Sunflower is grown worldwide for oil production. In Australia, sunflower is under intense competition from canola as an oil crop. Confectionery sunflower aimed for the overseas snack food market is a potential opportunity for Australian farmers due to its ability to provide off-season supply to the major market located mainly in the northern hemisphere. To serve this aim, new confectionery sunflower hybrids adapted to Australian production system with drought tolerance, large achenes, high self-fertility and rust resistance are of paramount importance. The objectives of this project were to understand the genetic inheritance and genetic linkage relationships of the above traits and also to identify linked DNA markers with the potential for marker-assisted selection (MAS). The inheritance of achene-length was studied in a 12 x 12 diallel and a 14 x 12 North Carolina design II (NC II) mating design. Achene-length was evaluated under three environments for each mating design. Genetic correlation among all five achene-size related traits (achene-length, -width, - thickness and also kernel-length and -width) and 100-achene weight were moderate to high. Narrow-and broad-sense heritability for achene-length was moderate to high and similar for each design. The general combining ability (GCA) and maternal effects were found to be the main genetic factors controlling achene-length and each accounted for around 45% of the total genotypic variance. The inheritance of self-fertility (SF) was assessed with the same 12 x 12 diallel mating design evaluated in two environments. The 12 parents also displayed various levels of SF in addition to a wide range of achene-length. Negative genetic correlations between SF and all five achene-size related traits and 100-achene weight were observed. Modelling achene-length as a covariate revealed that certain pre-pollination floret characteristics represented by achene-length at maturity strongly affects SF in sunflower. When the effect of achene-length was removed statistically as a covariate, the specific combining ability (SCA) effect increased dramatically and became the major factor (other than pre-pollination floret characteristics) for SF determination and accounted for 65% of the total variance. Long achene genotypes tended to have low SF and a positive SCA effect was observed more frequently in F1 hybrids that involved small achene lines. The broad sense heritability was moderate (0.663 ± 0.017), while the estimate of narrow-sense heritability was nearly zero. A segregating F6:7 recombinant inbred line population with 239 progeny was developed from a cross between HaR4, a low delta (Δ), high transpiration efficiency (TE), sunflower line with rust resistance but relatively low SF, and SA52 with all the characteristics in the opposite direction. The population was evaluated in two environments for three TE-related traits including Δ, specific leaf weight (SLW) and chlorophyll content (CC) and four agronomic traits i.e. days to flowering (DTF), plant height (PlantH), SF and rust resistance (RustR). A linkage map 1074.6 cM in length with 138 SSR and 37 ISSR markers consisting of 19 linkage groups was constructed. Spatially adjusted BLUPs were used in QTL analysis for individual and combined environments. Altogether, 10 QTL were identified for Δ, SLW and CC at individual environments, and 7 were detected by a combined analysis. Sixteen QTL were identified for 4 agronomic traits and 14 of them were confirmed by a combined analysis. Significant linkage among all three TE related traits was discovered on linkage group 4 (LG4), where alleles from one parent had the same direction of influence on TE which suggested either coupling phase linkage or pleiotropy. QTL for SF and RustR were closely linked on LG13. An F2 population with 502 progeny developed from a cross between Jumbo, a large achene confectionery sunflower line, and RIL25, an oilseed small achene line, was evaluated for five achene-size related traits in a single field trial. Using a subset of 178 progeny a framework genetic linkage map, 899.7 cM in length, containing 128 SSR markers and 23 ISSR markers was constructed with 18 linkage groups. Based on the results of a simulated QTL analysis, a modified selective genotyping strategy was employed for QTL analysis with 178 F2 individuals (128 randomly selected, 25 shortest achene F2’s and 25 longest achene F2’s). Altogether 18 achene-size related QTL with small effects were identified. Achene-size related genes characteristically expressed additive gene action although several alleles were partially recessive towards the large achene parent. The 18 identified achene-size related QTL were validated in the same diallel mating experiment mentioned above. Significant marker-trait associations were detected for 15 QTL. In addition to 12 significant alleles detected from the F2 population, 12 additional alleles associated with achene-size traits were revealed after the analysis with the diallel. These markers are ready to be used in MAS for confectionery sunflower breeding. Great steps have been made in obtaining essential knowledge of inheritance and linkage of target traits for breeding confectionery sunflower adapted to Australian production environments. The identified markers can be used in MAS and further enhance the breeding process.

