patterns of population differentiation in a Brassica rapa core collection

• Published in: Theoretical and applied genetics Vol. 122; no. 6; pp. 1105 - 1118
• Main Authors: Pino Del Carpio, Dunia, Basnet, Ram Kumar, De Vos, Ric C. H, Maliepaard, Chris, Visser, Richard, Bonnema, Guusje
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Berlin/Heidelberg : Springer-Verlag 01-04-2011; Springer-Verlag; Springer; Springer Nature B.V
• Subjects: aflp; Agriculture; association; Biochemistry; Biological and medical sciences; Biomedical and Life Sciences; Biotechnology; Botanical research; Brassica rapa; Brassica rapa - anatomy & histology; Brassica rapa - chemistry; Brassica rapa - genetics; Brassica rapa - metabolism; Cell differentiation; Cell physiology; Classical genetics, quantitative genetics, hybrids; Cluster Analysis; Crosses, Genetic; Cruciferae; Databases, Genetic; frequencies; Fundamental and applied biological sciences. Psychology; Genetic aspects; Genetic diversity; Genetic Markers; Genetic research; Genetic Variation; Genetics of eukaryotes. Biological and molecular evolution; landraces; Life Sciences; Metabolism; Metabolites; metabolomics; Microsatellite Repeats; microsatellites; morphological traits; Morphology; Original Paper; Plant Biochemistry; Plant Breeding/Biotechnology; Plant Genetics and Genomics; Plant physiology and development; Population genetics; Principal Component Analysis; Pteridophyta, spermatophyta; spectroscopy; Spectrum analysis; Vegetals; Netherlands; Core Collection; Membership Probability; Morphological Trait; Random Forest; Chinese Cabbage; Brassica rapa; Cruciferae; Dicotyledones; Angiospermae; Samplings; Collection; Genetics; Spermatophyta; Agriculture; Differentiation
• ISSN: 0040-5752; 1432-2242
• DOI: 10.1007/s00122-010-1516-1

With the recent advances in high throughput profiling techniques the amount of genetic and phenotypic data available has increased dramatically. Although many genetic diversity studies combine morphological and genetic data, metabolite profiling has yet to be integrated into these studies. For our study we selected 168 accessions representing the different morphotypes and geographic origins of Brassica rapa. Metabolite profiling was performed on all plants of this collection in the youngest expanded leaves, 5 weeks after transplanting and the same material was used for molecular marker profiling. During the same season a year later, 26 morphological characteristics were measured on plants that had been vernalized in the seedling stage. The number of groups and composition following a hierarchical clustering with molecular markers was highly correlated to the groups based on morphological traits (r = 0.420) and metabolic profiles (r = 0.476). To reveal the admixture levels in B. rapa, comparison with the results of the programme STRUCTURE was needed to obtain information on population substructure. To analyze 5546 metabolite (LC-MS) signals the groups identified with STRUCTURE were used for random forests classification. When comparing the random forests and STRUCTURE membership probabilities 86% of the accessions were allocated into the same subgroup. Our findings indicate that if extensive phenotypic data (metabolites) are available, classification based on this type of data is very comparable to genetic classification. These multivariate types of data and methodological approaches are valuable for the selection of accessions to study the genetics of selected traits and for genetic improvement programs, and additionally provide information on the evolution of the different morphotypes in B. rapa.