North American pitseed goosefoot (Chenopodium berlandieri) is a genetic resource to improve Andean quinoa (C. quinoa)

Pitseed goosefoot ( Chenopodium berlandieri ) is a free-living North American member of an allotetraploid complex that includes the Andean pseudocereal quinoa ( C. quinoa ). Like quinoa, pitseed goosefoot was domesticated, possibly independently, in eastern North America (subsp. jonesianum ) and Mesoamerica (subsp. nuttaliae ). To test the utility of C. berlandieri as a resource for quinoa breeding, we produced the whole-genome DNA sequence of PI 433,231, a huauzontle from Puebla, México. The 1.295 Gb genome was assembled into 18 pseudomolecules and annotated using RNAseq data from multiple tissues. Alignment with the v.2.0 genome of Chilean-origin C. quinoa cv. ‘QQ74’ revealed several inversions and a 4A-6B reciprocal translocation. Despite these rearrangements, some quinoa x pitseed goosefoot crosses produce highly fertile hybrids with faithful recombination, as evidenced by a high-density SNP linkage map constructed from a Bolivian quinoa ‘Real-1’ × BYU 937 (Texas coastal pitseed goosefoot) F 2 population. Recombination in that cross was comparable to a ‘Real-1’ × BYU 1101 (Argentine C. hircinum ) F 2 population. Furthermore, SNP-based phylogenetic and population structure analyses of 90 accessions supported the hypothesis of multiple independent domestications and descent from a common 4 × ancestor, with a likely North American Center of Origin.