John Forster

La Trobe University · AgriBio Centre for AgriBioscience

Potatoes are an important human food crop, but have a number of yield limiting factors, including disease susceptibility. Potato virus Y (PVY) is found worldwide, and is one of the main virus problems for potato growers. PVY is transmitted by aphids and mechanically by machinery, tools and people, and symptoms are variable across cultivars and stra...

Development of grass–endophyte associations with minimal or no detrimental effects in combination with beneficial characteristics is important for pastoral agriculture. The feasibility of enhancing production of an endophyte-derived beneficial alkaloid through introduction of an additional gene copy was assessed in a proof-of-concept study. Sexual...

Ascochyta blight (AB), caused by Ascochyta fabae Speg., is an economically important disease that has been reported in most of the faba bean growing regions worldwide. Breeding for resistance is the most environmentally acceptable and economically feasible method to address the disease, for which a detailed understanding of the genetic basis of AB...

Key message Exploitation of data from a ryegrass breeding program has enabled rapid development and implementation of genomic selection for sward-based biomass yield with a twofold-to-threefold increase in genetic gain. Abstract Genomic selection, which uses genome-wide sequence polymorphism data and quantitative genetics techniques to predict pla...

A conventional potato breeding strategy uses targeted outcrossing, followed by phenotypic recurrent selection over a series of generations to identify improved cultivars. This paper reviews recent research in Australia aimed at improving the efficiency of such breeding. To develop marker-assisted selection (MAS) for traits of interest, our initial...

We have developed the first comprehensive simulator for polyploid genomes (PolySim), and demonstrated its value by performing large‐scale simulations to examine the effect of different population parameters on the evolution of polyploids. PolySim is unlimited in terms of ploidy, population size, or number of simulated loci. Our process considered t...

Table S2 Perennial ryegrass genetic map information and comparative genome analysis to rice and B. distachyon.

Table S3 Allele‐specific expression (ASE) sampling probabilities.

Table S4 Description of lines used in each of the 4 species.

Figure S1 Canola SNP coverage of the agronomically important trait blackleg disease resistance.

Figure S2 Gene ontology analysis in canola.

Table S1 Lentil genetic distance matrix.

Molecular characterisation has convincingly demonstrated some types of horizontal gene transfer in eukaryotes, but nuclear gene transfer between distantly related eukaryotic groups appears to have been rare. For angiosperms (flowering plants), nuclear gene transfer events identified to date have been confined to genes originating from prokaryotes o...

The application of genomics in crops has the ability to significantly improve genetic gain for agriculture. Many marker-dense tools have been developed but few have seen broad adoption in plant genomics due to issues of significant variations of genome size, levels of ploidy, single nucleotide polymorphism (SNP) frequency and reproductive habit. Wh...

RNA-Seq methodology has been used to generate a comprehensive transcriptome sequence resource for perennial ryegrass, an important temperate pasture grass species. A total of 931,547,255 reads were obtained from libraries corresponding to 19 distinct tissue samples, including both vegetative and reproductive stages of development. Assembly of data...

RNA sequencing (RNA-Seq) is a deep sequencing method used for transcriptome profiling. RNA-Seq assemblies have successfully been used for a broad variety of applications, such as gene characterisation, functional genomic studies, and gene expression analysis, particularly useful in the absence of a well-studied genome reference sequence. This study...

Lentil (Lens culinaris Medik.) is a diploid (2n = 2x = 14), self-pollinating, cool-season, grain legume that is cultivated worldwide and is highly valuable due to its high protein content. However, lentil production is constrained by many factors including biotic stresses, majority of which are fungal diseases such as ascochyta blight (AB), fusariu...

Flowering in perennial ryegrass (Lolium perenne L.) is induced by a period of short days and low temperatures (vernalisation), followed by long-day photoperiod conditions. Genetic linkage mapping and association genetics studies have collectively identified 36 quantitative trait loci for flowering time which were distributed across all seven linkag...

Competition with weeds is a major constraint to production of field pea in Australia, exacerbated by limited herbicide control options. Metribuzin is considered to be a safe herbicide, but may be phytotoxic to both weeds and target crop. A preliminary glasshouse-based assay was used to identify the optimal concentration required for discrimination...

Phalaris aquatica is a cool-season perennial grass species that is extensively cultivated in Australia, with additional usage in other areas of the world. Phalaris displays a number of desirable agronomic characteristics, although unfavourable traits include excessive seed shattering, sensitivity to aluminium toxicity, and several toxicosis syndrom...

Symbiotic associations between tall fescue grasses and asexual Epichloë fungal endophytes exhibit biosynthesis of alkaloid compounds causing both beneficial and detrimental effects. Candidate novel endophytes with favourable chemotypic profiles have been identified in germplasm collections by screening for genetic diversity, followed by metabolite...

Genomic selection (GS) has been recognized as offering numerous potential benefits for ryegrass (Lolium perenne L.) breeding. While the theoretical benefits of GS in ryegrass breeding are clear, the best way to apply GS in practical breeding programs remains to be determined. The present study aimed to investigate genomic breeding options that best...

