Southern Cross Plant Science

The evolution of Brassica napus FLOWERING LOCUST paralogues in the context of inverted chromosomal duplication blocks

Jing Wang et al. — Wed, 15 May 2013 16:10:00 PDT

Background

The gene FLOWERING LOCUS T (FT) and its orthologues play a central role in the integration of flowering signals within Arabidopsis and other diverse species. Multiple copies of FT, with different cis-intronic sequence, exist and appear to operate harmoniously within polyploid crop species such as Brassica napus (AACC), a member of the same plant family as Arabidopsis.

Results

We have identified six BnFT paralogues from the genome of B. napus and mapped them to six distinct regions, each of which is homologous to a common ancestral block (E) of Arabidopsis chromosome 1. Four of the six regions were present within inverted duplicated regions of chromosomes A7 and C6. The coding sequences of BnFT paralogues showed 92-99% identities to each other and 85-87% identity with that of Arabidopsis. However, two of the paralogues on chromosomes A2 and C2, BnA2.FT and BnC2.FT, were found to lack the distinctive CArG box that is located within intron 1 that has been shown in Arabidopsis to be the binding site for theFLC protein. Three BnFT paralogues (BnA2.FT, BnC6.FT.a and BnC6.FT.b) were associated with two major QTL clusters for flowering time. One of the QTLs encompassing two BnFT paralogues (BnC6.FT.a and BnC6.FT.b) on chromosome C6 was resolved further using near isogenic lines, specific alleles of which were both shown to promote flowering. Association analysis of the three BnFT paralogues across 55 cultivars of B. napus showed that the alleles detected in the original parents of the mapping population used to detect QTL (NY7 and Tapidor) were ubiquitous amongst spring and winter type cultivars of rapeseed. It was inferred that the ancestral FT homologues in Brassica evolved from two distinct copies, one of which was duplicated along with inversion of the associated chromosomal segment prior to the divergence of B. rapa (AA) and B. oleracea (CC). At least ten such inverted duplicated blocks (IDBs) were identified covering a quarter of the whole B. napus genome.

Conclusion

Six orthologues of Arabidopsis FT were identified and mapped in the genome of B. napus which sheds new light on the evolution of paralogues in polyploidy species. The allelic variation of BnFT paralogues results in functional differences affecting flowering time between winter and spring type cultivars of oilseed Brassica. The prevalent inverted duplicated blocks, two of which were located by four of the six BnFT paralogues, contributed to gene duplications and might represent predominant pathway of evolution in Brassica.

QTLs for phosphorus deficiency tolerance detected in upland NERICA varieties

Yohei Koide et al. — Wed, 08 May 2013 20:10:48 PDT

Phosphorous (P) deficiency is a major yield limiting factor in rice (Oryza sativa L.) production. The interspecific New Rice for Africa (NERICA) varieties combine general stress tolerance from African cultivated rice (Oryza glaberrima Steud) with characteristics associated with high yield from O. sativa. However, little is known about their ability to tolerate P deficiency. Here, we examined the variation for tolerance to P deficiency among the 18 upland NERICAs and their parents in multi-year field experiments. The good performance under P deficiency of the O. glaberrima parent CG 14 and some NERICAs suggested that these tolerant NERICAs contain loci associated with P deficiency tolerance inherited from CG 14. Additionally, four QTL clusters for P deficiency tolerance were detected on chromosomes 4, 6 and 11 using F₃ lines derived from the cross between the P deficiency tolerant variety NERICA10 and a Japonica-type sensitive variety ‘Hitomebore’. These QTLs represent the first step in identifying stress tolerance genes from O. glaberrima that could subsequently be used to enhance P deficiency tolerance in O. sativa.

A rich TILLING resource for studying gene function in Brassica rapa

Pauline Stephenson et al. — Tue, 07 May 2013 22:58:34 PDT

Background

The Brassicaceae family includes the model plant Arabidopsis thaliana as well as a number of agronomically important species such as oilseed crops (in particular Brassica napus, B. juncea and B. rapa) and vegetables (eg. B. rapa and B. oleracea).

