scholarly journals Mapping of resistance to corn borers in a MAGIC population of maize

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
José Cruz Jiménez-Galindo ◽  
Rosa Ana Malvar ◽  
Ana Butrón ◽  
Rogelio Santiago ◽  
Luis Fernando Samayoa ◽  
...  
Keyword(s):  
Agronomic Traits ◽  
Sesamia Nonagrioides ◽  
Nucleotide Polymorphisms ◽  
Genetic Determinants ◽  
Multiple Traits ◽  
Corn Borer ◽  
Large Variability ◽  
Corn Borers ◽  
Important Pest ◽  
Magic Population

Abstract 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.

scholarly journals Relationships between Stalk Resistance and Corn Borers, Agronomic Traits, and Cell Wall Hydroxycinnamates in a Set of Recombinant Inbred Lines from a Maize MAGIC Population

Agronomy ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1132
Author(s):  
Ana López-Malvar ◽  
Zoila Reséndiz ◽  
Rogelio Santiago ◽  
José Cruz Jiménez-Galindo ◽  
Rosa Ana Malvar
Keyword(s):  
Cell Wall ◽  
Recombinant Inbred ◽  
Agronomic Traits ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Corn Borer ◽  
Corn Borers ◽  
Grain Moisture ◽  
Resistant Lines ◽  
Magic Population

Corn borers are the most important pest affecting maize. Resistance to corn borer attack may compromise plant fitness being detrimental for some important agronomic traits such as yield. Against the attack of this pest, cell wall-bound hydroxycinnamates have been previously described as a possible defense mechanism. In this study, agronomic characterization and cell wall-bound hydroxycinnamates quantification was performed in a subset of Recombinant Inbred Lines (RILs) from a Multiparent Advanced Generation Intercross (MAGIC) population that showed contrasting behavior against corn borer attack. Resistant lines showed greater concentration of p-coumaric acid, the only hydroxycinnamate that could have a role in the resistance in these particular materials. In addition, results indicated that resistant lines showed precocity, low grain moisture at harvest, and reduced plant height, thus, selecting for resistance may be detrimental for yield. In this way, a breeding strategy directly targeting grain yield in order to tolerate corn borer attack would be the recommended one.

scholarly journals Agronomic performance of maize populations divergently selected for diferulate cross-linkage

2016 ◽  
Vol 154 (7) ◽  
pp. 1270-1279 ◽  
Author(s):  
R. SANTIAGO ◽  
J. BARROS-RIOS ◽  
A. ALVAREZ ◽  
R. A. MALVAR
Keyword(s):  
Cell Wall ◽  
Grain Yield ◽  
Plant Height ◽  
Agronomic Traits ◽  
Divergent Selection ◽  
Flowering Plant ◽  
Corn Borer ◽  
Corn Borers ◽  
Maize Populations ◽  
Grain Moisture

SUMMARYThe direct response of a divergent selection programme for total cell wall ester-linked diferulate concentration in maize pith stalk tissues and its indirect effect on cell wall degradability and corn borer resistance have been previously evaluated. Since increased total diferulate concentration is expected to improve crop performance in response to corn borers, the objective of the present research was to evaluate the indirect response of the divergent selection for diferulates on agronomic traits under corn borer infestation. For this purpose, five maize populations with contrasting total diferulate concentrations were evaluated four environments for performance under protected and infested conditions. Measured traits were: days to anthesis, days to silking, plant height, stalk lodging, grain moisture at harvest and grain yield. High diferulate populations showed a significant reduction in anthesis (precocity), and were 11 cm taller than the starting population, while low diferulate populations were 9 cm shorter, and showed nearly 1 t/ha lower grain yield than the original and high diferulate populations. The analysis showed that cycles of selection were positively correlated with flowering, plant height and grain yield. The infestations with borers produced >1 t/ha of reduction in grain yield; although the higher diferulate populations showed a better performance under infestation than the low diferulate populations. This positive effect on the grain yield by increasing diferulate content can be considered an extra in order to breed for resistance to corn borers.

