No description available.

No description available.

<p>While local adaptation has been frequently demonstrated via reciprocal transplant experiments, our understanding of the genetic basis of it remains minimal. There is a notable lack of studies that identify naturally segregating variants, determine the traits controlled by these variants and characterize their fitness effects in the field. Such studies are critical for understanding how spatially varying selective pressures can drive population divergence and maintain genetic variation. The experiments presented here aim to characterize the genetic basis of local adaptation to serpentine soils in Mimulus guttatus. First, I show that serpentine and non-serpentine populations of M. guttatus are locally adapted to soil habitat wherein non-serpentine plants are unable to survive on serpentine soils. Serpentine tolerance appears to come at a cost as serpentine plants are smaller in the juvenile stage than non-serpentine plants when grown at non-serpentine field sites. These size differences may limit the competitive ability of serpentine tolerant plants in non-serpentine habitats which tend to be more heavily vegetated than serpentine habitats. Next I identify environmental variables that are important selective agents in the serpentine habitat. Using hydroponic assays to isolate an individual chemical variable of serpentine soils - low calcium levels to high magnesium levels (low Ca:Mg ratio) - I show that serpentine and non-serpentine populations of M. guttatus have significant differences in tolerance to low Ca:Mg. I then characterize the genetic basis of these ecotypic differences in survival and tolerance using quantitative trait locus (QTL) mapping. I identify a single, major QTL that controls both the ability to survive on serpentine soils and tolerance to low Ca:Mg ratio which suggests that M. guttatus populations have adapted to serpentine soils through an ability to tolerate the low levels of Ca while simultaneously not suffering from Mg toxicity. Furthermore, I show that this same QTL controls ability to survive on serpentine soils in a second, geographically distant population. However, preliminary work suggests that the two populations are not equally tolerant to each other's soils indicating that either other loci also contribute to serpentine tolerance and these are not shared between the two serpentine populations or that there are different serpentine tolerance alleles at the major QTL are not functionally equivalent. This work addresses long-standing questions in evolutionary biology regarding the number and effect size of loci that underlie adaptive traits by identifying a large effect locus that contributes to adaptive differences between M. guttatus populations.</p> / Dissertation

Fusarium Head Blight (FHB) is a destructive disease caused by Fusarium graminearum that affects wheat (Triticum aestivum L.) worldwide. Breeding for resistance to FHB is arguably the best way to combat this disease. However, FHB resistance is highly complex and phenotypic screening is difficult. Molecular markers are a promising tool but breeding programs face the challenge of allocating resources in such a way that the optimum balance between phenotypic and genotypic selection is reached. An F2:3 population derived from a resistant x susceptible cross was subjected to phenotypic and genotypic selection. For phenotyping, a novel air separation method was used to measure percentage of damaged kernels (FDK). Heritability estimates were remarkably high, which was attributed to the type of cross and the quality of phenotyping. Genotypic selection was done by selecting resistance alleles at quantitative trait loci (QTL) on the 3BS (Fhb1) and the 2DL chromosomes. Fhb1 conferred a moderate but stable FHB resistance while the 2DL QTL conferred a surprisingly high level of resistance but with significant interaction with the environment. Phenotypic selection conferred higher or lower genetic gains than genotypic selection, depending on the selection intensity. Based on these results, different selection strategies are discussed.

A whole genome scan was conducted to identify and fine map QTL regions for ultrasound and carcass merit traits in beef cattle. A total of 465 steers and bulls, genotyped for 4592 SNPs, were analysed for 16 ultrasound and carcass merit traits using interval mapping, single marker regression and Bayesian shrinkage approaches. Thirty QTL and 22 SNPs associated with traits were identified by interval mapping and single marker regression respectively. In Bayesian shrinkage estimation, 218 QTL were identified, wherein 11 of the 30 QTL identified by interval mapping were confirmed. The proportions of QTL variance on the trait variations estimated by Bayesian shrinkage analysis were relatively small. They ranged from 0.1 to 4.8% compared to 6.1 to 11.7% in interval mapping because the QTL in Bayesian approach were adjusted to remove effects of other QTL in the genome. These results are useful for detection of underlying causative QTN variants. / Animal Science

