Identification of QTL for sugar-related traits in a sweet x grain sorghum (Sorghum bicolor L. Moench) recombinant inbred population

QTL for stem sugar-related and other agronomic traits were identified in a converted sweet (R9188) × grain (R9403463-2-1) sorghum population. QTL analyses were conducted using phenotypic data for 11 traits measured in two field experiments and a genetic map comprising 228 SSR and AFLP markers grouped into 16 linkage groups, of which 11 could be assigned to the 10 sorghum chromosomes (SBI-01 to SBI-10). QTL were identified for all traits and were generally co-located to five locations (SBI-01, SBI-03, SBI-05, SBI-06 and SBI-10). QTL alleles from R9188 were detected for increased sucrose content and sugar content on SBI-01, SBI-05 and SBI-06. R9188 also contributed QTL alleles for increased Brix on SBI-05 and SBI-06, and increased sugar content on SBI-03. QTL alleles from R9403463-2-1 were found for increased sucrose content and sucrose yield on SBI-10, and increased glucose content on SBI-07. QTL alleles for increased height, later flowering and greater total dry matter yield were located on SBI-01 of R9403463-2-1, and SBI-06 of R9188. QTL alleles for increased grain yield from both R9403463-2-1 and R9188 were found on SBI-03. As an increase in stem sugars is an important objective in sweet sorghum breeding, the QTL identified in this study could be further investigated for use in marker-assisted selection of sweet sorghum.

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

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 x 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.

A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits

Background: Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology (DArT) is a hybridization-based technology that is increasingly being adopted by barley researchers. There is a need to integrate the information generated by DArT with previous data produced with gel-based marker technologies. The goal of this study was to build a high-density consensus linkage map from the combined datasets of ten populations, most of which were simultaneously typed with DArT and Simple Sequence Repeat (SSR), Restriction Enzyme Fragment Polymorphism (RFLP) and/or Sequence Tagged Site (STS) markers. Results: The consensus map, built using a combination of JoinMap 3.0 software and several purpose-built perl scripts, comprised 2,935 loci (2,085 DArT, 850 other loci) and spanned 1,161 cM. It contained a total of 1,629 'bins' (unique loci), with an average inter-bin distance of 0.7 ± 1.0 cM (median = 0.3 cM). More than 98% of the map could be covered with a single DArT assay. The arrangement of loci was very similar to, and almost as optimal as, the arrangement of loci in component maps built for individual populations. The locus order of a synthetic map derived from merging the component maps without considering the segregation data was only slightly inferior. The distribution of loci along chromosomes indicated centromeric suppression of recombination in all chromosomes except 5H. DArT markers appeared to have a moderate tendency toward hypomethylated, gene-rich regions in distal chromosome areas. On the average, 14 ± 9 DArT loci were identified within 5 cM on either side of SSR, RFLP or STS loci previously identified as linked to agricultural traits. Conclusion: Our barley consensus map provides a framework for transferring genetic information between different marker systems and for deploying DArT markers in molecular breeding schemes. The study also highlights the need for improved software for building consensus maps from high-density segregation data of multiple populations.

Developmental and physiological traits associated with high yield and stay-green phenotype in wheat

Water availability is a key limiting factor in wheat production in the northern grain belt of Australia. Varieties with improved adaptation to such conditions are actively sought. The CIMMYT wheat line SeriM82 has shown a significant yield advantage in multi-environment screening trials in this region. The objective of this study was to identify the physiological basis of the adaptive traits underpinning this advantage. Six detailed experiments were conducted to compare the growth, development, and yield of SeriM82 with that of the adapted cultivar, Hartog. The experiments were undertaken in field environments that represented the range of moisture availability conditions commonly encountered by winter crops grown on the deep Vertosol soils of this region. The yield of SeriM82 was 6-28% greater than that of Hartog, and SeriM82 exhibited a stay-green phenotype by maintaining green leaf area longer during the grain-filling period in all environments where yield was significantly greater than Hartog. However, where the availability of deep soil moisture was limited, SeriM82 failed to exhibit significantly greater yield or to express the stay-green phenotype. Thus, the stay-green phenotype was closely associated with the yield advantage of SeriM82. SeriM82 also exhibited higher mean grain mass than Hartog in all environments. It is suggested that small differences in water use before anthesis, or greater water extraction from depth after anthesis, could underlie the stay-green phenotype. The inability of SeriM82 to exhibit stay-green and higher yield where deep soil moisture was depleted indicates that extraction of deep soil moisture is important.

