Biology subjects

Papa, R.

Publications and source records attributed to Papa, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Multi-omic analysis reveals the genetic architecture of water-deficit stress in Phaseolus vulgaris

Common bean (Phaseolus vulgaris L.) is one of the most important grain legumes for direct human consumption. Currently, 60% of its production is estimated to be at risk due to drought. However, the genetic basis of common beans drought resistance is poorly understood. To this end, we assessed the genetic architecture of drought-responsive changes in a whole genome-sequenced population of 218 common bean accessions. Using multi-omics-based trait evaluation, including lipidomics, photosynthetic and agronomic traits, followed by multi-omics genome-wide association studies (moGWAS), yielded in the detection of a myriad of moQTL for photosynthesis and yield, as well as the levels of various lipids. QTL associated with glycolipids, which are integral to photosynthesis, since they constitute the major membrane components of chloroplasts, were identified. In addition, we molecularly validated several lipid-related candidate genes via P. vulgaris hairy root transformation as well as transient expression in tobacco. In particular, a lipoxygenase and an allene oxide synthase were identified as explaining the variation in triacylglycerol by oxylipin production. These data provide a blueprint for multi-omics-assisted improvement of crop water stress resilience.

plant biology↗

bioRxiv2025

Polygenic basis of incipient reproductive isolation in hybridizing populations is revealed by pangenomic and epigenetic divergence

Incipient reproductive isolation in the presence of gene flow has traditionally been attributed to a small number of major-effect loci under strong selection, representing only a minor fraction of the genome. Using the Heliconius erato adaptive radiation--a butterfly species with populations at varying levels of genetic differentiation--we employed a pan-genome approach to investigate genome-wide mutational divergence, epigenetic changes, and structural variation contributing to divergence. In contrast to earlier studies that identified only a few highly divergent loci, our high-resolution analysis reveals widespread divergence across the genome, suggesting polygenic barriers to gene flow. Epigenetic divergence assessed using ATAC-seq, highlights population-specific differences in chromatin accessibility, which may reflect SNPs distribution or precede genetic differentiation by reshaping regulatory landscapes. We also identified new structural variants, including polymorphic indels in open chromatin, that further associate with genomic divergence. Together, these findings show that the genomic landscape of H. erato is shaped by a dynamic interplay of mutational changes, epigenetic modifications, and structural variation. We emphasize the role of developmental, behavioral, and ecological adaptations and provide a broader perspective on the functional genetic basis of genome-wide divergence in Heliconius. This emerging polygenic framework offers a more detailed understanding of how reproductive barriers evolve under ongoing gene flow.

evolutionary biology↗

bioRxiv2025

WntA expression and wing transcriptomics illuminate the evolution of stripe patterns in skipper butterflies

Skippers (Hesperiidae) form a distinct lineage of butterflies where the developmental mechanisms of color patterning have seldom been studied. The wing patterns of skippers often consist of median stripes, and classic comparative morphology studies suggest these elements are homologous to the Central Symmetry System (CSS) found in nymphalid butterflies. Consistent with this hypothesis, we show here that expression of the signaling ligand gene WntA, a marker of the CSS in nymphalids, prefigures the position of the main wing patterns of the silver-spotted skipper Epargyreus clarus. Notably, WntA expression is associated with different color outputs in the forewing vs. hindwing, validating a theory of pattern homology from the mid-twentieth century. To further gain insights into the genes associated with this patterning process, we generated an annotated genome for E. clarus and performed an RNAseq study profiling gene expression along the proximo-distal (P-D) axis of early pupal wings. These data suggest that the transcription factor genes lobe, u-shaped, and odd-paired are expressed in restricted P-D sections of the wing similarly to WntA, indicating they may participate in the patterning of the CSS. In addition, inverted expression patterns of dachsous and four-jointed, as well as the expression of transcription factors with roles in specifying proximal (homothorax, tiptop/teashirt) and distal (vestigial, scalloped) section of ths Drosophila wing disk, suggest a deep conservation of wing P-D patterning process between Diptera and Lepidoptera. This work highlights the developmental homology between the CSS of Hesperiidae and Nymphalidae, and enriches our knowledge of patterning mechanisms in lepidopteran wings. Summary StatementThis study reveals how skipper butterfly wing stripes share deep developmental origins with other butterflies, offering fresh insight into wing pattern evolution.

developmental biology↗

bioRxiv2025

Genotype by Environment Interaction influenced the content of crude protein and total amino acids in lentil varieties

