Biology subjects

Giuliano, G.

Publications and source records attributed to Giuliano, G..

6 recordsLinked to original sources

bioRxiv2024

A novel tomato inter-specific (Solanum lycopersicum var. cerasiforme and S. pimpinellifolium) MAGIC population facilitates trait association and candidate gene discovery in untapped exotic germplasm

We developed a novel eight-way tomato multi-parental advanced generation inter-cross (MAGIC) population to improve the accessibility of the genetic resources of tomato relatives to geneticists and breeders. The inter-specific MAGIC population (ToMAGIC) was obtained by inter-crossing four accessions each of Solanum lycopersicum var. cerasiforme (SLC) and S. pimpinellifolium (SP), which respectively are the weedy relative and the ancestor of cultivated tomato. The eight exotic ToMAGIC founders were selected based on a representation of the genetic diversity and geographical distribution of the two taxa. The resulting MAGIC population comprises 354 lines which were genotyped using a new 12k tomato Single Primer Enrichment Technology (SPET) panel and yielded 6,488 high-quality SNPs. The genotyping data revealed a high degree of homozygosity (average 93.69%), an absence of genetic structure, and a balanced representation (11.62% to 14.16%) of the founder genomes. To evaluate the potential of the ToMAGIC population for tomato genetics and breeding, a proof-of-concept was conducted by phenotyping it for fruit size, plant pigmentation, leaf morphology, and earliness traits. Genome-wide association studies (GWAS) identified strong associations for the studied traits, pinpointing both previously identified and novel candidate genes near or within the linkage disequilibrium blocks. Domesticated alleles for fruit size were recessive and were found, at low frequencies, in wild/ancestral populations. Our findings demonstrate that the newly developed ToMAGIC population is a valuable resource for genetic research in tomato, offering significant potential for identifying new genes that govern key traits in tomato breeding. ToMAGIC lines displaying a pyramiding of traits of interest could have direct applicability for integration into breeding pipelines providing untapped variation for tomato breeding.

plant biology↗

bioRxiv2023

Integration of QTL and transcriptome approaches for the identification of genes involved in tomato response to nitrogen deficiency

Optimising plant nitrogen (N) usage and inhibiting N leaching loss in the soil-crop system is crucial to maintain crop yield and reduce environmental pollution. This study aimed at identifying quantitative trait loci (QTL) and differential expressed genes (DEGs) between two N treatments in order to list candidate genes related to nitrogen-related contrasting traits in tomato varieties. We characterised a genetic diversity core-collection (CC) and a multi-parental advanced generation intercross (MAGIC) tomato population grown in greenhouse under two nitrogen levels and assessed several N-related traits and mapped QTLs. Transcriptome response under the two N conditions was also investigated through RNA sequencing of fruit and leaves in four parents of the MAGIC population. Significant differences in response to N input reduction were observed at the phenotypic level for biomass and N-related traits. Twenty-seven (27) QTLs were detected for three target traits (Leaf N content, leaf Nitrogen Balance Index and petiole NO3- content), ten and six at low and high N condition, respectively; while 19 QTLs were identified for plasticity traits. At the transcriptome level, 4,752 and 2,405 DEGs were detected between the two N conditions in leaves and fruits, respectively, among which 3,628 (50.6%) in leaves and 1,717 (71.4%) in fruit were genotype specific. When considering all the genotypes, 1,677 DEGs were shared between organs or tissues. Finally, we integrated DEGs and QTLs analyses to identify the most promising candidate genes. The results highlighted a complex genetic architecture of N homeostasis in tomato and novel putative genes useful for breeding improved-NUE tomato. HighlightTomato response to nitrogen deficiency is genetically controlled by a few QTLs and impacts the expression of a large number of genes, among which some are good targets for breeding sober varieties.

plant biology↗

bioRxiv2023

The irregular fruit green netting: An eggplant domestication trait controlled by the SmGLK2 gene with implications in fruit colour diversification

The distribution of chlorophylls in the eggplant (Solanum melongena) fruit peel can be uniform or display an irregular green netting pattern. The fruit green netting phenotype, manifested as a gradient of dark green netting, more intense in the proximal part of the fruit on a pale green background, is commonly present in eggplant wild relatives as well as in some eggplant landraces. During domestication and modern breeding of eggplant, uniform fruit colour has been selected. However, the fruit green netting contributes to a greater diversity of fruit colours. Here, we have used over 2,300 individuals from several germplasm and experimental populations, including a multi-parental MAGIC population for candidate genomic region identification, an F2 population for BSA-Seq, and advanced backcrosses for edges-to-core fine mapping, to determine that SmGLK2 is the gene underlying the irregular netting in eggplant fruits. We have also analysed the gene sequence of 178 S. melongena accessions and 22 wild relative species for tracing the evolutionary changes that the gene has undergone over the course of domestication. Three different mutations were identified leading to the absence of netting. The main causative indel results in the appearance of a premature stop codon disrupting the protein conformation and function, which was confirmed by Western blotting analysis and confocal microscopy observations. SmGLK2 has a major role in the regulation of chlorophyll biosynthesis in eggplant fruit peel, and therefore in eggplant fruit photosynthesis.