RNA-Seq using second-generation sequencing technologies permits generation of a reference unigene set for a given species, in the absence of a well-annotated genome sequence, supporting functional genomics studies, gene characterisation and detailed expression analysis for specific morphophysiological or environmental stress response traits. A refe...

Lentil (Lens culinaris Medik.) is a self-pollinating, diploid, annual, cool-season, food legume crop that is cultivated throughout the world. Ascochyta blight (AB), caused by Ascochyta lentis Vassilievsky, is an economically important and widespread disease of lentil. Development of cultivars with high levels of durable resistance provides an envir...

Frequency distribution histogram. This file contains frequency histograms generated from AB resistance scores from lentil germplasm lines.

List of A. lentis isolate used for phenotyping. This file contain details of different A. lentis isolates used for phenotyping lentil mapping populations and the validation panel.

Consensus genetic linakge map statistics. This file contains details of different markers (SSRs and SNPs) and their corresponding positions on different LGs.

Linkage map statistics from IH × NF, IH × DIG, and NF × DIG maps. This file contains details of different markers (SSRs and SNPs) and their corresponding positions on different LGs.

BLASTN results of the markers. The data represents the BLASTN-based sequence analysis of DNA sequences underlying SNP markers assigned to three maps against M. truncatula genome (Mt4.0) and DNA sequences underlying SNP markers assigned on the Sharpe et al. (2013) map.

Comparison between linkage groups of IH × NF, IH × DIG, and NF × DIG maps. This file shows visual representation of the comparison of (A) all LGs in three different maps and the common marker loci between them, (B) LG5 from three maps and the common marker loci between them, (C) LG7 from three maps and the common marker loci between them, (D) LG6 f...

Frequency distribution histogram. This file contains frequency histograms generated from AB resistance scores in IH × NF and IH × DIG mapping populations.

Comparison between linkage groups of IH × NF, IH × DIG maps with consensus linkage map. This file shows visual representation of the comparison of (A) all LGs in IH × NF and IH × DIG maps with consensus map and the common marker loci between them, (B) LG5 from three maps and the common marker loci between them, (C) LG6 from three maps and the commo...

List of validation panel lines. The table provides the list of lentil validation panel lines used for marker validation with their respective germplasm category.

Phenotypic scores and genotypic data of the lentil germplasm set for the validation of AB resistance markers. This file contains the phenotypic scores of AB infection on lentil germplasm panel inoculated with A. lentis isolate FT12013 alongside genotyped markers for three QTL regions.

Potato (Solanum tuberosum L.) breeders consider a large number of traits during cultivar development and progress in conventional breeding can be slow. There is accumulating evidence that some of these traits, such as yield, are affected by a large number of genes with small individual effects. Recently, significant efforts have been applied to the...

Italian ryegrass is one of the most important temperate forage grasses on a global basis Improvement of both dry matter yield and quality of herbage have been major objectives of pastur grass breeding over the last century. F1 and F2 progeny sets derived from controlled pair-crosse between selected Italian ryegrass genotypes have been evaluated for...

Temperate pasture grasses form symbiotic associations with asexual fungal endophytes of the genus Epichloe. Viabilities of both seed and endophyte were assessed in cultivars of perennial ryegrass and tall fescue following different accelerated ageing (AA) treatments based on variations of relative humidity (RH) (80-100%) and duration at elevated te...

Faba bean (Vicia faba L.) is one of the most important cool-season legume species that is cultivated world-wide to produce protein-rich grain not only for human consumption but also for animal feed. A number of transcriptome sampling studies have previously been performed for faba bean, with an emphasis on specific developmental stages or environme...

Field pea is an important grain legume known for its nutritional value and rotational benefits including improving the soil fertility status through nitrogen fixation. However, one of the key constraints to Australian field pea production is weed competition due to the shortage of herbicide control options. Metribuzin is considered a safe herbicide...

RNA-Seq using second-generation sequencing technologies allows the generation of a reference unigene set for a given species, in the absence of a well-annotated genome sequence. Such a reference set will not only assist in functional genomics and gene characterisation, but also enable detailed expression analysis for the evaluation of specific morp...

The narrow genetic base of grain legume cultivars coupled with low utilization of genetic resources are the major factors limiting the breeding gains for these crops globally. Exploitation of new and diverse sources of variation is needed for the genetic enhancement of grain legumes including lentil. Knowledge of genetic variation and genetic relat...

Background. Multiplexed sequencing is commonly performed on massively parallel short-read sequencing platforms such as Illumina, and the efficiency of library normalisation can affect the quality of the output dataset. Although several library normalisation approaches have been established, none are ideal for highly multiplexed sequencing due to is...

Results of the TapeStation and MC assay. (A) The TapeStation results for the short DNA fragments, KAPA fragment and a single sequencing library, showing size distribution of dsDNA. The High Sensitivity D1000 kit (Agilent) was used for the short DNA and KAPA fragments. The y = 0 and x = 0 axes show the fluorescence intensity and DNA fragment size, r...

Quantification results of the 67 single libraries (12-cycled) with MC assay-, TapeStation-, and NanoDrop-based methods Sample unique identifier (e.g., A1) shows location in a 96-well microtiter plate during the MC assay. NTC stands for ’no-template control’. An empty cell in the result of the TapeStation-based method indicates that the DNA amount w...

