Title page, table of contents and abstract only. The complete thesis in print form is available from the University of Adelaide Library. / Variation in quantity and quality of gluten proteins is largely responsible for the genotypic differences associated with the dough rheological parameters, maximum resistance (R[subscript]max) and extensibility (Ext.). In the context of bread making, doughs characteristic of good quality have moderate to high extensograph maximum resistance (R[subscript]max) and high extensibility (Ext.). The term usually applied to describe the balance between these two parameters is dough strength. Generally, weak doughs perform poorly in baking tests and as dough strength increases, bread making quality also increases. Important proteins that constitute the 'gluten complex' include high molecular weight glutenin subunits (HMW-GSs) and low molecular weight glutenin subunits (LMW-GSs). These proteins, which interact to produce large polymeric proteins, are coded at the Glu-1 and Glu-3 loci on group 1 chromosomes, respectively. Extensive allelic variation exists a1 each of the G/u-1 and Glu-3 loci. Field trials (4 years) and physical dough quality tests on harvested grain from a set of near-isogenic lines, differing in glutenin composition, were used to investigate the effect of numerous glutenin alleles on dough rheological parameters. Glutenin allele main effects were ranked as follows: Glu-A1 a = p = b > c for R[subscript]max and Glu-A1 a = b = p > C for Ext.; Glu-B1 i ≥ b = c > d = a for R[subscript]max and Glu-B1 a = i = c ≥ b ≥ d for Ext.; Glu-D1d > Glu-D1a = Glu-D1b ≥ Glu-D1f for R[subscript]max and Glu-D1 a = b = f ≥ d for Ext.; Glu-A3 d = b ≥ c = f ≥ a > e for R[subscript]max and Glu-A3 b = a = d = c = f ≥ e for Ext.; Glu-B3 g ≥ b = m ≥ d = i = h = f≥ a ≥ c for R[subscript]max and Glu-B3 i = d ≥ g = f = m ≥ b = c = h = a for Ext.; Glu-D3 a-Gli-D1 = f ≥ c = d = a ≥ b for R[subscript]max and Glu-D3 d ≥ a-Gli-D1 ≥ a ≥ b = c = f for Ext. The influence of protein content and two-way glutenin allele interactions are also discussed. Another aspect of this work investigated the relationship between HMW-GS expression levels and quality. RP-HPLC was used to quantify the proportion (% area) of individual HMW-GSs relative to total HMW-GSs. Except for Glu-BId (6+8*), the B-genome contributed the highest percentage of HMW-GSs and was significantly higher (P<O.OO1) in cultivars that contained the Glu-BIal allele. A high proportion of IBx subunits compared to IDx subunits (= 2.3, Glu-B1al) correlated with varieties reported to have extra strong dough properties, while a 1Bx:1Dx ratio of = 1.3 (Glu-B1 i, f, c, u and ak) was typical of varieties with moderate to high dough strength characteristics. In varieties which contain Glu-B1 alleles reported to produce weak: doughs the 1Bx:I1Dx value was = 1.0 (Glu-B1e) and = 0.6 (Gfu-B1). This suggests that the overall proportion of Glu-B1 subunits has a major influence on dough strength and that the proportion of 1Bx relative to 1Dx subunits, as determined by RP-HPLC, could be used to predict dough quality. RP-HPLC analysis also enabled the identification of varieties that contained the Glu-B1al allele and overexpressed subunit Glu-B1 7x, including the most likely source of this allele in bread wheat cultivars. Novel HMW-GS alleles in related wheat species with good quality potential were also identified. A simple small-scale screening assay was developed to efficiently assess the protein quality attributes associated with accessions of synthetic hexaploids, T tauschii and T dicoccoides. Development of the Turbidity assay is described and was used in conjunction with SE-HPLC and SDS-PAGE to conflrm and characterise previously undescribed HMW-GSs. The HMW-GS composition of T dicoccoides is discussed in detail where there were 49 HMW-GSs which combined to produce 54 different HMW-GS banding patterns. Accordingly, allelic designations were tentatively assigned to either individual or subunit pairs and these are also Teported in this manuscript. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1277743 / Thesis (Ph.D.) -- University of Adelaide, School of Agriculture, Food and Wine, 2007

