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The sustainability of maize cultivation would benefit tremendously from early sowing, but is hampered by low temperatures during early development in temperate climates. We show that allelic variation within the gene encoding subunit M of the NADH-dehydrogenase-like (NDH) complex (ndhm1) in a European maize landrace affects several quantitative traits that are relevant during early development in cold climates through NDH-mediated cyclic electron transport around photosystem I, a process crucial for photosynthesis and photoprotection. Beginning with a genome-wide association study for maximum potential quantum yield of photosystem II in dark-adapted leaves (Fv/Fm), we capitalized on the large phenotypic effects of a hAT transposon insertion in ndhm1 on multiple quantitative traits (early plant height [EPH], Fv/Fm, chlorophyll content, and cold tolerance) caused by the reduced protein levels of NDHM and associated NDH components. Analysis of the ndhm1 native allelic series revealed a rare allele of ndhm1 that is associated with small albeit significant improvements of Fv/Fm, photosystem II efficiency in light-adapted leaves (ΦPSII), and EPH compared with common alleles. Our work showcases the extraction of favorable alleles from locally adapted landraces, offering an efficient strategy for broadening the genetic variation of elite germplasm by breeding or genome editing., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists.)

Genomic prediction (GP) using haplotypes is considered advantageous compared to GP solely reliant on single nucleotide polymorphisms (SNPs), owing to haplotypes' enhanced ability to capture ancestral information and their higher linkage disequilibrium with quantitative trait loci (QTL). Many empirical studies supported the advantages of haplotype-based GP over SNP-based approaches. Nevertheless, the performance of haplotype-based GP can vary significantly depending on multiple factors, including the traits being studied, the genetic structure of the population under investigation, and the particular method employed for haplotype construction. In this study, we compared haplotype and SNP based prediction accuracies in four populations derived from European maize landraces. Populations comprised either doubled haploid lines (DH) derived directly from landraces, or gamete capture lines (GC) derived from crosses of the landraces with an inbred line. For two different landraces, both types of populations were generated, genotyped with 600k SNPs and phenotyped as lines per se for five traits. Our study explores three prediction scenarios: (i) within each of the four populations, (ii) across DH and GC populations from the same landrace, and (iii) across landraces using either DH or GC populations. Three haplotype construction methods were evaluated: 1. fixed-window blocks (FixedHB), 2. LD-based blocks (HaploView), and 3. IBD-based blocks (HaploBlocker). In within population predictions, FixedHB and HaploView methods performed as well as or slightly better than SNPs for all traits. HaploBlocker improved accuracy for certain traits but exhibited inferior performance for others. In prediction across populations, the parameter setting from HaploBlocker which controls the construction of shared haplotypes between populations played a crucial role for obtaining optimal results. When predicting across landraces, accuracies were low for both, SNP and haplotype approaches, but for specific traits substantial improvement was observed with HaploBlocker. This study provides recommendations for optimal haplotype construction and identifies relevant parameters for constructing haplotypes in the context of genomic prediction., Competing Interests: Author MM was employed by the company Bayer CropScience Deutschland GmbH. Author DVT was employed by the company Strube Research GmbH & Co. KG. Authors AH, ThP, and MO were employed by the company KWS SAAT SE & Co. KGaA. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. The authors declare that this study received funding from Federal Ministry of Education and Research (BMBF, Germany) under the Plant Breeding Research for the Bioeconomy initiative (funding ID: 031B0195, project MAZE), the Bavarian State Ministry of the Environment and Consumer Protection through the BayKlimaFit project network (project TGC01GCUFuE69741, “Improving cold tolerance in maize”), and KWS SAAT SE & Co. KGaA (KWS) through PhD fellowships (MM and AH). The funder was not involved in the study design, collection, analysis, interpretation of data, the writing of this article or the decision to submit it for publication., (Copyright © 2024 Lin, Mayer, Valle Torres, Pook, Hölker, Presterl, Ouzunova and Schön.)

European flint landraces are a major class of maize possessing favorable alleles for improving host resistance to Gibberella ear rot (GER) disease which reduces yield and contaminates the grains with mycotoxins. However, the incorporation of these landraces into breeding programs requires a clear understanding of the effectiveness of their introgression into elite materials. We evaluated 15 pre-selected doubled haploid (DH) lines from two European flint landraces, "Kemater Landmais Gelb" (KE) and "Petkuser Ferdinand Rot" (PE), together with two adapted elite flint lines and seven standard lines for GER severity as the main trait, and several adaptation traits (plant height, days to silking, seed-set, plant vigor) across four environments. From this evaluation, three KE DH lines and one PE DH line, with the lowest GER severity, were selected and used as donor parents that were crossed with the two adapted and GER susceptible flint lines (Flint1 and Flint2) to develop six bi-parental DH populations with 34-145 DH lines each. Each DH population was evaluated across two locations. Correlations between GER severity, which was the target trait, and adaptation traits were weak (-0.02 to 0.19). GER severity of lines from PE landrace was on average 2-fold higher than lines from KE landrace, indicating a clear superiority of the KE landrace lines. Mean GER severity of the DH populations was 39.4-61.0% lower than the adapted elite flint lines. All KE-derived DH populations were on average more resistant (27.0-36.7%) than the PE-derived population (51.0%). Highly resistant lines (1.3-5.2%) were found in all of the populations, suggesting that the DH populations can be successfully integrated into elite breeding programs. The findings demonstrate that selected KE landrace lines used as donors were effective in improving GER resistance of the adapted elite inbreds., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Akohoue et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Pearl millet [Pennisetum glancum (L.) R. Br.] landraces provide nutritional quality and security under the harsh environmental conditions of Rajasthan, India. Using amplified fragment length polymorphism (AFLP), this study investigated pearl millet genetic diversity patterns and related the results to farmers' local knowledge and seed systems. Thirty-nine cultivars were assessed: 14 farmer landraces from western Rajasthan, 13 farmer landraces from eastern Rajasthan, and 12 control cultivars. Shannons' information index for western (H = 0.34) and eastern (H = 0.32) Rajasthan landraces was up to 14% higher than in composite-based improved cultivars. Analysis of molecular variance (AMOVA) revealed that variation within landrace populations was much higher than between regional samples. In the west, intra-village variation was higher than inter-village variation. In the east, variation between landrace groups bearing a specific name was higher than intra-group variation. Gene flow, inferred from genetic distances between populations, was used as an indicator for seed exchange between farmers. In western Rajasthan, seed exchange appears to be especially dynamic, as gene flow was greater than [N.sub.e]m = 25 among most of its populations. Farmers' knowledge of local cultivars and seed systems was, for the most part, supported by the AFLP analysis. These results are relevant for in situ maintenance and breeding strategies with a view to improving traditional cultivars, specifically performance and yielding stability., NATURAL OCCURRENCES, as well as human activities, can lead to phenotypic crop diversity within a given production system (e.g., Sperling et al., 1993; Bellon and Brush, 1994; Louette et al., [...]

