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Lupins are underutilised pulse crops subject to increasing interest for human consumption of the high‐protein grain. They are also valued as a source of animal nutrition and make an excellent break crop in agricultural production systems. Like other orphan legumes, the genomic revolution has made it cost‐effective to also apply modern genetic and genomic approaches in lupins. These have predominantly been conducted in the two major domesticated lupin species, namely, narrow‐leafed lupin (NLL; Lupinus angustifolius) and white lupin (Lupinus albus), with transcriptome studies also emerging in other domesticated and undomesticated species. This review provides an overview of the current lupin genomic resources developed including two reference genomes for NLL and white lupin, several transcriptome resources and the development of pan‐genomes for NLL and white lupin, and describes how these offer great potential to increase grain yield and quality for these recently domesticated pulse crops. Furthermore, we highlight the importance of lupins to further our understanding of many aspects of fundamental legume biology. Combined, this will aid breeders and growers to improve lupin crops to help meet the increasing demand for plant protein in more sustainable cropping systems.

Narrow-leafed lupin (NLL, Lupinus angustifolius) is a promising legume crop that produces seeds with very high protein content. However, NLL accumulates toxic quinolizidine alkaloids (QAs) in most of its tissues, including the seeds. To determine the level of in situ biosynthesis in the seeds, we compared the accumulation of QAs with the expression of the biosynthetic gene lysine decarboxylase (LDC) in developing seeds and pods of a bitter (high-QA) variety of NLL. While QAs accumulated steadily in seeds until the drying phase, LDC expression was comparatively very low throughout seed development. In contrast, both QA accumulation and LDC expression peaked early in pods and decreased subsequently, reaching background levels at the onset of drying. We complemented these studies with MS imaging, which revealed the distribution patterns of individual QAs in cross-sections of pods and seeds. Finally, we show that a paternal bitter genotype does not influence the QA levels of F₁ seeds grown on a maternal, low-QA genotype. We conclude that the accumulation of QAs in seeds of bitter NLL is mostly, if not exclusively, transported from other tissues. These results open the possibility of using transport engineering to generate herbivore-resistant bitter NLL varieties that produce QA-free seeds.

Lupins (Lupinus spp.) are nitrogen-fixing legumes that accumulate toxic alkaloids in their protein-rich beans. These anti-nutritional compounds belong to the family of quinolizidine alkaloids (QAs), which are of interest to the pharmaceutical and chemical industries. To unleash the potential of lupins as protein crops and as sources of QAs, a thorough understanding of the QA pathway is needed. However, only the first enzyme in the pathway, lysine decarboxylase (LDC), is known. Here, we report the transcriptome of a high-QA variety of narrow-leafed lupin (L. angustifolius), obtained using eight different tissues and two different sequencing technologies. In addition, we present a list of 33 genes that are closely co-expressed with LDC and that represent strong candidates for involvement in lupin alkaloid biosynthesis. One of these genes encodes a copper amine oxidase able to convert the product of LDC, cadaverine, into 1-piperideine, as shown by heterologous expression and enzyme assays. Kinetic analysis revealed a low K M value for cadaverine, supporting a role as the second enzyme in the QA pathway. Our transcriptomic data set represents a crucial step towards the discovery of enzymes, transporters, and regulators involved in lupin alkaloid biosynthesis.

Narrow-leafed lupin (Lupinus angustifolius) is an important dryland crop, providing a protein source in global grain markets. While agronomic practices have successfully controlled many dicot weeds among narrow-leafed lupins, the closely related sandplain lupin (Lupinus cosentinii) has proven difficult to control, reducing yield and harvest quality. Here, we successfully trained a segmentation model to detect sandplain lupins and differentiate them from narrow-leafed lupins under field conditions. The deep learning model was trained using 9171 images collected from a field site in the Western Australian grain belt. Images were collected using an unoccupied aerial vehicle at heights of 4, 10, and 20 m. The dataset was supplemented with images sourced from the WeedAI database, which were collected at 1.5 m. The resultant model had an average precision of 0.86, intersection over union of 0.60, and F1 score of 0.70 for segmenting the narrow-leafed and sandplain lupins across the multiple datasets. Images collected at a closer range and showing plants at an early developmental stage had significantly higher precision and recall scores (p-value < 0.05), indicating image collection methods and plant developmental stages play a substantial role in the model performance. Nonetheless, the model identified 80.3% of the sandplain lupins on average, with a low variation (±6.13%) in performance across the 5 datasets. The results presented in this study contribute to the development of precision weed management systems within morphologically similar crops, particularly for sandplain lupin detection, supporting future narrow-leafed lupin grain yield and quality.