genetics↗

bioRxiv2022

A multi-omic Nicotiana benthamiana resource for fundamental research and biotechnology

Nicotiana benthamiana is an invaluable model plant and biotechnology platform. To further improve its usefulness and versatility, we have produced high quality chromosome level genome assemblies and multi-omic datasets for both the ubiquitously used LAB strain and a distantly related wild accession, QLD, as well as mapping their single nucleotide polymorphisms with two additional laboratory and four additional wild accessions. LAB and QLD have many genetic, functional, and metabolic differences. These coupled with their high inter-fertility and equally efficient transient and stable transformation and genome editing provide a powerful resource partnership. Their [~]3Gb allotetraploid genomes show advanced diploidisation with major chromosome loss and rearrangement, extensive homoeologous gene loss, and widespread segmental allopolyploidy. Recent bursts of Copia mobility, not seen in other Nicotiana genomes, have probably aided N. benthamianas adaptation to a spectrum of Australian ecologies.

plant biology↗

bioRxiv2022

Mutations in the SmAPRR2 transcription factor suppressing chlorophyll pigmentation in the eggplant fruit peel are key drivers of a diversified colour palette

Understanding the mechanisms by which chlorophylls are synthesized in the eggplant (Solanum melongena) fruit peel is of great relevance for eggplant breeding. A multi-parent advanced generation inter-cross (MAGIC) population and a germplasm collection have been screened for green pigmentation in the fruit peel and used to identify candidate genes for this trait. A genome-wide association study (GWAS) performed with 420 MAGIC individuals revealed a major association on chromosome 8 close to a gene similar to APRR2. Two variants in SmAPRR2, predicted as having a high impact effect, were associated with the absence of fruit chlorophyll pigmentation in the MAGIC population, and a large deletion of 5.27 kb was found in two reference genomes of accessions without chlorophyll in the fruit peel. The validation of the candidate gene SmAPRR2 was performed by its sequencing in a set of MAGIC individuals and through its de novo assembly in 277 accessions from the G2P-SOL eggplant core collection. Two additional mutations in SmAPRR2 associated with the lack of chlorophyll were identified in the core collection set. The phylogenetic analysis of APRR2 reveals orthology within Solanaceae and suggests that specialization of APRR2-like genes occurred independently in Cucurbitaceae and Solanaceae. A strong geographical differentiation was observed in the frequency of predominant mutations in SmAPRR2, resulting in a lack of fruit chlorophyll pigmentation and suggesting that this phenotype may have arisen and been selected independently several times. This study represents the first identification of a major gene for fruit chlorophyll pigmentation in the eggplant fruit.

genetics↗

bioRxiv2021

European Vintage tomatoes galore: a result of farmers combinatorial assorting/swapping of a few diversity rich loci

A comprehensive collection of 1,254 tomato accessions corresponding to European heirlooms and landraces, together with modern varieties, early domesticates and wild relatives, were analyzed by genotyping by sequencing. A continuous genetic gradient between the vintage and modern varieties was observed. European vintage tomatoes displayed very low genetic diversity, with only 298 loci out of 64,943 variants being polymorphic at the 95% threshold. European vintage tomatoes could be classified in several genetic groups. Two main clusters consisting of Spanish and Italian accessions showed a higher genetic diversity than the rest varieties, suggesting that these regions might be independent secondary centers of diversity and with a different history. Other varieties seem to be the result of a more recent complex pattern of migrations and hybridizations among the European regions. Several polymorphic loci were associated in a GWAS with fruit morphological traits in the European vintage collection, and the corresponding alleles were found to contribute to the distinctive phenotypic characteristic of the genetic varietal groups. The few highly polymorphic loci associated with morphological traits in an otherwise diversity-poor genome suggests a history of balancing selection, in which tomato farmers maintained the morphological variation by applying a high selective pressure within different varietal types. HighlightThe high phenotypic diversity observed among European vintage varieties was created by traditional farmers by combining very few polymorphic loci subjected to balancing selection.

plant biology↗