegetation indices of canopy level (collected using a UAV platform) in drought-sensitive genotypes of maize crops under WD conditions, thus indicating its effectiveness in the classification of drought-tolerant genotypes.

Combining datasets for maize root seedling traits increases the power of GWAS and genomic prediction accuracies

The identification of genomic regions associated with root traits and the genomic prediction of untested genotypes can increase the rate of genetic gain in maize breeding programs targeting roots traits. Here, we combined two maize association panels with different genetic backgrounds to identify single nucleotide polymorphisms (SNPs) associated with root traits, and used a genome-wide association study (GWAS) and to assess the potential of genomic prediction for these traits in maize. For this, we evaluated 377 lines from the Ames panel and 302 from the Backcrossed Germplasm Enhancement of Maize (BGEM) panel in a combined panel of 679 lines. The lines were genotyped with 232 460 SNPs, and four root traits were collected from 14-day-old seedlings. We identified 30 SNPs significantly associated with root traits in the combined panel, whereas only two and six SNPs were detected in the Ames and BGEM panels, respectively. Those 38 SNPs were in linkage disequilibrium with 35 candidate genes. In addition, we found higher prediction accuracy in the combined panel than in the Ames or BGEM panel. We conclude that combining association panels appears to be a useful strategy to identify candidate genes associated with root traits in maize and improve the efficiency of genomic prediction.

Genetic Parameters for Selected Traits of Inbred Lines of Maize (Zea mays L.)

This paper presents an estimation of the parameters connected with the additive (a) effect, additive by additive (aa) epistatic effect, and additive by additive by additive (aaa) interaction gene effect for nine quantitative traits of maize (Zea mays L.) inbred lines. To our knowledge, this is the first report about aaa interaction of maize inbred lines. An analysis was performed on 252 lines derived from Plant Breeding Smolice Ltd. (Smolice, Poland)—Plant Breeding and Acclimatization Institute-National Research Institute Group (151 lines) and Małopolska Plant Breeding Ltd. (Kobierzyce, Poland) (101 lines). The total additive effects were significant for all studied cases. Two-way and three-way significant interactions were found in most analyzed cases with a considerable impact on phenotype. Omitting the inclusion of higher-order interactions effect in quantitative genetics may result in a substantial underestimation of additive QTL effects. Expanding models with that information may also be helpful in future homozygous line crossing projects.

Genomic insights into historical improvement of heterotic groups during modern hybrid maize breeding

Single-cross maize hybrids display superior heterosis and are produced from crossing two parental inbred lines belonging to genetically different heterotic groups. Here we assembled 1,604 historically utilized maize inbred lines belonging to various female heterotic groups (FHGs) and male heterotic groups (MHGs), and conducted phenotyping and genomic sequencing analyses. We found that the FHGs and MHGs have undergone both convergent and divergent changes for different sets of agronomic traits. Using genome-wide selection scans and association analyses, we identified a large number of candidate genes that contributed to the improvement of agronomic traits of the FHGs and MHGs. Moreover, we observed increased genetic differentiation between the FHGs and MHGs across the breeding eras, and we found a positive correlation between increasing heterozygosity levels in the differentiated genes and heterosis in hybrids. Furthermore, we validated the function of two selected genes and a differentiated gene. This study provides insights into the genomic basis of modern hybrid maize breeding.

Crucial factors for the feasibility of commercial hybrid breeding in food crops

There is an ongoing societal debate about plant breeding systems and their impact on stakeholders in food systems. Hybrid breeding and hybrid seed have become controversial topics as they are believed to mostly serve high-tech agricultural systems. This article focuses on the perspective of commercial plant breeders when developing new cultivars of food crops. Arguably, hybrid breeding is the most effective breeding system for genetic improvement of crops, enhancing yields, improving product quality and increasing resistance against (a)biotic stresses. Nonetheless, hybrid breeding is not commercially applied in all crops. We analyse how biological and economic factors determine whether a commercial plant breeder opts for the hybrid system or not. We show that the commercial feasibility of hybrid breeding depends on the crop and business case. In conclusion, the commercial application of hybrid breeding in crops seems to be hampered mostly by high costs of seed production. Case studies regarding the hybrid transitions in maize, wheat and potato are included to illustrate these findings.

