Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 8 de 8
Filter
Add more filters










Database
Language
Publication year range
1.
Plant Genome ; 13(2): e20027, 2020 07.
Article in English | MEDLINE | ID: mdl-33016606

ABSTRACT

DNA methylation is a mechanism of epigenetic modification in eukaryotic organisms. Generally, methylation within genes promoter inhibits regulatory protein binding and represses transcription, whereas gene body methylation is associated with actively transcribed genes. However, it remains unclear whether there is interaction between methylation levels across genic regions and which site has the biggest impact on gene regulation. We investigated and used the methylation patterns of the bread wheat cultivar Chinese Spring to uncover differentially expressed genes (DEGs) between roots and leaves, using six machine learning algorithms and a deep neural network. As anticipated, genes with higher expression in leaves were mainly involved in photosynthesis and pigment biosynthesis processes whereas genes that were not differentially expressed between roots and leaves were involved in protein processes and membrane structures. Methylation occurred preponderantly (60%) in the CG context, whereas 35 and 5% of methylation occurred in CHG and CHH contexts, respectively. Methylation levels were highly correlated (r = 0.7 to 0.9) between all genic regions, except within the promoter (r = 0.4 to 0.5). Machine learning models gave a high (0.81) prediction accuracy of DEGs. There was a strong correlation (p-value = 9.20×10-10 ) between all features and gene expression, suggesting that methylation across all genic regions contribute to gene regulation. However, the methylation of the promoter, the CDS and the exon in CG context was the most impactful. Our study provides more insights into the interplay between DNA methylation and gene expression and paves the way for identifying tissue-specific genes using methylation profiles.


Subject(s)
DNA Methylation , Triticum , Epigenesis, Genetic , Machine Learning , Promoter Regions, Genetic , Triticum/genetics
2.
PLoS One ; 13(9): e0203283, 2018.
Article in English | MEDLINE | ID: mdl-30231049

ABSTRACT

Stripe rust, caused by the fungal pathogen Puccinia striiformis Westend. f. sp. tritici Eriks, is an important disease of bread wheat (Triticum aestivum L.) worldwide and there is an indication that it may also become a serious disease of durum wheat (T. turgidum L. var. durum). Therefore, we investigated the genetic architecture underlying resistance to stripe rust in adapted durum wheat germplasm. Wheat infection assays were conducted under controlled conditions in Canada and under field conditions in Mexico. Disease assessments were performed on a population of 155 doubled haploid (DH) lines derived from the cross of Kofa (susceptible) and W9262-260D3 (moderately resistant) and on a breeding panel that consisted of 92 diverse cultivars and breeding lines. Both populations were genotyped using the 90K single-nucleotide polymorphism (SNP) iSelect assay. In the DH population, QTL for stripe rust resistance were identified on chromosome 7B (LOD 6.87-11.47) and chromosome 5B (LOD 3.88-9.17). The QTL for stripe rust resistance on chromosome 7B was supported in the breeding panel. Both QTL were anchored to the genome sequence of wild emmer wheat, which identified gene candidates involved in disease resistance. Exome capture sequencing identified variation in the candidate genes between Kofa and W9262-260D3. These genetic insights will be useful in durum breeding to enhance resistance to stripe rust.


Subject(s)
Basidiomycota/pathogenicity , Plant Diseases/genetics , Plant Diseases/microbiology , Triticum/genetics , Triticum/microbiology , Canada , Chromosome Mapping , Chromosomes, Plant/genetics , Disease Resistance/genetics , Genes, Plant , Haploidy , Mexico , Phenotype , Plant Breeding , Polymorphism, Single Nucleotide , Quantitative Trait Loci
4.
PLoS One ; 12(4): e0175285, 2017.
Article in English | MEDLINE | ID: mdl-28399136

ABSTRACT

Breeding for solid-stemmed durum (Triticum turgidum L. var durum) and common wheat (Triticum aestivum L.) cultivars is one strategy to minimize yield losses caused by the wheat stem sawfly (Cephus cinctus Norton). Major stem-solidness QTL have been localized to the long arm of chromosome 3B in both wheat species, but it is unclear if these QTL span a common genetic interval. In this study, we have improved the resolution of the QTL on chromosome 3B in a durum (Kofa/W9262-260D3) and common wheat (Lillian/Vesper) mapping population. Coincident QTL (LOD = 94-127, R2 = 78-92%) were localized near the telomere of chromosome 3BL in both mapping populations, which we designate SSt1. We further examined the SSt1 interval by using available consensus maps for durum and common wheat and compared genetic to physical intervals by anchoring markers to the current version of the wild emmer wheat (WEW) reference sequence. These results suggest that the SSt1 interval spans a physical distance of 1.6 Mb in WEW (positions 833.4-835.0 Mb). In addition, minor QTL were identified on chromosomes 2A, 2D, 4A, and 5A that were found to synergistically enhance expression of SSt1 to increase stem-solidness. These results suggest that developing new wheat cultivars with improved stem-solidness is possible by combining SSt1 with favorable alleles at minor loci within both wheat species.


