Tropical Maize Research Articles

QTL mapping and genome-wide association analysis reveal genetic loci and candidate gene for resistance to gray leaf spot in tropical and subtropical maize germplasm.

Using QTL mapping and GWAS, two candidate genes (Zm00001d051039 and Zm00001d051147) were consistently identified across the three different environments and BLUP values. GWAS analysis identified the candidate gene, Zm00001d044845. These genes were subsequently validated to exhibit a significant association with maize gray leaf spot (GLS) resistance. Gray leaf spot (GLS) is a major foliar disease of maize (Zea mays L.) that causes significant yield losses worldwide. Understanding the genetic mechanisms underlying gray leaf spot resistance is crucial for breeding high-yielding and disease-resistant varieties. In this study, eight tropical and subtropical germplasms were crossed with the temperate germplasm Ye107 to develop a nested association mapping (NAM) population comprising 1,653 F2:8 RILs, consisting of eight recombinant inbred line (RIL) subpopulations, using the single-seed descent method. The NAM population was evaluated for GLS resistance in three different environments, and genotyping by sequencing of the NAM population generated 593,719 high-quality single-nucleotide polymorphisms (SNPs). Linkage analysis and genome-wide association studies (GWASs) were conducted to identify candidate genes regulating GLS resistance in maize. Both analyses identified 25 QTLs and 149 SNPs that were significantly associated with GLS resistance. Candidate genes were screened 20Kb upstream and downstream of the significant SNPs, and three novel candidate genes (Zm00001d051039, Zm00001d051147, and Zm00001d044845) were identified. Zm00001d051039 and Zm00001d051147 were located on chromosome 4 and co-localized in both linkage (qGLS4-1 and qGLS4-2) and GWAS analyses. SNP-138,153,206 was located 0.499kb downstream of the candidate gene Zm00001d051039, which encodes the protein IN2-1 homolog B, a homolog of glutathione S-transferase (GST). GSTs and protein IN2-1 homolog B scavenge reactive oxygen species under various stress conditions, and GSTs are believed to protect plants from a wide range of biotic and abiotic stresses by detoxifying reactive electrophilic compounds. Zm00001d051147 encodes a probable beta-1,4-xylosyltransferase involved in the biosynthesis of xylan in the cell wall, enhancing resistance. SNP-145,813,215 was located 2.69kb downstream of the candidate gene. SNP-5,043,412 was consistently identified in three different environments and BLUP values and was located 8.788kb downstream of the candidate gene Zm00001d044845 on chromosome 9. Zm00001d044845 encodes the U-box domain-containing protein 4 (PUB4), which is involved in regulating plant immunity. qRT-PCR analysis showed that the relative expression levels of the three candidate genes were significantly upregulated in the leaves of the TML139 (resistant) parent, indicating that these three candidate genes could be associated with resistance to GLS. The findings of this study are significant for marker-assisted breeding aimed at enhancing resistance to GLS in maize and lay the foundation for further elucidation of the genetic mechanisms underlying resistance to gray leaf spot in maize and breeding of new disease-resistant varieties.

Mining of Oil Content Genes in Recombinant Maize Inbred Lines with Introgression from Temperate and Tropical Germplasm.

The oil content of maize kernels is essential to determine its nutritional and economic value. A multiparent population (MPP) consisting of five recombinant inbred line (RIL) subpopulations was developed to elucidate the genetic basis of the total oil content (TOC) in maize. The MPP used the subtropical maize inbred lines CML312 and CML384, along with the tropical maize inbred lines CML395, YML46, and YML32 as the female parents, and Ye107 as the male parent. A genome-wide association study (GWAS) was performed using 429 RILs of the multiparent population across three environments, employing 584,847 high-quality single nucleotide polymorphisms (SNPs). Furthermore, linkage analysis was performed in the five subpopulations to identify quantitative trait loci (QTL) linked to TOC in maize. Through QTL mapping and GWAS, 18 QTLs and 60 SNPs that were significantly associated with TOC were identified. Two novel candidate genes, Zm00001d029550 and Zm00001d029551, related to TOC in maize and located on chromosome 1 were reported, which have not been previously reported. These genes are involved in biosynthesis, lipid signal transduction, plant development and metabolism, and stress responses, potentially influencing maize TOC. Haplotype analysis of Zm00001d029550 and Zm00001d029551 revealed that Hap3 could be considered a superior haplotype for increasing TOC in maize. A co-located SNP (SNP-75791466) on chromosome 1, located 5648 bp and 11,951 bp downstream of the candidate genes Zm00001d029550 and Zm00001d029551, respectively, was found to be expressed in various maize tissues. The highest expression was observed in embryos after pollination, indicating that embryos are the main tissue for oil accumulation in maize. This study provides a theoretical basis for understanding the genetic mechanisms underlying maize TOC and developing high-quality, high-oil maize varieties.

