Nucleotide Variation In The Phytoene Synthase (ClPsy1) Gene Contributes To Golden Flesh In Watermelon (Citrullus Lanatus L.)

doi:10.21203/rs.3.rs-655111/v1

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Research Article

Nucleotide Variation In The Phytoene Synthase (ClPsy1) Gene Contributes To Golden Flesh In Watermelon (Citrullus Lanatus L.)

https://doi.org/10.21203/rs.3.rs-655111/v1

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published 11 Oct, 2021

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Vitamin A deficiency is a worldwide public nutrition problem, and β-carotene is the precursor for vitamin A synthesis. Watermelon with golden flesh (gf, due to accumulated abundance of β-carotene) is an important germplasm resource. In this study, a genetic analysis of gf segregating populations indicated that gf was controlled by a single recessive gene. BSA-seq and an initial linkage analysis placed the gf locus in a 290-Kb region on watermelon chromosome 1. Further fine mapping in a large population with over 1,000 F₂ plants narrowed this region to 39.08 Kb harboring two genes, Cla97C01G008760 and Cla97C01G008770, which encode phytoene synthase (ClPsy1) and GATA zinc finger domain-containing protein, respectively. Gene sequence alignment and expression analysis between parental lines revealed Cla97C01G008760 as the best possible candidate gene for gf trait. Nonsynonymous SNP mutations in the first exon of ClPsy1 between parental lines cosegregated with the gf trait only among individuals in the genetic population but were not related to flesh color in natural watermelon panels. Promoter sequence analysis of 26 watermelon accessions revealed two SNPs in the cis-acting element sequences corresponding to MYB and MYC2 transcription factors. RNA-seq data and qRT-PCR verification showed that two MYBs and one MYC2 exhibited expression trends similar as ClPsy1 in the parental lines, which may thus play roles in the regulation of ClPsy1 expression. Our research findings indicate that the gf trait is determined not only by ClPsy1 but also by ClLCYB, ClCRTISO and ClNCED7, which play important roles in β-carotene accumulation in watermelon flesh.

Agronomy

Biotechnology and Bioengineering

Watermelon

Flesh color

Phytoene synthase

β-carotene

A gene controlling the golden flesh trait in watermelon was firstly discovered and fine-mapped to a 39.08-Kb region on chromosome 1 through a forward genetic strategy, and Cla97C01G008760 (annotated as phytoene synthase protein, ClPsy1) was recognized as the most likely candidate gene.

Watermelon (Citrullus lanatus L.) is a commercial Cucurbitaceae crop that is cultivated worldwide and consumed fresh. The flesh color of watermelon is an important trait based on consumer demands and market requirements. The genetic diversity of multiple flesh colors (red, pink, orange, canary yellow, pale yellow, white and pale green) in watermelon is caused by genome domestication and human breeding selection (Guo et al., 2019). Carotenoids are the main pigment responsible for formation of the watermelon flesh color. Specifically, lycopene is the key pigment responsible for the red and pink flesh colors (Sun et al., 2018), whereas β-carotene, tetra-cis-lycopene, and ξ-carotene are responsible for the orange flesh color (Branham et al., 2017). In addition, violaxanthin and lutein are the two main pigments responsible for the formation of canary and pale yellow flesh, and violaxanthin is significantly more abundant in canary yellow than in pale yellow watermelon (Yuan et al., 2015 and Fang et al., 2020). White-fleshed watermelon contains only small amounts of lutein and violaxanthin (Lv et al., 2015). Carotenoids, which form part of the human diet, serve as precursors of vitamin A and substrates for many nutrients and also exhibit antioxidant activity. Although these compounds are indispensable for health, humans are incapable of de novo carotenoid synthesis (Rodriguez-Concepcion et al., 2018). The World Health Organization (WHO) estimates that approximately 190 million preschool children are deficient in vitamin A, and vitamin A deficiency is one of the major public health problems in the world. β-Carotene is the precursor for vitamin A synthesis, and the consumption of horticulture crops with high levels of β-carotene (golden flesh), which constitute an important germplasm resource, is an effective strategy for preventing vitamin A deficiency.

