Dissertations / Theses on the topic 'Crop and pasture improvement (incl. selection and breeding)'

Kiwifruit are of huge economic importance for New Zealand representing 29 percent of total horticultural exports. Fruit size is the biggest determinant of what consumers are willing to pay, and there is also a positive relationship between consumer preference for flavour and percentage dry matter. The two main cultivars exported from New Zealand are Actinidia chinensis ‘Hort 16A’ (gold kiwifruit) and A. deliciosa ‘Hayward’ (green kiwifruit). Under current commercial practice the only product allowed for use on kiwifruit to increase fruit size in New Zealand is Benefit®. Benefit® has been shown to induce different results when applied to A. chinensis and A. deliciosa, whereas synthetic plant growth regulators such as the cytokinin-like substance N-(2- chloro-4-pyridyl)-N’-phenylurea (CPPU) have been found to promote similar increases in fresh weight of fruit in both cultivars. Final fruit size is determined by both cell division and cell enlargement. It was been shown that fresh weight can be increased in both of the major Actinidia cultivars even though their physiology differs. Hormonal control of fruit size in relation to cell division and cell enlargement phases of fruit growth was studied in both A. chinensis and A. deliciosa. CPPU was applied to both cultivars in a growth response experiment where fruit were collected throughout the growing season. The objective of this experiment was to create growth curves, to compare and contrast the effect on A. chinensis and A. deliciosa, and to provide material for hormone analysis. Application of CPPU was found to significantly increase the fresh weight of both A. chinensis and A. deliciosa fruit (46.98 and 31.34 g increases respectively), and alter the ratio of inner and outer pericarps of A. chinensis fruit. CPPU and Benefit® were applied individually and together to both cultivars. It was found that only A. chinesis fruit were affected by the application of Benefit®; fresh weight was increased by 26.38 g, and percentage dry matter was significantly reduced. There was a statistically significant (p < 0.05) interaction between CPPU and Benefit® when applied to A. chinensis. 3,5,6-trichloro-2-pyridyloxyacetic acid (3,5,6-TPA) was applied to A. deliciosa on two application dates at three concentrations and was found to decrease fresh weight of fruit, but significantly increase percentage dry matter regardless of application date or concentration. Lastly CPPU and 1-naphthalene acetic acid (NAA) were applied to A. deliciosa at two application dates and in all combinations. Application date affected the response to both a low concentration of CPPU and NAA. A synergistic interaction was observed when CPPU was applied early plus NAA late (CPPU early (4.53 g increase) plus NAA late (13.29 g) < CPPU early plus NAA late (33.85 g). Finally endogenous hormone content was studied. Methods were developed and tested for the simultaneous analysis of both indole-3-acetic acid (IAA) and cytokinins. Freeze dried fruit were purified using Waters Sep-pak® cartridges and Oasis® columns then IAA was quantified by high pressure liquid chromatography. Preliminary results indicate a correlation between application of CPPU and endogenous IAA, high concentrations of IAA correlated well with periods of rapid fruit growth particularly for CPPU treated fruit.

Some aspects of the presence of systemic endophytic fungi in agriculturally important New Zealand grasses were studied in relation to plant breeding. Seedling resistance to adult Argentine stem weevil feeding in perennial ryegrass, Italian ryegrass and tall fescue was found to be related to the presence of their respective Acremonium endophytes in the seed rather than to plant genetic resistance. In addition a study of perennial ryegrass revealed that this resistance was independent of endophyte viability. The seedling resistance conferred by the endophyte of Italian ryegrass was found to be beneficial for field establishment. This endophyte differs from that in perennial ryegrass and tall fescue in that it does not confer resistance to Argentine stem weevil on mature plants, but only on seedlings. The extent of plant genetic seedling tolerance to adult Argentine stem weevil feeding was limited to broad inter-specific differences, with tall fescue more tolerant than perennial ryegrass and both of these more tolerant than Italian ryegrass. This ranking corresponds with previous observations on feeding preference on mature plants. A study of factors affecting the concentration of endophyte mycelia in infected seed of perennial ryegrass revealed that plant genetic factors had little effect. The major factors studied were: 1) the endophyte concentration in the maternal parent plant directly influenced the endophyte concentration in the seed. 2) nitrogen fertilizer applications to a seed crop reduced the concentration of mycelia in the seed, with earlier applications having a greater effect. 3) application of the fungicide propiconazole (Tilt) to a seed crop reduced the endophyte concentration in the seed. 4) the endophyte concentration in the seed was found to directly influence the endophyte concentration in seedlings, six month old plants and that of seed harvested from a first year seed crop. As there have been no previous reports of tetraploid perennial ryegrass cultivars with endophyte an experiment was conducted to determine if these could be developed by the standard procedure of colchicine treatment. The results revealed that endophyte was retained following colchicine treatment.

