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Keywords:

  • association mapping;
  • complex traits;
  • genetic architecture;
  • genotyping;
  • phenotyping

Contents

 Summary909
I.Introduction910
II.Genotyping910
III.Phenotyping911
IV.Study designs912
V.The genetics of the ‘omics’912
VI.Missing heritability: the dark matter of the genome913
VII.Gene interactions914
VIII.Many rare alleles914
IX.Looking in the wrong place914
X.Looking but not seeing915
XI.Needles in a haystack915
XII.Confounding effects916
XIII.Replicating and verifying associations916
XIV.The genetic architecture of quantitative traits in plants917
XV.Outlook918
 Acknowledgements919
 References919

Summary

Association mapping is rapidly becoming the main method for dissecting the genetic architecture of complex traits in plants. Currently most association mapping studies in plants are preformed using sets of genes selected to be putative candidates for the trait of interest, but rapid developments in genomics will allow for genome-wide mapping in virtually any plant species in the near future. As the costs for genotyping are decreasing, the focus has shifted towards phenotyping. In plants, clonal replication and/or inbred lines allows for replicated phenotyping under many different environmental conditions. Reduced sequencing costs will increase the number of studies that use RNA sequencing data to perform expression quantitative trait locus (eQTL) mapping, which will increase our knowledge of how gene expression variation contributes to phenotypic variation. Current population sizes used in association mapping studies are modest in size and need to be greatly increased if mutations explaining less than a few per cent of the phenotypic variation are to be detected. Association mapping has started to yield insights into the genetic architecture of complex traits in plants, and future studies with greater genome coverage will help to elucidate how plants have managed to adapt to a wide variety of environmental conditions.