Sequence and structure of in-house Y-shaped adaptor. (A) The PE1_adp_(+) and PE2_adp_(-) oligonucleotides were ordered from Integrated DNA Technologies (IDT; IA, USA). Asterisk (*) between nucleotides denotes a phosphorothioate modification. (B) PE1_adp_(+) and PE2_adp_(-) oligonucleotides were annealed through incubation at 94°C for 1 minutes, and...

Schematic explanation for the library quantification experiments and library pooling procedure

Coefficient of determination (R2) between the PRN from MiSeq sequencing and sum of dRFU values, depending on temperature ranges of the MC assay. The vertical and horizontal axes denote lower and upper range of the temperatures (°C) of the MC assay, respectively. The highest coefficient of determination (R2 = 0.823), which is from the PRN and dRFU v...

Quantification results of the 75 single libraries with MC assay-, and MiSeq sequencing-based methods Sample unique identifier shows location in a 96-well microtiter plate during the MC assay. NTC stands for ‘no-template control’. The average PRN was 1.33.

Quantification results of the 67 single libraries libraries (14-cycled) with MC assay-, and MiSeq sequencing-based methods Sample unique identifier shows location in a 96-well microtiter plate during the MC assay. NTC stands for ‘no-template control’. Single libraries were pooled according to the MC assay-based method. The D7 sample was not pooled,...

Correlation analysis between the sum of dRFU values between 75 and 95°C and quantification results from the TapeStation (A) and NanoDrop-based (B) methods

Details of the cost and processing duration assumption for the library normalisation or quantification methods. Price information for the major reagents was obtained from the websites of suppliers. Micropipette tips and 96-well microtiter plates are included in the consumables, and the per-sample cost for each of those was estimated as US0.04. SPRI...

Result of MC assay-based quantification and library normalisation procedure. A report file of the MC assay was exported from the CFX ConnectTM Real-Time PCR Detection System, and summation of dRFU between 86 and 95°C (A) was calculated for each single library. The sample ID 34 was excluded from the following procedure, as the summation was below 10...

Details for cost-reduced PCR amplicon sequencing library preparation with fragmentation produced by the MspJI restriction endonuclease. A cumulative length of 15 kb of DNA sequence can be enriched through 5 PCRs (3 kb × 5 reactions) using the MyFiTM DNA polymerase.

The ryegrass (Lolium) species, perennial ryegrass (Lolium perenne L.) and Italian ryegrass (Lolium multiflorum Lam.), are the two most important pasture grass species for global temperate regions and are also useful for amenity purposes. Due to an outbreeding reproductive habit, high levels of genetic heterogeneity are present within cultivated var...

Key message A targeted amplicon-based genotyping-by-sequencing approach has permitted cost-effective and accurate discrimination betweenryegrass species (perennial, Italian and inter-species hybrid), and identification of cultivars based on bulked samples. Abstract Perennial ryegrass and Italian ryegrass are the most important temperate forage spe...

Genomic selection (GS) provides an attractive option for accelerating genetic gain in perennial ryegrass (Lolium perenne L.) improvement given the long cycle times of most current breeding programs. The present study used simulation to investigate the level of genetic gain and inbreeding obtained from GS breeding strategies compared with traditiona...

Quantification of forage quality is essential for the identification of elite genotypes in forage grass breeding. Perennial ryegrass is the most important temperate species for global pastoral agriculture. However, the protein content of ryegrass generally exceeds the requirements of a grazing animal, and the ratio of water soluble carbohydrate (WS...

Fragmentation at random nucleotide locations is an essential process for preparation of DNA libraries to be used on massively parallel short-read DNA sequencing platforms. Although instruments for physical shearing, such as the Covaris S2 focused-ultrasonicator system, and products for enzymatic shearing, such as the Nextera technology and NEBNext...

Relatively modest levels of genetic gain have been achieved in conventional ryegrass breeding when compared to cereal crops such as maize, current estimates indicating an annual improvement of 0.25–0.6% in dry matter production. This property is partially due to an inability to effectively exploit heterosis through the formation of F1 hybrids. Cont...

Field pea (Pisum sativum L.) is a grain legume crop that is cultivated for either human or livestock consumption. Development of varieties adapted to damaging abiotic and biotic stresses is a major objective for field pea breeding. Bacterial blight is a serious disease caused by the pathogenic agents Pseudomonas syringae pv. syringae and Pseudomona...

Background: Field pea (Pisum sativum L.) is a cool-season grain legume that is cultivated world-wide for both human consumption and stock-feed purposes. Enhancement of genetic and genomic resources for field pea will permit improved understanding of the control of traits relevant to crop productivity and quality. Advances in second-generation sequ...

Perennial ryegrass (Lolium perenne L.) is one of the most important species for temperate pastoral agriculture, forming associations with genetically diverse groups of mutualistic fungal endophytes. However, only two taxonomic groups (E. festucae var. lolii and LpTG-2) have so far been described. In addition to these two well-characterised taxa, a...