A comprehensive study of the genomic differentiation between temperate Dent and Flint maize

An ARF gene mutation creates flint kernel architecture in dent maize

Dent and flint kernel architectures are important characteristics that affect the physical properties of maize kernels and their grain end uses. The genes controlling these traits are unknown, so it is difficult to combine the advantageous kernel traits of both. We found mutation of ARFTF17 in a dent genetic background reduces IAA content in the seed pericarp, creating a flint-like kernel phenotype. ARFTF17 is highly expressed in the pericarp and encodes a protein that interacts with and inhibits MYB40, a transcription factor with the dual functions of repressing PIN1 expression and transactivating genes for flavonoid biosynthesis. Enhanced flavonoid biosynthesis could reduce the metabolic flux responsible for auxin biosynthesis. The decreased IAA content of the dent pericarp appears to reduce cell division and expansion, creating a shorter, denser kernel. Introgression of the ARFTF17 mutation into dent inbreds and hybrids improved their kernel texture, integrity, and desiccation, without affecting yield.

Identifying QTLs involved in hybrid performance and heterotic group complementarity: new GWAS models applied to factorial and admixed diallel maize hybrid panels

KEY MESSAGE

An original GWAS model integrating the ancestry of alleles was proposed and allowed the detection of background specific additive and dominance QTLs involved in heterotic group complementarity and hybrid performance. Maize genetic diversity is structured into genetic groups selected and improved relative to each other. This process increases group complementarity and differentiation over time and ensures that the hybrids produced from inter-group crosses exhibit high performances and heterosis. To identify loci involved in hybrid performance and heterotic group complementarity, we introduced an original association study model that disentangles allelic effects from the heterotic group origin of the alleles and compared it with a conventional additive/dominance model. This new model was applied on a factorial between Dent and Flint lines and a diallel between Dent-Flint admixed lines with two different layers of analysis: within each environment and in a multiple-environment context. We identified several strong additive QTLs for all traits, including some well-known additive QTLs for flowering time (in the region of Vgt1/2 on chromosome 8). Yield trait displayed significant non-additive effects in the diallel panel. Most of the detected Yield QTLs exhibited overdominance or, more likely, pseudo-overdominance effects. Apparent overdominance at these QTLs contributed to a part of the genetic group complementarity. The comparison between environments revealed a higher stability of additive QTL effects than non-additive ones. Several QTLs showed variations of effects according to the local heterotic group origin. We also revealed large chromosomic regions that display genetic group origin effects. Altogether, our results illustrate how admixed panels combined with dedicated GWAS modeling allow the identification of new QTLs that could not be revealed by a classical hybrid panel analyzed with traditional modeling.

Genomic analysis of a new heterotic maize group reveals key loci for pedigree breeding

Genome-wide analyses of maize populations have clarified the genetic basis of crop domestication and improvement. However, limited information is available on how breeding improvement reshaped the genome in the process of the formation of heterotic groups. In this study, we identified a new heterotic group (X group) based on an examination of 512 Chinese maize inbred lines. The X group was clearly distinct from the other non-H&L groups, implying that X × HIL is a new heterotic pattern. We selected the core inbred lines for an analysis of yield-related traits. Almost all yield-related traits were better in the X lines than those in the parental lines, indicating that the primary genetic improvement in the X group during breeding was yield-related traits. We generated whole-genome sequences of these lines with an average coverage of 17.35× to explore genome changes further. We analyzed the identity-by-descent (IBD) segments transferred from the two parents to the X lines and identified 29 and 28 IBD conserved regions (ICRs) from the parents PH4CV and PH6WC, respectively, accounting for 28.8% and 12.8% of the genome. We also identified 103, 89, and 131 selective sweeps (SSWs) using methods that involved the π, Tajima's D, and CLR values, respectively. Notably, 96.13% of the ICRs co-localized with SSWs, indicating that SSW signals concentrated in ICRs. We identified 171 annotated genes associated with yield-related traits in maize both in ICRs and SSWs. To identify the genetic factors associated with yield improvement, we conducted QTL mapping for 240 lines from a DH population (PH4CV × PH6WC, which are the parents of X1132X) for ten key yield-related traits and identified a total of 55 QTLs. Furthermore, we detected three QTL clusters both in ICRs and SSWs. Based on the genetic evidence, we finally identified three key genes contributing to yield improvement in breeding the X group. These findings reveal key loci and genes targeted during pedigree breeding and provide new insights for future genomic breeding.

