Revealing gene regulation and associations through biological networks

Christophe Liseron-Monfils, Doreen Ware
2015 Current Plant Biology  
D. Ware). the wild varieties or ancestors of extant crop plants to recover lost genetic diversity. Such (re) discovery of lost alleles could help meet challenging breeding goals such as conferring tolerance to drought, salinity, and other stresses [1, 2] . Historically, the methods of choice for identifying candidate loci/genes primarily involved identification of quantitative trait loci (QTLs). In such analyses, phenotypic observations are associated with genetic region segregation, taking
more » ... ntage of linkage disequilibrium. In crop species, one aim of QTL analysis is to define genetic regions responsible for architectural and stress-related phenotypes, e.g., the response to water deficit and the efficiency of nitrogen use [3] [4] [5] . However, these genetic regions can be very large, due to the size of the QTL confidence intervals. To discover the causal genes, it is required to manually parse ∼100 candidate genes per locus. Sometimes, the number of candidate genes can be reduced using fine mapping, by finding additional makers within the QTL interval. Nevertheless, the process of narrowing a QTL is highly time-consuming [6] . Moreover, the outcome is not always guaranteed, as it depends upon the rate of crossing-over in the http://dx.
doi:10.1016/j.cpb.2015.11.001 fatcat:oz6mwmi6nrgnlgmnahp7bc7yim