The accuracy of varietal selection using factor analytic models for multi-environment plant breeding trials

Modeling of cultivar x trial effects for multienvironment trials (METs) within a mixed model framework is now common practice in many plant breeding programs. The factor analytic (FA) model is a parsimonious form used to approximate the fully unstructured form of the genetic variance-covariance matrix in the model for MET data. In this study, we demonstrate that the FA model is generally the model of best fit across a range of data sets taken from early generation trials in a breeding program. In addition, we demonstrate the superiority of the FA model in achieving the most common aim of METs, namely the selection of superior genotypes. Selection is achieved using best linear unbiased predictions (BLUPs) of cultivar effects at each environment, considered either individually or as a weighted average across environments. In practice, empirical BLUPs (E-BLUPs) of cultivar effects must be used instead of BLUPs since variance parameters in the model must be estimated rather than assumed known. While the optimal properties of minimum mean squared error of prediction (MSEP) and maximum correlation between true and predicted effects possessed by BLUPs do not hold for E-BLUPs, a simulation study shows that E-BLUPs perform well in terms of MSEP.

Strawberry breeding in a subtropical environment

Strawberry breeding aims to provide cultivars that maximise consumer satisfaction and producer profitability in a changing environment. In this paper some concepts of profitability, consumer satisfaction and sustainability are explored for a subtropical climate using Queensland Australia, and Florida USA, as examples. The typical production environment is annual autumn planting of bare rooted runners into polythene covered raised beds at about 40000 plants/ha. Harvesting is late autumn to early spring, with fruit arriving at the major markets up to 2000km away from the production area within 1-4 days of harvest. The basic premise in the breed-big work is that consumers must enjoy the experience of eating strawberries, and that perceived flavour, sweetness, and juiciness are the major contributors to this experience. Using market chain information, we developed a basic value model comprised of costs, returns, and sustainability of market. To this basic outline are applied operational descriptors, such as 'speed of harvest', and associated plant characteristics, such as 'fruit display'. The expression of each plant characteristic is ascribed a value or level and together numerically describe the phenotype. This description is mathematically manipulated to provide a 'value index' for the cultivar. Nine cultivars including 'Strawberry Festival', 'Kabarla', 'DPI Rubygem' and 'Sweet Charlie' are described, and environmental issues that may impact on the subtropical strawberry breeding objectives are discussed. Product differentiation and the use of exotic germplasm as a new source of genes for flavour and resistance to disease and environmental stress will likely be the cornerstones of future progress in subtropical strawberry breeding. This approach should satisfy both consumers and producers.

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.

Growth responses of sugarcane to mycorrhizal spore density and phosphorus rate

Arbuscular mycorrhizal (AM) fungi, commonly found in long-term cane-growing fields in northern Queensland, are linked with both negative and positive growth responses by sugarcane (Saccharum spp.), depending on P supply. A glasshouse trial was established to examine whether AM density might also have an important influence on these growth responses. Mycorrhizal spores (Glomus clarum), isolated from a long-term cane block in northern Queensland, were introduced into a pasteurised low-P cane soil at 5 densities (0, 0.06, 0.25, 1, 4 spores/g soil) and with 4 P treatments (0, 8.2, 25, and 47 mg/kg). At 83 days after planting, sugarcane tops responded positively to P fertilizer, although responses attributable to spore density were rarely observed. In one case, addition of 4 spores/g led to a 53% yield response over those without AM at 8 mgP/kg, or a relative benefit of 17 mg P/kg. Root colonisation was reduced for plants with nil or 74 mg P/kg. For those without AM, P concentration in the topmost visible dewlap (TVD) leaf increased significantly with fertiliser P (0.07 v. 0.15%). However, P concentration increased further with the presence of AM spores. Irrespective of AM, the critical P concentration in the TVD leaf was 0.18%. This study confirms earlier reports that sugarcane is poorly responsive to AM. Spore density, up to 4 spores/g soil, appears unable to influence this responsiveness, either positively or negatively. Attempts to gain P benefits by increasing AM density through rotation seem unlikely to lead to yield increases by sugarcane. Conversely, sugarcane grown in fields with high spore densities and high plant-available P, such as long-term cane-growing soils, is unlikely to suffer a yield reduction from mycorrhizal fungi.