Scholars began studying the inheritance of the watermelon flesh color as early as 1937(Porter, 1937). Canary yellow (C) is dominant to other colors (c) except white (Wf), which is epistatic to canary yellow (B) (Wehner, 2007). Coral red (Y) is more common than orange (y^O) and salmon yellow (y), and orange (y^O) dominates salmon yellow (y). In addition, canary yellow (C) is epistatic to Y and influenced by inhibitor of canary yellow (i-C), and a homozygous gene results in red flesh even in the presence of C (Henderson et al., 1998). Bang et al. (2010) reported that the py gene controls the formation of pale yellow-fleshed watermelon. To date, many scientists have summarized a series of QTLs or genes related to watermelon flesh color. In 2003, two red flesh-related QTLs, which were detected in groups 2 and 8, were first reported (Hashizume et al., 2003). The biosynthesis of carotenoids has been well studied in plants (Sun et al., 2018) and reported in watermelon. qFC.1 is reportedly related to β-carotene in a 2.4-Mb region on chromosome 1 that contains ClPsy1 (Branham et al., 2017). The pale green flesh color is also regulated by the major effective QTL qfc10.1 located on chromosome 10 spanning an approximately 519-Kb region, and Cla97C10G185970, annotated as plastid lipid-associated protein, was identified as the most candidate gene (Pei et al., 2021). The red flesh color gene ClLCYB (lycopene beta-cyclase) has been fine mapped to chromosome 4 (Liu et al., 2015; Wang et al., 2019). Zhang and colleagues found that the ClLCYB protein abundance, instead of the ClLCYB transcript level, is negatively correlated with lycopene accumulation (Zhang et al., 2020). Genes located in the carotenoid metabolic pathway are not the only factors responsible for flesh color formation. Y^scr (a single dominant gene), which has been fine mapped to an approximately 40-Kb region on chromosome 6, generates the scarlet red flesh color rather than the common red flesh color in watermelon. Four genes encoding glycine-rich cell wall structural proteins are regarded as candidate genes (Li et al., 2020). ClPHT4;2 regulates chromoplast development, and the expression level of ClPHT4;2 in red-fleshed accessions is approximately 10-fold higher than that in white-fleshed accessions. In addition, the overexpression of ClPHT4;2 lead to a high accumulation of carotenoids (Zhang et al., 2017).

The gf trait has been reported in some plants, such as cauliflower (Li et al., 2001), cassava (Welsch et al., 2010), melon (Tzuri et al., 2015), rice (Bai et al., 2016), wheat (Wang et al., 2014), potato (Mortimer et al., 2016) and banana (Paul et al., 2017), and the Psy and Or genes are involved in the formation of this trait. SlPsy1 is related to carotenoid accumulation in ripening tomato fruits (Fantini et al., 2013), and the silencing of SlPsy1 in tomato using CRISPR/Cas9 changes the flesh color from red to yellow (Dahan-Meir et al., 2018). In watermelon and citrus, the types and expression patterns of the Psy genes are similar to those found in tomato (Peng et al., 2013; Lv et al., 2015). Together with the DXS, LCYB, CHY and ZEP genes, Psy always affects the gf trait at the transcriptional level (Pons et al., 2014, Zeng et al., 2015, Farre et al., 2016).

The chromoplast is the main location for carotenoid accumulation, and enhancing the metabolic capacity would be beneficial for gf trait formation. The Or gene is known to play a role in carotenoid generation and chromoplast differentiation and exhibits chaperone activity for regulating Psy at the posttranscriptional level (Welsch et al., 2018). Or can also increase carotenoid accumulation by inhibiting hydroxylase and degradative reactions (Chayut et al., 2017), and overexpression of the Or gene in potato and white maize endosperm could enhance carotenoid synthesis by approximately 6- and 32-fold, respectively (Li et al., 2012, Berman et al., 2017). The carotenoid content cannot be enhanced by overexpression of the Or gene in tissues with abundant β-carotenoid accumulation (Shumskaya et al., 2012).

