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Laboratory experiments, genetic simulation, and theoretical analyses were performed to address several objectives related to the use of genetic markers in plant breeding programs. Two software packages were developed: GREGOR provides flexible and efficient computer algorithms for performing genetic simulation experiments, and KIN provides improved methods for estimating coancestry from known pedigrees. Random amplified polymorphic DNA (RAPD) markers were investigated in elite barley lines, and estimates of genetic distance based on RAPD markers were compared to estimates based on coancestry. Both types of estimate can provide information that is useful to breeders and geneticists. Genetic simulation was used to investigate the power, accuracy and precision of several methods that are available for analyzing quantitative trait loci (QTL). In most cases, simplified methods of QTL analysis based on linear regression were similar or superior to more complex methods based on mixture models. Methods for genetic analysis using selective genotyping and pooled DNA were also investigated. These methods may allow precise estimates of the positions of markers and QTL to be made.

The purpose of this experiment is to test the relative yields of grain from across-bred grains s.s compared with self fertilized seed of the same varieties. It was originally purported to make these tests with both wheat and barley. However, owing to unfavorable greenhouse conditions the wheat plants bloomed very poorly and the crosses made set very little seed so the wheat was dropped and the work done entirely with barley. Before entering into the details of the work conducted, a brief review will be made of small grain breeding work at other places. The Agricultural Experiment Station of Wisconsin has only recently issued a bulletin on barley cultivation. Barley being one of the principal crops of Wisconsin, the Experiment Station has made considerable effort to improve the seed production. Individual selection and crossbreeding have been carried on extensively. Up to the present time no cross-bred varieties have been developed that compare favorably with the pure strains. Their great work has been in individual selection and the production of the so-called pedigree barleys. They started by procuring foundation stock from the best varieties in the United States and Canada. These were planted in small plats and watched carefully during their growth. At harvest time the best heads were selected from the best plants. These were in turn grovm in centgener beds and again selected. After five years of this close selection larger quantities of seed were saved and planted. The sixth year small quantities of this seed were sent out to co-operating students all over the state. In this way the new varieties were disseminated throughout the state and were soon available to every farmer in the state. The Wisconsin station bred for large yields, for resistance to smuts, and for uniformity in size and quality of grain, in length and strength of straw and in time of germination and maturity. In twelve years time sixteen different strains of pedigree barley were developed that were superior to the old strains.The six-row bearded was found to be superior to all other varieties. Minnesota has probably done as much or more work than any other State in breeding and improving wheat. The Experiment station has been working for twenty-five years to produce improved strains for the use of Minnesota farmers and have been well repaid in many cases. Their work has been along the usual lines of cross breeding and selection. Two kinds of cross breeding were practiced - out-crosses and in-crosses. Out-crosses were made between plants of different varieties and in-crosses between plants of the same variety. The seed from these crosses was planted and the best one plant from each arose selected to continue the breeding. This individual selection was continued for several years before it was put out as a new variety. In this way several new varieties were developed that yielded very creditably with the best of the old varieties. However, it was found that large numbers had to be worked with in order to get even one cross that was good. The vast majority of them were no good. While out-crosses were harder to get than in-crosses, they gave more evidence of being crossed than did the in-crosses. Only one of the in-crosses showed enough variation from the parent stock to indicate that it was hybrid. Some of the best known varieties originating from crosses are the Fife and Blue stem wheats. After establishing a new variety it was disseminated throughout the state in much the same way as the barley varieties were in Wisconsin. The gain to the farmers of the state by this practice has been immense. It made available for the farmer pedigreed seed that was far superior to the scrub stock commonly used. The Nebraska Experiment station nas done a great deal of wheat breeding work in last twenty years, mainly along lines of selection. In former years the greater part of the wheat grown in Nebraska was spring wheat. The wields were not what they should be so attention was turned to winter wheats. The experiment station took the matter up and has developed a winter wheat that has increased the yield five bushels and more per acre. The variety found to be best suited to Nebraska was the Turkey Red. Dr. T. L. Lyon undertook to improve this variety by a systematic method of selection. To start with he took one thousand select heads and planted them in separate rows in the nursery. The second year the best heads from these rows were planted. This was continued for three years, some of the poorest being discarded each year. At the end of three years. The seed was planted in thirtieth-acre plats. For five years this was continued until good comparisons could be made of the various strains. Then the wheat was sold in ten bushel lots, in different sections of the state on the condition that the buyer should seed according to instructions and make a report on the results. The reports showed that an average of twenty-one tests in twenty counties gave a net increase of four bushels per acre over the local Turkey Red Wheat. In only three instances did the local wheat excel the improved strains. Dr. Hjalmar Wilssen of the Swedish Experiment Station, has done a great deal of breeding work with small grains. He has made selections tending toward improvement along all lines. In some instances he has been successful and in others very unsuccessful. He found that deficiencies of technical nature could be overcome, such as length of spikelet but where the foundation principles were concerned it was more difficult and sometimes impossible. One of his failures was an attempt to breed few stronger culms in barley. One of the most valuable barleys grown in Sweden was disposed to lodge or fall down. Nilsson tried to remedy this by selection. He spent years of hard work on the problem but never accomplished anything and finally gave it up. He later accomplished his end problem by producing another strain of barley which had as good quality as the old, and at the same time had strong culms. / Master of Science