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

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

Phytosociological Study of Weed Communities in Zea Mays Cultivation: Contributions to Sustainable Development Goals (SDG'S) in the Ecuadorian Tropics

Objective: This study investigates the phytosociological characteristics of weed communities associated with Zea mays cultivation in different zones of the Ecuadorian tropics, aiming to identify and classify weeds to develop effective management strategies that enhance productivity while minimizing environmental impacts Theoretical Framework: The research is based on the concept that weeds, or 'noxious weeds,' significantly challenge maize cultivation by competing for essential resources. Theories related to plant competition and agroecosystem sustainability underpin the study Method: The methodology involves a phytosociological survey across five farms in Mocache, Ventanas, and Balzar. Using 45 quadrats of 50 x 50 cm in a zigzag pattern across one-hectare plots, weed species were identified and quantified. Data were analyzed to calculate biodiversity and importance value indices. Results and Discussion: Mocache had the highest weed population, while Balzar exhibited greater species diversity. Similarity indices, including Jaccard and Bray-Curtis, revealed distinct patterns in species distribution and dominance. These findings are discussed in the context of sustainable agriculture, highlighting the implications for weed management and acknowledging potential limitations due to environmental variability. Research Implications: The study provides insights into sustainable weed management in maize agroecosystems, contributing to strategies aligned with SDG 2 (Zero Hunger) and SDG 15 (Life on Land), promoting practices that enhance food security and biodiversity conservation. Originality/Value: This research offers a novel phytosociological analysis of weed communities in tropical maize cultivation, contributing to sustainable agriculture and aligning with global sustainability goals.

Genome-wide association analysis of grain yield and Striga hermonthica and S. asiatica resistance in tropical and sub-tropical maize populations

BackgroundGenetic improvement for Striga hermonthica (Sh) and S. asiatica (Sa) resistance is the most economical and effective control method to enhance the productivity of maize and other major cereal crops. Hence, identification of quantitative trait loci (QTL) associated with Striga resistance and economic traits will guide the pace and precision of resistance breeding in maize. The objective of this study was to undertake a genome-wide association analysis of grain yield and Sh and Sa resistance among tropical and sub-tropical maize populations to identify putative genetic markers and genes for resistance breeding. 126 maize genotypes were evaluated under controlled environment conditions using artificial infestation of Sh and Sa. The test genotypes were profiled for grain yield (GY), Striga emergence counts at 8 (SEC8) and 10 (SEC10) weeks after planting, and Striga damage rate scores at 8 (SDR8) and 10 (SDR10) weeks after planting. Population structure analysis and genome-wide association mapping were undertaken based on 16,000 single nucleotide polymorphism (SNP) markers.ResultsA linkage disequilibrium (LD) analysis in 798,675 marker pairs revealed that 21.52% of pairs were in significant linkage (P < 0.001). Across the chromosomes, the LD between SNPs decayed below a critical level (r2 = 0.1) at a map distance of 0.19 Mbp. The genome-wide association study identified 50 significant loci associated with Sh resistance and 22 significant loci linked to Sa resistance, corresponding to 39 and 19 candidate genes, respectively.ConclusionThe study found non-significant QTL associated with dual resistance to the two examined Striga species Some of the detected genes reportedly conditioned insect and pathogen resistance, plant cell development, variable senescence, and pollen fertility. The markers detected in the present study for Sa resistance were reported for the first time. The gene Zm00001eb219710 was pleiotropic, and conditioned GY and SEC10, while Zm00001eb165170 affected SDR8 and SDR10, and Zm00001eb112030 conditioned SDR8 and SDR10 associated with Sh resistance. The candidate genes may facilitate simultaneous selection for Sh and Sa resistance and grain yield in maize after further validation and introgression in breeding pipelines. Overall, we recommend breeding maize specifically for resistance to each Striga species using germplasm adapted to the endemic region of each parasite.

