Identification of inheritance manner and responsible locus (Acsh) related to seed-shattering in grain amaranthus (Amaranthus cruentus)

Amaranthus (Amaranthus spp.) is one of the crops considered superfoods, given that this grain is enriched for minerals, protein, and vitamins. Most cultivars of this species exhibit seed-shattering, resulting in a reduction in seed yield, but it is expected that this undesirable trait can be improved by further breeding. However, the genetic mechanism of seed-shattering in this organism remains largely unknown. In the present study, we compared two amaranthus isolates, the A. cruentus grain cultivar ‘New Aztec’ (NA) (which exhibits seed-shattering) and Amaranthus spp. Accession DB9350 (DB) (which lacks seed-shattering). In initial experiments, we conducted morphological observations of the spikelets and utricles in these two strains. NA, and not DB, showed a horizontal dehiscence line on the utricle, resulting in easy detachment of the upper part of the pericarp and seed release. Next, we investigated the presence or absence of seed-shattering in the F₁ and F₂ progeny of an NA×DB cross. Notably, all F₁ plants (n=10) showed shattering traits. In contrast, F₂ plants (n = 106) exhibited segregation, yielding 82 and 24 plants showing shattering and non-shattering traits (respectively), consistent with the segregation ratio expected for Mendelian inheritance (3:1, χ²= 0.314, p = 0.575). To elucidate the genetics of this trait, we performed bulked segregant analysis and linkage analysis in the F₂ progeny. This analysis identified a locus, designated Acsh, in the 15.2–16.0 Mbp range of Chromosome 2B; the genotype at this locus co-segregated with the seed-shattering phenotype. Together, these data demonstrated that the seed-shattering trait in A. cruentus is a dominant, single-gene, qualitative trait regulated by Acsh. These results are expected to facilitate the breeding of non-shattering cultivars in grain amaranthus.