Deterministic and stochastic modelling of impacts from genomic selection and phenomics on genetic gain for perennial ryegrass dry matter yield.

Increasing the efficiency of current forage breeding programs through adoption of new technologies, such as genomic selection (GS) and phenomics (Ph), is challenging without proof of concept demonstrating cost effective genetic gain (∆G). This paper uses decision support software DeltaGen (tactical tool) and QU-GENE (strategic tool), to model and assess relative efficiency of five breeding methods. The effect on ∆G and cost ($) of integrating GS and Ph into an among half-sib (HS) family phenotypic selection breeding strategy was investigated. Deterministic and stochastic modelling were conducted using mock data sets of 200 and 1000 perennial ryegrass HS families using year-by-season-by-location dry matter (DM) yield data and in silico generated data, respectively. Results demonstrated short (deterministic)- and long-term (stochastic) impacts of breeding strategy and integration of key technologies, GS and Ph, on ∆G. These technologies offer substantial improvements in the rate of ∆G, and in some cases improved cost-efficiency. Applying 1% within HS family GS, predicted a 6.35 and 8.10% ∆G per cycle for DM yield from the 200 HS and 1000 HS, respectively. The application of GS in both among and within HS selection provided a significant boost to total annual ∆G, even at low GS accuracy rA of 0.12. Despite some reduction in ∆G, using Ph to assess seasonal DM yield clearly demonstrated its impact by reducing cost per percentage ∆G relative to standard DM cuts. Open-source software tools, DeltaGen and QuLinePlus/QU-GENE, offer ways to model the impact of breeding methodology and technology integration under a range of breeding scenarios.

The Impact of Alkaloid-Producing Epichloë Endophyte on Forage Ryegrass Breeding: A New Zealand Perspective.

For 30 years, forage ryegrass breeding has known that the germplasm may contain a maternally inherited symbiotic Epichloë endophyte. These endophytes produce a suite of secondary alkaloid compounds, dependent upon strain. Many produce ergot and other alkaloids, which are associated with both insect deterrence and livestock health issues. The levels of alkaloids and other endophyte characteristics are influenced by strain, host germplasm, and environmental conditions. Some strains in the right host germplasm can confer an advantage over biotic and abiotic stressors, thus acting as a maternally inherited desirable 'trait'. Through seed production, these mutualistic endophytes do not transmit into 100% of the crop seed and are less vigorous than the grass seed itself. This causes stability and longevity issues for seed production and storage should the 'trait' be desired in the germplasm. This makes understanding the precise nature of the relationship vitally important to the plant breeder. These Epichloë endophytes cannot be 'bred' in the conventional sense, as they are asexual. Instead, the breeder may modulate endophyte characteristics through selection of host germplasm, a sort of breeding by proxy. This article explores, from a forage seed company perspective, the issues that endophyte characteristics and breeding them by proxy have on ryegrass breeding, and outlines the methods used to assess the 'trait', and the application of these through the breeding, production, and deployment processes. Finally, this article investigates opportunities for enhancing the utilisation of alkaloid-producing endophytes within pastures, with a focus on balancing alkaloid levels to further enhance pest deterrence and improving livestock outcomes.

Multi-Trait Genomic Prediction Improves Predictive Ability for Dry Matter Yield and Water-Soluble Carbohydrates in Perennial Ryegrass.

In perennial ryegrass (Lolium perenne L), annual and seasonal dry matter yield (DMY) and nutritive quality of herbage are high-priority traits targeted for improvement through selective breeding. Genomic prediction (GP) has proven to be a valuable tool for improving complex traits and may be further enhanced through the use of multi-trait (MT) prediction models. In this study, we evaluated the relative performance of MT prediction models to improve predictive ability for DMY and key nutritive quality traits, using two different training populations (TP1, n = 463 and TP2, n = 517) phenotyped at multiple locations. MT models outperformed single-trait (ST) models by 24% to 59% for DMY and 67% to 105% for nutritive quality traits, such as low, high, and total WSC, when a correlated secondary trait was included in both the training and test set (MT-CV2) or in the test set alone (MT-CV3) (trait-assisted genomic selection). However, when a secondary trait was included in training set and not the test set (MT-CV1), the predictive ability was not statistically significant (p > 0.05) compared to the ST model. We evaluated the impact of training set size when using a MT-CV2 model. Using a highly correlated trait (rg = 0.88) as the secondary trait in the MT-CV2 model, there was no loss in predictive ability for DMY even when the training set was reduced to 50% of its original size. In contrast, using a weakly correlated secondary trait (rg = 0.56) in the MT-CV2 model, predictive ability began to decline when the training set size was reduced by only 11% from its original size. Using a ST model, genomic predictive ability in a population unrelated to the training set was poor (rp = -0.06). However, when using an MT-CV2 model, the predictive ability was positive and high (rp = 0.76) for the same population. Our results demonstrate the first assessment of MT models in forage species and illustrate the prospects of using MT genomic selection in forages, and other outcrossing plant species, to accelerate genetic gains for complex agronomical traits, such as DMY and nutritive quality characteristics.

