ObjectiveSeedling stage plays a vital role in plant growth and development. Up to date there are no reports about genetic mechanism of epistasis interaction during seedling growth in Populus euphratica.

MethodIn this study, a full-sib F₁ population including 408 individuals was derived from Populus euphratica × Populus euphratica. Dynamic growth data of four phenotypes were measured, including the taproot length, shoot length, total lateral root length, and number of lateral roots. Based on a high-density genetic linkage map, 2HIGWAS was employed to identify QTL-QTL interactions associated with four phenotypes.

ResultFinally, a total of 83 pairs of QTL-QTL interactions were detected, including 83 SNPs. The taproot length, shoot length, total lateral root length and number of lateral roots found 24 pairs, 20 pairs, 24 pairs and 15 pairs epistatic interactions, respectively, and the epistatic interactions of main root length, stem height and lateral root length were distributed in linkage groups 1, 19, and 17, respectively. In addition, we conducted functional annotations for the SNPs with significant QTL-QTL epistatic interactions, and 19 QTLs were annotated with candidate genes.

ConclusionInteractions associated with total lateral root length had higher heritability, and most of the SNPs were located in linkage group 17, which might be important candidate gene regions. This work may provide guidance for molecular marker-assisted breeding of Populus euphratica and other forest trees.