Variables for the accelerated ageing (AA) test, methods for reducing fungal contamination during the AA test, using the conductivity test as a vigour test, the effect of seed size on seed vigour and the relationship between laboratory test results and field perfonnance in selected Brassica spp were investigated. In the first experiment, three seed lots of turnip rape hybrid (B. rapa x campestris), turnip (B. campestris) and forage rape (B. napus); and seven seed lots of Asian rape (B. napus), six seed lots of Asian kale (B. oleraceae var. alboglabra L.) and five seed lots of choisum (B. rapa var. pekinensis) with germinations above 90% were aged at two different temperatures (41 and 42°C ± 0.3°C) and three ageing times (24, 48 and 72 ± 15 minutes). The second experiment was divided into three sections. In the first, the same seed lots and species were aged at one temperature (41°C) and time (72 h), but either 40 ml of saturated salts; KCl (83%RH), NaCl (76%RH), NaBr (55%RH); or distilled water (96%RH) were used as the ageing solutions. In the second, one turnip rape hyprid seed lot was aged at three temperatures (41, 42 and 45°C) and two times (72 and 96h), again using the three saturated salts and distilled water as ageing solutions. In the third, three turnip rape hybrid seed lots and three Asian kale seed lots were surface sterilised (1 % sodium hypochlorite) prior to ageing at one temperature (41°C) and time (72 h). In the third experiment, the same species and seed lots used in experiment one at their original seed moisture content (SMC) were tested for conductivity after soaking in deionised water for 4, 8, 12, 16, 20 and 24 h. They were then re-tested after the SMC had been adjusted to 8.5%. In the fourth experiment, three seed lots of forage rape and three seed lots of Asian kale were graded into three seed size categories; large (retained on a 2.0 mm screen), medium (retained on a 1.7 mm screen) and small (passed through a 1.7 mm screen). Graded seeds were then tested for standard germination, AA (41°C/48 h) and conductivity (measured at 16 and 24 h). In the final experiment, the relationships between laboratory tests for the six species (each consisting of three seed lots), field emergence from three sowings, and cold room emergence were evaluated. Both time and temperature influenced post-AA germination. Increasing the ageing period from 48 to 72 hours at 41°C, and 24 to 48 hours at 42°C resulted in decreased mean germination percentage for all species but not always clear separation of seed lots. While there were sometimes few differences between ageing at 41°C and 42°C, the former is preferred because it is already the temperature used for other species. For Asian rape, choisum and turnip, the previously recommended testing conditions of 41°C/72 h provided good seed lot separation, but for Asian kale and turnip rape hybrid, AA testing at 41°C/48 h provided better results. Seed moisture content after ageing ranged from 29-37% depending on species. Fungal growth on seeds during the ageing period appeared to reduce post-ageing germination in some seed lots . Substituting saturated salts for distilled water did not stress seed lots in the AA test, due to the lowered RH%, the exception being seed lots 1210 and 1296. For forage and Asian species, seed lot germination mostly remained above 90% when aged for 72 h at lowered RH%. Increasing the ageing duration from 72 to 96 hours resulted in some decreases in post-AA germination but no clear separation of seed lots. Surface sterilising the seeds prior to the AA test resulted in a lower incidence of contaminant fungi which was associated with a lower percentage of abnormal seedlings. The conductivity test was mostly able to identify vigour differences among forage and Asian vegetable brassica seed lots. Differences in conductivity readings were observed among seed lots in all species. Increasing the period of imbibition resulted in increased conductivity from most seed lots but radicle emergence occurred after 16-20 h of imbibition. Variation was observed in the time to reach 95% maximum of the imbibition curve for most species. Conductivity readings at 16 h would avoid possible influences of radicle emergence on results. Adjusting the SMC to 8.5% resulted in reduced variation in conductivity among replicates of seed lots, due to a reduction in imbibition damage. Seed size had a significant effect on both post-AA germination and conductivity results. In forage rape, large size seeds had higher post-AA germination cf. medium cf. small size seeds. In Asian kale, large size seeds had higher post-AA germination compared with small size seeds. For both forage rape and Asian kale, large size seeds had lower conductivity readings cf. small size seeds. The correlation analyses demonstrated significant relationships between AA testing and field emergence parameters (percentage emergence, emergence index and emergence rate). Significant relationships were also observed between conductivity testing and these field emergence parameters. Based on the correlation analysis, AA testing at 41°C/48 hand/or 42°C/48 h could be recommended to be used as an AA test for turnip and Asian rape; and 41°C/48 hand/or 41°C/72 h for Asian kale and choisum. Based on the correlation analysis, conductivity testing at 16 h can be used to predict the field emergence potential of forage and Asian vegetable seed lots. Vigour tests were consistently able to provide better indicators of field perfonnance than the standard germination test, although these relationships did vary with the different field sowings.