Induction of anthocyanin in the inner epidermis of red onion leaves by environmental stimuli and transient expression of transcription factors.

KEY MESSAGE: Novel imaging approaches have allowed measurements of the anthocyanin induction in onion epidermal cells that can be induced through water stress or transient expression of exogenous transcription factors. Environmental and genetic mechanisms that allow the normally colourless inner epidermal cells of red onion (Allium cepa) bulbs to accumulate anthocyanin were quantified by both absorbance ratios and fluorescence. We observed that water-stressing excised leaf segments induced anthocyanin formation, and fluorescence indicated that this anthocyanin was spectrally similar to the anthocyanin in the outer epidermal cells. This environmental induction may require a signal emanating from the leaf mesophyll, as induction did not occur in detached epidermal peels. Exogenous transcription factors that successfully drive anthocyanin biosynthesis in other species were also tested through transient gene expression using particle bombardment. Although the petunia R2R3-MYB factor AN2 induced anthocyanin in both excised leaves and epidermal peels, several transcription factors including maize C1 and Lc inhibited normal anthocyanin development in excised leaves. This inhibition may be due to moderate levels of conservation between the exogenous transcription factors and endogenous Allium transcription factors. The over-expressed exogenous transcription factors cannot drive anthocyanin biosynthesis themselves, but bind to the endogenous transcription factors and prevent them from driving anthocyanin biosynthesis.

The Onion (Allium cepa L.) R2R3-MYB Gene MYB1 Regulates Anthocyanin Biosynthesis.

Bulb color is an important consumer trait for onion (Allium cepa L., Allioideae, Asparagales). The bulbs accumulate a range of flavonoid compounds, including anthocyanins (red), flavonols (pale yellow), and chalcones (bright yellow). Flavonoid regulation is poorly characterized in onion and in other plants belonging to the Asparagales, despite being a major plant order containing many important crop and ornamental species. R2R3-MYB transcription factors associated with the regulation of distinct branches of the flavonoid pathway were isolated from onion. These belonged to sub-groups (SGs) that commonly activate anthocyanin (SG6, MYB1) or flavonol (SG7, MYB29) production, or repress phenylpropanoid/flavonoid synthesis (SG4, MYB4, MYB5). MYB1 was demonstrated to be a positive regulator of anthocyanin biosynthesis by the induction of anthocyanin production in onion tissue when transiently overexpressed and by reduction of pigmentation when transiently repressed via RNAi. Furthermore, ectopic red pigmentation was observed in garlic (Allium sativum L.) plants stably transformed with a construct for co-overexpression of MYB1 and a bHLH partner. MYB1 also was able to complement the acyanic petal phenotype of a defined R2R3-MYB anthocyanin mutant in Antirrhinum majus of the asterid clade of eudicots. The availability of sequence information for flavonoid-related MYBs from onion enabled phylogenetic groupings to be determined across monocotyledonous and dicotyledonous species, including the identification of characteristic amino acid motifs. This analysis suggests that divergent evolution of the R2R3-MYB family has occurred between Poaceae/Orchidaceae and Allioideae species. The DNA sequences identified will be valuable for future analysis of classical flavonoid genetic loci in Allium crops and will assist the breeding of these important crop species.

Inhibition of platelet activation by lachrymatory factor synthase (LFS)-silenced (tearless) onion juice.

