comparative methods for association studies a case study on metabolite variation in a brassica rapa core collection比较关联方法研究一个案例研究在芸苔属植物代谢物变化拉伯核心集合.pdfVIP

Comparative Methods for Association Studies: A Case Study on Metabolite Variation in a Brassica rapa Core Collection 1. 1,3. 2,3 1 ˜ Dunia Pino Del Carpio , Ram Kumar Basnet , Ric C. H. De Vos , Chris Maliepaard , Maria Joao Paulo4, Guusje Bonnema1,3* 1 Laboratory of Plant Breeding, Wageningen University, Wageningen, The Netherlands, 2 Plant Research International, Wageningen University and Research Centre (Wageningen-UR), Wageningen, The Netherlands, 3 Centre for BioSystems Genomics, Wageningen, The Netherlands, 4 Biometris-Applied Statistics, Wageningen University and Research Center, Wageningen, The Netherlands Abstract Background: Association mapping is a statistical approach combining phenotypic traits and genetic diversity in natural populations with the goal of correlating the variation present at phenotypic and allelic levels. It is essential to separate the true effect of genetic variation from other confounding factors, such as adaptation to different uses and geographical locations. The rapid availability of large datasets makes it necessary to explore statistical methods that can be computationally less intensive and more flexible for data exploration. Methodology/Principal Findings: A core collection of 168 Brassica rapa accessions of different morphotypes and origins was explored to find genetic association between markers and metabolites: tocopherols, carotenoids, chlorophylls and folate. A widely used linear model with modifications to account for population structure and kinship was followed for association mapping. In addition, a machine learning