Using morphological traits to identify persistent lucernes for dryland agriculture in NSW, Australia

This paper reports on several studies conducted to better understand the variability between lucerne cultivars and lines, and use this to predict persistence in dryland grazing pastures in eastern Australia. Morphological traits of 20 cultivars/lines were measured in irrigated and dryland spaced plant experiments. Studies were also conducted to describe variation among lucernes in their utilisation of starch and responses to water deficit, pests and diseases. Multiple regression analyses were used to develop simple models where the measured traits could be used to predict persistence of lucerne lines in dryland evaluation experiments. Although there was significant variation among cultivars/lines in most measured traits, no single trait reliably predicted persistence of cultivars/lines in dryland evaluation experiments. However, variation in persistence at both sites could be explained by models developed by multiple regression using differences in the mean lengths of the longest stems at 10% flower in summer and winter. Persistent lucernes were those that had relatively long stems in summer and short stems in winter. Water use efficiencies, starch utilisation patterns and resistances to pests and diseases of different lucernes provided some improvement to this simple model, but these improvements were not consistent.

Genotypic variation in seedling root architectural traits and implications for drought adaptation in wheat (Triticum aestivum L.)

Root system characteristics are of fundamental importance to soil exploration and below-ground resource acquisition. Root architectural traits determine the in situ space-filling properties of a root system or root architecture. The growth angle of root axes is a principal component of root system architecture that has been strongly associated with acquisition efficiency in many crop species. The aims of this study were to examine the extent of genotypic variability for the growth angle and number of seminal roots in 27 current Australian and 3 CIMMYT wheat (Triticum aestivum L.) genotypes, and to quantify using fractal analysis the root system architecture of a subset of wheat genotypes contrasting in drought tolerance and seminal root characteristics. The growth angle and number of seminal roots showed significant genotypic variation among the wheat genotypes with values ranging from 36 to 56 (degrees) and 3 to 5 (plant-1), respectively. Cluster analysis of wheat genotypes based on similarity in their seminal root characteristics resulted in four groups. The group composition reflected to some extent the genetic background and environmental adaptation of genotypes. Wheat cultivars grown widely in the Mediterranean environments of southern and western Australia generally had wider growth angle and lower number of seminal axes. In contrast, cultivars with superior performance on deep clay soils in the northern cropping region, such as SeriM82, Baxter, Babax, and Dharwar Dry exhibited a narrower angle of seminal axes. The wheat genotypes also showed significant variation in fractal dimension (D). The D values calculated for the individual segments of each root system suggested that, compared to the standard cultivar Hartog, the drought-tolerant genotypes adapted to the northern region tended to distribute relatively more roots in the soil volume directly underneath the plant. These findings suggest that wheat root system architecture is closely linked to the angle of seminal root axes at the seedling stage. The implications of genotypic variation in the seminal root characteristics and fractal dimension for specific adaptation to drought environment types are discussed with emphasis on the possible exploitation of root architectural traits in breeding for improved wheat cultivars for water-limited environments.

