Search

The fresh or dried fruit, although eaten in remote Aboriginal communities, is never sold for consumption as a whole fruit in commercial marketplaces. The flavour is considered by most to be rather acrid to be eaten whole in anything but small quantities, although as a flavouring ingredient, it imparts an attractive zest to food products. Definitive validated data on mean bush tomato production and price are difficult to obtain, but variability in production, prices and supply reliability is apparent. Fruit is most commonly traded in the dried form, though fresh fruit is also traded. Australian native plants have in general evolved under nutrient-deficient conditions and particularly so with regard to phosphorus nutrition. Accordingly, it is often opined that restricted fertilizer application is preferable for such plants during the course of cultivation. Bush tomato is a perennial crop and, once planted, can be expected to last many years by taking advantage of the plants' propensity for copious suckering.

The narrow genetic base of commercial arabica resulting from intensive selection for quality during domestication and self-pollination has been well documented, raising the need for new diverse germplasm sources. Beans of 232 diverse arabica coffee accessions originating from 27 countries were harvested from the germplasm collection at CATIE, Costa Rica. Substantial variation was observed for bean morphology including 100 bean weight, bean length, width, thickness and bulk density. Non-volatiles including caffeine and trigonelline were analysed and showed larger variation in range than has previously been reported. Results of targeted analysis of 18 volatiles from 35 accessions also showed significant variation, with coefficients of variation from 140% for 4-vinylguaiacol to 62% for geraniol. There were strong correlations between some volatile compounds, suggesting that representative volatiles used in selection would save analytical costs. However, no strong correlation was found between bean morphology and the levels of non-volatile or volatile compounds, implying that it is difficult to select for low or high composition of these compounds based on bean physical characteristics. Utilizing the large variation observed for bean morphology and biochemical traits, it should be possible to select for desirable combinations of traits in arabica coffee breeding.

The properties of sorghum starch may influence digestibility and nutritional value in animal and human diets and the processing performance of starch in industrial applications. The variation in grain composition and starch physiochemical properties was evaluated. The DNA sequence of three starch synthesis genes was surveyed and an association approach used to investigate the genetic basis of phenotypic differences in sorghum. Single nucleotide polymorphisms (SNPs) in SSIIa distinguish three haplotypes that were associated with significant differences in gelatinisation temperature and thousand-kernel weight. SSIIa haplotype (H1) accessions had a significantly lower mean gelatinisation temperature of 80.5 °C compared to 87.6 °C and 91.5 °C for H2 and H3, respectively. Polymorphisms in SBEIIb were associated with a 12 °C difference in gelatinisation temperature and GBSSI polymorphisms with total starch content. The SNPs identified provide a genetic explanation for variation in starch properties in sorghum.

Twenty genic- and genomic SSR markers were used to study genetic diversity and geographical differentiation of barley from 29 countries through analysis of a worldwide collection of 304 ICARDA’s barley landraces. Of these, 19 loci were highly polymorphic in the material studied. Based on Nei-distance matrix, Principal Component Analysis (PCoA) and cluster analysis using UPGMA associated with AMOVA the data revealed countries’ grouping within regions. Three distinct germplasm pools were identified in the landraces. The first of these was from Eastern Africa (Eritrea and Ethiopia) and South America (Ecuador, Peru and Chile) suggesting that barley introduced to South America might have originated specifically from East Africa or that they share a common genetic basis for adaptation. The second was the Caucasus (Armenia and Georgia) and the third included the remaining regions of Central Asia, Near East, Northern Africa and Eastern Asia. Genetic diversity of barley subspecies (Six-rowed barley, Two-rowed barley, H. spontaneum C. Koch and H. agriocrithon Aberg) also discriminates them into three groups: cultivated barleys (Six-rowed barley and Two-rowed barley), wild barley H. spontaneum and subspecies H. agriocrithon. These results associated with parsimony analysis demonstrate that H. agriocrithon and H. spontaneum might be distinct and do not support a hybrid origin for H. agriocrithon suggesting further investigation of the basis of more intense sampling of the two subspecies H. spontaneum and H. agriocrithon.

