The use of genetic correlations to evaluate associations between SNP markers and quantitative traits

Open-pollinated progeny of Corymbia citriodora established in replicated field trials were assessed for stem diameter, wood density, and pulp yield prior to genotyping single nucleotide polymorphisms (SNP) and testing the significance of associations between markers and assessment traits. Multiple individuals within each family were genotyped and phenotyped, which facilitated a comparison of standard association testing methods and an alternative method developed to relate markers to additive genetic effects. Narrow-sense heritability estimates indicated there was significant additive genetic variance within this population for assessment traits ( h ˆ 2 =0.28to0.44 ) and genetic correlations between the three traits were negligible to moderate (r G = 0.08 to 0.50). The significance of association tests (p values) were compared for four different analyses based on two different approaches: (1) two software packages were used to fit standard univariate mixed models that include SNP-fixed effects, (2) bivariate and multivariate mixed models including each SNP as an additional selection trait were used. Within either the univariate or multivariate approach, correlations between the tests of significance approached +1; however, correspondence between the two approaches was less strong, although between-approach correlations remained significantly positive. Similar SNP markers would be selected using multivariate analyses and standard marker-trait association methods, where the former facilitates integration into the existing genetic analysis systems of applied breeding programs and may be used with either single markers or indices of markers created with genomic selection processes.

Career adaptability predicts subjective career success above and beyond personality traits and core self-evaluations

The Career Adapt-Abilities Scale (CAAS) measures career adaptability as a higher-order construct that integrates four psychosocial resources of employees for managing their career development: concern, control, curiosity, and confidence. The goal of the present study was to investigate the validity of the CAAS with regard to its effects on two indicators of subjective career success (career satisfaction and self-rated career performance) above and beyond the effects of employees' Big Five personality traits and core self-evaluations. Data came from a large and heterogeneous sample of employees in Australia (N=1723). Results showed that overall career adaptability positively predicted career satisfaction and self-rated career performance above and beyond the Big Five personality traits and core self-evaluations. In addition, concern and confidence positively predicted the two indicators of subjective career success. The findings provide further support for the incremental validity of the CAAS.

QTL associated with barley (Hordeum vulgare) feed quality traits measured through in situ digestion

Barley (Hordeum vulgare) is a major feed source for the intensive livestock industry. Competitiveness against other cereal grains depends largely on the price per unit of expressed feed quality. The traits which contribute to feed quality in barley are largely quantitative in nature but little is known about their genetic control. A study to identify the quantitative trait loci (QTLs) associated with feed quality was performed using a F6-derived recombinant inbred barley population. Samples from each line were incubated in the rumen of fistulated cattle, recovered, washed and dried for determination of in situ dry matter digestibility. Additionally, both pre- and post-digestion samples were analysed to quantify the content of key quality components relating to acid detergent fibre, total starch and protein. The data was used to identify trait-associated QTLs. Genetic analysis identified significant QTLs on chromosomes 2H, 5H and 7H. Genetic markers linked to these QTL should provide an effective tool for the selection and improvement of feed barley in the future.

Genetic correlations of young bull reproductive traits and heifer puberty traits with female reproductive performance in two tropical beef genotypes in northern Australia

Genetic correlations of young bull and heifer puberty traits with measures of early and lifetime female reproductive performance were estimated in two tropical beef cattle genotypes. Heifer age at puberty was highly (r(g) = -0.71 +/- 0.11) and moderately (r(g) = -0.40 +/- 0.20) genetically correlated with pregnancy rate at first annual mating (mating 1) and lifetime annual calving rate, respectively in Brahman (BRAH). In Tropical Composite (TCOMP), heifer age at puberty was highly correlated with reproductive outcomes from the first re-breed (mating 2), mainly due to its association with lactation anoestrous interval (r(g) = 0.72 +/- 0.17). Scrotal circumference were correlated with heifer age at puberty (r(g) = -0.41 +/- 0.11 at 12 months in BRAH; -0.30 +/- 0.13 at 6 months in TCOMP) but correlations were lower with later female reproduction traits. Bull insulin-like growth factor-I was correlated with heifer age at puberty (r(g) = -0.56 +/- 0.11 in BRAH; -0.43 +/- 0.11 in TCOMP) and blood luteinising hormone concentration was moderately correlated with lactation anoestrous interval (r(g) = 0.59 +/- 0.23) in TCOMP. Semen quality traits, including mass activity, motility and percent normal sperm were genetically correlated with lactation anoestrus and female lifetime female reproductive traits in both genotypes, but the magnitudes of the relationships differed with bull age at measurement. Preputial eversion and sheath scores were genetically associated with lifetime calving and weaning rates in both genotypes. Several of the early-in-life male and female measures examined were moderately to highly genetically correlated with early and lifetime female reproduction traits and may be useful as indirect selection criteria for improving female reproduction in tropical breeds in northern Australia.

