Periodic Reporting for period 4 - G2P-SOL (Linking genetic resources, genomes and phenotypes of Solanaceous crops)
Reporting period: 2020-03-01 to 2021-12-31
G2P-SOL aims at bringing into full fruition the seeds from tens of thousands of genetic accessions of the four major Solanaceous food crops (potato, tomato, pepper and eggplant) that are stored in ‘genebanks’ worldwide. Understanding and utilising this genetic diversity is key to the sustainability of agriculture in the face of a changing environment and the appearance of new pests and diseases. This is currently hampered by the scarce publicly available information on the variability of collections preserved in different genebanks. In order to raise awareness of the available diversity and stimulate its usage in breeding programmes, G2P-SOL wants to make all the genetic material that is presently stored in genebanks, and the linked phenotypic and genetic information, available to the general public, scientists and breeders. The main objectives of the project are the following:
Inventory and conservation
The accessions of potato, tomato, pepper, eggplant and their wild relatives present in key European and international genebanks will be catalogued for wider use in farming and breeding. In the project, a network of repositories will be established where the germplasm is conserved and distributed to stakeholders on request. Additionally, a web-based G2P-SOL gateway will be set up, where the information is centrally made available in a unified, systemized and user-friendly way.
Description and assessment
G2P-SOL will assess the genetic relationships, levels of diversity and extent of duplication in the collections and will establish worldwide core collections, representing a large portion of the global genotypic and phenotypic variation for each of the four crops. Core collections will be characterized for agronomic and fruit/tuber quality traits, for metabolic profiles and for response to a set of biotic and abiotic stresses.
Pre-breeding
Important traits with regard to pathogen-, pest-, and abiotic stress resistance, as well as yield and quality from wild, non-adapted germplasm will be introduced into elite germplasm which is adapted to field conditions and food systems. These novel sources for variation will be used for phenotyping and genotyping. Elite material will be made available for pre-breeding and to end-users.
Dissemination, valorisation and training
All data and germplasm collected and produced during the project will be made publicly accessible through the G2P-SOL gateway. The cross-sectoral partners of G2P-SOL will organize workshops and training schools aimed at public and private sector breeders and farmers associations, in order to promote the inclusion of the genetic materials and the newly gained knowled.
breeders and farmers associations, in order to promote the inclusion of the genetic materials and the newly gained knowled.
Inventory and conservation
The accessions of potato, tomato, pepper, eggplant and their wild relatives present in key European and international genebanks will be catalogued for wider use in farming and breeding. In the project, a network of repositories will be established where the germplasm is conserved and distributed to stakeholders on request. Additionally, a web-based G2P-SOL gateway will be set up, where the information is centrally made available in a unified, systemized and user-friendly way.
Description and assessment
G2P-SOL will assess the genetic relationships, levels of diversity and extent of duplication in the collections and will establish worldwide core collections, representing a large portion of the global genotypic and phenotypic variation for each of the four crops. Core collections will be characterized for agronomic and fruit/tuber quality traits, for metabolic profiles and for response to a set of biotic and abiotic stresses.
Pre-breeding
Important traits with regard to pathogen-, pest-, and abiotic stress resistance, as well as yield and quality from wild, non-adapted germplasm will be introduced into elite germplasm which is adapted to field conditions and food systems. These novel sources for variation will be used for phenotyping and genotyping. Elite material will be made available for pre-breeding and to end-users.
Dissemination, valorisation and training
All data and germplasm collected and produced during the project will be made publicly accessible through the G2P-SOL gateway. The cross-sectoral partners of G2P-SOL will organize workshops and training schools aimed at public and private sector breeders and farmers associations, in order to promote the inclusion of the genetic materials and the newly gained knowled.
breeders and farmers associations, in order to promote the inclusion of the genetic materials and the newly gained knowled.
Inventory and conservation:
A common descriptor system has been developed for the four crops. Existing passport and phenotypic data, including images, have been collected for approximately 55,000 accessions of the four crops, as detailed in Table 1:
All data have been uploaded on the G2P-SOL gateway (http://www.g2p-sol.eu/G2P-SOL-gateway.html) and are publicly accessible to all users since Jan 1st, 2020.
Description and assessment
Low density genotyping protocols, able to score 2.000-5.000 genetic loci have been optimized and utilized to genotype approximately 38.000 accessions and prebreeding lines from the four crops, as detailed in Table 2.
The data have been added to the G2P-SOL gateway. The pepper data are public, those from the other three crops will be made public upon publication of the relative papers.
Five core collections (tomato, eggplant, pepper, South American and European potatoes), composed of 300-400 individuals each and representing the global or (in the case of potato) regional diversity of these crops have been constructed on the basis of phenotypic parameters and the low density genotyping data, and distributed to the phenotyping partners. At least two field trials/crop have been conducted for all five core collections. Phenotyping has been conducted using common protocols and metabolic profiling has been completed for tomato, eggplant and pepper. Trials for selected biotic/abiotic stress resistance traits have been also conducted.
The core collections of tomato and eggplant have been resequenced to 20x depth, while those of potato and pepper have been subjected to high density genotyping. Additionally, 16 genotypes of pepper, 47 wild accessions of eggplant, 30 of potato and 42 of tomato were resequenced to 20x-40x depth, for a total of over 5 Terabases.
