QTL analysis in multiple sorghum populations facilitates the dissection of the genetic and physiological control of tillering

Tillering in sorghum can be associated with either the carbon supply–demand (S/D) balance of the plant or an intrinsic propensity to tiller (PTT). Knowledge of the genetic control of tillering could assist breeders in selecting germplasm with tillering characteristics appropriate for their target environments. The aims of this study were to identify QTL for tillering and component traits associated with the S/D balance or PTT, to develop a framework model for the genetic control of tillering in sorghum. Four mapping populations were grown in a number of experiments in south east Queensland, Australia. The QTL analysis suggested that the contribution of traits associated with either the S/D balance or PTT to the genotypic differences in tillering differed among populations. Thirty-four tillering QTL were identified across the populations, of which 15 were novel to this study. Additionally, half of the tillering QTL co-located with QTL for component traits. A comparison of tillering QTL and candidate gene locations identified numerous coincident QTL and gene locations across populations, including the identification of common non-synonymous SNPs in the parental genotypes of two mapping populations in a sorghum homologue of MAX1, a gene involved in the control of tiller bud outgrowth through the production of strigolactones. Combined with a framework for crop physiological processes that underpin genotypic differences in tillering, the co-location of QTL for tillering and component traits and candidate genes allowed the development of a framework QTL model for the genetic control of tillering in sorghum.

Phenotyping novel stay-green traits to capture genetic variation in senescence dynamics

Stay-green plants retain green leaves longer after anthesis and can have improved yield, particularly under water limitation. As senescence is a dynamic process, genotypes with different senescence patterns may exhibit similar final normalised difference vegetative index (NDVI). By monitoring NDVI from as early as awn emergence to maturity, we demonstrate that analysing senescence dynamics improves insight into genotypic stay-green variation. A senescence evaluation tool was developed to fit a logistic function to NDVI data and used to analyse data from three environments for a wheat (Triticum aestivum L.) population whose lines contrast for stay-green. Key stay-green traits were estimated including, maximum NDVI, senescence rate and a trait integrating NDVI variation after anthesis, as well as the timing from anthesis to onset, midpoint and conclusion of senescence. The integrative trait and the timing to onset and mid-senescence exhibited high positive correlations with yield and a high heritability in the three studied environments. Senescence rate was correlated with yield in some environments, whereas maximum NDVI was associated with yield in a drought-stressed environment. Where resources preclude frequent measurements, we found that NDVI measurements may be restricted to the period of rapid senescence, but caution is required when dealing with lines of different phenology. In contrast, regular monitoring during the whole period after flowering allows the estimation of senescence dynamics traits that may be reliably compared across genotypes and environments. We anticipate that selection for stay-green traits will enhance genetic progress towards high-yielding, stay-green germplasm.

Markers for seedling and adult plant crown rot resistance in four partially resistant bread wheat sources

Key message: QTLidentified for seedling and adult plant crown rot resistance in four partially resistant hexaploid wheat sources. PCR-based markers identified for use in marker-assisted selection. Abstract: Crown rot, caused by Fusarium pseudograminearum, is an important disease of wheat in many wheat-growing regions globally. Complete resistance to infection by F. pseudograminearum has not been observed in a wheat host, but germplasm with partial resistance to this pathogen has been identified. The partially resistant wheat hexaploid germplasm sources 2-49, Sunco, IRN497 and CPI133817 were investigated in both seedling and adult plant field trials to identify markers associated with the resistance which could be used in marker-assisted selection programs. Thirteen different quantitative trait loci (QTL) conditioning crown rot resistance were identified in the four different sources. Some QTL were only observed in seedling trials whereas others appeared to be adult plant specific. For example while the QTL on chromosomes 1AS, 1BS, and 4BS contributed by 2-49 and on 2BS contributed by Sunco were detected in both seedling and field trials, the QTL on 1DL present in 2-49 and the QTL on 3BL in IRN497 were only detected in seedling trials. Genetic correlations between field trials of the same population were strong, as were correlations between seedling trials of the same population. Low to moderate correlations were observed between seedling and field trials. Flanking markers, most of which are less than 10 cM apart, have now been identified for each of the regions associated with crown rot resistance.

