Molecular and phenotypic characterization of the Ethiopian nested association mapping (EtNAM) population, an advanced genetic tool to map quantitative trait loci (QTL) in durum wheat

The core purpose of this PhD project was to exploit the molecular and phenotypic diversity of Ethiopian durum wheat NAM population (EtNAM) to identify genetic loci relevant to agronomic importance. We produced Ethiopian durum wheat NAM population (EtNAM) using Ethiopian durum wheat landraces by using methods of (Buckler et al., 2009) which are composed by a set of recombinant inbred lines (RILs). The efficacy of QTL discovery and QTL dissection principally depends on the genetic diversity and structure of the material under study, and on the marker density and molecular information available. As a result, the NAM design should provide increased QTL mapping definition, leading to the discovery of candidate genes underpinning the phenotypes of interest. Quantitative trait locus (QTL) analysis is a statistical method that links two types of information phenotypic data (trait measurements) and genotypic data (usually molecular markers) in an attempt to explain the genetic basis of variation in complex traits. This project has resulted in many findings that can contribute for the scientific community and for human welfare. The Ethiopian durum wheat NAM (EtNAM) founders are 50 landraces providing valuable traits, intercrossed to a recurrent durum wheat line with an international background (Asassa). The resulting population is composed by fifty independent interconnected bi-parental families, for a total of 6,280 RILs. This mapping tool represents the most advanced genetic tool in durum wheat, built with Ethiopian landrace materials. Subgroups of 12 families, 100 RILs each were selected for genomic and phenotypic characterization and for further Genome Wide Association studies. We argue that the EtNAM may act as a breeding tool and a research tool, supporting the identification of QTL of agronomic relevance and their incorporation in pre-breeding materials. High through put genomic characterization of a subset of 12 EtNAM families, represented by 1,200 RILs have showed elevated allelic variation and a genetic structure with RILs closing the gap between local and international allele pools. The EtNAM shows high minor allele frequency and fast linkage disequilibrium decay, suggesting elevated QTL mapping power and definition. This study is the first to describe an advanced multiparental population build with Ethiopian durum wheat. The information that we have generated is also valuable to identify QTL for important agronomic and diseases resistance traits. Phenotypic characterization on a subset of 12 EtNAM families revealed that the EtNAM population has wider variability that can be utilized further in breeding for better production and association mapping identified 237 marker trait associations (MTAs) in total between SNP markers and 12 quantitative traits. The main objectives of this project were to understand the diversity and genetic bases of agronomic traits in durum wheat through various techniques. The techniques that we used to dissect the diversity of EtNAM were found to be effective to meet the objectives. The EtNAM population exhibited high genotypic and phenotypic diversity that can be utilized in the development and improvement of new crop varieties and in quantitative trait locus (QTL) mapping for identification of genetic variations useful for breeding and genetics programs to boost productivity under increased human population and climate change. The EtNAM population is a promising resource to be characterized for different environments, as could help as pre-breeding material. The information that we have generated is also valuable for the choice of parental lines to use in crosses for breeding purposes. We studied subset of the EtNAM population and a more profound result could have been found if the entire population was considered.