Advantages of continuous genotype values over genotype classes for GWAS in higher polyploids: a comparative study in hexaploid chrysanthemum

Background: Association studies are an essential part of modern plant breeding, but are limited for polyploid crops. The increased number of possible genotype classes complicates the differentiation between them. Available methods are limited with respect to the ploidy level or data producing technologies. While genotype classification is an established noise reduction step in diploids, it gains complexity with increasing ploidy levels. Eventually, the errors produced by misclassifications exceed the benefits of genotype classes. Alternatively, continuous genotype values can be used for association analysis in higher polyploids. We associated continuous genotypes to three different traits and compared the results to the output of the genotype caller SuperMASSA. Linear, Bayesian and partial least squares regression were applied, to determine if the use of continuous genotypes is limited to a specific method. A disease, a flowering and a growth trait with h(2) of 0.51, 0.78 and 0.91 were associated with a hexaploid chrysanthemum genotypes. The data set consisted of 55,825 probes and 228 samples. Results: We were able to detect associating probes using continuous genotypes for multiple traits, using different regression methods. The identified probe sets were overlapping, but not identical between the methods. Baysian regression was the most restrictive method, resulting in ten probes for one trait and none for the others. Linear and partial least squares regression led to numerous associating probes. Association based on genotype classes resulted in similar values, but missed several significant probes. A simulation study was used to successfully validate the number of associating markers. Conclusions: Association of various phenotypic traits with continuous genotypes is successful with both uni- and multivariate regression methods. Genotype calling does not improve the association and shows no advantages in this study. Instead, use of continuous genotypes simplifies the analysis, saves computational time and results more potential markers

Integrating gene expression and GO classification for PCA by preclustering

Contains fulltext : 83407.pdf (publisher's version ) (Open Access)10 p

PERGOLA: fast and deterministic linkage mapping of polyploids

Background: A large share of agriculturally and horticulturally important plant species are polyploid. Linkage maps are used to locate associations between genes and traits by breeders and geneticists. Linkage map creation for polyploid species is not supported by standard tools. We want to overcome this limitation and validate our results with simulation studies. Results: We developed PERGOLA, a deterministic and heuristic method that addresses this problem. We show that it creates correct linkage groups, marker orders and distances for simulated and real datasets. We compare it to existing tools and demonstrate that it overcomes limitations in ploidy and outperforms them in computational time and mapping accuracy. We represent linkage maps as dendrograms and show that this has advantages in the comparison of different maps. Conclusions: PERGOLA can be used successfully to calculate linkage maps for diploid and polyploid species and outperforms existing tools

Exercise intensity modulates capillary perfusion in correspondence with ACE I/D modulated serum angiotensin II levels

During exercise the renin–angiotensin system is stimulated. We hypothesized that the increase in serum angiotensin II (AngII) levels after exercise is dependent on exercise intensity and duration and secondly that people with the ACE-II genotype will show a higher increase in AngII serum levels. We also assumed that perfusion of upper limbs is transiently reduced with maximal cycling exercise and that subjects with the ACE-II compared to the ACE-ID/DD genotype will have a higher capillary perfusion due to lower AngII levels. Ten healthy subjects completed a maximal exercise test, a 12-min exercise test at ventilatory threshold and a 3-min test at the respiratory compensation point. AngII serum levels and capillary recruitment of the skin in the third finger were measured before and after exercise and breath-by-breath gas exchange during exercise was assessed. Baseline levels of AngII levels were lower prior to the 3-min test which took place on average 5 days after the last exercise. A two-fold increase compared to baseline levels was found for AngII only immediately after the 3-min test and not after the maximal exercise test and 12-min of exercise. Subjects without the I allele showed a decrease in AngII values after the maximal test in contrast to subjects with the ACE-II/ID genotype. Subjects with the ACE-II genotype had a 1.8 times significant higher capillary perfusion in the finger after exercise. A trend was observed for a 34.3% decreased capillary recruitment in the ACE-ID/DD genotype after exercise. We conclude that the rise in AngII after exercise is intensity dependent and that variability in serum AngII and capillary perfusion is related to the ACE I/D polymorphism

Additional file 1 of Advantages of continuous genotype values over genotype classes for GWAS in higher polyploids: a comparative study in hexaploid chrysanthemum

Association scores. Tab-separated data file with q-values (LR), VIM-scores (PLS) and BFs (bayz) for all probes for all three traits. (TSV 4970 kb

Additional file 1 of PERGOLA: fast and deterministic linkage mapping of polyploids

Supplementary image. PDF including the additional tanglegrams and results of the simulation study. (PDF 355 kb