Non-cellulosic cell wall polysaccharides are subject to genotype × environment effects in sorghum (Sorghum bicolor) grain

Sorghum is a staple food for half a billion people and, through growth on marginal land with minimal inputs, is an important source of feed, forage and increasingly, biofuel feedstock. Here we present information about non-cellulosic cell wall polysaccharides in a diverse set of cultivated and wild Sorghum bicolor grains. Sorghum grain contains predominantly starch (64–76) but is relatively deficient in other polysaccharides present in wheat, oats and barley. Despite overall low quantities, sorghum germplasm exhibited a remarkable range in polysaccharide amount and structure. Total (1,3;1,4)-β-glucan ranged from 0.06 to 0.43 (w/w) whilst internal cellotriose:cellotetraose ratios ranged from 1.8 to 2.9:1. Arabinoxylan amounts fell between 1.5 and 3.6 (w/w) and the arabinose:xylose ratio, denoting arabinoxylan structure, ranged from 0.95 to 1.35. The distribution of these and other cell wall polysaccharides varied across grain tissues as assessed by electron microscopy. When ten genotypes were tested across five environmental sites, genotype (G) was the dominant source of variation for both (1,3;1,4)-β-glucan and arabinoxylan content (69–74), with environment (E) responsible for 5–14. There was a small G × E effect for both polysaccharides. This study defines the amount and spatial distribution of polysaccharides and reveals a significant genetic influence on cell wall composition in sorghum grain.

Epidemiology and genetic diversity of Tobacco streak virus and related subgroup 1 ilarviruses

A quarter of Australia’s sunflower production is from the central highlands region of Queensland and is currently worth six million dollars ($AUD) annually. From the early 2000s a severe necrosis disorder of unknown aetiology was affecting large areas of sunflower crops in central Queensland, leading to annual losses of up to 20%. Other crops such as mung bean and cotton were also affected. This PhD study was undertaken to determine if the causal agent of the necrosis disorder was of viral origin and, if so, to characterise its genetic diversity, biology and disease cycle, and to develop effective control strategies. The research described in this thesis identified Tobacco streak virus (TSV; genus Ilarvirus, family Bromoviridae) as the causal agent of the previously unidentified necrosis disorder of sunflower in central Queensland. TSV was also the cause of commonly found diseases in a range of other crops in the same region including cotton, chickpea and mung bean. This was the first report from Australia of natural field infections of TSV from these four crops. TSV strains have previously been reported from other regions of Australia in several hosts based on serological and host range studies. In order to determine the relatedness of previously reported TSV strains with TSV from central Queensland, we characterised the genetic diversity of the known TSV strains from Australia. We identified two genetically distinct TSV strains from central Queensland and named them based on their major alternative hosts, TSV-parthenium from Parthenium hysterophorus and TSV-crownbeard from Verbesina encelioides. They share only 81 % total-genome nucleotide sequence identity. In addition to TSV-parthenium and TSV-crownbeard from central Queensland, we also described the complete genomes of two other ilarvirus species. This proved that previously reported TSV strains, TSV-S isolated from strawberry and TSV-Ag from Ageratum houstonianum, were actually the first record of Strawberry necrotic shock virus from Australia, and a new subgroup 1 ilarvirus, Ageratum latent virus. Our results confirmed that the TSV strains found in central Queensland were not related to previously described strains from Australia and may represent new incursions. This is the first report of the genetic diversity within subgroup 1 ilarviruses from Australia. Based on field observations we hypothesised that parthenium and crownbeard were acting as symptomless hosts of TSV-parthenium and TSV-crownbeard, respectively. We developed strain-specific multiplex PCRs for the three RNA segments to accurately characterise the range of naturally infected hosts across central Queensland. Results described in this thesis show compelling evidence that parthenium and crownbeard are the major (symptomless) alternative hosts of TSV-parthenium and TSV-crownbeard. While both TSV strains had wide natural host ranges, the geographical distribution of each strain was closely associated with the respective distribution of their major alternative hosts. Both TSV strains were commonly found across large areas of central Queensland, but we only found strong evidence for the TSV-parthenium strain being associated with major disease outbreaks in nearby crops. The findings from this study demonstrate that both TSV-parthenium and TSV-crownbeard have similar life cycles but some critical differences. We found both TSV strains to be highly seed transmitted from their respective major alternative hosts from naturally infected mother plants and survived in seed for more than 2 years. We conclusively demonstrated that both TSV strains were readily transmitted via virus-infected pollen taken from the major alternative hosts. This transmission was facilitated by the most commonly collected thrips species, Frankliniella schultzei and Microcephalothrips abdominalis. These results illustrate the importance of seed transmission and efficient thrips vector species for the effective survival of these TSV strains in an often harsh environment and enables the rapid development of TSV disease epidemics in surrounding crops. Results from field surveys and inoculation tests indicate that parthenium is a poor host of TSV-crownbeard. By contrast, crownbeard was naturally infected by, and an experimental host of TSV-parthenium. However, this infection combination resulted in non-viable crownbeard seed. These differences appear to be an effective biological barrier that largely restricts these two TSV strains to their respective major alternative hosts. Based on our field observations we hypothesised that there were differences in relative tolerance to TSV infection between different sunflower hybrids and that seasonal variation in disease levels was related to rainfall in the critical early crop stage. Results from our field trials conducted over multiple years conclusively demonstrated significant differences in tolerance to natural infections of TSV-parthenium in a wide range of sunflower hybrids. Glasshouse tests indicate the resistance to TSV-parthenium identified in the sunflower hybrids is also likely to be effective against TSV-crownbeard. We found a significant negative association between TSV disease incidence in sunflowers and accumulated rainfall in the months of March and April with increasing rainfall resulting in reduced levels of disease. Our results indicate that the use of tolerant sunflower germplasm will be a critical strategy to minimise the risk of TSV epidemics in sunflower.

