Academic literature on the topic 'Horticultural crop improvement (incl. selection and breeding)'

Crop losses from winter injury and spring frosts which involve freezing injury are of major importance to the Canadian horticultural industry, whereas chilling injury which is produced at temperatures just above freezing is of minor importance. The technology to prevent crop losses from freezing injury to horticultural crops is well developed and includes site selection; plant protection with covers, protected-environmental structures heaters, and wind machines; control of ice-nucleating bacteria; selection of management practices to maximize plant resistance; and breeding for resistance. Improvement of this technology can be expected with further research. Increased knowledge of the basic physiology of freezing injury and the genetics of freezing resistance will be especially important to achieving technological advances in the prevention of freezing injury to horticultural crops.Key words: Cold hardiness, freezing injury, chilling injury, acclimation, frost protection

Improving fruit quality is an important but challenging breeding goal in winter squash. Squash breeding in general is resource-intensive, especially in terms of space, and the biology of squash makes it difficult to practice selection on both parents. These restrictions translate to smaller breeding populations and limited use of greenhouse generations, which in turn, limit genetic gain per breeding cycle and increases cycle length. Genomic selection is a promising technology for improving breeding efficiency; yet, few studies have explored its use in horticultural crops. We present results demonstrating the predictive ability of whole-genome models for fruit quality traits. Predictive abilities for quality traits were low to moderate, but sufficient for implementation. To test the use of genomic selection for improving fruit quality, we conducted three rounds of genomic recurrent selection in a butternut squash (Cucurbita moschata) population. Selections were based on a fruit quality index derived from a multi-trait genomic selection model. Remnant seed from selected populations was used to assess realized gain from selection. Analysis revealed significant improvement in fruit quality index value and changes in correlated traits. This study is one of the first empirical studies to evaluate gain from a multi-trait genomic selection model in a resource-limited horticultural crop.

Breeders of horticultural food crops are usually concerned with multiple traits related to yield and quality as well as other traits such as biotic and abiotic stresses. Yield in these crops is not solely tonnage of biomass produced in the field. Rather, it is the proportion of the crop that can be harvested and brought to market in a condition and at a price acceptable to the consumer. Quality may include flavor, color, shape, size, degree of damage, nutrient levels, and traits that permit greater perceived food safety or environmental sustainability. Some traits may exhibit phenotypic associations. Traits with unfavorable associations will be of concern to the breeder if the cause is unfavorably correlated genetic effects, especially those resulting from pleiotropy. Several multiple trait selection schemes have been developed, including independent culling levels, tandem selection, and index selection. These schemes can result in improvement even for traits with unfavorable associations. However, the breeder must have a strong rationale for each trait addressed in a breeding program because each additional trait necessitates larger breeding populations and more resources. Thus, the breeder's first challenge for each crop is to determine which traits are most important and which issues are most amenable to a breeding solution.

Horticultural crops include a diverse array of crops comprising fruits, vegetables, nuts, flowers, aromatic and medicinal plants. They provide nutritional, medicinal, and aesthetic benefits to mankind. However, these crops undergo many biotic (e.g., diseases, pests) and abiotic stresses (e.g., drought, salinity). Conventional breeding strategies to improve traits in crops involve the use of a series of backcrossing and selection for introgression of a beneficial trait into elite germplasm, which is time and resource consuming. Recent new plant breeding tools such as clustered regularly interspaced short palindromic repeats (CRISPR) /CRISPR-associated protein-9 (Cas9) technique have the potential to be rapid, cost-effective, and precise tools for crop improvement. In this review article, we explore the CRISPR/Cas9 technology, its history, classification, general applications, specific uses in horticultural crops, challenges, existing resources, associated regulatory aspects, and the way forward.

The present experiment was conducted during rabi 2017 at ICAR- Indian Institute of Horticultural Research, Bengaluru to assess the variability present in the germplasm and their usefulness in breeding of high yielding vegetable type cluster bean (Cyamopsis tetragonoloba L.). Total 38 diverse cluster bean germplasm from different sources were used to evaluate the variability, character association and their contribution towards pod yield. Characters like number of pods per plant, pod length, pod weight, plant height, number of clusters per plant, pods per cluster showed high coefficient of variations and high heritability with high genetic gain indicating their suitability for effective selection. Analysis of phenotypic and genotypic correlation co-efficient and path analysis revealed that traits like pod length, pod diameter, pod weight and seeds per pod had significant positive correlation with pod yield. Hence, selection for high pod weight with indirect selection for pod length will bring worthwhile improvement in yield.