The objective of this thesis was to construct radiation hybrid (RH) maps and estimate linkage disequilibrium (LD) using high density SNP markers on chromosomes 19 (BTA19) and 29 (BTA29) and use these as a tool to detect QTL in dairy and beef cattle. We have constructed RH maps of BTA19 and BTA29 consisting of 555 and 253 SNP markers respectively using a 12,000 rad whole genome RH panel. When aligned with the third draft of bovine genome sequence assembly, there was a significant internal rearrangement of the markers involving displacement, inversion and flips within the scaffolds with some scaffolds being misplaced in the genome assembly. Many of these mapped markers (370 and 186 SNP markers on BTA19 and 29 respectively) were further utilized to quantify the extent of LD using the square of the correlation coefficient (r2) and to study the pattern of selection signatures in beef (Angus) and dairy (Holstein) breeds of Bos taurus. Along the chromosomes, patterns of LD were variable in both breeds and a minimum of 30,000 informative and evenly spaced markers would be required for whole genome association studies in cattle. In addition, chromosomal regions showing evidence of selection for economically important traits in Angus and Holstein were identified. Furthermore, the dense SNP markers were used to perform chromosome-wide scan to detect QTL for different economically important traits in beef and dairy cattle. Two approaches, single marker LD regression and Bayesian Monte Carlo Markov Chain, were used to map QTL. QTL for 10 and 5 traits in dairy cattle and for 2 and 1 trait in beef cattle on BTA19 and 29 respectively were detected using both approaches of QTL mapping. The QTL detected in this study are a step towards the identification of positional candidate genes controlling these traits. In addition, we have detected several SNPs influencing economically important traits in both beef and dairy cattle. Some SNPs have been validated in an independent cattle population and has the potential of being utilized in the marker assisted selection of cattle. / Animal Science

Recent initiatives for biofuel production have increased research and development of sweet sorghum. Currently, the initial major limitation to integrating sweet sorghum into existing production systems is the lack of sweet sorghum hybrids adapted to industrial production systems. Hybrid development is now underway, and the application of genetic markers can be used to define the genetic basis of sugar yield and its components, as well as reduce the time required to deliver new sweet sorghum hybrids to market. The purpose of this research was to further characterize the genetic components that influence sweet sorghum productivity, agronomics, and composition. Specifically, a grain x sweet sorghum recombinant inbred line (RIL) population developed for quantitative trait locus (QTL) analysis related to sugar production was evaluated for 24 phenotypic traits including brix, percent moisture, and biomass yield across four environments. The 185 F4 RILs were derived from the parents 'BTx3197' and 'Rio', which are pithy stalk grain and juicy stalk sweet sorghums respectively. Following screening, two genetic maps were constructed with 372 and 381 single nucleotide polymorphisms (SNPs) evaluated using an Illumina GoldenGate assay. Analysis of the data in QTL Cartographer revealed a major and previously reported QTL for soluble solids on chromosome 3, but in contrast to previous studies, this QTL co-localized with other QTLs that have a negative influence on biomass and seed production. Therefore, selection for this QTL may not be advantageous. Because only a few QTLs for percent moisture were found, the results indicated that the pithy stalk phenotype does not have a major effect on percent moisture as measured in this study. Thus, breeding for high or low moisture content will be more challenging than previously expected. The absence of dominance effects indicated that brix must be high in both parents to produce high brix in the hybrid.

During the last decades the climate has been changing more rapidly than in the preceding periods. This is for instance characterized by an increase in temperature. Interestingly, such changes in the environment are not necessarily constant over time as they often show high levels of fluctuation. Organisms are exposed to these changes and respond to them and a recent theoretical model predicts that fluctuations in the environment are important for populations’ response to climate change. The aim of this thesis is to investigate how populations respond to a changing environment, including fluctuations. My thesis is based on the previously mentioned theoretical model and I used a suite of laboratory experiments on the seed beetle Callsosobruchus maculatus, to test the model predictions in a quantitative genetic framework. First, I assessed the genetic architecture of several life history and morphological traits in order to verify that there is sufficient additive genetic variation for the population to respond to changes in the environment. Second, I tested the detailed model predictions explicitly, by investigating whether different types of environmental fluctuations matter for a population’s response. Third, I investigated changes in quantitative genetic variation after i) a rapid shift in temperature and ii) long term selection under increasing temperature including fluctuations. Fourth, I concentrated on sex differences in response to temperature, and finally, I assessed the relative importance of genetic and nongenetic inheritance for traits that differ in their plastic response to a change in the environment. I found that environmental fluctuations are highly important for a population’s response to environmental change. I could detect changes in a set of quantitative genetic parameters, suggesting that a population’s potential to respond to selection, environmental sensitivity and the evolution of phenotypic plasticity are affected by the selective past. I also found that sexes differ in additive genetic variation and plasticity and that parental effects may play an important role in the evolutionary process. Therefore, future studies would benefit greatly from considering details of the selective past and especially environmental fluctuations during attempts to predict how populations respond to a changing environment, particularly with regards to climate change.