Although the Psy gene plays an important role in carotenoid synthesis in many plants, molecular markers developed based on forward genetics results have more effective applications in breeding. In watermelon, the gf trait remains poorly understood. The objectives of our study were to understand the genetic basis of the golden flesh color trait in watermelon and identify the genes responsible for this important trait in segregating populations. Suggestions for marker-assisted selection (MAS) for the golden trait are also provided based on the results.

Plant materials and phenotype evaluation

“Cream of Saskatchewan” (COS) with a pale-yellow flesh color and the watermelon accession PI 192938 with the gf trait (orange flesh) were used as the parental materials for obtaining the F₁, and F₂ and backcross populations. COS was kindly provided by Angela R. Davis at the U.S. Department of Agriculture, Agricultural Research Service, South Central Agricultural Research Laboratory, and PI 192938 was obtained from the U.S. National Plant Germplasm System. All the experimental materials were grown in a greenhouse at the Xiangyang Experimental Agricultural Farm of Northeast Agricultural University, Harbin, China, from 2018 to 2020. The F₂ populations were planted in 2018 and 2019 (93 and 297 plants, respectively) to verify the genetic segregation ratio and initial mapping, and BC₁P₁ (37 plants) and BC₁P₂ (84 plants) populations were planted in 2019 to further confirm their genetic inheritance. A total of 1,003 F₂ individuals were planted in 2020 for recombinant selection and fine mapping. Fifteen days after planting, each plant was numbered with a tag, and young and disease-free leaves were sampled and freshly frozen for DNA extraction using the improved hexadecyl trimethyl ammonium bromide (CTAB) method. All the plants were artificially pollinated, and this date was recorded; and 35 to 40 days after pollination, the fruits were collected, cross-cut and photographed for flesh evaluation.

BSA-seq and initial mapping

Equal amounts of genomic DNA from 20 pale yellow and 20 gf individuals were selected from 297 F₂ plants (in 2019) for flesh color gene pool construction. The two gene pools and genomic DNA of the parental lines were resequenced at the BGI Research Institute using the Illumina HiSeq Xten platform (at least 20× coverage genome sequencing depth for each sample) for BSA-seq analysis. The sequence data were aligned to the reference genome 97103 v2 (ftp://cucurbitgenomics.org/pub/cucurbit/genome/watermelon/97103/v2/) using Burrows-Wheeler Aligner (BWA, Li and Durbin, 2009) to obtain the snp.vcf file. The SNP sites were identified with SAMtools software (Li et al., 2009). Different homozygous sites in the two gene pools of the F₂ population were extracted to calculate the SNP variation frequency and analyze the regions significantly associated with the gf trait. Subsequently, 500 bp before and after the SNP site sequences were extracted from the resequencing data for molecular marker exploitation.

Candidate cleaved amplified polymorphic sequence (CAPS) loci were detected using SNP2CAPS software (Thomas et al., 2004) with the snp.vcf file. According to the BSA-seq results, CAPS loci evenly distributed in the initial chromosome region were designed with nine restriction endonucleases (HincII, MspI, BsrI, MboI, TaqI, AluI, XhoI, DraI and BsaHI) using Primer Premier v6.24. The protocols used for PCR amplification, mixing and enzyme digestion were previously described. SNP sites that could not be converted into CAPS markers were designed as Kompetitive Allele Specific PCR (KASP) markers and genotyped at the Vegetable Research Center of the Beijing Academy of Agricultural and Forestry Sciences. Individuals with recessive traits in the F₂ population planted in 2019 were selected and genotyped for initial mapping.

Fine mapping and candidate gene sequence analysis

A total of 1,003 F₂ individuals were sown in a greenhouse in the spring of 2020, and the two flanking markers in the initial mapping region were used for recombinant selection. All recombinants were transplanted to the greenhouse at the Xiangyang Experimental Agricultural Station of Northeast Agricultural University, Harbin China, and self-pollinated to obtain F_2:3 families. The flesh color of mature fruit was recorded, photographed and genotyped using new markers in the initial mapping segment to detect recombinant events for narrowing down the target region. The F_2:3 seeds of recombinants with dominant traits were planted with 30 plants of each family in the autumn of 2020. The genotype of the recombinants with dominant traits was confirmed according to the flesh color segregation in their F_2:3 families. Recombinants from the initial mapping panel were also selected to facilitate fine mapping.

