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

Abstract

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 nally delimited to a 611.78 Kb 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. Notably, the adjacent distribution candidates No2 and No3, as well as No4 and No5, were con rmed to derive from longer transcripts designated as No2_3 and No4_5, respectively. 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 non-stripes relative to stripes contrast to other candidates. Transcriptome analysis identi ed 356 DEGs between striped and non-striped peels, with genes involved in photosynthesis and chloroplast development down-regulated in non-stripes but calcium ion binding related genes up-regulated. Additionally, 38 DEGs were annotated as transcription factors, with the majority up-regulated in non-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 insight into the genomic structure of ClSP locus and valuable candidates.

Primary mapping of quantitative trait loci regulating multivariate horticultural phenotypes of watermelon (Citrullus lanatus L.)

“…Many QTL studies have been performed by using the developed biparental mapping populations (F 2 and F 3 ) and recombinant inbred lines. These studies identified that the differentiated watermelon rind strip pattern is generally controlled by a stable major effect genetic locus positioned on Chr-06 ( Park et al., 2016 ; Zhang et al., 2018 ; Wu et al., 2019 ; Guo et al., 2019 ; Yue et al., 2021 ; Wang et al., 2022 ; Liang et al., 2022 ) and Chr-09 ( Maragal et al., 2022 ), except the minor variations in genetic positions found in this study. Our genetic mapping study exhibited the contrasted QTL results as compared to the earlier reported QTLs.…”

The HD-ZIP Gene Family in Watermelon: Genome-Wide Identification and Expression Analysis under Abiotic Stresses

“…The qRT-PCR amplification was performed on a StepOnePlus Real-Time PCR system (Applied Biosystems, Foster, MN, USA). Using the housekeeping gene ClACT ( Cla007792 ) as the internal reference, the relative expression level for each selected gene was calculated using the 2 −∆∆Ct method, as described in our previous study [ 21 , 22 ]. All primers of ClHDZs are listed in Table S1 .…”

Retrospective Genetic Analysis of Qualitative and Quantitative Traits in Sweet Watermelon (Citrullus lanatus var. lanatus): A Review

“…The dark-green rind stripe pattern is controlled by a single dominant gene, designated as Cla019205 [34]. Yue et al [62] identified a single dominant gene, denoted as ClSP, controlling the stripe pattern of the fruit.…”

“…Genes involved in chloroplast development and photosynthesis were downregulated in the light-green striped genotype. Some 38 DEGs were up-regulated in dark-green striped phenotype [62]. Guo et al [63] identified the gene designated as Cla97C06G126710 (which encodes a WD40-repeat protein) regulating stripe rind presence in watermelon.…”