Fructans are polysaccharides that are made up mainly of fructose. They are non-digestible carbohydrates and act as prebiotics to selectively promote the growth of colonic bifidobacteria, thereby improving human gut health. Fructans are present in the grain of wheat (Triticum aestivum L.), a staple food crop. Until now, there has been no research on genetic improvement of the concentration of fructans in wheat grain, partly because it has been difficult to accurately measure. One aim of this research project was to develop a simple and effective method to measure the fructan concentration in wheat grain. This was achieved by modifying a method that involves extraction of fructans from wheat grain followed by enzymatic hydrolysis to break down fructans into monosaccharides and quantification by anion-exchange liquid chromatography coupled with pulsed amperometric detection. The modified procedure is reliable and allows the handling of large numbers of flour samples at a relatively low cost, and can therefore be useful for assessing large numbers of wheat breeding lines. Using this method, grain samples taken from a diverse set of 117 wheat cultivars and breeding lines, including parents of mapping populations, were analysed for grain fructan concentration. There was significant genotypic variation among these materials, with grain fructan concentration ranging from 0.3 to 2.3% of grain dry weight. There was no evidence of strong genotype-byenvironment interaction; the fructan concentrations of the same genotypes were positively correlated over different environments in Australia. Genetic mapping was carried out to detect and map loci affecting grain fructan concentration in wheat using a doubled haploid population derived from a cross between Berkut (high fructan) and Krichauff (low fructan). Grain samples were obtained from two field sites in South Australia and one in Kazakhstan. Fructan concentration varied widely within the population (0.6-2.6% of grain dry weight), with heritability estimated as h² = 0.71. A linkage map of 528 molecular markers covering 21 wheat chromosomes was used for locating quantitative trait loci (QTL). Genetic mapping identified two major QTLs on chromosomes 6D and 7A, with the (high fructan concentration) alleles contributed from Berkut, contributing to a 30-40% increase in wheat grain fructan compared to the Krichauff alleles. Effects of these chromosome regions were validated in additional environments and in another mapping population, Sokoll/Krichauff, with the favourable alleles contributed from Sokoll. The major QTL on chromosome 7A was in the same region with a reported fructosyltransferase orthologue (AB029888), while the major QTL on chromosome 6D seemed to be co-located with a reported gene encoding for a fructan-degrading enzyme 1-exohydrolase (1-FEHw2). It is concluded that grain fructan concentration of wheat can be improved by breeding and that molecular markers could be used to select effectively for favourable alleles in two regions of the wheat genome. / Thesis (Ph.D.) - University of Adelaide, School of Agriculture, Food and Wine, 2009

Fructans are polysaccharides that are made up mainly of fructose. They are non-digestible carbohydrates and act as prebiotics to selectively promote the growth of colonic bifidobacteria, thereby improving human gut health. Fructans are present in the grain of wheat (Triticum aestivum L.), a staple food crop. Until now, there has been no research on genetic improvement of the concentration of fructans in wheat grain, partly because it has been difficult to accurately measure. One aim of this research project was to develop a simple and effective method to measure the fructan concentration in wheat grain. This was achieved by modifying a method that involves extraction of fructans from wheat grain followed by enzymatic hydrolysis to break down fructans into monosaccharides and quantification by anion-exchange liquid chromatography coupled with pulsed amperometric detection. The modified procedure is reliable and allows the handling of large numbers of flour samples at a relatively low cost, and can therefore be useful for assessing large numbers of wheat breeding lines. Using this method, grain samples taken from a diverse set of 117 wheat cultivars and breeding lines, including parents of mapping populations, were analysed for grain fructan concentration. There was significant genotypic variation among these materials, with grain fructan concentration ranging from 0.3 to 2.3% of grain dry weight. There was no evidence of strong genotype-byenvironment interaction; the fructan concentrations of the same genotypes were positively correlated over different environments in Australia. Genetic mapping was carried out to detect and map loci affecting grain fructan concentration in wheat using a doubled haploid population derived from a cross between Berkut (high fructan) and Krichauff (low fructan). Grain samples were obtained from two field sites in South Australia and one in Kazakhstan. Fructan concentration varied widely within the population (0.6-2.6% of grain dry weight), with heritability estimated as h² = 0.71. A linkage map of 528 molecular markers covering 21 wheat chromosomes was used for locating quantitative trait loci (QTL). Genetic mapping identified two major QTLs on chromosomes 6D and 7A, with the (high fructan concentration) alleles contributed from Berkut, contributing to a 30-40% increase in wheat grain fructan compared to the Krichauff alleles. Effects of these chromosome regions were validated in additional environments and in another mapping population, Sokoll/Krichauff, with the favourable alleles contributed from Sokoll. The major QTL on chromosome 7A was in the same region with a reported fructosyltransferase orthologue (AB029888), while the major QTL on chromosome 6D seemed to be co-located with a reported gene encoding for a fructan-degrading enzyme 1-exohydrolase (1-FEHw2). It is concluded that grain fructan concentration of wheat can be improved by breeding and that molecular markers could be used to select effectively for favourable alleles in two regions of the wheat genome. / Thesis (Ph.D.) - University of Adelaide, School of Agriculture, Food and Wine, 2009