Candidate gene annotation in the fine-mapping region was performed with the reference genome (97103 v2). A coding sequence comparison was first performed with the resequencing data, and the results were further confirmed with the sequences from the gene cloning results to detect nonsynonymous SNPs and gene structure variations between COS and PI 192938. To examine the allele diversity of ClPsy1 among natural watermelon populations, resequencing data from 24 watermelon accessions (5 varieties resequenced in our previous study and 19 varieties resequencing data acquired from Guo et al., (2014) were used to extract the sequences of ClPsy1 for comparison.

RNA-seq

Flesh samples of COS and PI 192938 were collected from the center area of four parental fruits at 10, 18, 26, 34 and 42 days after pollination (DAP). The flesh tissues were immediately frozen in liquid nitrogen and stored at -80°C for RNA extraction. Three out of five watermelon fruits with similar growth conditions were collected per sample. Flesh samples with three replicates at each stage were sent to Biomarker Technologies for RNA-seq with an Illumina HiSeq 2000 system. RNA-seq library construction and data analysis were performed according to the protocols described by Zhong et al. (2011) and Guo et al. (2013). Bowtie and Trapnell (Langmead et al. 2009) software were used for identification of fragment mismatches and read alignment to the watermelon genome (Guo et al. 2013). The number of reads mapped to each watermelon gene model was obtained and then standardized to the number of reads per kilobase of transcript per million mapped reads (RPKM). The RNA-seq data of COS were sent to the NCBI database with the SRA number PRJNA587316, whereas the SRA number of the PI 192938 flesh RNA-seq data was PRJNA733842. The flesh tissue samples of COS and PI 192938 were collected at the same time.

Gene expression analysis

The RNA Simple Total RNA Kit (Tiangen, China) and ReverTra Ace qPCR RT Kit (TOYOBO, Osaka, Japan) were used for total RNA extraction and cDNA synthesis, respectively. Specific primers for candidate genes (Cla97C01G008760 and 196920), transcription factors (TFs; Cla97C10G196920, Cla97C02G046390 and Cla97C06G112130) and carotenoid metabolic pathway genes [ClZDS (Cla97C06G118930), ClNCED-7 (Cla97C07G137260), ClCRTISO (Cla97C10G200950), ClCHYB (Cla97C05G090480), ClLCYB (Cla97C04G070940), ClPDS (Cla97C07G142100), ClNCED-1 (Cla97C01G024630), and ClCHXE (Cla97C01G002480)] were designed for gene expression analysis through quantitative real-time polymerase chain reaction (qRT-PCR) (Table 3). SYBR Green Master Mix (Novogene, Beijing) was used to perform the qRT-PCRs in the QTOWER Real-Time PCR System (Analytik Jena, Germany) according to the manufacturer’s instructions. qRT-PCR amplification and mixing were performed as previously described. Each experiment was performed with three biological repetitions and three technical repetitions, and relative gene expression levels were determined using the 2^ΔΔCT method (Bustin et al 2009).

Promoter region cloning and candidate transcription factor prediction

The promoter region of ClPsy1 was cloned with genomic DNA from five watermelon accessions with different flesh colors, namely, COS, PI 192938, LSW-177 (red flesh), PI 635597 (canary yellow flesh) and PI 186490 (white flesh), using the primers listed in Table 2. Cis-elements in each promoter were predicted using PlantCARE online software (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/), and the five promoter sequences were compared to detect the variation. SNPs or structural alterations located in cis-elements were selected as important loci. The resequencing data of 24 other watermelon accessions were also used to extract the sequences of the ClPsy1 promoter and thus detect the variation diversity. The RNA-seq data of COS and PI 192938 flesh tissues were used to preliminarily view the expression patterns of the TFs that may bind with the cis-elements located in the variation region. TFs exhibiting expression patterns similar to that of ClPsy1 between COS and PI 192938 may be regarded as important factors for further verification.

Statistical analysis

The genetic analysis and evaluations of the differences in gene expression were performed using SPSS v.21.0 software (SPSS Inc., Chicago, IL, USA). Prism 7.0 software was used (GraphPad Inc., La Jolla, CA, USA) for illustration preparation.

