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FT ; K between 1 and 10 subpopulations, with a total of , population 2, includes several types: pak choi, winter oil, iterations for MCMC repetitions and burn in of , The auto-scaled data from the 26 morphological traits were Of the accessions, were assigned to a group with a used for principal components analysis PCA. PCA is the probability value of p [ 0. The morphotypes with amounts of variance and cumulative explained variances highest levels of admixture were the winter oil accessions per component.

FT and population 2 PC? To test the correlation between the clusters calculated with the phenotypic and genotypic marker data, a Mantel test Multivariate analyses was applied in R packages ape4 and ecodist Goslee and Urban ; Mantel Based on the allelic frequency classi- showed that most of the accessions were included into fication, STRUCTURE result assigns the accessions to subgroups that had non-significant bootstrap values.

In the GeneSrF web-based application this However, the hierarchical clustering results are mostly subgroup classification was inserted as the class file and the supported by the results obtained with STRUCTURE and 5, LC—MS mass scan data were input as the equivalent represent the classification based on morphotype and the of the expression data file. We considered the mean class geographical origin. Colors in the second column indicate geographic origin; red company line, yellow Asia, blue Europe, green America.

Bootstrap values higher than 20 are indicated color figure online few small groups of accessions Fig. The separation into these subgroups is not supported by high bootstrap values. The most relevant loadings for the PC1 were mostly leaf characteristics and flowering time and for PC2 the most important loadings were a combination of leaf and flower characteristics Table 2.

Correlation analysis of the 26 morphological traits showed significant and high correlations within leaf, flower and plant architecture traits, high values were also found between leaf area and width and flower traits area and width in corre- spondence to a possible modularity and genetic co-regulation of these developmental traits data not shown.

Leaf traits Leaf length LL Length from base of petiole to tip of lamina cm 0. Flower traits Corolla length CL Symmetric length between petals mm Plant architecture trait Leaf number LN Number of the leaves when the first flower opens However, the winter oil, mizuna and few Chinese cabbages; and group composition of each group showed a high correspondence IV consists of 47 accessions mainly CC accessions and with the four subpopulations found with molecular marker modern company CC accessions.

From these 31 YS and SO and 1 winter oil accession; group II includes accessions, 12 were also differently classified when 33 accessions of the following types: broccoletto, European molecular marker data were used for the hierarchical clus- vegetable and fodder turnips; group III, the most admixed tering Fig.

These accessions have an admixed group in terms of morphotypes and its relationship to the genetic nature, which allows for flexibility in terms of group STRUCTURE subgroups, is composed by 81 accessions of assignment Table S1. Bootstrap values higher than 20 are indicated. Comparison of blocks from the same year, by means of linear correlation regression analysis, resulted in average r2 values of 0.

Comparison of results between years gave an average r2 value of 0. These results indicate that the LC—MS pro- files of mass scan signals obtained from each accession are highly repeatable within and between years. Based on this biological repetition experiment on 17 homogeneous lines, we can assume that the metabolite profiles observed within the B.

Further- more, the LC—MS profiling was repeated with leaf samples from a group of nine accessions of the pak choi morphotype, which are genetically heterogeneous. The samples were taken from two plants grown in two blocks in the same year Clustering based on information from centro- types indicated that the variation found within accessions bootstrap values 99 or is lower than the variation between accessions as observed by clustering Fig. Comparison of morphological, metabolic and molecular group classification Although the bootstrap values obtained with hierarchical clustering were low the distance values were used to test the correlation between results with the different datasets.

The Mantel test between morphological and molecular distances revealed a strong and significant correlation value Fig. In the comparison between nine pak choi accessions. The number of variables metabolite: Population 1 Population 2 Population 3 Population 4 mass scan number from the original dataset that can summarize, in a small subset, the differences between the Population 1 classes 4 population subgroups was estimated. The mean Population 2 0.

In the variable selection using all data a number of Among 3 For the Within 1, Fixation index Correlation analysis between these individual mass FST: 0. Ric de Vos unpublished results. The mean allele number per SSR over all loci in feoylquinic acid, chlorogenic acid, coumaroylquinic acid, the four sub-populations is 4.

The highest mean value for quercetin 3- 2-feruloylsophoroside 7-diglucoside and ka- alleles was found in population 1 VT? FT European empferol coffeoyl tetraglucoside. The mass signals repre- turnip and broccoletto group and population 2 PC? T senting these 35 compounds were further used to construct with a value of 5. Two biological replicates were The genetic diversity corrected for sample size He cal- included in these cluster analyses, an oil type RO18 and a culated over the four populations ranged from 0.

FT European turnip and population 4 and group 3 PC? The oil group SO, YS and group of 0. FT European turnip and broccoletto group and groups, the summer and spring oil accessions, with population 2 PC? T pak choi and turnip group of 0. FT - population 2 PC? AMOVA results indicate that the highest per- Discussion centage of variation is found within populations Table 5. With the recent advances in high throughput profiling techniques the amount of genetic and phenotypic data Random forest classification and identification available has increased dramatically.

Although many of variables studies combine morphological and genetic data, metabo- lite profiling has yet to be integrated into diversity studies. The For our research we composed a B. In con- way the effect of population confounding. Random has undergone during centuries of cultivation. For future research high position and developmental traits. However, like in the study of Zhao et al. Because the same result is Besides the classification purposes of this study, the obtained when the morphological and metabolic data are value of multivariate data analysis to reveal morphotypes included in the cluster analysis we can also conclude that ancestry and evolutionary processes should be acknowl- only a few genes are involved in the emergence of crop edged.

It has been suggested that in B. In the study of genetic rela- highly correlated to the groups based on morphological tionships among cultivated types of B. Furthermore, the four admixture, which indicate the presence of genetic back- subpopulations show correspondence to the B.

This ancestry origin Asia and Europe. In our study we made use of SSRs with known evolution of the B. Our R package for gene selection and classification using random forest.

BMC Bioinform statistical approaches have been successful to unravel the Diaz-Uriarte R, Alvarez de Andres S Gene selection and complexity of the data and to establish relationships classification of microarray data using random forest. BMC between accessions using genetic markers, morphological Bioinform data and metabolite profiles. Dixon GR Vegetable Brassicas and related crucifers. Evol Bioinform Online —50 a high correlation with the genetic classification.

Trends Genet —48 hierarchical clustering of molecular data was not sufficient Gomez-Campo C Developments in plant genetics and to reveal the level of admixture in B. Biology of Brassica coenospecies. Mol Ecol Notes — methodological approach is valuable for the selection of Hartings H, Berardo N, Mazzinelli GF, Valoti P, Verderio A et al Assessment of genetic diversity and relationships among accessions to study the genetics of selected traits and for maize Zea mays L.

Italian landraces by morphological traits genetic improvement programs. This project was co financed by the Centre mining with R. R package version 1. PLoS tions in Brassica crop species. BMC Genet Chinese Brassica campestris vegetables: Chinese cabbage, purple Mantel N The detection of disease clustering and a generalized cai-tai, choysum, pakchoi, and turnip. HortScience — regression approach. Crop Sci BMC. Bioinformatics — Cockerham CC Variance of gene frequencies.

Evolution Nei M Estimation of average heterozygosity and genetic —84 distance from a small number of individuals. Genetics — Cockerham CC Analysis of gene frequencies. Evol Bioinform Online derivatives in turnip tops Brassica rapa L. Topolski , J. View on PubMed. Save to Library Save. Create Alert Alert. Share This Paper. Background Citations. Methods Citations. Results Citations. Tables and Topics from this paper.

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