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Crown rust, caused by the fungus Puccinia coronata, is a severe disease negatively impacting seed quality and yield in oat (Avena sativa). Host genetic resistance is the primary means for controlling this disease. The most extensive oat map contains nearly 2,500 genetic markers, many of which are restriction and amplified fragment length polymorphic (RFLP or AFLP) markers. However, the use of more abundant single nucleotide polymorphic (SNP) markers combined with diversity arrays technology (DArT) would be more advantageous for marker assisted breeding (MAB) and genome wide selection (GWS) applications due to the availability of high density genotyping technologies. The purpose of using this technology is to improve the competitiveness of oat by producing varieties with durable resistance to crown rust and desirable traits that will benefit oat growers in the U.S. Panels of winter and spring oat were evaluated for resistance to crown rust in four field environments in Texas, Louisiana, Minnesota, and North Dakota during a two-year study in 2010 and 2011. Plants representing 702 elite lines of oat were phenotyped for crown rust resistance and found to have highly diverse responses. The winter oat lines demonstrated the best crown rust resistance and are expected to yield the most QTL to be used in developing durable crown rust resistance. Heritability of crown rust resistance in this study ranged from 0.88 to 0.90 in spring and winter oats, respectively. Crown rust measurements were also found to be repeatable. Repeatability ranged from 0.56 to 0.88 at Castroville, TX in 2011 and 2010, respectively in spring oats and from 0.79 at St. Paul, MN in 2011 to 0.96 at Castroville, TX in 2010 in winter oats. Oat lines contributed by states along the Puccinia pathway in Texas, Louisiana, Minnesota, North Dakota, and Wisconsin on average exhibited the best crown rust resistance as compared to other areas in the country where spring and winter oat are grown. GGE biplot analysis indicated that Castroville, TX was the most representative and most ideal testing location. The above results are expected to increase knowledge of the genetic diversity of the oat germplasm, yield comprehensive genotyping and phenotyping information for North American oat breeding programs, and to promote further use of GWS and MAB for key traits regarding disease resistance in oat. Future work is to conclude the association mapping process by completing genotypic analysis.

A ferrugem alaranjada da cana-de-açúcar, causada pelo fungo Puccinia kuehnii, é atualmente a doença que mais preocupa o setor sucroenergético brasileiro, devido a sua introdução recente no país e aos prejuízos causados em indústrias canavieiras ao redor do mundo. A doença é controlada com variedades resistentes e por isso há a necessidade de maiores informações sobre a reação das cultivares mais importantes no Brasil. Os objetivos deste trabalho foram: (i) avaliar a reação de variedades de cana-de-açúcar à ferrugem alaranjada, em condições de infecção natural no campo; (ii) determinar a melhor época para avaliação da doença; (iii) estabelecer um método, em casa de vegetação e com inoculação artificial do patógeno, para seleção rápida de variedades com resistência no campo. Dezessete variedades foram avaliadas quanto às suas reações a P. kuehnii em dois experimentos de campo, plantados em abril e julho de 2011; neste último, após a colheita em maio de 2012, a cana-soca também foi avaliada. Para multiplicar e uniformizar a distribuição do inóculo, a variedade suscetível SP89-1115 foi usada como bordadura e plantada entre os blocos e em duas linhas, dividindo cada experimento ao meio. Avaliou-se a severidade da doença a cada 15 dias e, a partir destes dados, calculou-se a área abaixo da curva de progresso da doença (AACPD) e obteve-se a severidade máxima da doença. Para identificar o melhor período de avaliação, realizou-se análise de correlação entre a AACPD e cada levantamento de severidade. Em casa de vegetação, seis variedades com reações distintas à doença, com base nos resultados obtidos no campo, foram inoculadas com uma suspensão de 104 urediniósporos viáveis mL-1 de P. kuehnii, com auxílio de pulverizador manual, 60 dias após o plantio. As plantas foram mantidas por 24 horas em câmara de orvalho e, posteriormente, transferidas para casa de vegetação. Foram determinados os períodos de incubação e latência, o número de pústulas por cm2 e a severidade da doença. Oito das 17 variedades avaliadas no campo mostraram alta resistência à doença. As cultivares RB72454 e SP89-1115 foram as mais suscetíveis, seguidas da SP79-2233; por isso, o cultivo das mesmas não é