Chapter 13 - Translating genetics into genomics: From QTL identification to candidate gene discovery in rice

Abstract

Quantitative trait loci (QTL) are major contributors to genetic variation in natural populations and have paramount importance in plant breeding programs for crop improvement. Before the initiation of genome sequencing programs, understanding the genetic basis of complex traits remained challenging and biometrical assumptions based on phenotype were used to predict the genetic control of these traits. However, after the advent of molecular markers and next-generation sequencing technologies, a major leap was made toward identifying the genomic regions regulating phenotypic plasticity in quantitative traits. This chapter briefly discusses the genetic basis of quantitative traits with a focus on translating conventional genetics knowledge into modern genomics evidence. We provide an overview of sources of genetic variation, different types of QTLs, mapping methods and software, mining of QTL regions for the discovery of trait-linked candidate genes, and exploitation of major effect QTLs and functionally characterized genes for improvement of yield, quality, and stress tolerance in one of the most produced and consumed food grain crop, the rice. This information could help molecular rice breeders in understating the genetics of complex agronomic traits with the possibility to exploit it for further crop improvement.