Biology subjects

Rocchetti, L.

Publications and source records attributed to Rocchetti, L..

8 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

Genomic insights into the local adaptation of spontaneously occurring populations of olive trees (Olea europaea ssp. europaea var. sylvestris) in the Mediterranean Basin

Living organisms are increasingly threatened by significant environmental changes, primarily driven by human-induced global alterations. Understanding and forecasting species adaptive responses to these environmental changes is therefore crucial for enhancing conservation efforts. In the Mediterranean Basin (MB), the average temperature is rising at a rate 20% faster than the global average, placing regional biodiversity at heightened risk. The study of local adaptation is thus particularly relevant. In the western MB, spontaneously occurring olive populations consist of both wild olives and admixed resulting of crop-to-wild gene flow. The wild is likely harbouring adaptive genetic variation shaped by local environmental pressures. In this study, we analysed target genomic sequencing data from spontaneously occurring populations (comprising both wild and admixed trees) as well as cultivated olive trees. We performed selective sweep and GEA analyses in wild olives to identify genomic regions associated with environmental variables. Our findings identified signatures of adaptation particularly associated with precipitation and temperature. Notably, admixed individuals retained many wild candidate SNPs in their genomes suggesting that they might retain a certain level of adaptation to their local environment. Those results are in line with recent studies suggesting hybrids could adapt more rapidly to novel environments than their parental populations. Key-words: Local adaptation, selective sweep detection, crop-to-wild gene flow, Olea europaea L., population genomics, genome-environment association

evolutionary biology↗

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↗

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↗