Genetic variability, combining ability and molecular diversity-based parental line selection for heterosis breeding in field corn (Zea mays L.)

Background

The demand of maize crop is increasing day by day, hence to reduce the production and demand gap, there is a need to extract the high yielding parental lines to improve per se yield of the hybrids, which could help to enhance the productivity in maize crops.

Methods and results

The present investigation was carried out to select the best medium maturing inbred lines, among a set of 118 inbred lines. Based on the Duncan multiple range test, out of 118 lines, 16 inbred lines were selected on the basis of its high yield per se and flowering time. The molecular diversity was carried out using SSR markers linked to heterotic QTL and up on diversity analysis it classified selected genotypes in to three distinct groups. Among the selected inbred lines, a wider genetic variability and molecular diversity were observed. A total of 39 test crosses were generated after classifying 16 inbred lines in to three testers and thirteen lines (based on per se grain yield and molecular diversity) and crossing them in line × tester manner.

Conclusion

Combining ability analysis of these parental lines showed that female parents, PML 109, PML 110, PML 111, PML 114 and PML 116 showed additive effect for KRN and grain yield, whereas male parents, PML 46, and PML 93 showed epistatic effect for KRN and PML 102 showed epistatic effect for grain yield. The generated information in the present investigation may be exploited for heterosis breeding in filed corn.

Key messages

To tackle the balanced dietary requirement of Indian population; we focused to enhance the productivity of maize hybrids using genetically broad based, elite, diverse inbred lines. Combination of selection criterion, not only augment the productivity but also improves the quality of hybrid/s.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11033-022-07295-3.

Optimized Transformation and Gene Editing of the B104 Public Maize Inbred by Improved Tissue Culture and Use of Morphogenic Regulators

Plant transformation is a bottleneck for the application of gene editing in plants. In Zea mays (maize), a breakthrough was made using co-transformation of the morphogenic transcription factors BABY BOOM (BBM) and WUSCHEL (WUS) to induce somatic embryogenesis. Together with adapted tissue culture media, this was shown to increase transformation efficiency significantly. However, use of the method has not been reported widely, despite a clear need for increased transformation capacity in academic settings. Here, we explore use of the method for the public maize inbred B104 that is widely used for transformation by the research community. We find that only modifying tissue culture media already boosts transformation efficiency significantly and can reduce the time in tissue culture by 1 month. On average, production of independent transgenic plants per starting embryo increased from 1 to 4% using BIALAPHOS RESISTANCE (BAR) as a selection marker. In addition, we reconstructed the BBM-WUS morphogenic gene cassette and evaluated its functionality in B104. Expression of the morphogenic genes under tissue- and development stage-specific promoters led to direct somatic embryo formation on the scutellum of zygotic embryos. However, eight out of ten resulting transgenic plants showed pleiotropic developmental defects and were not fertile. This undesirable phenotype was positively correlated with the copy number of the morphogenic gene cassette. Use of constructs in which morphogenic genes are flanked by a developmentally controlled Cre/LoxP recombination system led to reduced T-DNA copy number and fertile T0 plants, while increasing transformation efficiency from 1 to 5% using HIGHLY-RESISTANT ACETOLACTATE SYNTHASE as a selection marker. Addition of a CRISPR/Cas9 module confirmed functionality for gene editing applications, as exemplified by editing the gene VIRESCENT YELLOW-LIKE (VYL) that can act as a visual marker for gene editing in maize. The constructs, methods, and insights produced in this work will be valuable to translate the use of BBM-WUS and other emerging morphogenic regulators (MRs) to other genotypes and crops.

