Genomic Sequence of Canadian Chenopodium berlandieri : A North American Wild Relative of Quinoa

• Published in: Plants (Basel) 2023-01, Vol.12 (3), p.467
• Main Authors: Samuels, Mark E, Lapointe, Cassandra, Halwas, Sara, Worley, Anne C
• Format: Article
• Language: English
• Subjects: Adaptation; Agriculture; Assembly; Chenopodium berlandieri; Chenopodium quinoa; Chloroplasts; Diploids; DNA barcoding; Domestication; Fertilization; Food; Gene sequencing; Genes; Genetics; genome assembly; genome sequencing; Genomes; Germplasm; Indigenous peoples; Morphology; Native North Americans; Nucleotide sequence; pitseed goosefoot; Quinoa; Salinity tolerance; Seeds; Self-fertilization; Soil salinity; Wet climates; Whole genome sequencing
• ISSN: 2223-7747; 2223-7747
• DOI: 10.3390/plants12030467

(pitseed goosefoot) is a widespread native North American plant, which was cultivated and consumed by indigenous peoples prior to the arrival of European colonists. is closely related to, and freely hybridizes with the domesticated South American food crop . As such it is a potential source of wild germplasm for breeding with , for improved quinoa production in North America. The genome sequence could also be a useful source of information for improving quinoa adaptation. To this end, we first optimized barcode markers in two chloroplast genes, and . Together these markers can distinguish from the morphologically similar Eurasian invasive (lamb's quarters). Second, we performed whole genome sequencing and preliminary assembly of a accession collected in Manitoba, Canada. Our assembly, while fragmented, is consistent with the expected allotetraploid structure containing diploid sub-genomes A and B. The genome of our accession is highly homozygous, with only one variant site per 3-4000 bases in non-repetitive sequences. This is consistent with predominant self-fertilization. As previously reported for the genome of a partly domesticated Mexican accession of , our genome assembly is similar to that of Somewhat unexpectedly, the genome of our accession had almost as many variant sites when compared to the Mexican , as compared to . Despite the overall similarity of our genome sequence to that of , there are differences in genes known to be involved in the domestication or genetics of other food crops. In one example, our genome assembly appears to lack one functional copy of the (salt overly sensitive 1) gene. is involved in soil salinity tolerance, and by extension may be relevant to the adaptation of to the wet climate of the Canadian region where it was collected. Our genome assembly will be a useful tool for the improved cultivation of quinoa in North America.