Faster breeding of new crops for high quality nutrition: quinoa as example and target crop

Faster breeding of new crops for high quality nutrition: quinoa as example and target crop


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Landbouw, Water, Voedsel>Sleuteltechnologieën LWV>Biotechnologie en Veredeling






Society demands more plant based protein foods in our diet to achieve a Circular Agriculture with smaller foot print and less emissions. To achieve this we need to produce new specialist protein crops. Quinoa is one those new crops that fit well in such diets, but we need varieties with higher protein content and yield to reduce cost price and improve quality. Quinoa breeding – as quinoa is a new crop - is still in its infancy. For new crops such as quinoa new key breeding technologies need to be developed, e.g. flexible genotyping tools that can be applied to biodiversity analysis and genetic linkage mapping, as well as advanced phenotyping tools. This project aims to develop both genetic key technologies and phenotyping key technologies for quinoa, and new crops in general. We believe this will be an ideal opportunity to enable a leap in the key breeding technologies and in the level of breeding in new crops. Quinoa is chosen as a model for new crops, because it is already an interesting target crop as the level of consumption of locally grown quinoa increases in NL and EU. The Dutch seed industry has a large opportunity for growth in NL and international seed sales of quinoa. First steps towards advanced breeding techniques have been set (e.g. the genome of quinoa was co-published by Wageningen UR (WUR) in Nature in 2017). WUR has developed its own quinoa varieties performing well across Europe, Turkey and even in the Andes. The combination of disease resistance, good yield, photoperiod insensitivity and the non-bitter seed coat make these varieties very popular. Most other varieties of quinoa have a bitter outer layer with saponins; these have to be removed via a costly process that also creates large losses. Non-bitter varieties are ideal for food ingredients from fractions (high starch, high protein) for specific applications. Even quinoa milk is a potential product. Having higher protein contents and yields is key to successfully develop such new food products. The consortium wants to make better use of quinoa genetic resources and wants to promote the further genetic improvement of germplasm in order to produce improved quinoa varieties to support their business and ambitions. There is a need to broaden the genetic diversity in the non-bitter breeding pool for which new germplasm from Ecuador will be tested and crossed with WUR germplasm. For these reasons, a consortium of Dutch and Ecuadorian companies involved in quinoa grain production and seed sales, production chain management and processing, and an international company involved in development of new key technologies for breeding together with WUR Plant Breeding have set out to develop such key breeding technologies (large scale genotyping technologies for new crops, large scale phenotyping platform, better use of heterosis by developing tools to implement hybrids based on cytoplasmic male sterility in new crops) and to test germplasm with higher protein for applications in food ingredients. The project contributes to Circular Agriculture by enabling local production of protein-rich quinoa to alleviate increasing environmental pressure in original production area in the Andes and long distance transport of food and their minerals. Further, as quinoa products contain high amounts of essential amino acids and can easily be incorporated in our meals, quinoa also contributes to the protein transition towards more plant based proteins with less mineral emissions. Furthermore, quinoa is a climate resilient crop that can grow in adverse conditions (e.g short seasons, low rainfall, high salinity), therefore also contributing to climate neutral agriculture.

Doel van het project

The demand for substitution of animal based protein foods by plant protein foods from new crops is increasing sharply, and is also needed to create a closed Circular Agriculture; quinoa can play a role, but only when the genetic improvement of quinoa is accelerated to achieve higher quality and yield and lower cost prices.

Relatie met missie (Motivatie)

Reason for submitting project: what is the urgency for the sector
The consortium is active in quinoa breeding and marketing for some years now, and one of its members is active in developing key genetics technologies. WUR has developed highly popular non-bitter varieties that are commercialized by the consortium. There is a need for more varieties that are locally adapted to the Netherlands, but also to many other regions in the world where production of Dutch quinoa varieties can greatly expand, enabling "short chains" better suited to Circular Agriculture. The ambition of the consortium is to become one of the strongest developers of quinoa varieties and quinoa food products. The key genetics technology wants to show the applicability in new crops. It is the vision of the consortium that quinoa can become a good addition to our diet, replacing in part animal protein. Further improvement in grain yield and protein content and yield are necessary to realize this ambition as this will lead to lower cost and lower land use. Improving genetic tools and broadening the germplasm of non-bitter quinoa is very urgent as the current variety base is very narrow.
State of the Art (see Appendix 2 for more details)
Global consumption of quinoa is over 200,000 tonnes annually and increasing at over 10 % per year. The consortium's varieties are used on over 5,000 ha today (12,000 tonnes) and this area is expanding fast. Potential grain yield of quinoa is about 6 t/ha, and 4 t/ha has been achieved in the Netherlands. Average farmer yield is about 2-3 t/ha, so there is much room for productivity increase. Current protein content is 12-18 % in dry matter and the target is 15-20 %. Today, only 9 non-bitter varieties exist in the EU (8 from WUR). A set of 400 Ecuadorian lines is available to the project providing a huge genetic variation. WUR has a mapping population with 800 F2-genotypes and their F3-families. The consortium has facilities for agronomy evaluation and evaluation of quinoa ingredient products. The state of the art in genetics in quinoa is also clear from the Nature publication on the genome of quinoa (Jarvis et al, 2017), which shows that the genome sequence has been assembled and that 82 % of the sequence length has been mapped onto a linkage map in 18 linkage groups. This provides the basis for the design of probes for the Allegro system. Genetic linkage mapping in quinoa for the target traits is still missing. Greenfood50 and WUR have developed a dry separation process that in combination with new higher protein quinoa will lead to unprecedented quinoa food ingredients.

