"With 15 plants, we are able to cover 100% of the allelic variability available within the beta genus, supplementing the genetic resources already used at present".
Contents
1. Collection of 10,000 accessions
2. Analysis of the 3,000 accessions retained
3. Choice of the 15 accessions selected
4. Crossing with the elite germplasm
Testimonial
Mitchell McGrath, Chairman of the AKER program's Scientific Committee
Preamble: expanding genetic variability
More and more is known about sugar beet's diploid genome: nine basic chromosomes, 760cM, genomic sequence acquired (750Mb, 55,000 genes). A number of genomic tools are available (SSR markers, numerous genetic maps, BAC banks, EST sequences, etc.) or being developed (SNP markers, physical map).
We can see that the genetic variability used in breeding is increasingly limited. However, the genetic improvement of plants depends primarily on this variability being continuously incorporated. Estimates show that the variability currently used represents less than 20% of the total available, which highlights the importance of expanding this variability from the start of the AKER program.
1. Collection of 10,000 accessions
The allelic variability of the sugar beet species is kept primarily in two international gene banks: GRIN-ARS and EURISCO. The first, www.ars-grin.gov, located in the United States, is collecting and multiplying genetic resources; it is available to users online. The second, www.eurisco.ecpgr.org, located in Europe, lists all the species from the beta genus and redirects users to the holding organization. In total, 46 organizations holding genetic material have been identified.
The potentially usable resources are estimated at 10,000 reference plants. The first task as part of the AKER program's WP2 (characterization and exploitation of natural diversity) has been to draw up an inventory of these plants that are available around the world. Out of the total, one third come from the United States and one third from Germany, with the rest split between the other countries.
Work needed to be carried out to "clean up" this information. At the start of 2013, the inventory and analysis of the 10,000 plants available made it possible to select the 3,000 that have been retained. This is what we call the reference collection. Within it, one third of the plants are wild beets (beta maritima, macrocarpa, adanensis, patula), with the rest cultivated sugar beet or related beet (garden, fodder beet).
2. Analysis of the 3,000 plants retained
DNA samples have been taken from these 3,000 plants in order to carry out genotyping. Then, they have been subject to molecular marking in connection with the AKER program's WP3 (sequencing and development of markers for genotyping).
Two types of markers have been used: SNP (Single Nucleotide Polymorphism), based on the breeding material, and DArT (Diversity Array Technology), based on all the elements, including wild germplasm. The first SNP analyses (378) have been carried out in Europe, with the second DArT analyses (4,500) performed in Australia. In total, these analyses represent 12 million molecular marking points.
3. Selection of the 15 reference plants
The WP2 team has run a reference collection software on 800 of the 4,500 analyses carried out with the DArT markers.
The aim is to measure the differences and calculate the allelic richness and genetic distances, representing the diversity. Taken two by two, the greater the total difference, the greater the distance. On all the reference plants, and for equivalent distances, the inclusion of new allelic features, to a greater or lesser degree, will be essential for breeders.
The result obtained has made it possible to select several sets of 15 interesting plants. These sets will be gradually sequenced between now and the end of 2013 by the WP3 team, with a view to ultimately choosing just one. However, the AKER program's researchers already know that 15 plants make it possible to cover 100% of the allelic variability available within the beta genus, supplementing the genetic resources already used at present. Together, the reference plants make up a representative sample of the total genetic richness.
This work is confirming the assumption set out initially, i.e. that a small number of plants selected with relevant tools and methods makes it possible to represent the bulk of the genetic diversity.
4. Crossing with the elite germplasm
In spring 2013, the WP2 team carried out F1 crossings of the sets of the 15 plants retained with the elite germplasm (existing genetic material component).
The seeds resulting from these crossings have been collected. DNA samples have been taken to check that there was no contamination in the genetic material obtained. The first backcrossings have been carried out for the annual plants, which will be followed by the biennial plants next year.
The program will continue in 2015 with second-generation backcrossings, continuing to use the elite germplasm, in 2016 with the self-fertilization from the second-generation backcrossing, and in 2017 with the production of hybrids.
As a result of this work, very large volumes of data are being collected and analyzed. In 2015 and 2016 for instance, 60,000 DNA samples will be taken from the plants obtained through the various crossings.
Testimonial
Mitchell McGrath,
Chairman of the AKER program's Scientific Committee,
Geneticist in the US Department of Agriculture's (USDA) beet and soya unit
"The AKER program is very ambitious, but it has already accomplished great things"
It is a great pleasure and honor to serve the AKER project as a member of the scientific committee. Having worked with sugar beet breeding, genetics and genomics in the United States for over 17 years, it is clear that meeting the challenges addressed by the AKER project is essential for continued breeding progress for improved sugar beet varieties, as well as sustained profitability for sugar beet growers around the world.
Early in the project, where we are now, AKER partners and scientists have done a fantastic job in characterizing the diversity present in the species. As sugar beet carries only a small fraction of this species diversity, it represents a rich source of genetic novelty that has great potential for sugar beet improvement.
Indeed, many important traits have already been captured in sugar beet from the wild species, and this AKER goal is to systematically capture this diversity into sugar beet so that it might be deployed to meet continued challenges faced by sugar beet growers and processors.
Over the next few years, new methods by which this novel diversity can be evaluated are being developed in the AKER project that will allow greater precision and higher efficiency in breeding, which will help not only in meeting AKER's goals, but assist the entire sugar beet breeding and genetics community.
Certainly, the AKER project is very ambitious, and already has accomplished a great deal by carefully thinking about the current variety development process and bringing new genetic resources and modern technology to bear on long-standing challenges for increasing agricultural productivity. It is a pleasure to be able to play some small part in this process.
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