Biology subjects

Kroc, M.

Publications and source records attributed to Kroc, M..

4 recordsLinked to original sources

bioRxiv2026

Multi-omics insights into quinolizidine alkaloid biosynthetic architecture in narrow-leafed lupin genotypes with contrasting alkaloid regulation

Quinolizidine alkaloids restrict the use of lupin seeds as food and feed. In narrow-leafed lupin, low-alkaloid content in most cultivars has been traced to the recessive iucundus locus, with the RAP2-7 transcription factor as a candidate regulator, yet the molecular basis of alternative low-alkaloid sources remains unclear. Here we provide a comparative view of alkaloid pathway and its regulation across two genetic backgrounds, the iucundus and Iucundus contrast and the Bryansk low-alkaloid background carrying the Iucundus-type RAP2-7 allele. This multi-omic framework integrates alkaloid profiling and transcriptomics alongside RAP2-7 DNA binding characterization, and sequence-level motif and variant analyses. Alkaloid profiles revealed genotype-specific differences, with Bryansk lines showing a distinct, sparteine-enriched and lupanine-depleted chemotype relative to iucundus and Iucundus. Using Iucundus line as a reference, transcriptome analyses highlighted candidate genes associated with low-alkaloid iucundus and Bryansk backgrounds, spanning enzymes, transporters and putative regulators. Consistent with a key role of RAP2-7, DAP-seq summits in Iucundus and Bryansk contained a clear AP2-like motif, whereas the iucundus background showed both strong depletion of high-confidence peaks and no defined motif. In silico modelling of RAP2-7 bound to its DNA motif, combined with DAP-seq and expression data, supported reduced binding of the iucundus variant relative to Iucundus, as well as a crucial mutation within the promoter of key acyltransferase (LaAT). Collectively, these data extend lupin transcriptomic resources and refine models of alkaloid biosynthesis beyond classical iucundus sources, and within this comparative framework, provide the first comprehensive molecular characterization of Bryansk low-alkaloid lines.

genomics↗

bioRxiv2024

Genetic and phenotypic characterization of global Lupinus albus genetic resources for the development of a CORE collection

Lupinus albus is a food grain legume recognized for its high levels of seed protein (30-40%) and oil (6-13%), and its adaptability to different climatic and soil conditions. To develop the next generation of L. albus cultivars, we need access to well-characterized, genetically and phenotypically diverse germplasm. Here we evaluated more than 2000 L. albus accessions with passport data based on 35 agro-morphological traits to develop Intelligent CORE Collections. The reference CORE (R-CORE), representing global diversity, exemplified the genotypic variation of cultivars, breeding/research materials, landraces and wild relatives. A subset of 300 R-CORE accessions was selected as a training CORE (T-CORE), representing the diversity in the entire collection. We divided the L. albus R-CORE into four phenotypic groups (A1, A2, A3 and B) based on principal component analysis, with groups A3 and B distinguished by pod shattering and seed ornamentation, respectively. The coefficient of additive genetic variation differed across morphological traits, phenotypic groups, geographic regions, and according to biological status. These CORE collections will facilitate agricultural research by identifying the genes responsible for desirable traits in crop improvement programs, and by shedding light on the use of orphan genetic resources for origin and domestication studies in L. albus. Understanding the variation in these genetic resources will allow us to develop sustainable tools and technologies that address global challenges such as providing healthy and sustainable diets for all, and contrasting the current climate change crisis.

plant biology↗

bioRxiv2024

The unexplored diversity of wild lupins provides rich genomic resources and insights into lupin evolution

Lupin crops provide nutritious seeds as an excellent source of dietary protein. However, extensive genomic resources are needed for the adaptation of lupin crops, particularly to improve their nutritional value and facilitate their adaptation to harsh environments caused by the changing climate. Such resources can be derived from crop wild relatives, which represent a large untapped source of genetic variation for crop improvement. Here we describe the first whole-genome sequences of the cross-compatible species Lupinus cosentinii (Mediterranean) and its pan-Saharan wild relative L. digitatus, which are well adapted to drought-prone environments and partially domesticated. We found that both species are tetraploids, with similar genome structures, distributions of gene duplications, and numbers of expanded and contracted gene families. The expansion and contraction of gene families that determine seed size, a paradigmatic domestication trait, indicates that gene duplication may have led to morphological adaptations in L. cosentinii and L. digitatus differing from those in L. albus, a domesticated lupin used as a reference. Seed size may therefore reflect convergent evolution mechanisms that play a key role in lupin domestication.

plant biology↗

bioRxiv2020

Pangenome of white lupin provides insights into the diversity of the species

BackgroundWhite 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 is still missing. ResultsHere, we report the genome sequencing of several accessions that were used to establish a white lupin pangenome. We defined core genes that are present in all individuals and variable genes that are absent in some and may represent a gene pool for stress adaptation. We believe that the identification of novel genes, together with a more comprehensive reference sequence, represents a significant improvement of the white lupin genetic resources. As an example, we used this pangenome to identify selection footprints and to provide a candidate gene for one of the main QTLs associated with late flowering in Ethiopian lupin types. A 686 nucleotide deletion was identified in exon 3 of the LaFTa1 (Lupinus albus Flowering Time a1) gene that suggests a molecular origin for this trait of importance, defining the need for vernalization in some lupins. ConclusionsThe white lupin pangenome provides a novel genetic resource to better understand how domestication has shaped the genomic variability amongst this crop. It will be of major importance for breeders to select new breeding traits and incorporate them into new, more efficient and robust cultivars in order to face a growing demand for plant protein sources, notably in Europe.

plant biology↗