Genetic diversity and epidemiology of Tobacco streak virus and related subgroup 1 Ilarviruses

A quarter of Australia’s sunflower production is from the central highlands region of Queensland and is currently worth six million dollars ($AUD) annually. From the early 2000s a severe necrosis disorder of unknown aetiology was affecting large areas of sunflower crops in central Queensland, leading to annual losses of up to 20%. Other crops such as mung bean and cotton were also affected. This PhD study was undertaken to determine if the causal agent of the necrosis disorder was of viral origin and, if so, to characterise its genetic diversity, biology and disease cycle, and to develop effective control strategies. The research described in this thesis identified Tobacco streak virus (TSV; genus Ilarvirus, family Bromoviridae) as the causal agent of the previously unidentified necrosis disorder of sunflower in central Queensland. TSV was also the cause of commonly found diseases in a range of other crops in the same region including cotton, chickpea and mung bean. This was the first report from Australia of natural field infections of TSV from these four crops. TSV strains have previously been reported from other regions of Australia in several hosts based on serological and host range studies. In order to determine the relatedness of previously reported TSV strains with TSV from central Queensland, we characterised the genetic diversity of the known TSV strains from Australia. We identified two genetically distinct TSV strains from central Queensland and named them based on their major alternative hosts, TSV-parthenium from Parthenium hysterophorus and TSV-crownbeard from Verbesina encelioides. They share only 81 % total-genome nucleotide sequence identity. In addition to TSV-parthenium and TSV-crownbeard from central Queensland, we also described the complete genomes of two other ilarvirus species. This proved that previously reported TSV strains, TSV-S isolated from strawberry and TSV-Ag from Ageratum houstonianum, were actually the first record of Strawberry necrotic shock virus from Australia, and a new subgroup 1 ilarvirus, Ageratum latent virus. Our results confirmed that the TSV strains found in central Queensland were not related to previously described strains from Australia and may represent new incursions. This is the first report of the genetic diversity within subgroup 1 ilarviruses from Australia. Based on field observations we hypothesised that parthenium and crownbeard were acting as symptomless hosts of TSV-parthenium and TSV-crownbeard, respectively. We developed strain-specific multiplex PCRs for the three RNA segments to accurately characterise the range of naturally infected hosts across central Queensland. Results described in this thesis show compelling evidence that parthenium and crownbeard are the major (symptomless) alternative hosts of TSV-parthenium and TSV-crownbeard. While both TSV strains had wide natural host ranges, the geographical distribution of each strain was closely associated with the respective distribution of their major alternative hosts. Both TSV strains were commonly found across large areas of central Queensland, but we only found strong evidence for the TSV-parthenium strain being associated with major disease outbreaks in nearby crops. The findings from this study demonstrate that both TSV-parthenium and TSV-crownbeard have similar life cycles but some critical differences. We found both TSV strains to be highly seed transmitted from their respective major alternative hosts from naturally infected mother plants and survived in seed for more than 2 years. We conclusively demonstrated that both TSV strains were readily transmitted via virus-infected pollen taken from the major alternative hosts. This transmission was facilitated by the most commonly collected thrips species, Frankliniella schultzei and Microcephalothrips abdominalis. These results illustrate the importance of seed transmission and efficient thrips vector species for the effective survival of these TSV strains in an often harsh environment and enables the rapid development of TSV disease epidemics in surrounding crops. Results from field surveys and inoculation tests indicate that parthenium is a poor host of TSV-crownbeard. By contrast, crownbeard was naturally infected by, and an experimental host of TSV-parthenium. However, this infection combination resulted in non-viable crownbeard seed. These differences appear to be an effective biological barrier that largely restricts these two TSV strains to their respective major alternative hosts. Based on our field observations we hypothesised that there were differences in relative tolerance to TSV infection between different sunflower hybrids and that seasonal variation in disease levels was related to rainfall in the critical early crop stage. Results from our field trials conducted over multiple years conclusively demonstrated significant differences in tolerance to natural infections of TSV-parthenium in a wide range of sunflower hybrids. Glasshouse tests indicate the resistance to TSV-parthenium identified in the sunflower hybrids is also likely to be effective against TSV-crownbeard. We found a significant negative association between TSV disease incidence in sunflowers and accumulated rainfall in the months of March and April with increasing rainfall resulting in reduced levels of disease. Our results indicate that the use of tolerant sunflower germplasm will be a critical strategy to minimise the risk of TSV epidemics in sunflower.