The association between individual plant performance and seed yield variability within and between field pea crops was investigated. In 1988/89 six F8 genotypes with morphologically distinct characteristics were selected from a yield evaluation trial. Analysis of the individual plant performance within these crops indicated an association between low seed yields and the location and dispersion of plant harvest index (PHI) and plant weight (PWT) distributions. The analyses also showed there was a strong linear relationship between the seed weight (SWT) and PWT of the individual plants within each crop, and that the smallest plants tended to have the lowest PHI values. A series of 20 simulations was used to formalize the relationships between SWT, PWT and PHI values within a crop into a principal axis model (PAM). The PAM was based on a principal axis which represented the linear relationship between SWT and PWT, and an ellipse which represented the scatter of data points around this line. When the principal axis passed through the origin, the PHI of a plant was independent of its PWT and the mean PHI was equal to the gradient of the axis. However, when the principal axis had a negative intercept then the PHI was dependent on PWT and a MPW was calculated. In 1989/90 four genotypes were sown at five plant populations, ranging from 9 to 400 plants m⁻². Significant seed and biological yield differences were detected among genotypes at 225 and 400 plants m⁻². The plasticity of yield components was highlighted, with significant genotype by environment interactions detected for each yield component. No relationship was found between results for yield components from spaced plants and those found at higher plant populations. The two highest yielding genotypes (CLU and SLU) showed either greater stability or higher genotypic means for PHI than genotypes CVN and SVU. Despite significant skewness and kurtosis in the SWT, PWT, and PHI distributions from the crops in this experiment, the assumptions of the PAM held. The lower seed yield and increased variability in PHI values for genotype CVN were explained by its higher MPW and the positioning of the ellipse closer to the PWT axis intercept than in other genotypes. For genotype SVU, the lower seed yield and mean PHI values were explained by a lower slope for the principal axis. Both low yielding genotypes were originally classified as having vigorous seedling growth and this characteristic may be detrimental to crop yields. A method for selection of field pea genotypes based on the PAM is proposed. This method enables the identification of weak competitors as single plants, which may have an advantage over vigorous plants when grown in a crop situation.

Lolium perenne is one of the most important forage crops globally and in New Zealand. Lotus corniculatus is a dicotyledonous forage that contains valuable traits such as high levels of condensed tannins, increased digestibility, and high nitrogen fixing abilities. However, conventional breeding between these two forage crops is impossible due to their markedly different taxonomic origin. Protoplast fusion (somatic hybridisation) provides an opportunity for gene introgression between these two species. This thesis describes the somatic hybridisation, the regeneration and the molecular analysis of the putative somatic hybrid plants obtained between L. perenne and L. corniculatus. Callus and cell suspensions of different cultivars of L. perenne were established from immature embryos and plants were regenerated from the callus. Of the 10 cultivars screened, cultivars Bronsyn and Canon had the highest percentage of callus induction at 36% each on 5 mg/L 2,4-D. Removal of the palea and lemma which form the seed coat was found to increase callus induction ability of the embryos. Plant regeneration from the callus was achieved when the callus was plated on LS medium supplemented with plant growth regulators at different concentrations. Variable responses to shoot regeneration was observed between the different cultivars with the cv Kingston having the lowest frequency of shoot formation (12%). Different factors affecting the protoplast isolation of L. perenne were investigated. The highest protoplast yield of 10×10⁶ g⁻¹FW was obtained when cell suspensions were used as the tissue source, with enzyme combination 'A' (Cellulase Onozuka RS 2%, Macerozyme R-10 1%, Driselase 0.5%, Pectolyase 0.2%), for 6 h incubation period in 0.6 M mannitol. Development of microcolonies was only achieved when protoplasts were plated on nitrocellulose membrane with a L. perenne feeder layer on PEL medium. All the shoots regenerated from the protoplast-derived calli were albino shoots. The highest protoplast yield (7×10⁶ g⁻¹FW) of L. corniculatus was achieved from cotyledons also with enzyme combination 'A' (Cellulase Onozuka RS 2%, Macerozyme R-10 1%, Driselase 0.5%, Pectolyase 0.2%), for 6 h incubation period in 0.6 M mannitol. The highest plating efficiency for L. corniculatus of 1.57 % was achieved when protoplasts were plated on nitrocellulose membrane with a L. perenne feeder layer on PEL medium. The highest frequency of shoot regeneration (46%) was achieved when calli were plated on LS medium with NAA (0.1 mg/L) and BA (0.1 mg/L). Protoplast fusion between L. perenne and L. corniculatus was performed using the asymmetric somatic hybridisation technique using PEG as the fusogen. L. perenne protoplasts were treated with 0.1 mM IOA for 15 min and L. corniculatus protoplasts were treated with UV at 0.15 J/cm² for 10 min. Various parameters affecting the fusion percentage were investigated. Successful fusions were obtained when the fusions were conducted on a plastic surface with 35% PEG (3350 MW) for 25 min duration, followed by 100 mM calcium chloride treatment for 25 min. A total of 14 putative fusion colonies were recovered. Shoots were regenerated from 8 fusion colonies. Unexpectedly, the regenerated putative hybrid plants resembled L. corniculatus plants. The flow cytometric profile of the putative somatic hybrids resembled that of L. corniculatus. Molecular analysis using SD-AFLP, SCARs and Lolium specific chloroplast microsatellite markers suggest that the putative somatic hybrids could be L. corniculatus escapes from the asymmetric protoplast fusion process. This thesis details a novel Whole Genome Amplification technique for plants using Strand Displacement Amplification technique.

