RT Journal Article
SR Electronic
T1 Genome-wide association study in the pseudocereal quinoa reveals selection pattern typical for crops with a short breeding history
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.12.03.410050
DO 10.1101/2020.12.03.410050
A1 Patiranage, Dilan S. R.
A1 Rey, Elodie
A1 Emrani, Nazgol
A1 Wellman, Gordon
A1 Schmid, Karl
A1 Schmöckel, Sandra M.
A1 Tester, Mark
A1 Jung, Christian
YR 2020
UL http://biorxiv.org/content/early/2020/12/05/2020.12.03.410050.abstract
AB Quinoa germplasm preserves useful and substantial genetic variation, yet it remains untapped due to a lack of implementation of modern breeding tools. We have integrated field and sequence data to characterize a large diversity panel of quinoa. Whole-genome sequencing of 310 accessions revealed 2.9 million polymorphic high confidence SNP loci. Highland and Lowland quinoa were clustered into two main groups, with FST divergence of 0.36 and fast LD decay of 6.5 and 49.8 Kb, respectively. A genome-wide association study uncovered 600 SNPs stably associated with 17 agronomic traits. Two candidate genes are associated with thousand seed weight, and a resistance gene analog is associated with downy mildew resistance. We also identified pleiotropically acting loci for four agronomic traits that are highly responding to photoperiod hence important for the adaptation to different environments. This work demonstrates the use of re-sequencing data of an orphan crop, which is partially domesticated to rapidly identify marker-trait association and provides the underpinning elements for genomics-enabled quinoa breeding.Competing Interest StatementThe authors have declared no competing interest.