Row spacing and planting density effects on the growth and yield of sugarcane. 1. Responses in fumigated and non-fumigated soil.

It has been reported that high-density planting of sugarcane can improve cane and sugar yield through promoting rapid canopy closure and increasing radiation interception earlier in crop growth. It is widely known that the control of adverse soil biota through fumigation (removes soil biological constraints and improves soil health) can improve cane and sugar yield. Whether the responses to high-density planting and improved soil health are additive or interactive has important implications for the sugarcane production system. Field experiments established at Bundaberg and Mackay, Queensland, Australia, involved all combinations of 2-row spacings (0.5 and 1.5 m), two planting densities (27 000 and 81 000 two-eyed setts/ha), and two soil fumigation treatments (fumigated and non-fumigated). The Bundaberg experiment had two cultivars (Q124, Q155), was fully irrigated, and harvested 15 months after planting. The Mackay experiment had one cultivar (Q117), was grown under rainfed conditions, and harvested 10 months after planting. High-density planting (81 000 setts/ha in 0.5-m rows) did not produce any more cane or sugar yield at harvest than low-density planting (27 000 setts/ha in 1.5-m rows) regardless of location, crop duration (15 v. 10 months), water supply (irrigated v. rainfed), or soil health (fumigated v. non-fumigated). Conversely, soil fumigation generally increased cane and sugar yields regardless of site, row spacing, and planting density. In the Bundaberg experiment there was a large fumigation x cultivar x density interaction (P<0.01). Cultivar Q155 responded positively to higher planting density in non-fumigated soil but not in fumigated soil, while Q124 showed a negative response to higher planting density in non-fumigated soil but no response in fumigated soil. In the Mackay experiment, Q117 showed a non-significant trend of increasing yield in response to increasing planting density in non-fumigated soil, similar to the Q155 response in non-fumigated soil at Bundaberg. The similarity in yield across the range of row spacings and planting densities within experiments was largely due to compensation between stalk number and stalk weight, particularly when fumigation was used to address soil health. Further, the different cultivars (Q124 and Q155 at Bundaberg and Q117 at Mackay) exhibited differing physiological responses to the fumigation, row spacing, and planting density treatments. These included the rate of tiller initiation and subsequent loss, changes in stalk weight, and propensity to lodging. These responses suggest that there may be potential for selecting cultivars suited to different planting configurations.

Row spacing and planting density effects on the growth and yield of sugarcane. 3. Responses with different cultivars.

The promotion of controlled traffic (matching wheel and row spacing) in the Australian sugar industry is necessitating a widening of row spacing beyond the standard 1.5 m. As all cultivars grown in the Australian industry have been selected under the standard row spacing there are concerns that at least some cultivars may not be suitable for wider rows. To address this issue, experiments were established in northern and southern Queensland in which cultivars, with different growth characteristics, recommended for each region, were grown under a range of different row configurations. In the northern Queensland experiment at Gordonvale, cultivars Q187((sic)), Q200((sic)), Q201((sic)), and Q218((sic)) were grown in 1.5-m single rows, 1.8-m single rows, 1.8-m dual rows (50 cm between duals), and 2.3-m dual rows (80 cm between duals). In the southern Queensland experiment at Farnsfield, cvv. Q138, Q205((sic)), Q222((sic)) and Q188((sic)) were also grown in 1.5-m single rows, 1.8-m single rows, 1.8-m dual rows (50 cm between duals), while 1.8-m-wide throat planted single row and 2.0-m dual row (80 cm between duals) configurations were also included. There was no difference in yield between the different row configurations at Farnsfield but there was a significant row configuration x cultivar interaction at Gordonvale due to good yields in 1.8-m single and dual rows with Q201((sic)) and poor yields with Q200((sic)) at the same row spacings. There was no significant difference between the two cultivars in 1.5-m single and 2.3-m dual rows. The experiments once again demonstrated the compensatory capacity that exists in sugarcane to manipulate stalk number and individual stalk weight as a means of producing similar yields across a range of row configurations and planting densities. There was evidence of different growth patterns between cultivars in response to different row configurations (viz. propensity to tiller, susceptibility to lodging, ability to compensate between stalk number and stalk weight), suggesting that there may be genetic differences in response to row configuration. It is argued that there is a need to evaluate potential cultivars under a wider range of row configurations than the standard 1.5-m single rows. Cultivars that perform well in row configurations ranging from 1.8 to 2.0 m are essential if the adverse effects of soil compaction are to be managed through the adoption of controlled traffic.

