SUMMARY: Food legumes are crucial for all agriculture‐related societal challenges, including climate change mitigation, agrobiodiversity conservation, sustainable agriculture, food security and human health. The transition to plant‐based diets, largely based on food legumes, could present major opportunities for adaptation and mitigation, generating significant co‐benefits for human health. The characterization, maintenance and exploitation of food‐legume genetic resources, to date largely unexploited, form the core development of both sustainable agriculture and a healthy food system. INCREASE will implement, on chickpea (Cicer arietinum), common bean (Phaseolus vulgaris), lentil (Lens culinaris) and lupin (Lupinus albus and L. mutabilis), a new approach to conserve, manage and characterize genetic resources. Intelligent Collections, consisting of nested core collections composed of single‐seed descent‐purified accessions (i.e., inbred lines), will be developed, exploiting germplasm available both from genebanks and on‐farm and subjected to different levels of genotypic and phenotypic characterization. Phenotyping and gene discovery activities will meet, via a participatory approach, the needs of various actors, including breeders, scientists, farmers and agri‐food and non‐food industries, exploiting also the power of massive metabolomics and transcriptomics and of artificial intelligence and smart tools. Moreover, INCREASE will test, with a citizen science experiment, an innovative system of conservation and use of genetic resources based on a decentralized approach for data management and dynamic conservation. By promoting the use of food legumes, improving their quality, adaptation and yield and boosting the competitiveness of the agriculture and food sector, the INCREASE strategy will have a major impact on economy and society and represents a case study of integrative and participatory approaches towards conservation and exploitation of crop genetic resources.

Summary: White lupin is an old crop with renewed interest due to its seed high protein content and high nutritional value. Despite a long domestication history in the Mediterranean basin, modern breeding efforts have been fairly scarce. Recent sequencing of its genome has provided tools for further description of genetic resources but detailed characterization of genomic diversity is still missing. Here, we report the genome sequencing of 39 accessions that were used to establish a white lupin pangenome. We defined 32 068 core genes that are present in all individuals and 14 822 that are absent in some and may represent a gene pool for breeding for improved productivity, grain quality, and stress adaptation. We used this new pangenome resource to identify candidate genes for alkaloid synthesis, a key grain quality trait. The white lupin pangenome provides a novel genetic resource to better understand how domestication has shaped the genomic variability within this crop. Thus, this pangenome resource is an important step towards the effective and efficient genetic improvement of white lupin to help meet the rapidly growing demand for plant protein sources for human and animal consumption.

SUMMARY: Legumes represent an important component of human and livestock diets; they are rich in macro‐ and micronutrients such as proteins, dietary fibers and polyunsaturated fatty acids. Whilst several health‐promoting and anti‐nutritional properties have been associated with grain content, in‐depth metabolomics characterization of major legume species remains elusive. In this article, we used both gas chromatography–mass spectrometry (GC‐MS) and liquid chromatography–mass spectrometry (LC‐MS) to assess the metabolic diversity in the five legume species commonly grown in Europe, including common bean (Phaseolus vulgaris), chickpea (Cicer arietinum), lentil (Lens culinaris), white lupin (Lupinus albus) and pearl lupin (Lupinus mutabilis), at the tissue level. We were able to detect and quantify over 3400 metabolites covering major nutritional and anti‐nutritional compounds. Specifically, the metabolomics atlas includes 224 derivatized metabolites, 2283 specialized metabolites and 923 lipids. The data generated here will serve the community as a basis for future integration to metabolomics‐assisted crop breeding and facilitate metabolite‐based genome‐wide association studies to dissect the genetic and biochemical bases of metabolism in legume species.

Unravelling the biosynthetic pathway of quinolizidine alkaloids (QAs), regarded as antinutritional compounds of narrow-leafed lupin (NLL) seeds, is fundamental to best exploit NLL as food or feed. We investigated 12 candidate genes connected to QA biosynthesis, selecting them by transcriptomic and genomic approaches, from the landscape of genes differentially expressed in leaves of the high- and low-alkaloid NLL accessions. Linkage analysis enabled the assessment of the location of the candidate genes in relation to iucundus, a major locus of unknown identity, that confers reduced QA content in seeds. The key finding was the identification of APETALA2/ethylene response transcription factor, RAP2-7, cosegregating with the iucundus locus and located within a region with highly significant QTLs that affect QA composition. We additionally identified a 4-hydroxy-tetrahydrodipicolinate synthase (DHDPS) gene involved in L-lysine biosynthesis as being closely linked to iucundus. The distributed location of other remaining candidates (including previously known QA genes) across different linkage groups, also indirectly supports the transcription factor as a possible regulator of lupin alkaloid biosynthesis. Our findings provide crucial insight into QA biosynthesis in NLL. Additionally, we evaluated and selected appropriate reference genes for qRT-PCRs to analyse the expression levels of QA genes in NLL.

White lupin (Lupinus albus L.) has unexploited potential as a crop plant due to its high seed yield as well as protein and oil content in seeds. Well-characterized collections of gene resources are very important for breeding as a source of genetic variation. This paper presents the results of analyses for total content and qualitative composition of alkaloids in seeds of 367 L. albus accessions from the Polish Genebank. Accessions were divided into four classes of origin: wild collected material, land races, breeding lines, and cultivars. Apart from the expected broad variation as well as strong differentiation in the alkaloid content, a clear influence of domestication was observed. This was shown as an apparent decrease in the alkaloid content in breeding lines and cultivars classes. The total alkaloid content varies from 0.02 to 12.73% of the seed dry weight. Six major alkaloids (abundance >1%) were revealed: lupanine (28.22–94.49%, mean 76.06% in total content), 13-hydroxylupanine (0.10–32.78%, mean 8.23%), multiflorine (0.00–21.67%, mean 5.52%), albine (0.00–18.55%, mean 4.48%), angustifoline (0.24–12.14%, mean 2.07%), 11,12-seco-12,13-didehydromultiflorine (0.00–12.28%, mean 1.74%). Owing to its abundance, lupanine was found to be the most closely correlated to the total alkaloid content.