Southern Cross Plant Science

The gene for fragrance in rice

Louis MT Bradbury et al. — Wed, 03 Oct 2012 21:27:35 PDT

The endosperm morphology of rice and its wild relatives as observed by scanning electron microscopy

Shabana Kasem et al. — Mon, 09 May 2011 22:55:40 PDT

While cultivated rice, Oryza sativa, is arguably the world’s most important cereal crop, there is little comparative morphological information available for the grain of rice wild relatives. In this study, the endosperm of 16 rice wild relatives were compared to O. sativa subspecies indica and O. sativa subspeciesjaponica using scanning electron microscopy. Although the aleurone, starch granules, protein bodies and endosperm cell shapes of the cultivated and non-cultivated species were similar, several differences were observed. The starch granules of some wild species had internal channels that have not been reported in cultivated rice. Oryza longiglumis, Microlaena stipoides and Potamophila parviflora, had an aleurone that was only one-cell thick in contrast to the multiple cell layers observed in the aleurone of the remainingOryza species. The similarity of the endosperm morphology of undomesticated species with cultivated rice suggests that some wild species may have similar functional properties. Obtaining a better understanding of the wild rice species grain ultrastructure will assist in identifying potential opportunities for development of these wild species as new cultivated crops or for their inclusion in plant improvement programmes.

Population structure, effective population size and adverse effects of stocking in the endangered Australian eastern freshwater cod Maccullochella ikei

Catherine J. Nock et al. — Thu, 27 Jan 2011 20:15:21 PST

Microsatellite markers were used to examine spatio-temporal genetic variation in the endangered eastern freshwater cod Maccullochella ikei in the Clarence River system, eastern Australia. High levels of population structure were detected. A model-based clustering analysis of multilocus genotypes identified four populations that were highly differentiated by F-statistics (FST = 0· 09 − 0· 49; P < 0· 05), suggesting fragmentation and restricted dispersal particularly among upstream sites. Hatchery breeding programmes were used to re-establish locally extirpated populations and to supplement remnant populations. Bayesian and frequency-based analyses of hatchery fingerling samples provided evidence for population admixture in the hatchery, with the majority of parental stock sourced from distinct upstream sites. Comparison between historical and contemporary wild-caught samples showed a significant loss of heterozygosity (21%) and allelic richness (24%) in the Mann and Nymboida Rivers since the commencement of stocking. Fragmentation may have been a causative factor; however, temporal shifts in allele frequencies suggest swamping with hatchery-produced M. ikei has contributed to the genetic decline in the largest wild population. This study demonstrates the importance of using information on genetic variation and population structure in the management of breeding and stocking programmes, particularly for threatened species.

Trans-specific single nucleotide polymorphisms in Eucalyptus wood quality genes

Timothy Sexton et al. — Thu, 16 Dec 2010 16:57:24 PST

Seasonality of flowering in Corymbia citriodora subsp variegata (Spotted gum)

M Abasolo et al. — Thu, 16 Dec 2010 16:52:32 PST

High-throughput DNA extraction from forest trees

Mervyn Shepherd et al. — Thu, 16 Dec 2010 16:45:39 PST

It is difficult to extract pure high-quality DNA from trees, which may not be amenable to advances in extraction methods suitable for other plants. A new commercial high-throughput DNA extraction system, using a silica binding matrix for purification and a multisample mixer mill for tissue disruption, was evaluated for its suitability with Eucalyptus spp., Pinus spp., and Araucaria cunninghamii (hoop pine). DNA suitable for a range of molecular biology applications was successfully extracted from all genera. The method was highly reliable when tested in more than 500 preparations and could be adapted to different tree species with relatively minor modifications.

Genetic control of propagation traits in a single Corymbia torelliana × Corymbia variegata family

Mervyn Shepherd et al. — Thu, 16 Dec 2010 16:23:16 PST

Genetic control of vegetative propagation traits was described for a second-generation, outbred, intersectional hybrid family (N = 208) derived from two species, Corymbia torelliana (F. Muell.) K.D. Hill & L.A.S. Johnson and Corymbia variegata (F. Muell.) K.D. Hill & L.A.S. Johnson, which contrast for propagation characteristics and in their capacity to develop lignotubers. Large phenotypic variances were evident for rooting and most other propagation traits, with significant proportions attributable to differences between clones (broad-sense heritabilities 0.2–0.5). Bare root assessment of rooting rate and root quality parameters tended to have the highest heritabilities, whereas rooting percentage based on root emergence from pots and shoot production were intermediate. Root biomass and root initiation had the lowest heritabilities. Strong favourable genetic correlations were found between rooting percentage and root quality traits such as root biomass, volume, and length. Lignotuber development on a seedling was associated with low rooting and a tendency to poor root quality in cuttings and was in accord with the persistence of species parent types due to gametic phase disequilibrium. On average, nodal cuttings rooted more frequently and with higher quality root systems, but significant cutting type × genotype interaction indicated that for some clones, higher rooting rates were obtained from tips. Low germination, survival of seedlings, and rooting rates suggested strong hybrid breakdown in this family.

