Applications of pedigree-based genome mapping in wheat and barley breeding programs.

The aim of the pedigree-based genome mapping project is to investigate and develop systems for implementing marker assisted selection to improve the efficiency of selection and increase the rate of genetic gain in breeding programs. Pedigree-based whole genome marker application provides a vehicle for incorporating marker technologies into applied breeding programs by bridging the gap between marker-trait association and marker implementation. We report on the development of protocols for implementation of pedigree-based whole genome marker analysis in breeding programs within the Australian northern winter cereals region. Examples of applications from the Queensland DPI&F wheat and barley breeding programs are provided, commenting on the use of microsatellites and other types of molecular markers for routine genomic analysis, the integration of genotypic, phenotypic and pedigree information for targeted wheat and barley lines, the genomic impacts of strong selection pressure in case study pedigrees, and directions for future pedigree-based marker development and analysis.

Mapping species differences for adventitious rooting in a Corymbia torelliana x Corymbia citriodora subspecies variegata hybrid

Quantitative trait loci (QTL) detection was carried out for adventitious rooting and associated propagation traits in a second-generation outbred Corymbia torelliana x Corymbia citriodora subspecies variegata hybrid family (n=186). The parental species of this cross are divergent in their capacity to develop roots adventitiously on stem cuttings and their propensity to form lignotubers. For the ten traits studied, there was one or two QTL detected, with some QTL explaining large amounts of phenotypic variation (e.g. 66% for one QTL for percentage rooting), suggesting that major effects influence rooting in this cross. Collocation of QTL for many strongly genetically correlated rooting traits to a single region on linkage group 12 suggested pleiotropy. A three locus model was most parsimonious for linkage group 12, however, as differences in QTL position and lower genetic correlations suggested separate loci for each of the traits of shoot production and root initiation. Species differences were thought to be the major source of phenotypic variation for some rooting rate and root quality traits because of the major QTL effects and up to 59-fold larger homospecific deviations (attributed to species differences) relative to heterospecific deviations (attributed to standing variation within species) evident at some QTL for these traits. A large homospecific/heterospecific ratio at major QTL suggested that the gene action evident in one cross may be indicative of gene action more broadly in hybrids between these species for some traits.

Development of hazard site surveillance programs for forest invasive species: A case study from Brisbane, Australia

Hazard site surveillance is a system for post-border detection of new pest incursions, targeting sites that are considered potentially at high risk of such introductions. Globalisation, increased volumes of containerised freight and competition for space at domestic ports means that goods are increasingly being first opened at premises some distance from the port of entry, thus dispersing risk away from the main inspection point. Hazard site surveillance acts as a backstop to border control to ensure that new incursions are detected sufficiently early to allow the full range of management options, including eradication and containment, to be considered. This is particularly important for some of the more cryptic forest pests whose presence in a forest often is not discovered until populations are already high and the pest is well established. General requirements for a hazard site surveillance program are discussed using a program developed in Brisbane, Australia, in 2006 as a case study. Some early results from the Brisbane program are presented. In total 67 species and 5757 individuals of wood-boring beetles have been trapped and identified during the program to date. Scolytines are the most abundant taxa, making up 83% of the catch. No new exotics have been trapped but 19 of the species and 60% of all specimens caught are exotics that are already established in Australia.

Harmonising GAP programs for fresh produce in ASEAN region

Many forces are driving the global demand for assurance that fruit and vegetables are safe to eat and of the right quality, and are produced and handled in a manner that does not cause harm to the environment and the health, safety and welfare of workers. The impact of these driving forces is that retailer requirements for suppliers to comply with Good Agricultural Practice (GAP) is increasing and governments are strengthening legal requirements for food safety, environmental protection, and worker health, safety and welfare. The implementation of GAP programs currently within the ASEAN (Association of South East Asian Nations) region varies, with some countries having government certified systems and others beginning the journey with awareness programs for farmers. Under a project funded by the ASEAN Australia Development Cooperation Program, a standard for ASEAN GAP has been developed to harmonise GAP Programs in the region. The goal is to facilitate trade between ASEAN countries and to global markets, improve viability for farmers, and help sustain a safe food supply and the environment. ASEAN GAP is an umbrella standard that individual member countries will benchmark their national programs against to gain equivalence. The scope of ASEAN GAP covers the production, harvesting and postharvest handling of fresh fruit and vegetables on farm and postharvest handling in locations where produce is packed for sale. ASEAN GAP consists of four modules covering food safety, environmental management, worker health, safety and welfare, and produce quality. Each module can be used alone or in combination with other modules. This enables progressive implementation of ASEAN GAP, module by module based on individual country priorities.