Separated by only 10-20 million years, Brassica species and Arabidopsis thaliana are closely related, and it is expected that knowledge obtained relating to Arabidopsis growth and development can be translated into Brassicas for crop improvement. Moreover, certain aspects of plant development are sufficiently different between Brassica and Arabidopsis to warrant studies to be carried out directly in the crop species. However, mutating individual genes in the amphidiploid Brassicas such as B. napus and B. juncea may, on the other hand, not give rise to expected phenotypes as the genomes of these species can contain up to six orthologues per single-copy Arabidopsis gene. In order to elucidate and possibly exploit the function of redundant genes for oilseed rape crop improvement, it may therefore be more efficient to study the effects in one of the diploid Brassica species such as B. rapa. Moreover, the ongoing sequencing of the B. rapa genome makes this species a highly attractive model for Brassica research and genetic resource development.

Results

Seeds from the diploid Brassica A genome species, B. rapa were treated with ethyl methane sulfonate (EMS) to produce a TILLING (Targeting Induced Local Lesions In Genomes) population for reverse genetics studies. We used the B. rapa genotype, R-o-18, which has a similar developmental ontogeny to an oilseed rape crop. Hence this resource is expected to be well suited for studying traits with relevance to yield and quality of oilseed rape. DNA was isolated from a total of 9,216 M₂ plants and pooled to form the basis of the TILLING platform. Analysis of six genes revealed a high level of mutations with a density of about one per 60 kb. This analysis also demonstrated that screening a 1 kb amplicon in just one third of the population (3072 M₂ plants) will provide an average of 68 mutations and a 97% probability of obtaining a stop-codon mutation resulting in a truncated protein. We furthermore calculated that each plant contains on average ~10,000 mutations and due to the large number of plants, it is predicted that mutations in approximately half of the GC base pairs in the genome exist within this population.

Conclusions

We have developed the first EMS TILLING resource in the diploid Brassica species, B. rapa. The mutation density in this population is ~1 per 60 kb, which makes it the most densely mutated diploid organism for which a TILLING population has been published. This resource is publicly available through the RevGenUK reverse genetics platform http://revgenuk.jic.ac.uk.

Traditionally used Thai medicinal plants: in vitro anti-inflammatory, anticancer and antioxidant activities

N Siriwatanametanon et al. — Tue, 07 May 2013 22:50:29 PDT

AIMS OF THE STUDY:

In order to assess traditional Thai claims about the therapeutic potential of medicinal plants and to select plants for future phytochemical research, nine plant species with anti-inflammatory uses were selected from Thai textbooks and assessed for their in vitro anti-inflammatory, antiproliferative and antioxidant activities.

METHODS:

Nuclear factor-kappaB (NF-kappaB) inhibitory effects in stably transfected HeLa cells were determined by luciferase assay, and effects on LPS-induced pro-inflammatory mediators prostaglandin E2 (PGE2), interleukin (IL)-6, IL-1beta, and tumour necrosis factor (TNF)alpha in primary monocytes were assessed by ELISA. Cytotoxic activities were examined against HeLa cells, human leukaemia CCRF-CEM cells and the multidrug-resistant CEM/ADR5000 subline using the MTT and XTT tests. However, a redox status has been linked with both inflammation and cancer, antioxidant effects were also assessed using the DPPH, lipid-peroxidation, and Folin-Ciocalteau methods.

RESULTS:

Among all the nine species, Gynura pseudochina var. hispida and Oroxylum indicum showed the most promising NF-kappaB inhibitory effects with the lowest IC(50) values (41.96 and 47.45 microg/ml, respectively). Muehlenbeckia platyclada did not inhibit the NF-kappaB activation but effectively inhibited the release of IL-6, IL-1beta and TNF-alpha with IC(50) values ranging between 0.28 and 8.67 microg/ml. Pouzolzia indica was the most cytotoxic against CCRF-CEM cells and the multidrug-resistant CEM/ADR5000 cells (9.75% and 10.48% viability, at 10 microg/ml, respectively). Rhinacanthus nasutus was the most potent cytotoxicity against HeLa cells (IC(50) 3.63 microg/ml) and showed specific cytotoxicity against the multidrug-resistant CEM/ADR5000 cells (18.72% viability at 10 microg/ml, p<0.0001 when compared to its cytotoxicity against CCRF-CEM cells). Moreover, Oroxylum indicum showed a high level of antioxidant activity by inhibiting lipid-peroxidation (IC(50) 0.08 microg/ml).

