Identification of environment types and adaptation zones with self-organizing maps; applications to sunflower multi-environment data in Europe.

KEY MESSAGE: We evaluate self-organizing maps (SOM) to identify adaptation zones and visualize multi-environment genotypic responses. We apply SOM to multiple traits and crop growth model output of large-scale European sunflower data. Genotype-by-environment interactions (G × E) complicate the selection of well-adapted varieties. A possible solution is to group trial locations into adaptation zones with G × E occurring mainly between zones. By selecting for good performance inside those zones, response to selection is increased. In this paper, we present a two-step procedure to identify adaptation zones that starts from a self-organizing map (SOM). In the SOM, trials across locations and years are assigned to groups, called units, that are organized on a two-dimensional grid. Units that are further apart contain more distinct trials. In an iterative process of reweighting trial contributions to units, the grid configuration is learnt simultaneously with the trial assignment to units. An aggregation of the units in the SOM by hierarchical clustering then produces environment types, i.e. trials with similar growing conditions. Adaptation zones can subsequently be identified by grouping trial locations with similar distributions of environment types across years. For the construction of SOMs, multiple data types can be combined. We compared environment types and adaptation zones obtained for European sunflower from quantitative traits like yield, oil content, phenology and disease scores with those obtained from environmental indices calculated with the crop growth model Sunflo. We also show how results are affected by input data organization and user-defined weights for genotypes and traits. Adaptation zones for European sunflower as identified by our SOM-based strategy captured substantial genotype-by-location interaction and pointed to trials in Spain, Turkey and South Bulgaria as inducing different genotypic responses.

Association between the UGT1A1 TA-repeat polymorphism and bilirubin concentration in patients with intermittent claudication: results from the CAVASIC study.

BACKGROUND: Bilirubin has antioxidative and cytoprotective properties. Low plasma concentrations of bilirubin are reportedly associated with the development of coronary and cerebrovascular disease, and bilirubin concentrations are strongly correlated with the enzyme activity of the hepatic uridine diphosphate glucuronosyltransferase (UGT1A1). The activity of UGT1A1 is influenced by a TA-repeat polymorphism in the promoter of the UGT1A1 gene (UDP glucuronosyltransferase 1 family, polypeptide A1). In a case-control study, we investigated the association between the UGT1A1 polymorphism, bilirubin concentration, and intermittent claudication. METHODS: We included 255 consecutive male patients presenting with intermittent claudication in the investigation and matched the patients by age and diabetes mellitus with 255 control individuals. RESULTS: Plasma bilirubin concentrations were significantly lower in patients than in controls [mean (SD), 12.5 (5.3) micromol/L vs 15.4 (7.9) micromol/L; P < 0.001]. We found a clear association between the number of TA repeats and plasma bilirubin concentration. Considering the 6/6 TA-repeat genotype as the wild type, we observed a slight increase in bilirubin concentration individuals with the heterozygous 6/7 genotype and pronounced increases for those with the homozygous 7/7 genotype. This association occurred in both controls and patients; however, patients and controls were not significantly different with respect to UGT1A1 TA-repeat genotype frequencies. CONCLUSIONS: Our study of a well-phenotyped group of patients with intermittent claudication and control individuals revealed a clear association between low bilirubin concentrations and peripheral arterial disease but no association between the UGT1A1 polymorphism and the disease.

APOA5 variants and metabolic syndrome in Caucasians.

Apolipoprotein A5 (APOA5) gene variants were reported to be associated with two components of metabolic syndrome (MetS): higher TG levels and lower HDL levels. Moreover, a recent Japanese case-control study found variant -1131T>C associated with MetS itself. Thus, our study systematically analyzed the APOA5 gene for association with lipid parameters, any other features of MetS, including waist circumference, glucose-related parameters, blood pressure, uric acid, and MetS itself in Caucasians. Ten polymorphisms were analyzed in a large fasting sample of the population-based Cooperative Health Research in the Region of Augsburg (KORA) survey S4 (n = 1,354; southern Germany) and in a second fasting sample, the Salzburg Atherosclerosis Prevention Program in Subjects at High Individual Risk (SAPHIR) study (n = 1,770; Austria). Minor alleles of variants -1131T>C, -3A>G, c.56C>G, 476G>A, and 1259T>C were significantly associated with higher TG levels in single polymorphism (P < 0.001) and haplotype (P G was associated with higher risk for MetS [odds ratio (95% confidence interval) = 1.43 (1.04, 1.99), P = 0.03 for KORA and 1.48 (1.10, 1.99), P = 0.009 for SAPHIR). Our study confirms the association of the APOA5 locus with TG and HDL levels in humans. Furthermore, the data suggest a different mechanism of APOA5 impact on MetS in Caucasians, as variant c.56C>G (not analyzed in the Japanese study) and not -1131T>C, as in the Japanese subjects, was associated with MetS.