Genetic dissection of maize plant architecture using a novel nested association mapping population

The leaf angle (LA), plant height (PH), and ear height (EH) are key plant architectural traits influencing maize (Zea mays L.) yield. However, their genetic determinants have not yet been well-characterized. Here, we developed a maize advanced backcross-nested association mapping population in Henan Agricultural University (HNAU-NAM1) comprised of 1,625 BC₁ F₄ /BC₂ F₄ lines. These were obtained by crossing a diverse set of 12 representative inbred lines with the common GEMS41 line, which were then genotyped using the MaizeSNP9.4K array. Genetic diversity and phenotypic distribution analyses showed considerable levels of genetic variation. We obtained 18-88 quantitative trait loci (QTLs) associated with LA, PH, and EH by using three complementary mapping methods, named as separate linkage mapping, joint linkage mapping, and genome-wide association studies. Our analyses enabled the identification of ten QTL hot-spot regions associated with the three traits, which were distributed on nine different chromosomes. We further selected 13 major QTLs that were simultaneously detected by three methods and deduced the candidate genes, of which eight were not reported before. The newly constructed HNAU-NAM1 population in this study will further broaden our insights into understanding of genetic regulation of plant architecture, thus will help to improve maize yield and provide an invaluable resource for maize functional genomics and breeding research.

Genomic Prediction of Complex Traits in an Allogamous Annual Crop: The Case of Maize Single-Cross Hybrids

For many plant and animal species, commercial products are hybrids between individuals from different genetic groups. For allogamous plant species such as maize, the breeding objective is to produce single-cross hybrid varieties from two inbred lines each selected in complementary groups. Efficient hybrid breeding requires methods that (1) quickly generate homozygous and homogeneous parental lines with high combining abilities, (2) efficiently choose among the large number of available parental lines the most promising ones, and (3) predict the performances of sets of non-phenotyped single-cross hybrids, or hybrids phenotyped in a limited number of environments, based on their relationship with another set of hybrids with known performances. The maize breeding community has been developing model-based prediction of hybrid performances well before the genomic era. This chapter (1) provides a reminder of the maize breeding scheme before the genomic era; (2) describes how genomic data were incorporated in the prediction models involved in different steps of genomic-based single-cross maize hybrid breeding; and (3) reviews factors affecting the accuracy of genomic prediction, approaches for optimizing GP-based single-cross maize hybrid breeding schemes, and ensuring the long-term sustainability of genomic selection.

Maize Transformation: From Plant Material to the Release of Genetically Modified and Edited Varieties

Over the past decades, advances in plant biotechnology have allowed the development of genetically modified maize varieties that have significantly impacted agricultural management and improved the grain yield worldwide. To date, genetically modified varieties represent 30% of the world's maize cultivated area and incorporate traits such as herbicide, insect and disease resistance, abiotic stress tolerance, high yield, and improved nutritional quality. Maize transformation, which is a prerequisite for genetically modified maize development, is no longer a major bottleneck. Protocols using morphogenic regulators have evolved significantly towards increasing transformation frequency and genotype independence. Emerging technologies using either stable or transient expression and tissue culture-independent methods, such as direct genome editing using RNA-guided endonuclease system as an in vivo desired-target mutator, simultaneous double haploid production and editing/haploid-inducer-mediated genome editing, and pollen transformation, are expected to lead significant progress in maize biotechnology. This review summarises the significant advances in maize transformation protocols, technologies, and applications and discusses the current status, including a pipeline for trait development and regulatory issues related to current and future genetically modified and genetically edited maize varieties.

A pan-genomic approach to genome databases using maize as a model system

Research in the past decade has demonstrated that a single reference genome is not representative of a species' diversity. MaizeGDB introduces a pan-genomic approach to hosting genomic data, leveraging the large number of diverse maize genomes and their associated datasets to quickly and efficiently connect genomes, gene models, expression, epigenome, sequence variation, structural variation, transposable elements, and diversity data across genomes so that researchers can easily track the structural and functional differences of a locus and its orthologs across maize. We believe our framework is unique and provides a template for any genomic database poised to host large-scale pan-genomic data.