High-throughput Phenotyping of Wheat Seminal Root Traits in a Breeding Context

Water availability is a major limiting factor for wheat (Triticum aestivum L.) in rain-fed agricultural systems worldwide. Root architecture has important functional implications for the timing and extent of soil water extraction, yet selection for root traits in wheat breeding programs has been largely limited due to the lack of suitable phenotyping methods. The aim of this research was to develop a low-cost high-throughput phenotyping method to facilitate selection for desirable root traits. We developed a method to assess ‘seminal root angle’ and ‘seminal root number’ in seedlings – two proxy traits associated to root architecture of mature wheat plants (1). The method involves measuring the angle between the first pair of seminal roots and the number of roots of wheat seedlings grown in transparent pots (Figure 1). Images captured at 5 to 10 days after sowing are analyzed to calculate seminal root angle and number. Performing this technique under “speed breeding” conditions (plants grown at a density of 600 plants / m2, under controlled temperature and constant light) allows the selection based on the desired root traits of up to 5 consecutive generations within 12 months. Alternatively, when focusing only on germplasm screening, up to 52 successive phenotypic assays can be conducted within 12 months. This approach has been shown to be highly reproducible, it requires little resource (time, space, and labour) and can be used to rapidly enrich breeding populations with desirable alleles for narrow root angle and a high number of seminal roots to indirectly target the selection of deeper root system with higher branching at depth. Such root characteristics are highly desirable in wheat to cope with the climate model projections, especially in summer rainfall dominant regions including some Australian, Indian, South American and African cropping regions, where winter crops mainly rely on deep stored water.

Integrating Rapid Phenotyping and Speed Breeding to Improve Stay-Green and Root Adaptation of Wheat in Changing, Water-Limited, Australian Environments

Temperatures have increased and in-crop rainfall decreased over recent decades in many parts of the Australian wheat cropping region. With these trends set to continue or intensify, improving crop adaptation in the face of climate change is particularly urgent in this, already drought-prone, cropping region. Importantly, improved performance under water-limitation must be achieved while retaining yield potential during more favourable seasons. A multi-trait-based approach to improve wheat yield and yield stability in the face of water-limitation and heat has been instigated in northern Australia using novel phenotyping techniques and a nested association mapping (NAM) approach. An innovative laboratory technique allows rapid root trait screening of hundreds of lines. Using soil grown seedlings, the method offers significant advantages over many other lab-based techniques. Another recently developed method allows novel stay-green traits to be quantified objectively for hundreds of genotypes in standard field trial plots. Field trials in multiple locations and seasons allow evaluation of targeted trait values and identification of superior germplasm. Traits, including yield and yield components are measured for hundreds of NAM lines in rain fed environments under various levels of water-limitation. To rapidly generate lines of interest, the University of Queensland “speed breeding” method is being employed, allowing up to 7 plant generations per annum. A NAM population of over 1000 wheat recombinant inbred lines has been progressed to the F5 generation within 18 months. Genotyping the NAM lines with the genome-wide DArTseq molecular marker system provides up to 40,000 markers. They are now being used for association mapping to validate QTL previously identified in bi-parental populations and to identify novel QTL for stay-green and root traits. We believe that combining the latest techniques in physiology, phenotyping, genetics and breeding will increase genetic progress toward improved adaptation to water-limited environments.

Inventories and significance of the genetic resources of an African mahogany species (Khaya senegalensis (Desr.) A. Juss.) assembled and further developed in Australia.

