Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 501720
Title Genome-wide association mapping and genomic prediction elucidate the genetic architecture of morphological traits in arabidopsis
Author(s) Kooke, Rik; Kruijer, Willem; Bours, Ralph; Becker, Frank; Kuhn, A.; Geest, Henri van de; Buntjer, Jaap; Doeswijk, Timo; Guerra, José; Bouwmeester, Harro; Vreugdenhil, Dick; Keurentjes, Joost J.B.
Source Plant Physiology 170 (2016)4. - ISSN 0032-0889 - p. 2187 - 2203.
DOI https://doi.org/10.1104/pp.15.00997
Department(s) Laboratory of Plant Physiology
Groep KoornneefGroep Koornneef
Biometris (WU MAT)
Biosystematics
PRI BIOS Applied Bioinformatics
EPS
Publication type Refereed Article in a scientific journal
Publication year 2016
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.

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