Strangers in a strange land: do life history traits differ for alien and native colonisers of novel environments?

Do alien invasive species exhibit life history characteristics that are similar to those of native species that have become pests in their continent of origin? We compared eucalypt specialists that have become pests in Australian plantations (natives) to those that have established overseas (aliens) using 13 life history traits and found that although traits that support rapid population build-up were shared, overall, aliens and native colonisers differed significantly. Distance from source (New Zealand vs. other) had no significant effect, but species that established more than 50 years ago exhibited different life history traits from those that established within the last 50 years, possibly because of more effective quarantine. Native and alien eucalypt insect invaders differed predominantly in traits that facilitate long-distance movement (pathway traits), compared to traits that facilitate establishment and spread. Aliens had longer adult flight seasons, were smaller and more closely host-associated (cryptic eggs and larvae), had lower incidence of diapause (i.e. were more seasonally plastic) and more generations per year than natives. Thus, studies of species invasive within their country of origin can shed light on alien invasions.

Coordination and plasticity in leaf anatomical traits of invasive and native vine species

Premise of the study: Plant invasiveness can be promoted by higher values of adaptive traits (e.g., photosynthetic capacity, biomass accumulation), greater plasticity and coordination of these traits, and by higher and positive relative influence of these functionalities on fitness, such as increasing reproductive output. However, the data set for this premise rarely includes linkages between epidermal–stomatal traits, leaf internal anatomy, and physiological performance.• Methods: Three ecological pairs of invasive vs. noninvasive (native) woody vine species of South-East Queensland, Australia were investigated for trait differences in leaf morphology and anatomy under varying light intensity. The linkages of these traits with physiological performance (e.g., water-use efficiency, photosynthesis, and leaf construction cost) and plant adaptive traits of specific leaf area, biomass, and relative growth rates were also explored.• Key results: Except for stomatal size, mean leaf anatomical traits differed significantly between the two groups. Plasticity of traits and, to a very limited extent, their phenotypic integration were higher in the invasive relative to the native species. ANOVA, ordination, and analysis of similarity suggest that for leaf morphology and anatomy, the three functional strategies contribute to the differences between the two groups in the order phenotypic plasticity > trait means > phenotypic integration.• Conclusions: The linkages demonstrated in the study between stomatal complex/gross anatomy and physiology are scarce in the ecological literature of plant invasiveness, but the findings suggest that leaf anatomical traits need to be considered routinely as part of weed species assessment and in the worldwide leaf economic spectrum.

Phenotyping novel stay-green traits to capture genetic variation in senescence dynamics

Stay-green plants retain green leaves longer after anthesis and can have improved yield, particularly under water limitation. As senescence is a dynamic process, genotypes with different senescence patterns may exhibit similar final normalised difference vegetative index (NDVI). By monitoring NDVI from as early as awn emergence to maturity, we demonstrate that analysing senescence dynamics improves insight into genotypic stay-green variation. A senescence evaluation tool was developed to fit a logistic function to NDVI data and used to analyse data from three environments for a wheat (Triticum aestivum L.) population whose lines contrast for stay-green. Key stay-green traits were estimated including, maximum NDVI, senescence rate and a trait integrating NDVI variation after anthesis, as well as the timing from anthesis to onset, midpoint and conclusion of senescence. The integrative trait and the timing to onset and mid-senescence exhibited high positive correlations with yield and a high heritability in the three studied environments. Senescence rate was correlated with yield in some environments, whereas maximum NDVI was associated with yield in a drought-stressed environment. Where resources preclude frequent measurements, we found that NDVI measurements may be restricted to the period of rapid senescence, but caution is required when dealing with lines of different phenology. In contrast, regular monitoring during the whole period after flowering allows the estimation of senescence dynamics traits that may be reliably compared across genotypes and environments. We anticipate that selection for stay-green traits will enhance genetic progress towards high-yielding, stay-green germplasm.