The role of root architectural traits in adaptation of wheat to water-limited environments

Better understanding of root system structure and function is critical to crop improvement in water-limited environments. The aims of this study were to examine root system characteristics of two wheat genotypes contrasting in tolerance to water limitation and to assess the functional implications on adaptation to water-limited environments of any differences found. The drought tolerant barley variety, Mackay, was also included to allow inter-species comparison. Single plants were grown in large, soil-filled root-observation chambers. Root growth was monitored by digital imaging and water extraction was measured. Root architecture differed markedly among the genotypes. The drought-tolerant wheat (cv. SeriM82) had a compact root system, while roots of barley cv. Mackay occupied the largest soil volume. Relative to the standard wheat variety (Hartog), SeriM82 had a more uniform rooting pattern and greater root length at depth. Despite the more compact root architecture of SeriM82, total water extracted did not differ between wheat genotypes. To quantify the value of these adaptive traits, a simulation analysis was conducted with the cropping system model APSIM, for a wide range of environments in southern Queensland, Australia. The analysis indicated a mean relative yield benefit of 14.5% in water-deficit seasons. Each additional millimetre of water extracted during grain filling generated an extra 55 kg ha-1 of grain yield. The functional implications of root traits on temporal patterns and total amount of water capture, and their importance in crop adaptation to specific water-limited environments, are discussed.

DNA markers linked to yield, yield components, and morphological traits in autotetraploid lucerne (Medicago sativa L.)

We have mapped and identified DNA markers linked to morphology, yield, and yield components of lucerne, using a backcross population derived from winter-active parents. The high-yielding and recurrent parent, D, produced individual markers that accounted for up to 18% of total yield over 6 harvests, at Gatton, south-eastern Queensland. The same marker, AC/TT8, was consistently identified at each individual harvest, and in individual harvests accounted for up to 26% of the phenotypic variation for yield. This marker was located in linkage group 2 of the D map, and several other markers positively associated with yield were consistently identified in this linkage group. Similarly, markers negatively associated with yield were consistently identified in the W116 map, W116 being the low-yielding parent. Highly significant positive correlations were observed between total yield and yield for harvests 1-6, and between total yield and stem length, tiller number, leaf yield/plant, leaf yield/5 stems, stem yield/plant, and stem yield/5 stems. Highly significant QTL were located for all these characters as well as for leaf shape and pubescence.

Responses in carcass lean pH at 24 hours post-mortem in lines of Large White pigs selected for growth rate on a fixed ration over a set time

A restricted maximum likelihood analysis applied to an animal model showed no significant differences (P > 0.05) in pH value of the longissimus dorsi measured at 24 h post-mortem (pH24) between high and low lines of Large White pigs selected over 4 years for post-weaning growth rate on restricted feeding. Genetic and phenotypic correlations between pH24 and production and carcass traits were estimated using all performance testing records combined with the pH24 measurements (5.05-7.02) on slaughtered animals. The estimate of heritability for pH24 was moderate (0.29 ± 0.18). Genetic correlations between pH24 and production or carcass composition traits, except for ultrasonic backfat (UBF), were not significantly different from zero. UBF had a moderate, positive genetic correlation with pH24 (0.24 ± 0.33). These estimates of genetic correlations affirmed that selection for increased growth rate on restricted feeding is likely to result in limited changes in pH24 and pork quality since the selection does not put a high emphasis on reduced fatness.

Heritability estimates for growth in the tropical abalone Haliotis asinina using microsatellites to assign parentage

The tropical abalone Haliotis asinina is a wild-caught and cultured species throughout the Indo-Pacific as well as being an emerging model species for the study of haliotids. H. asinina has the fastest recorded natural growth rate of any abalone and reaches sexual maturity within one year. As such, it is a suitable abalone species for selective breeding for commercially important traits such as rapid growth. Estimating the amount of variation in size that is attributable to heritable genetic differences can assist the development of such a selective breeding program. Here we estimated heritability for growth-related traits at 12 months of age by creating a single cohort of 84 families in a full-factorial mating design consisting of 14 sires and 6 dams. Of 500 progeny sampled, 465 were successfully assigned to their parents based on shared alleles at 5 polymorphic microsatellite loci. Using an animal model, heritability estimates were 0.48 ± 0.15 for shell length, 0.38 ± 0.13 for shell width and 0.36 ± 0.13 for weight. Genetic correlations were > 0.98 between shell parameters and weight, indicating that breeding for weight gains could be successfully achieved by selecting for shell length.