CONCLUSIONS:

This study provides in vitro evidence for the use of the Thai plants, most importantly Gynura pseudochina var. hispida, Oroxylum indicum and Muehlenbeckia platyclada as Thai anti-inflammatory remedies and these plants are now a priority for further phytochemical research.

Eucalypts for biofuel production in Northern Australia: identifying species from current and future testing programs

Mervyn Shepherd et al. — Tue, 07 May 2013 22:05:38 PDT

This RIRDC project identifies research needed to better define the choice of species and production systems for Eucalypts as a source of biomass for biofuel. This publication focuses on the unique opportunities for extensive areas available for Eucalypt production in Northern Australia. Small landholders and major forest producers could produce biofuels from Eucalypts.

Deviant near-infrared spectra allows identification of Corymbia hybrids

M Abasolo et al. — Sun, 05 May 2013 20:37:11 PDT

High throughput screening and detection of peptaibol antibiotics from the fermentation broth of trichoderma harzianum by LC-MS/MS

Shun Pan et al. — Wed, 01 May 2013 22:57:42 PDT

Towards a better understanding of medicinal uses of the brown seaweed Sargassum in Traditional Chinese Medicine: a phytochemical and pharmacological review

Lei Liu et al. — Wed, 01 May 2013 19:40:52 PDT

Ethnopharmacological relevance

For nearly 2000 years Sargassum spp., a brown seaweed, has been used in Traditional Chinese Medicine (TCM) to treat a variety of diseases including thyroid disease (e.g. goitre).

Aims of the review

To assess the scientific evidence for therapeutic claims made for Sargassum spp. in TCM and to identify future research needs.

Background and methods

A systematic search for the use of Sargassum in classical TCM books was conducted and linked to a search for modern phytochemical and pharmacological data on Sargassum spp. retrieved from PubMed, Web of Knowledge, SciFinder Scholar and CNKI (in Chinese).

Results and discussion

The therapeutic effects of Sargassum spp. are scientifically plausible and may be explained partially by keyin vivo and in vitro pharmacological activities of Sargassum, such as anticancer, anti-inflammatory, antibacterial and antiviral activities. Although the mechanism of actions is still not clear, the pharmacological activities could be mainly attributed to the major biologically active metabolites, meroterpenoids, phlorotanins and fucoidans. The contribution of iodine in Sargassum for treating thyroid related diseases seem to have been over estimated.

Conclusions

The bioactive compounds in Sargassum spp. appear to play a role as immunomodulators and could be useful in the treatment of thyroid related diseases such as Hashimoto's thyroiditis. Further research is required to determine both the preventative and therapeutic role of Sargassum spp. in thyroid health.

Review of local and traditional plant use by Australian migrant communities

Anna Du Chesne et al. — Thu, 18 Apr 2013 19:28:21 PDT

Factors affecting pharmacists' recommendations of CMs: a qualitative pilot study of Australian pharmacists

Sarah E. Culverhouse et al. — Thu, 18 Apr 2013 19:13:58 PDT

A simple HPLC method for detecting adulteration of ginkgo extracts with flavonol glycosides

Hans Wohlmuth et al. — Thu, 18 Apr 2013 19:13:55 PDT

The St George medicine chest research project

Peter Mouatt — Thu, 18 Apr 2013 18:17:37 PDT

Epigenetic profiling during Brassica rapa reproductive development

Justin A. Bloomfield et al. — Tue, 16 Apr 2013 23:56:46 PDT

Genomic regulation of seed development in Brassica

Graham J. King et al. — Tue, 16 Apr 2013 23:56:43 PDT

A hypomethylated population of Brassica rapa for forward and reverse epi-genetics

Stephen Amoah et al. — Tue, 16 Apr 2013 23:37:20 PDT

Background: Epigenetic marks superimposed on the DNA sequence of eukaryote chromosomes provide agility and plasticity in terms of modulating gene expression, ontology, and response to the environment. Modulating the methylation status of cytosine can generate epialleles, which have been detected and characterised at specific loci in several plant systems, and have the potential to generate novel and relatively stable phenotypes. There have been no systematic attempts to explore and utilise epiallelic variation, and so extend the range of phenotypes available for selection in crop improvement. We developed an approach for generating novel epialleles by perturbation of the DNA methylation status. 5- Azacytidine (5-AzaC) provides selective targeting of ^5mCG, which in plants is associated with exonic DNA. Targeted chemical intervention using 5-AzaC has advantages over transgenic or mutant modulation of methyltransferases, allowing stochastic generation of epialleles across the genome.