Row spacing and planting density effects on the growth and yield of sugarcane. 2. Strategies for the adoption of controlled traffic.

Controlled traffic (matching wheel and row spacing) is being promoted as a means to manage soil compaction in the Australian sugar industry. However, machinery limitations dictate that wider row spacings than the standard 1.5-m single row will need to be adopted to incorporate controlled traffic and many growers are reluctant to widen row spacing for fear of yield penalties. To address these concerns, contrasting row configuration and planting density combinations were investigated for their effect on cane and sugar yield in large-scale experiments in the Gordonvale, Tully, Ingham, Mackay, and Bingera (near Bundaberg) sugarcane-growing regions of Queensland, Australia. The results showed that sugarcane possesses a capacity to compensate for different row configurations and planting densities through variation in stalk number and individual stalk weight. Row configurations ranging from 1.5-m single rows (the current industry standard) to 1.8-m dual rows (50 cm between duals), 2.1-m dual (80 cm between duals) and triple ( 65 cm between triples) rows, and 2.3-m triple rows (65 cm between triples) produced similar yields. Four rows (50 cm apart) on a 2.1-m configuration (quad rows) produced lower yields largely due to crop lodging, while a 1.8-m single row configuration produced lower yields in the plant crop, probably due to inadequate resource availability (water stress/limited radiation interception). The results suggest that controlled traffic can be adopted in the Australian sugar industry by changing from a 1.5-m single row to 1.8-m dual row configuration without yield penalty. Further, the similar yields obtained with wider row configurations (2 m or greater with multiple rows) in these experiments emphasise the physiological and environmental plasticity that exists in sugarcane. Controlled traffic can be implemented with these wider row configurations (>2 m), although it will be necessary to carry out expensive modifications to the current harvester and haul-out equipment. There were indications from this research that not all cultivars were suited to configurations involving multiple rows. The results suggest that consideration be given to assessing clones with different growth habits under a range of row configurations to find the most suitable plant types for controlled traffic cropping systems.

Susceptibility of source plants to sugarcane Fiji disease virus influences the acquisition and transmission of the virus by the planthopper vector Perkinsiella saccharicida

Fiji leaf gall (FLG) caused by Sugarcane Fiji disease virus (SCFDV) is transmitted by the planthopper Perkinsiella saccharicida. FLG is managed through the identification and exploitation of plant resistance. The glasshouse-based resistance screening produced inconsistent transmission results and the factors responsible for that are not known. A series of glasshouse trials conducted over a 2-year period was compared to identify the factors responsible for the erratic transmission results. SCFDV transmission was greater when the virus was acquired by the vector from a cultivar that was susceptible to the virus than when the virus was acquired from a resistant cultivar. Virus acquisition by the vector was also greater when the vector was exposed to the susceptible cultivars than when exposed to the resistant cultivar. Results suggest that the variation in transmission levels is due to variation in susceptibility of sugarcane cultivars to SCFDV used for virus acquisition by the vector.

Is the distribution of Fiji leaf gall in Australian sugarcane explained by variation in the vector Perkinsiella saccharicida?