Title page, table of contents and abstract only. The complete thesis in print form is available from the University of Adelaide Library. / Variation in quantity and quality of gluten proteins is largely responsible for the genotypic differences associated with the dough rheological parameters, maximum resistance (R[subscript]max) and extensibility (Ext.). In the context of bread making, doughs characteristic of good quality have moderate to high extensograph maximum resistance (R[subscript]max) and high extensibility (Ext.). The term usually applied to describe the balance between these two parameters is dough strength. Generally, weak doughs perform poorly in baking tests and as dough strength increases, bread making quality also increases. Important proteins that constitute the 'gluten complex' include high molecular weight glutenin subunits (HMW-GSs) and low molecular weight glutenin subunits (LMW-GSs). These proteins, which interact to produce large polymeric proteins, are coded at the Glu-1 and Glu-3 loci on group 1 chromosomes, respectively. Extensive allelic variation exists a1 each of the G/u-1 and Glu-3 loci. Field trials (4 years) and physical dough quality tests on harvested grain from a set of near-isogenic lines, differing in glutenin composition, were used to investigate the effect of numerous glutenin alleles on dough rheological parameters. Glutenin allele main effects were ranked as follows: Glu-A1 a = p = b > c for R[subscript]max and Glu-A1 a = b = p > C for Ext.; Glu-B1 i ≥ b = c > d = a for R[subscript]max and Glu-B1 a = i = c ≥ b ≥ d for Ext.; Glu-D1d > Glu-D1a = Glu-D1b ≥ Glu-D1f for R[subscript]max and Glu-D1 a = b = f ≥ d for Ext.; Glu-A3 d = b ≥ c = f ≥ a > e for R[subscript]max and Glu-A3 b = a = d = c = f ≥ e for Ext.; Glu-B3 g ≥ b = m ≥ d = i = h = f≥ a ≥ c for R[subscript]max and Glu-B3 i = d ≥ g = f = m ≥ b = c = h = a for Ext.; Glu-D3 a-Gli-D1 = f ≥ c = d = a ≥ b for R[subscript]max and Glu-D3 d ≥ a-Gli-D1 ≥ a ≥ b = c = f for Ext. The influence of protein content and two-way glutenin allele interactions are also discussed. Another aspect of this work investigated the relationship between HMW-GS expression levels and quality. RP-HPLC was used to quantify the proportion (% area) of individual HMW-GSs relative to total HMW-GSs. Except for Glu-BId (6+8*), the B-genome contributed the highest percentage of HMW-GSs and was significantly higher (P<O.OO1) in cultivars that contained the Glu-BIal allele. A high proportion of IBx subunits compared to IDx subunits (= 2.3, Glu-B1al) correlated with varieties reported to have extra strong dough properties, while a 1Bx:1Dx ratio of = 1.3 (Glu-B1 i, f, c, u and ak) was typical of varieties with moderate to high dough strength characteristics. In varieties which contain Glu-B1 alleles reported to produce weak: doughs the 1Bx:I1Dx value was = 1.0 (Glu-B1e) and = 0.6 (Gfu-B1). This suggests that the overall proportion of Glu-B1 subunits has a major influence on dough strength and that the proportion of 1Bx relative to 1Dx subunits, as determined by RP-HPLC, could be used to predict dough quality. RP-HPLC analysis also enabled the identification of varieties that contained the Glu-B1al allele and overexpressed subunit Glu-B1 7x, including the most likely source of this allele in bread wheat cultivars. Novel HMW-GS alleles in related wheat species with good quality potential were also identified. A simple small-scale screening assay was developed to efficiently assess the protein quality attributes associated with accessions of synthetic hexaploids, T tauschii and T dicoccoides. Development of the Turbidity assay is described and was used in conjunction with SE-HPLC and SDS-PAGE to conflrm and characterise previously undescribed HMW-GSs. The HMW-GS composition of T dicoccoides is discussed in detail where there were 49 HMW-GSs which combined to produce 54 different HMW-GS banding patterns. Accordingly, allelic designations were tentatively assigned to either individual or subunit pairs and these are also Teported in this manuscript. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1277743 / Thesis (Ph.D.) -- University of Adelaide, School of Agriculture, Food and Wine, 2007

No abstract available. / Dissertation (MSc)--University of Pretoria, 2011. / Genetics / unrestricted

Somaclonal variation, to provide germplasm for crop improvement, must be screened, selected and characterized. Immature wheat, Triticum aestivum L., (PCYT-10) embryos (10-12 days old) were cultured on Hu rashige and Skoog (t1S) medium containing 0.5 mg L-1 6- furfurylaminopurine (kinet in) and 2, 3, or 4 mg L -1 of 1- methoxy-3,6- dichlorobenzoic acid (2,4-D). Dicamba, at 2 and 3 mg L -l and 0.2 mg L -1 2,4-D, produced 12.7%, 30.3%, and 28.2% of the somaclones, respectively. No plantlets were produced from other treatments. Variants were characterized by cytology, biochemistry and morphology. Somaclones showed significant differences in length and width of flag leaf, plant height, number of tillers, spike length, awn length, and number of seeds per main head when compared to parental controls for two sal fed recurrent generations. Number of spikelets per main head in the second generation showed no significant difference from controls. Stability and segregation of somaclones for measured traits indicated that genetic changes had occurred which could enhance wheat germplasm. Leaf isozymes of somaclones (SC 1 and sc 2 ) showed no variation in glutamine oxaloacetate transaminase (GOT) (E.C . 