Results: We demonstrate the potential of stochastic chemically-induced hypomethylation to generate novel and valuable variation for crop improvement. Systematic analysis of dose–response to 5-AzaC in B. rapa guided generation of a selfed stochastically hypomethylated population, used for forward screening of several agronomic traits. Dose–response was sigmoidal for several traits, similar to that observed for chemical mutagens such as EMS. We demonstrated transgenerational inheritance of some phenotypes. BraRoAZ is a unique hypomethylated population of 1000 E2 sib lines. When compared to untreated controls, 5-Aza C-treated lines exhibited reduced immuno-staining of ^5mC on pachytene chromosomes, and Methylation Sensitive Amplified Polymorphism (MSAP) profiles that were both divergent and more variable. There was coincident phenotypic variation among these lines for a range of seed yield and composition traits, including increased seed protein content and decreased oil content, as well as decreased erucic acid and corresponding increases in linoleic and/or palmitic acid. Each 5-AzaC-treated line represents a unique combination of hypomethylated epialleles.

Conclusions: The approach and populations developed are available for forward and reverse screening of epiallelic variation and subsequent functional and inheritance studies. The generation of stochastically hypomethylated populations has utility in epiallele discovery for a wide range of crop plants, and has considerable potential as an intervention strategy for crop improvement.

Novel microsatellite markers for the endangered Australian rainforest tree Davidsonia jerseyana (Cunoniaceae) and cross-species amplification in the Davidsonia genus

Frances G. Eliott et al. — Tue, 16 Apr 2013 23:26:28 PDT

Davidsonia jerseyana is an endangered rainforest tree endemic to far north-eastern New South Wales, Australia. The species occurs in small fragmented populations and has an edible plum-like fruit important to the Australian Native Food industry. Twenty one novel microsatellite markers were developed for D. jerseyana of which 13 were polymorphic for the species. Markers were characterised using 28 individuals, representing six populations from across the species geographic range. Species level analysis of the polymorphic markers revealed the mean number of alleles per locus was 3.154 (range 2–7) and mean expected and observed heterozygosities were 0.437 (range 0.035–0.725) and 0.044 (range 0–0.250) respectively. The heterozygote deficiency may indicate a predominantly selfing breeding system. All markers cross amplified in the other two Davidsonia species. These markers will be used to assess the genetic diversity, population structure and breeding systems in D. jerseyana and related taxa which will facilitate conservation management strategies.

Essential oil composition and antimicrobial activity of wild and cultivated mint timija (Mentha suaveolens subsp. timija (Briq.) Harley), an endemic and threatened medicinal species in Morocco

A Kasrati et al. — Tue, 16 Apr 2013 23:10:52 PDT

The hydro-distilled essential oils obtained from aerial parts of the wild (w) and cultivated (c) mint timija (Mentha suaveolens subsp. timija), an endemic medicinal species of Morocco, have been analyzed by GC–MS and screened for antimicrobial activity. In total, 35 compounds representing more than 98% of the oils were identified. Menthone (39.4(w)–10.8(c)%), pulegone (62.3(c)–34.3(w)%) and isomenthone (9.3(c)–7.8(w)%) were found as the main components for the two oils. The volatiles of the wild and cultivated material differed significantly in both the percentage of the main components and antimicrobial effect. Pulegone was more dominant in cultivated mint timija (62.3%) than in wild one (34.3%), while menthone was more abundant in the wild material (39.4%). In the antimicrobial assays, both oils displayed good to excellent activity against all microorganisms tested with the oil of the cultivated form being more active.