Agrobacterium-mediated Transformation of Tropical Maize Using Seedling Leaf Whorl Explants

Conventional maize transformation has largely relied on immature embryos as explants, and is thus often hampered by the limited access to high-quality immature embryos year-round. Here, we present a detailed protocol using seedling leaf whorls as alternative explants for tropical maize inbred transformation. This approach involves the use of a cassette that drives the expression of the morphogenic transcription factors (MTFs)Baby boom(Bbm) andWuschel2(Wus2), which have been shown to greatly enhance transformation efficiency. We outline here the steps required for the preparation of seedling leaf whorl explants and subsequentAgrobacteriuminfection, and describe the tissue culture regimen that results in transgenic plant regeneration. Because constitutive expression ofBbmandWus2prevents normal plant regeneration and the production of fertile plants, the cassette containing these genes must be excised. As such, we include the steps for theCre/loxP-mediated excision of the MTF gene cassette. The protocol outlines a year-round, more affordable, and efficient approach for carrying out maize transformation for crop improvement.

Integrated GWAS, linkage, and transcriptome analysis to identify genetic loci and candidate genes for photoperiod sensitivity in maize.

Maize photosensitivity and the control of flowering not only are important for reproduction, but also play pivotal roles in the processes of domestication and environmental adaptation, especially involving the utilization strategy of tropical maize in high-latitude regions. In this study, we used a linkage mapping population and an inbred association panel with the photoperiod sensitivity index (PSI) phenotyped under different environments and performed transcriptome analysis of T32 and QR273 between long-day and short-day conditions. The results showed that PSIs of days to tasseling (DTT), days to pollen shedding (DTP), and days to silking (DTS) indicated efficacious interactions with photoperiod sensitivity for maize latitude adaptation. A total of 48 quantitative trait loci (QTLs) and 252 quantitative trait nucleotides (QTNs) were detected using the linkage population and the inbred association panel. Thirteen candidate genes were identified by combining the genome-wide association study (GWAS) approach, linkage analysis, and transcriptome analysis, wherein five critical candidate genes, MYB163, bif1, burp8, CADR3, and Zm00001d050238, were significantly associated with photoperiod sensitivity. These results would provide much more abundant theoretical proofs to reveal the genetic basis of photoperiod sensitivity, which would be helpful to understand the genetic changes during domestication and improvement and contribute to reducing the barriers to use of tropical germplasm.

Differences in activity and stability drive transposable element variation in tropical and temperate maize.

Much of the profound interspecific variation in genome content has been attributed to transposable elements (TEs). To explore the extent of TE variation within species, we developed an optimized open-source algorithm, panEDTA, to de novo annotate TEs in a pangenome context. We then generated a unified TE annotation for a maize pangenome derived from 26 reference-quality genomes, which reveals an excess of 35.1 Mb of TE sequences per genome in tropical maize relative to temperate maize. A small number (n = 216) of TE families, mainly LTR retrotransposons, drive these differences. Evidence from the methylome, transcriptome, LTR age distribution, and LTR insertional polymorphisms reveals that 64.7% of the variability is contributed by LTR families that are young, less methylated, and more expressed in tropical maize, whereas 18.5% is driven by LTR families with removal or loss in temperate maize. Additionally, we find enrichment for Young LTR families adjacent to nucleotide-binding and leucine-rich repeat (NLR) clusters of varying copy number across lines, suggesting TE activity may be associated with disease resistance in maize.