The main restraint obstructing the wider adoption of lupins as protein crops is the presence of bitter and toxic quinolizidine alkaloids (QAs), whose contents might increase under exposure to stressful environmental conditions. A poor understanding of how QAs accumulate hinders the breeding of sweet varieties. Here, we characterize the expression profiles of QA-related genes, along with the alkaloid content, in various organs of sweet and bitter narrow-leafed lupin (NLL, Lupinus angustifolius L.). Special attention is paid to the RAP2-7 transcription factor, a candidate regulator of the QA pathway. We demonstrate the upregulation of RAP2-7 and other QA-related genes, across the aerial organs of a bitter cultivar and the significant correlations between their expression levels, thus supporting the role of RAP2-7 as an important regulatory gene in NLL. Moreover, we showed that the initial steps of QA synthesis might occur independently in all aerial plant organs sharing common regulatory mechanisms. Nonetheless, other regulatory steps might be involved in RAP2-7-triggered QA accumulation, given its expression pattern in leaves. Finally, the examination of QA-related gene expression in plants infected with Colletotrichum lupini evidenced no connection between QA synthesis and anthracnose resistance, in contrast to the important role of polyamines during plant–pathogen interactions.

Legumes are of great economic importance. Depending on the species, they are cultivated for food, fodder, green manure, and even as ornamentals. Legume seeds contain many valuable nutrients and also anti-nutritional substances. The aim of the study is to compare important seed quality traits in pea (Pisum sativum L.), faba bean (Vicia faba L.), white lupin (Lupinus albus L.), narrow-leafed lupin (Lupinus angustifolius L.), and yellow lupine (Lupinus luteus L.) to soybean (Glycine max (L.) Merr.). It was shown that the obtained parameters were significantly affected by the interaction of species with the years of study. Soybean was characterized by high seed and protein yield and favorable seed chemical composition (protein, fat, phosphorus, potassium, magnesium, and micronutrients, except manganese). Faba bean yields were high but varied over the years. Faba bean seeds were rich in phosphorus and copper. Pea yielded satisfactorily, and the seeds contained high iron and low fiber contents. Of the three lupin species, white lupin yielded the highest, while narrow-leafed and yellow lupin yields were low. However, yellow lupin seeds had a favorable chemical composition because they were rich in protein, calcium, phosphorus, magnesium, copper, and zinc. In conclusion, legumes are valued worldwide and could be a base for the development of many functional foods to promote human health.

Narrow-leafed lupin (Lupinus angustifolius L.) is the predominant grain legume crop in southern Australia, contributing half of the total grain legume production of Australia. Its yield in Australia is hampered by a range of subsoil constraints. The adaptation of lupin genotypes to subsoil constraints may be improved by selecting for optimal root traits from new and exotic germplasm sources. We assessed root trait diversity and genetic diversity of a core collection of narrow-leafed lupin (111 accessions) using 191 Diversity Arrays Technology (DArT) markers. The genetic relationship among accessions was determined using the admixture model in STRUCTURE. Thirty-eight root-associated traits were characterized, with 21 having coefficient of variation values >0.5. Principal coordinate analysis and cluster analysis of the DArT markers revealed broad diversity among the accessions. An ad hoc statistics calculation resulted in 10 distinct populations with significant differences among and within them (P < 0.001). The mixed linear model test in TASSEL showed a significant association between all root traits and some DArT markers, with the numbers of markers associated with an individual trait ranging from 2 to 13. The percentage of phenotypic variation explained by any one marker ranged from 6.4 to 21.8%, with 15 associations explaining >10% of phenotypic variation. The genetic variation values ranged from 0 to 7994, with 23 associations having values >240. Root traits such as deeper roots and lateral root proliferation at depth would be useful for this species for improved adaptation to drier soil conditions. This study offers opportunities for discovering useful root traits that can be used to increase the yield of Australian cultivars across variable environmental conditions.

