title: Genome-Wide Association Mapping and Genomic Prediction Elucidate the Genetic Architecture of Morphological Traits in Arabidopsis.
abstract: Quantitative traits in plants are controlled by a large number of genes and their interaction with the environment. To disentangle the genetic architecture of such traits, natural variation within species can be explored by studying genotype-phenotype relationships. Genome-wide association studies that link phenotypes to thousands of single nucleotide polymorphism markers are nowadays common practice for such analyses. In many cases, however, the identified individual loci cannot fully explain the heritability estimates, suggesting missing heritability. We analyzed 349 Arabidopsis accessions and found extensive variation and high heritabilities for different morphological traits. The number of significant genome-wide associations was, however, very low. The application of genomic prediction models that take into account the effects of all individual loci may greatly enhance the elucidation of the genetic architecture of quantitative traits in plants. Here, genomic prediction models revealed different genetic architectures for the morphological traits. Integrating genomic prediction and association mapping enabled the assignment of many plausible candidate genes explaining the observed variation. These genes were analyzed for functional and sequence diversity, and good indications that natural allelic variation in many of these genes contributes to phenotypic variation were obtained. For ACS11, an ethylene biosynthesis gene, haplotype differences explaining variation in the ratio of petiole and leaf length could be identified.
authors: Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.).
authors: Rik
authors: R
authors: Kooke
authors: Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.).
authors: Willem
authors: W
authors: Kruijer
authors: Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.).
authors: Ralph
authors: R
authors: Bours
authors: Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.).
authors: Frank
authors: F
authors: Becker
authors: Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.).
authors: André
authors: A
authors: Kuhn
authors: Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.).
authors: Henri
authors: H
authors: van de Geest
authors: Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.).
authors: Jaap
authors: J
authors: Buntjer
authors: Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.).
authors: Timo
authors: T
authors: Doeswijk
authors: Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.).
authors: José
authors: J
authors: Guerra
authors: Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.).
authors: Harro
authors: H
authors: Bouwmeester
authors: Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.).
authors: Dick
authors: 0000-0002-9014-9516
authors: D
authors: Vreugdenhil
authors: Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., R.B., A.K., H.B., D.V.); Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., F.B., J.J.B.K.); Centre for Biosystems Genomics, Wageningen Campus, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (R.K., H.v.d.G., D.V., J.J.B.K); Biometris, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (W.K.); PRI Bioinformatics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands (H.v.d.G.); and Keygene, Agro Business Park 90, 6708 PW Wageningen, the Netherlands (J.B., T.D., J.G.) joost.keurentjes@wur.nl.
authors: Joost J B
authors: 0000-0001-8918-0711
authors: JJ
authors: Keurentjes
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D002874:Chromosome Mapping; D002980:Climate; D056726:Genetic Association Studies; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods*; D005843:Geography; D040582:Inheritance Patterns / Q000235:genetics; D010641:Phenotype; D018515:Plant Leaves / Q000033:anatomy & histology / Q000235:genetics; D019655:Quantitative Trait, Heritable; D015203:Reproducibility of Results
chemical_list: D029681:Arabidopsis Proteins