Performance of tropical and subtropical maize inbred lines under well-watered and drought-stressed environments

Drought is a major constraint for maize production in sub-Saharan Africa. Developing high-yielding drought-tolerant maize germplasm will safeguard maize yields in the ever-increasing fluctuating rainfall conditions. This study aimed to identify high-yielding inbred lines with stable performance for utilization in hybrid production. One hundred eighty-two (182) maize inbred lines were evaluated under well-watered and drought-stressed conditions at Ukulinga, Makhathini, and Cedara research stations in KwaZulu-Natal, South Africa. The experiments were carried out in a 13 × 14 alpha lattice design with two replications. The inbred lines exhibited significant differences (p ≤ 0.001) for grain yield and yield-related traits under well-watered and drought-stressed environments. The GGE biplot identified three mega-environments, clearly separating drought-stressed from well-watered environments. Inbred lines TZISTR1190, TZISTR1231, TZISTR1261 and CML540 were superior under well-watered conditions, while TZISTR1164 and CML390 performed well under drought condition. TZISTR1190 displayed both high average yield and stability across environments. Inbred lines combining stable high yielding performance in optimum and stress conditions such as TZISTR1190 and TZISTR1231, can be incorporated into local maize breeding pipelines to develop stable high yielding resilient hybrids.

Genomic prediction of the performance of tropical doubled haploid maize lines under artificial Striga hermonthica (Del.) Benth. infestation.

Striga hermonthica (Del.) Benth., a parasitic weed, causes substantial yield losses in maize production in sub-Saharan Africa. Breeding for Striga resistance in maize is constrained by limited genetic diversity for Striga resistance within the elite germplasm and phenotyping capacity under artificial Striga infestation. Genomics-enabled approaches have the potential to accelerate identification of Striga resistant lines for hybrid development. The objectives of this study were to evaluate the accuracy of genomic selection for traits associated with Striga resistance and grain yield (GY) and to predict genetic values of tested and untested doubled haploid maize lines. We genotyped 606 doubled haploid lines with 8,439 rAmpSeq markers. A training set of 116 doubled haploid lines crossed to 2 testers was phenotyped under artificial Striga infestation at 3 locations in Kenya. Heritability for Striga resistance parameters ranged from 0.38-0.65 while that for GY was 0.54. The prediction accuracies for Striga resistance-associated traits across locations, as determined by cross-validation (CV) were 0.24-0.53 for CV0 and from 0.20 to 0.37 for CV2. For GY, the prediction accuracies were 0.59 and 0.56 for CV0 and CV2, respectively. The results revealed 300 doubled haploid lines with desirable genomic estimated breeding values for reduced number of emerged Striga plants (STR) at 8, 10, and 12 weeks after planting. The genomic estimated breeding values of doubled haploid lines for Striga resistance-associated traits in the training and testing sets were similar in magnitude. These results highlight the potential application of genomic selection in breeding for Striga resistance in maize. The integration of genomic-assisted strategies and doubled haploid technology for line development coupled with forward breeding for major adaptive traits will enhance genetic gains in breeding for Striga resistance in maize.

Registration of provitamin A‐enriched tropical maize inbred lines

AbstractVitamin A deficiency and its associated disorders are pervasive in sub‐Saharan Africa (SSA) including many middle‐ and low‐income countries across the world. Provitamin A‐enriched maize (Zea mays L.) inbred lines with desirable agronomic and adaptive traits have been developed and used to generate and commercialize maize varieties with medium to high levels of provitamin A in a few countries to curb vitamin A deficiency. Nonetheless, these inbred lines have not been made widely available to the public and private sector breeders in many countries. The main purpose for releasing the 21 provitamin A‐enriched tropical maize inbred lines (PI 705424–PI 705444, Reg. nos. GP‐624–GP‐644) is to supply maize breeders with elite source germplasm for increasing provitamin A and other carotenoids to much higher levels to offset losses during storage, natural degradation, and processing. These inbred lines were developed at the International Institute of Tropical Agriculture (IITA) from backcrosses of high β‐carotene temperate lines as donors and elite tropical lines as recipients. These inbred lines were developed through repeated self‐pollination with rigorous visual selection among and within lines for plant vigor, synchronous silk emergence and pollen shedding, low ear placement, and resistance to lodging and major tropical diseases, followed by selection for bright yellow to orange kernel color with semi flint to flint kernel texture after harvest. The released maize inbred lines will be diverse sources of favorable alleles to accelerate genetic gain in provitamin A and other beneficial carotenoid enrichment for human health.

