Variation in DNA methylation patterns of grapevine somaclones (Vitis vinifera L.)

<p>Abstract</p> <p>Background</p> <p>In traditional vine areas, the production should present a typicity that partly depends on the grapevine variety. Therefore, vine improvement is considered difficult because of the limited choice in the natural variability of the cultivars within the limits of their characteristics. A possibility to circumvent this problem is the use of somatic variability. <it>In vitro </it>somatic embryogenesis and organogenesis can lead to genotypic and phenotypic variations, described as somaclonal variation, that could be useful for the selection of improved grapevine genotypes.</p> <p>Results</p> <p>In order to study tissue culture-induced variation of grapevine, we have analysed 78 somaclones obtained from somatic embryos of two distinct cultivars using molecular marker techniques. SSRs were only useful to verify the conservation of the microsatellite genotype between the somaclones and the respective mother clones. AFLP polymorphism between mother clones and somaclones was 1.3–2.8 times higher to that found between clones. However, a majority of the somaclones (45/78) exhibited only few changes. Seven and five somaclones of 'Chardonnay 96' and 'Syrah 174', respectively, which covered at least all polymorphic loci found in AFLP analysis were used for MSAP study. All of the 120 polymorphic fragments were found only in the somaclones. The percentage of full methylation at CCGG recognition sites was slightly higher in somaclones due to more polymorphic bands generated after cleavage by <it>Eco</it>RI/<it>Hpa</it>II. Different digestion patterns revealed different methylation status, especially different levels of de-methylation, that are the consequence of the <it>in vitro </it>culture.</p> <p>Conclusion</p> <p>MSAP highlights DNA methylation variation in somaclones compared to mother clones and, therefore, is a powerful tool for genotypic characterisation of somatic embryo-derived grapevines. The detection of the same polymorphic bands in numerous somaclones of different cultivars suggests the possibility of hot spots of DNA methylation variation. SSR profiles of the 'Chardonnay' and 'Syrah' somaclones were the same as of the respective mother clones. The somaclones exhibited a higher AFLP variation than clones obtained via traditional clonal selection in the field. Therefore, somatic embryogenesis through <it>in vitro </it>culture technique could be useful for the selection of improved cultivars with subtle changes but conserving their main characteristics.</p

Genome-wide association study and genomic prediction of resistance to stripe rust in current Central and Northern European winter wheat germplasm

Stripe or yellow rust, caused by the fungus Puccinia striiformis Westend f. sp. tritici, is one of the most destructive wheat diseases. Sustainable management of wheat stripe rust can be achieved through the deployment of rust resistant cultivars. To detect effective resistance loci for use in breeding programs, an association mapping panel of 230 winter wheat cultivars and breeding lines from Northern and Central Europe was employed. Genotyping with the Illumina® iSelect® 25 K Infinium® single nucleotide polymorphism (SNP) genotyping array yielded 8812 polymorphic markers. Structure analysis revealed two subpopulations with 92 Austrian breeding lines and cultivars, which were separated from the other 138 genotypes from Germany, Norway, Sweden, Denmark, Poland, and Switzerland. Genome-wide association study for adult plant stripe rust resistance identified 12 SNP markers on six wheat chromosomes which showed consistent effects over several testing environments. Among these, two marker loci on chromosomes 2BS (RAC875_c1226_652) and 6AL (Tdurum_contig29607_413) were highly predictive in three independent validation populations of 1065, 1001, and 175 breeding lines. Lines with the resistant haplotype at both loci were nearly free of stipe rust symptoms. By using mixed linear models with those markers as fixed effects, we could increase predictive ability in the three populations by 0.13–0.46 compared to a standard genomic best linear unbiased prediction approach. The obtained results facilitate an efficient selection for stripe rust resistance against the current pathogen population in the Northern and Central European winter wheat gene pool.publishedVersio

Relationship between cardiovascular risk factors and biomarkers with necrotic core and atheroma size: a serial intravascular ultrasound radiofrequency data analysis