2. 6. 2.1. ), leucine aminopeptidase (LAP) (E.C. 3.4.11.1), or esterase (EST) (E.C. 3.4. 99) bands in 28% of the somaclones, 28% with light, and 44% missing a fast movind band. Approximately 30% of the normal group set no seeds. Mutants with the missing band were stable through the fourth-selfed generation, whereas, variants with the light EP band were still segregating . Plants with the missing EP band were morphologically normal compared to the parents except rachis internodes were longer than those of the parents. There was no correlation between the missing EP band and a missing chromosome in some mutants. The mutant may have been due to a point mutation, deletion, or activation of a repressor gene. Variants exhibited a wide range of protein density and missing or extra bands. Relative amounts of DNA per telophase nucleus were affected by inorganic salts and sucrose levels. Ploidy level increased with time within single-strength MS, but not within double MS medium. Cal li grown on the modified double MS medium exhibited a higher number of shoots than those grown on modified MS. Individual variants with desirable characteristics with high seed production, high protein levels, supernumerary spikelets, and larger flag leaves could be incorporated into a wheat improvement program.

The allohexaploid bread wheat (Triticum aestivum L.), evolved through a recent polyploidization event between tetraploid Triticum turgidum L. (AABB) and diploid Aegilops tauschii Coss. (DD), ~8,000 years ago. Contribution of only a subpopulation of Ae. tauschii to hexaploid evolution, followed by domestication and extensive breeding with the objective of higher yield gain and strict end-use quality determining the market classes of wheat, have created a genetic bottleneck. Synthetic hexaploid wheat (SHW) lines are generated to restore the diversity and exploit the genetic resource in the primary gene pool of wheat. However, there are challenges with recovering the phenotypes observed in the parental background in the hexaploid bread wheat in pre-breeding programs. To understand and characterize the barriers in utilizing the progenitor genetic diversity, the transcriptome of four SHW lines and their corresponding tetraploid and diploid parents across ten tissues, totalling to 240 samples, was analysed. The comparison of expression bias of homoeologues present as >18,000 triads (1:1:1) between parental in-silico SHW-like scenarios and SHWs, indicated a large-scale suppression of D subgenome homoeoalleles in SHWs. Tissue-specificity was not observed in the homoeologues of a large proportion of the triads. The next largest fractions were triads where all homoeologues displayed the same tissue-specific expression followed by those where only one of the homoeologues was tissue-specific. Several SHW-tissues showed moderate relationship between tissue-specificity of the homoeologues and expression bias of the corresponding triad. The repression of the genes of the D subgenome was also validated in the differential expression analysis using the entire high-confidence gene set of hexaploid wheat. Qualitative analysis of the transcripts revealed all five splicing events with predominance of retained introns, and more differentially-spliced transcripts were associated with the D homoeoalleles in most SHW-tissue contexts. The introgression patterns of the SHW-C66 into the elite bread wheat cultivar Carberry was analysed using a BC1F5 population. Large introgression of SHW-C66 were found closer to centromeric regions while smaller fragments were present towards the ends of the chromosomes. Correspondingly, the majority of the chromosomes showed higher recombination rates away from the centromere. The donor allele frequency was higher than the expected 25% for BC1F5 population in multiple regions of the A and B subgenomes but not in the D subgenome. In comparison, a preliminary analysis using an elite wheat × elite wheat doubled haploid population showed no subgenome-level variation in recombination rates or donor allele frequencies. In this thesis work, both functional genomic and structural genomic investigations using a set of SHW parents and their derivative population with elite wheat cultivars have unearthed some key patterns that add to the collective knowledge needed to fully exploit genetic resources in broadening the genetic diversity in wheat improvement programs.