Beat the stress: breeding for climate resilience in maize for the tropical rainfed environments

Intensive public sector breeding efforts and public-private partnerships have led to the increase in genetic gains, and deployment of elite climate-resilient maize cultivars for the stress-prone environments in the tropics. Maize (Zea mays L.) plays a critical role in ensuring food and nutritional security, and livelihoods of millions of resource-constrained smallholders. However, maize yields in the tropical rainfed environments are now increasingly vulnerable to various climate-induced stresses, especially drought, heat, waterlogging, salinity, cold, diseases, and insect pests, which often come in combinations to severely impact maize crops. The International Maize and Wheat Improvement Center (CIMMYT), in partnership with several public and private sector institutions, has been intensively engaged over the last four decades in breeding elite tropical maize germplasm with tolerance to key abiotic and biotic stresses, using an extensive managed stress screening network and on-farm testing system. This has led to the successful development and deployment of an array of elite stress-tolerant maize cultivars across sub-Saharan Africa, Asia, and Latin America. Further increasing genetic gains in the tropical maize breeding programs demands judicious integration of doubled haploidy, high-throughput and precise phenotyping, genomics-assisted breeding, breeding data management, and more effective decision support tools. Multi-institutional efforts, especially public-private alliances, are key to ensure that the improved maize varieties effectively reach the climate-vulnerable farming communities in the tropics, including accelerated replacement of old/obsolete varieties.

Major locus for spontaneous haploid genome doubling detected by a case-control GWAS in exotic maize germplasm

A major locus for spontaneous haploid genome doubling was detected by a case-control GWAS in an exotic maize germplasm. The combination of double haploid breeding method with this locus leads to segregation distortion on genomic regions of chromosome five. Temperate maize (Zea mays L.) breeding programs often rely on limited genetic diversity, which can be expanded by incorporating exotic germplasm. The aims of this study were to perform characterization of inbred lines derived from the tropical BS39 population using different breeding methods, to identify genomic regions showing segregation distortion in lines derived by the DH process using spontaneous haploid genome doubling (SHGD), and use case-control association mapping to identify loci controlling SHGD. Four different sets were used: BS39_DH and BS39_SSD were derived from the BS39 population by DH and single-seed descendent (SSD) methods, and BS39 × A427_DH and BS39 × A427_SSD from the cross between BS39 and A427. A total of 663 inbred lines were genotyped. The analyses of gene diversity and genetic differentiation for the DH sets provided evidence of the presence of a SHGD locus near the centromere of chromosome 5. The case-control GWAS for the DH set also pinpointed this locus. Haplotype sharing analysis showed almost 100% exclusive contribution of the A427 genome in the same region on chromosome 5 of BS39 × A427_DH, presumably due to an allele in this region affecting SHGD. This locus enables DH line production in exotic populations without colchicine or other artificial haploid genome doubling.

Genetic and molecular control of grain yield in maize

Understanding the genetic and molecular basis of grain yield is important for maize improvement. Here, we identified 49 consensus quantitative trait loci (cQTL) controlling maize yield-related traits using QTL meta-analysis. Then, we collected yield-related traits associated SNPs detected by association mapping and identified 17 consensus significant loci. Comparing the physical positions of cQTL with those of significant SNPs revealed that 47 significant SNPs were located within 20 cQTL regions. Furthermore, intensive reviews of 31 genes regulating maize yield-related traits found that the functions of many genes were conservative in maize and other plant species. The functional conservation indicated that some of the 575 maize genes (orthologous to 247 genes controlling yield or seed traits in other plant species) might be functionally related to maize yield-related traits, especially the 49 maize orthologous genes in cQTL regions, and 41 orthologous genes close to the physical positions of significant SNPs. In the end, we prospected on the integration of the public sources for exploring the genetic and molecular mechanisms of maize yield-related traits, and on the utilization of genetic and molecular mechanisms for maize improvement.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01214-3.