Genetic diversity and selection signatures in a gene bank panel of maize inbred lines from Southeast Europe compared with two West European panels

Southeast Europe (SEE) is a very important maize-growing region, comparable to the Corn belt region of the United States, with similar dent germplasm (dent by dent hybrids). Historically, this region has undergone several genetic material swaps, following the trends in the US, with one of the most significant swaps related to US aid programs after WWII. The imported accessions used to make double-cross hybrids were also mixed with previously adapted germplasm originating from several more distant OPVs, supporting the transition to single cross-breeding. Many of these materials were deposited at the Maize Gene Bank of the Maize Research Institute Zemun Polje (MRIZP) between the 1960s and 1980s. A part of this Gene Bank (572 inbreds) was genotyped with Affymetrix Axiom Maize Genotyping Array with 616,201 polymorphic variants. Data were merged with two other genotyping datasets with mostly European flint (TUM dataset) and dent (DROPS dataset) germplasm. The final pan-European dataset consisted of 974 inbreds and 460,243 markers. Admixture analysis showed seven ancestral populations representing European flint, B73/B14, Lancaster, B37, Wf9/Oh07, A374, and Iodent pools. Subpanel of inbreds with SEE origin showed a lack of Iodent germplasm, marking its historical context. Several signatures of selection were identified at chromosomes 1, 3, 6, 7, 8, 9, and 10. The regions under selection were mined for protein-coding genes and were used for gene ontology (GO) analysis, showing a highly significant overrepresentation of genes involved in response to stress. Our results suggest the accumulation of favorable allelic diversity, especially in the context of changing climate in the genetic resources of SEE.

A role for heritable transcriptomic variation in maize adaptation to temperate environments

Background

Transcription bridges genetic information and phenotypes. Here, we evaluated how changes in transcriptional regulation enable maize (Zea mays), a crop originally domesticated in the tropics, to adapt to temperate environments.

Result

We generated 572 unique RNA-seq datasets from the roots of 340 maize genotypes. Genes involved in core processes such as cell division, chromosome organization and cytoskeleton organization showed lower heritability of gene expression, while genes involved in anti-oxidation activity exhibited higher expression heritability. An expression genome-wide association study (eGWAS) identified 19,602 expression quantitative trait loci (eQTLs) associated with the expression of 11,444 genes. A GWAS for alternative splicing identified 49,897 splicing QTLs (sQTLs) for 7614 genes. Genes harboring both cis-eQTLs and cis-sQTLs in linkage disequilibrium were disproportionately likely to encode transcription factors or were annotated as responding to one or more stresses. Independent component analysis of gene expression data identified loci regulating co-expression modules involved in oxidation reduction, response to water deprivation, plastid biogenesis, protein biogenesis, and plant-pathogen interaction. Several genes involved in cell proliferation, flower development, DNA replication, and gene silencing showed lower gene expression variation explained by genetic factors between temperate and tropical maize lines. A GWAS of 27 previously published phenotypes identified several candidate genes overlapping with genomic intervals showing signatures of selection during adaptation to temperate environments.

Conclusion

Our results illustrate how maize transcriptional regulatory networks enable changes in transcriptional regulation to adapt to temperate regions.

Supplementary information

The online version contains supplementary material available at 10.1186/s13059-023-02891-3.

Genetic Engineering of Starch Biosynthesis in Maize Seeds for Efficient Enzymatic Digestion of Starch during Bioethanol Production

Maize accumulates large amounts of starch in seeds which have been used as food for human and animals. Maize starch is an importantly industrial raw material for bioethanol production. One critical step in bioethanol production is degrading starch to oligosaccharides and glucose by α-amylase and glucoamylase. This step usually requires high temperature and additional equipment, leading to an increased production cost. Currently, there remains a lack of specially designed maize cultivars with optimized starch (amylose and amylopectin) compositions for bioethanol production. We discussed the features of starch granules suitable for efficient enzymatic digestion. Thus far, great advances have been made in molecular characterization of the key proteins involved in starch metabolism in maize seeds. The review explores how these proteins affect starch metabolism pathway, especially in controlling the composition, size and features of starch. We highlight the roles of key enzymes in controlling amylose/amylopectin ratio and granules architecture. Based on current technological process of bioethanol production using maize starch, we propose that several key enzymes can be modified in abundance or activities via genetic engineering to synthesize easily degraded starch granules in maize seeds. The review provides a clue for developing special maize cultivars as raw material in the bioethanol industry.

QTL Mapping and a Transcriptome Integrative Analysis Uncover the Candidate Genes That Control the Cold Tolerance of Maize Introgression Lines at the Seedling Stage

Chilling injury owing to low temperatures severely affects the growth and development of maize (Zea mays.L) seedlings during the early and late spring seasons. The existing maize germplasm is deficient in the resources required to improve maize's ability to tolerate cold injury. Therefore, it is crucial to introduce and identify excellent gene/QTLs that confer cold tolerance to maize for sustainable crop production. Wild relatives of maize, such as Z. perennis and Tripsacum dactyloides, are strongly tolerant to cold and can be used to improve the cold tolerance of maize. In a previous study, a genetic bridge among maize that utilized Z. perennis and T. dactyloides was created and used to obtain a highly cold-tolerant maize introgression line (MIL)-IB030 by backcross breeding. In this study, two candidate genes that control relative electrical conductivity were located on MIL-IB030 by forward genetics combined with a weighted gene co-expression network analysis. The results of the phenotypic, genotypic, gene expression, and functional verification suggest that two candidate genes positively regulate cold tolerance in MIL-IB030 and could be used to improve the cold tolerance of cultivated maize. This study provides a workable route to introduce and mine excellent genes/QTLs to improve the cold tolerance of maize and also lays a theoretical and practical foundation to improve cultivated maize against low-temperature stress.