scholarly journals Role of Sesamia nonagrioides and Ostrinia nubilalis as Vectors of Fusarium spp. and Contribution of Corn Borer-Resistant Bt Maize to Mycotoxin Reduction

Toxins ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 780
Author(s):  
María Arias-Martín ◽  
Miriam Haidukowski ◽  
Gema P. Farinós ◽  
Belén Patiño
Keyword(s):  
Ostrinia Nubilalis ◽  
Fusarium Species ◽  
Animal Health ◽  
Economic Losses ◽  
Sesamia Nonagrioides ◽  
Bt Maize ◽  
Insecticidal Toxin ◽  
Corn Borer ◽  
Corn Borers ◽  
First Time

Maize expressing Cry1Ab insecticidal toxin (Bt maize) is an effective method to control Sesamia nonagrioides and Ostrinia nubilalis, the most damaging corn borers of southern Europe. In this area, maize is prone to Fusarium infections, which can produce mycotoxins that pose a serious risk to human and animal health, causing significant economic losses in the agrifood industry. To investigate the influence of corn borer damage on the presence of Fusarium species and their mycotoxins, Bt maize ears and insect-damaged ears of non-Bt maize were collected from commercial fields in three Bt maize growing areas in Spain, and differences in contamination were assessed. Additionally, larvae of both borer species were collected to evaluate their role as vectors of these molds. Non-Bt maize ears showed significantly higher presence of F. verticillioides, F. proliferatum, and F. subglutinans than Bt maize ears. For the first time, Fusarium species have been isolated from larvae of the two species. The most frequently found mycotoxins in ears were fumonisins, with non-Bt ears being significantly more contaminated than those of Bt maize. High levels of fumonisins were shown to correlate with the occurrence of corn borers in the ear and the presence of F. verticillioides and F. proliferatum.

scholarly journals Genetic Determinants of Neurobehavioral Responses to Caffeine Administration during Sleep Deprivation: A Randomized, Cross Over Study (NCT03859882)

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 555
Author(s):  
Mégane Erblang ◽  
Fabien Sauvet ◽  
Catherine Drogou ◽  
Michaël Quiquempoix ◽  
Pascal Van Beers ◽  
...  
Keyword(s):  
Sleep Deprivation ◽  
Nucleotide Polymorphisms ◽  
Genetic Determinants ◽  
Placebo Condition ◽  
Double Blind ◽  
Single Nucleotide ◽  
Psychomotor Vigilance Test ◽  
Tnf Α ◽  
And Performance ◽  
Psychomotor Vigilance

This study investigated whether four single nucleotide polymorphisms (SNPs) moderated caffeine effects on vigilance and performance in a double-blind and crossover total sleep deprivation (TSD) protocol in 37 subjects. In caffeine (2 × 2.5 mg/kg/24 h) or placebo-controlled condition, subjects performed a psychomotor vigilance test (PVT) and reported sleepiness every six hours (Karolinska sleepiness scale (KSS)) during TSD. EEG was also analyzed during the 09:15 PVT. Carriers of the TNF-α SNP A allele appear to be more sensitive than homozygote G/G genotype to an attenuating effect of caffeine on PVT lapses during sleep deprivation only because they seem more degraded, but they do not perform better as a result. The A allele carriers of COMT were also more degraded and sensitive to caffeine than G/G genotype after 20 h of sleep deprivation, but not after 26 and 32 h. Regarding PVT reaction time, ADORA2A influences the TSD effect but not caffeine, and PER3 modulates only the caffeine effect. Higher EEG theta activity related to sleep deprivation was observed in mutated TNF-α, PER3, and COMT carriers, in the placebo condition particularly. In conclusion, there are genetic influences on neurobehavioral impairments related to TSD that appear to be attenuated by caffeine administration. (NCT03859882).

scholarly journals Examining the effect of mitochondrial DNA variants on blood pressure in two Finnish cohorts