Genetic diversity analysis of tropical and sub-tropical maize germplasm for Striga resistance and agronomic traits with SNP markers.

Striga hermonthica (Sh) and S. asiatica (Sa) are major parasitic weeds limiting cereal crop production and productivity in sub-Saharan Africa (SSA). Under severe infestation, Striga causes yield losses of up to 100%. Breeding for Striga-resistant maize varieties is the most effective and economical approach to controlling the parasite. Well-characterized and genetically differentiated maize germplasm is vital to developing inbred lines, hybrids, and synthetic varieties with Striga resistance and desirable product profiles. The objective of this study was to determine the genetic diversity of 130 tropical and sub-tropical maize inbred lines, hybrids, and open-pollinated varieties germplasm using phenotypic traits and single nucleotide polymorphism (SNP) markers to select Striga-resistant and complementary genotypes for breeding. The test genotypes were phenotyped with Sh and Sa infestations using a 13x10 alpha lattice design with two replications. Agro-morphological traits and Striga-resistance damage parameters were recorded under a controlled environment. Further, high-density Diversity Array Technology Sequencing-derived SNP markers were used to profile the test genotypes. Significant phenotypic differences (P<0.001) were detected among the assessed genotypes for the assessed traits. The SNP markers revealed mean gene diversity and polymorphic information content of 0.34 and 0.44, respectively, supporting the phenotypic variation of the test genotypes. Higher significant variation was recorded within populations (85%) than between populations using the analysis of molecular variance. The Structure analysis allocated the test genotypes into eight major clusters (K = 8) in concordance with the principal coordinate analysis (PCoA). The following genetically distant inbred lines were selected, displaying good agronomic performance and Sa and Sh resistance: CML540, TZISTR25, TZISTR1248, CLHP0303, TZISTR1174, TZSTRI113, TZDEEI50, TZSTRI115, CML539, TZISTR1015, CZL99017, CML451, CML566, CLHP0343 and CML440. Genetically diverse and complementary lines were selected among the tropical and sub-tropical maize populations that will facilitate the breeding of maize varieties with Striga resistance and market-preferred traits.

Identification of candidate gene associated with maize northern leaf blight resistance in a multi-parent population

Key messageQTL mapping combined with genome-wide association studies, revealed a potential candidate gene for resistance to northern leaf blight in the tropical CATETO-related maize line YML226, providing a basis for marker-assisted selection of maize varietiesNorthern leaf blight (NLB) is a foliar disease that can cause severe yield losses in maize. Identifying and utilizing NLB-resistant genes is the most effective way to prevent and control this disease. In this study, five important inbred lines of maize were used as parental lines to construct a multi-parent population for the identification of NLB-resistant loci. QTL mapping and GWAS analysis revealed that QTL qtl_YML226_1, which had the largest phenotypic variance explanation (PVE) of 9.28%, and SNP 5-49,193,921 were co-located in the CATETO-related line YML226. This locus was associated with the candidate gene Zm00001d014471, which encodes a pentatricopeptide repeat (PPR) protein. In the coding region of Zm00001d014471, YML226 had more specific SNPs than the other parental lines. qRT-PCR showed that the relative expressions of Zm00001d014471 in inoculated and uninoculated leaves of YML226 were significantly higher, indicating that the expression of the candidate gene was correlated with NLB resistance. The analysis showed that the higher expression level in YML226 might be caused by SNP mutations. This study identified NLB resistance candidate loci and genes in the tropical maize inbred line YML226 derived from the CATETO germplasm, thereby providing a theoretical basis for using modern marker-assisted breeding techniques to select genetic resources resistant to NLB.

Simultaneous selection of several tropical maize hybrids under acidic soil conditions

Abstract Acidic soils present a major abiotic challenge for various crops, including maize. Such an environment may cause nutrient unavailability, leading to poor growth and yield. Selection using multiple traits enables breeders to select maize hybrids that appeal to preference. This research aimed to obtain information on the genetic variability and predict the selection response of tropical maize hybrids based on multiple traits. Fifty-two maize hybrids, including six checks, were evaluated under acidic soils using an augmented RCBD with three blocks for the check varieties. The results showed that the genotypes significantly affected several agronomic traits and yield. Moderate to high e heritability was found for most traits. The greatest positive direct effect on yield was demonstrated by ear diameter, stay-green, and shelling percentage. G13, G14, G49, G50, G35, G39, G09, and G51 were selected maize hybrids using the MGIDI method. Selection using multiple traits is expected to have selection precision while considering its strengths and weaknesses. The selected genotypes may be subjected to a multi-environment trial to understand the influence of genotype by environment interaction.