Can we abandon phosphorus starter fertilizer in maize? Results from a diverse panel of elite and doubled haploid landrace lines of maize (Zea mays L.)

The importance of phosphorus (P) in agriculture contrasts with the negative environmental impact and the limited resources worldwide. Reducing P fertilizer application by utilizing more efficient genotypes is a promising way to address these issues. To approach this, a large panel of maize (Zea mays L.) comprising each 100 Flint and Dent elite lines and 199 doubled haploid lines from six landraces was assessed in multi-environment field trials with and without the application of P starter fertilizer. The treatment comparison showed that omitting the starter fertilizer can significantly affect traits in early plant development but had no effect on grain yield. Young maize plants provided with additional P showed an increased biomass, faster growth and superior vigor, which, however, was only the case under environmental conditions considered stressful for maize cultivation. Importantly, though the genotype-by-treatment interaction variance was comparably small, there is genotypic variation for this response that can be utilized in breeding. The comparison of elite and doubled haploid landrace lines revealed a superior agronomic performance of elite material but also potentially valuable variation for early traits in the landrace doubled haploid lines. In conclusion, our results illustrate that breeding for P efficient maize cultivars is possible towards a reduction of P fertilizer in a more sustainable agriculture.

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.

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.

Maize Field Study Reveals Covaried Microbiota and Metabolic Changes in Roots over Plant Growth

Plant roots are colonized by microorganisms from the surrounding soil that belong to different kingdoms and form a multikingdom microbial community called the root microbiota. Despite their importance for plant growth, the relationship between soil management, the root microbiota, and plant performance remains unknown. Here, we characterize the maize root-associated bacterial, fungal, and oomycetal communities during the vegetative and reproductive growth stages of four maize inbred lines and the pht1;6 phosphate transporter mutant. These plants were grown in two long-term experimental fields under four contrasting soil managements, including phosphate-deficient and -sufficient conditions. We showed that the maize root-associated microbiota is influenced by soil management and changes during host growth stages. We identified stable bacterial and fungal root-associated taxa that persist throughout the host life cycle. These taxa were accompanied by dynamic members that covary with changes in root metabolites. We observed an inverse stable-to-dynamic ratio between root-associated bacterial and fungal communities. We also found a host footprint on the soil biota, characterized by a convergence between soil, rhizosphere, and root bacterial communities during reproductive maize growth. Our study reveals the spatiotemporal dynamics of the maize root-associated microbiota and suggests that the fungal assemblage is less responsive to changes in root metabolites than the bacterial community.

Influence of Endosperm Starch Composition on Maize Response to Fusarium temperatum Scaufl. & Munaut

Fusarium temperatum Scaufl. & Munaut is a newly described taxon belonging to the Fusarium fujikuroi species complex (FFSC) and a frequent causative factor of maize ear rot. The aim of the present study was to determine the responses to the disease in maize populations differing in endosperm features that were classified to flint, dent, and a group of plants with intermediate kernel characteristics. In inoculation studies, substantial variation of host response to the fungus was found among the tested maize types. The dent-type kernels contained significantly less amylose (28.27%) and exhibited significantly higher rates of infection (I_FER = 2.10) and contamination by beauvericin (7.40 mg kg⁻¹) than plants of the flint maize subpopulation. The study documents a significant positive correlation between the Fusarium ear rot intensity (I_FER) and ergosterol content (the R value ranged from 0.396 in 2015 to 0.735 in 2018) and between I_FER and the presence of beauvericin (the R value ranged from 0.364 in 2015 to 0.785 in 2017). The negative correlation between (I_FER) and amylose content (ranging from R = −0.303 to R= −0.180) stresses the role of the endosperm starch composition in the kernel resistance to Fusarium ear rot. The conducted study indicated that the risk of kernel infection and contamination with fungal metabolites (beauvericin and ergosterol) was associated with the maize type kernels.

Increasing calling accuracy, coverage, and read-depth in sequence data by the use of haplotype blocks

High-throughput genotyping of large numbers of lines remains a key challenge in plant genetics, requiring geneticists and breeders to find a balance between data quality and the number of genotyped lines under a variety of different existing genotyping technologies when resources are limited. In this work, we are proposing a new imputation pipeline (“HBimpute”) that can be used to generate high-quality genomic data from low read-depth whole-genome-sequence data. The key idea of the pipeline is the use of haplotype blocks from the software HaploBlocker to identify locally similar lines and subsequently use the reads of all locally similar lines in the variant calling for a specific line. The effectiveness of the pipeline is showcased on a dataset of 321 doubled haploid lines of a European maize landrace, which were sequenced at 0.5X read-depth. The overall imputing error rates are cut in half compared to state-of-the-art software like BEAGLE and STITCH, while the average read-depth is increased to 83X, thus enabling the calling of copy number variation. The usefulness of the obtained imputed data panel is further evaluated by comparing the performance of sequence data in common breeding applications to that of genomic data generated with a genotyping array. For both genome-wide association studies and genomic prediction, results are on par or even slightly better than results obtained with high-density array data (600k). In particular for genomic prediction, we observe slightly higher data quality for the sequence data compared to the 600k array in the form of higher prediction accuracies. This occurred specifically when reducing the data panel to the set of overlapping markers between sequence and array, indicating that sequencing data can benefit from the same marker ascertainment as used in the array process to increase the quality and usability of genomic data.