Lentil (Lens culinaris Medik) is a globally important grain legume valued for its high protein content and nutritional quality. However, the genetic and environmental factors influencing protein and amino acid composition, particularly the role of genotype x environment interaction (GEI), remain partially uncovered. This study evaluated 15 diverse lentil genotypes across seven agronomic trials spanning multiple years, sowing seasons, and locations to assess the effects of genotype, environment, and GEI on crude protein (CP), crude protein yield (CPY), total amino acids (TAA), and total amino acid yield (TAAY). Advanced statistical models such as AMMI, GGE, and WAASB were employed to dissect the contributions of genetic and environmental components and to identify stable, high-performing genotypes. Results revealed significant phenotypic variation for CP, Amino Acids (AA), and TAA among genotypes. Seasonal variation, especially between autumn and spring sowings, was the primary environmental driver of GEI for both CP and CPY. Notably, some landraces (PI_431710_LSP, PI_431739_LSP, PI_431753_LSP, IG_1959) demonstrated both high productivity and stability across environments, while others excelled in specific mega-environments identified through GGE analysis. Our findings emphasize the importance of integrating into lentil breeding programs, stability and adaptability, and a more comprehensive approach to measure the yield (e.g., CPY, MegaJoule, ammino acid composition and TAAY), which takes into account the quality and the effective energetic production of a crop. From this perspective, we highlight landraces as valuable sources of genetic diversity for improving yield. This work provides a foundation for targeted breeding strategies aimed at developing lentil varieties with enhanced protein content, balanced amino acid profiles, and resilience to environmental variability

genetics↗

bioRxiv2025

Newly-identified lentil genotypes adapted to Mediterraneanagro-ecosystems

Lentil cultivation and consumption promote human health and sustainable agriculture, making a significant contribution to the transition toward a plant-based diet. In Europe, lentil yields are still unstable, and the lack of breeding efforts limits the choice of farmers to few varieties. Here, we characterized 46 lentil genotypes, including local cultivars and landraces from diverse geographic origins, in Mediterranean agro-environments for flowering, architectural and production traits in seven field trials, over 3 years (2019-2021), in two localities (central and southern Italy) and during two sowing seasons (autumn and spring). We estimated the genetic merit of each genotype and identified outperforming genotypes for all traits. Indian ILL 11557AGL and Argentinian IL 4605AGL domesticated varieties resulted superior for earliness. Italian landraces and French cultivars achieved the highest values for first pod height, while landraces and breeding materials from Ethiopia, Syria and Iran were the best-yielding. Data from all seven trials were available for 16 genotypes, so we analyzed the genotype, environment and genotype x environment interaction (GEI) to identify specific genotypic adaptations. European cultivars performed well for architectural traits, whereas the best-yielding genotypes were Middle Eastern and Ethiopian landraces. Environmental effect on yield related to sowing season and locality was detected, with an overall higher yield in autumn compared to spring sowing trials and in central rather than southern Italy. By dissecting the GEI structure using additive main effect and multiplicative interaction (AMMI) analysis and Weighted Average of Absolute Scores (WAASB) index, we identified a group of Iranian landraces (PI 431633 AGL and PI 432033 LSP AGL) adapted to both autumn and spring sowing and one Ethiopian landrace (IG 1959 AGL) showing high yield stability across all environmental conditions. These findings provide a foundation to unlock the full potential of lentil cultivation in European and Mediterranean systems by identifying adapted, high-performing genotypes.

genetics↗

bioRxiv2025

Metabolite-based genome-wide association studies enable the dissection of the genetic bases of bioactive compounds in Chickpea seeds

Chickpea, is the second most consumed food legume, and significantly contributes to the human diet. Chickpea seeds are rich in a wide range of metabolites including bioactive specialized metabolites influencing nutritional qualities and human health. However, the genetic basis underlying the metabolite-based nutrient quality in chickpea remains poorly understood. Here we dissected the genetic architecture of seed metabolic diversity and explored how domestication shaped the chickpea metabolome. Through UPLC-MS we quantify over 3400 metabolic features in 509 chickpea seeds accessions from three independent multi-location field trials. The metabolite genome-wide association study (mGWAS) detected around 130,000 leading SNPs corresponding to 1890 metabolites across different environments. We further found and functionally validated a gene cluster of three CabHLH transcription factors that regulate soyasaponin biosynthesis in chickpea seeds. Our results reveal new insights on the effects of domestication process on chickpea metabolome. and provide valuable resources for the genetic improvement of the bioactive compounds in chickpea seeds.