Maize (Zea mays L.) cultivars with improved N-use efficiency would be beneficial for low-input production systems. Our objective was to estimate quantitative genetic parameters to optimize breeding programs for improving productivity under low N levels. Results of 21 field experiments with European breeding materials belonging to the flint and dent gene pool are presented. The study was performed during 1989 and 1999 at several locations in typical maize growing regions of Germany and France. All experiments were conducted at high (HN) and low (LN, no N fertilizer applied) N levels. Average grain yield was reduced by 37% at LN compared with HN. Coefficients of genotypic correlation between HN and LN were variable with an average of [r.sub.G] = 0.74 for grain yield and generally high for grain dry matter content. For grain yield, analyses of variance were computed from relative data, where plot values were expressed as percentage of the trial mean. Variances caused by genotype (G), G x location (L) interaction, and error effects were higher at LN compared with HN, with similar heritabilities at both N levels. For the untransformed data, components of variance were higher at HN than at LN. Genotype x N as well as G x L x N level interaction variances were significant in most experiments. Efficiency of improvement of grain yield at LN through indirect selection at HN was 70% compared with direct selection at LN. A trend toward increased efficiency of direct selection under LN conditions was evident with decreasing grain yield at LN., FROM 1960 to 1990, the use of N fertilizer in modern agricultural systems has increased in parts of Asia, North America, and West Europe (Food and Agricultural Organization of the [...]

In the desert region of Rajasthan, India, farmers mainly grow pearl millet [Pennisetum glaucum (L.) R. Br.] landraces. The adoption of modern cultivars is generally low because of their poor adaptation to extreme drought stress. The objective of this study was to evaluate the performance of six elite breeding populations and three landraces and to determine the heterotic pattern among the 36 diallel crosses of those populations. Field experiments were conducted in eight environments in India. Mean grain yields (GYs) in the three environments with favorable growing conditions were double to threefold those in the three arid environments. The elite populations generally showed higher GY than the landraces; stover yield (SY) was similar in both population types. The landraces flowered earlier, had a higher tillering potential, and smaller seeds. Mean level of midparent heterosis was generally low, ranging from 0.85% for time to flowering (TF) to 6.57% for SY. For GY, expression of heterosis for individual population crosses was between -14 and +30% under drought stress, and between -9 and +17% in the favorable environments. For SY, mean heterosis was always positive and higher than for GY. The elite x landrace population crosses with high mean GY and high levels of heterosis under drought stress could be beneficial to widen the germplasm base and to combine the high yield potential of elite materials with the good adaptation of the landraces., PEARL MILLET is a staple food crop in the semiarid and arid areas of Africa and Asia. In India, modern cultivars, both hybrids and open-pollinated cultivars, have been widely adopted [...]

Altering plant water use efficiency (WUE) is a promising approach for achieving sustainable crop production in changing climate scenarios. Here, we show that WUE can be tuned by alleles of a single gene discovered in elite maize (Zea mays) breeding material. Genetic dissection of a genomic region affecting WUE led to the identification of the gene ZmAbh4 as causative for the effect. CRISPR/Cas9-mediated ZmAbh4 inactivation increased WUE without growth reductions in well-watered conditions. ZmAbh4 encodes an enzyme that hydroxylates the phytohormone abscisic acid (ABA) and initiates its catabolism. Stomatal conductance is regulated by ABA and emerged as a major link between variation in WUE and discrimination against the heavy carbon isotope (Δ13C) during photosynthesis in the C4 crop maize. Changes in Δ13C persisted in kernel material, which offers an easy-to-screen proxy for WUE. Our results establish a direct physiological and genetic link between WUE and Δ13C through a single gene with potential applications in maize breeding., (© The Author(s) 2022. Published by Oxford University Press on behalf of American Society of Plant Biologists.)

Combined phenomic and genomic approaches are required to evaluate the margin of progress of breeding strategies. Here, we analyze 65 years of genetic progress in maize yield, which was similar (101 kg ha -1 year -1 ) across most frequent environmental scenarios in the European growing area. Yield gains were linked to physiologically simple traits (plant phenology and architecture) which indirectly affected reproductive development and light interception in all studied environments, marked by significant genomic signatures of selection. Conversely, studied physiological processes involved in stress adaptation remained phenotypically unchanged (e.g. stomatal conductance and growth sensitivity to drought) and showed no signatures of selection. By selecting for yield, breeders indirectly selected traits with stable effects on yield, but not physiological traits whose effects on yield can be positive or negative depending on environmental conditions. Because yield stability under climate change is desirable, novel breeding strategies may be needed for exploiting alleles governing physiological adaptive traits., (© 2022. The Author(s).)

Discovery and enrichment of favorable alleles in landraces are key to making them accessible for crop improvement. Here, we present two fundamentally different concepts for genome-based selection in landrace-derived maize populations, one based on doubled-haploid (DH) lines derived directly from individual landrace plants and the other based on crossing landrace plants to a capture line. For both types of populations, we show theoretically how allele frequencies of the ancestral landrace and the capture line translate into expectations for molecular and genetic variances. We show that the DH approach has clear advantages over gamete capture with generally higher prediction accuracies and no risk of masking valuable variation of the landrace. Prediction accuracies as high as 0.58 for dry matter yield in the DH population indicate high potential of genome-based selection. Based on a comparison among traits, we show that the genetic makeup of the capture line has great influence on the success of genome-based selection and that confounding effects between the alleles of the landrace and the capture line are best controlled for traits for which the capture line does not outperform the ancestral population per se or in testcrosses. Our results will guide the optimization of genome-enabled prebreeding schemes.