High-throughput genotyping of large numbers of lines remains a key challenge in plant genetics and breeding. Cost, precision, and throughput must be balanced to achieve optimal efficiency given available technologies and finite resources. Although genotyping arrays are still considered the gold standard in high-throughput quantitative genetics, recent advances in sequencing provide new opportunities. Both the quality and cost of genomic data generated based on sequencing are highly dependent on the used read-depth. In this work, we propose a new imputation pipeline (“HBimpute”) that uses haplotype blocks to detect individuals of the same genetic origin and subsequently uses all reads of those individuals in the variant calling. Thus, the obtained virtual read-depth is artificially increased, leading to higher calling accuracy, coverage, and the ability to call copy number variation based on low read-depth sequencing data. To conclude, our approach makes sequencing a cost-competitive alternative to genotyping arrays with the added benefit of allowing the calling of structural variation.

Joint analysis of days to flowering reveals independent temperate adaptations in maize

Domesticates are an excellent model for understanding biological consequences of rapid climate change. Maize (Zea mays ssp. mays) was domesticated from a tropical grass yet is widespread across temperate regions today. We investigate the biological basis of temperate adaptation in diverse structured nested association mapping (NAM) populations from China, Europe (Dent and Flint) and the United States as well as in the Ames inbred diversity panel, using days to flowering as a proxy. Using cross-population prediction, where high prediction accuracy derives from overall genomic relatedness, shared genetic architecture, and sufficient diversity in the training population, we identify patterns in predictive ability across the five populations. To identify the source of temperate adapted alleles in these populations, we predict top associated genome-wide association study (GWAS) identified loci in a Random Forest Classifier using independent temperate-tropical North American populations based on lines selected from Hapmap3 as predictors. We find that North American populations are well predicted (AUC equals 0.89 and 0.85 for Ames and USNAM, respectively), European populations somewhat well predicted (AUC equals 0.59 and 0.67 for the Dent and Flint panels, respectively) and that the Chinese population is not predicted well at all (AUC is 0.47), suggesting an independent adaptation process for early flowering in China. Multiple adaptations for the complex trait days to flowering in maize provide hope for similar natural systems under climate change.

A worldwide maize panel revealed new genetic variation for cold tolerance

A large association panel of 836 maize inbreds revealed a broader genetic diversity of cold tolerance, as predominantly favorable QTL with small effects were identified, indicating that genomic selection is the most promising option for breeding maize for cold tolerance. Maize (Zea mays L.) has limited cold tolerance, and breeding for cold tolerance is a noteworthy bottleneck for reaching the high potential of maize production in temperate areas. In this study, we evaluate a large panel of 836 maize inbred lines to detect genetic loci and candidate genes for cold tolerance at the germination and seedling stages. Genetic variation for cold tolerance was larger than in previous reports with moderately high heritability for most traits. We identified 187 significant single-nucleotide polymorphisms (SNPs) that were integrated into 159 quantitative trait loci (QTL) for emergence and traits related to early growth. Most of the QTL have small effects and are specific for each environment, with the majority found under control conditions. Favorable alleles are more frequent in 120 inbreds including all germplasm groups, but mainly from Minnesota and Spain. Therefore, there is a large, potentially novel, genetic variability in the germplasm groups represented by these inbred lines. Most of the candidate genes are involved in metabolic processes and intracellular membrane-bounded organelles. We expect that further evaluations of germplasm with broader genetic diversity could identify additional favorable alleles for cold tolerance. However, it is not likely that further studies will find favorable alleles with large effects for improving cold tolerance in maize.

Discovery of beneficial haplotypes for complex traits in maize landraces

Genetic variation is of crucial importance for crop improvement. Landraces are valuable sources of diversity, but for quantitative traits efficient strategies for their targeted utilization are lacking. Here, we map haplotype-trait associations at high resolution in ~1000 doubled-haploid lines derived from three maize landraces to make their native diversity for early development traits accessible for elite germplasm improvement. A comparative genomic analysis of the discovered haplotypes in the landrace-derived lines and a panel of 65 breeding lines, both genotyped with 600k SNPs, points to untapped beneficial variation for target traits in the landraces. The superior phenotypic performance of lines carrying favorable landrace haplotypes as compared to breeding lines with alternative haplotypes confirms these findings. Stability of haplotype effects across populations and environments as well as their limited effects on undesired traits indicate that our strategy has high potential for harnessing beneficial haplotype variation for quantitative traits from genetic resources.

Genetic variations present in landraces are critical for crop genetic improvement. Here, the authors map haplotype-trait associations in ~1000 doubled haploid lines derived from three European maize landraces and identify beneficial haplotypes for quantitative traits that are not present in breeding lines.

