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Breeding forage and grain legumes to increase EU's and China's protein self-sufficiency

Periodic Reporting for period 2 - EUCLEG (Breeding forage and grain legumes to increase EU's and China's protein self-sufficiency)

Berichtszeitraum: 2019-03-01 bis 2020-08-31

EUCLEG aims at providing tools and knowledge to improve the genetic progress in five major legume species: two forages, alfalfa and red clover, and three grain legumes, pea, faba bean and soybean. This implies genotyping, phenotyping and statistical work.
In WP1, we develop molecular and genomic tools. For the two outbreeding forage crops, we use genotyping by sequencing (GBS) to obtain marker frequency from pooled individuals of each accession (pool-GBS). For the three autogamous grain legumes, we use SNP array technology to obtain genotype data of accessions.
In WP2, we structure and improve access to data on European and Chinese plant genetic resources collections. We identify gaps (both passport and phenotypic data) in existing information systems and encourage collection holders to close these gaps. We create an efficient infrastructure for the central management of the data collected during the project (the Progeno database). Finally, the legal challenges and risks associated with the exchange of plant genetic resources and their data, but also intellectual property issues, are considered.
In WP3, we aim at describing the genetic structure of germplasm collections using both phenotypic traits and molecular markers. Trials are established in a network of environments in EU and China. Relevant phenotypic traits are evaluated: germination, crop establishment, biotic and abiotic stress, forage and seed yield, forage quality. An description of Chinese and European germplasm, an overview of genotype x environment interaction and an identification of promising germplasm are provided. The genetic structure of the germplasm is described with genotype data obtained in WP1.
In WP4, we aim at identifying genes, alleles and molecular markers that explain a large part of the phenotypic variation available for traits involved in crop yield and its stability including resistance to biotic and abiotic stresses. The WP2 database containing genotype data is used for genome-wide association analyses (GWAS).
Genomic selection, a form of marker-assisted selection, is more efficient than phenotypic selection in many cases. WP5 deliver knowledge and tools to breeders to implement genomic selection in their breeding programs. A user-friendly tool is developed for managing data and performing the calculation of breeding values (BV) and genomic breeding values (GEBV). The effects of several determinants of the accuracy of the equation of prediction of GEBV are tested and we aim at proposing several breeding solutions including genomic selection.
WP6 disseminates the project outcomes to the scientific community and transfer the innovations to stakeholders.
All this information will help to create high yielding and stress tolerant varieties of forage and grain legumes. At the end, an expansion of legume cultivation under a broad range of conditions, from South to North, West to East of Europe and China is expected.
In WP1, genotype data have been generated:
1. Alfalfa – Europe: 1016 accessions were genotyped (186K SNP). CAAS-IAS: 220 individuals were genotyped using whole genome sequencing (560K SNP).
2. Red clover: 641 accessions were genotyped. Allele frequency data for 65K SNP markers are available in Progeno.
3. Faba bean: 400 accessions were genotyped with a 50K Faba bean Axiom array. Genotype data for 35K markers are available in Progeno.
4. Pea: 260 accessions were genotyped using the 13K GenoPea array. Genotype data for 12K markers are available in Progeno.
5. Soybean: 479 European and 326 Chinese accessions were genotyped using the 355K SoySNP array. Genotype data is uploaded to Progeno, analysed and a publication is in preparation.
In WP2, inventories of plant genetic resources of the five focus species in Europe and China were compiled. Two surveys were sent to EUCLEG partners and EURISCO data providers. Gap analyses between the EURISCO system and the European Central Crop Databases were carried out. As a whole, data are available and there is a basic willingness to provide these data.
A central infrastructure for project data management was set up in the Progeno system. Upload and check routines were implemented and support is provided to users. Genotype and phenotype data are being imported on a regular basis. A policy brief is in progress to describe challenges and risks related to the exchange of plant genetic resources and associated data.
After accomplishing successfully the challenging task to establish the list of accessions and detailed protocols for each species (WP3 and WP4), 34 field trials were sown in Europe and China. Collecting data is in progress and data are deposited on Progeno. Because of COVID-19 pandemic, some measurements could not be performed or were delayed during the spring 2020. First significant results related to identification of promising legume populations were obtained.
For WP4, a larger number of accessions were sown at several of the locations at which WP3 trials were established to achieve the resolution required to perform GWAS. With some exceptions, the activities are progressing as expected. For the evaluation of traits related to biotic and abiotic stress and seedling vigour, experiments have been established under controlled conditions. Most data are available by now, and what is missing will be completed in early 2021. The datasets generated are uploaded in Progeno as soon as they are ready.
The first main goal of WP5 has been achieved with the implementation in Progeno software of routines allowing to calculate BV and GEBV. A documentation has been written to perform those calculations on Progeno and EUCLEG members have been trained.
In WP6, a collaborative website has been created for sharing of project outcomes and project newsletters have been produced and distributed. EUCLEG partners are continuing to engage with stakeholders and the public on an on-going basis. Results have been presented at a number of scientific conferences and several papers have been published in peer reviewed journals.
Genotype and phenotype data are the foundations for marker assisted breeding. For all five species, genome-wide genotype data are available. With exceptions (Covid-19), phenotyping is also progressing as expected. The data generated are of excellent quality for GWAS and GS analyses that are already initiated in red clover and soybean. The Progeno database contains an unprecedented amount of data on phenotypes and genotypes on five legume species. In addition, two interfaces, for basic and expert users, have been provided for the estimation of EBV and GEBV and trainings have been organised. Exchange of and access to data on genetic resources is being improved substantially.
Most outcomes will inevitably be towards the end of the project. A few scientific papers are published and partners are participating to dissemination in international conferences, national and local events related to legume crop production.
All this progress will in turn lead to strategies for more rapid breeding of new varieties that will help to increase the use of legumes in livestock and arable farming in Europe and China, and thus contribute to the overall objectives of the project.
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