The resequencing of the tomato and eggplant core collections generated, respectively, 30.1 M and 51.6 M Single Nucleotide Polymorphisms (SNPs) of which, after filtering, 1.02 M and 1.32 M were used for Genome Wide Association mapping. The numbers of SNPs were much lower for pepper and potato, which were subjected to GBS (Table 3). These SNPs were used together with tens (potato) or hundreds (tomato, eggplant, pepper) traits measured in the core collections for Genome Wide Association Studies, generating thousands of highly significant SNP/trait associations.
Pre-breeding
Over 50 segregating populations of the four crops, derived from intra- or inter-specific crosses are being assessed for a variety of novel quality- and disease resistance-related traits. A number of known agronomic traits have been introgressed into novel elite germplasm in a first wave of pre-breeding, and a number of novel traits have been validated for use in a second wave of prebreeding, as detailed below. The numbers of these traits are well above the 2-3 traits/crop that were initially planned.
Eggplant: known 6; novel 11; Pepper: known 6; novel 7; Tomato: known 8; novel 3; Potato: known 3; novel 4. (Table 4).
Dissemination, valorisation and training
The project results have been disseminated, up to now, through 69 press releases, the participation to 36 conferences/workshops/scientific events and 52 peer-reviewed, open access scientific papers. A list of all publications can be found on the G2P-SOL website (http://www.g2p-sol.eu/Publications.html). Two early stage training schools on the use of genetic resources have been organized, respectively, in Hyderabad, India and Lima, Perù two advanced training schools in Wageningen, the Netherlands and and on line. The project’s final workshop (http://www.g2p-sol.eu/G2P%2DSOL%2DFinal%2DWorkshop.html) attracted over 1,000 participants from 61 countries (Figure 1). The project’s Twitter account (@solgenetics) has gained over 300 followers.
A common descriptor system has been developed for the four crops. Existing passport and phenotypic data, including images, have been collected for approximately 55,000 accessions of the four crops, as detailed in Table 1:
All data have been uploaded on the G2P-SOL gateway (http://www.g2p-sol.eu/G2P-SOL-gateway.html) and are publicly accessible to all users since Jan 1st, 2020.
Description and assessment
Low density genotyping protocols, able to score 2.000-5.000 genetic loci have been optimized and utilized to genotype approximately 38.000 accessions and prebreeding lines from the four crops, as detailed in Table 2.
The data have been added to the G2P-SOL gateway. The pepper data are public, those from the other three crops will be made public upon publication of the relative papers.
Five core collections (tomato, eggplant, pepper, South American and European potatoes), composed of 300-400 individuals each and representing the global or (in the case of potato) regional diversity of these crops have been constructed on the basis of phenotypic parameters and the low density genotyping data, and distributed to the phenotyping partners. At least two field trials/crop have been conducted for all five core collections. Phenotyping has been conducted using common protocols and metabolic profiling has been completed for tomato, eggplant and pepper. Trials for selected biotic/abiotic stress resistance traits have been also conducted.
The core collections of tomato and eggplant have been resequenced to 20x depth, while those of potato and pepper have been subjected to high density genotyping. Additionally, 16 genotypes of pepper, 47 wild accessions of eggplant, 30 of potato and 42 of tomato were resequenced to 20x-40x depth, for a total of over 5 Terabases.
The resequencing of the tomato and eggplant core collections generated, respectively, 30.1 M and 51.6 M Single Nucleotide Polymorphisms (SNPs) of which, after filtering, 1.02 M and 1.32 M were used for Genome Wide Association mapping. The numbers of SNPs were much lower for pepper and potato, which were subjected to GBS (Table 3). These SNPs were used together with tens (potato) or hundreds (tomato, eggplant, pepper) traits measured in the core collections for Genome Wide Association Studies, generating thousands of highly significant SNP/trait associations.
Pre-breeding
Over 50 segregating populations of the four crops, derived from intra- or inter-specific crosses are being assessed for a variety of novel quality- and disease resistance-related traits. A number of known agronomic traits have been introgressed into novel elite germplasm in a first wave of pre-breeding, and a number of novel traits have been validated for use in a second wave of prebreeding, as detailed below. The numbers of these traits are well above the 2-3 traits/crop that were initially planned.
Eggplant: known 6; novel 11; Pepper: known 6; novel 7; Tomato: known 8; novel 3; Potato: known 3; novel 4. (Table 4).
Dissemination, valorisation and training
The project results have been disseminated, up to now, through 69 press releases, the participation to 36 conferences/workshops/scientific events and 52 peer-reviewed, open access scientific papers. A list of all publications can be found on the G2P-SOL website (http://www.g2p-sol.eu/Publications.html). Two early stage training schools on the use of genetic resources have been organized, respectively, in Hyderabad, India and Lima, Perù two advanced training schools in Wageningen, the Netherlands and and on line. The project’s final workshop (http://www.g2p-sol.eu/G2P%2DSOL%2DFinal%2DWorkshop.html) attracted over 1,000 participants from 61 countries (Figure 1). The project’s Twitter account (@solgenetics) has gained over 300 followers.
The pre-existing phenotypic and passport information gathered, the novel genotypic and phenotypic information produced, and the novel traits validated constitute the single largest, publicly funded, dataset of its kind on Solanaceous crops, and are being organised in a user-friendly gateway. This dataset and gateway will tremendously increase the value of the germplasm collections, promoting the use of biodiverse germplasm by all users, including SMEs and public sector breeders.