“Noisy beets”: impact of phenotyping errors on genomic predictions for binary traits in <Emphasis Type="Italic">Beta vulgaris</Emphasis>

Background

Noise (errors) in scientific data is endemic and may have a detrimental effect on statistical analyses and experimental results. The effects of noisy data have been assessed in genome-wide association studies for case-control experiments in human medicine. Little is known, however, on the impact of noisy data on genomic predictions, a widely used statistical application in plant and animal breeding.

Results

In this study, the sensitivity to noise in the data of five classification methods (K-nearest neighbours—KNN, random forest—RF, ridge logistic regression—LR, and support vector machines with linear or radial basis function kernels) was investigated. A sugar beet population of 123 plants phenotyped for a binary trait and genotyped for 192 SNP (single nucleotide polymorphism) markers was used. Labels (0/1 phenotype) were randomly sampled to generate noise. From the base scenario without errors in the labels, increasing proportions of noisy labels—up to 50 %—were generated and introduced in the data.

Conclusions

Local classification methods—KNN and RF—showed higher tolerance to noisy labels compared to methods that leverage global data properties—LR and the two SVM models. In particular, KNN outperformed all other classifiers with AUC (area under the ROC curve) higher than 0.95 up to 20 % noisy labels. The runner-up method, RF, had an AUC of 0.941 with 20 % noise.

     

Combining abilities of sugar beet genotypes for root- and sugar-related traits under multi-environment trials

The improvement of sugar-related factors is associated with root traits in sugar beet. The objectives of the present study were to assess variations of sugar- and root yield (RY)-related traits and to estimate general (GCA) and specific (SCA) combining abilities of several lines, testers and hybrids under various environmental conditions. A line × tester mating design was used to develop 28 hybrids from seven lines × four testers. Presently, root- and sugar-related traits were recorded in parental lines, hybrids and five local ('Pars', 'Torbat' and 'Ekbatan') and international ('Kermit' and 'Tous') check varieties in the eight combinations of location and growing season. Mean RY and sugar yield (SY) were 44.81 t/ha and 7.57 t/ha, respectively. Genotypes tested had 16.91% sugar content (SC) and 13.64% white sugar content (WSC) across trials. No one genotype was found to have high levels for all traits, but several had above mean sugar-related or RY traits. L7T2 as the best hybrid for RY and SY yielded 37.0% and 34.4% more than the checks’ mean, whereas ratios for the best hybrid (L7T4) for SC and WSC were 8.2% and 4.3%, respectively. Additive variance was significant for all traits, whereas dominance component was only significant for RY. Several parental lines had stable GCA effects with respect to direction and magnitude for WSC, RY and SC in environments. L7 and T2 for RY and SY and L3 and T4 for SC and WSC were identified as the best combiners with high GCA effects, and their use might increase favourable alleles in further breeding programmes for traits tested. Estimated heritability for the combined environments was lower for sugar-related traits (54.01%–59.39%) compared with those for RY traits (73.68%–74.21%). Overall, given heritability and additive variances estimated the identification of environmentally stable GCA and SCA effects and might help to increase efficiency of selection of superior cultivars with respect to sugar traits.     

Root traits and yield in sugar beet: identification of AFLP markers associated with root elongation rate

Morpho-physiological and molecular analysis were conducted to identify useful root indexes of sugar beet nutrient uptake capacity and productivity. Root architectural parameters, root elongation rate, sulfate uptake rate and glucose and fructose content in the root apex, traits involved in the plant response to sulfate stress, were evaluated in 18 sugar beet genotypes characterized by different root yield. Morpho-physiological traits, determined on 11-day-old seedlings grown in hydroponics under sulfate deprivation, showed variations from 59 to 197% and were significantly correlated (P < 0.01) with root yield. Under field conditions, the highest root yield genotype (L18), which has the highest root phenotypic values following sulfate shortage, also showed the greatest root length density and leaf relative water content, with respect to the lowest root yield genotype (L01). Bulk segregant analysis based on AFLP analysis, done on a segregating progeny obtained from the cross between the two lines L01 × L18, allowed the identification of two AFLP markers associated to the root elongation rate parameter that showed the highest variation among all the analyzed root traits. The genetic diversity of root adaptive traits and the use of marker-assisted selection aimed at increasing sugar yield under water and nutrient stress in sugar beet breeding programmes are discussed.     

Quantitative characterization of flavonoid compounds in Rooibos tea (Aspalathus linearis) by LC-UV/DAD

Rooibos tea originates from the leaves and stems of the indigenous South African plant Aspalathus linearis. It has gained much attention for clinical purposes in the case of nervous tension, allergies (dermatitis), and various indigestive problems. Recently, antioxidative activity was also attributed to the tea on the basis of its flavonoid content. Therefore, an HPLC method using a C(18) reversed phase column was developed for the assay of 10 flavonoids in aqueous and methanolic infusions. Main compounds determined were the dihydrochalcone aspalthin, rutin, and orientin, and their content was in the range of 1.0 to 1.3 mg/g. The identity of detected flavonoids was confirmed by comparing their retention times and UV and MS spectra with those of corresponding standards. In addition, the MS analysis showed evidence of the presence of other compounds such as nothofagin, dihydroisoorientin, and dihydroorientin.     