Low pH adaptation of tropical exotic acid tolerance yellow maize donor lines in sub-tropical breeding programs

Soil acidity is one of the most important constraints to maize production in Angola, where both yellow and white maize is essential for food and feed requirements. In this study, four yellow acid soil tolerant donor lines from the International Maize and Wheat Improvement Centre (CIMMYT)—Colombia were crossed with ten yellow elite lines adapted to the mid-altitude climatic conditions developed by CIMMYT—Zimbabwe, in order to identify donor lines, which can be potential sources of acid tolerance genes in breeding programs in Angola and within the mid-altitude climatic zones. The two groups of parents were crossed using a line by tester mating design, yielding 36 crosses with sufficient seed, which were evaluated alongside six acid tolerant commercial hybrids, during the 2014–16 cropping seasons at nine sites, representing acid and non-acid soils in Angola and Zimbabwe. A significant (p < 0.05) line and line × tester effect for grain yield performance was observed across acid and non-acid conditions. Acid tolerance donor lines CY3 and CY1 showed the highest positive GCA effects for grain yield. In addition, crosses involving these two donor lines had the best yielding ability and stability under both acid and non-acid conditions. For instance, the crosses CH142464 (ZY2 × CY3) and, CH142447 (ZY2 × CY1) were the best combinations for grain yield performance under both acid and non-acid soil conditions, and were stable compared to the commercial check hybrids. Crosses involving the acid tolerant donor lines mostly flowered earlier than the commercial checks. Overall, the data showed the potential of tropically-adapted exotic yellow maize acid tolerance donor lines in improving productivity of sub-tropical maize under both low-pH and well-managed soil conditions.

Combining ability and heterosis of tropical maize under acidic soil conditions

Combining ability and heterosis of tropical maize under acidic soil conditions

Dissection of Common Rust Resistance in Tropical Maize Multiparent Population through GWAS and Linkage Studies.

Common rust (CR), caused by Puccina sorghi, is a major foliar disease in maize that leads to quality deterioration and yield losses. To dissect the genetic architecture of CR resistance in maize, this study utilized the susceptible temperate inbred line Ye107 as the male parent crossed with three resistant tropical maize inbred lines (CML312, D39, and Y32) to generate 627 F7 recombinant inbred lines (RILs), with the aim of identifying maize disease-resistant loci and candidate genes for common rust. Phenotypic data showed good segregation between resistance and susceptibility, with varying degrees of resistance observed across different subpopulations. Significant genotype effects and genotype × environment interactions were observed, with heritability ranging from 85.7% to 92.2%. Linkage and genome-wide association analyses across the three environments identified 20 QTLs and 62 significant SNPs. Among these, seven major QTLs explained 66% of the phenotypic variance. Comparison with six SNPs repeatedly identified across different environments revealed overlap between qRUST3-3 and Snp-203,116,453, and Snp-204,202,469. Haplotype analysis indicated two different haplotypes for CR resistance for both the SNPs. Based on LD decay plots, three co-located candidate genes, Zm00001d043536, Zm00001d043566, and Zm00001d043569, were identified within 20 kb upstream and downstream of these two SNPs. Zm00001d043536 regulates hormone regulation, Zm00001d043566 controls stomatal opening and closure, related to trichome, and Zm00001d043569 is associated with plant disease immune responses. Additionally, we performed candidate gene screening for five additional SNPs that were repeatedly detected across different environments, resulting in the identification of five candidate genes. These findings contribute to the development of genetic resources for common rust resistance in maize breeding programs.