plant biology↗

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

Landscape genomics highlights the adaptive evolution of chickpea

Environmental heterogeneity and human-mediated dispersal have jointly shaped the genetic diversity and local adaptation of crop species. Understanding the genetic basis of these processes is essential for improving crops across diverse agro-environmental conditions. We characterized population structure and geographic patterns of genetic diversity in 532 chickpea genotypes spanning most of the cultivated range. Using redundancy analysis on 208 georeferenced landrace-derived genotypes from the Mediterranean Basin to Central Asia, we identified genotype-environment associations (GEAs) and traced adaptive variation along historical Silk Road routes. Both environmental and geographic factors significantly shaped chickpea diversity. GEA loci were enriched for genes involved in heat and drought tolerance, while key geographic regions harbored reservoirs of adaptive alleles and early-flowering genotypes, supporting flowering time as an escape strategy from terminal stress. These findings provide a genomic framework for integrating climate-adaptive alleles into chickpea breeding programs targeting drought- and heat-prone environments.

genomics↗

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↗

bioRxiv2024

A long non-coding RNA at the cortex locus controls adaptive colouration in butterflies

Evolutionary variation in the wing pigmentation of butterflies and moths offers striking examples of adaptation by crypsis and mimicry. The cortex locus has been independently mapped as the locus controlling colour polymorphisms in 14 lepidopteran species, suggesting it acts as a genomic hotspot for the diversification of wing patterns, but functional validation through protein-coding knockouts has proven difficult to obtain. Our study unveils the role of a novel long non-coding RNA (lncRNA) which we name ivory, transcribed from the cortex locus, in modulating colour patterning in butterflies. Strikingly, ivory expression prefigures most melanic patterns during pupal development, suggesting an early developmental role in specifying scale identity. To test this, we generated CRISPR mosaic knock-outs in five nymphalid butterfly species and show that ivory mutagenesis yields transformations of dark pigmented scales into white or light-coloured scales. Genotyping of Vanessa cardui germline mutants associates these phenotypes to small on-target deletions at the conserved first exon of ivory. In contrast, cortex germline mutant butterflies with confirmed null alleles lack any wing phenotype, and exclude a colour patterning role for this adjacent gene. Overall, these results show that a lncRNA acts as a master switch of colour pattern specification, and played key roles in the adaptive diversification of colour patterns in butterflies. Significance statementDeciphering the genetic underpinnings of adaptive variation is fundamental for a comprehensive understanding of evolutionary processes. Long non-coding RNAs (lncRNAs) represent an emerging category of genetic modulators within the genome, yet they have been overlooked as a source of phenotypic diversity. In this study, we unveil the pivotal role of a lncRNA in orchestrating colour transitions between dark and light patterns during butterfly wing development. Remarkably, this lncRNA gene is nested within the cortex locus, a genetic region known to control multiple cases of adaptive variation in butterflies and moths, including iconic examples of natural selection. These findings highlight the significant influence of lncRNAs in developmental regulation, and also underscore their potential as key genetic players in the evolutionary process itself.

evolutionary biology↗

bioRxiv2023

Adaptive gene loss in the common bean pan-genome during range expansion and domestication

The common bean (Phaseolus vulgaris L.) is a crucial grain legume crop [1,2] whose life history offers an ideal evolutionary model to identify and study adaptive variants in wild and domestication populations [3]. Here we present the first common bean pan-genome based on five high-quality genomes and whole-genome reads representing 339 genotypes. We found [~]243 Mb of additional sequences containing 7,495 protein-coding genes missing from the reference, constituting 51% of the total presence/absence variations (PAVs). There were more putatively deleterious mutations in PAVs than core genes, probably reflecting the lower effective population size of PAVs as well as fitness advantages due to the purging effect of gene loss. Our results suggest strong pan-genome shrinkage occurred during wild range expansion from Mexico to South America, with more PAV loss per individual in Andean vs Mesoamerican populations. Selection signatures during wild spreading and domestication were also associated with PAV loss involved in important adaptive traits. Our findings provide evidence that partial or complete gene loss was a key adaptive trait leading to localized and genome-wide reductions. This novel result has major implications for the understanding of the process of plant adaptation and claims for a paradigm shift in evolutionary genetics. Moreover, the common bean pan-genome is a valuable resource for food legume research and breeding towards climate change mitigation, and sustainable agriculture.

evolutionary biology↗

bioRxiv2023

Genotype combinations drive variability in the microbiome configuration of the rhizosphere of Maize/Bean intercropping system