The forest tree species Khaya senegalensis (Desr.) A. Juss. occurs in a belt across 20 African countries from Senegal-Guinea to Sudan-Uganda where it is a highly important resource. However, it is listed as Vulnerable (IUCN 2015-3). Since introduction in northern Australia around 1959, the species has been planted widely, yielding high-value products. The total area of plantations of the species in Australia exceeds 15,000 ha, mostly planted in the Northern Territory since 2006, and includes substantial areas across 60-70 woodlots and industrial plantations established in north-eastern Queensland since the early-1990s and during 2005-2007 respectively. Collaborative conservation and tree improvement by governments began in the Northern Territory and Queensland in 2001 based on provenance and other trials of the 1960s-1970s. This work has developed a broad base of germplasm in clonal seed orchards, hedge gardens and trials (clone and progeny). Several of the trials were established collaboratively on private land. Since the mid-2000s, commercial growers have introduced large numbers of provenance-bulk and individual-tree seedlots to establish industrial plantations and trials, several of the latter in collaboration with the Queensland Government. Provenance bulks (>140) and families (>400) from 17 African countries are established in Australia, considered the largest genetic base of the species in a single country outside Africa. Recently the annual rate of industrial planting of the species in Australia has declined, and R&D has been suspended by governments and reduced by the private sector. However, new commercial plantings in the Northern Territory and Queensland are proposed. In domesticating a species, the strategic importance of a broad genetic base is well known. The wide range of first- and advanced-generation germplasm of the species established in northern Australia and documented in this paper provides a sound basis for further domestication and industrial plantation and woodlot expansion, when investment conditions are favourable

Molecular Characterization of Viruses Causing the Cassava Brown Streak Disease Epidemic in Eastern Africa

Cassava brown streak disease (CBSD) was described for the first time in Tanganyika (now Tanzania) about seven decades ago. Tanganyika (now Tanzania) about seven decades ago. It was endemic in the lowland areas of East Africa and inland parts of Malawi and caused by Cassava brown streak virus (CBSV; genus Ipomovirus; Potyviridae). However, in 1990s CBSD was observed at high altitude areas in Uganda. The causes for spread to new locations were not known.The present work was thus initiated to generate information on genetic variability, clarify the taxonomy of the virus or viruses associated with CBSD in Eastern Africa as well as to understand the evolutionary forces acting on their genes. It also sought to develop a molecular based diagnostic tool for detection of CBSD-associated virus isolates. Comparison of the CP-encoding sequences of CBSD-associated virus isolates collected from Uganda and north-western Tanzania in 2007 and the partial sequences available in Genbank revealed occurrence of two genetically distinct groups of isolates. Two isolates were selected to represent the two groups. The complete genomes of isolates MLB3 (TZ:Mlb3:07) and Kor6 (TZ:Kor6:08) obtained from North-Western (Kagera) and North-Eastern (Tanga) Tanzania, respectively, were sequenced. The genomes were 9069 and 8995 nucleotides (nt), respectively. They translated into polyproteins that were predicted to yield ten mature proteins after cleavage. Nine proteins were typical in the family Potyviridae, namely P1, P3, 6K1, CI, 6K2, VPg, NIa-Pro, NIb and CP, but the viruses did not contain HC-Pro. Interestingly, genomes of both isolates contained a Maf/HAM1-like sequence (HAM1h; 678 nucleotides, 25 kDa) recombined between the NIb and CP domains in the 3’-proximal part of the genomes. HAM1h was also identified in Euphorbia ringspot virus (EuRSV) whose sequence was in GenBank. The HAM1 gene is widely spread in both prokaryotes and eukaryotes. In yeast (Saccharomyces cerevisiae) it is known to be a nucleoside triphosphate (NTP) pyrophosphatase. Novel information was obtained on the structural variation at the N-termini of polyproteins of viruses in the genus Ipomovirus. Cucumber vein yellowing virus (CVYV) and Squash vein yellowing virus (SqVYV) contain a duplicated P1 (P1a and P1b) but lack the HC-Pro. On the other hand, Sweet potato mild mottle virus (SPMMV), has a single but large P1 and has HC-Pro. Both virus isolates (TZ:Mlb3:07 & TZ:Kor6:08) characterized in this study contained a single P1 and lacked the HC-Pro which indicates unique evolution in the family Potyviridae. Comparison of 12 complete genomes of CBSD-associated viruses which included two genomes characterized in this study, revealed genetic identity of 69.0–70.3% (nt) and amino acid (aa) identities of 73.6–74.4% at polyprotein level. Comparison was also made among 68 complete CP sequences, which indicated 69.0-70.3 and 73.6-74.4 % identity at nt and aa levels, respectively. The genetic variation was large enough for dermacation of CBSD-associated virus isolates into two distinct species. The name CBSV was retained for isolates that were related to CBSV isolates available in database whereas the new virus described for the first time in this study was named Ugandan cassava brown streak virus (UCBSV) by the International Committee on Virus Taxonomy (ICTV). The isolates TZ:Mlb3:07 and TZ:Kor6:08 belong to UCBSV and CBSV, respectively. The isolates of CBSV and UCBSV were 79.3-95.5% and 86.3-99.3 % identitical at nt level, respectively, suggesting more variation amongst CBSV isolates. The main sources of variation in plant viruses are mutations and recombination. Signals for recombination events were detected in 50% of isolates of each virus. Recombination events were detected in coding and non-coding (3’-UTR) sequences except in the 5’UTR and P3. There was no evidence for recombination between isolates of CBSV and UCBSV. The non-synonomous (dN) to synonomous (dS) nucleotide substitution ratio (ω) for the HAM1h and CP domains of both viruses were ≤ 0.184 suggesting that most sites of these proteins were evolving under strong purifying selection. However, there were individual amino acid sites that were submitted to adaptive evolution. For instance, adaptive evolution was detected in the HAM1h of UCBSV (n=15) where 12 aa sites were under positive selection (P< 0.05) but not in CBSV (n=12). The CP of CBSV (n=23) contained 12 aa sites (p<0.01) while only 5 aa sites in the CP gene of UCBSV were predicted to be submitted to positive selection pressure (p<0.01). The advantages offered by the aa sites under positive selection could not be established but occurrence of such sites in the terminal ends of UCBSV-HAMIh, for example, was interpreted as a requirement for proteolysis during polyprotein processing. Two different primer pairs that simultaneously detect UCBSV and CBSV isolates were developed in this study. They were used successfully to study distribution of CBSV, UCBSV and their mixed infections in Tanzania and Uganda. It was established that the two viruses co-infect cassava and that incidences of co-infection could be as high as 50% around Lake Victoria on the Tanzanian side. Furthermore, it was revealed for the first time that both UCBSV and CBSV were widely distributed in Eastern Africa. The primer pair was also used to confirm infection in a close relative of cassava, Manihot glaziovii (Müller Arg.) with CBSV. DNA barcoding of M. glaziovii was done by sequencing the matK gene. Two out of seven M. glaziovii from the coastal areas of Korogwe and Kibaha in north eastern Tanzania were shown to be infected by CBSV but not UCBSV isolates. Detection in M. glaziovii has an implication in control and management of CBSD as it is likely to serve as virus reservoir. This study has contributed to the understanding of evolution of CBSV and UCBSV, which cause CBSD epidemic in Eastern Africa. The detection tools developed in this work will be useful in plant breeding, verification of the phytosanitary status of materials in regional and international movement of germplasm, and in all diagnostic activities related to management of CBSD. Whereas there are still many issues to be resolved such as the function and biological significance of HAM1h and its origin, this work has laid a foundation upon which the studies on these aspects can be based.