Genetic association studies in Eucalyptus pilularis Smith (blackbutt)

Timothy R. Sexton et al. — Thu, 16 Dec 2010 14:32:24 PST

Breeding for wood quality is limited by the long generation times and the delay before wood quality can be measured reliably. Association studies allow links between phenotype and genotype to be made, and are a prelude to accelerated domestication of trees by molecular breeding approaches. This study uses association genetics to identify DNA polymorphisms that correlate with solid wood properties of Eucalyptus pilularis Smith (blackbutt). We undertook extensive phenotyping of dimensional stability, growth and structural wood properties on a nine-year-old progeny trial established by Forests NSW at Hannam Vale, near Port Macquarie in NSW. A subset of 372 phenotyped individuals representing 284 families collected from 37 provenances was used as the association population for genotypic assessment. Fifty-two out of 127 novel DNA polymorphisms were surveyed within four candidate genes, CCR, CAD, MYB1 and MYB2. Several putative associations between wood quality traits and selected DNA polymorphisms are reported, along with the likely mechanism of action on wood quality. Association studies such as this will facilitate non-destructive DNA tests for heritable wood properties that can be used to enrich breeding populations at any developmental stage with desirable alleles. Keywords: wood properties; phenotypic variation; genetic variation; molecular markers; selection; marker-aided selection; Eucalyptus pilularis

Identification of QTLs associated with variations in grain protein concentration in two-row barley

L C. Emebiri et al. — Tue, 09 Nov 2010 17:22:10 PST

Grain protein concentration (GPC) is arguably the most important factor when marketing malting barleys. Excessively high and excessively low GPC are both undesirable for malting and brewing. GPC variation is influenced to a high degree by the environment and exhibits relatively large genotype x environment interaction. Identification of molecular markers linked to genes influencing GPC would allow barley breeders to select for GPC independent of environmental effects. A genetic linkage map with 270 markers was constructed to identify the genetic basis for variation in GPC, using 180 doubled haploid lines from a cross of VB9524 and ND11231*12. The parental genotypes were chosen on the basis of their known low GPC phenotype and their lack of common ancestry. A combination of composite interval and multiple-trait quantitative trait locus (QTL) mapping approach allowed the identification of QTLs with specific impact on GPC, and those likely to depend on or be influenced by variations in grain yield and heading date. The study identified a major QTL with a 'stable' and specific effect on GPC and located near the centromeric region of chromosome 5H. The QTL accounted for ∼21% of the phenotypic variation in this trait. The allele for reduced GPC at this region was inherited from the ND11231*12 parent, with additive effect of ∼1% in GPC. Additional QTLs with minor effects (5-10% explained variation) were also detected on chromosome 2H, 4H, and 7H. The parent VB9524 was the source of the low GPC alleles at these regions.

Application of SSR markers in the construction of Australian barley genetic maps

Gary A. Ablett et al. — Tue, 09 Nov 2010 17:11:40 PST

Simple sequence repeat (SSR) or microsatellite markers were examined for polymorphisms among the parents of 12 barley mapping populations. Of 259 SSRs screened, 149 were mapped on 1 or more of the 12 doubled haploid populations studied. The relative genetic positions of the 149 mapped SSR markers on Australian varieties are presented in the form of a consensus map. A database was created based on the results of screenings of barley varieties with a series of SSR markers. Details of the markers are at: http://www.scu.edu.au/ research/ cpcg/Barley/index.php. A procedure is suggested for mapping new populations with microsatellites using this information and information available on other databases. These 12 populations have been mapped with SSR markers that act as 'anchors' for other types of genetic markers and for traits of interest. Some challenges in mapping SSRs were detailed. Multi-locus markers can cause confusion since one marker can map at different locations. Polymorphisms should be confirmed in new mapping varieties since some variation of allele size is seen in different sources of varieties of the same name, possibly due to differences in sources of germplasm. Lack of standardisation between laboratories or between analytical systems may also lead to differences in called allele sizes. SSRs proved to be adaptable to several technologies and economical, providing a preferred marker system for mapping new barley populations and to 'anchor' other types of markers.

