Publications by authors named "Luis Fernando Samayoa"

8 Publications

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Genome-wide association analysis of the strength of the MAMP-elicited defense response and resistance to target leaf spot in sorghum.

Sci Rep 2020 11 30;10(1):20817. Epub 2020 Nov 30.

Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695-7613, USA.

Plants have the capacity to respond to conserved molecular features known as microbe-associated molecular patterns (MAMPs). The goal of this work was to assess variation in the MAMP response in sorghum, to map loci associated with this variation, and to investigate possible connections with variation in quantitative disease resistance. Using an assay that measures the production of reactive oxygen species, we assessed variation in the MAMP response in a sorghum association mapping population known as the sorghum conversion population (SCP). We identified consistent variation for the response to chitin and flg22-an epitope of flagellin. We identified two SNP loci associated with variation in the flg22 response and one with the chitin response. We also assessed resistance to Target Leaf Spot (TLS) disease caused by the necrotrophic fungus Bipolaris cookei in the SCP. We identified one strong association on chromosome 5 near a previously characterized disease resistance gene. A moderately significant correlation was observed between stronger flg22 response and lower TLS resistance. Possible reasons for this are discussed.
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http://dx.doi.org/10.1038/s41598-020-77684-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7704633PMC
November 2020

The genetic architecture of the maize progenitor, teosinte, and how it was altered during maize domestication.

PLoS Genet 2020 05 14;16(5):e1008791. Epub 2020 May 14.

Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.

The genetics of domestication has been extensively studied ever since the rediscovery of Mendel's law of inheritance and much has been learned about the genetic control of trait differences between crops and their ancestors. Here, we ask how domestication has altered genetic architecture by comparing the genetic architecture of 18 domestication traits in maize and its ancestor teosinte using matched populations. We observed a strongly reduced number of QTL for domestication traits in maize relative to teosinte, which is consistent with the previously reported depletion of additive variance by selection during domestication. We also observed more dominance in maize than teosinte, likely a consequence of selective removal of additive variants. We observed that large effect QTL have low minor allele frequency (MAF) in both maize and teosinte. Regions of the genome that are strongly differentiated between teosinte and maize (high FST) explain less quantitative variation in maize than teosinte, suggesting that, in these regions, allelic variants were brought to (or near) fixation during domestication. We also observed that genomic regions of high recombination explain a disproportionately large proportion of heritable variance both before and after domestication. Finally, we observed that about 75% of the additive variance in both teosinte and maize is "missing" in the sense that it cannot be ascribed to detectable QTL and only 25% of variance maps to specific QTL. This latter result suggests that morphological evolution during domestication is largely attributable to very large numbers of QTL of very small effect.
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http://dx.doi.org/10.1371/journal.pgen.1008791DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7266358PMC
May 2020

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

BMC Plant Biol 2019 Oct 17;19(1):431. Epub 2019 Oct 17.

Misión Biológica de Galicia, Spanish National Research Council (CSIC), Apartado 28, 36080, Pontevedra, Spain.

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

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

Conclusions: We developed a mapping population which allowed a finer dissection of the genetics of maize resistance to corn borers and a solid nomination of candidate genes based on functional information. The population, given its large variability, was also adequate to map multiple traits and study the relationship between them.
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http://dx.doi.org/10.1186/s12870-019-2052-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6796440PMC
October 2019

The genetic architecture of teosinte catalyzed and constrained maize domestication.

Proc Natl Acad Sci U S A 2019 03 6;116(12):5643-5652. Epub 2019 Mar 6.

Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706;

The process of evolution under domestication has been studied using phylogenetics, population genetics-genomics, quantitative trait locus (QTL) mapping, gene expression assays, and archaeology. Here, we apply an evolutionary quantitative genetic approach to understand the constraints imposed by the genetic architecture of trait variation in teosinte, the wild ancestor of maize, and the consequences of domestication on genetic architecture. Using modern teosinte and maize landrace populations as proxies for the ancestor and domesticate, respectively, we estimated heritabilities, additive and dominance genetic variances, genetic-by-environment variances, genetic correlations, and genetic covariances for 18 domestication-related traits using realized genomic relationships estimated from genome-wide markers. We found a reduction in heritabilities across most traits, and the reduction is stronger in reproductive traits (size and numbers of grains and ears) than vegetative traits. We observed larger depletion in additive genetic variance than dominance genetic variance. Selection intensities during domestication were weak for all traits, with reproductive traits showing the highest values. For 17 of 18 traits, neutral divergence is rejected, suggesting they were targets of selection during domestication. Yield (total grain weight) per plant is the sole trait that selection does not appear to have improved in maize relative to teosinte. From a multivariate evolution perspective, we identified a strong, nonneutral divergence between teosinte and maize landrace genetic variance-covariance matrices (G-matrices). While the structure of G-matrix in teosinte posed considerable genetic constraint on early domestication, the maize landrace G-matrix indicates that the degree of constraint is more unfavorable for further evolution along the same trajectory.
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http://dx.doi.org/10.1073/pnas.1820997116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6431195PMC
March 2019

Modifications to a LATE MERISTEM IDENTITY1 gene are responsible for the major leaf shapes of Upland cotton (Gossypium hirsutum L.).

Proc Natl Acad Sci U S A 2017 01 20;114(1):E57-E66. Epub 2016 Dec 20.

Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695-7620;

Leaf shape varies spectacularly among plants. Leaves are the primary source of photoassimilate in crop plants, and understanding the genetic basis of variation in leaf morphology is critical to improving agricultural productivity. Leaf shape played a unique role in cotton improvement, as breeders have selected for entire and lobed leaf morphs resulting from a single locus, okra (l-D), which is responsible for the major leaf shapes in cotton. The l-D locus is not only of agricultural importance in cotton, but through pioneering chimeric and morphometric studies, it has contributed to fundamental knowledge about leaf development. Here we show that an HD-Zip transcription factor homologous to the LATE MERISTEM IDENTITY1 (LMI1) gene of Arabidopsis is the causal gene underlying the l-D locus. The classical okra leaf shape allele has a 133-bp tandem duplication in the promoter, correlated with elevated expression, whereas an 8-bp deletion in the third exon of the presumed wild-type normal allele causes a frame-shifted and truncated coding sequence. Our results indicate that subokra is the ancestral leaf shape of tetraploid cotton that gave rise to the okra allele and that normal is a derived mutant allele that came to predominate and define the leaf shape of cultivated cotton. Virus-induced gene silencing (VIGS) of the LMI1-like gene in an okra variety was sufficient to induce normal leaf formation. The developmental changes in leaves conferred by this gene are associated with a photosynthetic transcriptomic signature, substantiating its use by breeders to produce a superior cotton ideotype.
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http://dx.doi.org/10.1073/pnas.1613593114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5224360PMC
January 2017

Hydroxycinnamate Synthesis and Association with Mediterranean Corn Borer Resistance.

J Agric Food Chem 2016 Jan 12;64(3):539-51. Epub 2016 Jan 12.

Misión Biológica de Galicia (CSIC) , Apartado 28, 36080 Pontevedra, Spain.

Previous results suggest a relationship between maize hydroxycinnamate concentration in the pith tissues and resistance to stem tunneling by Mediterranean corn borer (MCB, Sesamia nonagrioides Lef.) larvae. This study performs a more precise experiment, mapping an F2 derived from the cross between two inbreds with contrasting levels for hydroxycinnamates EP125 × PB130. We aimed to co-localize genomic regions involved in hydroxycinnamate synthesis and resistance to MCB and to highlight the particular route for each hydroxycinnamate component in relation to the better known phenylpropanoid pathway. Seven quantitative trait loci (QTLs) for p-coumarate, two QTLs for ferulate, and seven QTLs for total diferulates explained 81.7, 26.9, and 57.8% of the genotypic variance, respectively. In relation to borer resistance, alleles for increased hydroxycinnamate content (affecting one or more hydroxycinnamate compounds) could be associated with favorable effects on stem resistance to MCB, particularly the putative role of p-coumarate in borer resistance.
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http://dx.doi.org/10.1021/acs.jafc.5b04862DOI Listing
January 2016

Identification of QTL for resistance to Mediterranean corn borer in a maize tropical line to improve temperate germplasm.

BMC Plant Biol 2015 Nov 4;15:265. Epub 2015 Nov 4.

Misión Biológica de Galicia, Spanish National Research Council (CSIC), P.O. Box 28, 36080, Pontevedra, Spain.

Background: A QTL mapping study for maize resistance to the Mediterranean corn borer (MCB) was performed with a RIL population derived from the cross B73 × CML103. To develop commercial inbreds of maize resistant to the MCB for use in Europe, it would be useful to transfer resistance from tropical germplasm like the subtropical inbred CML103 to temperate lines. The inbred B73 was chosen as representative of the Stiff Stock heterotic group, a major heterotic group used in hybrid grown in both North American and Europe. The objectives were to study the architecture of genetic factors for resistance to MCB and to check the feasibility of using marker-assisted selection (MAS) for transferring those genetic factors.

Results: Eight quantitative trait loci (QTL) were declared significant for resistance traits and eight QTL were located for agronomic traits. Alleles from CML103 at QTL significant for tunnel length could reduce tunnel length made for MCB in inbred B73 in more than 8 cm; favorable alleles for yield were also found in CML103 and no genetic correlation coefficient between tunnel length and yield was detected.

Conclusions: MAS for transferring resistance genes to corn borer attack from CML103 to B73 could be successful based on cross validation results and a negative effect on yield would not be expected.
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http://dx.doi.org/10.1186/s12870-015-0652-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4632334PMC
November 2015

Genome-wide association study reveals a set of genes associated with resistance to the Mediterranean corn borer (Sesamia nonagrioides L.) in a maize diversity panel.

BMC Plant Biol 2015 Feb 5;15:35. Epub 2015 Feb 5.

Misión Biológica de Galicia, Spanish National Research Council (CSIC), P.O. Box 28, 36080, Pontevedra, Spain.

Background: Corn borers are the primary maize pest; their feeding on the pith results in stem damage and yield losses. In this study, we performed a genome-wide association study (GWAS) to identify SNPs associated with resistance to Mediterranean corn borer in a maize diversity panel using a set of more than 240,000 SNPs.

Results: Twenty five SNPs were significantly associated with three resistance traits: 10 were significantly associated with tunnel length, 4 with stem damage, and 11 with kernel resistance. Allelic variation at each significant SNP was associated with from 6 to 9% of the phenotypic variance. A set of genes containing or physically close to these SNPs are proposed as candidate genes for borer resistance, supported by their involvement in plant defense-related mechanisms in previously published evidence. The linkage disequilibrium decayed (r(2) < 0.10) rapidly within short distance, suggesting high resolution of GWAS associations.

Conclusions: Most of the candidate genes found in this study are part of signaling pathways, others act as regulator of expression under biotic stress condition, and a few genes are encoding enzymes with antibiotic effect against insects such as the cystatin1 gene and the defensin proteins. These findings contribute to the understanding the complex relationship between plant-insect interactions.
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http://dx.doi.org/10.1186/s12870-014-0403-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4340109PMC
February 2015