Metabolism of stevioside and rebaudioside A from Stevia rebaudiana extracts by human microflora

Stevia rebaudiana standardized extracts (SSEs) are used as natural sweeteners or dietary supplements in different countries for their content of stevioside or rebaudioside A. These compounds possess up to 250 times the sweetness intensity of sucrose, and they are noncaloric and noncariogenic sweeteners. The aim of this study was to investigate the in vitro transformation of stevioside and rebaudioside A after incubation with human microflora, the influence of these sweeteners on human microbial fecal community and which specific groups metabolize preferentially stevioside and rebaudioside A. The experiments were carried out under strict anaerobic conditions in batch cultures inoculated with mixed fecal bacteria from volunteers. The hydrolysis was monitored by HPLC coupled to photodiode array and mass spectrometric detectors. Isolated bacterial strains from fecal materials incubated in selective broths were added to stevioside and rebaudioside A. These sweeteners were completely hydrolyzed to their aglycon steviol in 10 and 24 h, respectively. Interestingly, the human intestinal microflora was not able to degrade steviol. Furthermore, stevioside and rebaudioside A did not significantly influence the composition of fecal cultures; among the selected intestinal groups, bacteroides were the most efficient in hydrolyzing Stevia sweeteners to steviol.     

Sources of resistance to diseases of sugar beet in related Beta germplasm: II. Soil-borne diseases

Between 580 and 700 accessions of related cultivated and wild species of the genus Beta were assessed for resistance to four soil-borne diseases of sugar beet: two seedling damping-off diseases caused by the fungi Aphanomyces cochlioides and Pythium ultimum and two diseases of more mature plants, Rhizoctonia root and crown rot, caused by the fungus R. solani, and Rhizomania, caused by Beet necrotic yellow vein virus (BNYVV), a furovirus transmitted by the plasmodiophorid Polymyxa betae. Analysis of resistance data (assessed on an international standardised 1–9 scale of Resistance Scores) indicated that the highest levels of resistance ({RS} 2) to A. cochlioides and P. ultimum were to be found amongst accessions of the more distantly related sections Corollinae (93% of accessions tested) and Procumbentes (10%), respectively; although useful levels could also be found in the more closely related, and sexually compatible, section Beta (1–6%). Resistance to Rhizoctonia was also found in section Beta (5–7%), depending on whether field or glasshouse tests were used, but there was little evidence of generally high levels of resistance to Rhizomania among accessions of this section. None of the accessions of sections Corollinae and Procumbentes exhibited any notable resistance to Rhizoctonia. However, all sections Procumbentes and some sections Corollinae (4%) accessions were highly resistant to Rhizomania. Individuals with high levels of resistance to Rhizomania were identified from within some section Beta and Corollinae accessions, in which there was evidence of segregation.     

Molecular and morpho-physiological characterization of sea,ruderal and cultivated beets

Beta vulgaris genetic resources are essential for broadening genetic base of sugar beet and developing cultivars adapted to adverse environmental conditions. Wild beets (sea beets, B. vulgaris spp. maritima and their naturalized introgressions with cultivated beets known as ruderal beets) harbor substantial genetic diversity that could be useful for beet improvement. Here, we compared molecular and morpho-physiological traits of wild beets collected on the Adriatic coast of Italy with sugar beet using eight primer-pairs amplifying 194 polymorphic fragments and four root traits (glucose and fructose content in the root tip, root elongation rate, number of the of root tips, total root length and its distribution among diameters ranges). Genetic diversity was higher in the sea beet accession, which may be due to the highly variable selection pressures that occur in heterogeneous ecological niches, compared with the ruderal and cultivated beets. Sea and sugar beet accessions showed contrasting root patterns in response to sulfate deprivation: sugar beet showed an increase of reducing sugars in the root tips and higher root elongation rate, and the sea beet accession showed an increase in root tip number, total root length and fine root length (average diameter < 0.5 mm). The ruderal beet showed intermediary responses to sea and sugar beet accessions. AFLP and morpho-physiological cluster analyzes showed sea, ruderal and cultivated beets to be genetically distinct groups. The results of this study indicate variability in response to sulfate deprivation is present in undomesticated beets that could be deployed for sugar beet improvement.     

The extent of non-Born-Oppenheimer coupling in the reaction of Cl(2P) with para-H2

Elementary triatomic reactions offer a compelling test of our understanding of the extent of electron-nuclear coupling in chemical reactions, which is neglected in the widely applied Born-Oppenheimer (BO) approximation. The BO approximation predicts that in reactions between chlorine (Cl) atoms and molecular hydrogen, the excited spin-orbit state (Cl*) should not participate to a notable extent. We report molecular beam experiments, based on hydrogen-atom Rydberg tagging detection, that reveal only a minor role of Cl*. These results are in excellent agreement with fully quantum-reactive scattering calculations based on two sets of ab initio potential energy surfaces. This study resolves a previous disagreement between theory and experiment and confirms our ability to simulate accurately chemical reactions on multiple potential energy surfaces.