TY - BOOK

T1 - Association mapping of biorefinery traits relevant for development of dual-purpose varieties of winter wheat

AU - Malik, Pernille Louise

PY - 2019

Y1 - 2019

N2 - A Fast growing world population is putting tremendous pressure on future food and energy security especially as the heavily exploited fossil fuel resources are depleting. A more sustainable utilization of the agricultural land is therefore required for shifting the input stream of biorefineries towards lignocellulosic plant material. Wheat is the second most grown crop worldwide, leaving a large amount of biomass material as agricultural by-products. Application of the straw biomass as a feedstock for production of biofuels, sugars for bio-based chemicals or biogas in 2nd generation biorefineries, is therefore of interest. Conventional wheat breeding programs have mainly focused on grain yield, while no effort has been made towards traits relevant for conversion of straw biomass in biorefineries. In order to increase the value of wheat, breeding for dual-purpose varieties, producing high grain yields for food sector as well as high straw yields for biorefinery purposes, may be a solution. Novel genetic markers are required to obtain dual-purpose varieties, as they can help breeders select cultivars with a good quality in terms of biorefinery traits (i.e. straw yield and saccharification potential) without compromising grain yield. The purpose of this PhD thesis was to analyse whether genome-wide association studies (GWAS) will be a suitable analytical tool for discovery of marker trait associations for biorefinery traits in popular breeding designs such as active breeding nurseries and multi-cross populations. With this knowledge, selection of dual-purpose cultivars in common wheat breeding programmes would be facilitated. ASRemel-R was used to model data and obtain trait mean estimates of the unbalanced breeding designs. The usability of diverse GWAS algorithms to analyse data of an active breeding nurseries and multi-cross population were then evaluated. The effect of including different covariates to control for population structure and family relatedness was further investigated. The best GWAS algorithm was selected based on Quantile-Quantile-plots and its ability to detected method on detection of heritability for monosaccharide release was also analysed in a subset of samples. Utilization of GWAS as a genetic association tool to discover MTAs in standard breeding designs were achievable by applying the FarmCPU algorithm. MTAs for both standard agricultural traits and biorefinery traits were identified in common wheat varieties using activebreeding nurseries or multi-cross designs, consequently showing that breeding toward dualpurpose varieties is possible. MTAs were discovered for straw yield on chromosome 3A, 3D and 7A, while MTAs for saccharification potential were present on many different chromosomes, where 6A seems to be common location of MTAs for release of all monosaccharides. Furthermore, detection of the heritability for saccharification potentials was dependent on temperature of hydrothermal pretreatment, with optimal detection at lower temperatures. Breeding for biorefinery traits in common wheat without compromising grain yield seems promising. However, larger wheat collections with more variation in biorefinery traits should be included, in order to increase the likelihood of obtaining higher SNP effects and consequently stronger KASP markers for biorefinery traits marker-trait associations (MTAs) was assessed. Associations between 15K SNP markers, and the standard agronomic traits (grain yield, plant height, lodging resistance, Septoria tritici blotch, and harvest index) and the biorefinery traits (straw yield and release of monosaccharides from straw after enzymatic saccharification) were analysed by GWAS. The effect of the pretreatment

AB - A Fast growing world population is putting tremendous pressure on future food and energy security especially as the heavily exploited fossil fuel resources are depleting. A more sustainable utilization of the agricultural land is therefore required for shifting the input stream of biorefineries towards lignocellulosic plant material. Wheat is the second most grown crop worldwide, leaving a large amount of biomass material as agricultural by-products. Application of the straw biomass as a feedstock for production of biofuels, sugars for bio-based chemicals or biogas in 2nd generation biorefineries, is therefore of interest. Conventional wheat breeding programs have mainly focused on grain yield, while no effort has been made towards traits relevant for conversion of straw biomass in biorefineries. In order to increase the value of wheat, breeding for dual-purpose varieties, producing high grain yields for food sector as well as high straw yields for biorefinery purposes, may be a solution. Novel genetic markers are required to obtain dual-purpose varieties, as they can help breeders select cultivars with a good quality in terms of biorefinery traits (i.e. straw yield and saccharification potential) without compromising grain yield. The purpose of this PhD thesis was to analyse whether genome-wide association studies (GWAS) will be a suitable analytical tool for discovery of marker trait associations for biorefinery traits in popular breeding designs such as active breeding nurseries and multi-cross populations. With this knowledge, selection of dual-purpose cultivars in common wheat breeding programmes would be facilitated. ASRemel-R was used to model data and obtain trait mean estimates of the unbalanced breeding designs. The usability of diverse GWAS algorithms to analyse data of an active breeding nurseries and multi-cross population were then evaluated. The effect of including different covariates to control for population structure and family relatedness was further investigated. The best GWAS algorithm was selected based on Quantile-Quantile-plots and its ability to detected method on detection of heritability for monosaccharide release was also analysed in a subset of samples. Utilization of GWAS as a genetic association tool to discover MTAs in standard breeding designs were achievable by applying the FarmCPU algorithm. MTAs for both standard agricultural traits and biorefinery traits were identified in common wheat varieties using activebreeding nurseries or multi-cross designs, consequently showing that breeding toward dualpurpose varieties is possible. MTAs were discovered for straw yield on chromosome 3A, 3D and 7A, while MTAs for saccharification potential were present on many different chromosomes, where 6A seems to be common location of MTAs for release of all monosaccharides. Furthermore, detection of the heritability for saccharification potentials was dependent on temperature of hydrothermal pretreatment, with optimal detection at lower temperatures. Breeding for biorefinery traits in common wheat without compromising grain yield seems promising. However, larger wheat collections with more variation in biorefinery traits should be included, in order to increase the likelihood of obtaining higher SNP effects and consequently stronger KASP markers for biorefinery traits marker-trait associations (MTAs) was assessed. Associations between 15K SNP markers, and the standard agronomic traits (grain yield, plant height, lodging resistance, Septoria tritici blotch, and harvest index) and the biorefinery traits (straw yield and release of monosaccharides from straw after enzymatic saccharification) were analysed by GWAS. The effect of the pretreatment

M3 - Ph.D. thesis

BT - Association mapping of biorefinery traits relevant for development of dual-purpose varieties of winter wheat

PB - Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen

ER -