Fiji leaf gall (FLG) is an important virally induced disease in Australian sugarcane. It is confined to southern canegrowing areas, despite its vector, the delphacid planthopper Perkinsiella saccharicida, occurring in all canegrowing areas of Queensland and New South Wales. This disparity between distributions could be a result of successful containment of the disease through quarantine and/or geographical barriers, or because northern Queensland populations of Perkinsiella may be poorer vectors of the disease. These hypotheses were first tested by investigating variation in the ITS2 region of the rDNA fragment among eastern Australian and overseas populations of Perkinsiella. The ITS2 sequences of the Western Australian P. thompsoni and the Fijian P. vitiensis were distinguishable from those of P. saccharicida and there was no significant variation among the 26 P. saccharicida populations. Reciprocal crosses of a northern Queensland and a southern Queensland population of P. saccharicida were fertile, so they may well be conspecific. Single vector transmission experiments showed that a population of P. saccharicida from northern Queensland had a higher vector competency than either of two southern Queensland populations. The frequency of virus acquisition in the vector populations was demonstrated to be important in the vector competency of the planthopper. The proportion of infected vectors that transmitted the virus to plants was not significantly different among the populations tested. This study shows that the absence of FLG from northern Queensland is not due to a lack of vector competency of the northern population of P. saccharicida.

Breeding Ananas for the cut-flower and garden markets

Only small quantities of Ananas have been marketed as cut flowers or as potted plants for garden use in Australia. Worldwide there have, until very recent times, been no breeding programs to develop ornamental characteristics and hence the choice of cultivars has been limited mainly to semi-domesticated selections or those developed by amateur enthusiasts. Interest in developing Ananas selections specifically for the ornamental market is now increasing. A small program has operated in Australia since 1995. In this program, a total of 4,700 seedlings were generated over three generations using various parental combinations of Ananas comosus var. comosus, A. comosus var. bracteatus, A. comosus var. ananassoides 'FRF223', A. comosus var. erectifolious 'Selvagem 6' and Ananas macrodontes 'I.26-803'. Several selections have been developed for the garden and or cut-flower market. Characteristics represented include a pink or red syncarp, dark red-brown foliage and a dwarf, clumping growth habit. While a surprising display of ornamental diversity exists within Ananas, the genus is limited in comparison to the other bromeliad genera. Opportunity might exist however to introgress characteristics such as additional foliage colours, plant morphology and syncarp colours from other genera into Ananas.

"On-the-go" NIT technology to assess protein and moisture during harvest of wheat breeding trials.

In this study, we investigated the application of “on-the-go” assessment of wheat protein and moisture under a breeding trial situation.

Revenue diversification opportunities from sugarcane

Sugarcane is a major global agricultural crop that produces significant quantities of sugar and biomass in tropical and sub-tropical regions. Over many centuries, the crop has been grown primarily for its high sugar content which traditionally contributes over 95% of the revenue derived from the crop. While the production of renewable electricity from bagasse and rum from molasses has a long history, in more recent decades significant advances have been made in the production of cogeneration products and fuel ethanol at large scale. Sugarcane biorefineries producing fuels, green chemicals, biopolymers and bio-products offer great potential for improving the profitability of sugarcane production. This paper will address the opportunities available for sugarcane biorefineries to contribute to future profitability and sustainability of the sugarcane industry.

The use of an acetoacetyl-CoA synthase in place of a -ketothiolase enhances poly-3-hydroxybutyrate production in sugarcane mesophyll cells

