Biology subjects

Pieri, A.

Publications and source records attributed to Pieri, A..

9 recordsLinked to original sources

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↗

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↗

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

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↗

bioRxiv2020

Increased and ectopic expression of Triticum polonicum VRT-A2 underlies elongated glumes and grains in hexaploid wheat in a dosage-dependent manner

Flower development is a major determinant of yield in crops. In wheat, natural variation for the size of spikelet and floral organs is particularly evident in Triticum polonicum, a tetraploid subspecies of wheat with long glumes, lemmas, and grains. Using map-based cloning, we identified VRT2, a MADS-box transcription factor belonging to the SVP family, as the gene underlying the T. polonicum long-glume (P1) locus. The causal P1 mutation is a sequence re-arrangement in intron-1 that results in both increased and ectopic expression of the T. polonicum VRT-A2 allele. Based on allelic variation studies, we propose that the intron-1 mutation in VRT-A2 is the unique T. polonicum species defining polymorphism, which was later introduced into hexaploid wheat via natural hybridizations. Near-isogenic lines differing for the P1 locus revealed a gradient effect of P1 across florets. Transgenic lines of hexaploid wheat carrying the T. polonicum VRT-A2 allele show that expression levels of VRT-A2 are highly correlated with spike, glume, grain, and floral organ length. These results highlight how changes in expression profiles, through variation in cis-regulation, can impact on agronomic traits in a dosage-dependent manner in polyploid crops. One-sentence summaryAn intron-1 rearrangement in the MADS-box transcription factor VRT-A2 leads to its misexpression and defines the long-glume phenotype of Polish wheat (T. polonicum).

plant biology↗

bioRxiv2018

Long non-coding RNAs in wild wheat progenitors

Triticum urartu and Aegilops tauschii are the diploid progenitors of the hexaploid Triticum aestivum (AuAuBBDD), donors of the Au and D genome respectively. In this work we investigate the long noncoding RNAs (lncRNAs) component of the genomes of these two wild wheat relatives. Sixty-eight RNA-seq libraries generated from several organs and conditions were retrieved from public databases. We annotated and characterized 14,515 T. urartu and 20,908 Ae. tauschii bona-fide lncRNA transcripts that show features similar to those of other plant and animal counterparts. Thousands of lncRNAs were found significantly modulated in different organs and exhibited organ specific expression, with a predominant accumulation in the spike, fostering the hypothesis of their crucial role in reproductive organs. Most of the organ-specific lncRNAs were found associated with transposable elements (TEs), indicating the possible role of TEs in lncRNA origin, differentiation and function. The majority of T. urartu and Ae. tauschii lncRNAs appear to be species-specific; nevertheless, we found some lncRNAs conserved between the two wheat progenitors, highlighting the presence and conservation of exonic splicing enhancers sites in multi-exon conserved lncRNAs. In addition, we found cases of lncRNA conservation and their cis regulatory regions spanning the wheat pre-domestication and post-domestication period. Altogether, these results represent the first comprehensive genome-wide encyclopedia of lncRNAs in wild wheat relatives, and they provide clues as to the hidden regulatory pathway mediated by long noncoding RNAs in these largely unexplored wheat progenitors.

plant biology↗