CsKIP1.7A, a gene involved in fruit development, contributes to the yield heterosis formation of hybrid F1 in cucumber.

Heterosis has been widely applied in crops production. Nonetheless, how to determine the favorable recombination of non-alleles remains elusive. Due to the uncertainty of genetic recombination, hybrids with strong heterosis tend to be selected empirically, by developing and testing a tremendous number of combinations. Here, we found some individuals in recombinant inbred lines (RILs, F₉) that were generated from hybrid F₁ (HRF₁) with heterosis performed transgressive segregation for yield in multiple environments. The result suggested that the formation of yield heterosis in hybrid was caused by the effective recombination of genes or QTLs. We performed multiple regression analysis (MRA) and redundancy analysis (RDA) using 11 traits measured in four environments. Of these traits, percentage of female flowers (PFF), fruit length (FL), fruit neck length (FNL), vine length (VL) and vine diameter (VD) contributed to increase yield. Moreover, the genes or QTL of yield contributor traits were identified by the molecular mapping strategy. We predicted a fl7.1 candidate gene that encoding a KIP1-like protein through correlation analysis between haplotype and fruit length phenotype. Based on the phenomenon some RILs individuals performed transgressive segregation and genetic theory, we proposed the model that the genetic sources of heterosis are contributed by combination of heterozygotic advantages and genetic recombination effects. Our work provides the theoretical basis for the pyramid of contributor genes or QTL for yield heterosis. This work also may facilitate Marker-assisted Selection for promote hybrid pyramid breeding and makes yield increasing more predictable in cucumber.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-025-01551-7.