Genetic variation is the basis of selection, evolution and breeding. Maize landraces represent a rich source of allelic diversity, but their efficient utilization in breeding and research has been hampered by their heterogeneous and heterozygous nature and insufficient information about most accessions. While molecular inventories of germplasm repositories are growing steadily, linking these data to meaningful phenotypes for quantitative traits is challenging. Here, we present comprehensive molecular and phenotypic data for ∼1,000 doubled-haploid (DH) lines derived from three pre-selected European maize landraces. Due to their full homozygosity, the DH lines can be multiplied ad libitum and represent a powerful biological resource available to the community. The DH lines allow high-precision phenotyping in repeated experiments and reveal the full additive genetic variance of the population. The DH lines were evaluated for nine agronomically important, quantitative traits in multi-environment field trials comprising seven locations and two years. The DH populations revealed high genetic variance and high heritability for the analysed traits. The DH lines were genotyped with 600k SNP markers. After stringent quality filtering 500k markers remained for further analyses. This is the largest resource of landrace derived DH material in maize, unprecedented in its structure and dimension. The presented data are ideal for linking molecular variation to meaningful phenotypes. They can be used for genome-wide association studies, genomic prediction, and population genetic analyses as well as for developing and testing statistical methods. All plant material is available to the community for conducting additional experiments, extending the panel of traits and environments, and for testing the landrace-derived lines in combination with other genetic material., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2022 The Author(s). Published by Elsevier Inc.)

Key Message: High genetic variation in two European maize landraces can be harnessed to improve Gibberella ear rot resistance by integrated genomic tools. Fusarium graminearum (Fg) causes Gibberella ear rot (GER) in maize leading to yield reduction and contamination of grains with several mycotoxins. This study aimed to elucidate the molecular basis of GER resistance among 500 doubled haploid lines derived from two European maize landraces, "Kemater Landmais Gelb" (KE) and "Petkuser Ferdinand Rot" (PE). The two landraces were analyzed individually using genome-wide association studies and genomic selection (GS). The lines were genotyped with a 600-k maize array and phenotyped for GER severity, days to silking, plant height, and seed-set in four environments using artificial infection with a highly aggressive Fg isolate. High genotypic variances and broad-sense heritabilities were found for all traits. Genotype-environment interaction was important throughout. The phenotypic (r) and genotypic ([Formula: see text]) correlations between GER severity and three agronomic traits were low (r =  - 0.27 to 0.20; [Formula: see text]=  - 0.32 to 0.22). For GER severity, eight QTLs were detected in KE jointly explaining 34% of the genetic variance. In PE, no significant QTLs for GER severity were detected. No common QTLs were found between GER severity and the three agronomic traits. The mean prediction accuracies ([Formula: see text]) of weighted GS (wRR-BLUP) were higher than [Formula: see text] of marker-assisted selection (MAS) and unweighted GS (RR-BLUP) for GER severity. Using KE as the training set and PE as the validation set resulted in very low [Formula: see text] that could be improved by using fixed marker effects in the GS model.

Key Message: NCLB is the most devastating leaf disease in European maize, and the introduction of Brazilian resistance donors can efficiently increase the resistance levels of European maize germplasm. Northern corn leaf blight (NCLB) is one of the most devastating leaf pathogens in maize (Zea mays L.). Maize cultivars need to be equipped with broad and stable NCLB resistance to cope with production intensification and climate change. Brazilian germplasm is a great source to increase low NCLB resistance levels in European materials, but little is known about their effect in European environments. To investigate the usefulness of Brazilian germplasm as NCLB resistance donors, we conducted multi-parent QTL mapping, evaluated the potential of marker-assisted selection as well as genome-wide selection of 742 F 1 -derived DH lines. The line per se performance was evaluated in one location in Brazil and six location-by-year combinations (= environments) in Europe, while testcrosses were assessed in two locations in Brazil and further 10 environments in Europe. Jointly, we identified 17 QTL for NCLB resistance explaining 3.57-30.98% of the genotypic variance each. Two of these QTL were detected in both Brazilian and European environments indicating the stability of these QTL in contrasting ecosystems. We observed moderate to high genomic prediction accuracies between 0.58 and 0.83 depending on population and continent. Collectively, our study illustrates the potential use of tropical resistance sources to increase NCLB resistance level in applied European maize breeding programs.

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.

Key Message: Doubled-haploid libraries from landraces capture native genetic diversity for a multitude of quantitative traits and make it accessible for breeding and genome-based studies. Maize landraces comprise large allelic diversity. We created doubled-haploid (DH) libraries from three European flint maize landraces and characterized them with respect to their molecular diversity, population structure, trait means, variances, and trait correlations. In total, 899 DH lines were evaluated using high-quality genotypic and multi-environment phenotypic data from up to 11 environments. The DH lines covered 95% of the molecular variation present in 35 landraces of an earlier study and represent the original three landrace populations in an unbiased manner. A comprehensive analysis of the target trait plant development at early growth stages as well as other important agronomic traits revealed large genetic variation for line per se and testcross performance. The majority of the 378 DH lines evaluated as testcrosses outperformed the commercial hybrids for early development. For total biomass yield, we observed a yield gap of 15% between mean testcross yield of the commercial hybrids and mean testcross yield of the DH lines. The DH lines also exhibited genetic variation for undesirable traits like root lodging and tillering, but correlations with target traits early development and yield were low or nonsignificant. The presented diversity atlas is a valuable, publicly available resource for genome-based studies to identify novel trait variation and evaluate the prospects of genomic prediction in landrace-derived material.