Genomic loci associated with grain yield under well-watered and water-stressed conditions in multiple bi-parental maize populations

Smallholder maize farming systems in sub-Saharan Africa (SSA) are vulnerable to drought-induced yield losses, which significantly impact food security and livelihoods within these communities. Mapping and characterizing genomic regions associated with water stress tolerance in tropical maize is essential for future breeding initiatives targeting this region. In this study, three biparental F3 populations composed of 753 families were evaluated in Kenya and Zimbabwe and genotyped with high-density single nucleotide polymorphism (SNP) markers. Quantitative trait loci maping was performed on these genotypes to dissect the genetic architecture for grain yield (GY), plant height (PH), ear height (EH) and anthesis-silking interval (ASI) under well-watered (WW) and water-stressed (WS) conditions. Across the studied maize populations, mean GY exhibited a range of 4.55–8.55 t/ha under WW and 1.29–5.59 t/ha under WS, reflecting a 31–59% reduction range under WS conditions. Genotypic and genotype-by-environment (G × E) variances were significant for all traits except ASI. Overall broad sense heritabilities for GY were low to high (0.25–0.60). For GY, these genetic parameters were decreased under WS conditions. Linkage mapping revealed a significant difference in the number of QTLs detected, with 93 identified under WW conditions and 41 under WS conditions. These QTLs were distributed across all maize chromosomes. For GY, eight and two major effect QTLs (&amp;gt;10% phenotypic variation explained) were detected under WW and WS conditions, respectively. Under WS conditions, Joint Linkage Association Mapping (JLAM) identified several QTLs with minor effects for GY and revealed genomic region overlaps in the studied populations. Across the studied water regimes, five-fold cross-validation showed moderate to high prediction accuracies (−0.15–0.90) for GY and other agronomic traits. Our findings demonstrate the polygenic nature of WS tolerance and highlights the immense potential of using genomic selection in improving genetic gain in maize breeding.

Growth and yield of tropical maize landraces and commercial genotypes in Yucatan, Mexico

The state of Yucatan, known for its shallow Leptosol soils poses challenges to agriculture. Therefore, this study focused on examining ecophysiological attributes influencing the growth and yield determinants of six maize genotypes. The study assessed vegetative characteristics, growth rates, dry matter allocation, grain yield, and harvest index. All maize genotypes exhibited early maturity, a favorable trait under the climate conditions of Yucatan. Most genotypes exhibited superior growth rate and dry matter content when compared to the landrace Elotillo. Stem and grain were identified as the primary organs for dry matter accumulation, with 36% and 22% respectively. The highest grain yield was noted in hybrids Impacto and DK-390. This study provided valuable information for farmers in selecting suitable maize genotypes in Yucatan, although additional evaluations of different genotypes and management conditions are recommended.

Exploiting genomic tools for genetic dissection and improving the resistance to Fusarium stalk rot in tropical maize.

A stable genomic region conferring FSR resistance at ~250 Mb on chromosome 1 was identified by GWAS. Genomic prediction has the potential to improve FSR resistance. Fusarium stalk rot (FSR) is a global destructive disease in maize; the efficiency of phenotypic selection for improving FSR resistance was low. Novel genomic tools of genome-wide association study (GWAS) and genomic prediction (GP) provide an opportunity for genetic dissection and improving FSR resistance. In this study, GWAS and GP analyses were performed on 562 tropical maize inbred lines consisting of two populations. In total, 15 SNPs significantly associated with FSR resistance were identified across two populations and the combinedPOP consisting of all 562 inbred lines, with the P-values ranging from 1.99 × 10-7 to 8.27 × 10-13, and the phenotypic variance explained (PVE) values ranging from 0.94 to 8.30%. The genetic effects of the 15 favorable alleles ranged from -4.29 to -14.21% of the FSR severity. One stable genomic region at ~ 250Mb on chromosome 1 was detected across all populations, and the PVE values of the SNPs detected in this region ranged from 2.16 to 5.18%. Prediction accuracies of FSR severity estimated with the genome-wide SNPs were moderate and ranged from 0.29 to 0.51. By incorporating genotype-by-environment interaction, prediction accuracies were improved between 0.36 and 0.55 in different breeding scenarios. Considering both the genome coverage and the threshold of the P-value of SNPs to select a subset of molecular markers further improved the prediction accuracies. These findings extend the knowledge of exploiting genomic tools for genetic dissection and improving FSR resistance in tropical maize.