ShadowBoxer and LocusEater: programs to optimise experimental design and multiplexing strategies for genetic mark-recapture

Genetic mark–recapture requires efficient methods of uniquely identifying individuals. 'Shadows' (individuals with the same genotype at the selected loci) become more likely with increasing sample size, and bias harvest rate estimates. Finding loci is costly, but better loci reduce analysis costs and improve power. Optimal microsatellite panels minimize shadows, but panel design is a complex optimization process. locuseater and shadowboxer permit power and cost analysis of this process and automate some aspects, by simulating the entire experiment from panel design to harvest rate estimation.

Use of part records in Merino breeding programs - The inheritance of wool growth and fibre traits during different times of the year to determine their value in Merino breeding programs

Fibre diameter can vary dramatically along a wool staple, especially in the Mediterranean environment of southern Australia with its dry summers and abundance of green feed in spring. Other research results have shown a very low phenotypic correlation between fibre diameter grown between seasons. Many breeders use short staples to measure fibre diameter for breeding purposes and also to promote animals for sale. The effectiveness of this practice is determined by the relative response to selection by measuring fibre traits on a full 12 months wool staple as compared to measuring them only on part of a staple. If a high genetic correlation exists between the part record and the full record, then using part records may be acceptable to identify genetically superior animals. No information is available on the effectiveness of part records. This paper investigated whether wool growth and fibre diameter traits of Merino wool grown at different times of the year in a Mediterranean environment, are genetically the same trait, respectively. The work was carried out on about 7 dyebanded wool sections/animal.year, on ewes from weaning to hogget age, in the Katanning Merino resource flocks over 6 years. Relative clean wool growth of the different sections had very low heritability estimates of less than 0.10, and they were phenotypically and genetically poorly correlated with 6 or 12 months wool growth. This indicates that part record measurement of clean wool growth of these sections will be ineffective as indirect selection criteria to improve wool growth genetically. Staple length growth as measured by the length between dyebands, would be more effective with heritability estimates of between 0.20 and 0.30. However, these measurements were shown to have a low genetic correlation with wool grown for 12 months which implies that these staple length measurements would only be half as efficient as the wool weight for 6 or 12 months to improve total clean wool weight. Heritability estimates of fibre diameter, coefficient of variation of fibre diameter and fibre curvature were relatively high and were genetically and phenotypically highly correlated across sections. High positive phenotypic and genetic correlations were also found between fibre diameter, coefficient of variation of fibre diameter and fibre curvature of the different sections and similar measurements for wool grown over 6 or 12 months. Coefficient of variation of fibre diameter of the sections also had a moderate negative phenotypic and genetic correlation with staple strength of wool staples grown over 6 months indicating that coefficient of variation of fibre diameter of any section would be as good an indirect selection criterion to improve stable strength as coefficient of variation of fibre diameter for wool grown over 6 or 12 months. The results indicate that fibre diameter, coefficient of variation of fibre diameter and fibre curvature of wool grown over short periods of time have virtually the same heritability as that of wool grown over 12 months, and that the genetic correlation between fibre diameter, coefficient of variation of fibre diameter and fibre curvature on part and on full records is very high (rg > 0.85). This indicates that fibre diameter, coefficient of variation of fibre diameter and fibre curvature on part records can be used as selection criteria to improve these traits. However, part records of greasy and clean wool growth would be much less efficient than fleece weight for wool grown over 6 or 12 months because of the low heritability of part records and the low genetic correlation between these traits on part records and on wool grown for 12 months.

Evaluating progress in weed eradication programs

Evaluating progress towards eradication is critically important because weed eradication programs are very expensive and may take more than 10 years to complete. The degree of confidence that can be placed in any measure of eradication progress is a function of the effort that has been invested in finding new infestations and in monitoring known infestations. Determining eradication endpoints is particularly difficult, since plants may be extremely difficult to detect when at low densities and it is virtually impossible to demonstrate seed bank exhaustion. Recent work suggests that an economic approach to this problem should be adopted. They propose some rules of thumb to determine whether to continue an eradication program or switch to an alternative management strategy.