Development of recombinant coat protein antibody based IC-RT-PCR for detection and discrimination of sugarcane streak mosaic virus isolates from Southern India

Sugarcane streak mosaic virus (SCSMV), causes mosaic disease of sugarcane and is thought to belong to a new undescribed genus in the family Potyviridae. The coat protein (CP) gene from the Andhra Pradesh (AP) isolate of SCSMV (SCSMV AP) was cloned and expressed in Escherichia coli. The recombinant coat protein was used to raise high quality antiserum. The CP antiserum was used to develop an immunocapture reverse transcription-polymerase chain reaction (IC-RT-PCR) based assay for the detection and discrimination of SCSMV isolates in South India. The sequence of the cloned PCR products encoding 3'untranslated region (UTR) and CP regions of the virus isolates from three different locations in South India viz. Tanuku (Coastal Andhra Pradesh), Coimbatore (Tamil Nadu) and Hospet (Karnataka) was compared with that of SCSMV AP The analysis showed that they share 89.4, 89.5 and 90% identity respectively at the nucleotide level. This suggests that the isolates causing mosaic disease of sugarcane in South India are indeed strains of SCSMV In addition, the sensitivity of the IC-RT-PCR was compared with direct antigen coating-enzyme linked immunosorbent assay (DAC-ELISA) and dot-blot immunobinding assays and was found to be more sensitive and hence could be used to detect the presence of virus in sugarcane breeding, germplasm centres and in quarantine programs.

Aquaculture Asia, Vol. 8, No. 2, pp.1-47, April-June 2003

*Table of Contents* Sustainable Aquaculture Peter Edwards writes on rural aquaculture: Peri-urban aquaculture in Kolkata A case of informal shrimp farmers association and its role in sustainable shrimp farming in Tamil Nadu, India M. Kumaran, N. Kalaimani, K. Ponnusamy, V.S. Chandrasekaran, D. Deboral Vimala Diffusion and adoption of shrimp farming technologies M. Kumaran, K. Ponnusamy and N. Kalaimani Farmers as Scientists: Aquaculture education in India - opportunities for global partnership M.C. Nandeesha Information system of fish germplasm resources in China Yang Ningsheng, Ge Chanshui, Ouyang Haiying, Yuan Yongming Status and development needs of freshwater crustacean aquaculture in China Xu Pao Research and Farming Techniques Aquaculture fundamentals: Getting the most out of your feed Part II: The role of macronutrients Simon Wilkinson Fish breeding in captivity - some innovative adaptations of technology by Bengal farmers N.R. Chattopadhyay Scientific guidelines for farmers engaged in freshwater prawn farming in India Vishal Saxena Marine Finfish Section News and publications Status and development of mariculture in Indonesia Ketut Sugama Aquatic Animal Health Use of probiotics in larval rearing of new candidate species Rehana Abidi Advice on aquatic animal health care: Problems in shrimp culture during the wet season (Thai/English languages) Pornlerd Chanratchakool