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jaakko Laaksonen ◽  
Pashupati P. Mishra ◽  
Ilkka Seppälä ◽  
Leo-Pekka Lyytikäinen ◽  
Emma Raitoharju ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Mitochondrial Dna ◽  
Genome Wide Association Study ◽  
Rare Variants ◽  
Meta Analysis ◽  
Noncommunicable Diseases ◽  
Nucleotide Polymorphisms ◽  
Genetic Determinants ◽  
Genome Wide ◽  
Mitochondrial Dna Variants

AbstractHigh blood pressure (BP) is a major risk factor for many noncommunicable diseases. The effect of mitochondrial DNA single-nucleotide polymorphisms (mtSNPs) on BP is less known than that of nuclear SNPs. We investigated the mitochondrial genetic determinants of systolic, diastolic, and mean arterial BP. MtSNPs were determined from peripheral blood by sequencing or with genome-wide association study SNP arrays in two independent Finnish cohorts, the Young Finns Study and the Finnish Cardiovascular Study, respectively. In total, over 4200 individuals were included. The effects of individual common mtSNPs, with an additional focus on sex-specificity, and aggregates of rare mtSNPs grouped by mitochondrial genes were evaluated by meta-analysis of linear regression and a sequence kernel association test, respectively. We accounted for the predicted pathogenicity of the rare variants within protein-encoding and the tRNA regions. In the meta-analysis of 87 common mtSNPs, we did not observe significant associations with any of the BP traits. Sex-specific and rare-variant analyses did not pinpoint any significant associations either. Our results are in agreement with several previous studies suggesting that mtDNA variation does not have a significant role in the regulation of BP. Future studies might need to reconsider the mechanisms thought to link mtDNA with hypertension.

scholarly journals Nonsynonymous single nucleotide polymorphisms of NHE3 differentially decrease NHE3 transporter activity

2015 ◽  
Vol 308 (9) ◽  
pp. C758-C766 ◽  
Author(s):  
Xinjun Cindy Zhu ◽  
Rafiquel Sarker ◽  
John R. Horton ◽  
Molee Chakraborty ◽  
Tian-E Chen ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Large Fraction ◽  
Regulatory Protein ◽  
Nucleotide Polymorphisms ◽  
Genetic Determinants ◽  
Single Nucleotide ◽  
Mutant Proteins ◽  
Homologous Protein ◽  
Genetic Abnormalities ◽  
The Impact

Genetic determinants appear to play a role in susceptibility to chronic diarrhea, but the genetic abnormalities involved have only been identified in a few conditions. The Na+/H+ exchanger 3 (NHE3) accounts for a large fraction of physiologic intestinal Na+ absorption. It is highly regulated through effects on its intracellular COOH-terminal regulatory domain. The impact of genetic variation in the NHE3 gene, such as single nucleotide polymorphisms (SNPs), on transporter activity remains unexplored. From a total of 458 SNPs identified in the entire NHE3 gene, we identified three nonsynonymous mutations (R474Q, V567M, and R799C), which were all in the protein's intracellular COOH-terminal domain. Here we evaluated whether these SNPs affect NHE3 activity by expressing them in a mammalian cell line that is null for all plasma membrane NHEs. These variants significantly reduced basal NHE3 transporter activity through a reduction in intrinsic NHE3 function in variant R474Q, abnormal trafficking in variant V567M, or defects in both intrinsic NHE3 function and trafficking in variant R799C. In addition, variants NHE3 R474Q and R799C failed to respond to acute dexamethasone stimulation, suggesting cells with these mutant proteins might be defective in NHE3 function during postprandial stimulation and perhaps under stressful conditions. Finally, variant R474Q was shown to exhibit an aberrant interaction with calcineurin B homologous protein (CHP), an NHE3 regulatory protein required for basal NHE3 activity. Taken together, these results demonstrate decreased transport activity in three SNPs of NHE3 and provide mechanistic insight into how these SNPs impact NHE3 function.