Doctor of Philosophy / Genetics - Plant Pathology / Jesse A. Poland / The global population is estimated to reach 9.1 billion by 2050. Together with climate change, insuring food security for this population presents a significant challenge to agriculture. In this context, a large number of breeding objectives must be targeted. The focus of the work presented here is to explore genomic approaches for tapping exotic germplasm for valuable alleles to increased yield, disease resistance and abiotic stress tolerance. The loss of genetic diversity in bread wheat (Triticum aestivum L.) due to bottlenecks during polyploidization, domestication and modern plant breeding can be compensated by introgressing novel exotic germplasm. Here, the potential of genomic selection (GS) for rapid introgression of synthetic derived wheat is evaluated in field trials. Overall, the GS models had moderate predictive ability. However, prediction accuracies were lower than expected likely due to complex and confounding physiological effects. As such, implementation of rapid cycle GS for introgression of exotic alleles is possible but might not perform very well with synthetic derived wheat. Disease resistance is another important trait affecting grain yield. Stem rust (Puccinia graminis f. sp. tritici) has historically caused severe yield loss of wheat worldwide. In a quantitative trait loci (QTL) mapping study with a synthetic-derived mapping population, QTLs for resistance to stem rust races TRTTF and QTHJC were identified on chromosomes 1AS, 2BS, 6AS and 6AL. Some of these genes could be new resistance genes and useful for marker-assisted selection (MAS). In addition to food insecurity through lack of sufficient source of calories, nutrient deficiency is considered the ‘hidden hunger’ and can lead to serious disorders in humans. Through biofortification, essential nutrients are increased in staple crops for improved quality of food and human health. A high-throughput elemental profiling experiment was performed with the same synthetic derived mapping population to study the wheat ionome. Twenty-seven QTL for different elements in wheat shoots and two QTL in roots were identified. Four “hotspots” for nutrient accumulation in the shoots were located on chromosomes 5AL, 5BL, 6DL and 7AL. Overall, exotic germplasm is a valuable source of favorable alleles, but improved breeding methodologies are needed to rapidly utilize this diversity.

L’optimisation de la biomasse produite par les taillis à courte rotation de peupliers représente un enjeu majeur pour la production de biocarburants de deuxième génération. Dans ce contexte, ce travail vise à faciliter le développement à court terme de nouvelles variétés clonales de peuplier permettant la production d’une ressource de qualité en s’intéressant plus particulièrement à l’architecture génétique de la résistance à la rouille foliaire et de la qualité du bois chez le peuplier noir (Populus nigra), espèce parente des hybrides cultivés. Des marqueurs SNP ont été développés à partir du séquençage de 665 fragments de gènes dans un panel de 21 individus. Ces derniers ont été associés à des marqueurs SSR et AFLP pour construire de nouvelles cartes génétiques sur une famille de 324 plein-frères clonés. Une technique de phénotypage à haut débit basée sur la spectrométrie à proche infrarouge a été développée pour prédire les teneurs en composés chimiques du bois ainsi que le rendement en saccharification. La mise en évidence d’une variabilité génétique importante pour l’ensemble des caractères a permis de cartographier les régions génomiques impliquées dans leur variation. Parmi les 11 QTL détectés pour la résistance, un QTL à effet majeur co-localise avec un QTL majeur associé à la résistance à la rouille foliaire du saule. Pour la qualité du bois, 15 QTL à effet faible à moyen ont été détectés, dont un cartographié sur le chromosome XIII qui colocalise avec des QTL précédemment identifiés chez le peuplier pour les teneurs en sucres et en lignines. Ce travail de thèse ouvre des perspectives d’identification de gènes sous-jacents aux QTL par génétique d’association. / Improvement of lignocellulosic resources from poplar short rotation coppices is a major challenge for the production of second generation biofuels. In this context, the present work aims at optimizing short term creation and deployment of improved poplar clonal varieties through the dissection of genetic control of both leaf rust resistance and wood quality in black poplar (Populus nigra), one of the parental species of cultivated hybrids. SNP markers have been developed from the resequencing of 665 gene fragments in a discovery panel of 21 individuals. These markers were combined with SSRs and AFLPs to build new genetic maps in a pedigree composed of 324 cloned full-sibs. High throughput phenotyping based on near infrared spectroscopy has been used to predict wood chemical contents and saccharification yield. High genetic variability expressed in all traits allowed the identification of genomic regions controlling this variation. Of the 11 QTL mapped for resistance, one major QTL co-localized with a major QTL previously detected for leaf rust resistance in willow. For wood quality, 15 QTL with low to moderate effect have been identified. Interestingly, one QTL mapped on chromosome XIII and colocalized with sugar and lignin contents QTL previously detected in poplar. Present results open perspectives towards the identification of candidate genes underlying the detected QTL through association genetics.