Adaptive introgression from maize has facilitated the establishment of teosinte as a noxious weed in Europe

Global trade has considerably accelerated biological invasions. The annual tropical teosintes, the closest wild relatives of maize, were recently reported as new agricultural weeds in two European countries, Spain and France. Their prompt settlement under climatic conditions differing drastically from that of their native range indicates rapid genetic evolution. We performed a phenotypic comparison of French and Mexican teosintes under European conditions and showed that only the former could complete their life cycle during maize cropping season. To test the hypothesis that crop-to-wild introgression triggered such rapid adaptation, we used single nucleotide polymorphisms to characterize patterns of genetic variation in French, Spanish, and Mexican teosintes as well as in maize germplasm. We showed that both Spanish and French teosintes originated from Zea mays ssp. mexicana race "Chalco," a weedy teosinte from the Mexican highlands. However, introduced teosintes differed markedly from their Mexican source by elevated levels of genetic introgression from the high latitude Dent maize grown in Europe. We identified a clear signature of divergent selection in a region of chromosome 8 introgressed from maize and encompassing ZCN8, a major flowering time gene associated with adaptation to high latitudes. Moreover, herbicide assays and sequencing revealed that French teosintes have acquired herbicide resistance via the introgression of a mutant herbicide-target gene (ACC1) present in herbicide-resistant maize cultivars. Altogether, our results demonstrate that adaptive crop-to-wild introgression has triggered both rapid adaptation to a new climatic niche and acquisition of herbicide resistance, thereby fostering the establishment of an emerging noxious weed.

European maize genomes highlight intraspecies variation in repeat and gene content

The diversity of maize (Zea mays) is the backbone of modern heterotic patterns and hybrid breeding. Historically, US farmers exploited this variability to establish today’s highly productive Corn Belt inbred lines from blends of dent and flint germplasm pools. Here, we report de novo genome sequences of four European flint lines assembled to pseudomolecules with scaffold N50 ranging from 6.1 to 10.4 Mb. Comparative analyses with two US Corn Belt lines explains the pronounced differences between both germplasms. While overall syntenic order and consolidated gene annotations reveal only moderate pangenomic differences, whole-genome alignments delineating the core and dispensable genome, and the analysis of heterochromatic knobs and orthologous long terminal repeat retrotransposons unveil the dynamics of the maize genome. The high-quality genome sequences of the flint pool complement the maize pangenome and provide an important tool to study maize improvement at a genome scale and to enhance modern hybrid breeding.

De novo genome assemblies of four European flint maize lines and comparison with two US Corn Belt genomes provide insights into the dynamics of intraspecies variation in repeat and gene content in maize genomes.

Dark response genes: a group of endogenous pendulum/timing players in maize?

MAIN CONCLUSION

Maize has a set of dark response genes, expression of which is influenced by multiple factor and varies with maize inbred lines but without germplasm specificity. The response to photoperiod is a common biological issue across the species kingdoms. Dark is as important as light in photoperiod. However, further in-depth understanding of responses of maize (Zea mays) to light and dark transition under photoperiod is hindered due to the lack of understanding of dark response genes. With multiple public "-omic" datasets of temperate and tropical/subtropical maize, 16 maize dark response genes, ZmDRGs, were found and had rhythmic expression under dark and light-dark cycle. ZmDRGs 6-8 were tandemly duplicated. ZmDRGs 2, 13, and 14 had a chromosomal collinearity with other maize genes. ZmDRGs 1-11 and 13-16 had copy-number variations. ZmDRGs 2, 9, and 16 showed 5'-end sequence deletion mutations. Some ZmDRGs had chromatin interactions and underwent DNA methylation and/or m6A mRNA methylation. Chromosomal histones associated with 15 ZmDRGs were methylated and acetylated. ZmDRGs 1, 2, 4, 9, and 13 involved photoperiodic phenotypes. ZmDRG16 was within flowering-related QTLs. ZmDRGs 1, 3, and 6-11 were present in cis-acting expression QTLs (eQTLs). ZmDRGs 1, 4, 6-9, 11, 12, and 14-16 showed co-expression with other maize genes. Some of ZmDRG-encoded ZmDRGs showed obvious differences in abundance and phosphorylation.

CONCLUSION

Sixteen ZmDRGs 1-16 are associated with the dark response of maize. In the process of post-domestication and/or breeding, the ZmDRGs undergo the changes without germplasm specificity, including epigenetic modifications, gene copy numbers, chromatin interactions, and deletion mutations. In addition to effects by these factors, ZmDRG expression is influenced by promoter elements, cis-acting eQTLs, and co-expression networks.

