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Genetic factors and genes underpinning drought response in wheat

Webster, Hollie (2014) Genetic factors and genes underpinning drought response in wheat. PhD thesis, Murdoch University.

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Pollen fertility is one of the main factors limiting yield in crops such as rice and wheat, both highly inbreeding species (Wang et al., 2003). Water deficit during reproductive stage growth can result in pollen sterility due to impaired carbohydrate supply (sucrose/glucose) to pollen and supporting tissues such as the tapetum. In cereal species, and monocotyledons in general, viable pollen development is accompanied by starch accumulation in amounts that are sufficient to support pollen germination and pollen tube growth (Franchi et al., 1996). Cereal pollen grains rendered sterile by the down regulation of the sugar transport gene IVR1 lack starch (Sheoran and Saini 1996) and have failed or impaired intine formation (Lalonde et al., 1997). IVR1 down regulation results in incomplete or total absence of sucrose cleavage to the hexose sugars glucose and fructose (the final energy substrates used in plant metabolism to support pollen development), resulting an accumulation of sucrose despite the high energy demand of the developing tissues (Dorion et al., 1996).

The mechanisms underlying the sensitivity of pollen and the tapetum to abiotic stress (water deficit) provide a basis for developing molecular approaches aimed at increasing stress tolerance (Parish and Li 2010). This thesis has characterized the cell wall invertase gene family in detail in order to provide DNA sequence signatures that allow the expression of specific genes to be followed. The study demonstrated IVR1.1-­‐3B expression was confined to leaves while IVR1-­‐4A and IVR1-­‐5B represented genes expressed during early head development. Two double haploid lines identified from a population of 225 lines derived from a cross between the varieties Westonia and Kauz showed significant differences in response to water deficit stress induced grain set reduction and expression of IVR1 isoforms IVR1-­‐4A and IVR1-­‐5B. The differences in expression were investigated in more detail using a large-­‐scale RNASeq study, which indicated there was a significant expression response to water deficit in a suite of genes involved in carbohydrate metabolism. In addition IVR1 expression analysis was validated using SQ-­‐PCR, which highlighted significant differences in response to water deficit stress. Rice was used as a benchmark for selecting genes in this study.

The external phenotype, penultimate leaf internode auricle distance 5cm (Zadoks growth stages Z39/40), was validated as an indicator of pollen meiosis completion. A significant developmentally related drought escape QTL was identified on chromosomes 5B and 5D. High resolution mapping of the group 5 chromosomes (using a 90K SNP chip) enabled a high density of markers to be located across the chromosome 5B QTL in particular, and identified water deficit responsive UDP-­‐glucose 6-­‐dehydrogenase (from the KEGG carbohydrate metabolism pathway) as a gene of interest. A global analysis using RNASeq data identified a more extensive suite of anther-­‐specific genes that were water deficit responsive. In turn this suit of genes provided the basis for defining a set of molecular markers to screen for variation in drought responsiveness in wheat varieties.

Although this work has focussed on a developmental stage specific water deficit response, it is evident the thesis contributes to the wider body of information becoming available for wheat, much of which now indicates it should be feasible to define a haplotype for wheat using the allelic variation in genes associated with drought tolerance in different environments. Results from this study have shown that reproductive stage water deficit tolerance is a complex quantitative trait and that it may be more useful to quantify a risk factor value using a suite of markers, rather than a plus/minus analysis of single markers. We propose the network of carbohydrate metabolism genes defined in this thesis would make significant contributions to risk factor analyses in early selection or backcrossing for sensitivity in particular environments.

Item Type: Thesis (PhD)
Murdoch Affiliation(s): School of Veterinary and Life Sciences
Supervisor(s): Appels, Rudi, Dell, Bernard and Fosu-Nyarko, John
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