The present investigation was carried out during 2014-15 and 2015–16 at Horticultural Research Station, Ananthrajupet, DRYSRHU, Andhra Pradesh to assess the genetic diversity in muskmelon, Cucumis melo. Genetic divergence evaluated using Mahalanobis D2 analysis revealed less to moderate diversity among fourty two genotypes. The cluster analysis of muskmelon exhibited a moderate clustering pattern and grouped genotypes into five distinct clusters with maximum of 37 genotypes in cluster I, two in cluster IV and one in each of cluster II, III and V. The highest inter-cluster distance (80.61) between Cluster III and IV indicating the genotypes of these clusters may give heterotic response and leads to better segregants. Among the morphological traits studied, fruit length (23.69%), pulp thickness (17.07%) and fruit girth (16.84%) contributed major share in the divergence of the genotypes which can be utilized for selection of individual genotypes for future crop improvement programme. Most of the genotypes accommodated into single cluster, probably they may share genetic similarity. The genotypes Papayee S-1, IC 321371, Kundan, Muskan and Arka Jeet, being divergent from others may serve as potential parents for breeding programmes.

Abstract Breeding low-chilling peach and nectarine cultivars began in Florida in 1953. Objectives were to produce low-chilling, early-ripening peach cultivars with fruit qualities equal to temperate-zone cultivars. Low chilling was essential for local adaptation (4). Early ripening was essential to allow production of the earliest-season peaches on the domestic market with little competition from other states and to allow harvest of the crop during the relatively dry period of late April and May. Feral selections descended from Spanish seed introductions through St. Augustine, Fla., seed importations from Okinawa, and ‘Hawaiian’, a South China clone, served as the main sources of low chilling (18). These sources were hybridized with high-chilling U.S. clones having commercial fruit qualities. Resultant seedlings were selected for best adaptation and improvement in fruit qualities above that of the low-chilling parents. Chilling requirements of progeny were near midparent values; chilling requirements of the F2 seedlings ranged from equal to the low parent to equal to the high parent (14), indicating that many genes are involved in chilling. Selections were intermated, and low-chilling progeny were hybridized with other high-chilling U.S. clones, resulting in more progenies for further selection. Commercial fruit size and satisfactory horticultural qualities were obtained after six generations of crosses and backcrosses. Clonal selections made during these six generations and in subsequent generations serve as the basis for most low-chilling cultivars currently grown in Florida, southern Texas, and southern California. Selections from this program are either grown commercially or being evaluated in many tropical and tropical highland areas of the world (11, 16, 19, 24).

Pumpkins and squash, Cucurbita species, are valued horticultural products almost everywhere. They have been cultivated and subjected to consumer-oriented selection for thousands of years. Under this consumer orientation, they have been improved culinarily and diversified into the wonderful array of fruit sizes, shapes, and colors that are seen today. Besides their value as food items, pumpkins and squash are associated by people with abundance, warmth, sexuality, and life itself. My current objective is to provide a succinct perspective on the process of consumer-oriented exploitation of pumpkin and squash genetic resources. I briefly review the etymology, taxonomy and gross morphology of Cucurbita plants. A view is presented of how gathering, nurturing, domestication and cultivation of Cucurbita, species-specific and consumer-driven, maintained some of the parallels among species but also magnified the phenotypic differences among them. At greater length are considered the differences in resource allocation required for the preferential consumer-driven production of mature versus young fruits. Environmental effects, abiotic and biotic, are briefly mentioned, as are some of the potential benefits of biotechnology, genetic engineering, mapping, genomics, and gene editing as cognates for breeding. Finally, I consider the processes and needs for collection, maintenance, characterization, and availability of Cucurbita genetic resources and the dangers imposed by under-informed administrators in academia and cavalier governmental regulatory statutes toward future consumer-oriented improvement of pumpkins and squash.