recomendado. As variedades RB925211, SP81-3250, RB855156 e RB92579 tiveram reação intermediária, sendo que as duas primeiras apresentaram maiores níveis da doença. Avaliações realizadas no mês de março foram as que mais se correlacionaram com a AACPD, portanto este é o melhor período para determinar a reação de variedades de cana-de-açúcar à ferrugem alaranjada. O comportamento das variedades em casa de vegetação foi semelhante ao observado no campo, especialmente em relação às cultivares suscetíveis e resistentes. Assim, o método aplicado em casa de vegetação mostrou potencial para selecionar, em poucos dias, cultivares com resistência à doença no campo, além de economizar espaço, mão de obra e de ser facilmente executado. / Currently, sugarcane orange rust, caused by Puccinia kuehnii, is the disease that most concerns the Brazilian sugarcane industry, due to its recent introduction in the country and the damage caused to sugarcane industries all over the world. The disease is controlled with resistant varieties; hence there is a need for more information about the reaction of the major cultivars in Brazil. The objectives of this work were: (i) to evaluate the reaction of sugarcane varieties to orange rust in field, under natural infection conditions; (ii) to determine the best time for disease assessment; (iii) to establish a method in greenhouse, based on artificial inoculation, for rapid selection of field resistant varieties. Seventeen varieties were studied in two field experiments, planted in April and July 2011; in the latter, after the harvest in May 2012, the ratoon was also evaluated. The susceptible variety SP89-1115 was used as border and planted between the blocks in two lines, dividing each experiment in two halves in order to multiply and standardize the inoculum in the area. Disease severity was evaluated every 15 days and the area under disease progress curve (AUDPC) was calculated and the maximum disease severity was obtained. To identify the best time for disease assessment, a correlation analysis between the AUDPC and each disease severity assessment was done. In greenhouse, six varieties with different reactions to the disease based on results obtained in field were inoculated with a suspension of 104 viable urediniospores mL-1 of P. kuehnii with a manual sprayer 60 days after planting. Plants were maintained in dew chamber for 24 hours and afterwards they were transferred to the greenhouse. The incubation and latent period were determined as well as the number of pustules cm-2 and disease severity. Eight out of 17 varieties evaluated in field showed high disease resistance. The varieties RB72454 and SP89-1115 were the most susceptible, followed by SP79-2233; therefore, their commercial cultivation is not recommended. The varieties RB925211, SP81-3250, RB855156 and RB92579 had intermediate reaction, with the first two showing higher disease levels. Evaluations performed in March showed the highest correlation with AUDPC, thus this period is the best for determining sugarcane reaction to orange rust. The varieties reaction in greenhouse was similar to that observed in the field, particularly in relation to susceptible and resistant cultivars. So, the method applied in greenhouse showed potential to select, in a few days, field disease-resistant varieties, besides saving space and labor and being easily implemented.

Thesis (MSc)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Wheat rust, caused by the Puccinia spp., is a global biotic cause of wheat yield losses. This disease can effectively be combatted by implementing rust resistant wheat cultivars. The release of new resistant wheat cultivars is however prolonged due to the time needed to fix resistance genes in a good quality background and develop pure breeding wheat lines. The aim of this study was the pyramiding of novel species derived leaf and stripe rust resistance genes in bread wheat lines through the utilization of high throughput marker assisted selection and microspore derived doubled haploid technology. / AFRIKAANSE OPSOMMING: Koringroes het wêreldwyd verliese in koringopbrengste tot gevolg. Dit word veroorsaak deur die Puccinia fungi. Hierdie siekte kan effektief beveg word deur die verbouing van roesbestande kultivars. Die vrystel van nuwe weerstandbiedende kultivars is egter ‘n langdurige proses weens die tyd verbonde daaraan om weerstandsgene te fikseer in ‘n genetiese agtergrond met ‘n goeie kwaliteit en om dan suiwertelende lyne te ontwikkel. Die doelwit van hierdie studie was om nuwe spesie-verhaalde blaar- en streeproes weestandsgene in koringlyne te stapel met behulp van merker bemiddelde seleksie en mikrospoor geassosieerde verdubbelde haploïede tegnologie.