The germination and early growth of Australian rainforest cabinet timber species were examined. The species were chosen from shade sensitive early secondary to shade tolerant climax successional groups. The germination of 35 Queensland rainforest timber species and effectiveness of pre-germination treatments were studied. Five distinct patterns of germination are outlined and linked to fruiting season and geographic location. Twenty Queensland cabinet timber species seedlings were subsequently grown in three light regimes and two nutrient treatments. Growth and photosynthetic responses to light and nutrient treatments were examined. The quantity and quality of solar radiation were altered by the use of painted polyfilm in order to simulate natural rainforest light regimes. Growth responses were variable across treatments and between species. A factorial analysis of variance was conducted to evaluate the effects of light (high-80% full sunlight and R:FR 1.01, low-8% full sunlight and R:FR 0.63), nitrogen (control, added nitrogen) and successional status (early secondary, late secondary, climax). Under high light conditions the cabinet timber species significantly increased their total number of leaves, branching, rate of photosynthesis, transpiration and stomatal conductance. Under low light conditions a significant increase in internode length, single leaf area, leaf blade length, slenderness (height/diameter ratio) and relative crown depth was observed. The light treatments did not have a significant effect on stem elongation rate, relative stem elongation rate or total leaf area. The added nitrogen treatment produced a significant increase in stem elongation rate, relative stem elongation rate, internode length, single leaf area, total leaf area, leaf blade length and relative crown depth. Additional nitrogen did not have a significant effect on slenderness (height/diameter ratio), branching, rate of photosynthesis and stomatal conductance. The combination of high light conditions and added nitrogen treatment significantly increased diameter increment rate, relative diameter increment rate and water use efficiency in the species being trialed. Low light conditions combined with added nitrogen significantly increased specific leaf area. Early secondary species exhibited the greatest stem elongation rate, relative stem elongation rate, diameter increment rate and relative diameter increment rate compared to late secondary and climax species. Early secondary species had the lowest total number of leaves at the end of the experiment. Climax species had significantly lower stem elongation rate, relative stem elongation rate, diameter increment rate, relative diameter increment rate, leaf blade length and height/diameter ratio than secondary species. Under low light conditions, early secondary species exhibited the highest mean specific leaf area whilst climax species had the lowest specific leaf area. The potential application of these findings to rainforest cabinet timber farm forestry is discussed.

A degree of in-crop management could provide growers with the option to manipulate growth and development in line with ambient weather conditions. Studies presented in this thesis explored this opportunity, and data so far collected support the 'nutrient diversion' hypothesis that internal resource availability and allocation play important roles in regulation of growth partitioning and phenological development. Different levels of defoliation were conducted on maize and cotton plants growing under contrasting water conditions to measure the effect of partial defoliation on their growth and production. In the environment of water stress with low average control yield, defoliation significantly diminished the negative impact caused by water deficit and led to smaller water-deficit-induced decrease of grain yield of maize plants and harvestable product of cotton plants. The relative yield advantage of defoliated plants in the water deficit environment can be attributed to defoliation-induced improvement in water status later in the growth cycle as reflected in measures of photosynthetic rate and stomatal conductance. Early-stage defoliation, removing different parts of maize plants, resulted in varied developmental responses. Removing only the fully exposed leaf blades did not delay the onset of tassel initiation, but tassel initiation and tassel emergence were significantly delayed by either removal of all the shoot tissues above the second ligule or removal of only the expanding leaves at a height just above the soil surface(with the first three or four fully exposed leaves left intact). Continued removal of the expanding leaves delayed tassel initiation further. This indicates the important role that expanding leaves play in control of the transition to reproductive growth. The elongation rate of leaf primordia underwent a gradual decrease as maize plants increased in size with time. The gradual decrease in rate of leaf primordium elongation and the resultant change in shoot apical architecture (described by relative length of leaf primordia) were strongly associated with floral induction. It is proposed that plant internal resource competition lessened the nutrient supply to the shoot apices and, therefore, affected leaf primordium growth and meristem identity simultaneously. The dynamic competition and interdependency among various plant parts were explored using a dynamic model constructed to simulate resource allocation and growth partitioning at the whole plant level.