Onion and garlic are renowned for their roles as functional foods. The health benefits of garlic are attributed to di-2-propenyl thiosulfinate (allicin), a sulfur compound found in disrupted garlic but not found in disrupted onion. Recently, onions have been grown with repressed lachrymatory factor synthase (LFS) activity, which causes these onions to produce increased amounts of di-1-propenyl thiosulfinate, an isomer of allicin. This investigation into the key health attributes of LFS-silenced (tearless) onions demonstrates that they have some attributes more similar to garlic and that this is likely due to the production of novel thiosulfinate or metabolites. The key finding was that collagen-induced in vitro platelet aggregation was significantly reduced by tearless onion extract over normal onion extract. Thiosulfinate or derived compounds were shown not to be responsible for the observed changes in the inflammatory response of AGS (stomach adenocarcinoma) cells to tumor necrosis factor alpha (TNFα) when pretreated with model onion juices. A preliminary rat feeding trial indicated that the tearless onions may also play a key role in reducing weight gain.

Fast phenotyping of LFS-silenced (tearless) onions by desorption electrospray ionization mass spectrometry (DESI-MS).

Fast MS techniques have been applied to the analysis of sulfur volatiles in Allium species and varieties to distinguish phenotypes. Headspace sampling by proton transfer reaction (PTR) MS and surface sampling by desorption electrospray ionization (DESI) MS were used to distinguish lachrymatory factor synthase (LFS)-silenced (tearless; LFS-) onions from normal, LFS-active (tear-inducing; LFS+), onions. PTR-MS showed lower concentrations of the lachrymatory factor (LF, 3) and dipropyl disulfide 12 from tearless onions. DESI-MS of the tearless onions confirmed the decreased LF 3 and revealed much higher concentrations of the sulfenic acid condensates. Using DESI-MS with MS(2) could distinguish zwiebelane ions from thiosulfinate ions. DESI-MS gave reliable fast phenotyping of LFS+ versus LFS- onions by simply scratching leaves and recording the extractable ions for <0.5 min. DESI-MS leaf compound profiles also allowed the rapid distinction of a variety of Allium cultivars to aid plant breeding selections.

Genomics of biotrophic, plant-infecting plasmodiophorids using in vitro dual cultures.

The plasmodiophorids are a phylogenetically distinct group of parasitic protists that infect plants and stramenopiles, causing several important agricultural diseases. Because of the obligate intracellular part of their lifecycle, none of the plasmodiophorids has been axenically cultured. Further, the molecular biology of the plasmodiophorids is poorly understood because pure cultures are not available from any species. We report on an in-vitro dual culture system of the plasmodiophorids Plasmodiophora brassicae and Spongospora subterranea with their respective plant hosts, Brassica rapa and Solanum tuberosum. We show that these plasmodiophorids are capable of initiating and maintaining stable, long-term plant cell callus cultures in the absence of exogenous plant growth regulators. We show that callus cultures harbouring S. subterranea provide an excellent starting material for gene discovery from this organism by constructing a pilot-scale DNA library. Bioinformatic analysis of the sequences established that almost all of the DNA clones from this library were from S. subterranea rather than the plant host. The Spongospora genome was found to be rich in retrotransposable elements, and Spongospora protein-coding genes were shown to contain introns. The sequence of a near full-length non-LTR retrotransposon was obtained, the first transposable element reported from a cercozoan protist.

Efficient Agrobacterium tumefaciens-mediated transformation and regeneration of garlic (Allium sativum) immature leaf tissue.

Transgenic garlic (Allium sativum) plants have been recovered directly from immature leaf material by selective culture following Agrobacterium-mediated transformation. This method involved the use of a binary vector containing the mgfp-ER reporter gene and hpt selectable marker, and followed a similar protocol developed previously for the transformation of immature onion embryos. The choice of tissue and post-transformation selection procedure resulted in a large increase in recovery of transgenic plants compared with previously confirmed allium transformation protocols. The presence of transgenes in the genome of the plants was confirmed using Southern analysis. This improvement in frequency and the use of clonal commercial "Printanor" germplasm now makes possible the integration of useful agronomic and quality traits into this crop.

Silencing onion lachrymatory factor synthase causes a significant change in the sulfur secondary metabolite profile.