The gf trait in watermelon is controlled by a simply inherited gene

The carotenoid composition and content in the mature flesh of COS and PI 192938 were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) in our previous study (Fang et al. 2020). β-carotene and violaxanthin appeared to be the two pigments showing major differences in content between the two parental materials, and the contents in PI 192938 (16.133 ± 0.952 µg/g) were approximately 53.2-fold higher than those in COS (0.033 ± 0.004 µg/g). Based on the flesh color associated with the two pigments, we speculated that the high accumulation of β-carotene in PI 192938 may be the main reason for the gf trait (Fig. 1a). The flesh color of F₁ was canary yellow, similar to that of COS, and four flesh categories were segregated in the F₂ generation: gf, pale yellow, canary yellow and gf mixed with canary yellow (Fig. 1b). F₂ individuals can also be divided into gf and non-gf groups (pale yellow, canary yellow and gf mixed with canary yellow, Fig. 1c to e). According to these classification criteria, the COS×PI 192938-F₂ population in 2018 (84 individuals in total) consisted of 17 gf and 67 non-gf plants and exhibited a 1:3 genetic ratio (χ² = 1.016, p = 0.313), whereas in 2019, 279 F₂ individuals consisted of 74 gf and 205 non-gf plants, which was also consistent with the 1:3 genetic ratio (χ² = 0.345, p = 0.557). For generation of a backcross population between F₁ and COS, none of the individuals exhibited the gf color. In the backcross population derived from F₁ and PI 192938, 39 plants had the gf color, and 45 plants had a non-gf color, which corresponded to a ratio of 1:1 (χ² = 0.429, p = 0.513, Table 1). Based on the above results, we conclude that the gf trait in watermelon flesh is controlled by a simply inherited gene and that pale yellow flesh is partly dominant to the gf color.

BSA-seq and recombinant deletion of the gf locus in a 39‑Kb region identified ClPsy1 as a candidate gene

After filtering low-quality and short reads, 125,549,810 and 60,739,330 clean read pairs were obtained for COS and PI 192938 with approximately 10.01 (28.76× depth coverage) and 8.56 (22.87× depth coverage) Gbp clean bases, respectively, and Q30 values above 89.89% were found. A total of 86.50% and 92.48% of these clean reads of COS and PI 192938, respectively, were successfully mapped to the reference genome, and 68,585,634 and 68,541,696 clean read pairs were generated from the gf pool (25.7× depth coverage and 92.35% properly mapped ratio) and pale-yellow flesh pool (25.88× depth coverage and 93.16% properly mapped ratio), respectively, through the Illumina high-throughput sequencing platform. A total of 366,358 and 374,417 SNPs were identified between the reference genome and the two gene pools, respectively. The SNP index for each identified SNP was calculated, and the average SNP index was computed in a 1-Mb interval using a 10-Kb sliding window. By combining the SNP index information from the gf color pool and pale-yellow flesh pool, the ΔSNP index was calculated and plotted against the genome positions. According to the ΔSNP index value, an obvious signal related to the gf color was detected on chromosome 1, spanning approximately 2.99 Mb (from 8,912,000 bp to 11,900,000 bp, Fig. 2a).

A total of 30 CAPS and two KASP markers evenly distributed in BSA-seq chromosome segments were developed based on parental line resequencing data, and 10 markers (eight CAPS markers and two KASP markers) were used for initial mapping after polymorphism detection among COS, PI 192938 and their F₁ generation. Individuals with a recessive phenotype (gf trait) from 2019 were selected for genotyping with the 10 polymorphic markers. The candidate region was narrowed to a physical distance of 290.214 Kb (from 9,272,322 bp to 9,562,536 bp) using 11 recessive-trait plants (including nine recombinants) between the CAPS markers Chr01_9272322 and Chr01_9562536 with one and two recombinants (Fig. 2b). To further narrow down the initial mapping region precisely, a larger COS×PI 192938-F₂ segregating population including 1,003 individuals was subjected to genotyping of the primary flanking markers Chr01_9242322 and Chr01_9562536 in the spring of 2020. A total of 20 recombinants were screened for further fine mapping of the gf gene. Another nine polymorphic markers were developed to genotype the 20 recombinants. The target trait genotype of the dormant recombinants was confirmed based on phenotypic segregation in their F₃ families. Finally, the gf locus was delimited between the CAPS markers Chr01_9440282 and Chr01_9479366 (physical distance of approximately 39.08 Kb) with two and nine recombinants, respectively (Fig. 2c).