Key Messages: Sixty-nine quantitative trait nucleotides conferring maize resistance to Gibberella ear rot were detected, including eighteen novel loci. Four candidate genes were predicted, and four kompetitive allele-specific PCR markers were developed. Maize Gibberella ear rot (GER), caused by Fusarium graminearum, is one of the most devastating diseases in maize-growing regions worldwide. Enhancing maize cultivar resistance to this disease requires a comprehensive understanding of the genetic basis of resistance to GER. In this study, 334 maize inbred lines were phenotyped for GER resistance in five environments and genotyped using the Affymetrix CGMB56K SNP Array, and a genome-wide association study of resistance to GER was performed using a 3V multi-locus random-SNP-effect mixed linear model. A total of 69 quantitative trait nucleotides (QTNs) conferring resistance to GER were detected, and all of them explained individually less than 10% of the phenotypic variation, suggesting that resistance to GER is controlled by multiple minor-effect genetic loci. A total of 348 genes located around the 200-kb genomic region of these 69 QTNs were identified, and four of them (Zm00001d029648, Zm00001d031449, Zm00001d006397, and Zm00001d053145) were considered candidate genes conferring susceptibility to GER based on gene expression patterns. Moreover, four kompetitive allele-specific PCR markers were developed based on the non-synonymous variation of these four candidate genes and validated in two genetic populations. This study provides useful genetic resources for improving resistance to GER in maize., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Key Message: A genomic segment on maize chromosome 7 influences carbon isotope composition, water use efficiency, and leaf growth sensitivity to drought, possibly by affecting stomatal properties. Climate change is expected to decrease water availability in many agricultural production areas around the globe. Therefore, plants with improved ability to grow under water deficit are urgently needed. We combined genetic, phenomic, and physiological approaches to understand the relationship between growth, stomatal conductance, water use efficiency, and carbon isotope composition in maize (Zea mays L.). Using near-isogenic lines derived from a maize introgression library, we analysed the effects of a genomic region previously identified as affecting carbon isotope composition. We show stability of trait expression over several years of field trials and demonstrate in the phenotyping platform Phenodyn that the same genomic region also influences the sensitivity of leaf growth to evaporative demand and soil water potential. Our results suggest that the studied genomic region affecting carbon isotope discrimination also harbours quantitative trait loci playing a role in maize drought sensitivity possibly via stomatal behaviour and development. We propose that the observed phenotypes collectively originate from altered stomatal conductance, presumably via abscisic acid.

With 1 figure and 6 tables In maize ( Zea mays L.), as in other cross-pollinated crops, a high mutational load of deleterious recessive alleles hampers the use of landraces in hybrid breeding. The in vivo doubled haploid (DH) technology meanwhile offers great promise in purging such alleles. This approach was employed to three European flint type landraces. Eighty DH lines were evaluated for testcross performance under three farming conditions. Mean testcross performance of DH lines was similar to that of their parental landraces but 22–26% lower than that of present elite flint lines. Highly significant genetic variance existed in each of the three DH-line groups. Coefficients of genetic variation ranged from 6.7 to 7.4. DH-lines derived from ‘Lucq de Béarn’ displayed specific adaptation to N deficiency. The 10% (out of 80) best DH lines surpassed the first-cycle lines by 11% in testcross grain yield and remained only 13% below the elite lines. Altogether, the DH approach proved to be a highly effective tool for gaining access to the hitherto hardly tapped broad genetic diversity of landraces in research and breeding. [ABSTRACT FROM AUTHOR]

Abstract Maize varieties with improved nitrogen(N)-use efficiency under low soil N conditions can contribute to sustainable agriculture. Tests were carried to see whether selection of European elite lines at low and high N supply would result in hybrids with differential adaptation to these contrasting N conditions. The objective was to analyze whether genotypic differences in N uptake and N-utilization efficiency existed in this material and to what extent these factors contributed to adaptation to low N supply. Twenty-four hybrids developed at low N supply (L × L) were compared with 25 hybrids developed at high N supply (H × H). The N uptake was determined as total above-ground N in whole plants, and N-utilization efficiency as the ratio between grain yield and N uptake in yield trials at four locations and at three N levels each. Highly significant variations as a result of hybrids and hybrids × N-level interaction were observed for grain yield as well as for N uptake and N-utilization efficiency in both hybrid types. Average yields of the L × L hybrids were higher than those of the H × H hybrids by 11.5% at low N supply and 5.4% at medium N level. There was no significant yield difference between the two hybrid types at high N supply. The L × L hybrids showed significantly higher N uptake at the low (12%) and medium (6%) N levels than the H × H hybrids. In contrast, no differences in N-utilization efficiency were observed between the hybrid types. These results indicate that adaptation of hybrids from European elite breeding material to conditions with reduced nitrogen input was possible and was mainly the result of an increase in N-uptake efficiency. [ABSTRACT FROM AUTHOR]

Farmers in western Rajasthan (north-west India) produce and maintain their landrace populations of pearl millet through their own distinct seed management practices. The objective of this study was to characterize morphological and agronomic variability of different traits between and within three farmers' populations using quantitative–genetic parameters. Populations examined were a typical landrace and two modified landraces, which were generated through farmer introgression of modern varieties with different levels of subsequent selection. From these three populations, 100 random full-sib progenies were evaluated in field trials at two locations in western Rajasthan over two years. Significant genetic variation existed within the three populations. Estimates of heritability were moderate to high for all observed traits. Predicted selection response for grain yield across environments was 1.6% for the typical landrace and 2.2% for both the modified landraces. Results suggest that the introgression of modern varieties into landraces had increased the genetic diversity. Therefore, farmers' current breeding activities could open up new resources for plant breeding programmes aiming at plant improvement for the semiarid zones of India. [ABSTRACT FROM AUTHOR]