Pachymetra chaunorhiza is an important soilborne pathogen of sugarcane and is found only in Australia. Pachymetra root rot is managed primarily by growing resistant cultivars, which are chosen for planting based on oospore levels in the soil. This management strategy does not account for differences in virulence among Pachymetra populations, despite previous research demonstrating that two genetically distinct groups of Pachymetra occur, which may differ in pathogenicity. Higher than expected yield losses have been associated with high oospore levels under some cultivars with intermediate resistance to the pathogen. Increased virulence of Pachymetra towards specific cultivars, following long-term exposure to that cultivar, could explain these reports of high yield losses in intermediate cultivars. This research project aimed to deliver knowledge of the genetic and pathogenic variation among Pachymetra populations in different growing regions and following long-term exposure to different cultivars. The level of genetic and pathogenic variation among Pachymetra populations and the factors contributing to pachymetra root rot were investigated in a series of field trials, glasshouse experiments and laboratory molecular analyses. Results from field experiments generally support the current guidelines used for Pachymetra management. No evidence was found to support the hypothesis that planting the same intermediate cultivar over multiple crop cycles could lead to higher than expected yield losses due to pachymetra root rot. Yield losses of 17 percent were associated with continual cropping of Q208A in a field trial near Bundaberg, in the southern Queensland sugarcane-growing region. A range of putative Pachymetra genes were identified which could play a role in pathogenicity. Collectively, the findings from this research supported the conclusion that two genetically distinct groups of Pachymetra occur in growing regions a) north of Townsville and b) south of Townsville, as previously reported. Three potential native hosts of Pachymetra were also identified, including Themeda australis and this finding supports the theory that lighter soil types are conducive to pachymetra root rot.

Aerobic rice is becoming a more promising rice cultivation system due to increasing water scarcity for irrigation and occurrence of drought, especially in Australia. Rice cultivation on aerobic soil under rainfed conditions has shown potential for successful rice cultivation in tropical climate. Strategic irrigation during the critical growth period can help reduce the water demand on farm. Central Queensland has an annual rainfall of ca. 800 mm, and about 600 mm occurs during the wet season from December to March; whereas parts of the wet tropical north Queensland receive ca. 3000 mm annual rainfall, and about 1893 mm during the wet season from December to March. The study was carried out at Alton Downs, central Queensland (dry tropics) and South Johnstone, north Queensland (wet tropics) to investigate the phenological, physiological and agronomical responses of 13 different rice varieties with a view to identifying suitable varieties for dry land cultivation. The objectives were to assess rice varieties under i) rainfed conditions in the wet and dry tropics, ii) rainfed conditions and strategic irrigation condition in the dry tropics, and to iii) identify the physiological, phenological and agronomical traits of rice adaptation under aerobic conditions in the dry and wet tropics. In the dry tropics, the strategic irrigation was provided by drip irrigation and was scheduled when the rice plants showed water deficit symptoms (corresponding to the refill point at 21 mm /100 mm soil water). The average yield of rice varieties under strategic irrigation was significantly higher and the variety best yield (AAT 4) produced up to 5.23 t/ha in the year 2015 under strategic irrigation. The average yield of varieties was increased from 1.5 times (AAT 4) to 16.8 times (AAT 15) with strategic irrigation, as compared to rainfed conditions. The average water productivity was increased by 100 % in 2014 and by 110.3 % in 2015 using strategic irrigation as compared to rainfed. The average water productivity was 0.24 t/ML (in 2014) and 0.61 t/ML (in 2015) under strategic irrigation, whereas it was 0.12 t/ML (in 2014) and 0.29 t/ML (in 2015) under rainfed conditions. The high yielding varieties were early flowering types, which escaped the terminal drought caused by lower rainfall during the flowering stage, whereas the late varieties such as AAT 10, AAT 11 and AAT 15 were among the highest yielders in the wet tropics under rainfed conditions. The greater yield was associated with greater panicle fertility, leaf area index , higher photosynthetic rate and water use efficiency during flowering, and one of the high yielding varieties (AAT 3) had the highest photosynthetic rate during the grain filling period in both strategic irrigation and rainfed conditions. Root dry weight and root weight density in the top soil layer at 0–15 cm were found to be related to yield under strategic irrigation, but the varietal characteristic of deep rooting was not correlated with yield. It is important to consider variations in flowering time, yield potential and drought patterns while developing varieties for aerobic conditions, as the drought reduced the panicle filling percentage to 1% under rainfed conditions. The variety with most stable and consistent yield at Alton Downs was AAT 6, and had the lowest coefficient of variation across the years whereas the variety AAT 13 was found to be more responsive with better growing conditions at Alton Downs under rainfed conditions. The varieties when sown late, late flowering varieties were subjected to cold and terminal drought reducing the yield. AAT 6 and AAT 13 are both early flowering varieties. In the wet tropical environment, the crop received rainfall until harvesting time. The favourable physiological characteristic of high yielding varieties such as AAT 4 and AAT 6 in the dry tropics was greater water use efficiency, and the agronomic characteristics were higher panicle fertility, higher effective tillers per plant and grains per panicle. In the wet tropics (South Johnstone), the high yielding variety AAT 10 was characterised by high harvest index, longest panicle length, higher effective tillers, higher panicle fertility and higher water use efficiency. In South Johnstone, the days to flowering did not have any effect on the yield of varieties. The varieties those producing least yield under rainfed conditions at Alton Downs were among the highest yielders in South Johnstone. The high yielding varieties maintained greater effective tillers per plant, heavier 1000 grain weight, greater harvest index and fertility. Reliable soil moisture favoured photosynthetic rate and water use efficiency and the associated larger flag leaf area contributed significantly to higher yields at wet tropical South Johnstone as compared to dry tropical Alton Downs. Strategic irrigation in dry tropical environments could allow plants to cope with water stress caused by less rainfall during the grain filling period. Similar yield was achieved under strategic irrigation for late flowering varieties as under rainfed conditions for early flowering varieties. The varieties responded with an average increase of 11.87 kg/ha and 15.80 kg/ha with each additional 1 mm water application in 2014 and 2015 respectively. This shows that there is great commercial scope for strategic irrigation during water deficit periods, created by little or no rainfall, during critical crop growth periods for rice in the dry tropical environment of central Queensland. In conclusion, this thesis increases the understanding the role of strategic irrigation and varietal characteristics for rice cultivation under the dry tropical agro‐ecological domain of central Queensland and the wet tropical conditions of north Queensland. Higher productivity of aerobic rice in dry tropical central Queensland is achieved with early flowering varieties, supported by strategic irrigation management during the water shortage periods, with higher water use efficiency, greater number of spikelets, higher panicle fertility. In the wet tropical environment of northern Queensland, yield variation between varieties was not significantly affected by the days to flowering. However, further study for selection of varieties from more diverse germplasm for plant water status and fertility, and different water management strategies under aerobic conditions needs, to be explored, to achieve the rice yield that can assure the commercial opportunity for rice production in the dry and wet tropical environments of Queensland, Australia.