Through a single genetic transformation in onion (Allium cepa), a crop recalcitrant to genetic transformation, we suppressed the lachrymatory factor synthase gene using RNA interference silencing in six plants. This reduced lachrymatory synthase activity by up to 1,544-fold, so that when wounded the onions produced significantly reduced levels of tear-inducing lachrymatory factor. We then confirmed, through a novel colorimetric assay, that this silencing had shifted the trans-S-1-propenyl-l-cysteine sulfoxide breakdown pathway so that more 1-propenyl sulfenic acid was converted into di-1-propenyl thiosulfinate. A consequence of this raised thiosulfinate level was a marked increase in the downstream production of a nonenzymatically produced zwiebelane isomer and other volatile sulfur compounds, di-1-propenyl disulfide and 2-mercapto-3,4-dimethyl-2,3-dihydrothiophene, which had previously been reported in trace amounts or had not been detected in onion. The consequences of this dramatic simultaneous down- and up-regulation of secondary sulfur products on the health and flavor attributes of the onion are discussed.

Intron-rich gene structure in the intracellular plant parasite Plasmodiophora brassicae.

Plasmodiophora brassicae, a pathogen of Brassicaceae plants, is grouped within the eukaryotic supergroup, the Rhizaria. Although a large diversity of protists is found in the Rhizaria, genomes of organisms within the group have barely been examined. In this study, we identified DNA sequences spanning or flanking 24 P. brassicae genes, eventually sequencing close to 44 kb of genomic DNA. Evidence from this preliminary genome survey suggested that splicing is an important feature of P. brassicae gene expression; the P. brassicae genes were rich in spliceosomal introns and two mini-exons of less than 20 bp were identified. Consensus splice sites and branch-point sequences in P. brassicae introns were similar to those found in other eukaryotes. Examination of the promoter and transcription start sites of genes indicated that P. brassicae transcription is likely to begin from initiator elements rather than TATA-box containing promoters. Where neighbouring genes were confirmed, intergenic distances were short, ranging from 44 to 470 bp, but a number of larger DNA fragments containing no obvious genes were also sequenced.

Identification of genes from the obligate intracellular plant pathogen, Plasmodiophora brassicae.

Plasmodiophora brassicae is an intracellular pathogen that infects plants in the Brassicaceae family. Although an important pathogen group, information on the genomic makeup of the plasmodiophorids is almost completely lacking. We performed suppression subtractive hybridization (SSH) between RNA from P. brassicae-infected and uninfected Arabidopsis tissue, then screened 232 clones from the resulting SSH library. In addition, we used an oligo-capping procedure to screen 305 full-length cDNA clones from the infected tissue. A total of 76 new P. brassicae gene sequences were identified, the majority of which were extended to full length at the 5' end by the use of RACE amplification. Many of the unisequences were predicted to contain signal peptides for ER translocation. Although we located few sequences in total, these markedly increase available data from the plasmodiophorids, and provide new opportunities to examine plasmodiophorid biology. Our study also points towards the best methods for future plasmodiophorid gene discovery.

Agrobacterium-mediated transformation of Sclerotinia sclerotiorum.

Ascospores from the phytopathogenic fungus Sclerotinia sclerotiorum were transformed to hygromycin B resistance by co-cultivation with Agrobacterium tumefaciens. Transformed spores germinated and grew on PDA supplemented with 100 ug/ml hygromycin B. The presence of mitotically stable hph gene integration at random sites in the genome was confirmed by PCR and Southern blot analysis. A transformation frequency of 8 x 10(-5) was achieved in five separate experiments. This study is the first report of success co-cultivating A. tumefaciens with S. sclerotiorum. This report of a reproducible Agrobacterium-mediated transformation method should allow the development of T-DNA tagging as a system for insertional mutagenesis in S. sclerotiorum and provide a simple and reliable method for genetic manipulation.

Agrobacterium tumefaciens-mediated transformation of leek (Allium porrum) and garlic (Allium sativum).

Transgenic leek (Allium porrum) and garlic (Allium sativum) plants have been recovered by the selective culturing of immature leek and garlic embryos via Agrobacterium-mediated transformation using a method similar to that described by Eady et al. (Plant Cell Rep 19:376-381, 2000) for onion transformation. This method involved the use of a binary vector containing the m-gfp-ER reporter gene and nptII selectable marker, and followed the protocol developed previously for the transformation of onions with only minor modifications pertaining to the post-transformation selection procedure which was simplified to have just a single selection regime. Transgenic cultures were selected for their ability to express the m-gfp-ER reporter gene and grown in the presence of geneticin (20 mg/l). The presence of transgenes in the genome of the plants was confirmed using TAIL-PCR and Southern analysis. This is the first report of leek and "true seed" garlic transformation. It now makes possible the integration of useful agronomic and quality traits into these crops.