Background
Green flesh color, resulting from the accumulation of chlorophyll, is one of the most important commercial traits for the fruits. The genetic network regulating green flesh formation has been studied in tomato, melon and watermelon. However, little is known about the inheritance and molecular basis of green flesh in cucumber. This study sought to determine the main genomic regions associated with green flesh. Three F
2
and two BC
1
populations derived from the 9110Gt (cultivated cucumber, green flesh color) and PI183967 (wild cucumber, white flesh color) were used for the green flesh genetic analysis. Two F
2
populations of them were further employed to do the map construction and quantitative trait loci (QTL) study. Also, a core cucumber germplasms population was used to do the GWAS analysis.
Results
We identified three indexes, flesh color (FC), flesh extract color (FEC) and flesh chlorophyll content (FCC) in three environments. Genetic analysis indicated that green flesh color in 9110Gt is controlled by a major-effect QTL. We developed two genetic maps with 192 and 174 microsatellite markers respectively. Two novel inversions in Chr1 were identified between cultivated and wild cucumbers. The major-effect QTL,
qgf5.1
, was identified using FC, FEC and FCC index in all different environments used. In addition, the same
qgf5.1
, together with
qgf3.1
, was identified via GWAS. Further investigation of two candidate regions using pairwise LD correlations, combined with genetic diversity of
qgf5.1
in natural populations, it was found that
Csa5G021320
is the candidate gene of
qgf5.1
. Geographical distribution revealed that green flesh color formation could be due to the high latitude, which has longer day time to produce the photosynthesis and chlorophyll synthesis during cucumber domestication and evolution.
Conclusions
We first reported the cucumber green flesh color is a quantitative trait. We detected two novel loci
qgf5.1
and
qgf3.1
, which regulate the green flesh formation in cucumber. The QTL mapping and GWAS approaches identified several candidate genes for further validation using functional genomics or forward genetics approaches. Findings from the present study provide a new insight into the genetic control of green flesh in cucumber.
Electronic supplementary material
The online version of this article (10.1186/s12870-019-1835-6) contains supplementary material, which is available to authorized users.