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Quinoa genome could see 'super-food' prices tumble  

Quinoa plant            quinoa food  

Growing quinoa plant, and quinoa used for cooking: Images borrowed from: McGrath, 2017 ; DETOXINISTA


Background

Chenopodium quinoa (quinoa) is a south American harvested plant with the common descriptors of "super food" and "mother grain". This crop has increased in international demand over the last 10 years due to its nutritious and gluten-free properties. Quinoa primarily grows in high altitude and cool temperatures which limits possible land for crop growth. The increased demand and stagnant supply has contributed to quinoa's heightened price (McGrath, 2017).

 A recently published sequence of the quinoa genome could lead to a solution for the shortage of the plant (Jarvis et al.,2017). Once genes that can beneficially alter quinoa are identified, quinoa can be breed for traits that optimize production rates. For example, shorter stockier plants could boost production by decreasing the amount fallen over plants. Scientist hope modifications to the quinoa genome could lead to crop production in a variety of soils, thus increasing world wide farming areas for quinoa. Modifications to the quinoa genome could lead to an increased supply that could decrease quinoa's price as low as that of wheat (McGrath, 2017).


Research project

Using current genomics tools, Jarvis et al., developed a chromosome-scale reference genome for quinoa (2017). Additionally, two ancestral diploid versions modern quinoa and multiple tetraploid species were sequenced to further identify quinoa sub-genomes (Figure 1) and to find preserved regions in the genome with desirable traits. Quinoa orthologues to closely related species lead to identification of 97.3% of quinoa genes. One of the first genes to be identified was a transcription factor that could be involved in saponin formation. Saponin is a bitter tasting compound that quinoa uses as an environmental defense. From this project, we have at least one gene that can be reduced or eliminated to make quinoa more profitable by reducing treatment costs to remove the compound.

 3 typestree

Figure 1. Multiple genomes were sequenced, including 3 species in the Chenopodium genus, to construct a philogenetic tree of quinoa.

Discovery science or testing a hypothesis?

The quinoa project can be classified as discovery science since there was no established testable hypothesis. Jarvis et al, primarily focused on sequencing the quinoa genome and identifying quinoa genes that could be alternated for optimized crop production.

Genomics technology

A wide array of genomics technologies were utilized for the successful sequencing of quinoa. First, the coastal Chilean quinoa fragmented genome was sequenced using single-molecule real-time (SMRT) sequencing from Pacific Biosciencies (PacBio). The sequenced genome was computationally assembled into scaffolds using chromosome-constant and optical maps. Structures similar to chromosomes called psuedomolecules were assembled from scaffolds using linkage maps. RNA-seq and PacBio isoform were used to predict protein-coding and microRNA genes. Linkage mapping and bulk segregant analysis were used to find a single gene that controls seed saponins as well as other correlated genes.

Take home message

Through a vast number of genomics technologies, the majority of the quinoa genome has been sequenced. Nine hundred and fifty six quinoa genes have been identified and annotated. With the improved sequencing of the quinoa genome, genes such as one predicted to control sapoin production, can be selected against by humans to decrease the processing costs to prepare quinoa for distribution. Other genes can be selected for to improve the production rate of the plant that can ultimately increase the supply and decrease the cost of the internationally in demand quinoa plant.

Evaluation of project

Overall, I am impressed by the techniques used in this project as well as the possible international impacts. This project is very thorough. Jarvis et al., commonly used multiple genomics technologies for one experiment. For example, when assembling the quinoa genome after sequencing, researchers used both optical and chromosome-contact maps. Optical maps from BioNano provide genetic information about molecular organization. Chromosome-contact maps look at overall conformation of chromosomes. When determining gene function, researchers looked at both ancestral forms or quinoa as well as closely related species. By looking at the same quinoa genome using multiple technologies as well as multiple references, findings seem more compelling that if only one technology was used.

This project was successful in identifying and annotating 956 (97.3%) genes in the quinoa genome. However I am curious about the sequencing or annotating limitations that explain why 2.7% of the genes are still not identified. I am also still curious about previous limitations that only allowed for partial quinoa genome sequencing.

Due to the primarily sequencing nature of this project, and because of the multiple technologies used throughout the project, Jarvis et al., were able to provide their results in a very compelling way. However, they identified potential genes primarily by comparing sequences of orthologue genes of closely related species. However, by using primarily orthologue sequences, we may not detect genes novel to quinoa.

The work by Jarvis et al., is very exciting. Many people across the world have begun to eat quinoa, this finding allows for the possibility of greater production rates of the coveted plant. Often times, scientific discoveries are amazing, but there's not a large audience to applaud them. Quinoa has a large consumer market that could be thrilled by the news. Additionally this project has the potential to lead to direct job creation, economic improvement and could ultimately give access to a cheaper nutritional food source for countries in desperate need. Although a small percentage of the quinoa genome still needs to be annotated, knowing most of the quinoa genome establishes the possibility for future beneficial genome modifications.


Sources

Jarvis DE et al., 2017. The genome of Chenopodium quinoa. Nature 542:307-312. http://dx.doi.org/10.1038/nature21370                                     

McGrath M. 2017. Quinoa genome could see 'super-food' prices tumble. BBC science and environment; [cited 208 Jan 27]. Available from: http://www.bbc.com/news/science-environment-38908321

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