Modelling the effect of plant water use traits on yield and stay-green expression in sorghum

Post-rainy sorghum (Sorghum bicolor (L.) Moench) production underpins the livelihood of millions in the semiarid tropics, where the crop is affected by drought. Drought scenarios have been classified and quantified using crop simulation. In this report, variation in traits that hypothetically contribute to drought adaptation (plant growth dynamics, canopy and root water conducting capacity, drought stress responses) were virtually introgressed into the most common post-rainy sorghum genotype, and the influence of these traits on plant growth, development, and grain and stover yield were simulated across different scenarios. Limited transpiration rates under high vapour pressure deficit had the highest positive effect on production, especially combined with enhanced water extraction capacity at the root level. Variability in leaf development (smaller canopy size, later plant vigour or increased leaf appearance rate) also increased grain yield under severe drought, although it caused a stover yield trade-off under milder stress. Although the leaf development response to soil drying varied, this trait had only a modest benefit on crop production across all stress scenarios. Closer dissection of the model outputs showed that under water limitation, grain yield was largely determined by the amount of water availability after anthesis, and this relationship became closer with stress severity. All traits investigated increased water availability after anthesis and caused a delay in leaf senescence and led to a ‘stay-green’ phenotype. In conclusion, we showed that breeding success remained highly probabilistic; maximum resilience and economic benefits depended on drought frequency. Maximum potential could be explored by specific combinations of traits.

Agronomic indices, growth, yield-contributing traits, and yield of dry-seeded rice under varying herbicides

Dry-seeded rice (DSR) is an emerging resource-conserving technology in many Asian countries, but weeds remain the major threat to the production of DSR systems. A field study was conducted in 2012 and 2013 at the International Rice Research Institute (IRRI), Los Baños, Philippines, to evaluate the performance of sole and sequential applications of preemergence (oxadiazon and pendimethalin), early postemergence (butachlor + propanil and thiobencarb + 2,4-D), and late postemergence herbicides (bispyribac-sodium and fenoxaprop + ethoxysulfuron) with different modes of action in comparison to manual weeding in DSR. The sequential applications of all preemergence and postemergence herbicides reduced weed density and biomass by 80–100% compared to the nontreated plots. The sole application of postemergence herbicides reduced weed density by only 44–54% and weed biomass by 51–61%, whereas oxadiazon alone reduced weed density and biomass by 96–100%. All herbicide treatments and manual weeding significantly affected tiller number, biomass, crop growth rate, agronomic indices, yield-contributing parameters (panicle density and filled grains), and yield (biological and grain) of rice. The highest grain yield was obtained in the manually weeded plots (5.9–6.1 t ha−1) and the plots treated with oxadiazon alone (5.4–5.6 t ha−1) and oxadiazon followed by postemergence herbicides (5.2–5.8 t ha−1). The lowest paddy yield (0.22 t ha−1) was achieved in the nontreated plots followed by the plots treated with the sole application of bispyribac-sodium and fenoxaprop + ethoxysulfuron. The results suggest that oxadiazon is the best broad-spectrum and economically effective herbicide when applied alone or in combination with other effective postemergence herbicides with different modes of action, depending on the weed species present in the field.

Factors affecting log traits and green rotary-peeled veneer recovery from temperate eucalypt plantations

High levels of percentage green veneer recovery can be obtained from temperate eucalypt plantations. Recovery traits are affected by site and log position in the stem. Of the post-felling log traits studied, out-of-roundness was the best predictor of green recovery.

High-throughput Phenotyping of Wheat Seminal Root Traits in a Breeding Context

Water availability is a major limiting factor for wheat (Triticum aestivum L.) in rain-fed agricultural systems worldwide. Root architecture has important functional implications for the timing and extent of soil water extraction, yet selection for root traits in wheat breeding programs has been largely limited due to the lack of suitable phenotyping methods. The aim of this research was to develop a low-cost high-throughput phenotyping method to facilitate selection for desirable root traits. We developed a method to assess ‘seminal root angle’ and ‘seminal root number’ in seedlings – two proxy traits associated to root architecture of mature wheat plants (1). The method involves measuring the angle between the first pair of seminal roots and the number of roots of wheat seedlings grown in transparent pots (Figure 1). Images captured at 5 to 10 days after sowing are analyzed to calculate seminal root angle and number. Performing this technique under “speed breeding” conditions (plants grown at a density of 600 plants / m2, under controlled temperature and constant light) allows the selection based on the desired root traits of up to 5 consecutive generations within 12 months. Alternatively, when focusing only on germplasm screening, up to 52 successive phenotypic assays can be conducted within 12 months. This approach has been shown to be highly reproducible, it requires little resource (time, space, and labour) and can be used to rapidly enrich breeding populations with desirable alleles for narrow root angle and a high number of seminal roots to indirectly target the selection of deeper root system with higher branching at depth. Such root characteristics are highly desirable in wheat to cope with the climate model projections, especially in summer rainfall dominant regions including some Australian, Indian, South American and African cropping regions, where winter crops mainly rely on deep stored water.