A research study was conducted with nine dwarf Roselle germplasm of H. sabdariffa var. sabdariffa at College of Horticulture, Sri Konda Laxman Telangana State Horticultural University, Hyderabad, Telangana State, India during first week, October, 2019 to 2nd week, January, 2020. The analysis of variance for yield and its contributing characters was found to be significant for all the characters. Based on mean performance, the Roselle accession SAS-14139-1 was the best performance for yield, number of fruits per plant and plant height. Seven accessions produced green calices with red tinging, which are having good demand in the market. Good amount of genetic variability was associated with the germplasm for majority of the characters. Significant differences (p<0.05) were observed for yield characters of the accessions. This is an indication that there is a store of genetic variability that can be exploited for the improvement of Roselle in India. There was also pronounced variation in yield and other morphological parameters, suggesting the possibility of evolving higher yield variants of Roselle through proper selection. High heritability was registered with plant height, number of branches per plant and fruit yield per plant. The present study identified agronomically better germplasm for yield exploitation coupled with high heritability characters for future varietal development and use as parents in further breeding programmes in Roselle, a future reliable vegetable crop.

Abstract The Rosaceae crop family (including almond, apple, apricot, blackberry, peach, pear, plum, raspberry, rose, strawberry, sweet cherry, and sour cherry) provides vital contributions to human well-being and is economically significant across the U.S. In 2003, industry stakeholder initiatives prioritized the utilization of genomics, genetics, and breeding to develop new cultivars exhibiting both disease resistance and superior horticultural quality. However, rosaceous crop breeders lacked certain knowledge and tools to fully implement DNA-informed breeding—a “chasm” existed between existing genomics and genetic information and the application of this knowledge in breeding. The RosBREED project (“Ros” signifying a Rosaceae genomics, genetics, and breeding community initiative, and “BREED”, indicating the core focus on breeding programs), addressed this challenge through a comprehensive and coordinated 10-year effort funded by the USDA-NIFA Specialty Crop Research Initiative. RosBREED was designed to enable the routine application of modern genomics and genetics technologies in U.S. rosaceous crop breeding programs, thereby enhancing their efficiency and effectiveness in delivering cultivars with producer-required disease resistances and market-essential horticultural quality. This review presents a synopsis of the approach, deliverables, and impacts of RosBREED, highlighting synergistic global collaborations and future needs. Enabling technologies and tools developed are described, including genome-wide scanning platforms and DNA diagnostic tests. Examples of DNA-informed breeding use by project participants are presented for all breeding stages, including pre-breeding for disease resistance, parental and seedling selection, and elite selection advancement. The chasm is now bridged, accelerating rosaceous crop genetic improvement.

This thesis reports the cell culture establishment and a somatic cell selection system optimized for the isolation of chlorsulfuron-resistant variants in asparagus (Asparagus officinalis L.). The development of this cell selection system benefited the isolation of chlorsulfuron-resistant variants from an elite asparagus genotype. A cell culture system, suitable for somatic cell selection, was established for asparagus genotype CRD 168. Friable callus was initiated from etiolated shoots in darkness and used to produce a high density of single cells in suspension. Cell density was estimated based on a linear relationship with settled cell volume. A mean plating efficiency of 0.19 % was recorded between 1-4x10⁵ cells/Petri dish. In vitro cell selection techniques were developed to identify mutant asparagus cells with resistance to a sulfonylurea herbicide, chlorsulfuron. A few key aspects were important to achieve this: a cell culture system for cell selection was initially established; a toxic concentration for the complete growth inhibition of the wild type asparagus cells was defined; rare, resistant cell colonies were isolated and characterized; and chlorsulfuron-resistant plants were regenerated. From about 50 million cells, 165 cell colonies were isolated in the presence of 8 nM chlorsulfuron. Characterization of these selected cell colonies yielded 24 escapes, 98 unstable variants, and 43 stable-resistant variants. Callus cultures from 34 of these stable variants retained resistance following 11 months growth in the absence of the selection agent. Plants were regenerated from 36 of these stable herbicide-resistant variants. Six of these chlorsulfuron-resistant variants were screened for their degree of resistance to chlorsulfuron, cross resistance to other acetohydroxyacid synthase (AHAS) inhibiting herbicides and AHAS enzyme activity. Cross resistance to imazamox was evident in four of the resistant variants, while lack of cross resistance to metsulfuron methyl was observed in all six resistant variants. A varying degree of resistance to chlorsulfuron was observed among the resistant variants. Both in the original and secondary callus, an uninhibited AHAS enzyme activity in all six resistant variants was recorded in the presence of high chlorsulfuron concentration (70-140 nM), compared to the total inhibition in the wild type. One chlorsulfuron-resistant variant, R-45, was used to compare the biochemical and physiological basis of resistance with the wild type. The AHAS enzyme activity in the tissue culture and greenhouse foliage of R-45 was significantly higher in the presence of up to 280 nM chlorsulfuron compared with the wild type. Chlorsulfuron retention was considerably higher due to the reduction of epicuticular wax deposits on the foliage of R-45, in comparison with the wild type. Consequently, the resistant line absorbed at least 1.6 fold more chlorsulfuron than the wild type plants. Therefore, foliar application of 15 g a.i./ha Glean (commercial formulation of chlorsulfuron) produced typical symptoms of chlorosis in R-45, similar to the wild type, in the greenhouse plants. Somatic cell selection was carried out using two elite asparagus genotypes, CRD 74 and Clone X. Of the 33 rare cell colonies isolated from Clone X, 22 unstable variants and 6 escapes were discarded. All five remaining resistant variants produced plants. One of the stable-resistant variants (Clone X-24) was evaluated for resistance to chlorsulfuron. Both in vitro shoot cultures and greenhouse-grown plants of Clone X-24 showed increased resistance to chlorsulfuron compared with the wild type. The AHAS enzyme activity in the foliar extracts also showed the presence of higher enzyme activity in Clone X-24.

