Identification of novel loci and alleles for drought and heat stress tolerance in wheat

Abstract

Wheat is one of the most important food sources worldwide contributing to around 20 % of the total calories and proteins in the human diet. However, many wheat growing regions of the world are affected by drought and heatwave events every year, threatening global food security. Whereas responses to drought and heat stress have been studied extensively in wheat, the combination of both environmental stresses has just recently become a matter of research. To ensure future food productivity, the genetic improvement of crops for combined drought and heat stress tolerance and the development of high-throughput phenotyping methods are required. With the aim to identify novel loci for drought and heat stress tolerance at early grain-filling, which then could be used in future wheat breeding, a worldwide collection of 315 diverse wheat genotypes was analysed using genome-wide association (Chapter 2). Experiments were carried out in a semi-controlled facility over two successive years, subjecting plants to either drought or combined drought and heat treatments. We identified a total of 452 quantitative trait loci (QTL) for flag leaf water potential, spike length, spike number, aboveground biomass, harvest index, screenings (i.e., percentage of small seeds), single seed weight, seed number and seed weight under drought, for the heat response under drought and under combined drought and heat stress. 134 of the QTL for seed weight were independent from flowering time and several QTL were novel with favourable alleles widespread in Asian landraces. A target QTL on the short arm of chromosome 6A was validated under semi-controlled field conditions using near-isogenic lines (NILs). The allele donated by the non-Australian parent contributed to higher seed weight, thousand kernel weight and seed number under drought and heat stress, being consistent with allelic effects observed in the genome-wide association study. NILs targeting a region on chromosome 6B, which had been identified during the genomewide association studies, were phenotyped in a gravimetric platform with precision irrigation to assess the QTL effect on plant water use, photosynthesis-related traits and yield components (Chapter 3). Plants were grown in pots and exposed to either drought or combined drought and heat stress three days after anthesis, similar to the treatment applied in the genome-wide association studies. Allelic effects on seed weight, single seed weight and seed number under drought and combined drought and heat stress were consistent with previous results. An increase in yield was also associated with thicker leaves, a higher photosynthetic capacity as well as a better acclimation to different water availabilities and a higher water use efficiency. Using gene expression analysis, we could narrow down the target region to a total of 41 candidate genes. The majority of these genes have not been previously characterized under drought or heat stress and might serve as candidate genes for crop improvement in dry and hot climates. Further analysis regarding their involvement in the observed changes in physiology and yield components is required. Manual threshing and phenotyping of the spikes from the genome-wide association studies was work- and time-intensive and is often affected by human errors. We, therefore, decided to develop a method that was more accurate and faster for measuring wheat seed set components under different abiotic stresses using computed tomography (Chapter 4). The X-ray computed tomographic analysis was carried out on 291 spikes of wheat plants which had been exposed to either drought or combined drought and heat stress during the second year of genome-wide association study. An algorithm was developed and evaluated comparing actual measurements of seed weight and seed number per spike to the virtual measurements. Results demonstrated that our computed tomography pipeline could evaluate these traits with an accuracy of 0.70- 0.99. Subsequently, the algorithm was used to acquire further grain set characteristics such as seed weight along the spike, single seed weight, seed size, seed shape and seed surface area, enabling a detailed analysis of the performance of genotypically very diverse wheat accessions under both stress regimes. In conclusion, this study has contributed to the genetic dissection of combined drought and heat stress as well as the implementation of a more accurate and faster phenotyping platform for the evaluation of yield components. Markers have been developed for two target loci offering potential for marker-assisted selection in wheat breeding programs.