BIOBREED – a new project on marker assisted population breeding in wheat with resistance to common bunt

The paper describes the BIOBREED project

Association Mapping for Common Bunt Resistance in Wheat

Common bunt, caused by Tilletia caries and T. foetida, is a fungal disease of wheat world wide. Infection, occurring via seed borne teliospores, is generally controlled by the application of seed treatments prior to sowing. Farming systems like organic agriculture with a very limited range of organic seed treatments available rely heavily on common bunt resistance genes within wheat. In the framework of the BIOBREED project an association study in winter wheat was conducted, aiming at the identification of genetic loci linked to resistance towards common bunt in wheat. 152 European wheat cultivars were phenotyped for their resistance reaction for the two consecutive years 2011/12 at Agrologica research station at Mariager. Infection was scored as percent infected ears. The scorings were log-transformed to fit a disease scoring scale ranging from 1 to 9. The association analysis was performed for each year separately as well as for the mean scoring of the two years. The wheat cultivars were genotyped with DArT markers, yielding 1832 polymorphic loci. The association analysis was conducted using the computer program Genstat, with the ASReml module. Minimun allele frequency for the association analysis was set to 0.07. 13 out of the total of1832 marker in our study were linked to common bunt resistance in wheat (-log10(P) >3). These marker are located on 8 out of the 21 wheat chromosomes. Comparisons of these findings with other published results are difficult since only very little is known about the chromosomal location of common bunt resistance genes/QTL in wheat. Chromosome 2B was previously reported to carry gene(s) for common bunt resistance. Findings of our analysis are in accordance with this: 4 of the linked marker resided on this chromosome. Further, another two linked marker were found on chromosome 2D, another chromosome previously reported to carry common bunt resistance genes. Our study shows the possibilities of finding makers linked to common bunt resistance in wheat, and of using these markers for marker assisted selection of wheat cultivars tailored for the needs of organic agriculture

Common bunt resistant wheat composite cross populations

Utilising diverse populations instead of single line varieties is expected to lead to a number of advantages in cereal production. These include reduced epidemics of plant diseases, improved weed competition and better exploitation of soil nutrients, resulting in improved yield stability. However, a number of challenges must be met before diverse wheat populations can be introduced into commercial wheat production: one of these is the development of breeding technologies based on mass selection which enable breeders and farmers to improve specific traits in populations and maintain diversity at the same time. BIOBREED is a project started in Denmark in 2011 to meet these challenges for wheat population breeding. The project is focusing on the development of tools and methods for mass selection of traits relevant for organic and low input production, where it is expected that the highest benefits of utilizing diverse populations can be achieved. BIOBREED focuses on three main aspects of wheat population breeding for organic and low input production systems: i) common bunt (caused by Tilletia caries) resistance, ii) selection for improved protein content and iii) the influence on population diversity of different selection pathways. Selection for common bunt resistance in wheat composite cross populations 33 crosses were made between 23 common bunt resistant winter wheat varieties in order to generate two populations. Progeny of all crosses was bulked in the F 3 to constitute the first population Pop.No.Sel. Prior to the creation of the second population Pop.Sel, the F 3 of the parental crosses was sown as head-rows with common bunt infection. Only lines that showed resistance to common bunt were used to create Pop.Sel. in generation F 4 . Afterwards the two populations were grown with and without inoculation with common bunt in order to i) select for bunt resistance and ii) to be able to compare the effect on diversity of this selection step. Preliminary results show a higher level of common bunt resistance in Pop.Sel in the first year. Single seed sorting for protein content Prior to sowing the F 5 seed of the population Pop.Sel, the seed were sorted individually for protein content using a BoMill IQ Grain Quality Sorter 1002S. The fraction of seeds containing the 10% highest and another fraction containing the 10% lowest protein content were selected. The four populations, Pop.No.Sel, Pop.Sel, and Pop.Sel.high. Protein and Pop.Sel.low.Protein and the parental lines were sown in a randomized complete block yield trial at two locations in Denmark in order to assess their yield and quality parameters such as protein content and baking quality of the parents and there derived populations. Results are expected in the summer 2013. Diversity of wheat composite cross populations. The practical question of “how much diversity is needed in populations?” has not been answered yet. BIOBREED will aim to to quantify the levels of diversity in wheat composite cross populations after the different selection steps i) cultivation with and without common bunt inoculum, and ii) sorting for single protein content. In a fist attempt SSR markers will be used to describe the influence these different selection pathways will have on the population diversity. 90 SSR markers—about two markers per chromosome arm—will be used to describe the initial genetic diversity of the 23 parental lines. F 6 seed of the different populations will be analysed with the same markers and population diversity after different selection pathways will be quantified