Wheat is a major source of calories and protein for humans worldwide. Wheat is the most widely grown crop, with cultivation areas and production systems on every continent. The cultivated land area is vast because of its importance and adaptability to various environmental conditions. Global wheat production has not kept up with the growing population, provoking the need to develop new methods and techniques to increase genetic gains. The first research chapter of this Ph.D. dissertation involves performing genome-wide association studies (GWAS) to identify and examine transferability of marker-trait associations (MTAs) across environments. I evaluated yield and yield components traits among 270 soft red winter (SRW) wheat varieties. The population consists of experimental breeding lines adapted to the Midwestern and eastern United States and developed by public university breeding programs. Phenotypic data from a two-year field study and a 45K-SNP marker dataset were analyzed by FarmCPU model to identify MTAs for yield related traits. Grain yield was positively correlated with thousand kernel weight, biomass, and grain weight per spike while negatively correlated with days to heading and maturity. Sixty-one independent loci were identified for agronomic traits, including a region that with –logP of 16.35, which explained 18% of the variation in grain yield. Using 12 existing datasets from other states and seasons, in addition to my own data, I examined the transferability of significant MTAs for grain yield and days to heading across homogenous environments. For grain yield and days to heading, I only observed 6 out of 28 MTAs to hold up across homogenous environments. I concluded that not all marker-trait associations can be detected in other environments.

In the second research chapter of this Ph.D. dissertation, I dissected yield component traits under contrasting nitrogen environments by using field-based low-throughput phenotyping. I characterized grain yield formation and quality attributes in soft red winter wheat. Using a split-block design, I studied responses of 30 experimental lines, as sub-plot, to high nitrogen and low nitrogen environment, as main-plot, for two years. Differential N environments were imposed by the application, or lack thereof, of spring nitrogen application in a field, following a previous corn harvest. In this study, I measured agronomic traits, in-tissue nitrogen concentrations, nitrogen use efficiency, nitrogen harvest index and end-use quality traits on either all or subset of the germplasm. My data showed that biomass, number of spikes and total grain numbers per unit area were most sensitive to low nitrogen while kernel weight remained stable across environments. Significant genotype x N-environment interaction allowed me to select N-efficient germplasm, that can be used as founding parents for a potential breeding population specifically for low-N environments. I did this selection on the basis of superior agronomic traits and the presence of the desirable gluten quality alleles such as Glu-A1b (2*) and Glu-D1d (5+10).

Project involves various methods of triploid identification in citrus fruit.. Seedlessness is a desirable horticultural attribute in Citrus and is positively associated with triploidy. The conventional cytological method for triploid identification is a laborious technique as it involves the preparation of foot-tips for chromosomal analysis. Isozymes and digital densitometry, however, offer the facility to distinguish triploid Citrus from large populations of seedlings both quickly and cheaply. Where there are no gene-dosage regulation effects, greater band density, reflecting increased enzyme activity, should be evident in the allozyme contributed by the diploid gamete for a heterozygous locus. To achieve this, appropriate methods of sample preparation, isozyme electrophoresis and digital densitometry were established. The isozymes of four enzymes, malate dehydrogenase, 6-phosphogluconate dehydrogenase, shikimate dehydrogenase, and phosphoglucose isomerase were investigated for band density differences between allozymes. Polyacrylamide gel electrophoresis was employed to study the isozymes of these four enzymes and band density was measured using a digital densitometer. Of the 4 enzymes investigated only allozymes for shikimate dehydrogenase exhibited consistent differences over a wide range of Citrus cultivars. Greater band density was evident in the allozyme contributed by the diploid gamete. The band density ratio between allozymes for triploid Citrus was close to 0.5, while for diploid Citrus band density ratios were close to 1.0. This effect is due to the extra protein coded by the additional gene dose and was not observed in diploids. Shikimate dehydrogenase proved to be an accurate molecular marker for distinguishing between diploid and triploid Citrus.