Mapping and QTL analysis of the barley population Tallon x Kaputar

Mehmet Cakir et al. — Sun, 07 Nov 2010 18:55:22 PST

A genetic map of barley with 224 AFLP and 39 simple sequence repeat (SSR) markers was constructed using a doubled haploid (DH) mapping population from a cross between the varieties Tallon and Kaputar. Linkage groups were assigned to individual barley chromosomes using the published map locations of the SSR markers as reference points. This genetic map was used to identify markers with linkage to agronomic, disease, and quality traits in barley. The population, which comprised 65 lines, was tested in a range of environments across Australia. Quantitative trait loci (QTLs) analyses were performed using software packages MapMaker, MapManager, and Qgene. Significant associations with markers were found for several traits. Grain yield showed significant association with regions on chromosomes 2H, 3H, and 5H over a range of sites throughout Australia. Regions on chromosomes 2H and 3H explained 30% and 26% of variation in lodging, respectively. Among quality traits, diastatic power was associated with regions on chromosomes 1H, 2H, and 5H (R2 = 37%). Hot water extract was associated with a region on chromosome 6H and a marker not assigned to a chromosome (R2 = 45%). There were also environment-specific QTLs for the traits analysed. The markers identified here present an opportunity for marker assisted selection of lines for these traits in barley breeding programs.

Phylogenetics and revised taxonomy of the Australian freshwater cod genus, Maccullochella (Percichthyidae)

Catherine J. Nock et al. — Tue, 28 Sep 2010 16:46:35 PDT

Determining the phylogenetic and taxonomic relationships among allopatric populations can be difficult, especially when divergence is recent and morphology is conserved. We used mitochondrial sequence data from the control region and three protein-coding genes (1253 bp in total) and genotypes determined at 13 microsatellite loci to examine the evolutionary relationships among Australia’s largest freshwater fish, the Murray cod, Maccullochella peelii peelii, from the inland Murray–Darling Basin, and its allopatric sister taxa from coastal drainages, the eastern freshwater cod, M. ikei, and Mary River cod, M. peelii mariensis. Phylogenetic analyses provided strong support for taxon-specific clades, with a clade containing both of the eastern taxa reciprocally monophyletic to M. peelii peelii, suggesting a more recent common ancestry between M. ikei and M. peelii mariensis than between the M. peelii subspecies. This finding conflicts with the existing taxonomy and suggests that ancestral Maccullochella crossed the Great Dividing Range in the Pleistocene and subsequently diverged in eastern coastal drainages. Evidence from the present study, in combination with previous morphological and allozymatic data, demonstrates that all extant taxa are genetically and morphologically distinct. The taxonomy of Maccullochella is revised, with Mary River cod now recognised as a species, Maccullochella mariensis, a sister species to eastern freshwater cod, M. ikei. As a result of the taxonomic revision, Murray cod is M. peelii.

Evolutionary history and population genetics of the endangered eastern freshwater cod Maccullochella ikei

Catherine J. Nock et al. — Wed, 22 Sep 2010 20:05:29 PDT

Conservation genetics of the eastern freshwater cod (Maccullochella ikei)

Catherine J. Nock et al. — Wed, 22 Sep 2010 20:05:27 PDT

The evolutionary origins of the Australian Elapid snakes

Catherine J. Nock et al. — Wed, 22 Sep 2010 20:05:24 PDT

Chloroplast genome sequences from total DNA for plant identification

Catherine J. Nock et al. — Tue, 21 Sep 2010 19:47:19 PDT

Chloroplast DNA sequence data are a versatile tool for plant identification or barcoding and establishing genetic relationships among plant species. Different chloroplast loci have been utilized for use at close and distant evolutionary distances in plants, and no single locus has been identified that can distinguish between all plant species. Advances in DNA sequencing technology are providing new cost-effective options for genome comparisons on a much larger scale. Universal PCR amplification of chloroplast sequences or isolation of pure chloroplast fractions, however, are nontrivial. We now propose the analysis of chloroplast genome sequences from massively parallel sequencing (MPS) of total DNA as a simple and cost-effective option for plant barcoding, and analysis of plant relationships to guide gene discovery for biotechnology. We present chloroplast genome sequences of five grass species derived from MPS of total DNA. These data accurately established the phylogenetic relationships between the species, correcting an apparent error in the published rice sequence. The chloroplast genome may be the elusive single-locus DNA barcode for plants.