SNP in starch biosynthesis genes associated with nutritional and functional properties of rice

Ardashir Kharabian-Masouleh et al. — Tue, 12 Mar 2013 20:29:36 PDT

Starch is a major component of human diets. The relative contribution of variation in the genes of starch biosynthesis to the nutritional and functional properties of the rice was evaluated in a rice breeding population. Sequencing 18 genes involved in starch synthesis in a population of 233 rice breeding lines discovered 66 functional SNPs in exonic regions. Five genes, AGPS2b, Isoamylase1, SPHOL, SSIIb and SSIVb showed no polymorphism. Association analysis found 31 of the SNP were associated with differences in pasting and cooking quality properties of the rice lines. Two genes appear to be the major loci controlling traits under human selection in rice, GBSSI (waxy gene) and SSIIa. GBSSI influenced amylose content and retrogradation. Other genes contributing to retrogradation were GPT1, SSI, BEI and SSIIIa. SSIIa explained much of the variation in cooking characteristics. Other genes had relatively small effects.

Horticultural development of bush food plants and rights of Indigenous people as traditional custodians – the Australian Bush Tomato (Solanum centrale) example: a review

L Slade Lee — Thu, 07 Mar 2013 19:35:14 PST

New crops are regularly being introduced into cultivation, typically accompanied by a very small agricultural knowledge base. Often, there is a lack of agronomic research information or production experience upon which to rely, nor plant varieties optimised for an agricultural system. The challenges of a new industry may be compounded by a lack of consumer awareness of the new product and value-chain models need to be developed to suit the product. Frequently the plant species being developed into a new crop is one traditionally used as a food source or for medicinal or other applications by Indigenous people. Thus a complex series of additional factors comes into play – consent of the original custodians, respect and acknowledgement of their traditional knowledge that may be exploited, and totemic, kinship and spiritual associations that may be impacted. Establishing benefit sharing for the hereditary stewards, and protection of traditional collective intellectual property is an important ethical consideration. In the 21st century, the previous unjust exploitation of the traditional knowledge of the original custodians without acknowledgement or benefit sharing, is no longer accepted. However, prevailing strategies to safeguard intellectual property and traditional knowledge associated with native plants, for instance, to ensure that benefit is captured for Indigenous hereditary custodians may be lacking or may contravene Indigenous customary law. Where scientific, cultural, ethical, legal and commercial issues interact at the emergence of a new crop industry, stakeholders from various perspectives will bring critical, sometimes conflicting, impediments to resolve. The challenges that arise in the commercial exploitation of the Australian Bush Tomato, Solanum centrale, and its horticultural development, are reviewed and the approaches to their resolution are discussed.

Development of heartwood in response to water stress for radiata pine in Southern New South Wales, Australia

Julian Moreno Chan et al. — Wed, 06 Mar 2013 17:50:51 PST

Heartwood development and other functional changes in stem conductance in response to water stress in radiata pine were investigated using two contrasting climatic areas (high-altitude sub-alpine vs. warm–dry inland) of the Hume region of New South Wales, Australia. The study included mature (34.5–36.5 years old) and young stands (10–11 years old) measured under normal climate and during an extreme drought. The effect of water stress on heartwood development was examined using sapwood percentage, sapwood saturation, development of dry sapwood and evidence of cavitation in sapwood. Trees at the warm–dry site developed heartwood at faster rates than on the high-altitude site. At breast height, the mature stands of the warm–dry site had 8–14 % less sapwood. Extensive cavitation towards the sapwood/heartwood boundary occurred in some of the mature and young stands on the warm–dry site. We postulated that in water-limiting environments, cavitation of the inner sapwood precedes heartwood formation and is an adaptation mechanism that regulates stem conductance capacity and thus water use in the tree. The drought of 2006 led to decreases in moisture associated with cavitation not previously reported for radiata pine and demonstrated the drought hardiness of the species. In the warm–dry site, breast-height sapwood saturation dropped to 58 and 82 % for suppressed and average-sized trees in a mature unthinned stand; and 75–78 % for two young stands. These saturation levels, however, only imply average values as some cells cavitated whilst others were fully saturated. Cavitation occurred in a localized fashion affecting small to large groups of cells.