Assessing the genetic variability of plant performance under heat and drought scenarios can contribute to reduce the negative effects of climate change. We propose here an approach that consisted of (1) clustering time courses of environmental variables simulated by a crop model in current (35 years × 55 sites) and future conditions into six scenarios of temperature and water deficit as experienced by maize (Zea mays L.) plants; (2) performing 29 field experiments in contrasting conditions across Europe with 244 maize hybrids; (3) assigning individual experiments to scenarios based on environmental conditions as measured in each field experiment; frequencies of temperature scenarios in our experiments corresponded to future heat scenarios (+5°C); (4) analyzing the genetic variation of plant performance for each environmental scenario. Forty-eight quantitative trait loci (QTLs) of yield were identified by association genetics using a multi-environment multi-locus model. Eight and twelve QTLs were associated to tolerances to heat and drought stresses because they were specific to hot and dry scenarios, respectively, with low or even negative allelic effects in favorable scenarios. Twenty-four QTLs improved yield in favorable conditions but showed nonsignificant effects under stress; they were therefore associated with higher sensitivity. Our approach showed a pattern of QTL effects expressed as functions of environmental variables and scenarios, allowing us to suggest hypotheses for mechanisms and candidate genes underlying each QTL. It can be used for assessing the performance of genotypes and the contribution of genomic regions under current and future stress situations and to accelerate breeding for drought-prone environments., (© 2016 American Society of Plant Biologists. All Rights Reserved.)

Key Message: Dents were more heat tolerant than Flints. QTL for heat tolerance with respect to grain yield at field conditions were identified considering multiple populations and environments. High temperatures have the potential to cause severe damages to maize production. This study aims to elucidate the genetic mechanisms of heat tolerance under field conditions in maize and the genome regions contributing to natural variation. In our study, heat tolerance was assessed on a multi-environment level under non-controlled field conditions for a set of connected intra- and interpool Dent and Flint populations. Our findings indicate that Dent are more heat tolerant during adult stage than Flint genotypes. We identified 11 quantitative trait loci (QTL) including 2 loci for heat tolerance with respect to grain yield. Furthermore, we identified six heat-tolerance and 112 heat-responsive candidate genes colocating with the previously mentioned QTL. To investigate their contribution to the response to heat stress and heat tolerance, differential expression and sequence variation of the identified candidate genes should be subjected to further research.

Main Conclusion: Pearl millet wild relatives harbour novel alleles which could be utilized to broaden genetic base of cultivated species. Genomics-informed pre-breeding is needed to speed up introgression from wild to cultivated gene pool in pearl millet. Rising episodes of intense biotic and abiotic stresses challenge pearl millet production globally. Wild relatives provide a wide spectrum of novel alleles which could address challenges posed by climate change. Pre-breeding holds potential to introgress novel diversity in genetically narrow cultivated Pennisetum glaucum from diverse gene pool. Practical utilization of gene pool diversity remained elusive due to genetic intricacies. Harnessing promising traits from wild pennisetum is limited by lack of information on underlying candidate genes/QTLs. Next-Generation Omics provide vast scope to speed up pre-breeding in pearl millet. Genomic resources generated out of draft genome sequence and improved genome assemblies can be employed to utilize gene bank accessions effectively. The article highlights genetic richness in pearl millet and its utilization with a focus on harnessing next-generation Omics to empower pre-breeding., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

The genetic dissection of root architecture and functions allows for a more effective and informed design of novel root ideotypes and paves the way to evaluate their effects on crop resilience to a number of abiotic stresses. In maize, limited attention has been devoted to the genetic analysis of root architecture diversity at the early stage. The difference in embryonic (including seminal and primary) root architecture between the maize reference line B73 (which mostly develops three seminal roots) and the landrace Gaspé Flint (with virtually no seminal roots) was genetically dissected using a collection of introgression lines grown in paper rolls and pots. Quantitative trait locus (QTL) analysis identified three QTLs controlling seminal root number (SRN) on chromosome bins 1.02, 3.07, and 8.04-8.05, which collectively explained 66% of the phenotypic variation. In all three cases, Gaspé Flint contributed the allele for lower SRN. Primary root dry weight was negatively correlated with SRN (r= -0.52), and QTLs for primary root size co-mapped with SRN QTLs, suggesting a pleiotropic effect of SRN QTLs on the primary root, most probably caused by competition for seed resources. Interestingly, two out of three SRN QTLs co-mapped with the only two known maize genes (rtcs and rum1) affecting the number of seminal roots. The strong additive effect of the three QTLs and the development of near isogenic lines for each QTL in the elite B73 background provide unique opportunities to characterize functionally the genes involved in root development and to evaluate how root architecture affects seedling establishment, early development, and eventually yield in maize., (© The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.)

Northern corn leaf blight (NCLB) caused by the hemibiotrophic fungus Exserohilum turcicum is an important foliar disease of maize that is mainly controlled by growing resistant maize cultivars. The Htn1 locus confers quantitative and partial NCLB resistance by delaying the onset of lesion formation. Htn1 represents an important source of genetic resistance that was originally introduced from a Mexican landrace into modern maize breeding lines in the 1970s. Using a high-resolution map-based cloning approach, we delimited Htn1 to a 131.7-kb physical interval on chromosome 8 that contained three candidate genes encoding two wall-associated receptor-like kinases (ZmWAK-RLK1 and ZmWAK-RLK2) and one wall-associated receptor-like protein (ZmWAK-RLP1). TILLING (targeting induced local lesions in genomes) mutants in ZmWAK-RLK1 were more susceptible to NCLB than wild-type plants, both in greenhouse experiments and in the field. ZmWAK-RLK1 contains a nonarginine-aspartate (non-RD) kinase domain, typically found in plant innate immune receptors. Sequence comparison showed that the extracellular domain of ZmWAK-RLK1 is highly diverse between different maize genotypes. Furthermore, an alternative splice variant resulting in a truncated protein was present at higher frequency in the susceptible parents of the mapping populations compared with in the resistant parents. Hence, the quantitative Htn1 disease resistance in maize is encoded by an unusual innate immune receptor with an extracellular wall-associated kinase domain. These results further highlight the importance of this protein family in resistance to adapted pathogens.

