The research presented in this thesis is an original contribution towards greater understanding of genetics of adaptation of yellow lupin to dryland conditions. I, Muhammad Munir Iqbal, declare that this thesis is my own work and does not contain any material that has been accepted for the award of any other degree or diploma in any university or other tertiary institute. To the best of my knowledge, it contains no copy or paraphrase of materials previously published by any other person or

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... f, except where due reference is made. I, Muhammad Munir Iqbal, carried out the design and conducted the field and laboratory work related to this thesis after consultation with my supervisors. The thesis is presented on the format of independent research papers (to be published either individually or combined), preceded by a general introduction and review of literature and followed by a general discussion. As the research experiment chapters are written in a separate manuscript format, some unavoidable repetition of basic information (especially introduction and materials and methods) does occur. The research experiment chapters were written by myself and co-authors were involved in planning, discussion of results, structure of chapters and editorial comments to finalize them. Muhammad Munir Iqbal ii I dedicate my thesis to my beloved wife, our lovely daughter, loving parents, caring siblings and my kind supervisors iii ABSTRACT Narrow-leafed lupin (Lupinus angustifolius L.,) is a well-established widely grown lupin crop species in acidic sandy soils of Western Australia. However, it is largely used as a low value animal feed, and is falling out of crop rotations, replaced by higher value canola. Yellow lupin (Lupinus luteus L.) offers some additional advantages over narrow-leafed lupin as it has higher seed protein content that works well in aquaculture and is better adapted to acidic and waterlogged soils than narrow-leafed lupin. However, low yields especially in low rainfall environments limit grower uptake. If adaptation to dryland environments can be improved, yellow lupin would become a credible break crop species in Australia. The history of yellow lupin breeding in Australia is short having been active between the years 1990 and 2005 and resulted in two cultivars. Yellow lupin breeders used the same strategy as for narrow-leafed lupin breeding: strong selection for vernalization insensitive, temperature responsive early phenology suited to short seasons in the northern wheatbelt. However, a consequence of this strong phenological selection was yellow lupin and narrow-leafed lupin cultivars that have limited yield potential in regions with longer seasons, as the early crop produces low above-and below-ground biomass. This begs the questionwhat more can be done? In recent studies on wild yellow lupin by Berger et al (2014) , it was observed that phenology, productivity, water-use, stress onset under terminal drought and drought tolerance are all correlated. Under adequate vegetative phase water supply, high rainfall ecotypes are later flowering, more productive, but use more water and experience water stress earlier than their low rainfall, earlier, less productive counterparts. However, perhaps to compensate for this, high rainfall ecotypes exhibit more drought tolerance per se, falling to lower critical leaf water potentials while retaining higher leaf water content under drought than low rainfall ecotypes iv can. This suggests that while productivity and phenology are linked in yellow lupin, it may be possible to enhance the drought tolerance if we cross high and low rainfall ecotypes. The recombinant inbred-line (RIL) population was derived from high rainfall wild x low rainfall domesticated parents used in present study essentially represents that cross (Chapter # 3). The results revealed that whole recombinant inbred line (RIL) population followed a drought escape strategy under water-deficit treatment where early and late flowering genotypes extended phenology in the same way, similar patterns were observed under well-watered treatment against the expectations. We conclude that the drought escape response under well-watered treatment was because of the short season of WA where this study was conducted as a sudden temperature increase above 35 °C in mid-October did not allow the crop to prolong its life cycle under wellwatered conditions and forced it to stop its physiological processes earlier. vi Overall, this study significantly contributes to the current understanding of the yellow lupin adaptation under water-deficit and genetic control of key domestication traits in yellow lupin along with the development of genomic tools including the first linkage map of yellow lupin. vii