The Chromosome Scaffold Based Quinoa Genome: Its Building and Its Use to Find the Non-Bitter Mutations in Quinoa

The pseudomolecule genome assembly of quinoa (Chenopodium quinoa Willd.) presented here is based on a PacBio/BioNano/Dovetail-assembly combined with segregation analysis to arrive at nine A-genome and nine B-genome chromosomes. Genetic maps were created from two populations: Kurmi (non-bitter) x 0654 (bitter), based on RNAseq-markers (30X lllumina 2500 PE) from developing seeds of 50 progeny; and Atlas (non-bitter) x Carina Red (bitter), based on shallow DNAseq 'context' markers (Illumina 2500 PE, 1X for the 94 genotypes and 30X for the parents) based on allele counts over a stretch of 500 successive variant calls in 94 progeny. BLASTN of KASP-markers from the genetic map of Maughan et al. (2012) allowed the assigning of the KASP-markers to the assembly scaffolds. With 6,000 markers in the three maps together, it proved possible to group 600 scaffolds covering more than 85 % of the assembly into 18 new linkage groups which are the basis of the new pseudomolecule-based genome assembly. The maps and genome assembly also allowed for the identification of the probable mutation underlying the presence and absence of saponins, which are compounds in the outer layer of quinoa seeds that cause the bitter taste of unprocessed seeds. In both mapping populations, the non-bitter locus was found on Chr16 with underlying mutations in the same bHlH transcription factor causing down-regulation of the saponin pathway (an SNP in Kurmi x 0654 and an insertion in Atlas x Carina Red population).