Improving waterlogging tolerance in barley with molecular and physiological markers

Over 17 million km\\(^2\\) of land surface is affected by flooding every year, resulting in severe damages to plants and yield losses in agricultural production around the globe. While the importance of plant breeding for waterlogging tolerance has long been on the agenda, the progress in the field is handicapped by the physiological and genetic complexity of this trait. The main feature of waterlogged soils is oxygen deprivation, due to slow gas diffusion in water. Decreased oxygen content in waterlogged soils leads to oxygen deficiency, resulting in reduced energy availability for plants. Plant adaptation to waterlogged conditions requires a set of morphological and physiological/biochemical changes. The formation of aerenchyma is one of the most crucial adaptive traits for waterlogging tolerance in wetland species such as rice. Enzymatic scavenging may also contribute to waterlogging tolerance by providing detoxification of reactive oxygen species (ROS). In this thesis, the changes of root porosity (an indicator of aerenchyma formation in roots) and activities in leaves of four major antioxidant enzymes was reported, in six barley genotypes contrasting in waterlogging tolerance. Soil waterlogging caused significant increases in adventitious root porosity in all genotypes. Waterlogging tolerant genotypes showed not only significantly higher adventitious root porosity than sensitive genotypes (P < 0.01) but also much faster development of aerenchyma. In contrast, antioxidant enzyme activities in leaves did not correlate with waterlogging tolerance. Quantifying aerenchyma formation after 7 days of waterlogging can be a fast and reliable approach for the selection of waterlogging tolerant barley genotypes, which is supported by measurements of redox potential (an indicator of anaerobic conditions). This protocol was also used to identify quantitative trait loci (QTL) in a doubled haploid population of barley from the cross between Yerong (tolerant) and Franklin (sensitive) genotypes. The QTL for aerenchyma formation and root porosity were at the same location as one of the major QTL for waterlogging tolerance. The major QTL for aerenchyma formation after 7 days waterlogging treatment on chromosome 4H explained 42.8% of the phenotypic variance. Seven new markers were developed and added onto this region on chromosome 4H. These markers can be effectively used in marker assisted selection to improve waterlogging tolerance in barley. A wild barley genotype TAM407227 showed very good tolerance to waterlogging and, therefore, provides a useful resource for breeding waterlogging tolerant barley. A high density linkage map was constructed between the wild barley and a cultivated barley Franklin (waterlogging sensitive) using 163 doubled haploid lines. A total of 17 QTL were detected for various traits under waterlogging and control conditions. A new major allele for waterlogging tolerance and aerenchyma formation under waterlogging conditions was identified. The QTL for aerenchyma formation on chromosome 4H explained 76.8% phenotypic variance with a LOD value of 51.4. The high density linkage maps and the QTL for aerenchyma formation can be effectively used for further fine mapping, QTL positional cloning, and marker assisted selection. Breeding for abiotic stress tolerant crops has drawn increased attention and a large number of QTL for drought, salinity, and waterlogging tolerance in barley have been detected. However, very few QTL have been successfully used in marker assisted selection in breeding programs. We summarized 632 QTL for drought, salinity and waterlogging tolerance in barley. Among all these QTL, 195 major QTL with a LOD value above 3.0 were used to conduct metaanalysis to refine QTL positions for use in marker assisted selection. Meta-analysis was used to map the summarized major QTL for drought, salinity, and waterlogging tolerance from different mapping populations onto the barley physical map. The positions of identified meta-QTL (MQTL) were used to search for candidate genes for drought, salinity, and waterlogging tolerance in barley. Two meta-QTL, MQTL3H.4 and MQTL6H.2, were found to be associated with drought tolerance. Fine mapped QTL for salinity tolerance, HvNax4 and HvNax3, were validated on MQTL1H.4 and MQTL7H.2, respectively. MQTL2H.1 and MQTL5H.3 are also the target regions for improving salinity tolerance in barley. MQTL4H.4 with a fine mapped QTL for aerenchyma formation under waterlogging conditions is the main region controlling waterlogging tolerance in barley. Detected and refined MQTL and candidate genes are crucial for future successful marker assisted selection in barley breeding.