Engineering the production of polyhydroxyalkanoates (PHAs) into high biomass bioenergy crops has the potential to provide a sustainable supply of bioplastics and energy from a single plant feedstock. One of the major challenges in engineering C-4 plants for the production of poly[(R)-3-hydroxybutyrate] (PHB) is the significantly lower level of polymer produced in the chloroplasts of mesophyll (M) cells compared to bundle sheath (BS) cells, thereby limiting the full PHB yield-potential of the plant. In this study, we provide evidence that the access to substrate for PHB synthesis may limit polymer production in M chloroplasts. Production of PHB in M cells of sugarcane is significantly increased by replacing -ketothiolase, the first enzyme in the bacterial PHA pathway, with acetoacetyl-CoA synthase. This novel pathway enabled the production of PHB reaching an average of 6.3% of the dry weight of total leaf biomass, with levels ranging from 3.6 to 11.8% of the dry weight (DW) of individual leaves. These yields are more than twice the level reported in PHB-producing sugarcane containing the -ketothiolase and illustrate the importance of producing polymer in mesophyll plastids to maximize yield. The molecular weight of the polymer produced was greater than 2x10(6)Da. These results are a major step forward in engineering a high biomass C-4 grass for the commercial production of PHB.

Sugarcane smut after three years: a policy retrospective.

The detection of sugarcane smut disease (Ustilago scitaminea) in the Bundaberg-Childers region of eastern Australia in 2006 triggered a comprehensive and united response from BSES Limited, Queensland Government and CANEGROWERS. The response to sugarcane smut in the Bundaberg-Childers area was the first test for the Emergency Plant Pest Response Deed, an agreement between Australian governments and plant industries to facilitate a response to a plant pest incursion. As part of this response and the subsequent inquiry, economic models of the likely pattern of spread and cost of the smut epidemic were prepared. This paper reviews the predictions of those models in the light of the subsequent three years' experience. It examines reasons for divergence from the modelled outcomes, some of which were good approximations of actual experience.

Interactions between rotation breaks, tillage and N management on sugarcane grown at Bundaberg and Ingham.

The impact of cropping histories (sugarcane, maize and soybean), tillage practices (conventional tillage and direct drill) and fertiliser N in the plant and 1st ratoon (1R) crops of sugarcane were examined in field trials at Bundaberg and Ingham. Average yields at Ingham (Q200) and Bundaberg (Q151) were quite similar in both the plant crop (83 t/ha and 80 t/ha, respectively) and the 1R (89 t/ha v 94 t/ha, respectively), with only minor treatment effects on CCS at each site. Cane yield responses to tillage, break history and N fertiliser varied significantly between sites. There was a 27% yield increase in the plant crop from the soybean fallow at Ingham, with soybeans producing a yield advantage over continuous cane, but there were no clear break effects at Bundaberg - possibly due to a complex of pathogenic nematodes that responded differently to soybeans and maize breaks. There was no carryover benefit of the soybean break into the 1R crop at Ingham, while at Bundaberg the maize break produced a 15% yield advantage over soybeans and continuous cane. The Ingham site recorded positive responses to N fertiliser addition in both the plant (20% yield increase) and 1R (34% yield increase) crops, but there was negligible carryover benefit from plant crop N in the 1R crop, or of a reduced N response after a soybean rotation. By contrast, the Bundaberg site showed no N response in any history in the plant crop, and only a small (5%) yield increase with N applied in the 1R crop. There was again no evidence of a reduced N response in the 1R crop after a soybean fallow. There were no significant effects of tillage on cane yields at either site, although there were some minor interactions between tillage, breaks and N management in the 1R crop at both sites. Crop N contents at Bundaberg were more than 3 times those recorded at Ingham in both the plant and 1R crops, with N concentrations in millable stalk at Ingham suggesting N deficiencies in all treatments. There was negligible additional N recovered in crop biomass from N fertiliser application or soybean residues at the Ingham site. There was additional N recovered in crop biomass in response to N fertiliser and soybean breaks at Bundaberg, but effects were small and fertiliser use efficiencies poor. Loss pathways could not be quantified, but denitrification or losses in runoff were the likely causes at Ingham while leaching predominated at Bundaberg. Results highlight the complexity involved in developing sustainable farming systems for contrasting soil types and climatic conditions. A better understanding of key sugarcane pathogens and their host range, as well as improved capacity to predict in-crop N mineralisation, will be key factors in future improvements to sugarcane farming systems.