Plant Breeding Institute

Genome wide association mapping in Quinoa


Quinoa (Chenopodium quinoa) is a traditional Andean crop that was domesticated around 5000-7000 years ago. The production and consumption of Quinoa have rapidly expanded in recent years, due to its broad adaptability and nutritional value. Despite its long history of domestication, modern breeding and genetic improvement programs were started only a few decades ago. Now with the availability of the genome sequence, we can use genomics to improve Quinoa and spread its production even far beyond from its origin.
Quinoa germplasm possesses great genetic diversity. Adaptation and cultivation of Quinoa in Northern Europe can profit from its diversity. Understanding the genetics underlying agronomically important traits is essential for fast improvement of crops. Genome-Wide Association Studies (GWAS) based on single nucleotide polymorphisms, which rely on linkage disequilibrium and historical recombination in large diverse populations is an effective way of identifying candidate genes/loci that control agronomically important traits.

In this study, we aimed to identify candidate genes for agronomically important traits by genome-wide association study in Quinoa. We phenotyped a diversity panel of Quinoa obtained from different geographical locations in field trials at the Kiel University (Northern Germany). All the accessions on the diversity panel have already been re-sequenced. Using the phenotypic and the sequencing data, we will be able to identify candidate genes for relevant traits for adaptation of Quinoa to different climatic conditions. These candidate genes will facilitate the marker-assisted selection in modern breeding programs by accelerating the breeding progress.

We performed field trials with a diversity panel of 350 quinoa accessions. The accessions displayed large phenotypic variation with regard to flowering time and other agronomically important traits. All the accessions of the diversity panel were sequenced by a whole-genome re-sequencing approach. We identified SNPs based on the QQ74 genome V2 reference assembly. We obtained ~3 million high-quality SNPs, which we used to identify significant associations between SNPs and important traits, such as flowering time, panicle length, plant height, saponin content, TKW, and seed yield. Presently, we are identifying candidate genes for agronomically important traits. We observed rapid LD decay in the diversity panel, indicating a weak genome-wide footprint of breeding and selection in the history of Quinoa. We aim to use sequence variations to select promising accessions as crossing partners to breed new varieties well adapted to European climate conditions. Our study provides resources for fast track genetic improvement of the underutilized pseudocereal quinoa. This will enable harnessing its undiscovered potential in sustainable agricultural production

Project team
-    Prof. Dr. Christian Jung
-    Dr. Nazgol Emrani
-    M. Sc. Dilan Sarange
-    M. Sc. Nathaly Maldonado
-    B. Sc. Federico Barbier
-    Monika Bruisch
-    Brigitte Neidhardt-Olf

Scientific Partners
-    Prof. Mark Tester (King Abdullah University of Science and Technology, KAUST).
-    Prof. Dr. Karl Schmid (University of Hohenheim)
-    Jun.-Prof. Dr. Sandra M. Schmöckel (University of Hohenheim)
-    Dr. Kevin Murphy (Washington state university)

Patirange D.S.R, Emrani N., Asare E., Böndel B K., Wellman G., Rey E., Schmöckel S., Schmid K., Tester M., Jung C. (2020). Genome-wide association mapping for flowering time in Quinoa. International Symposium of the Society for Plant Breeding (GPZ). Digital breeding. 11-13 February 2020, Tulln, Austria. Oral presentation
Patirange D.S.R., Emrani N., and Jung C., (2019). Unraveling genetic mechanisms of flowering time control in Quinoa. KLS Retreat, 21-22 November 2019, Schleswig, Germany. Oral presentation
Patirange D.S.R., Emrani N., and Jung C., (2019). Genome-wide association mapping for flowering time in Quinoa. Kiel Plant Center Mini‐Symposium, 7 November 2019, Kiel, Germany. Oral presentation
Patirange D.S.R., Maldonado N., Emrani N., and Jung C., (2019). Unraveling genetic mechanisms of flowering time control in Quinoa. Genome Research for Plant Breeding GPZ Conference, 28-29 March 2019, Schleswig, Germany. Poster presentation
Sarange D., N. Emrani and C. Jung. 2019. Flowering time regulation in Quinoa and related species of the Amaranthaceae family. XXVII. Plant & Animal Genome Conference. January 12-16, 2019, San Diego, USA.
Sarange D., N. Emrani and C. Jung. 2018. Unravelling genetic mechanisms of flowering time control in Quinoa. III. International Symposium: Genetic Variation of Flowering Time Genes and Applications for Crop Improvement. March 14-16, 2018, Kiel, Germany.

Financial Support (past three years)
Funding has been provided by the KAUST`s internal competitive research program under grant No. OSR-2016-CRG5-2966.


Updated: 29.06.2020                         Responsible for this webpage: Dilan Sarange