The occurrence of Boron (B) toxicity in Australian soils is recognised as a limiting factor for cereal productivity. A number of loci conferring tolerance to B toxicity have been identified in barley and chromosomally mapped. However, a lack of knowledge relating to the physiological and molecular events that occur under B toxicity and the molecular basis for B stress tolerance has been a bottleneck in harnessing available genetic diversity in barley and wheat. The recent advances in functional genomics provided an opportunity to examine B stress in barley in more detail. The aim of this project was to analyse genes differentially expressed under B stress in tolerant and intolerant barley to identify candidate genes involved in B toxicity tolerance. Two experimental approaches, Suppression Subtractive Hybridization (SSH) and microarray were adopted. Firstly, SSH was performed to examine gene expression in roots of selected tolerant and intolerant doubled haploid lines from a Clipper (B intolerant) X Sahara 3771 (B tolerant) mapping population, grown under moderate B stress. The SSH experiment aimed to investigate the early transcriptional response of B tolerant barley lines to B stress in order to identify the basis for B toxicity tolerance in roots. Differential screening of the subtracted library generated from B treated plants identified a total of 111 non-redundant clones up-regulated in bulked tolerant lines. On the other hand 94 clones were differentially expressed under non-treated conditions. Among the clones identified from subtracted library generated from B treated plants, metabolism was the largest functional category, representing 21% of the clones. The largest functional category in the subtracted library generated from non treated plants was cellular transport, representing 19% of the clones. Based on sequence similarity, about 170 transcripts identified in this experiment were assigned to chromosomal segments (bins) on the three homoeologous genomes of bread wheat. In total, 36 clones from the subtracted library generated from B treated plants were analysed as candidates. Nine were genetically mapped within the region of B tolerance QTL on three chromosomes (2H, 4H and 6H). The genes mapped to 4H and 6H QTL have the highest association with these loci in the Clipper X Sahara 3771 doubled haploid mapping population. A 4H B tolerance QTL candidate gene was identified as a B transporter gene with similarity to the Arabidopsis BOR1 gene. Genes identified to be differentially expressed in the tolerant lines from SSH suggest activation of a diverse defence response in the roots of barley plants under B stress. Data from SSH experiment indicate that cell wall-plasma membrane cytoskeleton continuum constitute the first action site against B toxicity and the influence of toxic B on K+ uptake could be the key initiating factor. In the second approach, the Affymetrix 22K Barley1 GeneChip(TM) was used to investigate B stress adaptation processes in barley. Gene expression was profiled in leaves of Sahara 3771 and Clipper plants grown under various B concentrations. The results show that the two genotypes respond differently to B toxicity. The B intolerance of Clipper is expressed through the induction of a high number of probe sets (2310) even at a low B concentration of 100 µM. In contrast, Sahara 3771 responded to a high B concentration (2000 µM) through the induction of only a few hundred (266) probe sets. In Sahara 3771 no change in the expression level of any probe sets was observed at 100 µM B. Altogether 286 probe sets showed differential expression in Sahara 3771 under three levels of B treatment (500, 1000 and 2000 µM). About 30% of these were down-regulated and about 70% were up-regulated in Sahara 3771 in response to B treatment. Most of the probe sets (59%) up-regulated in Sahara 3771 did not respond to B treatment in Clipper. These genes are either salt stress responsive or related to plant defense and thus could play a key role in protecting barley plants from the toxic effects of B. Two differentially expressed probe sets annotated as B transporters were identified between Sahara 3771 and Clipper under control condition. These two B transporter probe sets did not respond to B treatment but showed opposing expression patterns in the two varieties. One of these probe sets (Contig21126_at) is similar to the B transporter gene isolated from the SSH experiment that maps to the 4H tolerance locus. The map location and expression of this B transporter gene suggest that it could be the borate anion efflux transporter predicted by the proposed efflux model of B tolerance in Sahara 3771 barley. The other B transporter gene (Contig14139_at) showed over expression in Clipper under control condition and could be contributing to high B accumulation in Clipper which needs further investigation. Data from both experiments have indicated that B toxicity triggers oxidative stress and that jasmonate-based signaling plays a key role in B toxicity tolerance. SSH data indicate that Sahara 3771 which evolved in the harsh environment of Africa is more efficient in osmoregulation and ROS scavenging than Clipper. This trait is likely to give Sahara 3771 an edge over Clipper in tolerating toxic the effect of B. In addition to the efflux mechanism, which becomes less efficient with increasing B supply, Sahara 3771 appears to apply a number of other mechanisms for alleviating or withstanding toxic B induced stress to sustain growth. Some of these mechanisms are already known to be used by plants to cope with a number of stresses. / Thesis (Ph.D.) -- University of Adelaide, School of Agriculture, Food and Wine, 2008