Doctor of Philosophy / Genetics Interdepartmental Program / Bikram S. Gill / Leaf rust, caused by fungus Puccinia triticina, is an important foliar disease of wheat worldwide. Breeding for race-nonspecific resistant cultivars is the best strategy to combat this disease. Aegilops tauschii, D genome donor of hexaploid wheat, has provided resistance to several pests and pathogens of wheat. To identify potentially new adult plant resistance (APR) genes, 371 geographically diverse Ae. tauschii accessions were evaluated in field with leaf rust (LR) composite culture of predominant races. Accessions from Afghanistan only displayed APR whereas both seedling resistance and APR were common in the Caspian Sea region. Seventeen accessions with high APR were selected for production of synthetic hexaploid wheat (SHW), using ‘TetraPrelude’ and/or ‘TetraThatcher’ as tetraploid parents. Six SHWs were produced and evaluated for APR to LR and resistance to tan spot at seedling stage. Genetic analysis and mapping of APR introgressed from accession TA2474 was investigated in recombinant inbred lines (RIL) population derived from cross between SHW, TA4161-L3 and spring wheat cultivar, ‘WL711’. Genotyping-by-sequencing approach was used to genotype the RILs. Maximum disease severity (MDS) for LR was significantly correlated among all experiments and APR to LR was highly heritable trait in this population. Nine genomic regions significantly associated with APR to LR were QLr.ksu-1AL, QLr.ksu-1BS, QLr.ksu-1BL.1, QLr.ksu-1BL.2, QLr.ksu-2DS, QLr.ksu-2DL, QLr.ksu-5AL, QLr.ksu-5DL and QLr.ksu-6BL. Association of QLr.ksu-1BL.1 with marker Xwmc44 indicated this locus could be slow-rusting APR gene, Lr46/Yr29. QTLs detected on 2DS, 2DL and 5DL were contributed by TA4161-L3 and are novel, along with QLr.ksu-5AL. Tan spot, caused by necrotrophic fungus, Pyrenophora tritici-repentis, has recently emerged as a damaging disease of wheat worldwide. To identify QTLs associated with resistance to Race 1 of P. tritici-repentis, F[subscript]2:3 population derived from cross between SHW, TA4161-L1 and winter wheat cultivar, ‘TAM105’ was used. Two major effect QTLs, QTs.ksu-1AS.1 and QTs.ksu-7AS were significantly associated with tan spot resistance and contributed by TA4161-L1. QTs.ksu-7AS is a novel QTL and explained 17% of the phenotypic variation. Novel QTLs for APR to LR and tan spot identified in SHWs add new variation for broadening the gene pool of wheat and providing resources for breeding of durable resistant cultivars.

Molecular markers were used in an attempt to determine the phylogenetic relationships of hexaploid wheats within Triticum aestivum L. and to identify wheat cultivars. Random amplified polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP), gliadin protein and cytological analyses were used to assess phylogenetic relationships among five morphological groups of hexaploid wheat, namely, macha, common wheat, spelta, vavilovii and semi-wild wheat (SWW). RAPD and gliadin data were analysed using the NTSYS-pc computer program to generate Jaccard genetic similarity coefficients. Coefficients of genetic similarity in the cytological study were calculated based on the number of chiasmata in hybrids. Dendrograms were constructed based on these coefficients. The dendrogram based on RAPD analysis grouped 15 accessions into five distinct clusters which were in agreement with the morphology-based classification. The results indicated that common wheat was closely related to vavilovii. Spelta was less related to the common and vavilovii wheat cluster. SWW was distantly related to common wheat. Macha was the least related to the previous clusters. These results were consistent with those based on cytological analysis. The results of gliadin analysis were not completely consistent with those based on RAPD and cytological analyses. RFLP data showed that it was difficult to determine phylogenetic relationships among the five groups of hexaploid wheat based on variation in the intergenic spacer region of the 18-25S rRNA unit. Polymerase chain reaction analysis of the 5S rRNA unit and the internal transcribed spacer of the 18-25S rRNA unit did not show any polymorphism among and within the five groups of hexaploid wheat. Twelve mis-classified Triticum accessions were found in macha and vavilovii wheat collections and investigated using RAPD and cytological analyses. A dendrogram based on RAPD analysis classified the 12 accessions into either T. monococcum, T. turgidum spp. dicoccum or T. timopheevii. The results were in agreement with cytogenetic data and morphological observations. The genetic diversity of spelta and macha wheat was also investigated using RAPD analysis and the results were generally consistent with geographic origins. Macha wheat germplasm was found slightly more diverse than spelta wheat although macha has a restricted geographic origin. In addition, duplicate accessions of macha and spelta were identified based on RAPD analysis. In the study of wheat cultivar identification and pedigree assessment, 29 cultivars were investigated using RAPD analysis. Cultivar specific markers were found, and at least eight cultivars could be identified using these specific markers. Cultivar relationships based on genetic similarity values were consistent with knownpedigrees. The study demonstrated that RAPD analysis can be used for estimating the phylogenetic relationships among the five groups of hexaploid wheat, reclassifying misclassified wheat germplasm, surveying the genetic diversity of spelta and macha wheat and identifying common wheat cultivars and duplicated accessions in wheat germplasm collections.