We explored the impact of patient demographics, anthropometric measurements, cardiovascular risk factors, and soluble biomarkers on necrotic core and atheroma size in patients with coronary disease. The IBIS-2 trial enrolled 330 patients. In the multivariate analysis, at baseline, creatinine had a positive, whereas baseline mean lumen diameter and myeloperoxidase had a negative, independent association with percentage of necrotic core (PNC); while age, glomerular filtration rate <60, HbA1c, previous PCI or CABG and baseline % diameter stenosis were positively, and acute coronary syndromes (ACS) were negatively associated with baseline percentage atheroma volume (PAV). The variables associated with a decrease in PNC from baseline were darapladib, ACS and a large content of NC at baseline, while variables associated with an increase in PNC were previous stroke and % diameter stenosis at baseline. Those variables associated with a decrease in PAV from baseline were waist circumference, statin use, CD40L and baseline PAV, while the only variable associated with an increase in PAV was baseline diastolic blood pressure. Treatment with darapladib was associated with a decrease in necrotic core, but was not associated with a decrease in percentage atheroma volume. On the contrary, statin use was only associated with a decrease in percentage atheroma volume

Allocation of the oat powdery mildew resistance gene Pm3 to oat chromosome 1A

Besides the mode of inheritance, the knowledge of the chromosome location and allelic relationships are the essentials towards a successful deployment and stacking of divergent disease resistance genes for a given pathogen in breeding programs. Powdery mildew of oats, to which 11 major resistance genes in the host Avena sativa L. have been characterized so far, is a prevalent fungal disease of the crop in Northwestern Europe. In the present study, the resistance gene Pm3 was mapped by linkage analysis relative to molecular markers from oat consensus linkage group Mrg18 which was recently determined to represent oat chromosome 1A. Pm3 was located at 67.7–72.6 cM on Mrg18 of the oat consensus map, a position at which also stem and crown rust resistance genes Pg13 and Pc91 and a large cluster of resistance gene analogs have been previously mapped. The closely linked marker GMI_ES03_c2277_336 was found to be useful for the prediction of Pm3 in gene postulation studies. Although the major effect of the widespread gene got lost over time, the known genome location with associated markers will assist revealing in future genetic studies whether there is a possible residual effect of the gene contributing to adult plant resistance

Genetic Basis of Resistance to Warrior (-) Yellow Rust Race at the Seedling Stage in Current Central and Northern European Winter Wheat Germplasm

To evaluate genetic variability and seedling plant response to a dominating Warrior (-) race of yellow rust in Northern and Central European germplasm, we used a population of 229 winter wheat cultivars and breeding lines for a genome-wide association study (GWAS). A wide variation in yellow rust disease severity (based on infection types 1&ndash;9) was observed in this panel. Four breeding lines, TS049 (from Austria), TS111, TS185, and TS229 (from Germany), and one cultivar, TS158 (KWS Talent), from Germany were found to be resistant to Warrior (-) FS 53/20 and Warrior (-) G 23/19. The GWAS identified five significant SNPs associated with yellow rust on chromosomes 1B, 2A, 5B, and 7A for Warrior (-) FS 53/20, while one SNP on chromosome 5B was associated with disease for Warrior (-) G 23/19. For Warrior (-) FS 53/20, we discovered a new QTL for yellow rust resistance associated with the marker Kukri_c5357_323 on chromosome 1B. The resistant alleles G and T at the marker loci Kukri_c5357_323 on chromosome 1B and Excalibur_c17489_804 on chromosome 5B showed the largest effects (1.21 and 0.81, respectively) on the severity of Warrior (-) FS 53/20 and Warrior (-) G 23/19. Our results provide the basis for knowledge-based resistance breeding in the face of the enormous impact of the Warrior (-) race on wheat production in Europe

Genetics of the Inverse Relationship between Grain Yield and Grain Protein Content in Common Wheat