Geplande acties

WP 1. Implementation of a novel genotyping technology (Allegro genotyping technology from Tecan)
Year 1. Design probe set for at least 5000 potential SNP positions;
Year 2. Redesign probes sets if necessary
Year 3. No activities planned
Year 4. Finalize analysis and paper writing and reporting.
WP2 Use of the Allegro genotyping technology of Tecan in a biodiversity study in Ecuadorian germplasm
Year 1. Evaluate 96 lines, analyze probe design, optimize probe set, first biodiversity analysis
Year 2. Evaluate second 96 lines with optimized probe set (smaller set but overlapping fully with first)
Year 3. Evaluate remaining 192 lines, finalize full biodiversity analysis and probe design for quinoa biodiversity analysis.
The Ecuadorian germplasm (and DNA) will arrive in batches, so cannot all be analyzed in year 1.
Year 4. Finalize analysis and paper writing and reporting.
WP3 Use of the Allegro genotyping by sequencing technology to enlarging set of genotypes in a combined mapping population of quinoa
Already available: Genetic marker map on 94 genotypes (F2s) of the cross Atlas x Red Carina.
Year 1. Use Allegro genotyping technology in 80 genotypes (F2s) of cross Pasto x Red Carina
Year 2. Evaluate design of probes and if necessary redesign and then apply Allegro genotyping to an additional 130 genotypes of both crosses, to finally achieve a combined population of 300+ genotypes
Year 3. Evaluate design of probes and propose a set of high quality probes for genotyping in quinoa. Create combined linkage map.
Year 4. Finalize analysis and paper writing and reporting.
WP4 Development and use of large scale phenotyping platform of NPEC
(= Netherlands Plant-Ecophenotyping Centre) at Wageningen UR to assess genetic variation in yield potential and abiotic stress tolerance and resource use efficiency.
Year 1. Phenotype a mapping population of 200 genotypes
Year 2. Genetic linkage analysis combining data of WP 4 year 1 and WP3 Year 2; produce seed offspring of highly promising materials from year 1 for assessing parent offspring relationships or fine mapping.
Year 3. Phenotype 50 selected offspring (more replicates).
Year 4. Finalize analysis and paper writing and reporting.
WP5 Development of agronomy and genetic selection tools to improve nutritional quality of quinoa towards higher protein yield and content.
Year 1. Sample collection from practice and experiments (mapping populations) and breeding program. Analysis of protein content. Selection of best F3-genotypes from segregating F2-families for inbreeding towards to F4. Analyse same samples using NIRS to create NIRS calibration. Food product application tests with high and low protein samples.
Year 2. Apply NIRS calibration samples from selected offspring, select best genotypes for further inbreeding to F5. Food product application tests with high and low protein samples.
Year 3. Apply NIRS calibration samples from selected offspring, select best genotypes for further inbreeding to F6.
Year 4. Test in yield and protein content of selected F6 families in plots. Food product application tests with high and low protein samples.
WP6 Hybrid breeding
Year 1. cross CMS lines and with European non-bitter varieties (F1s and F2-families already obtained): select pollen sterile and fertile genotypes for bulk segregant analysis.
Year 2.Whole genome sequence analyse on CMS and fertile parent and two bulk segregant samples of fertile and non-fertile genotypes: identify restorer of fertility loci
Year 3. Sequences population of mitochondrial DNA of CMS and non-bitter parent to search for gene causing CMS.
Year 4. Select plants that carry fertile mitochondrial DNA but are homozygous for the non-functional restorer of fertility gene (homozygous rf rf): these are maintainer lines. Finalize design of using the markers/gene sequences for restorer genes and mitochondrial mutation to develop breeding scheme introgress both CMS and maintainer trait into elite materials.

Each year a project meeting will be held in the period April/May. This year (like last year) this is a virtual meeting, but with use of video to show the actual field/greenhouse and labtrials that are executed. Hopefully in July we can have a physical meeting in Wageningen.

Naam projectleider

Robert van Loo