Mismatch-specific endonucleases are efficient tools for the targeted scanning of populations for subtle DNA variations. Conventional protocols involve 5'-labeled amplicon substrates and the detection of digestion products by LIF electrophoresis. A shortcoming of such protocols, however, is the limited 5'-signal strength. Normally the sensitivity of fluorescent DNA analyzers is superior to that of intercalating dye/agarose systems, however, pooling capacities of the former and latter approaches to mismatch scanning are somewhat similar. Detection is further limited by significant background. We investigated the activity of CEL nucleases using amplicon substrates labeled both internally and at each 5'-terminus. The amplicons were generated from exon 8 of the rice starch synthase IIa encoding gene. Signal of both 5'-labels was significantly reduced by enzyme activity, while that of the internal label was largely unaffected. In addition, background resulting from internal labeling was a significant improvement on that associated with 5'-labeling. Sizing of the multilabeled substrates suggests that 5'-modification enhances exonucleolytic activity, resulting in the removal of the dye-labeled terminal nucleotides. We have developed an alternative approach to mismatch detection, in which amplicon labeling is achieved via the incorporation of fluorescently labeled deoxynucleotides, which we have named Endonucleolytic Mutation Analysis by Internal Labeling (EMAIL). The strength of the EMAIL assay was demonstrated by the reclassification of a rice line as being heterozygous for the starch gene. This cultivar was assigned as being homozygous by a previous resequencing study. EMAIL shows potential for the clear identification of multiple mutations amongst allelic pools.

Background: Both sorghum (Sorghum bicolor) and sugarcane (Saccharum officinarum) are members of the Andropogoneae tribe in the Poaceae and are each other's closest relatives amongst cultivated plants. Both are relatively recent domesticates and comparatively little of the genetic potential of these taxa and their wild relatives has been captured by breeding programmes to date. This review assesses the genetic gains made by plant breeders since domestication and the progress in the characterization of genetic resources and their utilization in crop improvement for these two related species. Genetic Resources: The genome of sorghum has recently been sequenced providing a great boost to our knowledge of the evolution of grass genomes and the wealth of diversity within S. bicolor taxa. Molecular analysis of the Sorghum genus has identified close relatives of S. bicolor with novel traits, endosperm structure and composition that may be used to expand the cultivated gene pool. Mutant populations (including TILLING populations) provide a useful addition to genetic resources for this species. Sugarcane is a complex polyploid with a large and variable number of copies of each gene. The wild relatives of sugarcane represent a reservoir of genetic diversity for use in sugarcane improvement. Techniques for quantitative molecular analysis of gene or allele copy number in this genetically complex crop have been developed. SNP discovery and mapping in sugarcane has been advanced by the development of high-throughput techniques for ecoTILLING in sugarcane. Genetic linkage maps of the sugarcane genome are being improved for use in breeding selection. The improvement of both sorghum and sugarcane will be accelerated by the incorporation of more diverse germplasm into the domesticated gene pools using molecular tools and the improved knowledge of these genomes.

Coffee is an important crop that provides a livelihood to millions of people living in developing countries. Production of genotypes with improved coffee quality attributes is a primary target of coffee genetic improvement programmes. Advances in genomics are providing new tools for analysis of coffee quality at the molecular level. The recent report of a genomic sequence for robusta coffee, Coffea canephora, is a major development. However, a reference genome sequence for the genetically more complex arabica coffee (C. arabica) will also be required to fully define the molecular determinants controlling quality in coffee produced from this high quality coffee species. Genes responsible for control of the levels of the major biochemical components in the coffee bean that are known to be important in determining coffee quality can now be identified by association analysis. However, the narrow genetic base of arabica coffee suggests that genomics analysis of the wild relatives of coffee (Coffea spp.) may be required to find the phenotypic diversity required for effective association genetic analysis. The genomic resources available for the study of coffee quality are described and the potential for the application of next generation sequencing and association genetic analysis to advance coffee quality research are explored. (C) 2016 Society of Chemical Industry

Ripening of the grape berry immediately precedes harvesting and is the key phase which determines the composition of wine and table grapes. Although it is apparent that changes in gene expression levels play a role in initiating ripening, it is unknown to what extent gene expression levels differ between cultivars during ripening. We have undertaken a comparison of a selection of wine grape cultivars using a 9200 feature cDNA microarray to gauge the extent to which transcript levels differ between wine grape cultivars in the berry skin during ripening. Clones for microarray slide fabrication were sourced from a cDNA library constructed from mRNA derived from randomly sampled berries. The berries were collected at weekly intervals over four weeks of berry development including veraison. The microarray slides were hybridised with Cy3 and Cy5 labelled cDNA derived from the skin of ripening berries of the cultivars Cabernet Sauvignon, Pinot Noir, Shiraz, Chardonnay, Riesling, Sauvignon Blanc and Semillon. Only a small proportion of the genes within the berry skin showed a three-fold or greater difference in expression level after ripening commenced. Most of the differences appear to arise from environmental signals rather than genome differences.