Conservação in vitro de germoplasma de Petiveria alliacea L. utilizando cultura de tecidos e criopreservação

A implementação de estratégias visando à conservação de espécies medicinais apresenta grande importância, tanto do ponto de vista ecológico quanto econômico. Petiveria alliacea L., espécie da família Phytolacaceae, conhecida como guiné, erva-de alho, erva-tipi ou amansa-senhor, pode ser encontrada desde a América Central até a América do Sul. Esta espécie possui ampla utilização medicinal, devido à presença, em sua composição, de vários polissulfetos, como o DTS (dibenziltrissulfeto), com propriedades antifúngica, antineoplásica e imunomodulatória, entre outras. O objetivo deste trabalho foi a conservação in vitro de germoplasma de Petiveria alliacea obtido de diferentes populações ocorrentes no Rio de Janeiro, através de métodos baseados em cultura de tecidos e criopreservação. Plantas obtidas através da germinação in vitro foram utilizadas como matrizes para a micropropagação através da multiplicação de meristemas pré-existentes em meio MS sem reguladores de crescimento, e embriões somáticos foram obtidos de forma direta a partir da cultura de explantes foliares das linhagens estudadas (Magé MG; Marechal Hermes MH; Niterói NT; Vila Isabel VI e Planta envasada AL), em presença de PIC (20μM) e 2,4D (22,6 μM), após 60 dias de cultivo. Os ápices caulinares das plantas micropropagadas e os embriões somáticos obtidos foram submetidos à criopreservação através de técnicas de vitrificação, encapsulamento-vitrificação e encapsulamento-desidratação, com a avaliação da pré-cultura e de soluções crioprotetoras (PVS2 e PVS3), em diferentes concentrações e tempos de exposição. Os resultados mostraram uma taxa de 100% de germinação in vitro. As condições para a pré-cultura de ápices foram padronizadas, entretanto não foram obtidos resultados positivos após o descongelamento. Por outro lado, os embriões da linhagem AL (linhagem embriogênica em cultura há 24 meses) mantiveram sua capacidade multiplicativa (100%) (embriogênese secundária) quando submetidos à desidratação em sacarose (0,5M) e expostos às soluções de vitrificação PVS2 e PVS3 pelos menores tempos (15 e 30 minutos). Os diferentes meios de recuperação apresentaram respostas variáveis em relação à capacidade multiplicativa dos embriões. O encapsulamento/vitrificação foi a técnica que promoveu maior tolerância dos embriões ao congelamento. A recuperação dos embriões através de multiplicação após a criopreservação abre uma perspectiva de conservação de genótipos com alta produção de polissulfetos, de interesse para a indústria farmacêutica

