Association genetics of complex traits in plants

Contents

	Summary	909
I.	Introduction	910
II.	Genotyping	910
III.	Phenotyping	911
IV.	Study designs	912
V.	The genetics of the ‘omics’	912
VI.	Missing heritability: the dark matter of the genome	913
VII.	Gene interactions	914
VIII.	Many rare alleles	914
IX.	Looking in the wrong place	914
X.	Looking but not seeing	915
XI.	Needles in a haystack	915
XII.	Confounding effects	916
XIII.	Replicating and verifying associations	916
XIV.	The genetic architecture of quantitative traits in plants	917
XV.	Outlook	918
	Acknowledgements	919
	References	919

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.