Thesis (MSc)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Wheat production is globally affected by several different wheat rust diseases. The rust diseases can effectively be controlled by the deployment of multiple resistance genes that confer durable resistance. One of the most effective strategies to incorporate resistance genes is by the implementation of recurrent mass selection as it maximizes opportunities for gene pyramiding. The implementation of a recurrent mass selection program in wheat can effectively be enhanced with the use of genetic male sterility and the incorporation of maker assisted-selection (MAS). The aim of the study was to pyramid wheat rust resistance genes in wheat lines by utilizing a male sterile mediated marker-assisted recurrent selection breeding (MS-MARS) scheme. An existing segregating MS-MARS base population and resistance donor lines carrying genes of interest (Sr26, Sr35 and Sr45) were used as female and male crossing parents. Potential markers for the genes of interest were first identified and validated on the male population. PCR based markers tested for Sr26 and Sr45 easily distinguished between resistant and non-resistant plants in the study, while markers tested for the detection of Sr35 and Sr45 in most instances failed to do so. The identified Sr26 marker (Sr26#43) was successfully added to the SU-PBL’s standardized marker set in a multiplex reaction. The standardized marker set and the co-dominant PCR marker for Sr45 were used to screen male and female populations before and after cross-pollination. Several wheat rust resistance genes were present in various frequencies in both male and female populations prior to the first crossing cycle, except Sr26 and Sr45. Increases in gene frequencies and combinations were obtained after the first crossing cycle, highlighting the effectiveness of the MS-MARS breeding strategy to improve gene frequencies of desirable genes. Two MS-MARS crossing cycles were successfully completed and large numbers of hybrid seeds were produced in a short period of time by selecting male sterile plants based on distinct characteristics induced by the dominant male sterility gene. Future studies will include the wide deployment of Sr26 and Sr45 in the MS-MARS breeding program as markers are now available and can be included in the SU-PBL’s standardized marker set for the effective detection of these genes, the development of gene-specific markers for Sr35 to ascertain the presence of the gene in the MS-MARS population and the specific selection of male sterile plants with wide open glumes to maximize outcrossing rates. / AFRIKAANSE OPSOMMING: Koring produksie word wêreldwyd aansienlik deur koringroes siektes geaffekteer. Die siektes kan doeltreffend beheer word deur die ontplooing van veelvuldige weerstandsgene, wat langdurige weerstand tot gevolg het. Een van die mees doeltreffendste strategieë om weerstandsgene in n koring plant te inkorporeer is deur die implementering van herhalende massa seleksie (HMS), siende dat dit geleenthede vir geen stapeling maksimaliseer. Die implementering van 'n HMS program in koring kan effektief aangewend word met behulp van genetiese manlike steriliteit en merker bemiddelde seleksie (MBS). Die doelwit van hierdie studie was om veelvuldige koringroes weerstandsgene in koring lyne te stapel met behulp van die manlik steriliteits merker bemiddelde herhalende seleksie (MS-MBHS)-telingsskema. ‘n Gevestigde segregerende MS-MARS basis populasie en donor lyne, wat die gene (Sr26, Sr35 en Sr45) van belang dra, was onderskeidelik as vroulike en manlike kruisingsouers gebruik. Potensiële molekulêre merkers vir die gene van belang was eers geidentifiseer in literatuur en op die donor lyne getoets, voordat dit vir die opsporing van die gene in die nageslag gebruik was. Polimerase ketting reaksie (PKR)-gebaseerde merkers wat getoets was vir Sr26 en Sr45, kon maklik tussen weerstand en nie-weerstandbiedende plante in die studie onderskei, terwyl ander merkers vir die opsporing van Sr35 en Sr45 nie so doeltreffend was nie. Die geidentifiseerde Sr26 merker was suksesvol bygevoeg tot die SU-PBL se gestandardiseerde merkerpaneel, in ‘n multipleks reaksie. Die gestandardiseerde merkerpaneel en die ko-dominante PKR merker vir Sr45 was gebruik om die manlike en vroulike populasie te analiseer vir die teenwoordigheid van verskeie weerstandsgene voor en na kruisbestuiwing. Merker analise het die teenwoordigheid van verskeie koringroes weerstandsgene in verskillende frekwensies in beide die manlike en vroulike populasie voor die eerste kruising siklus aangedui. Sr26 en Sr45 was egter afwesig in beide populasies. ‘n Toename in geen frekwensies en kombinasies was waargeneem na die eerste kruising siklus. Dit het gevolglik die doeltreffendheid van die MS-MARS teling strategie beklemtoon. Twee herhalende kruising siklusse was suksesvol voltooi en groot hoeveelhede bastersaad was verkry vanaf steriele plante wat geselekteer was op grond van unieke eienskappe wat hulle vertoon as gevolg van die manlike steriliteits geen. Toekomstige studies sluit in, die groot skaalse gebruik van Sr26 en Sr45 in die MS-MARS teelprogram aangesien merkers nou beskikbaar is en gebruik kan word in die MS-MARS teelprogram vir die doeltreffende opsporing van hierdie gene, die ontwikkeling van ‘n geen-spesifieke merker vir Sr35 om die teenwoordigheid van die geen in die MS-MARS populasie vas te stel, en die selektering van manlike steriele plante met wyd oop kaffies om kruisbestuiwing te verhoog.

