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

Kailiang Bo,Shaoyun Dong,Han Miao,Shengping Zhang,Weiping Wang,Shuang Wei,Xingfang Gu

doi:10.1186/s12870-019-1835-6

Kailiang Bo, Shaoyun Dong + Show 5 more

Open Access

https://doi.org/10.1186/s12870-019-1835-6

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Abstract

BackgroundGreen 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 F2 and two BC1 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 F2 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.ResultsWe 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.ConclusionsWe 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.

Highlights

Green flesh color, resulting from the accumulation of chlorophyll, is one of the most important commercial traits for the fruits
Phenotypic variation of flesh color (FC), flesh extract color (FEC) and flesh chlorophyll content (FCC) in F2 and BC1 populations Phenotypic data of FC, FEC and FCC were collected from the two parents, their F1, three F2, one BC1P1 and one BC1P2 populations in five experiments over two years (Fig. 1, Additional file 1: Table S1)
The frequency distributions of FC, FEC and FCC among the populations from different experiments are illustrated in Fig. 2c-e and Additional file 1: Figure S3

Summary

Introduction

Green flesh color, resulting from the accumulation of chlorophyll, is one of the most important commercial traits for the fruits. Chlorophyll and its natural or commercial derivatives have demonstrated to have antioxidant, and antimutagenic activity, and have function in modulating xenobiotic metabolizing enzymes, and induction of apoptotic events in cancer cell lines in vitro and in vivo experiments [6]. They have the ability to induce mammalian phase 2 proteins which protect cells against deleterious effect of oxidants and electrophiles [7]. Carotenoids including β–carotene, α-carotene, lutein, etc. are the important precursors of vitamin A, which is necessary for human health especially the eye health [8, 9]

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