Colletotrichum sublineolum is the causal agent of sorghum anthracnose, a very common and destructive fungal disease in warm and humid areas, especially in West and Central Africa. Use of host plant resistance is considered as the most important and effective control option for sorghum diseases. To achieve this goal, identification and mapping resistance genes is essential. In this study, we used an isolate of C. sublineolum, CsGL1, to screen our sorghum germplasm and identified a resistant inbred line, P9830. We developed a mapping population from a cross between P9830 and a susceptible line, TAM428, for this research. The population was advanced to the F₆ generation. Progenies were phenotyped at F₂, F₃ and F₆ generations for disease resistance against the pathogen, CsGL1. In the F₂ generation, 460 individuals showed resistance and 149 individuals showed susceptibility to CsGL1. This result fits the 3:1 segregation pattern expected for resistance controlled by a single gene. Bulked segregant analysis with next generation sequencing was used on selected F₆ recombinant inbred lines. A significant peak containing 153 SNPs was observed on the distal end of the long arm of chromosome 8. To verify resistance to CsGL1 was controlled by genes in this region, indel and SNP markers were used between 59.4Mbp and 60.6Mbp on chromosome 8 to fine map the resistance locus. One SNP marker located in the gene Sobic.008G166400 co-segregated with resistance, and another two indel markers were discovered to be tightly linked to the resistance locus. These three PCR-based SNP markers would be useful for marker-assisted selection for improving anthracnose resistance against CsGL1. Two candidate genes, Sobic.008G166400 and Sobic.008G166550, were found in the locus. Both of the genes encode LRR proteins implicated in plant disease defense response. The identity of DNA sequence between these two candidate genes is 94.1%, possibly the result of tandem duplication. Another possible ortholog in the region is Sobic.008G167500. Quantitative PCR analysis showed that the expression level of Sobic.008G166400 didn’t change significantly in a resistant RIL, 17-12 but was induced in a susceptible RIL, 13-31, after CsGL1 infection. In conclusion, we mapped two candidate genes conferring resistant to CsGL1 on chromosome 8, and Sobic.008G166400 is more likely of the two to be determined as the gene controlling resistance to CsGL1.

Comprehensive information of breeding germplasm is a necessity to develop effective strategies for accelerated breeding. I characterized Purdue University soft red winter wheat breeding population that was subjectof intensive germplasm introduction and introgression from exotic germplasm. Using genotyping-by-sequences (GBS) approach, I developed ~15,000 single nucleotide polymorphisms (SNPs) and studied extent of linkage disequilibrium (LD)and hidden population structure in the population.The extent of LD and its decay varied among chromosomes with chromosomes 2B and 7D showing the most extended islands of high-LDandslow rates of decay. Four sub-populations, two with North American origin and two with Australian and Chinese origins, were identified. Genome-wide scans for signatures of selection using FSTand hapFLK identified 13 genomic regions under selection, of which six loci (LT, Ppd-B1, Fr-A2, Vrn-A1, Vrn-B1, Vrn3) were associated with environmental adaptation and two loci were associated with disease resistance genes (Sr36 and Fhb1).