Subject(s)
Genes, Plant , Haplotypes , Triticum/genetics , Quantitative Trait Loci , Species Specificity , Triticum/classification
5.
PLoS One ; 12(1): e0170941, 2017.
Article in English | MEDLINE | ID: mdl-28135299

ABSTRACT

Association mapping is usually performed by testing the correlation between a single marker and phenotypes. However, because patterns of variation within genomes are inherited as blocks, clustering markers into haplotypes for genome-wide scans could be a worthwhile approach to improve statistical power to detect associations. The availability of high-density molecular data allows the possibility to assess the potential of both approaches to identify marker-trait associations in durum wheat. In the present study, we used single marker- and haplotype-based approaches to identify loci associated with semolina and pasta colour in durum wheat, the main objective being to evaluate the potential benefits of haplotype-based analysis for identifying quantitative trait loci. One hundred sixty-nine durum lines were genotyped using the Illumina 90K Infinium iSelect assay, and 12,234 polymorphic single nucleotide polymorphism (SNP) markers were generated and used to assess the population structure and the linkage disequilibrium (LD) patterns. A total of 8,581 SNPs previously localized to a high-density consensus map were clustered into 406 haplotype blocks based on the average LD distance of 5.3 cM. Combining multiple SNPs into haplotype blocks increased the average polymorphism information content (PIC) from 0.27 per SNP to 0.50 per haplotype. The haplotype-based analysis identified 12 loci associated with grain pigment colour traits, including the five loci identified by the single marker-based analysis. Furthermore, the haplotype-based analysis resulted in an increase of the phenotypic variance explained (50.4% on average) and the allelic effect (33.7% on average) when compared to single marker analysis. The presence of multiple allelic combinations within each haplotype locus offers potential for screening the most favorable haplotype series and may facilitate marker-assisted selection of grain pigment colour in durum wheat. These results suggest a benefit of haplotype-based analysis over single marker analysis to detect loci associated with colour traits in durum wheat.


Subject(s)
Breeding , Chromosome Mapping/methods , Food , Genetic Association Studies , Haplotypes/genetics , Polymorphism, Single Nucleotide/genetics , Triticum/genetics , Alleles , Color , Discriminant Analysis , Genetic Loci , Genetic Markers , Genetics, Population , Genome, Plant , Least-Squares Analysis , Linkage Disequilibrium/genetics , Phenotype , Principal Component Analysis , Quantitative Trait, Heritable
6.
J Sci Food Agric ; 97(3): 743-752, 2017 Feb.
Article in English | MEDLINE | ID: mdl-27145288

ABSTRACT

BACKGROUND: The structure of ß-glucan influences its use in cereal-based foods and feed. The objective of this study was to determine the effect of environment (E) and genotype (G) on ß-glucan fine structure and its genetic control in two-row spring barley with normal starch characteristics. RESULTS: A population of 89 recombinant inbred lines, derived from the cross of two-row spring barley genotypes Merit × H93174006 (H92076F1 × TR238), was characterized for concentration and structure of grain ß-glucan in two environments. Results showed that concentrations of ß-glucan, DP3, DP4 and DP3 + DP4 were positively correlated with each other, suggesting no preference for DP3 or DP4 subunit production in high- or low-ß-glucan lines. The concentrations of ß-glucan, DP3, DP4 and DP3:DP4 ratios were significantly influenced by genotype and environment. However, only DP3:DP4 ratio showed a significant effect of G × E interaction. Association mapping of candidate markers in 119 barley genotypes showed that marker CSLF6_4105 was associated with ß-glucan concentration, whereas Bmac504 and Bmac211 were associated with DP3:DP4 ratio. Bmac273e was associated with both ß-glucan concentration and DP3:DP4 ratio. CONCLUSION: The grain ß-glucan concentration and DP3:DP4 ratio are strongly affected by genotype and environment. Single-marker analyses suggested that the genetic control of ß-glucan concentration and DP3:DP4 ratio was linked to separate chromosomal regions on barley genome. © 2016 Society of Chemical Industry.


