A genome-wide association study investigating fumonisin contamination in a panel of tropical maize elite lines

Silva, Karla Jorge da; Guimarães, C. T.; Sousa, Sylvia Morais de; Bernardino, K. da C.; Trindade, R. dos S.; Queiroz, Valéria Aparecida Vieira; Conceição, R. R. P. da; Guilhen, José Henrique Soler; Oliveira, Natanael Tavares de; Damasceno, C. M. B.; Noda, R. W.; Dias, Luíz Antônio dos Santos; Guimarães, L. J. M.; Melo, Janaína de Oliveira; Pastina, Maria Marta

doi:10.1007/s10681-022-03082-0

Cited by 5 publications

(4 citation statements)

References 58 publications

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“…Fifteen publications were SNP-based QTL mapping studies which were used to collect relevant information required for the QTL meta-analysis ( Supplementary File 2 ) ( Chen et al., 2016 ; Giomi et al., 2016 ; Han et al., 2016 ; Kebede et al., 2016 ; Maschietto et al., 2017 ; Han et al., 2018 ; Galić et al., 2019 ; Wen et al., 2020 ; Yuan et al., 2020a ; Galiano-Carneiro et al., 2021 ; Giomi et al., 2021 ; Wen et al., 2021b ; Zhou et al., 2021 ; Feng et al., 2022 ; Guo et al., 2022 ). Seven papers were related to genome-wide association study and used to cross-validate the meta-analysis ( Butrón et al., 2019 ; Samayoa et al., 2019 ; Wu et al., 2020 ; Gaikpa et al., 2021 ; Gesteiro et al., 2021 ; Liu et al., 2021 ; da Silva et al., 2022 ).…”

Section: Resultsmentioning

confidence: 99%

Meta-analysis and co-expression analysis revealed stable QTL and candidate genes conferring resistances to Fusarium and Gibberella ear rots while reducing mycotoxin contamination in maize

Akohoue

Miedaner

2022

Front. Plant Sci.

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Fusarium (FER) and Gibberella ear rots (GER) are the two most devastating diseases of maize (Zea mays L.) which reduce yield and affect grain quality worldwide, especially by contamination with mycotoxins. Genetic improvement of host resistance to effectively tackle FER and GER diseases requires the identification of stable quantitative trait loci (QTL) to facilitate the application of genomics-assisted breeding for improving selection efficiency in breeding programs. We applied improved meta-analysis algorithms to re-analyze 224 QTL identified in 15 studies based on dense genome-wide single nucleotide polymorphisms (SNP) in order to identify meta-QTL (MQTL) and colocalized genomic loci for fumonisin (FUM) and deoxynivalenol (DON) accumulation, silk (SR) and kernel (KR) resistances of both FER and GER, kernel dry-down rate (KDD) and husk coverage (HC). A high-resolution genetic consensus map with 36,243 loci was constructed and enabled the projection of 164 of the 224 collected QTL. Candidate genes (CG) mining was performed within the most refined MQTL, and identified CG were cross-validated using publicly available transcriptomic data of maize under Fusarium graminearum infection. The meta-analysis revealed 40 MQTL, of which 29 were associated each with 2-5 FER- and/or GER-related traits. Twenty-eight of the 40 MQTL were common to both FER and GER resistances and 19 MQTL were common to silk and kernel resistances. Fourteen most refined MQTL on chromosomes 1, 2, 3, 4, 7 and 9 harbored a total of 2,272 CG. Cross-validation identified 59 of these CG as responsive to FER and/or GER diseases. MQTL ZmMQTL2.2, ZmMQTL9.2 and ZmMQTL9.4 harbored promising resistance genes, of which GRMZM2G011151 and GRMZM2G093092 were specific to the resistant line for both diseases and encoded “terpene synthase21 (tps21)” and “flavonoid O-methyltransferase2 (fomt2)”, respectively. Our findings revealed stable refined MQTL harboring promising candidate genes for use in breeding programs for improving FER and GER resistances with reduced mycotoxin accumulation. These candidate genes can be transferred into elite cultivars by integrating refined MQTL into genomics-assisted backcross breeding strategies.

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Section: Resultsmentioning

confidence: 99%

Meta-analysis and co-expression analysis revealed stable QTL and candidate genes conferring resistances to Fusarium and Gibberella ear rots while reducing mycotoxin contamination in maize

Akohoue

Miedaner

2022

Front. Plant Sci.