Grain protein content (GPC) is one of the most important criteria to determine the quality of common wheat (Triticum aestivum). One of the major obstacles for bread wheat production is the negative correlation between GPC and grain yield (GY). Previous studies demonstrated that the deviation from this inverse relationship is highly heritable. However, little is known about the genetics controlling these deviations in common wheat. To fill this gap, we performed quantitative trait locus (QTL) analysis for GY, GPC, and four derived GY-GPC indices using an eight-way multiparent advanced generation intercross population comprising 394 lines. Interval mapping was conducted using phenotypic data from up to nine environments and genotypic data from a 20k single-nucleotide polymorphism array. The four indices were highly heritable (0.76&ndash;0.88) and showed distinct correlations to GY and GPC. Interval mapping revealed that GY, GPC, and GY-GPC indices were controlled by 6, 12, and 12 unique QTL, of which each explained only a small amount of phenotypic variance (R2 &le; 10%). Ten of the 12 index QTL were independent of loci affecting GY and GPC. QTL regions harboured several candidate genes, including Rht-1, WAPO-A1, TaTEF-7A, and NRT2.6-7A. The study confirmed the usefulness of indices to mitigate the inverse GY-GPC relationship in breeding, though the selection method should reflect their polygenic inheritance

Loving the Alien: The Contribution of the Wild in Securing the Breeding of Cultivated Hexaploid Wheat and Oats

Cereal production is of strategic importance to the world economy. Although the primary aim of breeding programs is to develop cultivars with improved agronomic performance, including high grain yield and grain quality, as well as disease and lodging resistance, nowadays the adaptability to changing environmental conditions seems to be an extremely important feature. The achievement of these breeding objectives in diploid cereal species such as rice, barley, or maize is straightforward. The genetic improvement of polyploid crops such as hexaploid wheat and oats for increased crop production is highly demanding. Progenitor species and wild relatives, including taxa at lower ploidy levels, have preserved a high degree of useful genetic variation. The world’s genebank collections of wheat and oat germplasm provide extremely rich resources for future breeding and utilization. This review highlights the immense potential of cultivated wild relatives as donors of genes for a wide range of biotic and abiotic traits and their impact on wheat and oat breeding. This review covers methods allowing access to these genetic resources, and it highlights the most (and most recently)-exploited related species for gene introgression in wheat and oats. Further, it will also deal with the impact of genomics and cloned genes on the advanced discovery, characterization, and utilization of genetic resources in these two cereals

Searching for Novel Oat Crown Rust Resistance in Diploid Oat <i>Avena strigosa</i> Schreb. Reveals the Complexity and Heterogeneity of the Analyzed Genebank Accessions

Crown rust, one of the most destructive diseases of oat, regularly occurs worldwide and leads to significant yield losses. The constant evolution of the Puccinia coronata f. sp. avenae pathogen causes a rapid decline in the effectiveness of currently used crown rust resistance genes, so new ones are urgently needed. In this study, 39 accessions of Avena strigosa Schreb. from ten countries gathered from the Polish National Genebank were evaluated at the seedling stage for crown rust reaction using a detached leaf assay and five isolates of P. coronata with diverse virulence profiles. Ten plants of each accession were tested, and 28 diverse infection profiles (IPs) were defined. One hundred and sixty-eight out of 390 plants revealed an IP of unidentified resistance. Thirty-eight (97%) of the accessions studied showed a heterogeneous infection pattern, none of the accessions displayed homogeneous susceptibility, and one (51887) was homogeneously resistant to all races used. The obtained results confirmed the complexity and heterogeneity of the accessions gathered in the genebanks. A. strigosa preserved as complex populations could be a valuable source of resistance to crown rust and potentially other pathogens. The variability of the analyzed populations was ascertained by a detailed diversity analysis of the transformed resistance/susceptibility data. The averaged resistance rating for the genebank specimens available in the databases may be an obstacle in revealing the beneficial alleles of genes hidden among the plants representing accessions preserved as complex populations. Potential donors of effective resistance may be discovered even in accessions with general susceptibility, which is a promising alternative at a time when making new collections of wild and weedy accessions is under threat from agricultural practice and climate change