Improving Imputation Quality in BEAGLE for Crop and Livestock Data

Imputation is one of the key steps in the preprocessing and quality control protocol of any genetic study. Most imputation algorithms were originally developed for the use in human genetics and thus are optimized for a high level of genetic diversity. Different versions of BEAGLE were evaluated on genetic datasets of doubled haploids of two European maize landraces, a commercial breeding line and a diversity panel in chicken, respectively, with different levels of genetic diversity and structure which can be taken into account in BEAGLE by parameter tuning. Especially for phasing BEAGLE 5.0 outperformed the newest version (5.1) which in turn also lead to improved imputation. Earlier versions were far more dependent on the adaption of parameters in all our tests. For all versions, the parameter ne (effective population size) had a major effect on the error rate for imputation of ungenotyped markers, reducing error rates by up to 98.5%. Further improvement was obtained by tuning of the parameters affecting the structure of the haplotype cluster that is used to initialize the underlying Hidden Markov Model of BEAGLE. The number of markers with extremely high error rates for the maize datasets were more than halved by the use of a flint reference genome (F7, PE0075 etc.) instead of the commonly used B73. On average, error rates for imputation of ungenotyped markers were reduced by 8.5% by excluding genetically distant individuals from the reference panel for the chicken diversity panel. To optimize imputation accuracy one has to find a balance between representing as much of the genetic diversity as possible while avoiding the introduction of noise by including genetically distant individuals.

Mapping of resistance to corn borers in a MAGIC population of maize

BACKGROUND

Corn borers constitute an important pest of maize around the world; in particular Sesamia nonagrioides Lefèbvre, named Mediterranean corn borer (MCB), causes important losses in Southern Europe. Methods of selection can be combined with transgenic approaches to increase the efficiency and durability of the resistance to corn borers. Previous studies of the genetic factors involved in resistance to MCB have been carried out using bi-parental populations that have low resolution or using association inbred panels that have a low power to detect rare alleles. We developed a Multi-parent Advanced Generation InterCrosses (MAGIC) population to map with high resolution the genetic determinants of resistance to MCB.

RESULTS

We detected multiple single nucleotide polymorphisms (SNPs) of low effect associated with resistance to stalk tunneling by MCB. We dissected a wide region related to stalk tunneling in multiple studies into three smaller regions (at ~ 150, ~ 155, and ~ 165 Mb in chromosome 6) that closely overlap with regions associated with cell wall composition. We also detected regions associated with kernel resistance and agronomic traits, although the co-localization of significant regions between traits was very low. This indicates that it is possible the concurrent improvement of resistance and agronomic traits.

CONCLUSIONS

We developed a mapping population which allowed a finer dissection of the genetics of maize resistance to corn borers and a solid nomination of candidate genes based on functional information. The population, given its large variability, was also adequate to map multiple traits and study the relationship between them.

Technological advances in maize breeding: past, present and future

Maize has for many decades been both one of the most important crops worldwide and one of the primary genetic model organisms. More recently, maize breeding has been impacted by rapid technological advances in sequencing and genotyping technology, transformation including genome editing, doubled haploid technology, parallelled by progress in data sciences and the development of novel breeding approaches utilizing genomic information. Herein, we report on past, current and future developments relevant for maize breeding with regard to (1) genome analysis, (2) germplasm diversity characterization and utilization, (3) manipulation of genetic diversity by transformation and genome editing, (4) inbred line development and hybrid seed production, (5) understanding and prediction of hybrid performance, (6) breeding methodology and (7) synthesis of opportunities and challenges for future maize breeding.

Detecting Adaptive Differentiation in Structured Populations with Genomic Data and Common Gardens

Adaptation in quantitative traits often occurs through subtle shifts in allele frequencies at many loci-a process called polygenic adaptation. While a number of methods have been developed to detect polygenic adaptation in human populations, we lack clear strategies for doing so in many other systems. In particular, there is an opportunity to develop new methods that leverage datasets with genomic data and common garden trait measurements to systematically detect the quantitative traits important for adaptation. Here, we develop methods that do just this, using principal components of the relatedness matrix to detect excess divergence consistent with polygenic adaptation, and using a conditional test to control for confounding effects due to population structure. We apply these methods to inbred maize lines from the United States Department of Agriculture germplasm pool and maize landraces from Europe. Ultimately, these methods can be applied to additional domesticated and wild species to give us a broader picture of the specific traits that contribute to adaptation and the overall importance of polygenic adaptation in shaping quantitative trait variation.

Characterization of Proteome Variation During Modern Maize Breeding

The success of modern maize breeding has been demonstrated by remarkable increases in productivity with tremendous modification of agricultural phenotypes over the last century. Although the underlying genetic changes of the maize adaptation from tropical to temperate regions have been extensively studied, our knowledge is limited regarding the accordance of protein and mRNA expression levels accompanying such adaptation. Here we conducted an integrative analysis of proteomic and transcriptomic changes in a maize association panel. The minimum extent of correlation between protein and RNA levels suggests that variation in mRNA expression is often not indicative of protein expression at a population scale. This is corroborated by the observation that mRNA- and protein-based coexpression networks are relatively independent of each other, and many pQTLs arise without the presence of corresponding eQTLs. Importantly, compared with transcriptome, the subtypes categorized by the proteome show a markedly high accuracy to resemble the genomic subpopulation. These findings suggest that proteome evolved under a greater evolutionary constraint than transcriptome during maize adaptation from tropical to temperate regions. Overall, the integrated multi-omics analysis provides a functional context to interpret gene expression variation during modern maize breeding.