Key Message: The efficiency of marker-assisted selection for native resistance to European corn borer stalk damage can be increased when progressing from a QTL-based towards a genome-wide approach. Marker-assisted selection (MAS) has been shown to be effective in improving resistance to the European corn borer (ECB) in maize. In this study, we investigated the performance of whole-genome-based selection, relative to selection based on individual quantitative trait loci (QTL), for resistance to ECB stalk damage in European elite maize. Three connected biparental populations, comprising 590 doubled haploid (DH) lines, were genotyped with high-density single nucleotide polymorphism markers and phenotyped under artificial and natural infestation in 2011. A subset of 195 DH lines was evaluated in the following year as lines per se and as testcrosses. Resistance was evaluated based on stalk damage ratings, the number of feeding tunnels in the stalk and tunnel length. We performed individual- and joint-population QTL analyses and compared the cross-validated predictive abilities of the QTL models with genomic best linear unbiased prediction (GBLUP). For all traits, the GBLUP model consistently outperformed the QTL model despite the detection of QTL with sizeable effects. For stalk damage rating, GBLUP's predictive ability exceeded at times 0.70. Model training based on DH line per se performance was efficient in predicting stalk breakage in testcrosses. We conclude that the efficiency of MAS for ECB stalk damage resistance can be increased considerably when progressing from a QTL-based towards a genome-wide approach. With the availability of native ECB resistance in elite European maize germplasm, our results open up avenues for the implementation of an integrated genome-based selection approach for the simultaneous improvement of yield, maturity and ECB resistance.

Societal Impact Statement: Genebanks contribute to global food security, directly influencing societal well‐being, by providing access to seed or genetic material that is more resilient to pests, diseases, and environmental stresses. The ability to develop crops adapted to changing environmental conditions and with high nutritional value means societies can better cope with the adverse effects of climate change, safeguarding food production and rural livelihoods. Enhancing sustainable crop traits, such as improved water‐use efficiency and nutrient utilization, supports the transition toward more sustainable agricultural practices. New technologically advanced phenotyping tools are required to optimally realize the potential of these genetic resources, to identify plant genetic resources that will best enable us to address current global challenges. Summary: Plant genebanks have a crucial role as specialized repositories, preserving diverse plant genetic resources and providing essential access to researchers, breeders, and farmers for developing resilient crops. With over 7 million global accessions, these genebanks significantly contribute to global food security, climate change mitigation, and sustainable agriculture. This opinion paper, inspired by an international workshop in 2022 in Wageningen (Netherlands), focuses on the transformative impact of phenomics technology within genebanks, offering a view on its potential applications and implications for preserving and utilizing plant genetic resources. Discussions from the 2022 workshop organized by the International Plant Phenotyping Network are integrated, emphasizing the potential of phenomics for global collaboration without requiring major policy developments. The workshop prioritized traits like disease resistance and drought tolerance, highlighting roots as a critical organ for phenotyping. Participants expressed a keen interest in global collaboration, emphasizing the need for partnerships between genebanks and advanced phenotyping facilities. The workshop's outcomes underscore the transformative impact of phenomics on genebanks, promoting innovation, collaboration, and sustainable agricultural practices. These results will guide future pilot studies, marking a significant step toward integrating phenomics into genebank practices and ensuring the continued prosperity of plant genetic heritage. [ABSTRACT FROM AUTHOR]

Background: Accuracy of genomic prediction depends on the heritability of the trait, the size of the training set, the relationship of the candidates to the training set, and the Min (N QTL , M e) , where N QTL is the number of QTL and M e is the number of independently segregating chromosomal segments. Due to LD, the number Q e of independently segregating QTL (effective QTL) can be lower than Min (N QTL , M e) . In this paper, we show that Q e is inversely associated with the trait-specific genomic relationship of a candidate to the training set. This provides an explanation for the inverse association between Q e and the accuracy of prediction. Methods: To quantify the genomic relationship of a candidate to all members of the training set, we considered the k 2 statistic that has been previously used for this purpose. It quantifies how well the marker covariate vector of a candidate can be represented as a linear combination of the rows of the marker covariate matrix of the training set. In this paper, we used Bayesian regression to make this statistic trait specific and argue that the trait-specific genomic relationship of a candidate to the training set is inversely associated with Q e . Simulation was used to demonstrate the dependence of the trait-specific k 2 statistic on Q e , which is related to N QTL . Conclusions: The posterior distributions of the trait-specific k 2 statistic showed that the trait-specific genomic relationship between a candidate and the training set is inversely associated to Q e and N QTL . Further, we show that trait-specific genomic relationship between a candidate and the training set is directly related to the size of the training set. [ABSTRACT FROM AUTHOR]

Introgression libraries are valuable resources for QTL detection and breeding, but their development is costly and time-consuming. Selection strategies for the development of introgression populations with a limited number of individuals and high-throughput (HT) marker assays are required. The objectives of our simulation study were to design and compare selection strategies for the development of maize introgression populations of 100 lines with population sizes of 360-720 individuals per generation for different DH and S2 crossing schemes. Pre-selection for complete donor chromosomes or donor chromosome halves reduced the number of simultaneous backcross programs. The investigated crossing and selection schemes differed considerably with respect to their suitability to create introgression populations with clearly separated, evenly distributed target donor chromosome segments. DH crossing schemes were superior to S2 crossing schemes, mainly due to complete homozygosity, which greatly reduced the total number of disjunct genome segments in the introgression populations. The S2 crossing schemes were more flexible with respect to selection and provided economic alternatives to DH crossing schemes. For the DH crossing schemes, increasing population sizes gradually over backcross generations was advantageous as it reduced the total number of required HT assays compared to constant population sizes. For the S2 crossing schemes, large population sizes in the final backcross generation facilitated selection for the target segments in the final backcross generation and reduced fixation of large donor chromosome segments. The suggested crossing and selection schemes can help to make the genetic diversity of exotic germplasm available for enhancing the genetic variation of narrow-based breeding populations of crops.

