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News

Breeding: The CRISPR-Cas9 method (Part 1)

03/07/2019 - François-Xavier Branthôme - The 2019 Tomato News Conference - Avignon - Read in French
After the Conference…
The CRISPR-Cas9 method: now that genomics have become a reality, what innovations can we expect for tomato seed breeding? (Part 1)

Based on the presentation by Mathilde Causse (INRA) during the Tomato News Conference held in Avignon, 16-17 May 2019

The Tomato News Conference dedicated one session, chaired by Antonio Casana, President of TomatoEurope, to innovations and new contributions from research in the area of variety improvement with a view to developing the industry. Mrs. Mathilde Causse, Research Director of the Department for Genetics and Fruit and Vegetable Improvement (GAFL) at the INRA in Avignon, was the first to address the conference on this issue. She described the work that has been carried out with the aim of improving the understanding and management of the genetic and molecular bases of overall quality variability factors in tomatoes (organoleptic and nutritional). 

 Mathilde Causse

Research undertaken by Mathilde Causse is more specifically aimed at the sector of table tomatoes; but her presentation on 17 May nonetheless shows that the problems and solutions being considered for this sector are not very far removed from those that concern the processing tomato sector, and she explained how current technological advances have led to speedier and far more precise selection procedures.

"To quote the researchers of Cornell University, we are currently in the 4th phase of the evolution of plant selection. We can consider that during the first period of this process, selection was carried out by growers themselves. Then, during the 20th century, methods based on statistics and experimentation were introduced, leading to major improvements in varieties. At the end of the 20th century, in the 80s, researchers began to work with the molecular markers of DNA and started to use them in the field of genetics. Then, in the early years of the 21st century, we acquired knowledge of the entire genome, and entered the era of genome selection and editing."

 
 
Diagram created by researchers at Cornell University (USA)

"Whether working with table tomatoes for the fresh fruit and vegetable market or raw materials for processing, selection objectives in the tomato sector remain very similar: tomato producers must aim at improving yields, stability, early ripening and the capacity to adapt to growing conditions, particularly in terms of weather conditions, but also disease resistances, of which dozens have been identified around the world and currently represent a major challenge. As for processors, they want quality, firm fruit, good holding capacity before and after harvest, viscosity, and commercial aspects like sensory and nutritional qualities – features that are closely linked to the composition of the fruit and will be decisive factors in selling processed products.
Over time, researchers have provided and improved various responses to several of these objectives, attempting to offer a wide diversity of varieties that are adapted to different growing conditions. Today, the main challenge is to adapt crops in order to better take account of the agricultural environment, to consume less water, less health inputs, etc."

"Plant breeders have a wide range of tools to work with. Firstly, the plant material they use is very important, as we have access, in the tomato sector, to several wild relatives of the cultivated varieties; and these are very important because they represent a unique resource in terms of disease resistances. We also have a number of mutant populations, and when we identify an interesting gene/characteristic, it then becomes possible to easily transfer it into classic varieties. This field of research uses several different methods like the Genome Wide Association Study (which consists in analyzing a number of genetic variations found in a high number of individuals in order to study the correlation with phenotypic traits, editor's note). Researchers need to know the precise phenotype, and must be able to measure characteristics as accurately as possible. We have increasingly large number of selection criteria, like the size of cells or the precise composition of the fruit. In order to identify the genes found in a variety being studied, we use molecular markers. These markers allow us to follow a specific section of the chromosome that carries a "desirable gene" and to introduce it into a variety, instead of having to measure the complex phenotype over several generations.
"
 
 "We now know a lot more about the genome, to the point that selection and improvement methods have greatly evolved and currently provide optimized selection procedures. Among the most remarkable progressions in this evolution, one of the main ones was the publication in 2012 of the complete sequence of the tomato genome (which has 12 pairs of chromosomes), the result of work initiated by Professor Steve Tanksley at Cornell University, USA, in 2003, and carried out thanks to the contribution of new technologies based on progress achieved in human genetics, which allowed researchers to identify almost all of the 900 million base pairs that constitute the chromosomes. A publicly accessible website (http://solgenomics.net) was set up to allow researchers interested in these issues to access this essential information. After this stage (based on the sequencing of the Heinz 1706 variety), researchers were able to re-sequence several hundred important varieties in the context of a research project published in 2014, thereby identifying more than 10 million SNP (single nucleotide polymorphism: in the field of genetics, this is the variation of one single base pair of the genome between different individuals of the same species, editor's note), i.e. the variation of a base pair potentially responsible for the variations of any other characteristic. By achieving such unprecedented levels of precision, speed and efficiency, these results led, for example, to the differentiation of varieties that are very close to each other, yet in the context of greatly reduced sequencing costs.
In fact, these aspects of efficiency and cost reduction continue to improve rapidly today. At the same time, they have demonstrated, at the genomic level, a big drop in diversity in the range of tomato varieties available to growers. This is the reason why plant breeders must work with wild varieties like "cherry tomatoes" in order to recover a degree of the variability that has been lost but which could be interesting in terms of fruit qualities, adaptability to growing conditions, disease resistances, etc."

"All disease resistance genes have come from wild varieties. One interesting (but sometimes undesirable) aspect of these selection and improvement techniques is linked to the fact that the introgression of one section of a gene (generally a fairly sizable section) over several stages of crossbreeding into the genome of a cultivated variety is often accompanied by the introduction of undesirable sections carrying "bad genes" that are potentially harmful to the composition, size or other feature of the fruit.
Thanks to the use of molecular markers, and to the work carried out in the context of the Genome Wide Association Study, it has been possible to identify the genes responsible for a number of interesting traits, notably for the shape and size of the fruit, and it has also been possible to identify and map the genes involved in the processes of development and ripening of the fruit, those responsible for the infertility of flowers or for the "jointless" characteristic (very important for tomato processing), for reactions to abiotic stress (drought, heat, cold, etc.), and disease resistances
." 

See the link below for the second part of this dossier.

Some additional information
Find out more about Mathilde Causse and her work:
https://www6.paca.inra.fr/gafl_eng/Staff/Holders/Causse

Tools for seed-breeder 
 

This article refers to the Tomato News Conference held in Avignon (Fr) on 16 and 17 May 2019, during which the "2019 Processed Tomato Yearbook" was distributed to attendees. A copy of this book can be purchased from this website (go to GET LISTED) or fill in and post the order form.

Source: Tomato News conference, Interview Mathilde Causse (INRA)


 
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