According to the watermelon reference genome, the 39.08-Kb region contained only two annotated candidate genes, Cla97C01G008760 and Cla97C01G008770. Cla97C01G008760 encodes a phytoene synthase protein (ClPsy1), and Cla97C01G008770 was annotated as a GATA zinc finger domain-containing protein. To identify the candidate gene for the gf locus, we first analyzed the genomic variations in the two candidate genes between the parental lines with resequencing data. The results identified no polymorphic sites in Cla97C01G008770, whereas one nonsynonymous SNP mutation, SNP^9,448,870 (A→G, located in the first exon at the 9,448,870th bp position), was detected in the coding region of Cla97C01G008760 between COS and PI 192938. In COS, base A encodes glutamic acid (Glu), whereas in PI 192938, this base is mutated to base G, resulting in an amino acid change from Glu to lysine (Lys). To further confirm the sequence variation, we cloned the coding regions of the two candidate genes in COS and PI 192938. This SNP mutation was still found between the two parental lines. We further developed this nonsynonymous SNP into the KASP marker Chr01_9448870 and genotyped F₂ individuals from 2018 to 2019. As a result, ClPsy1^A:A exhibited the gf color, whereas ClPsy1^G:A/G:G showed a non-gf color, which indicated that Chr01_9448870 cosegregated with the phenotype in all the plants (Fig. 3a).

Although no variation in the Cla97C01G008770 gene sequence was found between COS and PI 192938, we found some polymorphic sites in the promoter region. To further confirm this hypothesis, we analyzed the gene expression patterns of the two candidate genes in COS and PI 192938 flesh tissues collected from different stages of flesh color formation. The results showed that the two parental lines exhibited similar expression trends across the five developmental stages (10, 18, 26, 34 and 42 DAP), and no significant difference in Cla97C01G008770 was found (Fig. 3b). For Cla97C01G008760 (ClPsy1), the two parental lines also showed similar expression patterns (the expression level was upregulated gradually during flesh maturation), but at 26 DAP, the allele of ClPsy1 in PI 192938 exhibited significantly higher expression than that in COS, and this increase continued to be observed until 42 DPA (mature stage, Fig. 3c). Our previous research also showed that 26 DAP may be an important developmental stage for flesh color formation (Fang et al., 2020). At this stage, the colored COS and PI 192938 watermelon flesh started to abundantly accumulate carotenoids. Hence, we hypothesized that ClPsy1 is the most likely candidate gene for the gf locus and is responsible for high β-carotene accumulation in watermelon.

Nucleotide variation in the ClPsy1 gene structure among natural watermelon accessions

To examine the allelic diversity of the ClPsy1 gene in natural watermelon groups, we examined the nucleotide variation of the ClPsy1 locus in 26 resequenced accessions with different flesh colors (red, orange, canary yellow, pale yellow, light green and white), including 18 C. lanatus, four C. mucosospermus and four C. amarus accessions (Fig. 4). SNP^9,448,870 was still present, but this mutation was not correlated with flesh color among the different watermelon accessions and exhibited no obvious difference between the cultivated and wild-type watermelon groups. These results indicated that this site may not affect carotenoid accumulation. In addition to SNP^9,448,870, another nonsynonymous SNP mutation, SNP^9,448,438 (C→T, located in the first exon at the 9,448,438th bp position), was also detected. Interestingly, SNP^9,448,438 existed only in the C. amarus group, resulting in an amino acid substitution from proline (Pro in the C. lanatus and C. mucosospermus groups) to serine (Ser in the C. amarus group).