‘Ellendale’ mandarin (Citrus reticulata Blanco) on seven commercially important rootstocks was assessed over a 26-year period on a site not previously planted to citrus. Tree yield data collected each season from 1969 to 1991 showed that yields were highest on ‘Lockyer’ rough lemon (C. jambhiri Lush) and lowest on ‘Emperor’ mandarin. Yields for the two citranges (C. sinensis (L.) Osbeck × Poncirus trifoliata (L.) Raf.), ‘Troyer’ and ‘Carrizo’, were intermediate, and somewhat higher than those for two selections of sweet orange (C. sinensis (L.) Osbeck), ‘Parramatta’ and ‘Joppa’. Linear regression was used to examine changes in yielding pattern across the 23 seasons of fruit production. This revealed that ‘Troyer’ was comparable with the rough lemon selections throughout most of the experiment and significantly higher than ‘Carrizo’ during certain periods in the middle of the experiment. Similarly, while ‘Joppa’ and ‘Parramatta’ produced near-identical results during most of the experiment, ‘Joppa’ out-performed ‘Parramatta’ toward the end of the experiment. ‘Emperor’ showed a low yield trend throughout the experiment, often more than 50 kg per tree per year less than the rough lemon and citrange selections. Detailed assessment of biennial bearing showed a significant pattern commencing when trees were approximately 15 years old and intensifying until the end of the experiment. However, rootstock had no effect on the biennial bearing behaviour of ‘Ellendale’ mandarin. Correlations of cumulative yields at each harvest date with the final cumulative yield (for 23 seasons of cropping) showed instability up until approximately the eighth year of cropping after which it increased steadily, suggesting that in similar experiments there may be only marginal value in assessing yields beyond about the 10th season. Fruit quality assessments made in two consecutive seasons showed expected trends, with rough lemon (both ‘Lockyer’ and ‘Mazoe’) producing the largest and heaviest fruit, with thicker rinds, lower juice content, and lower Brix. The citrange selections (‘Troyer’ and ‘Carrizo’) resulted in fruit quality comparable to the sweet oranges (‘Parramatta’ and ‘Joppa’), with ‘Troyer’ producing significantly higher Brix levels than any other rootstock. All rootstocks produced leaf nutrient levels close to the desirable range, with significant differences for the elements P, Mg, Ca, Mn, and B. These differences separated the seven rootstocks into categories consistent with their genetic relatedness.

Potamophila parviflora, a wild relative ofdomestic rice, is endemic to the north-eastern river systemsof New South Wales, Australia. It is the only member of the genus,and is habitat specific. Several new sites were found, mostly in theUpper Clarence catchment. Florets of P.parviflora were found to be 86%female-only, while 14% contained mature malereproductive parts, which occurred more often in the middle sectionof the panicle. Pollen was found to be necessary for the developmentof mature fruits. RAPD data showed that there is very little geneticvariation between individual plants, or between differentpopulations. An embryological study showed several irregularities inmegasporogenesis and megagametogenesis. No tetrads were observed inmegasporogenesis and the ovule is vacuolate at the megaspore mothercell stage. Megagametogenesis proceeded rapidly, nuclei within theovule were sometimes not spherical and varied in size, and sometimesthe antipodal cells doubled in number with a corresponding halving insize of the nuclei. Chromosome number varied between 2n = 24and 2n = 25, between and within populations. These resultsindicate that P. parvifloracould be a diplosporous apomict of the Antennaria type, althoughfurther works are required to provide conclusive proof.