Evaluation of weed eradication programs: containment and extirpation

Weed eradication programs often require 10 years or more to achieve their objective. It is important that progress is evaluated on a regular basis so that programs that are 'on track' can be distinguished from those that are unlikely to succeed. Earlier research has addressed conformity of eradication programs to the delimitation criterion. In this paper evaluation in relation to the containment and extirpation criteria is considered. Because strong evidence of containment failure (i.e. spread from infestations targeted for eradication) is difficult to obtain, it generally will not be practicable to evaluate how effective eradication programs are at containing the target species. However, chronic failure of containment will be reflected in sustained increases in cumulative infested area and thus a failure to delimit a weed invasion. Evaluating the degree of conformity to the delimitation and extirpation criteria is therefore sufficient to give an appraisal of progress towards the eradication objective. A significant step towards eradication occurs when a weed is no longer readily detectable at an infested site, signalling entry to the monitoring phase. This transition will occur more quickly if reproduction is prevented consistently. Where an invasion consists of multiple infestations, the monitoring profile (frequency distribution of time since detection) provides a summary of the overall effectiveness of the eradication program in meeting the extirpation criterion. Eradication is generally claimed when the target species has not been detected for a period equal to or greater than its seed longevity, although there is often considerable uncertainty in estimates of the latter. Recently developed methods, which take into consideration the cost of continued monitoring vs. the potential cost of damage should a weed escape owing to premature cessation of an eradication program, can assist managers to decide when to terminate weed eradication programs.

A review of Australian classical biological control of weeds programs and research activities over the past 12 years

Considerable progress has been made towards the successful classical biological control of many of Australia’s exotic weeds over the past decade. Some 43 new arthropod or pathogen agents were released in 19 projects. Effective biological control was achieved in several projects with the outstanding successes being the control of rubber vine, Cryptostegia grandiflora, and bridal creeper, Asparagus asparagoides. Significant developments also occurred in target prioritization, procedures for target and agent approval, funding, infrastructure and cooperation between agencies. Scientific developments included greater emphasis on climate matching, plant and agent phylogeny, molecular diagnostics, agent prioritization and agent evaluation.

Ageing delays the cellular stages of adventitious root formation in pine.

Vegetative propagation programs internationally are affected by the significant decline of rooting success as trees mature. This study compared the cellular stages of root formation in stem cuttings from 15-week-old (juvenile) and 9-y-old (mature) stock plants of the slash x Caribbean pine hybrid (Pinus elliottii var. elliottii x P. caribaea van hondurensis). The cellular stages of root formation were the same in both juvenile and mature cuttings, beginning with cell divisions of the vascular cambium forming callus tissue. Within the callus, tracheids differentiated and elongated to form root primordia. Roots in juvenile cuttings developed faster than those in mature cuttings and the juvenile cuttings had a much higher rooting percent at the end of the study (92% and 26% respectively). Cuttings of the two juvenile genotypes had more primary roots (5.5 and 3.3) than the three mature genotypes (0.96, 0.18 and 0.07). The roots of juvenile cuttings were more evenly distributed around the basal circumference when compared with those on cuttings from the mature genotypes. Further work is needed to improve understanding of physiological changes with maturation so that the rooting success and the speed of development in cuttings from mature stock plants can be optimised, hence improving genetic gain.

Cynodon transvaalensis x Cynodon dactylon Hybrid Green Couch Grass, Hybrid Bermuda Grass 'MS-Supreme'

Ploidy: triploid interspecific hybrid (3n = 27 chromosomes). Plant: habit prostrate, creeping, type mat-forming, height very short, longevity perennial, spreading laterally by stolons and rhizomes. Stolon: compound nodes with up to 3 leaves, internode length very short, internode thickness very thin, colour grey-brown (RHS N199A) when exposed to sunlight. Culms: length very short. Leaf blade: shape linear-triangular, length short, width narrow, colour dark green (RHS 137B). Ligule: dense row of short white hairs. Inflorescence: digitate with 3(-4) very short spicate racemes, peduncle very short. (All RHS colour chart numbers refer to 2001 edition.) PBR Certificate Number 2641, Application Number 2002/305, granted 24 February 2005.