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.

The role of fruit traits of bird-dispersed plants in invasiveness and weed risk assessment

Aim: Birds play a major role in the dispersal of seeds of many fleshy-fruited invasive plants. The fruits that birds choose to consume are influenced by fruit traits. However, little is known of how the traits of invasive plant fruits contribute to invasiveness or to their use by frugivores. We aim to gain a greater understanding of these relationships to improve invasive plant management. Location: South-east Queensland, Australia. Methods: We measure a variety of fruit morphology, pulp nutrient and phenology traits of a suite of bird-dispersed alien plants. Frugivore richness of these aliens was derived from the literature. Using regressions and multivariate methods, we investigate relationships between fruit traits, frugivore richness and invasiveness. Results: Plant invasiveness was negatively correlated to fruit size, and all highly invasive species had quite similar fruit morphology [smaller fruits, seeds of intermediate size and few (<10) seeds per fruit]. Lower pulp water was the only pulp nutrient trait associated with invasiveness. There were strong positive relationships between the diversity of bird frugivores and plant invasiveness, and in the diversity of bird frugivores in the study region and another part of the plants' alien range. Main conclusions: Our results suggest that weed risk assessments (WRA) and predictions of invasive success for bird-dispersed plants can be improved. Scoring criteria for WRA regarding fruit size would need to be system-specific, depending on the fruit-processing capabilities of local frugivores. Frugivore richness could be quantified in the plant's natural range, its invasive range elsewhere, or predictions made based on functionally similar fruits.

Detection and use of QTL for complex traits in multiple environments.

QTL mapping methods for complex traits are challenged by new developments in marker technology, phenotyping platforms, and breeding methods. In meeting these challenges, QTL mapping approaches will need to also acknowledge the central roles of QTL by environment interactions (QEI) and QTL by trait interactions in the expression of complex traits like yield. This paper presents an overview of mixed model QTL methodology that is suitable for many types of populations and that allows predictive modeling of QEI, both for environmental and developmental gradients. Attention is also given to multi-trait QTL models which are essential to interpret the genetic basis of trait correlations. Biophysical (crop growth) model simulations are proposed as a complement to statistical QTL mapping for the interpretation of the nature of QEI and to investigate better methods for the dissection of complex traits into component traits and their genetic controls.

Fruit traits of vertebrate-dispersed alien plants: smaller seeds and more pulp sugar than indigenous species

Vertebrates play a major role in dispersing seeds of fleshy-fruited alien plants. However, we know little of how the traits of alien fleshy fruits compare with indigenous fleshy fruits, and how these differences might contribute to invasion success. In this study, we characterised up to 38 fruit morphology, pulp nutrient and phenology traits of an assemblage of 34 vertebrate-dispersed alien species in south-eastern Queensland, Australia. Most alien fruits were small (81%\15 mm in mean width), and had watery fruit pulps that were high in sugars and low in nitrogen and lipids. When compared to indigenous species, alien fruits had significantly smaller seeds. Further, alien fruit pulps contained more sugar and more variable (and probably greater) nitrogen per pulp wet weight, and species tended to have longer fruiting seasons than indigenous species. Our analyses suggest that fruit traits could be important in determining invasiveness and could be used to improve pre- and post-border weed risk assessment.

Quantitative and molecular genetics of juvenile wood traits in radiata and slash/Caribbean pines.

