QTL mapping and genome-wide association study reveal two novel loci associated with green flesh color in cucumber

Abstract

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.

Quantitative trait loci and candidate genes responsible for pale green flesh colour in watermelon (Citrullus lanatus)

“…Compared with the pale yellow flesh COS, the pale green flesh ZXG01555 showed significantly higher chlorophyll content, indicating a key role of chlorophyll in green flesh formation. The results were consistent with Bo et al., (2019), who reported that cucumber green flesh colour formation resulted from chlorophyll accumulation. Our results revealed that green flesh colour was controlled by a major effective QTL.…”

Fine Mapping and Candidate Gene Identification for the CapUp Locus Controlling Fruit Orientation in Pepper (Capsicum spp.)

“…To understand the trend of fruit orientation in different pepper populations, identify the possible minor alleles that contribute to the few intermediate phenotypes, and determine the major locus controlling upright and pendent fruit orientations, we performed QTL and GWAS analyses. The combined use of QTLs and GWAS was previously shown to be a powerful approach for the identification of loci and candidate genes in pepper ( Han et al, 2018 ), as well as other crops ( He et al, 2017 ; Liu et al, 2018 ; Zhao et al, 2018 ; Bo et al, 2019 ; Siddique et al, 2019 ).…”

Molecularly tagged genes and quantitative trait loci in cucumber with recommendations for QTL nomenclature

“…54 ). The green flesh ( gf ) in immature cucumber, results of accumulation of chlorophyll, is controlled by two loci 55 .…”