Heterosis and Hybrid Crop Breeding: A Multidisciplinary Review

Although hybrid crop varieties are among the most popular agricultural innovations, the rationale for hybrid crop breeding is sometimes misunderstood. Hybrid breeding is slower and more resource-intensive than inbred breeding, but it allows systematic improvement of a population by recurrent selection and exploitation of heterosis simultaneously. Inbred parental lines can identically reproduce both themselves and their F1 progeny indefinitely, whereas outbred lines cannot, so uniform outbred lines must be bred indirectly through their inbred parents to harness heterosis. Heterosis is an expected consequence of whole-genome non-additive effects at the population level over evolutionary time. Understanding heterosis from the perspective of molecular genetic mechanisms alone may be elusive, because heterosis is likely an emergent property of populations. Hybrid breeding is a process of recurrent population improvement to maximize hybrid performance. Hybrid breeding is not maximization of heterosis per se, nor testing random combinations of individuals to find an exceptional hybrid, nor using heterosis in place of population improvement. Though there are methods to harness heterosis other than hybrid breeding, such as use of open-pollinated varieties or clonal propagation, they are not currently suitable for all crops or production environments. The use of genomic selection can decrease cycle time and costs in hybrid breeding, particularly by rapidly establishing heterotic pools, reducing testcrossing, and limiting the loss of genetic variance. Open questions in optimal use of genomic selection in hybrid crop breeding programs remain, such as how to choose founders of heterotic pools, the importance of dominance effects in genomic prediction, the necessary frequency of updating the training set with phenotypic information, and how to maintain genetic variance and prevent fixation of deleterious alleles.

CRISPR-Cas technology in corn: a new key to unlock genetic knowledge and create novel products

Since its inception in 2012, CRISPR-Cas technologies have taken the life science community by storm. Maize genetics research is no exception. Investigators around the world have adapted CRISPR tools to advance maize genetics research in many ways. The principle application has been targeted mutagenesis to confirm candidate genes identified using map-based methods. Researchers are also developing tools to more effectively apply CRISPR-Cas technologies to maize because successful application of CRISPR-Cas relies on target gene identification, guide RNA development, vector design and construction, CRISPR-Cas reagent delivery to maize tissues, and plant characterization, each contributing unique challenges to CRISPR-Cas efficacy. Recent advances continue to chip away at major barriers that prevent more widespread use of CRISPR-Cas technologies in maize, including germplasm-independent delivery of CRISPR-Cas reagents and production of high-resolution genomic data in relevant germplasm to facilitate CRISPR-Cas experimental design. This has led to the development of novel breeding tools to advance maize genetics and demonstrations of how CRISPR-Cas technologies might be used to enhance maize germplasm.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01200-9.

Genomic prediction across years in a maize doubled haploid breeding program to accelerate early-stage testcross testing

Genomic selection with a multiple-year training population dataset could accelerate early-stage testcross testing by skipping the first-stage yield testing, which significantly saves the time and cost of early-stage testcross testing. With the development of doubled haploid (DH) technology, the main task for a maize breeder is to estimate the breeding values of thousands of DH lines annually. In early-stage testcross testing, genomic selection (GS) offers the opportunity of replacing expensive multiple-environment phenotyping and phenotypic selection with lower-cost genotyping and genomic estimated breeding value (GEBV)-based selection. In the present study, a total of 1528 maize DH lines, phenotyped in multiple-environment trials in three consecutive years and genotyped with a low-cost per-sample genotyping platform of rAmpSeq, were used to explore how to implement GS to accelerate early-stage testcross testing. Results showed that the average prediction accuracy estimated from the cross-validation schemes was above 0.60 across all the scenarios. The average prediction accuracies estimated from the independent validation schemes ranged from 0.23 to 0.32 across all the scenarios, when the one-year datasets were used as training population (TRN) to predict the other year data as testing population (TST). The average prediction accuracies increased to a range from 0.31 to 0.42 across all the scenarios, when the two-years datasets were used as TRN. The prediction accuracies increased to a range from 0.50 to 0.56, when the TRN consisted of two-years of breeding data and 50% of third year's data converted from TST to TRN. This information showed that GS with a multiple-year TRN set offers the opportunity to accelerate early-stage testcross testing by skipping the first-stage yield testing, which significantly saves the time and cost of early-stage testcross testing.