Influence of single nucleotide polymorphisms on thrombin generation in factor V Leiden heterozygotes

2014 ◽  
Vol 111 (03) ◽  
pp. 438-446 ◽  
Author(s):  
Olivier Segers ◽  
Paolo Simioni ◽  
Daniela Tormene ◽  
Elisabetta Castoldi
Keyword(s):  
Thrombin Generation ◽  
Factor V Leiden ◽  
Individual Variability ◽  
Intermediate Phenotype ◽  
Individual Risk ◽  
Factor V ◽  
Nucleotide Polymorphisms ◽  
Factor X ◽  
Large Variability ◽  
Fv Leiden

SummaryCarriership of the factor V (FV) Leiden mutation increases the risk of venous thromboembolism (VTE) ~4-fold, but the individual risk of each FV Leiden carrier depends on several co-inherited risk and protective factors. Under the hypothesis that thrombin generation might serve as an intermediate phenotype to identify genetic modulators of VTE risk, we enrolled 188 FV Leiden heterozygotes (11 with VTE) and determined the following parameters: thrombin generation in the absence and presence of activated protein C (APC); plasma levels of prothrombin, factor X, antithrombin, protein S and tissue factor pathway inhibitor; and the genotypes of 24 SNPs located in the genes encoding these coagulation factors and inhibitors. Multiple regression analysis was subsequently applied to identify the (genetic) determinants of thrombin generation. The endogenous thrombin potential (ETP) showed a striking inter-individual variability among different FV Leiden carriers and, especially when measured in the presence of APC, correlated with VTE risk. Several SNPs in the F2 (rs1799963, rs3136516), F10 (rs693335), SERPINC1 (rs2227589), PROS1 (Heerlen polymorphism) and TFPI (rs5940) genes significantly affected the ETPAPC and/or the ETP+APC in FV Leiden carriers. Most of these SNPs have shown an association with VTE risk in conventional epidemiological studies, suggesting that the genetic dissection of thrombin generation leads to the detection of clinically relevant SNPs. In conclusion, we have identified several SNPs that modulate thrombin generation in FV Leiden heterozygotes. These SNPs may help explain the large variability in VTE risk observed among different FV Leiden carriers.

scholarly journals L2,1-norm regularized multivariate regression model with applications to genomic prediction

2021 ◽  
Author(s):  
Alain J Mbebi ◽  
Hao Tong ◽  
Zoran Nikoloski
Keyword(s):  
Variable Selection ◽  
Regression Model ◽  
Multivariate Regression ◽  
Statistical Testing ◽  
Supplementary Information ◽  
Nucleotide Polymorphisms ◽  
Multiple Traits ◽  
Multivariate Regression Model ◽  
Proposed Model ◽  
Iterative Optimization Algorithm

AbstractMotivationGenomic selection (GS) is currently deemed the most effective approach to speed up breeding of agricultural varieties. It has been recognized that consideration of multiple traits in GS can improve accuracy of prediction for traits of low heritability. However, since GS forgoes statistical testing with the idea of improving predictions, it does not facilitate mechanistic understanding of the contribution of particular single nucleotide polymorphisms (SNP).ResultsHere, we propose a L2,1-norm regularized multivariate regression model and devise a fast and efficient iterative optimization algorithm, called L2,1-joint, applicable in multi-trait GS. The usage of the L2,1-norm facilitates variable selection in a penalized multivariate regression that considers the relation between individuals, when the number of SNPs is much larger than the number of individuals. The capacity for variable selection allows us to define master regulators that can be used in a multi-trait GS setting to dissect the genetic architecture of the analyzed traits. Our comparative analyses demonstrate that the proposed model is a favorable candidate compared to existing state-of-the-art approaches. Prediction and variable selection with datasets from Brassica napus, wheat and Arabidopsis thaliana diversity panels are conducted to further showcase the performance of the proposed model.Availability and implementation: The model is implemented using R programming language and the code is freely available from https://github.com/alainmbebi/L21-norm-GS.Supplementary informationSupplementary data are available at Bioinformatics online.

scholarly journals Global Analysis of the Genetic Variations in miRNA-Targeted Sites and Their Correlations With Agronomic Traits in Rapeseed

