Common buckwheat (Fagopyrum esculentum Moench; 2n = 2x =16) is an outcrossing pseudocereal widely cultivated in the temperate zone. Buckwheat is fast-growing and is tolerant of cool climates and high elevations. The seeds of buckwheat contain a high level of starch and high quality of protein with a well-balanced amino acid profile without gluten. The genetic improvement of this minor yet important crop has achieved only limited success, mainly due to its heteromorphic self-incompatible (SI) system. Our challenge is to elucidate the characteristic heteromorphic SI system and genetically improve the agricultural traits of buckwheat.

We previously developed a self-compatible (SC) common buckwheat line by an interspecific cross between F. esculentum (SI species) and F. homotropicum (SC species). Here, we identified the genetic loci of the SI/SC trait and pre-harvest sprouting (PHS) tolerance, which is an important trait in buckwheat using three F2 populations (crosses A to C) derived from SI × SC lines. To construct genetic maps and performed quantitative trait loci (QTL) analysis efficiently, we developed the Ion AmpliSeq custom panel. Using this custom panel, we detected a single genetic locus which tightly linked with SI/SC trait. QTL analysis detected two, four, and two QTLs for PHS tolerance in crosses A, B, and C, respectively. We also detected some QTLs for maturity time.