Selecting for increased barley grain size

In this study, 120–144 commercial varieties and breeding lines were assessed for grain size attributes including plump grain (>2.8 mm) and retention (>2.5 mm+>2.8 mm). Grain samples were produced from replicated trials at 25 sites across four years. Climatic conditions varied between years as well as between sites. Several of the trial sites were irrigated while the remaining were produced under dryland conditions. A number of the dryland sites suffered severe drought stress. The grain size data was analysed for genetic (G), environmental (E) and genotype by environment (G×E) interactions. All analyses included maturity as a covariate. The genetic effect on grain size was greater than environmental or maturity effects despite some sites suffering terminal moisture stress. The model was used to calculate heritability values for each site used in the study. These values ranged from 89 to 98% for plump grain and 88 to 96% for retention. The results demonstrated that removing the sources of non-heritable variation, such as maturity and field effects, can improve genetic estimates of the retention and plump grain fractions. By partitioning all variance components, and thereby having more robust estimates of genetic differences, plant breeders can have greater confidence in selecting barley genotypes which maintain large, stable grain size across a range of environments.

The genetic effective and adult census size of an Australian population of tiger prawns (Penaeus esculentus)

This study compares estimates of the census size of the spawning population with genetic estimates of effective current and long-term population size for an abundant and commercially important marine invertebrate, the brown tiger prawn (Penaeus esculentus). Our aim was to focus on the relationship between genetic effective and census size that may provide a source of information for viability analyses of naturally occurring populations. Samples were taken in 2001, 2002 and 2003 from a population on the east coast of Australia and temporal allelic variation was measured at eight polymorphic microsatellite loci. Moments-based and maximum-likelihood estimates of current genetic effective population size ranged from 797 to 1304. The mean long-term genetic effective population size was 9968. Although small for a large population, the effective population size estimates were above the threshold where genetic diversity is lost at neutral alleles through drift or inbreeding. Simulation studies correctly predicted that under these experimental conditions the genetic estimates would have non-infinite upper confidence limits and revealed they might be overestimates of the true size. We also show that estimates of mortality and variance in family size may be derived from data on average fecundity, current genetic effective and census spawning population size, assuming effective population size is equivalent to the number of breeders. This work confirms that it is feasible to obtain accurate estimates of current genetic effective population size for abundant Type III species using existing genetic marker technology.

Effect of changes in hook pattern and size on catch rate, hooking location, injury and bleeding for a number of tropical reef fish species

The Queensland Great Barrier Reef line fishery in Australia is regulated via a range of input and output controls including minimum size limits, daily catch limits and commercial catch quotas. As a result of these measures a substantial proportion of the catch is released or discarded. The fate of these released fish is uncertain, but hook-related mortality can potentially be decreased by using hooks that reduce the rates of injury, bleeding and deep hooking. There is also the potential to reduce the capture of non-target species though gear selectivity. A total of 1053 individual fish representing five target species and three non-target species were caught using six hook types including three hook patterns (non-offset circle, J and offset circle), each in two sizes (small 4/0 or 5/0 and large 8/0). Catch rates for each of the hook patterns and sizes varied between species with no consistent results for target or non-target species. When data for all of the fish species were aggregated there was a trend for larger hooks, J hooks and offset circle hooks to cause a greater number of injuries. Using larger hooks was more likely to result in bleeding, although this trend was not statistically significant. Larger hooks were also more likely to foul-hook fish or hook fish in the eye. There was a reduction in the rates of injuries and bleeding for both target and non-target species when using the smaller hook sizes. For a number of species included in our study the incidence of deep hooking decreased when using non-offset circle hooks, however, these results were not consistent for all species. Our results highlight the variability in hook performance across a range of tropical demersal finfish species. The most obvious conservation benefits for both target and non-target species arise from using smaller sized hooks and non-offset circle hooks. Fishers should be encouraged to use these hook configurations to reduce the potential for post-release mortality of released fish.

The effect of foliar sprays of the synthetic auxin 3-5-6 TPA, on fruit drop, fruit size and seed development in three lychee (Litchi chinensis) cultivars: Tai So, Fay Zee Sui and Kwai Mai Pink.

Fruit drop in lychee can cause major yield losses in Australia, the severity varying with cultivar and season. Research in China, South Africa and Israel has demonstrated the potential for synthetic auxins used as foliar sprays to reduce fruit drop in lychee. Trials were initiated in Australia to test the efficacy of the synthetic auxin, 3-5-6 Trichloro-2-phridyl-oxyacetic acid (3-5-6 TPA) at 50 ppm on the cultivars Tai So, Fay Zee Sui and Kwai Mai Pink. Results indicate that in most cases the TPA reduced natural fruit drop however the size of the fruit at the time of application affects the response and the ideal application time varies with cultivar; approximately 13 mm fruit length in 'Kwai Mai Pink', 20 mm in 'Fay Zee Sui' and 27 mm in 'Tai So'. If applied too early in 'Tai So', it caused an increase in fruit drop. The TPA was most effective when natural fruit drop was high, reducing fruit drop from 74.7 to 34.9% in 'Kwai Mai Pink' and least effective when natural fruit drop was low. An increase in the percentage of fruit with poorly developed (chicken tongue) seed and slightly larger fruit size was also observed in treated trees.