Cynodon transvaalensis x Cynodon dactylon, Hybrid Green Couch Grass, Hybrid Bermuda Grass 'TL2'

Spontaneous mutation: In 1996, vegetative material (later designated ‘TL2’) taken from a disease resistant mutant plant on the fifteenth green at Novotel Palm Cove resort course near Cairns was included an on-going program of selection and testing of promising ‘Tifgreen’ mutants by Tropical Lawns Pty Ltd. Selection criteria: healthy vigorous growth during the tropical wet season, dense fine-textured appearance under close mowing, and dark green leaves. In subsequent trials, ‘TL2’ was identified as the outstanding plant among selections of mutant ‘Tifgreen’ genotypes from other north Queensland sites in terms of colour, texture and density for greens use. Propagation: vegetative. Breeder: Terry Anderlini, Gordonvale, QLD. PBR Certificate Number 2639, Application Number 2002/268, granted 24 February 2005.

Cynodon transvaalensis x Cynodon dactylon, Hybrid Green Couch Grass, Hybrid Bermuda Grass 'P18'

‘P18’ was first produced in 1992 and is a mutant genotype obtained from a hybrid Bermudagrass line believed to be ‘Tifdwarf’, which was grown in a greenhouse owned by H&H Seed Company in Yuma, Arizona. ‘P18’ was selected for its extremely fine leaf texture, its high shoot density under close mowing, its rapid growth rate, and its uniform dark green colour, and was subsequently evaluated for these traits and characteristics. Propagation: vegetative. Breeder: Howard E. Kaewer, Eden Prairie, MN, USA. PBR Application Number 2007/179, Certificate Number 3567, granted 13 August 2007.

Cynodon transvaalensis x Cynodon dactylon, Hybrid Green Couch Grass, Hybrid Bermuda Grass 'AGRD'

‘AGRD’ was selected by the breeder, Dr Warren Hunt, from a variant area of winter active turf (probably ‘Tifway’ or ‘Tifgreen’) on a Hong Kong Golf Course in Apr 1996. A selection of this material was imported through vegetative quarantine to New Zealand for evaluation. Following a favourable assessment of its potential as a warm-season turfgrass variety under New Zealand conditions made based on its superior comparative performance relative to other Cynodon accessions in glasshouse and field trials, the New Zealand registered variety ‘Grasslands AgRiDark’ was released in 1999. PBR Certificate Number 3716, Application Number 2004/299, granted 20 January 2009.

Salinity tolerance of twelve hybrid Bermudagrass (Cynodon Dactylon (L.) Pers. x C. Transvaalensis Burtt Davy) genotypes

Salinity is an increasingly important issue in both rural and urban areas throughout much of Australia. The use of recycled/reclaimed water and other sources of poorer quality water to irrigate turf is also increasing. Hybrid Bermudagrass (Cynodon dactylon (L.) Pers. x C. transvaalensis Burtt Davey), together with the parent species C. dactylon, are amongst the most widely used warm-season turf grass groups. Twelve hybrid Bermudagrass genotypes and one accession each of Bermudagrass (C. dactylon), African Bermudagrass (C. transvaalensis) and seashore paspalum (Paspalum vaginatum Sw.) were grown in a glasshouse experiment with six different salinity treatments applied hydroponically through the irrigation water (ECW = <0.1, 6, 12, 18, 24 or 30 dSm-1) in a flood-and-drain system. Each pot was clipped progressively at 2-weekly intervals over the 12-week experimental period to determine dry matter production; leaf firing was rated visually on 3 occasions during the last 6 weeks of salinity treatment. At the end of the experiment, dry weights of roots and crowns below clipping height were also determined. Clipping yields declined sharply after about the first 6 weeks of salinity treatment, but then remained stable at substantially lower levels of dry matter production from weeks 8 to 12. Growth data over this final 4-week experimental period is therefore a more accurate guide to the relative salinity tolerance of the 15 entries than data from the preceding 8 weeks. Based on these data, the 12 hybrid Bermudagrass genotypes showed moderate salinity tolerance, with FloraDwarfM, 'Champion Dwarf', NovotekM and 'TifEagle' ranking as the most salt tolerant and 'Patriot', 'Santa Ana', 'Tifgreen' and TifSport M the least tolerant within the hybrid group. Nevertheless, Santa Ana, for example, maintained relatively strong root growth as salinity increased, and so may show better salt tolerance in practice than predicted from the growth data alone. The 12 hybrid Bermudagrasses and the single African Bermudagrass genotype were all ranked above FloraTeXM Bermudagrass in terms of salt tolerance. However, seashore paspalum, which is widely acknowledged as a halophytic species showing high salt tolerance, ranked well above all 14 Cynodon genotypes in terms of salinity tolerance.