Genetic differentiation among and within three red mahoganies (series Annulares), Eucalyptus pellita, E. resinifera and E. scias (Myrtaceae)

Son Le et al. — Tue, 21 Sep 2010 19:47:15 PDT

The red mahogany group (Eucalyptus ser. Annulares Blakely) includes some of the most important commercial species (i.e. Eucalyptus urophylla S.T.Blake) worldwide for forestry in the subtropics and tropics. However, the taxonomic status of some species in this group is unclear and the relationship among and genetic structuring within some species is unresolved. The present study examined genetic variation at 13 microsatellite loci in E. pellita F.Muell., E. resinifera Smith and E. scias L.Johnson & K.Hill. Despite close geographical proximity and natural hybridisation in northern Queensland, E. resinifera and E. pellita remain genetically distinct as taxa. Within E. pellita, two genetic groups were clearly resolved, one from New Guinea and one from Queensland (Cape York Peninsula populations were not sampled). Geographic structuring was also evident in E. resinifera, with northern Queensland populations separating from those from Fraser Island southwards. Ecological factors and species disjunctions were implicated in the genetic substructuring of these two taxa because patterns of geographic variation aligned with biogeographical regions. E. scias was indistinguishable from southern E. resinifera and its three subspecies could not be resolved.

Polymorphic microsatellite loci for species of Australian freshwater cod, Maccullochella

Catherine J. Nock et al. — Tue, 21 Sep 2010 19:47:12 PDT

The Australian freshwater cod genus, Maccullochella is represented by three species: Murray cod, M. peelii peelii, eastern freshwater cod, M. ikei, and trout cod, M.macquariensis. Seven novel microsatellite loci from M. ikei and six previously published loci from M. peelii peelii were tested on wild populations of Murray, eastern and trout cod. Levels of polymorphism varied between species with 13 loci polymorphic in Murray cod, 9 in trout cod and 7 in eastern cod. Observed heterozygosities ranged from 0.053 to 0.842. This suite of microsatellite loci will facilitate future studies of the genetic status of wild and hatchery bred populations of Maccullochella.

Predicting pulp yield and pulp productivity of Eucalyptus dunnii using acoustic techniques

Carolyn A. Raymond et al. — Sun, 11 Jul 2010 17:56:22 PDT

The economics of kraft pulping are influenced by variation in wood density and chemistry, or their product, pulp productivity. The ability to predict basic density, pulp yield or pulp productivity before harvest would provide an economic advantage to the grower or processor. Acoustic velocity in green wood is correlated with both basic density and pulp yield, offering potential for rapid screening. We explored relationships between acoustic velocity, density, pulp yield and fibre length using data from Eucalyptus dunnii plantations in northern NSW, Australia. Acoustic velocity measured on logs accounted for 27% of the variation in pulp yield and 50% of variation in pulp productivity. The strong relationship between fibre length and pulp yield is proposed as a possible causal mechanism. A threshold acoustic velocity of 3.65 km s–1 was defined as the point at which logs would produce at least 250 kg of dry pulp per cubic metre of green wood. Removal of the worst 25% of logs, based on velocity, would give a 2.2% gain in pulp productivity which equates, in turn, to an additional 6.2 kg of pulp produced from every cubic metre of green wood. Keywords: acoustic properties; wood pulps; yields; wood density; fibre length; grading; segregation; Eucalyptus dunnii.

Non-destructive assessment of green density and moisture condition in plantation-grown radiata pine (Pinus radiata D. Don.) by increment core measurements

Julian Moreno Chan et al. — Sun, 11 Jul 2010 17:47:31 PDT

A novel protocol for non-destructive assessment of green density and moisture content via increment cores was validated for young (8–10 years) and mature trees (36 years) of radiata pine (Pinus radiata D. Don.). Initial procedures involved comparing 5- and 12-mm cores with fresh disks taken from young trees at breast height and felled during the winter, as well as methods for rehydrating the wood cores. Subsequently, the best method (12-mm cores) was validated with material collected in summer from both young and mature trees. The protocols developed require separate processing of sapwood and heartwood, and soaking the sapwood for 24 h to replace the moisture lost while coring. For young trees, bark-to-pith 12-mm cores accounted for between 64% and 66% of variation in green density of sapwood and between 51% and 72% of saturation percentage, as measured by destructively sampled disks. For mature trees, the average of two sides of 12-mm bark-to-bark cores accounted for 73% of variation in green density of sapwood, and 56% of saturation percentage as measured by destructive wedges. One or both sides of a bark-to-bark core accounted for between 72% and 80% of variation in whole-section green density, and between 70% and 79% of variation in sapwood percentage. The number of heartwood rings was better predicted from the average of two sides of the cores (R2 of 0.71). Whole-tree values (lower two logs) for sapwood green density and saturation were better predicted from the average of both sides of the bark-to-bark core (R2 of 0.76 and 0.57, respectively). Whole-tree values for whole-section green density could be predicted either by one side or two sides of the cores (R2 for 1 or 2 sides of 0.77 and 0.81). Finally, whole-tree sapwood volumetric percent was better predicted by the average of two sides of the cores (R2 of 0.81).