Candidate gene analysis of watermelon stripe pattern locus ClSP ongoing recombination suppression.

Xiaona Pan,Xian Zhang,Zhen Yue,Chunhua Wei,Lijuan Yin,Xing Yan,Chunxia Wang,Yaping He,Rongxue Ma,Denghu Cheng

doi:10.1007/s00122-021-03891-2

Abstract

Using two segregating population, watermelon stripe pattern underlying gene ClSP was delimited to a 611.78Kb region, consisting of four discrete haploblocks and ongoing recombination suppression. Stripe pattern is an important commodity trait in watermelon, displaying diverse types. In this study, two segregating populations were generated for genetic mapping the single dominant locus ClSP, which was finally delimited to a 611.78Kb interval with suppression of recombination. According to polymorphism sites detected among genotypes, four discrete haploblocks were characterized in this target region. Based on reference genomes, 81 predicted genes were annotated in the ClSP interval, including seven transcription factors namely as candidate No1-No7. Meanwhile, the ortholog gene of cucumber ist responsible for the irregular stripes was considered as candidate No8. Strikingly, gene structures of No1-No5 completely varied from their reference descriptions and subsequently re-annotated. For instance, the original adjacent distribution candidates No2 and No3 were re-annotated as No2_3, while No4 and No5 were integrated as No4_5. Sequence analysis demonstrated the third polymorphism in CDS of re-annotated No4_5 resulting in truncated proteins in non-stripe plants. Furthermore, only No4_5 was down-regulated in light green stripes relative to dark green stripes. Transcriptome analysis identified 356 DEGs between dark green striped and light green striped peels, with genes involved in photosynthesis and chloroplast development down-regulated in light green stripes but calcium ion binding related genes up-regulated. Additionally, 38 DEGs were annotated as transcription factors, with the majority up-regulated in light green stripes, such as ERFs and WRKYs. This study not only contributes to a better understanding of the molecular mechanisms underlying watermelon stripe development, but also provides new insights into the genomic structure of ClSP locus and valuable candidates.

Highlights

Watermelon (Citrullus lanatus L., 2n = 2x =22) belonging to Cucurbitaceae family, is cultivated world widely and consumed as one of the most favorite fresh fruits globally
At approximately 6 days after pollination (DAP, D6 in Fig. 1), the stripe pattern could be visually characterized and distinctly distinguished at 8 DAP (D8), which was subsequently defined as standard green rind with stripes or without stripes at mature fruit period (D23) according to the descriptions of similar rind phenotypes published recently (HeeBum et al 2015; Park et al 2016)
Rind types as the major objectives in watermelon breeding, have been further divided as the foreground stripe patterns and background rind colors. The former is diverse and characterized by the margin of stripes, the width of stripes, the intensity of stripe coloration, the conspicuousness of stripes, while the latter presents in various phenotypes (Kim et al 2015; Lou and Wehner 2016; Park et al 2016)

Summary

Introduction

According to the morphological descriptions of watermelon, rind types could be further divided into background rind color (light to dark green, yellow, or gray) and foreground stripe pattern (solid to stripe), the latter of which are diverse and further characterized in terms of the margin of stripes (welldefined, medium, and diffuse), the width of stripes (very narrow to very broad), the intensity of stripe coloration (unicolored, bicolored, marbled, or only vein), the conspicuousness of stripes (inconspicuous to very strong) (Gama et al 2015; Kim et al 2015). A more complex model was raised to explain the inheritance of fruit rind colors and stripe patterns, in which contains five alleles at the g locus, G (dark green rind color), gW (wide stripe), gM (medium stripe), gN (narrow stripe), and g (light green rind color), with the dominance G > gW > gM > gN > g (Lou and Wehner 2016). Regarding of other stripe patterns in watermelon, the intermittent rind phenotype of ‘Navajo Sweet’ showing narrow dark green stripes at the stem end of the fruit but being irregular around the fruit equator and nearly absent at the blossom end of the fruit, is regulated by a single recessive gene ins (Gusmini and Wehner 2006); the penciled (p) phenotype visualized as very narrow stripes on a light background rind of ‘Japan 6’ is recessive to the netted rind pattern of ‘China 23’ (Weetman 1937)

Methods

Results

Conclusion