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.

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.

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.

Plant microbiomes are increasingly recognized for their potential to help plants with critical functions such as nutrient acquisition. Nitrogen is the most limiting nutrient in agriculture and growers apply substantial amounts to meet crop needs. Only 50% of N fertilizers are generally taken up by plants and the rest is subject to loss which negatively affects environmental quality. Organic fertilizers such as cover crops and animal manure can help reduce this loss, though these materials must mineralize via microbial mediated processes before they are available for plant uptake, which makes managing fertility using these sources difficult. Some plants can scavenge nutrients from organic materials by stimulating positive priming processes in soil. Carrot (Daucus carota. L) is known as an N scavenging crop, making it an ideal model crop to study these interactions. In a greenhouse trial, soils were amended with an isotopically labeled corn residue to track N movement, and planted with one of five carrot genotypes expected to differ in nitrogen use efficiency (NUE). Changes in soil b-glucosidase activity, ammonium (NH₄⁺-N) and nitrate (NO₃^- -N) concentrations, soil bacterial community composition, weight and carbon and N concentrations, and total δ¹⁵N of above and below ground carrot biomass were determined. Results indicate that there are genetic differences in the ability of carrots to promote priming under N limited conditions, which could be exploited to enhance NUE in carrots. Soil microbial communities differed between genotypes, indicating that some of these microbes could play a role in the differential N scavenging responses observed, and/or contribute to other important functions such as resistance to pests. Endophytic microbes residing inside carrot taproots also have potential to contribute to NUE and other benefits, but are notoriously difficult to isolate and culture. New next generation sequencing technologies have revolutionized the study of microbiomes, though using these tools to study bacterial endophytes in plants is still difficult due to co-amplification of plant organelles. Consequently, a second study was conducted to determine if subjecting carrot tissues to hollow fiber microfiltration followed by enzymatic digestion could enhance recovery and amplification of bacterial endophytes. Carrot taproot digests were subject to amplification using a standard V3-V4 16S primer set, as well as two alternative (blocking and mismatch) primer sets that have prevented amplification of plastids/mitochondria in other plant species. Results indicate that the microfiltration/digestion procedure can increase the number of bacterial endophyte OTUs assigned and could be further optimized for use in carrots. The blocking and mismatch primer sets were not as effective in blocking co-amplification of plant products as they are in other studies, possibly due to the presence of a high number of chromoplasts in carrot tissues. Taxonomic assignment of bacterial endophytes differed significantly between the primer sets, indicating that multiple primer sets may be needed to fully characterize these communities in carrots. The enzymatic digestion procedure could artificially inflate certain taxa, which could be helpful if targeting specific taxa. These studies demonstrate that carrots are intimately connected with microbes residing in the soil and within their taproots, and further exploration of these plant-soil-microbial relationships could enhance the yield and sustainability of carrot production systems.

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.

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.

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).