Influence of Wounding and Temperature on Resistance of Maize Landraces From Mexico to Aflatoxin Contamination

Maize is a staple for billions across the globe. However, in tropical and sub-tropical regions, maize is frequently contaminated with aflatoxins by Aspergillus section Flavi fungi. There is an ongoing search for sources of aflatoxin resistance in maize to reduce continuous exposures of human populations to those dangerous mycotoxins. Large variability in susceptibility to aflatoxin contamination exists within maize germplasm. In Mexico, several maize landrace (MLR) accessions possess superior resistance to both Aspergillus infection and aflatoxin contamination but their mechanisms of resistance have not been reported. Influences of kernel integrity on resistance of four resistant and four susceptible MLR accessions were evaluated in laboratory assays. Wounds significantly (P < 0.05) increased susceptibility to aflatoxin contamination even when kernel viability was unaffected. Treatments supporting greater A. flavus reproduction did not (P > 0.05) proportionally support higher aflatoxin accumulation suggesting differential influences by some resistance factors between sporulation and aflatoxin biosynthesis. Physical barriers (i.e., wax and cuticle) prevented both aflatoxin accumulation and A. flavus sporulation in a highly resistant MLR accession. In addition, influence of temperature on aflatoxin contamination was evaluated in both viable and non-viable kernels of a resistant and a susceptible MLR accession, and a commercial hybrid. Both temperature and living embryo status influenced (P < 0.05) resistance to both aflatoxin accumulation and A. flavus sporulation. Lower sporulation on MLR accessions suggests their utilization would result in reduced speed of propagation and associated epidemic increases in disease both in the field and throughout storage. Results from the current study should encourage researchers across the globe to exploit the large potential that MLRs offer to breed for aflatoxin resistant maize. Furthermore, the studies provide support to the importance of resistance based on the living host and maintaining living status to reducing episodes of post-harvest contamination.

A Revolution toward Gene-Editing Technology and Its Application to Crop Improvement

Genome editing is a relevant, versatile, and preferred tool for crop improvement, as well as for functional genomics. In this review, we summarize the advances in gene-editing techniques, such as zinc-finger nucleases (ZFNs), transcription activator-like (TAL) effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR) associated with the Cas9 and Cpf1 proteins. These tools support great opportunities for the future development of plant science and rapid remodeling of crops. Furthermore, we discuss the brief history of each tool and provide their comparison and different applications. Among the various genome-editing tools, CRISPR has become the most popular; hence, it is discussed in the greatest detail. CRISPR has helped clarify the genomic structure and its role in plants: For example, the transcriptional control of Cas9 and Cpf1, genetic locus monitoring, the mechanism and control of promoter activity, and the alteration and detection of epigenetic behavior between single-nucleotide polymorphisms (SNPs) investigated based on genetic traits and related genome-wide studies. The present review describes how CRISPR/Cas9 systems can play a valuable role in the characterization of the genomic rearrangement and plant gene functions, as well as the improvement of the important traits of field crops with the greatest precision. In addition, the speed editing strategy of gene-family members was introduced to accelerate the applications of gene-editing systems to crop improvement. For this, the CRISPR technology has a valuable advantage that particularly holds the scientist's mind, as it allows genome editing in multiple biological systems.