Towards the positional cloning of yield QTL on chromosome 1B for drought tolerance in wheat
Date
2018
Authors
Tura, Habtamu
Editors
Advisors
Fleury, Delphine
Langridge, Peter
Garcia, Melissa
Langridge, Peter
Garcia, Melissa
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Abstract
Wheat feeds about 35% of the world’s population and its productivity needs to be increased by 2.8% every year. Drought and heat have been reported to decrease grain yield up to 70 %. Fine mapping and dissecting the physiological effects of quantitative trait loci (QTL) for yield enable to find molecular markers and genes for breeding drought tolerant varieties. Here we focus on QTL with strong effects on yield and yield-related traits that were previously found on the chromosome 1B in three bread wheat (Triticum aestivum L.) mapping populations grown under abiotic stress. These QTL were first identified under low rain fed environments in three continents (Australia, Mexico and India) using double-haploid (DH) lines from Excalibur x Kukri (Edwards, 2012) and RAC875 x Kukri DH (Bennett et. al., 2012). The yield QTL on chromosome 1B of Excalibur x Kukri DH was highly expressed under severe drought stressed environments (yield < 500kg/ha) of South Australia and was not under the influence of phenology genes, and so was chosen for fine mapping. QTL for plant growth, relative leaf expansion and transpiration rate were also detected on chromosome 1B in a third mapping population derived from Drysdale x Gladius recombinant inbred lines (RIL), grown in glasshouse under well-watered and drought conditions, using a LemnaTec high throughput image phenotyping platform (Parent et al. (2015). The aims of this project were to: find whether or plant growth and transpiration QTL in Drysdale x Gladius coincide with a grain yield QTL, (2) fine map the yield QTL in Excalibur/Kukri near-isogenic lines (3) align the QTL from the three mapping populations onto chromosome 1B physical map and identify the candidate genes underlying yield under drought and heat stressed environments. For aim 1, we selected Drysdale/Gladius RIL with recombination points in the region covering the QTL for growth and transpiration rate previously reported by Parent et al. (2015). We tested these RIL for two consecutive years (2014 and 2015) under severe drought and heat stresses in a rainout shelter (polytunnel). We found a yield QTL on chromosome 1B which was co-located with QTL for seeds/spikelet, seeds/spike, biomass, spike weight and plant height. All were expressed specifically under severe drought and high temperatures. Drysdale was the positive allele for all the QTL, except for plant height, and had a strong effect on number of seeds/spike under severe drought and heat stressed in Drysdale/Gladius. We also found that the yield QTL match a QTL for relative leaf area expansion rate and partially overlap with a QTL for transpiration rate. We hypothesized that Drysdale allele at the 1B loci contributes to biomass accumulation at early growth stage leading to a yield increase under dry and hot climate. We aligned all the QTL for yield, yield components and physiological traits (growth, relative leaf expansion and transpiration rate) that were detected on the chromosome 1B in the three mapping populations onto the reference sequence RefSeq v1.0 and found co-locations among the QTL at the three regions. In the first region (7 Mbp), we found a co-location of yield QTL (QYld.aww-1B.1) from RAC875/Kukri and QTL for yield components and relative leaf expansion rate from Drysdale/Gladius. The second region spined 18.3 Mbp covered yield QTL in the three mapping populations, and also QTL for growth, leaf area expansion and transpiration rate in Drysdale/Gladius. Co-location of the QTL for yield and yield components with the QTL for physiological traits suggests a pleiotropic effect of the same gene and is indicative of potential function of the gene. The third region covered 17 Mbp and harboured a co-located yield and yield components QTL from the three mapping populations. The co-located yield QTL from the three mapping populations in the third region covered a large interval that needed to be narrowed down to identify functional markers for molecular assisted breeding. We developed a high-resolution Excalibur/Kukri genetic map and fine mapped the yield QTL interval with SNP markers. Near-iso-genic lines (NIL) were developed from Excalibur/Kukri heterozygous inbred lines (RIL) (F2:5) that were recombinant in the yield QTL interval. The NIL were phenotyped under severe drought and high temperatures in a polytunnel using drip irrigation. We confirmed the yield and yield component QTL in Excalibur/Kukri NIL on the long arm of chromosome 1B. The Excalibur allele increased grain yield by 54.5%, biomass by 43%, fertile tillers by 32.8% and plant height by 14% compared to Kukri allele. The significant effect on grain yield resulted from significant number of productive tillers which was strongly correlated with seed number per plot. Based on the comparison of NIL haplotype, the yield QTL was narrowed down to 2.9 cM, corresponding to 2.2 Mbp on the chromosome 1B Chinese Spring reference sequence (IWGSC RefSeq v0.1). Using the Excalibur/Kukri NIL fine mapped yield QTL, we identified and annotated 42 genes on the 2.2 Mbp interval. Further expression analysis and characterization of the candidate gene/s will be necessary to identify the gene responsible for this grain yield QTL. In this work, we found that chromosome 1B carries a locus of 17 Mbp that contributes to yield in Excalibur/Kukri population, a second locus that we narrowed down to 2.2 Mbp and 42 genes in Excalibur/Kukri. The data generated from this research adds to the currently available body of scientific knowledge related to the chromosome 1B genomic regions controlling yield under dry and hot environments. It will enable to complete the positional cloning of 1B QTL for yield.
School/Discipline
School of Agriculture, Food and Wine
Dissertation Note
Thesis (Ph.D.) -- University of Adelaide, School of Agriculture, Food & Wine, 2018
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