A ferrugem alaranjada da cana-de-açúcar, causada pelo fungo Puccinia kuehnii, é atualmente a doença que mais preocupa o setor sucroenergético brasileiro, devido a sua introdução recente no país e aos prejuízos causados em indústrias canavieiras ao redor do mundo. A doença é controlada com variedades resistentes e por isso há a necessidade de maiores informações sobre a reação das cultivares mais importantes no Brasil. Os objetivos deste trabalho foram: (i) avaliar a reação de variedades de cana-de-açúcar à ferrugem alaranjada, em condições de infecção natural no campo; (ii) determinar a melhor época para avaliação da doença; (iii) estabelecer um método, em casa de vegetação e com inoculação artificial do patógeno, para seleção rápida de variedades com resistência no campo. Dezessete variedades foram avaliadas quanto às suas reações a P. kuehnii em dois experimentos de campo, plantados em abril e julho de 2011; neste último, após a colheita em maio de 2012, a cana-soca também foi avaliada. Para multiplicar e uniformizar a distribuição do inóculo, a variedade suscetível SP89-1115 foi usada como bordadura e plantada entre os blocos e em duas linhas, dividindo cada experimento ao meio. Avaliou-se a severidade da doença a cada 15 dias e, a partir destes dados, calculou-se a área abaixo da curva de progresso da doença (AACPD) e obteve-se a severidade máxima da doença. Para identificar o melhor período de avaliação, realizou-se análise de correlação entre a AACPD e cada levantamento de severidade. Em casa de vegetação, seis variedades com reações distintas à doença, com base nos resultados obtidos no campo, foram inoculadas com uma suspensão de 104 urediniósporos viáveis mL-1 de P. kuehnii, com auxílio de pulverizador manual, 60 dias após o plantio. As plantas foram mantidas por 24 horas em câmara de orvalho e, posteriormente, transferidas para casa de vegetação. Foram determinados os períodos de incubação e latência, o número de pústulas por cm2 e a severidade da doença. Oito das 17 variedades avaliadas no campo mostraram alta resistência à doença. As cultivares RB72454 e SP89-1115 foram as mais suscetíveis, seguidas da SP79-2233; por isso, o cultivo das mesmas não é recomendado. As variedades RB925211, SP81-3250, RB855156 e RB92579 tiveram reação intermediária, sendo que as duas primeiras apresentaram maiores níveis da doença. Avaliações realizadas no mês de março foram as que mais se correlacionaram com a AACPD, portanto este é o melhor período para determinar a reação de variedades de cana-de-açúcar à ferrugem alaranjada. O comportamento das variedades em casa de vegetação foi semelhante ao observado no campo, especialmente em relação às cultivares suscetíveis e resistentes. Assim, o método aplicado em casa de vegetação mostrou potencial para selecionar, em poucos dias, cultivares com resistência à doença no campo, além de economizar espaço, mão de obra e de ser facilmente executado. / Currently, sugarcane orange rust, caused by Puccinia kuehnii, is the disease that most concerns the Brazilian sugarcane industry, due to its recent introduction in the country and the damage caused to sugarcane industries all over the world. The disease is controlled with resistant varieties; hence there is a need for more information about the reaction of the major cultivars in Brazil. The objectives of this work were: (i) to evaluate the reaction of sugarcane varieties to orange rust in field, under natural infection conditions; (ii) to determine the best time for disease assessment; (iii) to establish a method in greenhouse, based on artificial inoculation, for rapid selection of field resistant varieties. Seventeen varieties were studied in two field experiments, planted in April and July 2011; in the latter, after the harvest in May 2012, the ratoon was also evaluated. The susceptible variety SP89-1115 was used as border and planted between the blocks in two lines, dividing each experiment in two halves in order to multiply and standardize the inoculum