Genome-wide association analysis for fumonisin content in maize kernels

Samayoa, Luis Fernando; Cao, Ana Rey; Santiago, Rogelio; Malvar, R. A.; Butrón, Ana

doi:10.1186/s12870-019-1759-1

Cited by 26 publications

(25 citation statements)

References 82 publications

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“…The plant material was obtained from the North Central Regional Plant Introduction Station from Iowa State University following the seeds import law applicable for Spain. The list of inbred lines used in this study along with their accession identifications at the North Central Regional Plant Introduction Station (NCRPIS) is available as additional file in Samayoa et al [59].…”

Section: Methodsmentioning

confidence: 99%

Genome-wide association analysis for maize stem Cell Wall-bound Hydroxycinnamates

et al. 2019

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BackgroundThe structural reinforcement of cell walls by hydroxycinnamates has a significant role in defense against pests and pathogens, but it also interferes with forage digestibility and biofuel production. Elucidation of maize genetic variations that contribute to variation for stem hydroxycinnamate content could simplify breeding for cell wall strengthening by using markers linked to the most favorable genetic variants in marker-assisted selection or genomic selection approaches.ResultsA genome-wide association study was conducted using a subset of 282 inbred lines from a maize diversity panel to identify single nucleotide polymorphisms (SNPs) associated with stem cell wall hydroxycinnamate content. A total of 5, 8, and 2 SNPs were identified as significantly associated to p-coumarate, ferulate, and total diferulate concentrations, respectively in the maize pith. Attending to particular diferulate isomers, 3, 6, 1 and 2 SNPs were related to 8–O–4 diferulate, 5–5 diferulate, 8–5 diferulate and 8–5 linear diferulate contents, respectively. This study has the advantage of being done with direct biochemical determinations instead of using estimates based on Near-infrared spectroscopy (NIRS) predictions. In addition, novel genomic regions involved in hydroxycinnamate content were found, such as those in bins 1.06 (for FA), 4.01 (for PCA and FA), 5.04 (for FA), 8.05 (for PCA), and 10.03 and 3.06 (for DFAT and some dimers).ConclusionsThe effect of individual SNPs significantly associated with stem hydroxycinnamate content was low, explaining a low percentage of total phenotypic variability (7 to 10%). Nevertheless, we spotlighted new genomic regions associated with the accumulation of cell-wall-bound hydroxycinnamic acids in the maize stem, and genes involved in cell wall modulation in response to biotic and abiotic stresses have been proposed as candidate genes for those quantitative trait loci (QTL). In addition, we cannot rule out that uncharacterized genes linked to significant SNPs could be implicated in dimer formation and arobinoxylan feruloylation because genes involved in those processes have been poorly characterized. Overall, genomic selection considering markers distributed throughout the whole genome seems to be a more appropriate breeding strategy than marker-assisted selection focused in markers linked to QTL.

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Section: Methodsmentioning

confidence: 99%

Genome-wide association analysis for maize stem Cell Wall-bound Hydroxycinnamates

et al. 2019

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“…So far, there is just one GWAS on resistance to fumonisin accumulation, which has confirmed that highly significant genotype × environment interaction as well as genetic variation for many genes with small effects would contribute to the high complexity of the inheritance of maize resistance to kernel contamination [ 69 ]. In the inbred panel of approximately 250 entries, 39 SNPs, clustered into 17 QTL, were significantly associated with resistance to fumonisin accumulation in maize kernels.…”

Section: Genome-wide Association Studies For Fer and Fumonisin Conmentioning

confidence: 99%

Genomics of Maize Resistance to Fusarium Ear Rot and Fumonisin Contamination

Santiago

Cao

Malvar

et al. 2020

Toxins

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Food contamination with mycotoxins is a worldwide concern, because these toxins produced by several fungal species have detrimental effects on animal and/or human health. In maize, fumonisins are among the toxins with the highest threatening potential because they are mainly produced by Fusarium verticillioides, which is distributed worldwide. Plant breeding has emerged as an effective and environmentally safe method to reduce fumonisin levels in maize kernels, but although phenotypic selection has proved effective for improving resistance to fumonisin contamination, further resources should be mobilized to meet farmers’ needs. Selection based on molecular markers linked to quantitative trait loci (QTL) for resistance to fumonisin contamination or/and genotype values obtained using prediction models with markers distributed across the whole genome could speed up breeding progress. Therefore, in the current paper, previously identified genomic regions, genes, and/or pathways implicated in resistance to fumonisin accumulation will be reviewed. Studies done until now have provide many markers to be used by breeders, but to get further insight on plant mechanisms to defend against fungal infection and to limit fumonisin contamination, the genes behind those QTLs should be identified.

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“…Moreover, in order to develop genetically resistant germplasm to Fusarium researchers carried out Quantitative Trait Locus (QTL) mapping analysis and GWAS by testing several distinct population structures (McMullen et al 2009;Yang et al 2010;Zila et al 2013Zila et al , 2014Warburton et al 2013;Chen et al 2016;Ju et al 2017;Maschietto et al 2017;Gaikpa and Miedaner 2019;Samayoa et al 2019;Septiani et al 2019).…”

Section: Introductionmentioning

confidence: 99%

A Genome-Wide Association Study To Understand the Effect of Fusarium verticillioides Infection on Seedlings of a Maize Diversity Panel

Stagnati

Rahjoo

Samayoa

et al. 2020

G3 Genes|Genomes|Genetics

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Fusarium verticillioides, which causes ear, kernel and stem rots, has been reported as the most prevalent species on maize worldwide. Kernel infection by F. verticillioides results in reduced seed yield and quality as well as fumonisin contamination, and may affect seedling traits like germination rate, entire plant seedling length and weight. Maize resistance to Fusarium is a quantitative and complex trait controlled by numerous genes with small effects. In the present work, a Genome Wide Association Study (GWAS) of traits related to Fusarium seedling rot was carried out in 230 lines of a maize association population using 226,446 SNP markers. Phenotypes were scored on artificially infected kernels applying the rolled towel assay screening method and three traits related to disease response were measured in inoculated and not-inoculated seedlings: plant seedling length (PL), plant seedling weight (PW) and germination rate (GERM). Overall, GWAS resulted in 42 SNPs significantly associated with the examined traits. Two and eleven SNPs were associated with PL in inoculated and not-inoculated samples, respectively. Additionally, six and one SNPs were associated with PW and GERM traits in not-inoculated kernels, and further nine and thirteen SNPs were associated to the same traits in inoculated kernels. Five genes containing the significant SNPs or physically closed to them were proposed for Fusarium resistance, and 18 out of 25 genes containing or adjacent to significant SNPs identified by GWAS in the current research co-localized within QTL regions previously reported for resistance to Fusarium seed rot, Fusarium ear rot and fumonisin accumulation. Furthermore, linkage disequilibrium analysis revealed an additional gene not directly observed by GWAS analysis. These findings could aid to better understand the complex interaction between maize and F. verticillioides.

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Genome-wide association analysis for fumonisin content in maize kernels

Cited by 26 publications

References 82 publications

Genome-wide association analysis for maize stem Cell Wall-bound Hydroxycinnamates

Genome-wide association analysis for maize stem Cell Wall-bound Hydroxycinnamates

Genomics of Maize Resistance to Fusarium Ear Rot and Fumonisin Contamination

A Genome-Wide Association Study To Understand the Effect of Fusarium verticillioides Infection on Seedlings of a Maize Diversity Panel

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