In plants with C4 photosynthesis, physiological mechanisms underlying variation in stable carbon isotope discrimination (Δ(13)C) are largely unknown, and genetic components influencing Δ(13)C have not been described. We analyzed a maize (Zea mays) introgression library derived from two elite parents to investigate whether Δ(13)C is under genetic control in this C4 species. High-density genotyping with the Illumina MaizeSNP50 Bead Chip was used for a detailed structural characterization of 89 introgression lines. Phenotypic analyses were conducted in the field and in the greenhouse for kernel Δ(13)C as well as plant developmental and photosynthesis-related traits. Highly heritable significant genetic variation for Δ(13)C was detected under field and greenhouse conditions. For several introgression library lines, Δ(13)C values consistently differed from the recurrent parent within and across the two phenotyping platforms. Δ(13)C was significantly associated with 22 out of 164 analyzed genomic regions, indicating a complex genetic architecture of Δ(13)C. The five genomic regions with the largest effects were located on chromosomes 1, 2, 6, 7, and 9 and explained 55% of the phenotypic variation for Δ(13)C. Plant development stage had no effect on Δ(13)C expression, as phenotypic as well as genotypic correlations between Δ(13)C, flowering time, and plant height were not significant. To our knowledge, this is the first study demonstrating Δ(13)C to be under polygenic control in the C4 species maize.

An association study conducted on 375 maize inbred lines indicates a strong relationship between Vgt1 polymorphisms and flowering time, extending former quantitative trait loci (QTL) mapping results. Analysis of allele frequencies in a landrace collection supports a key role of Vgt1 in maize altilatitudinal adaptation.

Maize (Zea mays L.) is particularly sensitive to chilling in the early growth stages. The objective of this study was to determine quantitative trait loci (QTL) for early plant vigour of maize grown under cool and moderately warm conditions in Central Europe. A population of 720 doubled haploid (DH) lines was derived from a cross between two dent inbred lines contrasting in early vigour and were genotyped with 188 SSR markers. The DH lines per se and their testcrosses with a flint line were evaluated in field experiments across 11 environments in 2001 and 2002. Plants were harvested after six to eight leaves had been fully developed to assess fresh matter yield as a criterion of early vigour. Seven QTL were detected for line performance and ten QTL for testcross performance, explaining 64 and 49% of the genetic variance. Six out of seven QTL detected in the lines per se were also significant in their testcrosses. Significant QTL x environment interaction was observed, but no relationship existed between the size of the QTL effects and the mean temperature in the individual environment. The correlation between fresh matter yield and days to silking was non-significant, indicating that differences in early plant vigour were not simply caused by maturity differences. For three additional chilling-related traits, leaf chlorosis, leaf purpling, and frost damage seven, six, and five QTL were detected, respectively. Three QTL for leaf chlorosis, two for leaf purpling, and two for frost damage co-localized with QTL for fresh matter yield. Results are considered as a reliable basis for further genetic, molecular, and physiological investigations.

We present a detailed analysis of linkage disequilibrium (LD) in the physical and genetic context of the barley gene Hv-eIF4E, which confers resistance to the barley yellow mosaic virus (BYMV) complex. Eighty-three SNPs distributed over 132 kb of Hv-eIF4E and six additional fragments genetically mapped to its flanking region were used to derive haplotypes from 131 accessions. Three haplogroups were recognized, discriminating between the alleles rym4 and rym5, which each encode for a spectrum of resistance to BYMV. With increasing map distance, haplotypes of susceptible genotypes displayed diverse patterns driven mainly by recombination, whereas haplotype diversity within the subgroups of resistant genotypes was limited. We conclude that the breakdown of LD within 1 cM of the resistance gene was generated mainly by susceptible genotypes. Despite the LD decay, a significant association between haplotype and resistance to BYMV was detected up to a distance of 5.5 cM from the resistance gene. The LD pattern and the haplotype structure of the target chromosomal region are the result of interplay between low recombination and recent breeding history.

With the intensification of global climate change and environmental stress, research on abiotic and biotic stress resistance in maize is particularly important. High temperatures and drought, low temperatures, heavy metals, salinization, and diseases are widespread stress factors that can reduce maize yields and are a focus of maize-breeding research. Molecular biology provides new opportunities for the study of maize and other plants. This article reviews the physiological and biochemical responses of maize to high temperatures and drought, low temperatures, heavy metals, salinization, and diseases, as well as the molecular mechanisms associated with them. Special attention is given to key transcription factors in signal transduction pathways and their roles in regulating maize stress adaptability. In addition, the application of transcriptomics, genome-wide association studies (GWAS), and QTL technology provides new strategies for the identification of molecular markers and genes for maize-stress-resistance traits. Crop genetic improvements through gene editing technologies such as the CRISPR/Cas system provide a new avenue for the development of new stress-resistant varieties. These studies not only help to understand the molecular basis of maize stress responses but also provide important scientific evidence for improving crop tolerance through molecular biological methods. [ABSTRACT FROM AUTHOR]

Northern corn leaf blight (NCLB), caused by Setosphaeria turcica , is a major fungal disease affecting maize production in sub-Saharan Africa. Utilizing host plant resistance to mitigate yield losses associated with NCLB can serve as a cost-effective strategy. In this study, we conducted a high-resolution genome-wide association study (GWAS) in an association mapping panel and linkage mapping with three doubled haploid (DH) and three F3 populations of tropical maize. These populations were phenotyped for NCLB resistance across six hotspot environments in Kenya. Across environments and genotypes, NCLB scores ranged from 2.12 to 5.17 (on a scale of 1–9). NCLB disease severity scores exhibited significant genotypic variance and moderate-to-high heritability. From the six biparental populations, 23 quantitative trait loci (QTLs) were identified, each explaining between 2.7% and 15.8% of the observed phenotypic variance. Collectively, the detected QTLs explained 34.28%, 51.37%, 41.12%, 12.46%, 12.11%, and 14.66% of the total phenotypic variance in DH populations 1, 2, and 3 and F3 populations 4, 5, and 6, respectively. GWAS, using 337,110 high-quality single nucleotide polymorphisms (SNPs), identified 15 marker–trait associations and several putative candidate genes linked to NCLB resistance in maize. Joint linkage association mapping (JLAM) identified 37 QTLs for NCLB resistance. Using linkage mapping, JLAM, and GWAS, several QTLs were identified within the genomic region spanning 4 to 15 Mbp on chromosome 2. This genomic region represents a promising target for enhancing NCLB resistance via marker-assisted breeding. Genome-wide predictions revealed moderate correlations with mean values of 0.45, 0.44, 0.55, and 0.42 for within GWAS panel, DH pop1, DH pop2, and DH pop3, respectively. Prediction by incorporating marker-by-environment interactions did not show much improvement. Overall, our findings indicate that NCLB resistance is quantitative in nature and is controlled by few major-effect and many minor-effect QTLs. We conclude that genomic regions consistently detected across mapping approaches and populations should be prioritized for improving NCLB resistance, while genome-wide prediction results can help incorporate both major- and minor-effect genes. This study contributes to a deeper understanding of the genetic and molecular mechanisms driving maize resistance to NCLB. [ABSTRACT FROM AUTHOR]