Analysis of 2479 ESTs from Vitis vinifera berry tissue and 2438 from leaf revealed that 1% of the ESTs match to known Vitis proteins, 72% to plant proteins, 11% to non-plant, and 16% had no match (P[N]>0.5). The levels of redundancy were similar in the leaf and berry libraries. Only 12% of the genes matched by the ESTs were common to both libraries indicating marked differences in the genes expressed in the two tissues. The abundance of transcripts with predicted cellular roles in leaf and berry were estimated by classifying the primary BLAST matches to known proteins (score >80) into functional categories. Thirty-six percent of the leaf transcripts were involved in photosynthesis, compared to 3% in the berry. This is a much higher proportion of transcripts involved with a function limited to specialized cells, than was found when transcripts of 33 human tissues were compared using a similar approach, suggesting plant cells may involve their cellular machinery to a greater extent in specialized activities than animal cells. Relatively enhanced expression of specific transcription factors, and genes involved in defense, detoxification, stress response, proteolysis, trafficing, and signal transduction, suggests berry tissue is actively engaged in responding to environmental stimuli.

The composition and yield of oil in 615 trees representing the natural populations of Melaleuca alternifolia, or tea tree, was investigated. A sixth distinct oil chemotype was identified. Of the six chemotypes, one chemotype is dominated by terpinen-4-ol, one by 1,8-cineole, one by terpinolene and the remaining three chemotypes are all dominated by 1,8-cineole and differ in either terpinen-4-ol or terpinolene content. Whilst most chemotypes are present throughout the distribution range, a definite correspondence of oil types with geographic location was found. Terpinen-4-ol types predominate in and around the Bungawalbin basin in the Casino area of northern New South Wales (NSW), high 1,8-cineole types predominate toward the southern end of the distribution around Grafton and terpinolene types predominate in southern Queensland. Preliminary formulae have been developed to allow comparisons of oil data obtained by steam distillation with a static headspace gas chromatography method.

Molecular techniques have created the opportunity for great advances in plant mutation genetics and the science of mutation breeding. The powerful targeted induced local lesions in genomes (TILLING) technique has introduced the possibility of reverse genetics-the ability to screen for mutations at the DNA level prior to assessing phenotype. Fundamental to TILLING is the induction of mutant populations (or alternatively, the identification of mutants in the environment); and mutation induction requires an understanding and assessment of the appropriate mutagen dose required. The techniques of mutation induction, dose optimization, and TILLING are explained.

Molecular techniques have created the opportunity for great advances in plant mutation genetics and the science of mutation breeding. The powerful targeted induced local lesions in genomes (TILLING) technique has introduced the possibility of reverse genetics-the ability to screen for mutations at the DNA level prior to assessing phenotype. Fundamental to TILLING is the induction of mutant populations (or alternatively, the identification of mutants in the environment); and mutation induction requires an understanding and assessment of the appropriate mutagen dose required. The techniques of mutation induction, dose optimization, and TILLING are explained.

Microarray analysis of Vitis vinifera cv. Shiraz developing berries has revealed the expression patterns of several categories of genes. Microarray slides were constructed from 4,608 PCR-amplified cDNA clones derived from a ripening grape berry cDNA library. The mRNA expression levels of the genes represented by these cDNAs were measured in flowers, week 2 post-flowering whole berries, week 5, week 8, week 10 (veraison, green berries), week 12 and week 13 berry skin. In addition, a comparison of RNA expression in pigmented and unpigmented berry skin at veraison (week 10) was undertaken. Image and statistical analysis revealed four sets of genes with distinctive and similar expression profiles over the course of berry development. The first set was composed of genes which had maximum RNA expression in flowers, followed by a steady decrease in expression. The most prominent group within this set were genes which have a role in photosynthesis. The second set of cDNAs was dominated by genes involved in flavonoid biosynthesis and had a peak of expression week 2 post-flowering. The data indicate co-ordinate regulation of flavonoid biosynthetic genes which code for the enzymes 4-coumarate-CoA ligase, chalcone synthase, chalcone isomerase, flavonone hydroxylase, anthocyanidin reductase and cytochrome b5. The third set of cDNAs exhibited maximum expression week 5 post-flowering, midway between flowering and veraison, a period of rapid berry growth. This set of cDNAs is dominated by genes which code for structural cell wall proteins. The fourth set of genes was dramatically up-regulated at veraison and remained up-regulated until 13 weeks post-flowering. This set of genes was composed of a diverse range of genes, a reflection of the complexity of ripening, most with no known function.

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.