Community Research and Development Information Service - CORDIS

Periodic Report Summary 1 - BREED4FUTURE (Breeding for a sustainable agriculture: quality and resistance in the frame of H2020)

1) A summary description of the Project objectives
The project titled “BREED4FUTURE” presents two main objectives: training and research activities: The training activities are related to the acquirement of relevant scientific and professional skills by Dr. Angel Fernandez i Marti to obtain new skills in Next Generation Sequencing Technologies (NGS) and disease resistance in plants. The research activities are aimed to identify the casual genes associated with disease resistance in a sustainable agriculture and understanding how plants defend themselves from pathogens. The specific research objectives proposed were: (i) to identify molecular mechanisms determining disease resistance across the Compositae and to establish syntenic relationships within the family as well as with other plant species (Rosaceae), (ii) to determine the different classes of resistance genes as a basis for a more efficient breeding for Durable Disease Resistance and a more efficient sustainable agriculture and (iii) to gain expertise in excellent research to be applied in commercial crops to reduce the gap between research and market in the landscape of H2020.
2) A description of the work performed since the beginning of the project

The period of the Outgoing phase at the Genome Center UCDavis was mainly focused on research training activities of Dr. Fernandez i Marti as mentioned in Annex 1, part B of the BREED4FUTURE project. The first part was oriented in learning molecular and bioinformatics tools. The second task consisted in the literature review on resistance genes and plant genome assembly methods.
The first and second task of his Work Plan (WP), as described on table 1 of the Part B, have successfully been accomplished. The fellow has phenotyped for recombination and spontaneous mutants of downy mildew resistance in three different populations of the lettuce cross ‘Kordaat’ X ‘Calmar’. Population 1: FKC1 individuals from a cross of the cultivars Kordaat (Dm1, Dm3, Dm4) X Calmar (Dm7, Dm8, Dm13). This population was screened for losses of Dm1 and Dm3 activity. Activity of Dm4 could not be tested in this population due to the lack of an isolate with the appropriate virulence phenotype. Activities of Dm7, Dm8, and Dm13 could not be tested due to unavoidable selfing of the maternal parent (Kordaat). Population 2: S2 (selfed twice) families of the lettuce cultivar, Diana (Dm1, Dm3, Dm7, Dm8). This population was screened for losses of all four specificities. Population 3: F3 recombinant-derived families. This population was derived by crossing Kordaat X Calmar F2 individuals, which exhibited recombination events between SCV12 and such that the recombinant allele retained Dm3.
Molecular analysis were conducted by using DNA molecular markers (RAPD, SCARs and SSRs).
The third activity of the WP has also been accomplished. The fellow attended successfully several bioinformatic courses at the Genome Center UCDavis.
Dr. Fernandez i Marti achieved task 4 of the WP 2. He gained experience by using available database from 25 plant genome sequences, such as Arabidopsis thaliana, Zea mays, Populus trichocarpa, Lactuca sativa, Theobroma cacao, Medicago truncatula, Vitis vinifera, Prunus persica, Fragaria vesca, Carica papaya, Solanum lycopersicum, Citrus clementina, and many others. These genomes were used for molecular evolution of resistance genes, comparative genomics and DNA variation (SNP, SSR and CNVs).
Task 5 of the WP2 was also accomplished. The fellow generated REN-SEQ libraries for 10 lettuce cultivars (Salinas, Serriola, Diana, Kordaat, Calmar, Greenlake, Maruska, Emperor, El Dorado and Cobhan Green). The aim of this task was dual. First of all, he wanted to set up a new protocol called REN-SEQ (Sequence Enrichment for Targeted Sequencing), by using the two most powerful NGS platforms “Illumina” and “PacBio”. The second aim was the reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregation populations. This method enables discovery and annotate of new pathogen resistance gene family members in plant genome sequences.
Task 6, 7 & 8 are being achieved. The fellow is still analyzing dates obtained by the Illumina and PacBio technologies. The REN-SEQ sequences obtained from the 10 cultivars have already assembled by using the Illumina platform. These dates are being compared and blasted against the lettuce reference genome “Salinas”. By the way, the same 10 samples are still being run at the PacBio platform. This experiment will serve us too to compare the efficiency and quality of the genomes of the two NGS platforms.
Furthermore, Dr. Fernandez i Marti, is being part of the international consortium for sequencing the novo the “almond genome”. This consortium is formed by researchers from Spain, Italy, France, Australia and USA. In addition to the novo sequencing, other 40 almond varieties are being re-sequenced and used for other genetic studies such as Variant calling, Population structure analysis, Linkage disequilibrium and GWAS analysis.
Concerning the task 8, 9 & 10, the fellow is about to send for publication to an international journal his first study of diversity evolution of resistance genes in the Compositae “Angel Fernandez i Marti, Sebastian Reyes-Chin-Wo, Marilena Christopoulou and Richard W. Michelmore (2016) Diversity and evolution of resistance genes in the compositae (in preparation)”. This study has already been presented this January 2016 at the Plant and Animal Genome Conference hold in San Diego (USA). Furthermore, two other publications are being drafting with his host researcher, Dr. Michelmore.
Also, it was presented at the PAG conference the first draft of the almond genome, and at the end of the year is expected to be published in an international journal “Tyler Alioto, Fernando Cruz, Jèssica Gómez Garrido, Leonor Frias, Paolo Ribeca, Konstantinos Alexiou, Werner Howad, Jordi Morata, Josep Mª Casacuberta Suñer, María José Rubio Cabetas, Marta Gut, Beatriz Galán, José L. Garcia, Amit Dhingra, Henry Duval, Ángel Fernández i Martí, Michelle Wirthensohn, Pere Arús (2016) A draft assembly of the almond genome (in preparation).
Another publication has been submitted to the journal Frontiers in Plant Science “Badenes, ML, Fernández i Marti A, Rios G and Rubio-Cabetas MJ (2016) Biotechnology applied to breeding of perennial tree species. Finally, another study where the fellow has actively participated has been presented in a international conference hold in June 2016 in Angers, France. Bielsa B, Fernandez i Marti A and Rubio-Cabetas MJ, “Identification of almond genomic regions in four 3-way interspecific hybrid progenies”. Early 2016, the editorial Springer has proposed to Dr. Fernandez i Marti to be the Editor in chief of the book “The almond tree genome”. In addition, the fellow is participating in the chapter “Molecular Breeding and Genomics, of the book “Almonds: Botany, Production and Uses” (Editor: Rafael Socias). Eds (CAB International) written by C Font i Forcada, R Sanchez-Perez, I Eduardo, W Shubiao, Fernandez i Marti A (2016).