in the area. Disease severity was evaluated every 15 days and the area under disease progress curve (AUDPC) was calculated and the maximum disease severity was obtained. To identify the best time for disease assessment, a correlation analysis between the AUDPC and each disease severity assessment was done. In greenhouse, six varieties with different reactions to the disease based on results obtained in field were inoculated with a suspension of 104 viable urediniospores mL-1 of P. kuehnii with a manual sprayer 60 days after planting. Plants were maintained in dew chamber for 24 hours and afterwards they were transferred to the greenhouse. The incubation and latent period were determined as well as the number of pustules cm-2 and disease severity. Eight out of 17 varieties evaluated in field showed high disease resistance. The varieties RB72454 and SP89-1115 were the most susceptible, followed by SP79-2233; therefore, their commercial cultivation is not recommended. The varieties RB925211, SP81-3250, RB855156 and RB92579 had intermediate reaction, with the first two showing higher disease levels. Evaluations performed in March showed the highest correlation with AUDPC, thus this period is the best for determining sugarcane reaction to orange rust. The varieties reaction in greenhouse was similar to that observed in the field, particularly in relation to susceptible and resistant cultivars. So, the method applied in greenhouse showed potential to select, in a few days, field disease-resistant varieties, besides saving space and labor and being easily implemented.

Doctor of Philosophy / Department of Plant Pathology / Bikram S. Gill / The wild relatives of crop plants are sources of useful genes, but such genes when transferred to agricultural crops are often associated with deleterious traits. Because most of the recombination and the disease resistance genes are localized towards the ends of wheat chromosomes, cryptic terminal alien segments, carrying rust resistance genes, were transferred from Aegilops geniculata (UgMg) and Ae. triuncialis (UtCt) into common wheat without the usual linkage drag. The alien segment with the leaf rust and stripe rust resistance genes Lr57 and Yr40 in translocation T5DL•5DS-5MgS(0.95) was found to be less than 3.3 cM in genetic length and spans less than four overlapping BAC/PAC clones of the syntenic rice chromosome arm 12L. The alien segment with leaf rust resistance gene Lr58, transferred from Ae. triuncialis, was found to be less than 5% of the chromosome arm 2BL of wheat in T2BS•2BL-2tL(0.95), further suggesting that it is feasible to transfer small alien segments with disease resistance genes. Resistance genes Lr57, Yr40 and Lr58 were transferred to Kansas hard red winter wheat cultivars by backcrossing and marker assisted selection. Tillering, a key component of grain yield, and seed color which influences seed dormancy and pre-harvest sprouting in wheat, are agronomically important domestication traits in wheat. A tiller inhibition mutant with monoculm phenotype was isolated and the mutated gene (tin3) was mapped on the distal region of chromosome arm 3AmL of T. monococcum. As a first step towards isolating candidate gene(s), the tin3 and the seed color gene (R-A1) of chromosome 3A were mapped in relation to physically mapped ESTs and STS markers developed based on synteny with rice. Physically mapped wheat ESTs provided a useful framework to identify closely related rice sequences and to establish the most likely syntenous region in rice for the wheat tin3 and R-A1 region. Comparative genomic analysis of the tin3 and R-A1 genomic regions with the corresponding region in rice localized the tin3 gene to a 324 kb region spanned by two overlapping BACs and the R-A1 gene was mapped to a single BAC of the colinear rice chromosome arm 1L.

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.

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.

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.