Dissecting the soybean grain yield (GY) to approach it as a sum of its associated processes seems a viable approach to explore this trait considering its complex multigenic nature. Monteith (1972, 1977) first defined potential yield as the result of three physiological efficiencies: light interception (Ei), radiation use efficiency (RUE) and harvest index (HI). Though this rationality is not recent, few works assessing these three efficiencies as strategies to improve crops have been carried out. This thesis approaches yield from the perspective of Ei, RUE, and HI to better understand yield as the result of genetic and physiological processes. This study reveals the phenotypic variation, heritability, genetic architecture, and genetic relationships for Ei, RUE, and HI and their relationships with GY and other physiological and phenological variables. Similarly, genomic prediction is presented as a viable strategy to partially overcome the tedious phenotyping of these traits. A large panel of 383 soybean recombinant inbred lines (RIL) with significant yield variation but shrinkage maturity was evaluated in three field environments. Ground measurements of dry matter, photosynthesis (A), transpiration (E), water use efficiency (WUE), stomatal conductance (gs), leaf area index (LAI) and phenology (R1, R5, R8) were measured. Likewise, RGB imagery from an unmanned aircraft system (UAS) were collected with high frequency (~12 days) to estimate the canopy dynamic through the canopy coverage (CC). Light interception was modeled through a logistic curve using CC as a proxy and later compared with the seasonal cumulative solar radiation collected from weather stations to calculate Ei. The total above ground biomass collected during the growing season and its respective cumulative light intercepted were used to derive RUE through linear models fitting, while apparent HI was calculated through the ratio seeds dry matter vs total above-ground dry matter. Additive-genetic correlations, genome wide association (GWA) and whole genome regressions (WGR) were performed to determine the relationship between traits, their association with genomic regions, and the feasibility of predicting these efficiencies through genomic information. Our results revealed moderate to high phenotypic variation for Ei, RUE, and HI. Additive-genetic correlation showed a strong relationship of GY with HI and moderate with RUE and Ei when the whole data set was considered, but negligible contribution of HI on GY when just the top 100 yielding RILs were analyzed. High genetic correlation to grain yield (GY) was also observed for A (0.87) and E (0.67), suggesting increase in GY can be achieved through the improvement of A or E. The GWA analyses showed that Ei is associated with three SNPs; two of them located on chromosome 7 and one on chromosome 11 with no previous quantitative trait loci (QTLs) reported for these regions. RUE is associated with four SNPs on chromosomes 1, 7, 11, and 18. Some of these QTLs are novel, while others are previously documented for plant architecture and chlorophyll content. Two SNPs positioned on chromosome 13 and 15 with previous QTLs reported for plant height and seed set, weight and abortion were associated with HI. WGR showed high predictive ability for Ei, RUE, and HI with maximum correlation ranging between 0.75 to 0.80. Both directed and undirected multivariate explanatory models indicate that HI has a strong relationship with A, average growth rate of canopy coverage for the first 40 days after planting (AGR40), seed-filling (SFL), and reproductive length (RL). According to the path analysis, increase in one standard unit of HI promotes changes in 0.5 standard units of GY, while changes in the same standard unit of RUE, and Ei produce increases on GY of 0.20 and 0.19 standard units. This study presents novel genetic knowledge for Ei, RUE, HI and GY along with a set of tools that may contribute to the development of new cultivars with enhanced light interception, light conversion and optimized dry matter partitioning in soybean. This work not only complements the physiological knowledge already available with the genetic control of traits directly associated with yield, but also represents a pioneer attempt to integrate traditional physiological traits into the breeding process in the context of physiological breeding

Phytophthora root and stem rot (PRSR), caused by oomycete Phytophthora sojae, is the most severe soil-borne disease of soybean (Glycine max (L.) Merr.) worldwide. The disease can be effectively managed by introducing resistance to P. sojae (Rps) genes into soybean cultivars by breeding, which requires continuous efforts on identification of resistance resources from soybean germplasm. Previously, two resistance genes, Rps2-cas (former name Rps2-das) and Rps14 (former name Rps1-f), were mapped by linkage analysis from soybean landraces, PI 594549 C and PI 340029, respectively. The resistance underlying PI 594592 also need further characterization given its broad resistance spectrum. In this study, Rps-2cas and Rps14 were further mapped, and Rps2-b, was identified and initial mapped from PI 594592. Thus, this thesis research was divided into three parts for three Rps genes.

The first part mainly focuses advances on Rps2-cas. Marker-assisted spectrum analysis was performed for Rps-2cas to confirm its potential in disease management. A high-quality genome assembly of PI 594549 C was generated, and KASP markers were developed based on comparison between new reference and Williams 82 reference genome. The gene was further mapped to a 32.67-kb region on PI 594549 C reference genome harboring three expressed NLRs by 24 recombinants screened from a large F₄ population. Comparative genomics analysis suggests the only intact NBS-LRR gene in the fine mapping region is the best candidate gene for Rps2cas, and its function was validated by stable transformation. Evidences from other high-quality assembly genomes suggest Rps2-cas originated from an ancient unequal crossing over event.

In the second part, Rps14 was further mapped using 21 recombinants identified from a F₃ population consisting of 473 plants. In commonly used Williams 82 reference genome, the assembly of fine mapping region was incomplete, and Rps14 region showed drastic variation in size and copy number of NLRs in 23 high-quality genome assemblies, suggesting the complexity of Rps14 region and high-quality reference sequence of donor line is required for isolation of Rps14 candidate genes. Marker assisted resistance test showed Rps14 had wider resistance spectrum to different P. sojae isolates comparing to other Rps genes on chromosome 3, and phylogenic analysis further supported the potential of Rps14 to be a novel resistance gene.

For the third part, an F₂ population derived from a cross between PI 594592 and Williams was tested by P. sojae race 1. The 3:1 and 1:2:1 Mendelian segregation ratios were observed in F₂ individuals and F_2:3 families, respectively, suggesting a single dominant Rps gene in PI 594592. The gene was initially mapped to the distal end chromosome 16 overlapped with Rps2, and the gene was tentatively named as Rps2-b. Polymorphic SSR markers and InDel markers designed based on re-sequencing data of PI 594592 and Williams was used to genotyping all the F_2:3 families, and a linkage map was constructed for Rps2-b. Rps2-b was mapped to a 461.8-kb region flanked by SSR marker Satt431 and InDel marker InDel3668 according to the reference genome (Wm82. a2). Marker-assisted resistance test showed Rps2-b hold a wide resistance spectrum.