In intercropping system, the interplay between cereals and legumes, which is strongly driven by complementarity of below-ground structures and their interactions with the soil microbiome, raises a fundamental query: Can different genotypes alter the configuration of the rhizosphere microbial communities? To address this issue, we conducted a field study, probing the effects of intercropping and diverse maize (Zea mays L.) and beans (Phaseolus vulgaris L., Phaseolus coccineus L.) genotype combinations. Our results unveil that intercropping condition alters the rhizosphere bacterial communities, but that the degree of this impact is substantially affected by specific genotype combinations. Overall, intercropping allows the recruitment of exclusive bacterial species and enhance community complexity. Nevertheless, combinations of maize and beans genotypes determine two distinct groups characterized by higher or lower bacterial community diversity and complexity, which are influenced by the specific bean line associated. Moreover, intercropped maize lines exhibit varying propensities in recruiting bacterial members with more responsive lines showing preferential interactions with specific microorganisms. Our study conclusively shows that genotype has an impact on the rhizosphere microbiome and that a careful selection of genotype combinations for both species involved is essential to achieve compatibility optimization in intercropping.

plant biology↗

bioRxiv2023

Nitrogen availability during domestication shaped the divergence of tetraploid wheat

The domestication of crops, with the development of the agroecosystems, is associated with major environmental changes and represent a model to test the role of phenotypic plasticity. Here we investigated 32 genotypes representing key stages of tetraploid wheat domestication. We developed a dedicated pipeline combining RNA-Seq data, estimates of evolvability and QST to characterize the plasticity of gene expression and identify signatures of selection under different nitrogen conditions. The analysis of gene expression diversity showed contrasting results between primary and secondary domestication in relation to nitrogen availability. Indeed, nitrogen triggered the expression of twice the number of genes in durum wheat compared to emmer and wild emmer. QST distributions and QST-FST comparisons revealed distinct selection signatures at each domestication stage. While primary domestication affected the expression of genes involved in biotic interactions, secondary domestication was associated with changes in expression of genes involved in metabolism of amino acids, particularly lysine. Selection signatures were found also in differentially expressed genes, specifically involved in nitrogen metabolism, such as glutamate dehydrogenase. Overall, our findings show that nitrogen availability had a pivotal role during the domestication and adaptive responses of a major food crop, with varying effects across different traits and growth conditions.

genetics↗

bioRxiv2023

The evolutionary history of the common bean (Phaseolus vulgaris) revealed by chloroplast and nuclear genomes.

The remarkable evolutionary history of the common bean (Phaseolus vulgaris L.) has led to the emergence of three wild main genepools corresponding to three different ecogeographic areas: Mesoamerica, the Andes and northern Peru/Ecuador. Recent works proposed novel scenarios and the northern Peru/Ecuador population has been described as a new species called P. debouckii, rekindling the debate about the origin of P. vulgaris. Here we shed light on the origin of P. vulgaris by analysing the chloroplast and nuclear genomes of a large varietal collection representing the entire geographical distribution of wild forms. We assembled 37 chloroplast genomes de novo and used them to construct a time frame for the divergence of the genotypes under investigation, revealing that the separation of the Mesoamerican and northern Peru/Ecuador genepools occurred [~]0.15 Mya. Our results clearly support a Mesoamerican origin of the common bean and reject the recent P. deboukii hypothesis. These results also imply two independent migratory events from Mesoamerica to the North and South Andes, probably facilitated by birds. Our work represents a paradigmatic example of the importance of taking into account recombination events when investigating phylogeny and of the analysis of wild forms when studying the evolutionary history of a crop species.

genetics↗

bioRxiv2022

CRISPR/Cas9-based repeat depletion for the high-throughput genotyping of complex plant genomes