Entre as principais demandas da agricultura brasileira nos últimos anos, destaca-se a necessidade de cultivares de soja com elevado potencial produtivo, resistentes/tolerantes a doenças, em especial à ferrugem asiática da soja e com ciclo reduzido. O trabalho teve como objetivo principal avaliar cruzamentos de soja em diferentes gerações de endogamia e seleção, com ênfase nos caracteres produtividade de grãos, resistência/tolerância à ferrugem e ciclo (precocidade). Os 49 cruzamentos foram obtidos em um dialelo parcial 7x7, avaliados nas gerações F2 e F2:3 por Oliveira (2011) e, neste trabalho, nas gerações F2:4, F2:5, F5:6 e F5:7. Um total de dez experimentos (combinações de anos agrícolas, locais e manejos de doenças) foram realizados em blocos aumentados e ou blocos casualizados. Os dois manejos de doenças compreenderam um experimento com controle das doenças de fim de ciclo (DFC) e da ferrugem, enquanto que no segundo experimento envolveu somente o controle das DFC. Os caracteres avaliados foram: produtividade de grãos (PG), peso de cem sementes (PCS, representando o tamanho das sementes), número de dias para a maturidade (NDM), altura da planta na maturidade (APM), acamamento (AC), valor agronômico (VA), notas de severidade da ferrugem (NF) e taxas de reação à ferrugem (TRF). As TRFs foram estimadas para cada caráter por meio da diferença entre as médias ajustadas de cada genótipo nos dois experimentos com manejos de doenças. Foram realizadas análises de variância, estimativas de herdabilidade, capacidades médias de combinação (CMC), correlações das CMC entre as gerações, correlações entre caracteres, seleção de linhagens experimentais superiores e estimativas dos ganhos com a seleção. As metodologias de avaliação da resistência (NF) e da tolerância (TRF) possibilitaram a discriminação de genótipos superiores quanto à reação à ferrugem, demonstrando evidências de serem complementares e úteis para uso em conjunto. Observou-se maior tendência de haver correlações das CMC entre as gerações para caracteres de alta herdabilidade. A magnitude da variabilidade dentro de cruzamentos oscilou em consequência da seleção e da abertura de progênies e ou linhagens para a maior parte dos caracteres. Apesar das correlações entre os caracteres (NDM x PG e NDM x NF), foram observados ganhos na seleção de genótipos superiores. Os genitores que mais contribuíram para a obtenção de linhagens experimentais com alta produtividade de grãos, resistentes/tolerantes à ferrugem e precoces foram M-Soy 8001 e IAC 100 no Grupo I e USP 70.080 e USP 70.123 no Grupo II do dialelo. / Among the main demands of Brazilian agriculture in recent years highlights the need for soybean cultivars with high yield potential, resistance / tolerance to diseases, mainly Asian soybean rust (FAS) and reduced cycle. The research aimed to study the genetic relationships of soybean crosses in different generations of inbreeding and selection, with an emphasis on the seed yield, resistance/tolerance to rust and cycle (earliness). The 49 crosses was obtained in a partial diallel 7x7, researching the generations F2 and F2: 3 by Oliveira (2011) and, in this work, the generations F2:4, F2:5, F5:6 and F5:7. A total of ten experiments (combinations of agricultural years, locations and disease managements) were performed in augmented block and or randomized complete-block designs. The two managements involved one experiment with control of the late season leaf diseases (DFC) and rust, whereas the second experiment only involved the control of the DFC. The following traits were evaluated : seed yield (PG), one hundred seed weight (PCS, representing the seed size), number of days to maturity (NDM), plant height at maturity (APM), lodging (AC), agronomic value (VA), notes of rust severity (NF) and the rust reaction rates (TRF). The TRFs for each trait were estimated by the difference between the adjusted means of each genotype in the two experiments with diseases managements. There were obtained analyses of variance and estimates of heritability, average combining ability (CMC), the CMC correlations between generations, correlations between traits, selection of superior experimental lines and the selection gains. The methodologies for measuring the rust resistance by severity notes (NF) and the rust tolerance (TRF) allowed the discrimination of genotypes and showed evidences of being complementary and with benefits for use together. Higher evidences of CMC correlations between generations were observed in the high heritability traits. The magnitude of the variability within crosses oscillated due the selection and the progeny/line opening, for most of the traits. Even with negative correlations between traits ( NDM x PG and NDM x NF), there were observed gains in the selection of superior genotypes. The parents who contributed most to obtain experimental lines with high seed yield, rust resistance / tolerance and earliness were M-Soy 8001 and IAC 100 in the Group I, and USP 70.080 and USP 70.123 in the Group II of the diallel.