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“…Different phenotypic responses of maize ( Zea mays L.) genotypes to distinct environments is a challenging task for cultivar recommendations in tropical and temperate environments. In fact, tropical environments are more prone to outbreaks of pests and diseases and exhibit major environmental differences between locations, years and seasons within years (Paterniani, 1990; Silva et al., 2022; Sandhu & Dhillon, 2021). Differential genotypic responses to these geographical and temporal variations comprise genotype‐by‐environment interaction (GEI), which can hinder effective cultivar recommendation (Crossa, 2012; Malosetti et al., 2013; van Eeuwijk et al., 2016).…”

Section: Introductionmentioning

confidence: 99%

Employing factor analytic tools for selecting high‐performance and stable tropical maize hybrids

et al. 2023

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Genotype‐by‐environment interaction (GEI) is a major concern in tropical maize breeding. Here, we used factor analytic mixed models (FAMM) to study GEI in a tropical maize dataset. Our goal was to select high‐performance and stable hybrids using factor analytic selection tools (FAST) derived from FAMM outputs. Because the dataset comprised two different planting seasons, we also investigated differences in the genetic gains between seasonal and general selection (i.e., for both seasons simultaneously). The trials were installed in a lattice design with 36 hybrids containing two replicates and blocks with six plants each. We evaluated 53 hybrids and seven checks in 48 environments, represented by a combination of locations, years and seasons. We fitted the FAMMs with distinct sets of factors. The best‐fitted FAMM was selected considering a parsimony‐explained variance balance. Using the best FAMM for both seasonal and general analyses, we estimated the following selection tools: overall performance (OP$\textit{OP}$); root mean square deviation (RMSD$\textit{RMSD}$), which represents general stability; and responsiveness , which represents specific stability. We selected hybrids based on an index built with OP$\textit{OP}$ and RMSD$\textit{RMSD}$. Five and three hybrids were selected considering both general and seasonal analyses for the first and second season, respectively. Two hybrids were amongst the top eight for both seasonal analyses (i.e., only first season and only second season simultaenously). Higher genetic gains may be obtained by employing FAMM and using FAST in each season rather than analysing both seasons in a joint fashion.

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“…Transcriptome analysis is a valuable tool in investigating the molecular mechanisms behind cereal resistance to fungal infections as the costs of this technique decrease and its applications become more widespread. For instance, RNA profiling of barley spikes showed that multiple defense mechanisms were activated in response to DON treatment as demonstrated by significant upregulation of gene transcripts encoding ABC transporters, UGT, cytochrome P450s, and glutathione-S-transferases [ 17 ]. In wheat, microarray analysis of spikelets from wheat near-isogenic lines revealed that the increased accumulation in gene transcripts encoding expansins and proline-rich proteins in the resistant cultivar resulted in cell wall modification, suggesting cell wall fortification may play a role in protecting the resistant cultivar [ 18 ].…”

Section: Introductionmentioning

confidence: 99%

Comparative transcriptomic analysis of wheat cultivars differing in their resistance to Fusarium head blight infection during grain-filling stages reveals unique defense mechanisms at play

Chen,

Guo,

et al. 2023

BMC Plant Biol

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Fusarium head blight (FHB) is a devastating fungal disease that poses a significant threat to wheat production, causing substantial yield losses. Understanding the molecular mechanisms of wheat resistance to FHB is crucial for developing effective disease management strategies. This study aimed to investigate the mechanisms of FHB resistance and the patterns of toxin accumulation in three wheat cultivars, Annong8455, Annong1589, and Sumai3, with different levels of resistance, ranging from low to high respectively, under natural field conditions. Samples were taken at three different grain-filling stages (5, 10, and 15 DPA) for gene expression analysis and phenotypic observation. Results found that toxin concentration was inversely correlated with varietal resistance but not correlated with disease phenotypes, indicating that toxin analysis is a more accurate measure of disease status in wheat ears and grains. Transcriptomic data showed that Sumai3 exhibited a stronger immune response during all stages of grain filling by upregulating genes involved in the active destruction of pathogens and removal of toxins. In contrast, Annong1589 showed a passive prevention of the spread of toxins into cells by the upregulation of genes involved in tyramine biosynthesis at the early stage (5 DPA), which may be involved in cell wall strengthening. Our study demonstrates the complexity of FHB resistance in wheat, with cultivars exhibiting unique and overlapping defense mechanisms, and highlights the importance of considering the temporal and spatial dynamics of gene expression in breeding programs for developing more resistant wheat cultivars.

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A genome-wide association study investigating fumonisin contamination in a panel of tropical maize elite lines

Cited by 5 publications

References 58 publications

Meta-analysis and co-expression analysis revealed stable QTL and candidate genes conferring resistances to Fusarium and Gibberella ear rots while reducing mycotoxin contamination in maize

Meta-analysis and co-expression analysis revealed stable QTL and candidate genes conferring resistances to Fusarium and Gibberella ear rots while reducing mycotoxin contamination in maize

Employing factor analytic tools for selecting high‐performance and stable tropical maize hybrids

Comparative transcriptomic analysis of wheat cultivars differing in their resistance to Fusarium head blight infection during grain-filling stages reveals unique defense mechanisms at play

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