Optimising between and within family selection for harvest weight in prawns with restricted harvest size.

Manual grading of prawns restricts the number that can be harvested. A restricted harvest size places a limit on the opposing within family and between family sources of selection pressure. A simulation study with inbreeding constrained at 0.5% per generation, a harvest size of 2000, heritability of 0.3, common family environmental effect of 0.1, indicates that maximum response to selection could be achieved with as few as 40 families. Increasing the number of families above 80 may reduce total selection response. It is important to be aware that increasing the number of families may not always yield a greater genetic response.

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

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.

Uncertainty in length measurements of live coral trout: implications for compliance and enforcement of minimum legal size limits.

Report on evidence of shrinkage of live coral trout during professional fishing operations on the Great Barrier Reef in 2000. Excel data includes the following fields: Column A. Fish (fish number from 1 -24) Column B. Bin (1-8, container the fish was held in during the experiment) Column C. Measure (1-7, number of the measurement of each fish) Column D. Observer (1 or 2, making the measurement) Column E. Time 2 Column F. Time (time of the day the measurement was made) Column G. FL (Fork Length) Column H. TL (Total Length) Column I. Difference (difference in length between measures) Column J. Order Column K. Temperature (surface water temp under the boat)

Raw data for "Linkage disequilibrium estimation of effective population size with immigrants from divergent populations: a case study on Spanish mackerel (Scomberomorus commerson)."

Abstract of Macbeth, G. M., Broderick, D., Buckworth, R. & Ovenden, J. R. (In press, Feb 2013). Linkage disequilibrium estimation of effective population size with immigrants from divergent populations: a case study on Spanish mackerel (Scomberomorus commerson). G3: Genes, Genomes and Genetics. Estimates of genetic effective population size (Ne) using molecular markers are a potentially useful tool for the management of endangered through to commercial species. But, pitfalls are predicted when the effective size is large, as estimates require large numbers of samples from wild populations for statistical validity. Our simulations showed that linkage disequilibrium estimates of Ne up to 10,000 with finite confidence limits can be achieved with sample sizes around 5000. This was deduced from empirical allele frequencies of seven polymorphic microsatellite loci in a commercially harvested fisheries species, the narrow barred Spanish mackerel (Scomberomorus commerson). As expected, the smallest standard deviation of Ne estimates occurred when low frequency alleles were excluded. Additional simulations indicated that the linkage disequilibrium method was sensitive to small numbers of genotypes from cryptic species or conspecific immigrants. A correspondence analysis algorithm was developed to detect and remove outlier genotypes that could possibly be inadvertently sampled from cryptic species or non-breeding immigrants from genetically separate populations. Simulations demonstrated the value of this approach in Spanish mackerel data. When putative immigrants were removed from the empirical data, 95% of the Ne estimates from jacknife resampling were above 24,000.

Patterns of seed bank and size asymmetry of plant growth across varying sites in the invasive Lantana camara L. (Verbenaceae)

Lantana camara L. (Verbenaceae) is a weed of great significance in Australia and worldwide, but little is known about connections among components of its life history. We document over a 3-year period, the links between L. camara seed-bank dynamics and its above-ground growth, including size asymmetry in four land-use types (a farm, a hoop pine plantation and two open eucalypt forests) invaded by the weed near Brisbane, Queensland Australia. Seed-bank populations varied appreciably across sites and in response to rainfall and control measures, and they were higher (~1,000 seeds/m2) when annual rainfall was 15-30 % below the long-term yearly average. Fire reduced seed-bank populations but not the proportion germinating (6-8 %). Nearly a quarter of fresh seeds remain germinable after 3 years of soil burial. For small seedlings (<10 cm high), the expected trade-offs in two life-history traits-survival and growth-did not apply; rather the observed positive association between these two traits, coupled with a persistent seed-bank population could contribute to the invasiveness of the plant. Relationships between absolute growth rate and initial plant size (crown volume) were positively linear, suggesting that most populations are still at varying stages of the exponential phase of the sigmoid growth; this trend also suggests that at most sites and despite increasing stand density and limiting environmental resources of light and soil moisture, lantana growth is inversely size asymmetric. From the observed changes in measures of plant size inequality, asymmetric competition appeared limited in all the infestations surveyed. © 2013 Crown Copyright as represented by: Department of Agriculture, Fisheries and Forestry, Australia.

