In contrast to most widespread broad-acre crops, the narrow-leafed lupin (Lupinus angustifolius L.) was domesticated very recently, in breeding programmes isolated in both space and time. Whereas domestication was initiated in Central Europe in the early twentieth century, the crop was subsequently industrialized in Australia, which now dominates world production. To investigate the ramifications of these bottlenecks, the genetic diversity of wild (n = 1,248) and domesticated populations (n = 95) was characterized using diversity arrays technology, and adaptation studied using G × E trials (n = 31) comprising all Australian cultivars released from 1967 to 2004 (n = 23). Principal coordinates analysis demonstrates extremely limited genetic diversity in European and Australian breeding material compared to wild stocks. AMMI analysis indicates that G × E interaction is a minor, albeit significant effect, dominated by strong responses to local, Western Australian (WA) optima. Over time Australian cultivars have become increasingly responsive to warm, intermediate rainfall environments in the northern WA grainbelt, but much less so to cool vegetative phase eastern environments, which have considerably more yield potential. G × E interaction is well explained by phenology, and its interaction with seasonal climate, as a result of varying vernalization responses. Yield differences are minimized when vegetative phase temperatures fully satisfy the vernalization requirement (typical of eastern Australia), and maximized when they do not (typical of WA). In breeding for WA optima, the vernalization response has been eliminated and there has been strong selection for terminal drought avoidance through early phenology, which limits yield potential in longer season eastern environments. Conversely, vernalization-responsive cultivars are more yield-responsive in the east, where low temperatures moderately extend the vegetative phase. The confounding of phenology and vernalization response limits adaptation in narrow-leafed lupin, isolates breeding programmes, and should be eliminated by widening the flowering time range in a vernalization-unresponsive background. Concomitantly, breeding strategies that will widen the genetic base of the breeding pool in an ongoing manner should be initiated.

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Phomopsis stem blight (PSB) caused by Diaporthe toxica is a major disease in narrow-leafed lupin ( Lupinus angustifolius L.). The F(2) progeny and the parental plants from a cross between a breeding line 75A:258 (containing a single dominant resistance gene Phr1 against the disease) and a commercial cultivar Unicrop (susceptible to the disease) were used for development of molecular markers linked to the disease resistance gene. Two pairs of co-dominant DNA polymorphisms were detected using the microsatellite-anchored fragment length polymorphism (MFLP) technique. Both pairs of polymorphisms were isolated from the MFLP gels, re-amplified by PCR, sequenced, and converted into co-dominant, sequence-specific and PCR-based markers. Linkage analysis by MAPMAKER suggested that one marker (Ph258M2) was 5.7 centiMorgans (cM) from Phr1, and the other marker (Ph258M1) was 2.1 cM from Ph258M2 but further away from Phr1. These markers are suitable for marker-assisted selection (MAS) in lupin breeding.

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T he main objective of a plant breeding program is selection of breeding lines which represent the greatest improvement relative to established varieties in terms of one or more traits. Therefore the effi ciency of a breeding program is measured through changes in yield performance over time (genetic gain). In statistical context it is expressed as potential genetic gain, measuring the average diff erence in performance among the lines entering the breeding program and those fi nally selected. The main concern in the selection process is the eff ect of V×E interactions, and the degree of uncertainty in identifi cation of varieties with broad or specifi c adaptation to the target environments. Effi cient analysis of multi-environment trials (METs) reduces the uncertainty and helps in understanding the V×E interactions.The linear mixed model approach to the analysis of plant breeding experiments, METs in particular, has become popular and widely used. These comprise: variance component models (Patterson et al.ABSTRACT Genetic gain is used as a long-term measure of the effi ciency of a breeding program. A spatial linear mixed model that includes a multiplicative mixed model (MMM) for the variety by environment (V×E) effect has been used for the analysis of 39 trials of 25 historical lupin varieties for the period of 1997 to 2006. The 25 varieties were produced by the Australian breeding effort from 1967 to 2007 and are a result from fi ve cycles of breeding. Genetic gain was assessed on the basis of the overall performance of the varieties across all environments based on the MMM results. The genetic gain from the fi rst early fl owering variety, Unicrop, to the highest yielding variety, Mandelup, represents a yield gain of 81% over 31 yr. The varieties' yield stability across the environments and their broad or specifi c adaptations are discussed.Abbreviations: AMMI, additive main eff ects and multiplicative interaction; AR1 × AR1, fi rst order autoregressive by fi rst order autoregressive; BLUE, best linear unbiased estimate; BLUP, best linear unbiased predictor; FA, factor analytic; GGE, genotype main eff ects and genotype × environment interaction; MET, multi-environment trials; MMM, multiplicative mixed model; PCA, principal components analysis; REML, residual maximum likelihood; REMLRT, residual maximum likelihood ratio test; V×E, variety by environment.