在异倍性水平多胚苗水稻的特征特性研究

通过无融合生殖方式固定水稻杂种优势是水稻育种中极具诱惑力的研究内容之一。自从1979年以来，我国水稻无融合生殖充种研究主要集中在筛选和鉴定水稻多胚苗材料。根据前人的研究结果，具有无融合生殖特性的植物大多数为多倍体。本试验以多胚苗水稻APIV及其衍生系为研究材料，在二倍体[APIV_((2))]、同源三倍体[APIV_((3))]和同源四倍体[APIV_((4))]水平，对其多个世代中的特征特性，其中包括形态学特征，遗传学和胚胎学特性进行了研究，旨在探讨在多倍性水平筛选水稻无融合生殖种质的可能性，获得如下主要研究结果： 1.在二倍体APIV_((2))的多个世代中，只发现单胚苗、双胚苗和三胚苗植株，多胚苗频率比较低(4.67～5.14%)，多胚苗性状的表达在一定程度上受到环境因素的影响，并且，多胚苗植株的成活率比较低(11.70～17.39%)，大部分多胚苗植株在三叶期之前死亡，这很可能与其胚乳的营养供应有关。根据APIV_((2))的多胚苗性状在多个自交世代和杂交世代中的表达特点，多胚苗性状不是显性性状，也不是隐性性状，而是一种比较特殊的数量性状。 2.胚胎学的研究结果表明，在APIV_((2))的2857个子房的胚囊中没有观察到与不定胚生殖有关的特异生殖现象;APIV_((2))在发生受精之前的胚囊构型包括正常蓼型胚囊（76.5%）、退化型胚囊（16.0%）和变异型胚囊（7.5%），在变异型胚囊中包括双卵卵器胚囊（86.7%）和三卵卵器胚囊（13.3%）;APIV_((2))的双受精与前人在正常二倍体水稻中所观察到的结果大致相符;在不同季节的颖花和同一季节同一稻穗的不同颖花内多卵和多胚苗频率存在着明显差异。 3.在同源四倍体水稻的诱导中对种芽进行预处理，促使其胚芽鞘明显伸长后再进行诱导处理是诱导成功的关键技术。在同源四倍体APIV_((4))的同一稻穗中强势颖花的多卵频率要明显地高于弱势颖花的多卵频率。在APIV_((4))去雄后的颖花中意外地观察到了单胚和双胚现象。同源四倍体水稻APIV_((4))的有性生殖能力明显变弱，在花药内正常花粉粒少而败育花粉粒多;在受精前正常胚囊数少而退化胚囊数比较多（36.0%）;花粉管进入胚囊的时间比较晚;双受精频率低而单受精频率高。 4.异倍性水稻间具有一定的可交配性，但其结实率比较低（0.20～-1.64%），通过常规杂交方法所获得的同源三倍体成活植株的频率更低（0.07%）。在湖南湘潭的秋季条件下同源三倍体水稻植株雄性完全败育，但有部分稻穗能结实（0.59%～7.71%)，由此可获得饱满种子和不饱满种子。 5.通过子房培养可以获得异倍性水稻间杂种植株。在APIV_((4))/APIV_((2))杂交组合的子房培养中出现了一株双胚苗;同源三倍体成活植株的获得率仍然比较低（0.78%），但比通过常规杂交法首先获得种子，进而获得同源三倍体成活植株的效率要倍出11.14倍。根据试验结果，提出了6个问题进行讨论。认为在杂交后代中有可能筛选到多胚苗发生频率更高的单株;多胚苗性状是比较复杂的数量性状;同源四倍体水稻的有性生殖能力明显变弱;通过合理配组和复重授粉可以提高异倍性水稻间的杂并结实率;通过子房培养可以明显提高获得同源三倍体成活植株的效率;在多倍体水稻中筛选无融合生殖种质在比二倍体水稻中筛选可能更容易成功。

抗盐、耐海水蔬菜的生物技术培育与海水无土栽培应用

本研究是以植物起源于海洋的系统进化理论和植物细胞的全能性理论为依据的。 对芹菜(Apium graveolensL．)、油菜(B. rapa, chinese group)、叶用甜菜(Beta vulgaris(L.)Koch, Cicla group)、甘蓝(B. oleraceae, acephala group)、豆瓣菜(A'asturtiumofficinale R．Br*.）、番杏（Tetragonla expansa Ait.)、菠菜(Spinacia oleracea　L．)等蔬菜种类进行大规模种质资源筛选和鉴定， 从芹菜、油菜、叶用甜菜等植物中筛选出20多种能够耐受l%NaCI或1/3海水盐度的蔬菜品系。在耐盐蔬菜品种资源筛选的基础上，为了证明用生物技术提高盐敏感蔬菜耐盐性的可行性，本研究以植物体外培养细胞体系为操作平台，对盐敏感的蔬菜一一豆瓣菜进行了生物技术改造。一方面，筛选豆瓣菜的耐盐细胞变异体并使得耐盐细胞再生植株，获得了耐1/3海水的豆瓣菜变异体;另一方面，通过将盐生植物山菠菜(Atriplex hortensisL)的耐盐相关基因，甜菜碱醛脱氢酶(BADH)基因转入豆瓣菜，使得BADH基因在豆瓣菜中过量表达和积累甜菜碱，提高了豆瓣菜的渗透调节能力，从而提高了豆瓣菜的耐盐性。同时，本研究还将所获得的多种抗盐、耐海水蔬菜材料以海水无土栽培的方式进行生产和应用， 取得了很好的效果。 本文的结果证明了在陆地淡水栽培的蔬菜和野生蔬菜资源中，存在着部分耐盐性较强的蔬菜种质;通过生物技术改造能够提高盐敏感蔬菜的耐盐性，并获得抗盐、耐海水的蔬菜新品系。对这些抗盐、耐海水蔬菜材料进行1/3海水无土栽培应用的成功结果表明，某些陆地蔬菜具有重新适应海洋生境的潜能。