Subject(s)
Dietary Carbohydrates/analysis , Gene-Environment Interaction , Glucosyltransferases/metabolism , Hordeum/chemistry , Plant Proteins/metabolism , Seeds/chemistry , beta-Glucans/analysis , Alberta , Altitude , Animal Feed/analysis , Animals , Carbohydrate Sequence , Cellulose/genetics , Cellulose/metabolism , Climate , Crosses, Genetic , Dietary Carbohydrates/metabolism , Genetic Markers , Glucosyltransferases/genetics , Hordeum/genetics , Hordeum/growth & development , Hordeum/metabolism , Humans , Nutritive Value , Plant Breeding , Plant Proteins/genetics , Seeds/genetics , Seeds/growth & development , Seeds/metabolism , Substrate Specificity , Tetroses/metabolism , Trioses/metabolism , beta-Glucans/chemistry , beta-Glucans/metabolism
7.
Anim Genet ; 44(2): 197-201, 2013 Apr.
Article in English | MEDLINE | ID: mdl-22670622

ABSTRACT

In dairy cows, there is evidence that failure to respond to superovulation protocols is a heritable trait. In women, genotyping for the p.N680S single nucleotide polymorphism (SNP) in the follicle-stimulating hormone receptor (FSHR) gene may help identify poor responders before ovarian stimulation is initiated. Our objectives were to identify SNPs in the coding region of the bovine FSHR gene and to investigate the effect of FSHR genotypes on superovulatory response in Holstein cattle. Sequencing of FSHR exons 1-10 revealed seven SNPs. Three were non-synonymous mutations (c.337C>G, c.871A>G and c.1973C>G). SNP c.337C>G encodes for a proline-to-alanine (p.Pro113Ala) amino acid replacement in the extracellular ligand-binding domain of the receptor. PCR-RFLP analyses showed that homozygous GG Holstein cows present a higher percentage of viable embryos, whereas GG and CG animals have less unfertilised oocytes. SNP c.871A>G results in an isoleucine-to-valine (p.Ile291Val) modification, and homozygous AA animals present lower embryo yield after superovulatory treatments. SNP c.1973C>G corresponds to a threonine-to-serine (p.The658Ser) modification in the intracellular carboxyl-terminal domain of the FSHR protein, and homozygous GG Holstein cows were associated with a lower embryo yield and a higher percentage of unfertilised oocytes. Our results suggest that specific alleles of the bovine FSHR gene are associated with variations in embryo yield and in the number of unfertilised oocytes.


Subject(s)
Cattle/genetics , Polymorphism, Single Nucleotide/genetics , Receptors, FSH/genetics , Superovulation/genetics , Amino Acid Sequence , Animals , Base Sequence , Female , Gene Frequency , Genotype , Molecular Sequence Data , Polymerase Chain Reaction/veterinary , Polymorphism, Restriction Fragment Length , Sequence Analysis, DNA/veterinary , Species Specificity
8.
Mol Reprod Dev ; 74(12): 1491-504, 2007 Dec.
Article in English | MEDLINE | ID: mdl-17410545

ABSTRACT

In mammals, the pre-Sertoli cell of the male genital ridge is the first cell type to display sex specific differentiation and differential gene expression. The genetic cascade driving the differentiation of pre-Sertoli cells and ultimately testis formation is beginning to be unravelled, but many questions remain. A better understanding of the transcriptome of pre-Sertoli cells immediately after sex determination is essential in order to further understand this differentiation process. A mouse model expressing Red Fluorescent Protein (RFP) under the control of a hybrid mouse/pig SRY promoter (HybSRYp-RFP) was used to purify cells from embryonic day 12.0 (e12.0) male genital ridges. To compare the transcriptomes of HybSRYp-RFP cell populations versus age matched whole female genital ridges, RNA was extracted and used to generate molecular probes that were hybridized onto Affymetrix Mouse Genome 430 2.0 micro-arrays. The expression of genes considered markers for pre-Sertoli cells, including Sox9, Mis, Dhh and Fgf9 were identified within the HybSRYp-RFP expressing cell population, while markers for germ cells (Oct4, SSEA-1) and endothelial cells (Ntrk3) were not identified. In contrast, markers for ovarian somatic cell expression, including Fst and Bmp2, were identified as overexpressed within the ovarian cell population. In a general fashion, genes identified as 2.5-fold over expressed in HybSRYp-RFP expressing cells coded notably for cell signalling and extra cellular proteins. The expression of Sox10, Stc2, Fgf18, Fgf13 and Wnt6 were further characterized via whole mount in situ hybridization (WISH) on male and female genital ridges between e11.5 and e14.5. Sox10, Fgf18, Fgf13 and Stc2 gene expression was detected within the male genital ridges while Wnt6 was found diffusely within both the male and female genital ridges. These data represent the earliest comprehensive microarray expression analysis of purified presumptive pre-Sertoli cells available to date.


Subject(s)
Gene Expression , Organogenesis/genetics , Sertoli Cells/metabolism , Testis/embryology , Animals , Cell Differentiation/genetics , Gene Expression Profiling , Luminescent Proteins/analysis , Luminescent Proteins/genetics , Male , Mice , Mice, Transgenic , Oligonucleotide Array Sequence Analysis , Signal Transduction/genetics , Testis/metabolism , Red Fluorescent Protein
SELECTION OF CITATIONS
SEARCH DETAIL
...