Heat stress has become one of the abiotic stresses that pose an increasing threat to maize production due to global warming. The Hsp20 gene family confers tolerance to various abiotic stresses in plants. However, very few Hsp20s have been identified in relation to maize thermotolerance. In this study, we conducted a comprehensive study of Hsp20s involved in thermotolerance in maize. A total of 33 maize Hsp20 genes (ZmHsp20s) were identified through scanning for a conserved α-crystalline domain (ACD), and they were categorized into 14 subfamilies based on phylogenetic analysis. These genes are distributed across all maize chromosomes and nine of them are in regions previously identified as heat-tolerance quantitative trait loci (hrQTL). These hrQTL-associated ZmHsp20s show variation in tissue-specific expression profiles under normal conditions, and seven of them possess 1–5 heat stress elements in their promoters. The integration of RNA-seq data with real-time RT-PCR analysis indicated that ZmHsp23.4, ZmHsp22.8B and ZmHsp18 were dramatically induced under heat stress. Additionally, these genes exhibited co-expression patterns with key ZmHsfs, which are crucial in the heat tolerance pathway. When a null mutant carrying a frame-shifted ZmHsp18 gene was subjected to heat stress, its survival rate decreased significantly, indicating a critical role of ZmHsp18 in maize thermotolerance. Our study lays the groundwork for further research into the roles of ZmHsp20s in enhancing maize's thermotolerance. [ABSTRACT FROM AUTHOR]

Waxy corn is a special type of maize primarily consumed as a fresh vegetable by humans. Nitrogen (N) plays an essential role in regulating the growth progression, maturation, yield, and quality of waxy maize. A reasonable N application rate is vital for boosting the accumulation of both N and carbon (C) in the grains, thereby synergistically enhancing the grain quality. However, the impact of varying N levels on the dynamic changes in N metabolism, carbohydrate formation, and anthocyanin synthesis in purple waxy corn kernels, as well as the regulatory relationships among these processes, remains unclear. To explore the effects of varying N application rates on the N metabolism, carbohydrate formation, and anthocyanin synthesis in kernels during grain filling, a two-year field experiment was carried out using the purple waxy maize variety Jinnuo20 (JN20). This study examined the different N levels, specifically 0 (N0), 120 (N1), 240 (N2), and 360 (N3) kg N ha−1. The results of the analysis revealed that, for nearly all traits measured, the N application rate of N2 was the most suitable. Compared to the N0 treatment, the accumulation and content of anthocyanins, total nitrogen, soluble sugars, amylopectin, and C/N ratio in grains increased by an average of 35.62%, 11.49%, 12.84%, 23.74%, 13.00%, and 1.87% under N2 treatment over five filling stages within two years, respectively, while the harmful compound nitrite content only increased by an average of 30.2%. Correspondingly, the activities of related enzymes also significantly increased and were maintained under N2 treatment compared to N0 treatment. Regression and correlation analysis results revealed that the amount of anthocyanin accumulation was highly positively correlated with the activities of phenylalanine ammonia-lyase (PAL) and flavanone 3-hydroxylase (F3H), but negatively correlated with anthocyanidin synthase (ANS) and UDP-glycose: flavonoid-3-O-glycosyltransferase (UFGT) activity, nitrate reductase (NR), and glutamine synthetase (GS) showed significant positive correlations with the total nitrogen content and lysine content, and a significant negative correlation with nitrite, while soluble sugars were negatively with ADP-glucose pyrophosphorylase (AGPase) activity, and amylopectin content was positively correlated with the activities of soluble starch synthase (SSS), starch branching enzyme (SBE), and starch debranching enzyme (SDBE), respectively. Furthermore, there were positive or negative correlations among the detected traits. Hence, a reasonable N application rate improves purple waxy corn kernel nutritional quality by regulating N metabolism, as well as carbohydrate and anthocyanin biosynthesis. [ABSTRACT FROM AUTHOR]

Commercial hybrids are the main germplasm source for developing maize lines in breeding programs in Brazil; additionally, nitrogen (N) is one the major limiting maize production in Brazilian tropical areas. Here, we assessed the combining ability among ten commercial hybrids under contrasting N inputs and selected the best parental hybrids to develop breeding populations for optimal and N-stress environments. We evaluated the 45 F1 crosses for agronomic traits under contrasting N inputs and over two summer seasons. A mixed model approach was used to estimate the variance components of general combining ability (GCA) and specific combining ability (SCA) as well as to predict the GCA and SCA effects. N-stress caused a reduction in GY (33.25%) of F1 crosses averaged across seasons. We found presence of combining ability (GCA and SCA) x N input interaction for grain yield (GY), days to pollen and plant stature. The parental hybrids showed differences in GCA for cycle and plant stature but not for GY, irrespective of N inputs. Additionally, the variance components of SCA were not significant (P>0.10) for GY under LN, whereas SCA was the major component accounting for variation among F1 crosses under HN. Based on estimates of GCA effects for cycle and plant height, we selected the hybrids BAL188, BM3061, GNZ7210, BRS1060 and DKB390 as sources of favorable alleles for earlier maturing and shorter stature maize for both N conditions and suggested that hybrids GNZ7201 and DKB390, and AG1051 and NS70, which presented very small estimates of SCA for GY, must be recombined to develop two synthetic populations to begin a reciprocal recurrent selection program, mainly for non N-stress environments. [ABSTRACT FROM AUTHOR]

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