Biology subjects

Rocchetti, L.

Publications and source records attributed to Rocchetti, L..

4 recordsLinked to original sources

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↗