Genomic regions influencing seminal root traits in barley

Water availability is a major limiting factor for crop production, making drought adaptation and its many component traits a desirable attribute of plant cultivars. Previous studies in cereal crops indicate that root traits expressed at early plant developmental stages, such as seminal root angle and root number, are associated with water extraction at different depths. Here, we conducted the first study to map seminal root traits in barley (Hordeum vulgare L.). Using a recently developed high-throughput phenotyping method, a panel of 30 barley genotypes and a doubled-haploid (DH) population (ND24260 × 'Flagship') comprising 330 lines genotyped with diversity array technology (DArT) markers were evaluated for seminal root angle (deviation from vertical) and root number under controlled environmental conditions. A high degree of phenotypic variation was observed in the panel of 30 genotypes: 13.5 to 82.2 and 3.6 to 6.9° for root angle and root number, respectively. A similar range was observed in the DH population: 16.4 to 70.5 and 3.6 to 6.5° for root angle and number, respectively. Seven quantitative trait loci (QTL) for seminal root traits (root angle, two QTL; root number, five QTL) were detected in the DH population. A major QTL influencing both root angle and root number (RAQ2/RNQ4) was positioned on chromosome 5HL. Across-species analysis identified 10 common genes underlying root trait QTL in barley, wheat (Triticum aestivum L.), and sorghum [Sorghum bicolor (L.) Moench]. Here, we provide insight into seminal root phenotypes and provide a first look at the genetics controlling these traits in barley.

Molecular Breeding for Complex Adaptive Traits: How Integrating Crop Ecophysiology and Modelling Can Enhance Efficiency

Progress in crop improvement is limited by the ability to identify favourable combinations of genotypes (G) and management practices (M) in relevant target environments (E) given the resources available to search among the myriad of possible combinations. To underpin yield advance we require prediction of phenotype based on genotype. In plant breeding, traditional phenotypic selection methods have involved measuring phenotypic performance of large segregating populations in multi-environment trials and applying rigorous statistical procedures based on quantitative genetic theory to identify superior individuals. Recent developments in the ability to inexpensively and densely map/sequence genomes have facilitated a shift from the level of the individual (genotype) to the level of the genomic region. Molecular breeding strategies using genome wide prediction and genomic selection approaches have developed rapidly. However, their applicability to complex traits remains constrained by gene-gene and gene-environment interactions, which restrict the predictive power of associations of genomic regions with phenotypic responses. Here it is argued that crop ecophysiology and functional whole plant modelling can provide an effective link between molecular and organism scales and enhance molecular breeding by adding value to genetic prediction approaches. A physiological framework that facilitates dissection and modelling of complex traits can inform phenotyping methods for marker/gene detection and underpin prediction of likely phenotypic consequences of trait and genetic variation in target environments. This approach holds considerable promise for more effectively linking genotype to phenotype for complex adaptive traits. Specific examples focused on drought adaptation are presented to highlight the concepts.

Dispersal and related life history traits in the Glanville fritillary butterfly

Most studies of life history evolution are based on the assumption that species exist at equilibrium and spatially distinct separated populations. In reality, this is rarely the case, as populations are often spatially structured with ephemeral local populations. Therefore, the characteristics of metapopulations should be considered while studying factors affecting life history evolution. Theoretical studies have examined spatial processes shaping the evolution of life history traits to some extent, but there is little empirical data and evidence to investigate model predictions. In my thesis I have tried to bridge the gap between theoretical and empirical studies by using the well-known Glanville fritillary (Melitaea cinxia) metapopulation as a model system. The long-term persistence of classic metapopulations requires sufficient dispersal to establish new local populations to compensate for local extinctions. Previous studies on the Glanville fritillary have shown that females establishing new populations are not a random sample from the metapopulation, but they are in fact more dispersive than females in old populations. Many other life-history traits, such as body size, fecundity and lifespan, may be related to dispersal rate. Therefore, I examined a range of correlated traits for their evolutionary and ecological consequences. I was particularly interested in how the traits vary under natural environmental conditions, hence all studies were conducted in a large (32 x 26 m) outdoor population cage built upon a natural habitat patch. Individuals for the experiments were sampled from newly-established and old populations within a large metapopulation. Results show that females originating from newly-established populations had higher within-habitat patch mobility than females from old populations. I showed that dispersal rate is heritable and that flight activity is related to variation in a gene encoding the glycolytic enzyme phosphoglucose isomerase. Both among-individual and among-population variation in dispersal are correlated with the reproductive performance of females, though I found no evidence for a trade-off between dispersal and fecundity in terms of lifetime egg production or clutch size. Instead, the results suggest that highly dispersive females from newly-established populations have a shorter lifespan than females from old populations, and that dispersive females may pay a cost in terms of reduced lifetime reproductive success due to increased time spent outside habitat patches. In summary, the results of this thesis show that genotype-dependent dispersal rate correlates with other life history traits in the Glanville fritillary, and that the rapid turnover of local populations (extinctions and re-colonisations) is likely to be the mechanism that maintains phenotypic variation in many life history traits at the metapopulation level.