Entre as principais demandas da agricultura brasileira nos últimos anos, destaca-se a necessidade de cultivares de soja com elevado potencial produtivo, resistentes/tolerantes a doenças, em especial à ferrugem asiática da soja e com ciclo reduzido. O trabalho teve como objetivo principal avaliar cruzamentos de soja em diferentes gerações de endogamia e seleção, com ênfase nos caracteres produtividade de grãos, resistência/tolerância à ferrugem e ciclo (precocidade). Os 49 cruzamentos foram obtidos em um dialelo parcial 7x7, avaliados nas gerações F2 e F2:3 por Oliveira (2011) e, neste trabalho, nas gerações F2:4, F2:5, F5:6 e F5:7. Um total de dez experimentos (combinações de anos agrícolas, locais e manejos de doenças) foram realizados em blocos aumentados e ou blocos casualizados. Os dois manejos de doenças compreenderam um experimento com controle das doenças de fim de ciclo (DFC) e da ferrugem, enquanto que no segundo experimento envolveu somente o controle das DFC. Os caracteres avaliados foram: produtividade de grãos (PG), peso de cem sementes (PCS, representando o tamanho das sementes), número de dias para a maturidade (NDM), altura da planta na maturidade (APM), acamamento (AC), valor agronômico (VA), notas de severidade da ferrugem (NF) e taxas de reação à ferrugem (TRF). As TRFs foram estimadas para cada caráter por meio da diferença entre as médias ajustadas de cada genótipo nos dois experimentos com manejos de doenças. Foram realizadas análises de variância, estimativas de herdabilidade, capacidades médias de combinação (CMC), correlações das CMC entre as gerações, correlações entre caracteres, seleção de linhagens experimentais superiores e estimativas dos ganhos com a seleção. As metodologias de avaliação da resistência (NF) e da tolerância (TRF) possibilitaram a discriminação de genótipos superiores quanto à reação à ferrugem, demonstrando evidências de serem complementares e úteis para uso em conjunto. Observou-se maior tendência de haver correlações das CMC entre as gerações para caracteres de alta herdabilidade. A magnitude da variabilidade dentro de cruzamentos oscilou em consequência da seleção e da abertura de progênies e ou linhagens para a maior parte dos caracteres. Apesar das correlações entre os caracteres (NDM x PG e NDM x NF), foram observados ganhos na seleção de genótipos superiores. Os genitores que mais contribuíram para a obtenção de linhagens experimentais com alta produtividade de grãos, resistentes/tolerantes à ferrugem e precoces foram M-Soy 8001 e IAC 100 no Grupo I e USP 70.080 e USP 70.123 no Grupo II do dialelo. / Among the main demands of Brazilian agriculture in recent years highlights the need for soybean cultivars with high yield potential, resistance / tolerance to diseases, mainly Asian soybean rust (FAS) and reduced cycle. The research aimed to study the genetic relationships of soybean crosses in different generations of inbreeding and selection, with an emphasis on the seed yield, resistance/tolerance to rust and cycle (earliness). The 49 crosses was obtained in a partial diallel 7x7, researching the generations F2 and F2: 3 by Oliveira (2011) and, in this work, the generations F2:4, F2:5, F5:6 and F5:7. A total of ten experiments (combinations of agricultural years, locations and disease managements) were performed in augmented block and or randomized complete-block designs. The two managements involved one experiment with control of the late season leaf diseases (DFC) and rust, whereas the second experiment only involved the control of the DFC. The following traits were evaluated : seed yield (PG), one hundred seed weight (PCS, representing the seed size), number of days to maturity (NDM), plant height at maturity (APM), lodging (AC), agronomic value (VA), notes of rust severity (NF) and the rust reaction rates (TRF). The TRFs for each trait were estimated by the difference between the adjusted means of each genotype in the two experiments with diseases managements. There were obtained analyses of variance and estimates of heritability, average combining ability (CMC), the CMC correlations between generations, correlations between traits, selection of superior experimental lines and the selection gains. The methodologies for measuring the rust resistance by severity notes (NF) and the rust tolerance (TRF) allowed the discrimination of genotypes and showed evidences of being complementary and with benefits for use together. Higher evidences of CMC correlations between generations were observed in the high heritability traits. The magnitude of the variability within crosses oscillated due the selection and the progeny/line opening, for most of the traits. Even with negative correlations between traits ( NDM x PG and NDM x NF), there were observed gains in the selection of superior genotypes. The parents who contributed most to obtain experimental lines with high seed yield, rust resistance / tolerance and earliness were M-Soy 8001 and IAC 100 in the Group I, and USP 70.080 and USP 70.123 in the Group II of the diallel.