High-throughput genotyping enables the large-scale analysis of genetic diversity in population genomics and genomewide association studies that combine the genotypic and phenotypic characterization of large collections of accessions. Sequencing-based approaches for genotyping are progressively replacing traditional genotyping methods due to the lower ascertainment bias. However, genome-wide genotyping based on sequencing becomes expensive in species with large genomes and a high proportion of repetitive DNA. Here we describe the use of CRISPR/Cas9 technology to deplete repetitive elements in the 3.76-Gb genome of lentil (Lens culinaris), 84% consisting of repeats, thus concentrating the sequencing data on coding and regulatory regions (single-copy regions). We designed a custom set of 566,766 gRNAs targeting 2.9 Gbp of repeats and excluding repetitive regions overlapping annotated genes and putative regulatory elements based on ATAC-Seq data. The novel depletion method removed [~]40% of reads mapping to repeats, increasing those mapping to single-copy regions by [~]2.6-fold. When analyzing 25 million fragments, this repeat-to-single-copy shift in the sequencing data increased the number of genotyped bases of [~]10-fold compared to non-depleted libraries. In the same condition, we were also able to identify [~]12-fold more genetic variants in the single-copy regions and increased the genotyping accuracy by rescuing thousands of heterozygous variants that otherwise would be missed due to low coverage. The method performed similarly regardless of the multiplexing level, type of library or genotypes, including different cultivars and a closely-related species (L. orientalis). Our results demonstrated that CRISPR/Cas9-driven repeat depletion focuses sequencing data on meaningful genomic regions, thus improving high-density and genome-wide genotyping in large and repetitive genomes.

genomics↗

bioRxiv2022

Selection and adaptive introgression guided the complex evolutionary history of European common bean

Domesticated crops have been disseminated by humans over vast geographic areas. After 1492, the common bean (Phaseolus vulgaris L.) was introduced in Europe. Here, we combine whole-genome profiling, metabolic fingerprinting and phenotypic characterisation, and we show that the first common bean cultigens successfully introduced into Europe were of Andean origin, after Francisco Pizarros expedition to northern Peru in 1529. We show that hybridisation, selection and recombination have shaped the genomic diversity of the European common bean in parallel with political constraints. There is clear evidence of adaptive introgression into the Mesoamerican-derived European genotypes, with 44 Andean introgressed genomic segments shared by more than 90% of European accessions and distributed across all chromosomes except PvChr11. Genomic scans for signatures of selection highlight the role of genes relevant to flowering and environmental adaptation, suggesting that introgression has been crucial for the dissemination of this tropical crop to the temperate regions of Europe.

genomics↗

bioRxiv2022

Evolutionary dynamics of genome size and content during the adaptive radiation of Heliconiini butterflies

Heliconius butterflies, a speciose genus of Mullerian mimics, represent a classic example of an adaptive radiation that includes a range of derived dietary, life history, physiological and neural traits. However, key lineages within the genus, and across the broader Heliconiini tribe, lack genomic resources, limiting our understanding of how adaptive and neutral processes shaped genome evolution during their radiation. We have generated highly contiguous genome assemblies for nine new Heliconiini, 29 additional reference-assembled genomes, and improve 10 existing assemblies. Altogether, we provide a major new dataset of annotated genomes for a total of 63 species, including 58 species within the Heliconiini tribe. We use this extensive dataset to generate a robust and dated heliconiine phylogeny, describe major patterns of introgression, explore the evolution of genome architecture, and the genomic basis of key innovations in this enigmatic group, including an assessment of the evolution of putative regulatory regions at the Heliconius stem. Our work illustrates how the increased resolution provided by such dense genomic sampling improves our power to generate and test gene-phenotype hypotheses, and precisely characterize how genomes evolve.

evolutionary biology↗

bioRxiv2022

A butterfly pan-genome reveals a large amount of structural variation underlies the evolution of chromatin accessibility

Despite insertions and deletions being the most common structural variants (SVs) found across genomes, not much is known about how much these SVs vary within populations and between closely related species, nor their significance in evolution. To address these questions, we characterized the evolution of indel SVs using genome assemblies of three closely related Heliconius butterfly species. Over the relatively short evolutionary timescales investigated, up to 18.0% of the genome was composed of indels between two haplotypes of an individual H. charithonia butterfly and up to 62.7% included lineage-specific SVs between the genomes of the most distant species (11 Mya). Lineage-specific sequences were mostly characterized as transposable elements (TEs) inserted at random throughout the genome and their overall distribution was similarly affected by linked selection as single nucleotide substitutions. Using chromatin accessibility profiles (i.e., ATAC-seq) of head tissue in caterpillars to identify sequences with potential cis-regulatory function, we found that out of the 31,066 identified differences in chromatin accessibility between species, 30.4% were within lineage-specific SVs and 9.4% were characterized as TE insertions. These TE insertions were localized closer to gene transcription start sites than expected at random and were enriched for several transcription factor binding site candidates with known function in neuron development in Drosophila. We also identified 24 TE insertions with head-specific chromatin accessibility. Our results show high rates of structural genome evolution that were previously overlooked in comparative genomic studies and suggest a high potential for structural variation to serve as raw material for adaptive evolution.

genomics↗