Genetic basis of maturity time is independent from that of flowering time and contributes to ecotype differentiation in common buckwheat (Fagopyrum esculentum Moench)

BACKGROUND: Common buckwheat is considered a quantitative short-day plant and is classified into the autumn (highly photoperiod sensitive), summer (weakly photoperiod sensitive), and intermediate ecotype. Understanding ecotype differentiation is essential for adaptive expansion and maximizing yield. The genetic analysis for ecotype has focused on photoperiod-dependent flowering time, whereas post-flowering traits such as seed set and maturity time might also regulate ecotype differentiation. RESULTS: A field experiment revealed that ecotype differentiation is mainly defined by the timing of seed set and maturation, whereas flowering time is less relevant. Thus, we focused on maturity time as a trait that defines the ecotype. To detect QTLs for maturity time, we developed two F(2) populations derived from early × late-maturing accessions and intermediate × late-maturing accessions. Using genotyping by random amplicon sequencing–direct analysis, we generated a high-density linkage map. QTL analysis detected two major QTLs for maturity time, one in each F(2) population. We also detected QTLs for flowering time at loci different from maturity time QTLs, which suggests that different genetic mechanisms regulate flowering and maturity. Association analysis showed that both QTLs for maturity time were significantly associated with variations in the trait across years. CONCLUSIONS: Maturity time appeared to be more suitable for explaining ecotype differentiation than flowering time, and different genetic mechanisms would regulate the timing of flowering and maturation. The QTLs and QTL-linked markers for maturity time detected here may be useful to extend the cultivation area and to fine-tune the growth period to maximize yield in buckwheat. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-022-03722-6.