Exploiting SPL genes to improve maize plant architecture tailored for high-density planting

Maize (Zea mays ssp. mays) is an agronomically important crop and also a classical genetic model for studying the regulation of plant architecture formation, which is a critical determinant of grain yield. Since the 1930s, increasing planting density has been a major contributing factor to the >7-fold increase in maize grain yield per unit land area in the USA, which is accompanied by breeding and utilization of cultivars characterized by high-density-tolerant plant architecture, including decreased ear height, lodging resistance, more upright leaves, reduced tassel branch number, and reduced anthesis-silking interval (ASI). Recent studies demonstrated that phytochrome-mediated red/far-red light signaling pathway and the miR156/SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) regulatory module co-ordinately regulate the shade avoidance response and diverse aspects of plant architecture in responding to shading in Arabidopsis. The maize genome contains 30 ZmSPL genes, and 18 of them are predicted as direct targets of zma-miR156s. Accumulating evidence indicates that ZmSPL genes play important roles in regulating maize flowering time, plant/ear height, tilling, leaf angle, tassel and ear architecture, and grain size and shape. Finally, we discuss ways to exploit maize SPL genes and downstream targets for improving maize plant architecture tailored for high-density planting.

In situ rumen degradation of kernels from short-season corn silage hybrids as affected by processing. Transl Anim Sci 2018;2:428-438. [PMID: 32704725 DOI: 10.1093/tas/txy084]

The objective of this in situ study was to evaluate the rumen degradability of kernels from short-season corn hybrids grown for silage in Western Canada (Lacombe, AB) and determine whether decreasing kernel particle size would enhance ruminal degradability in a similar manner for all hybrids. The study was a completely randomized design with 3 beef cows (replicates) and a 6 (hybrid) × 3 (particle size) factorial arrangement of treatments. Kernels were processed to generate three different particle sizes: large (2.3 mm), medium (1.4 mm), and small (0.7 mm). Processed samples were incubated in the rumen for 0, 3, 6, 12, 24, and 48 h using the in situ method and degradation kinetics of DM and starch were determined. Effective rumen degradability (ED) was estimated using a passage rate of 0.04 (ED4), 0.06 (ED6), and 0.08/h (ED8). Hybrids exhibited a range in whole plant DM content (23.7 to 25.0%), starch content (15.9 to 28.1% DM), kernel hardness (21.9 to 34.4 s/20 g) and density (3.57 to 4.18 g/mL), and prolamin content (8.24 to 11.34 g/100 g starch). Differences in digestion kinetics among hybrids were generally more pronounced for starch than DM. The hybrids differed in starch degradability (P < 0.05), with earlier maturing hybrids having lower A fraction, lower k _d, and lower ED, with hybrid effects on ED being accentuated with faster passage rate. Kernel DM content (r = -0.85, -0.87), hardness (r = -0.89, -0.86), and density (r = -0.84, -0.85) were negatively correlated with ED4 and ED8 of starch, respectively, due mainly to decreased k _d of fraction B. Reducing the particle size of kernels increased ED of starch due to increased A fraction and k _d of the B fraction. A tendency (P = 0.09) for hybrid × processing effects for ED6 and ED8 indicated that processing had greater effects on increasing ED of starch for earlier maturing hybrids. We conclude that short-season hybrids that mature early may have lower ED of DM and starch and would benefit from prolonged ensilage time. Kernel processing during silage making is recommended for short-season corn hybrids as a means of enhancing rumen availability of starch.

Assessing and Exploiting Functional Diversity in Germplasm Pools to Enhance Abiotic Stress Adaptation and Yield in Cereals and Food Legumes

There is a need to accelerate crop improvement by introducing alleles conferring host plant resistance, abiotic stress adaptation, and high yield potential. Elite cultivars, landraces and wild relatives harbor useful genetic variation that needs to be more easily utilized in plant breeding. We review genome-wide approaches for assessing and identifying alleles associated with desirable agronomic traits in diverse germplasm pools of cereals and legumes. Major quantitative trait loci and single nucleotide polymorphisms (SNPs) associated with desirable agronomic traits have been deployed to enhance crop productivity and resilience. These include alleles associated with variation conferring enhanced photoperiod and flowering traits. Genetic variants in the florigen pathway can provide both environmental flexibility and improved yields. SNPs associated with length of growing season and tolerance to abiotic stresses (precipitation, high temperature) are valuable resources for accelerating breeding for drought-prone environments. Both genomic selection and genome editing can also harness allelic diversity and increase productivity by improving multiple traits, including phenology, plant architecture, yield potential and adaptation to abiotic stresses. Discovering rare alleles and useful haplotypes also provides opportunities to enhance abiotic stress adaptation, while epigenetic variation has potential to enhance abiotic stress adaptation and productivity in crops. By reviewing current knowledge on specific traits and their genetic basis, we highlight recent developments in the understanding of crop functional diversity and identify potential candidate genes for future use. The storage and integration of genetic, genomic and phenotypic information will play an important role in ensuring broad and rapid application of novel genetic discoveries by the plant breeding community. Exploiting alleles for yield-related traits would allow improvement of selection efficiency and overall genetic gain of multigenic traits. An integrated approach involving multiple stakeholders specializing in management and utilization of genetic resources, crop breeding, molecular biology and genomics, agronomy, stress tolerance, and reproductive/seed biology will help to address the global challenge of ensuring food security in the face of growing resource demands and climate change induced stresses.