The Juvenile Wood Initiative (JWI) project has been running successfully since July 2003 under a Research Agreement with FWPA and Letters of Association with the consortium partners STBA (Southern Tree Breeding Association), ArborGen and FPQ (Forestry Plantations Queensland). Over the last five and half years, JWI scientists in CSIRO, FPQ, and STBA have completed all 12 major milestones and 28 component milestones according to the project schedule. We have made benchmark progress in understanding the genetic control of wood formation and interrelationships among wood traits. The project has made 15 primary scientific findings and several results have been adopted by industry as summarized below. This progress was detailed in 10 technical reports to funding organizations and industry clients. Team scientists produced 16 scientific manuscripts (8 published, 1 in press, 2 submitted, and several others in the process of submission) and 15 conference papers or presentations. Primary Scientific Findings. The 15 major scientific findings related to wood science, inheritance and the genetic basis of juvenile wood traits are: 1. An optimal method to predict stiffness of standing trees in slash/Caribbean pine is to combine gravimetric basic density from 12 mm increment cores with a standing tree prediction of MoE using a time of flight acoustic tool. This was the most accurate and cheapest way to rank trees for breeding selection for slash/Caribbean hybrid pine. This method was also recommended for radiata pine. 2. Wood density breeding values were predicted for the first time in the STBA breeding population using a large sample of 7,078 trees (increment cores) and it was estimated that selection of the best 250 trees for deployment will produce wood density gains of 12.4%. 3. Large genetic variation for a suite of wood quality traits including density, MFA, spiral grain, shrinkage, acoustic and non-acoustic stiffness (MoE) for clear wood and standing trees were observed. Genetic gains of between 8 and 49% were predicted for these wood quality traits with selection intensity between 1 to 10% for radiata pine. 4. Site had a major effect on juvenile-mature wood transition age and the effect of selective breeding for a shorter juvenile wood formation phase was only moderate (about 10% genetic gain with 10% selection intensity, equivalent to about 2 years reduction of juvenile wood). 5. The study found no usable site by genotype interactions for the wood quality traits of density, MFA and MoE for both radiata and slash/Caribbean pines, suggesting that assessment of wood properties on one or two sites will provide reliable estimates of the genetic worth of individuals for use in future breeding. 6. There were significant and sizable genotype by environment interactions between the mainland and Tasmanian regions and within Tasmania for DBH and branch size. 7. Strong genetic correlations between rings for density, MFA and MoE for both radiata and slash/Caribbean pines were observed. This suggests that selection for improved wood properties in the innermost rings would also result in improvement of wood properties in the subsequent rings, as well as improved average performance of the entire core. 8. Strong genetic correlations between pure species and hybrid performance for each of the wood quality traits were observed in the hybrid pines. Parental performance can be used to identify the hybrid families which are most likely to have superior juvenile wood properties of the slash/Caribbean F1 hybrid in southeast Queensland. 9. Large unfavourable genetic correlations between growth and wood quality traits were a prominent feature in radiata pine, indicating that overcoming this unfavourable genetic correlation will be a major technical issue in progressing radiata pine breeding. 10. The project created the first radiata pine 18 k cDNA microarray and generated 5,952 radiata pine xylogenesis expressed sequence tags (ESTs) which assembled into 3,304 unigenes. 11. A total of 348 genes were identified as preferentially expressed genes in earlywood or latewood while a total of 168 genes were identified as preferentially expressed genes in either juvenile or mature wood. 12. Juvenile earlywood has a distinct transcriptome relative to other stages of wood development. 13. Discovered rapid decay of linkage disequilibrium (LD) in radiata pine with LD decaying to approximately 50% within 1,700 base pairs (within a typical gene). A total of 913 SNPS from sequencing 177,380 base pairs were identified for association genetic studies. 14. 149 SNPs from 44 genes and 255 SNPs from a further 51 genes (total 95 genes) were selected for association analysis with 62 wood traits, and 30 SNPs were shortlisted for their significant association with variation of wood quality traits (density, MFA and MoE) with individual significant SNPs accounting for between 1.9 and 9.7% of the total genetic variation in traits. 15. Index selection using breeding objectives was the most profitable selection method for radiata pine, but in the long term it may not be the most effective in dealing with negative genetic correlations between wood volume and quality traits. A combination of economic and biological approaches may be needed to deal with the strong adverse correlation.