Effect of Time of Planting and Plant Size on the Productivity of ‘Festival’ and ‘Florida Fortuna’ Strawberry Plants in a Subtropical Environment

The effect of time of planting and plant size on the performance of ‘Festival’ and ‘Florida Fortuna’ strawberry (Fragaria ×ananassa) plants was studied at Nambour in southeastern Queensland, Australia, over 2 years. The main objective of the work was to determine whether small plants yielded proportionally less than large plants as planting was delayed. First, bare-rooted transplants of ‘Festival’ were divided into small (crown diameters ranging from 6 to 10 mm) or large plants (10 to 17 mm) and planted in late March, mid-April, or late April. Second, transplants of ‘Florida Fortuna’ were divided into small (5 to 8 mm) or large plants (8 to 17 mm) and planted in early April, mid-April, or early May. The early planting for each cultivar corresponded with the time that the transplants are first available from commercial strawberry nurseries. Yields were generally greater in plants planted in late March/early April compared with plants planted later. Differences in yield between the small and large plants were consistent across the different times of planting, with the small plants always having lower yields. Small transplants are an issue for the productivity of strawberry fields in this environment whether they are planted early or late. Producers should consider paying a premium for large transplants delivered early in the season.

NEESTIMATOR v2: re-implementation of software for the estimation of contemporary effective population size (N-e) from genetic data

NeEstimator v2 is a completely revised and updated implementation of software that produces estimates of contemporary effective population size, using several different methods and a single input file. NeEstimator v2 includes three single-sample estimators (updated versions of the linkage disequilibrium and heterozygote-excess methods, and a new method based on molecular coancestry), as well as the two-sample (moment-based temporal) method. New features include the following: (i) an improved method for accounting for missing data; (ii) options for screening out rare alleles; (iii) confidence intervals for all methods; (iv) the ability to analyse data sets with large numbers of genetic markers (10000 or more); (v) options for batch processing large numbers of different data sets, which will facilitate cross-method comparisons using simulated data; and (vi) correction for temporal estimates when individuals sampled are not removed from the population (Plan I sampling). The user is given considerable control over input data and composition, and format of output files. The freely available software has a new JAVA interface and runs under MacOS, Linux and Windows.

Principles and guidelines for managing cattle grazing in the grazing lands of northern Australia: stocking rates, pasture resting, prescribed fire, paddock size and water points - a review

Beef cattle grazing is the dominant land use in the extensive tropical and sub-tropical rangelands of northern Australia. Despite the considerable knowledge on land and herd management gained from both research and practical experience, the adoption of improved management is limited by an inability to predict how changes in practices and combinations of practices will affect cattle production, economic returns and resource condition. To address these issues, past Australian and international research relating to four management factors that affect productivity and resource condition was reviewed in order to identify key management principles. The four management factors considered were stocking rates, pasture resting, prescribed fire, and fencing and water point development for managing grazing distribution. Four management principles for sound grazing management in northern Australia were formulated as follows: (1) manage stocking rates to meet goals for livestock production and land condition; (2) rest pastures to maintain them in good condition or to restore them from poor condition to increase pasture productivity; (3) devise and apply fire regimes that enhance the condition of grazing land and livestock productivity while minimising undesirable impacts; and (4) use fencing and water points to manipulate grazing distribution. Each principle is supported by several more specific guidelines. These principles and guidelines, and the supporting research on which they are based, are presented.

Improved estimation of size-transition matrices using tag-recapture data

We derive a new method for determining size-transition matrices (STMs) that eliminates probabilities of negative growth and accounts for individual variability. STMs are an important part of size-structured models, which are used in the stock assessment of aquatic species. The elements of STMs represent the probability of growth from one size class to another, given a time step. The growth increment over this time step can be modelled with a variety of methods, but when a population construct is assumed for the underlying growth model, the resulting STM may contain entries that predict negative growth. To solve this problem, we use a maximum likelihood method that incorporates individual variability in the asymptotic length, relative age at tagging, and measurement error to obtain von Bertalanffy growth model parameter estimates. The statistical moments for the future length given an individual’s previous length measurement and time at liberty are then derived. We moment match the true conditional distributions with skewed-normal distributions and use these to accurately estimate the elements of the STMs. The method is investigated with simulated tag–recapture data and tag–recapture data gathered from the Australian eastern king prawn (Melicertus plebejus).

Plot size matters: interference from intergenotypic competition in plant phenotyping studies

Genetic and physiological studies often comprise genotypes diverse in vigour, size and flowering time. This can make the phenotyping of complex traits challenging, particularly those associated with canopy development, biomass and yield, as the environment of one genotype can be influenced by a neighbouring genotype. Limited seed and space may encourage field assessment in single, spaced rows or in small, unbordered plots, whereas the convenience of a controlled environment or greenhouse makes pot studies tempting. However, the relevance of such growing conditions to commercial field-grown crops is unclear and often doubtful. Competition for water, light and nutrients necessary for canopy growth will be variable where immediate neighbours are genetically different, particularly under stress conditions, where competition for resources and influence on productivity is greatest. Small hills and rod-rows maximise the potential for intergenotypic competition that is not relevant to a crop’s performance in monocultures. Response to resource availability will typically vary among diverse genotypes to alter genotype ranking and reduce heritability for all growth-related traits, with the possible exception of harvest index. Validation of pot experiments to performance in canopies in the field is essential, whereas the planting of multirow plots and the simple exclusion of plot borders at harvest will increase experimental precision and confidence in genotype performance in target environments.