Flowering is initiated in response to environmental cues, with the photoperiod and ambient temperature being the main ones. The regulatory pathways underlying floral transition are well studied in Arabidopsis thaliana but remain largely unknown in legumes. Here, we first applied an in silico approach to infer the regulatory inputs of four FT-like genes of the narrow-leafed lupin Lupinus angustifolius. We studied the roles of FTc1, FTc2, FTa1, and FTa2 in the activation of meristem identity gene AGL8 in response to 8 h and 16 h photoperiods, vernalization, and the circadian rhythm. We developed a set of regression models of AGL8 regulation by the FT-like genes and fitted these models to the recently published gene expression data. The importance of the input from each FT-like gene or their combinations was estimated by comparing the performance of models with one or few FT-like genes turned off, thereby simulating loss-of-function mutations that were yet unavailable in L. angustifolius. Our results suggested that in the early flowering Ku line and intermediate Pal line, the FTc1 gene played a major role in floral transition; however, it acted through different mechanisms under short and long days. Turning off the regulatory input of FTc1 resulted in substantial changes in AGL8 expression associated with vernalization sensitivity and the circadian rhythm. In the wild ku line, we found that both FTc1 and FTa1 genes had an essential role under long days, which was associated with the vernalization response. These results could be applied both for setting up new experiments and for data analysis using the proposed modeling approach.

Background & Aims Searching for root traits underpinning efficient nutrient acquisition has received increased attention in modern breeding programs aimed at improved crop productivity. Root models provide an opportunity to investigate root-soil interactions through representing the relationships between rooting traits and the non-uniform supply of soil resources. This study used simulation modelling to predict and identify phenotypic plasticity, root growth responses and phosphorus (P) use efficiency of contrasting Lupinus angustifolius genotypes to localised soil P in a glasshouse. Methods Two L. angustifolius genotypes with contrasting root systems were grown in cylindrical columns containing uniform soil with three P treatments (nil and 20 mg P kg⁻¹ either top-dressed or banded) in the glasshouse. Computer simulations were carried out with root architecture model ROOTMAP which was parameterized with root architectural data from an earlier published hydroponic phenotyping study. Results The experimental and simulated results showed that plants supplied with banded P had the largest root system and the greatest P-uptake efficiency. The P addition significantly stimulated root branching in the topsoil, whereas plants with nil P had relatively deeper roots. Genotype-dependent root growth plasticity in response to P supply was shown, with the greatest response to banded P. Conclusions Both experimental and simulation outcomes demonstrated that 1) root hairs and root proliferation increased plant Ρ acquisition and were more beneficial in the localised Ρ fertilisation scenario, 2) placing Ρ deeper in the soil might be a more effective fertilisation method with greater Ρ uptake than top dressing, and 3) the combination of Ρ foraging strategies (including root architecture, root hairs and root growth plasticity) is important for efficient Ρ acquisition from a localised source of fertiliser P.

The fungus, Diaporthe toxica, anamorph Phomopsis sp., previously classified as P. leptostromiformis, is a plant endophyte and occasional pathogen, causing Phomopsis stem blight. This disease is damaging not only to lupins but also to the animals grazing on infected plants, due to the toxic secondary metabolites called phomopsins. The aim of this work was to validate markers for resistance to Phomopsis stem blight in narrow-leafed lupins and identify novel germplasm with increased levels of resistance to the disease. Plant inoculations were performed using ten isolates of D. toxica, originating from Australia and Poland. The European core collection of L. angustifolius was evaluated both in a controlled environment and with field experiments to classify the accessions based on their resistance to the disease. Simultaneously, the accessions were assayed with disease resistance markers to identify donors of hypothetical resistance alleles. We have found that the European lupin germplasm collection preserves wild and domesticated donors of at least two resistance genes to Phomopsis stem blight, including Phr1 and PhtjR. Molecular markers PhtjM7, InDel2, and InDel10, tagging PhtjR gene, were applicable for marker-assisted selection targeting the European gene pool with an expected accuracy of 95%. None of diagnostic markers for the Phr1 locus was found useful for European breeding programs; two existing markers Ph258M1 and Ph258M2 were unreliable, due to a high percentage of false-positive results (up to 58%) and a high recombination rate between markers (~ 30%).