Comparative Transcriptome Analysis Provides Insights Into Yellow Rind Formation and Preliminary Mapping of the Clyr (Yellow Rind) Gene in Watermelon

Dongming Liu,Huihui Yang,Huayu Zhu,Luming Yang,Xiaochun Wei,Shichao Yang,Xiaojuan Wang,Yuxiang Yuan,Dongling Sun,Minjuan Zhang

doi:10.3389/fpls.2020.00192

Dongming Liu, Huihui Yang + Show 8 more

Open Access

https://doi.org/10.3389/fpls.2020.00192

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Abstract

As an important appearance trait, the rind color of watermelon fruit affects the commodity value and further determines consumption choices. In this study, a comparative transcriptome analysis was conducted to elucidate the genes and pathways involved in the formation of yellow rind fruit in watermelon using a yellow rind inbred line WT4 and a green rind inbred line WM102. A total of 2,362 differentially expressed genes (DEGs) between WT4 and WM102 at three different stages (0, 7, and 14 DAP) were identified and 9,770 DEGs were obtained by comparing the expression level at 7 DAP and 14 DAP with the former stages of WT4. The function enrichment of DEGs revealed a number of pathways and terms in biological processes, cellular components, and molecular functions that were related to plant pigment metabolism, suggesting that there may be a group of common core genes regulating rind color formation. In addition, next-generation sequencing aided bulked-segregant analysis (BSA-seq) of the yellow rind pool and green rind pool selected from an F2 population revealed that the yellow rind gene (Clyr) was mapped on the top end of chromosome 4. Based on the BSA-seq analysis result, Clyr was further confined to a region of 91.42 kb by linkage analysis using 1,106 F2 plants. These results will aid in identifying the key genes and pathways associated with yellow rind formation and elucidating the molecular mechanism of rind color formation in watermelon.

Highlights

Watermelon (Citrullus lanatus) is an important horticultural crop in the Cucurbitaceae family and is one of the top ten most consumed fresh fruits globally
The content of chlorophyll a and chlorophyll b was significantly reduced in the yellow rind line WT4, which was detected at a very low level, whereas the carotenoids were dramatically increased in WT4 at the same developmental stage (Figure 2)
124.71 Gb clean reads were obtained for the 18 cDNA libraries, ranging from 5.96 to 7.98 Gb reads per library

Summary

Introduction

Watermelon (Citrullus lanatus) is an important horticultural crop in the Cucurbitaceae family and is one of the top ten most consumed fresh fruits globally. Chlorophyll and carotenoids are the main pigments affecting watermelon rind coloration. Because of their essential role in harvesting light energy and converting it into chemical energy, chlorophyll is of great importance in photosynthesis (Fromme et al, 2003). The first section is synthesis of protoporphyrin IX from 5-aminolevulinic acid (ALA), the precursor of chlorophyll (Hotta et al, 1997). In this progress, ALA is condensed to the monopyrrole, porphobilinogen, and four molecules, and cyclic tetrapyrrole and uroporphyrinogen III would be synthesized (Grimm, 1998). The last section is the degradation of Chl a (Takamiya et al, 2000; Hörtensteiner, 2006)

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