Risk and Subtypes of Stroke Following New-Onset Postoperative Atrial Fibrillation in Coronary Bypass Surgery:A Population-Based Cohort Study

BACKGROUND: New‐onset postoperative atrial fibrillation (POAF) develops in approximately one‐third of patients undergoing cardiac surgery and is associated with a higher incidence of ischemic stroke and increased mortality. However, it remains unknown to what extent ischemic stroke events in patients with POAF are cardioembolic and whether anticoagulant therapy is indicated. We investigated the long‐term risk and pathogenesis of postoperative stroke in patients undergoing coronary artery bypass grafting experiencing POAF. METHODS AND RESULTS: This was a register‐based cohort study. Data from the WDHR (Western Denmark Heart Registry) were linked with the DNPR (Danish National Patient Register), the Danish National Prescription Register, and the Cause of Death Register. All stroke diagnoses were verified, and ischemic stroke cases were subclassified according to pathogenesis. Furthermore, investigations of all‐cause mortality and the use of anticoagulation medicine for the individual patient were performed. A total of 7813 patients without a preoperative history of atrial fibrillation underwent isolated coronary artery bypass grafting between January 1, 2010, and December 31, 2018, in Western Denmark. POAF was registered in 2049 (26.2%) patients, and a postoperative ischemic stroke was registered in 195 (2.5%) of the patients. After adjustment, there was no difference in the risk of ischemic stroke (hazard ratio [HR], 1.08 [95% CI, 0.74–1.56]) or all‐cause mortality (HR, 1.09 [95% CI, 0.98–1.23]) between patients who developed POAF and non‐POAF patients. Although not statistically significant, patients with POAF had a higher incidence rate (IR; per 1000 patient‐years) of cardioembolic stroke (IR, 1 [95% CI, 0.6–1.6] versus IR, 0.5 [95% CI, 0.3–0.8]), whereas non‐POAF patients had a higher incidence rate of large‐artery occlusion stroke (IR, 1.1 [95% CI, 0.8–1.5] versus IR, 0.7 [95% CI, 0.4–1.4]). Early initiation of anticoagulation medicine was not associated with a lower risk of ischemic stroke. However, patients with POAF were more likely to die of cardiovascular causes than non‐POAF patients (P<0.001). CONCLUSIONS: We found no difference in the adjusted risk of postoperative stroke or all‐cause mortality in POAF versus non‐POAF patients. Patients with POAF after coronary artery bypass grafting presented with a higher, although not significant, proportion of ischemic strokes of the cardioembolic type

Defining lncRNAs Correlated with CHO Cell Growth and IgG Productivity by RNA-Seq

How the long non-coding RNA (lncRNA) genome in recombinant protein producing Chinese hamster ovary (CHO) cell lines relates to phenotype is not well described. We therefore defined the CHO cell lncRNA transcriptome from cells grown in controlled miniature bioreactors under fed-batch conditions using RNA-Seq to identify lncRNAs and how the expression of these changes throughout growth and between IgG producers. We identify lncRNAs including Adapt15, linked to ER stress, GAS5, linked to mTOR signaling/growth arrest, and PVT1, linked to Myc expression, which are differentially regulated during fed-batch culture and whose expression correlates to productivity and growth. Changes in (non)-coding RNA expression between the seed train and the equivalent day of fed-batch culture are also reported and compared with existing datasets. Collectively, we present a comprehensive lncRNA CHO cell profiling and identify targets for engineering growth and productivity characteristics of CHO cells

Association Mapping for Common Bunt Resistance in Wheat Landraces and Cultivars

Common bunt is a seed borne disease of wheat whose importance is likely to increase due to the growing organic seed market, which, in addition to seed phytosanitary measures, relies on genetic resistances towards the disease. Genome wide association studies in wheat have been proven to be a useful tool in the detection of genetic polymorphisms underlying phenotypic trait variation in wheat. Here 248 wheat landraces and cultivars representing 130 years of breeding history were screened for two years in the field for their resistance reactions towards common bunt. The majority of lines exhibited high levels of susceptibility towards common bunt, while 25 accessions had less than 10% infection. Using Diversity Array Technology (DArT) markers for genotyping and correcting for population stratification by using a compressed mixed linear model, we identified two significant marker trait associations (MTA) for common bunt resistance, designated QCbt.cph-2B and QCbt.cph-7A, located on wheat chromosomes 2B and 7A, respectively. This shows that genome wide association studies (GWAS) are applicable in the search for genetic polymorphisms for resistance towards less studied plant diseases such as common bunt in the context of an under representation of resistant lines