Towards a whole-genome sequence for rye (Secale cereale L.)

We report on a whole-genome draft sequence of rye (Secale cereale L.). Rye is a diploid Triticeae species closely related to wheat and barley, and an important crop for food and feed in Central and Eastern Europe. Through whole-genome shotgun sequencing of the 7.9-Gbp genome of the winter rye inbred line Lo7 we obtained a de novo assembly represented by 1.29 million scaffolds covering a total length of 2.8 Gbp. Our reference sequence represents nearly the entire low-copy portion of the rye genome. This genome assembly was used to predict 27 784 rye gene models based on homology to sequenced grass genomes. Through resequencing of 10 rye inbred lines and one accession of the wild relative S. vavilovii, we discovered more than 90 million single nucleotide variants and short insertions/deletions in the rye genome. From these variants, we developed the high-density Rye600k genotyping array with 600 843 markers, which enabled anchoring the sequence contigs along a high-density genetic map and establishing a synteny-based virtual gene order. Genotyping data were used to characterize the diversity of rye breeding pools and genetic resources, and to obtain a genome-wide map of selection signals differentiating the divergent gene pools. This rye whole-genome sequence closes a gap in Triticeae genome research, and will be highly valuable for comparative genomics, functional studies and genome-based breeding in rye.

Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts

Through the local selection of landraces, humans have guided the adaptation of crops to a vast range of climatic and ecological conditions. This is particularly true of maize, which was domesticated in a restricted area of Mexico but now displays one of the broadest cultivated ranges worldwide. Here, we sequenced 67 genomes with an average sequencing depth of 18x to document routes of introduction, admixture and selective history of European maize and its American counterparts. To avoid the confounding effects of recent breeding, we targeted germplasm (lines) directly derived from landraces. Among our lines, we discovered 22,294,769 SNPs and between 0.9% to 4.1% residual heterozygosity. Using a segmentation method, we identified 6,978 segments of unexpectedly high rate of heterozygosity. These segments point to genes potentially involved in inbreeding depression, and to a lesser extent to the presence of structural variants. Genetic structuring and inferences of historical splits revealed 5 genetic groups and two independent European introductions, with modest bottleneck signatures. Our results further revealed admixtures between distinct sources that have contributed to the establishment of 3 groups at intermediate latitudes in North America and Europe. We combined differentiation- and diversity-based statistics to identify both genes and gene networks displaying strong signals of selection. These include genes/gene networks involved in flowering time, drought and cold tolerance, plant defense and starch properties. Overall, our results provide novel insights into the evolutionary history of European maize and highlight a major role of admixture in environmental adaptation, paralleling recent findings in humans.

Responses to Hypoxia and Endoplasmic Reticulum Stress Discriminate the Development of Vitreous and Floury Endosperms of Conventional Maize (Zea mays) Inbred Lines

Major nutritional and agronomical issues relating to maize (Zea mays) grains depend on the vitreousness/hardness of its endosperm. To identify the corresponding molecular and cellular mechanisms, most studies have been conducted on opaque/floury mutants, and recently on Quality Protein Maize, a reversion of an opaque2 mutation by modifier genes. These mutant lines are far from conventional maize crops. Therefore, a dent and a flint inbred line were chosen for analysis of the transcriptome, amino acid, and sugar metabolites of developing central and peripheral endosperm that is, the forthcoming floury and vitreous regions of mature seeds, respectively. The results suggested that the formation of endosperm vitreousness is clearly associated with significant differences in the responses of the endosperm to hypoxia and endoplasmic reticulum stress. This occurs through a coordinated regulation of energy metabolism and storage protein (i.e., zein) biosynthesis during the grain-filling period. Indeed, genes involved in the glycolysis and tricarboxylic acid cycle are up-regulated in the periphery, while genes involved in alanine, sorbitol, and fermentative metabolisms are up-regulated in the endosperm center. This spatial metabolic regulation allows the production of ATP needed for the significant zein synthesis that occurs at the endosperm periphery; this finding agrees with the zein-decreasing gradient previously observed from the sub-aleurone layer to the endosperm center. The massive synthesis of proteins transiting through endoplasmic reticulum elicits the unfolded protein responses, as indicated by the splicing of bZip60 transcription factor. This splicing is relatively higher at the center of the endosperm than at its periphery. The biological responses associated with this developmental stress, which control the starch/protein balance, leading ultimately to the formation of the vitreous and floury regions of mature endosperm, are discussed.

Comparative genomics provides insight into maize adaptation in temperate regions

A new study provides insights into the evolution of maize during its global spread into temperate regions from its origin in coastal Mexico.Please see related Research article: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1009-x.