QTL mapping of key phenological and morphological traits in grain amaranth (Amaranthus hypochondriacus L.)

Grain amaranth is a promising alternative food grain owing to its nutrient-rich composition and ability to grow under poor environmental conditions. In this study, we aimed to identify quantitative trait loci (QTLs) associated with key morphological and phenological traits using an F₂ population of Amaranthus hypochondriacus derived from two commercial cultivars, Golden and Pygmy Torch. Nine traits were evaluated across three cultivation trials, and single nucleotide polymorphism (SNP) genotyping conducted using double digest restriction site-associated DNA sequencing analysis. Genetic linkage maps were constructed based on SNP markers, and QTL analysis independently conducted for each trial. Three linkage maps were constructed, spanning 5640, 5970.3, and 6960.2 cM, respectively. In total, 12 QTLs were associated with the nine traits detected on Chr. 4, 6, 9, 10, and 16 in at least two cultivations, with QTL regions of the five traits overlapping on Chr. 4. Notably, seven QTLs (AhPH6, AhSTD4, AhNN4, AhBI4, AhHC16, AhIFC16, and AhSCC9) related to important morphological traits were consistently detected in all three cultivation trials. The study results provide valuable genetic insights for the improvement of A. hypochondriacus and suggest the possibility of using molecular markers for the selection of important traits to establish breeding programs more efficiently.