3) A description of the main results achieved so far
Dr. Fernandez i Marti is becoming an expert in NGS and bioinformatics tools associated to resistance genes in plants. Moreover, during this outgoing phase (from 1st to 24th month) he has set up different lab protocols and presented his results in international conferences. The results indicate that through the new technique RENSEQ is possible to discover and re-annotated new genes encoding NB-LRR proteins. In addition, different bioinformatics softwares have been compared in order to determine which one provides a better quality of their assemblies and annotation of resistance genes. Different spontaneous mutants have been too identified by using phenotype and DNA molecular markers. These individuals will be used for large scale DNA sequencing by using the Illumina and Pacbio platforms.

4) The expected final results and their potential impact and use (including the socio-economic impact and the wider societal implications of the project so far)

The understanding and identification of genes conferring disease resistance in the Compositae and Rosaceae will help in designing new breeding strategies in these two crop families. The elucidation of the different types of resistance will shed light on their involvement in plant evolution and plant breeding, thus optimizing their utilization in the present situation of growing global population and changing environments. Consequently, this knowledge will increase the efficiency in reducing vulnerability to epidemics and stabilizing the global food supply. DNA technological advances are producing novel and more efficient ways for identifying genetic variation for crop improvement. In particular, NGS and bioinformatics are revolutionizing the characterization of natural genetic variation. These new sequencing technologies will have tremendous impact on strategies for crop improvement and provide the opportunity for the analysis and improvement of a wide range of traits in plants that are inherited in a complex, including disease resistance. Furthermore, NGS will allow rapid, inexpensive and comprehensive analysis of germplasm as well as the identification of functional genes or variations affecting disease resistances.


Clara María Marín, (Research Director)
Tel.: +34 976716458
Fax: +34 976716335


Life Sciences
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