2021 ◽  
Vol 12 ◽  
Author(s):  
Pengfei Xu ◽  
Yantao Zhu ◽  
Yanfeng Zhang ◽  
Jianxia Jiang ◽  
Liyong Yang ◽  
...  
Keyword(s):  
Mirna Target ◽  
Target Genes ◽  
Rare Variants ◽  
Agronomic Traits ◽  
Global Analysis ◽  
Variant Calling ◽  
Genetic Variations ◽  
Nucleotide Polymorphisms ◽  
A Genome ◽  
Target Sites

MicroRNAs (miRNAs) and their target genes play vital roles in crops. However, the genetic variations in miRNA-targeted sites that affect miRNA cleavage efficiency and their correlations with agronomic traits in crops remain unexplored. On the basis of a genome-wide DNA re-sequencing of 210 elite rapeseed (Brassica napus) accessions, we identified the single nucleotide polymorphisms (SNPs) and insertions/deletions (INDELs) in miRNA-targeted sites complementary to miRNAs. Variant calling revealed 7.14 million SNPs and 2.89 million INDELs throughout the genomes of 210 rapeseed accessions. Furthermore, we detected 330 SNPs and 79 INDELs in 357 miRNA target sites, of which 33.50% were rare variants. We also analyzed the correlation between the genetic variations in miRNA target sites and 12 rapeseed agronomic traits. Eleven SNPs in miRNA target sites were significantly correlated with phenotypes in three consecutive years. More specifically, three correlated SNPs within the miRNA-binding regions of BnSPL9-3, BnSPL13-2, and BnCUC1-2 were in the loci associated with the branch angle, seed weight, and silique number, respectively; expression profiling suggested that the variation at these 3 miRNA target sites significantly affected the expression level of the corresponding target genes. Taken together, the results of this study provide researchers and breeders with a global view of the genetic variations in miRNA-targeted sites in rapeseed and reveal the potential effects of these genetic variations on elite agronomic traits.

scholarly journals INFLUENCE ON HOMEOSTASIS AS THE CRITERION FOR SELECTING SINGLE NUCLEOTIDE POLYMORPHISMS FOR THE STUDY OF METABOLIC SYNDROM IN THE KAZAKH POPULATION

REPORTS ◽  
2020 ◽  
Vol 5 (333) ◽  
pp. 86-93
Author(s):  
V.V. Benberin ◽  
◽  
T.A. Voshchenkova ◽  
A.A. Nagymtayeva ◽  
A.S. Sibagatova ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Traditional Approach ◽  
Population Based ◽  
Malignant Neoplasms ◽  
Nucleotide Polymorphisms ◽  
Genetic Determinants ◽  
Single Nucleotide ◽  
Sequence Of Events ◽  
Kazakh Population ◽  
Symptom Complex

Metabolic syndrome (MS) is increasingly cited as the world's leading health risk. The sequence of events toward multimorbidity in most cases passes through MS. According to the research, MS heritability ranges from 23 to 27% in Europeans, and 51 to 60% in Asians. The purpose of the review: to form a strategy for the selection of single nucleotide polymorphisms (SNPs) for the study of MS in the Kazakh population based on the effect of SNPs on homeostasis indicators The stable symptom complex of MS is a complicated dynamic system of successive accumulations of dysmetabolic disorders of homeostasis. This system starts the development of subsequent age-associated diseases), such as cardiometabolic, neurodegenerative, and malignant neoplasms. The system for selecting SNPs for the MS study, proposed on the basis of the concept of homeostasis dysfunction, assumes, in conditions of limited resources, to see the greatest level of their influence within the conditional framework of three genetic models of homeostasis dysregulation: insulin resistance , oxidative stress, and chronic inflammation. This approach is fundamentally different from the traditional approach involving candidate genes. It is expected that scientific research in this direction will contribute not only to the understanding of general biological processes, but also to the targeted search for genetic determinants and for new opportunities for personalized interventions.

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