Whole-Genome Resequencing of Near-Isogenic Lines Reveals a Genomic Region Associated with High Trans-Lycopene Contents in Watermelon

Lee, Siyoung; Park, Girim; Choi, Yunseo; Park, Seoyeon; Kim, Hoy‐Taek; Lee, Oakjin; Kim, Taebok; Park, Young-Hoon

doi:10.3390/plants11010008

Cited by 7 publications

(7 citation statements)

References 48 publications

(60 reference statements)

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“…The b-carotene and lycopene of F 2 individuals were extracted from freeze-dried watermelon flesh according to the method described by Lee et al (2022). Briefly, 0.1 g of finely crushed watermelon sample was added to 1 ml of ethanol containing 0.5 mM butylated hydroxytoluene and mixed carefully.…”

Section: Fruit Phenotype Analysismentioning

confidence: 99%

High-quality genome assembly and genetic mapping reveal a gene regulating flesh color in watermelon (Citrullus lanatus)

Nie

Kim²,

Lee³

et al. 2023

Front. Plant Sci.

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The unique color and type characteristics of watermelon fruits are regulated by many molecular mechanisms. However, it still needs to be combined with more abundant genetic data to fine-tune the positioning. We assembled genomes of two Korean inbred watermelon lines (cv. 242-1 and 159-1) with unique color and fruit-type characteristics and identified 23,921 and 24,451 protein-coding genes in the two genomes, respectively. To obtain more precise results for further study, we resequenced one individual of each parental line and an F2 population composed of 87 individuals. This identified 1,539 single-nucleotide polymorphisms (SNPs) and 80 InDel markers that provided a high-density genetic linkage map with a total length of 3,036.9 cM. Quantitative trait locus mapping identified 15 QTLs for watermelon fruit quality-related traits, including β-carotene and lycopene content in fruit flesh, fruit shape index, skin thickness, flesh color, and rind color. By investigating the mapping intervals, we identified 33 candidate genes containing variants in the coding sequence. Among them, Cla97C01G008760 was annotated as a phytoene synthase with a single-nucleotide variant (A → G) in the first exon at 9,539,129 bp of chromosome 1 that resulted in the conversion of a lysine to glutamic acid, indicating that this gene might regulate flesh color changes at the protein level. These findings not only prove the importance of a phytoene synthase gene in pigmentation but also explain an important reason for the color change of watermelon flesh.

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Section: Fruit Phenotype Analysismentioning

confidence: 99%

High-quality genome assembly and genetic mapping reveal a gene regulating flesh color in watermelon (Citrullus lanatus)

Nie

Kim²,

Lee³

et al. 2023

Front. Plant Sci.

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“…KASP TM markers UGA3_10738714, UGA3_10795402, and UGA3_11016809, associated with the Qdff3-1 loci conferring early maturity in watermelon, have been developed for breeding [32]. CAPS markers CIR6-M1 and CIR6-M4 are linked to trans-lycopene content [103]. Pei et al [104] developed a KASP marker to identify pale green coloured watermelon flesh.…”

Section: Molecular Markersmentioning

confidence: 99%

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

et al. 2022

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Understanding the genetic basis of a crop’s qualitative and quantitative traits is vital to designing market preferred varieties. The aim of this review is to present a retrospective genetic analysis of qualitative and quantitative phenotypic traits in sweet watermelon as a guide for trait integration and the development of novel varieties with yield potential and desirable horticultural attributes. The first section outlines genes conditioning the inheritance of plant architecture (e.g., leaf attributes and plant architecture), floral characters (flowering rate, sex expression, and male sterility), fruit traits (shape, colour, rind colour and stripe patterns and flesh colour) and seed morphology (seed length, width, size and coat colour). In the second section, developments in molecular markers and quantitative trait loci (QTL) to aid marker-assisted breeding are discussed. Further, the review highlights the clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) gene-editing technology and its scope in gene manipulations and new variety development. The information presented in this review is useful for optimised and demand-led breeding to develop new varieties to serve growers, consumers and the sweet watermelon industry.

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“… Jin et al (2019) also suggested the development of a CRTISO gene-based marker for orange flesh with high prolycopene content. Recently, Li et al (2020) and Lee et al (2021) described the markers distinguishing scarlet and coral red. However, no markers have been reported for selecting incomplete yellow, which is essential for breeding canary yellow- or red-fleshed watermelons.…”

Section: Introductionmentioning

confidence: 99%

“…The WGRS of a large number of watermelon accessions and genome-wide association study (GWAS) revealed sequence polymorphisms and genes for fruit-related traits, such as fruit shape, flesh color, rind patterns ( Park et al, 2018 ; Subburaj et al, 2019 ), and disease resistances, including gummy stem blight ( Lee et al, 2018 ). The WGRS of near-isogenic lines successfully revealed a locus related to the high lycopene content in a scarlet red-fleshed watermelon cultivar ( Lee et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Identification of a novel locus C2 controlling canary yellow flesh color in watermelons

Park,

Shahwar,

Jang

et al. 2023

Front. Genet.

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The flesh color of watermelon is an important trait that is determined by carotenoid composition and affects consumers’ fruit desirability. Although a complete dominant control by C locus (Cllcyb) for canary yellow flesh (CY) over red flesh has been reported, red and CY colors frequently appear as a mixed pattern in the same flesh (incomplete canary yellow, ICY) in F1 and inbred lines carrying dominant C alleles. Therefore, we examined the genetic control of the mixed color pattern in ICY using whole-genome resequencing of three ICY (ICY group) and three CY inbred lines (CY group), as well as genetic linkage mapping of an F2 population. The segregation pattern in 135 F2 plants indicated that CY is controlled by a single locus (named C2) dominant over ICY. The whole-genome resequencing of ICY and CY inbred lines revealed an ICY/CY-specific region of approximately 27.60–27.88 Mb on Chr. 2 that was polymorphic between the ICY and CY groups. Our genetic map, using nine cleaved amplified polymorphic sequence markers developed based on the single-nucleotide polymorphisms from the ICY/CY-specific region, confirmed that C2 is located on Chr. 2 and cosegregated with the marker (M7) derived from a non-synonymous single-nucleotide polymorphism of the pentatricopeptide repeat (PPR) gene (ClPPR, Cla97C02G039880). Additionally, 27 watermelon inbred lines of ICY, CY, and red flesh were evaluated using previously reported Cllcyb (C locus)-based markers and our C2 locus-linked ClPPR-based marker (M7). As a result, dominant alleles at the C2 locus were required to produce CY, in addition to dominant alleles at the C locus, while a recessive homozygous genotype at the C locus gave the red flesh irrespective of the genotype at the C2 locus. Using a ClPPR-based cleaved amplified polymorphic sequence developed in this study and Cllcyb-based markers, watermelon cultivars with CY, ICY, and red flesh could be successfully discerned, implying that the combined use of these markers will be efficient for marker-assisted selection of flesh color in watermelon breeding.

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Whole-Genome Resequencing of Near-Isogenic Lines Reveals a Genomic Region Associated with High Trans-Lycopene Contents in Watermelon

Cited by 7 publications

References 48 publications

High-quality genome assembly and genetic mapping reveal a gene regulating flesh color in watermelon (Citrullus lanatus)

High-quality genome assembly and genetic mapping reveal a gene regulating flesh color in watermelon (Citrullus lanatus)

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

Identification of a novel locus C2 controlling canary yellow flesh color in watermelons

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