chapter  5
60 Pages

Molecular Mapping of Complex Traits

WithMałgorzata Kaczmarek, Matthew N. Nelson, Wallace A. Cowling

Genetic variation underlying quantitative phenotypes such as plant yield, pathogen resistance, etc. result from a segregation of numerous quantitative trait loci (QTL), each explaining a portion of the total variation, and whose expression is modifi ed by interactions with other genes and the environment (Mackay 2001). The development of DNA markers enabled the construction of saturated genetic maps and localization of QTL for various phenotypes in various organisms (Glazier et al. 2002). Owing to their favorable genetic attributes, plants are used as model organisms for the study of quantitative traits. They are particularly suitable for high-resolution mapping and positional cloning. Much of the early work in this fi eld was carried out by crossing the individuals of distinct phenotypes to maximize both QTL effects and DNA marker polymorphisms and constructing large experimental populations. Precise evaluation of mean phenotypic values called for statistically signifi cant data obtained from replicated tests performed in different environmental conditions on either clonally reproduced genotypes or stable mapping populations such as recombinant inbred lines (RILs) or introgression lines (ILs). The creation of nearly isogenic lines (NILs) that differ only at a single region increased the precision of estimates of the effects of individual QTL or the interactions between QTLs (Paran and Zamir 2003). Although NILs can help to defi ne the position of a QTL to a small region and thereby provide a shortlist of candidate genes for further investigation, the identity of the gene(s) underlying a QTL must be confi rmed through the genetic and/or functional complementation and gene expression analysis (Paran and Zamir 2003). Two contrasting attributes of QTL analysis are: the relative simplicity of QTL mapping (to date ~ 1,750 papers have been published on QTL mapping in plants alone; www.ncbi.nlm.nih.gov; April 2010) versus the diffi culty in assigning genetic locus to the QTL (until 2005 only 12 genes underlying QTL loci have been cloned) (Mackay 2001).