Next generation sequencing is quickly emerging as the go-to tool for plant virologists when sequencing whole virus genomes, and undertaking plant metagenomic studies for new virus discoveries. This study aims to compare the genomic and biological properties of Bean yellow mosaic virus (BYMV) (genus Potyvirus), isolates from Lupinus angustifolius plants with black pod syndrome (BPS), systemic necrosis or non-necrotic symptoms, and from two other plant species. When one Clover yellow vein virus (ClYVV) (genus Potyvirus) and 22 BYMV isolates were sequenced on the Illumina HiSeq2000, one new ClYVV and 23 new BYMV sequences were obtained. When the 23 new BYMV genomes were compared with 17 other BYMV genomes available on Genbank, phylogenetic analysis provided strong support for existence of nine phylogenetic groupings. Biological studies involving seven isolates of BYMV and one of ClYVV gave no symptoms or reactions that could be used to distinguish BYMV isolates from L. angustifolius plants with black pod syndrome from other isolates. Here, we propose that the current system of nomenclature based on biological properties be replaced by numbered groups (I–IX). This is because use of whole genomes revealed that the previous phylogenetic grouping system based on partial sequences of virus genomes and original isolation hosts was unsustainable. This study also demonstrated that, where next generation sequencing is used to obtain complete plant virus genomes, consideration needs to be given to issues regarding sample preparation, adequate levels of coverage across a genome and methods of assembly. It also provided important lessons that will be helpful to other plant virologists using next generation sequencing in the future.

The narrow-leafed lupin (Lupinus angustifolius L.) is a legume with much to offer to agriculture and human wellbeing through its adaptation to nitrogen- and phosphorus-deficient, acid, sandy soils, and production of nutritious, very low glycemic index grain with manifold health benefits. However, the industry has exploited only a small fraction of the genetic and adaptive diversity of the species, reflecting a short and fragmented domestication history. Given declining global production, unlocking the potential residing in untapped sources of genetic diversity to maximise yield and value is critical for the future of the crop. To this end, a wide range of genetic resources is under evaluation. The Australian Lupin Collection comprises almost 4600 diverse, mostly wild accessions, many of which have been genotyped using DArT (Diversity Array Technology) markers, and collection sites characterised to facilitate ecophysiology of contrasting material. Additional exotic genetic resources include recombinant inbred line and mutant populations, as well as inter-specific crosses. These resources are being used to investigate specific adaptation and genetic and molecular control of key traits, all of which will be expedited by current efforts to provide a reference genome sequence for L. angustifolius. Genetic base broadening is the current breeding focus, combining distantly related wild and domestic material with elite cultivars in double-backcrosses or topcrosses, with dramatic effects on yield. In future this will be complemented by marker-based, targeted trait introgression to improve narrow-leafed lupin adaptation, quality/value, and fit into the farming system.

Selection for phomopsis stem blight disease (PSB) resistance is one of the key objectives in lupin (Lupinus angustifolius L.) breeding programs. A cross was made between cultivar Tanjil (resistant to PSB) and Unicrop (susceptible). The progeny was advanced into F(8) recombinant inbred lines (RILs). The RIL population was phenotyped for PSB disease resistance. Twenty plants from the RIL population representing disease resistance and susceptibility was subjected to next-generation sequencing (NGS)-based restriction site-associated DNA sequencing on the NGS platform Solexa HiSeq2000, which generated 7,241 single nucleotide polymorphisms (SNPs). Thirty-three SNP markers showed the correlation between the marker genotypes and the PSB disease phenotype on the 20 representative plants, which were considered as candidate markers linked to a putative R gene for PSB resistance. Seven candidate markers were converted into sequence-specific PCR markers, which were designated as PhtjM1, PhtjM2, PhtjM3, PhtjM4, PhtjM5, PhtjM6 and PhtjM7. Linkage analysis of the disease phenotyping data and marker genotyping data on a F(8) population containing 187 RILs confirmed that all the seven converted markers were associated with the putative R gene within the genetic distance of 2.1 CentiMorgan (cM). One of the PCR markers, PhtjM3, co-segregated with the R gene. The seven established PCR markers were tested in the 26 historical and current commercial cultivars released in Australia. The numbers of "false positives" (showing the resistance marker allele band but lack of the putative R gene) for each of the seven PCR markers ranged from nil to eight. Markers PhtjM4 and PhtjM7 are recommended in marker-assisted selection for PSB resistance in the Australian national lupin breeding program due to its wide applicability on breeding germplasm and close linkage to the putative R gene. The results demonstrated that application of NGS technology is a rapid and cost-effective approach in development of markers for molecular plant breeding.