To analyze the reason for the low ClPsy1 expression in COS, we cloned the 1,996-bp promoter sequence from four cultivated watermelon varieties: COS, PI 192938, LSW-177 (red flesh) and PI 635597 (canary yellow). The promoter sequences of 14 other cultivated watermelon accessions were extracted from their genome resequencing data. Interestingly, a total of six SNPs (SNP³⁴², SNP⁵⁹⁸, SNP⁸⁹⁸, SNP^1,257, SNP^1,634 and SNP^1,694) were detected in the COS promoter region compared with the other 17 watermelon accessions, which exhibited consistent promoter sequences. SNP⁵⁹⁸ and SNP^1,257 were located in the MYC- and MYB-binding sites, respectively, whereas the other four SNPs were not located in the sequence of any cis-acting element (Fig. 5a).

MYB and MYC2 may be important transcription factors regulating the expression level of ClPsy1

We then used the RNA-seq data of COS and PI 192938 flesh tissues (collected at 18, 26 and 42 DAP, data not shown in this manuscript) to obtain an overview of the expression patterns of all MYB and MYC TFs. A total of 65 MYB TFs with read per kilobase per million mapped reads (RPKM) values were detected, and only two MYB TFs (Cla97C10G196920 and Cla97C02G046390) exhibited expression tendencies similar to that of ClPsy1 in COS and PI 192938. An obvious significant difference in expression began to be observed at 26 DAP in PI 192938 compared with COS and continued to be observed at 42 DAP (mature stage). For all 22 MYC TFs, Cla97C06G112130 (annotated as a MYC2 transcription factor) also showed an obvious significant difference in expression between COS and PI 192938 at 26 DAP. We further examined the expression levels of Cla97C10G196920, Cla97C02G046390 and Cla97C06G112130 in COS and PI 192938 flesh tissues collected at five developmental stages by qRT-PCR to verify the expression pattern. The results showed the same tendency as the RNA-seq data (Fig. 5b to d). LSW-177 was a red flesh-colored watermelon accession with the same genotype in the gene sequence and promoter region as PI 192938. The RNA-seq data between COS and LSW-177 (red flesh) flesh tissues (BioProject number PRJNA338036) were also used for analyzing the expression levels of Cla97C10G196920, Cla97C02G046390 and Cla97C06G112130. The results showed that the three TFs also presented a higher expression level in LSW-177 than in COS (Fig. 8a to c). In watermelon fruit rinds, the expression levels of the three TFs were also clearly lower than those in the flesh of 97103 (red flesh), which indicated that these TFs may be expressed in tissues with high carotenoid accumulation according to the RNA-seq data of SRP012849 (Fig. 8d to f).

The conserved domains of Cla97C10G196920 (148 aa) and Cla97C02G046390 (110 aa) were extracted and compared to the Arabidopsis Information Resource (TAIR). The results showed that AtMYB21/AtMYB3, AtMYB24, AtMYB57, AtMYB59, and AtMYB48 were the first three (or two) homologs. Cla97C06G112130 has two conserved domains: the N-terminus of the bHLH-MYC and R2R3-MYB TFs and the N-terminus of a family of MYB and MYC transcription factors (156 aa). The other superfamily is the bHLH domain superfamily (70 aa), and AtMYC2 exhibited the highest homology. We speculated that ClMYB and ClMYC2 may be two important TFs regulating ClPsy1 expression due to variations in the binding sites in their promoter region between COS and PI 192938. Although MYB and MYC TFs have many functions, they have not been reported to play a role in flesh color formation in watermelon.

The gene expression and genotype variations in carotenoid pathway genes between COS and PI 192938 provide insight into gf trait formation in watermelon flesh

We examined the transcript abundances of ClPDS, ClZDS, ClCRTISO, ClLCYB, ClCHYB and ClNCED7 in COS and PI 192938 flesh tissues collected at five developmental stages (10, 18, 26, 34 and 42 DAP) by qRT-PCR (Fig. 6a to f). ClPDS, ClZDS and ClCRTISO exhibited the same expression trend as ClPsy1 between the two parental lines. The transcript abundance of PI 192938 was always higher than that of COS throughout all developmental stages, particularly at 26 DAP. It has been reported that ClLCYB regulates lycopene accumulation at the protein level (Zhang et al., 2020), and COS and PI 192938 have the same single-nucleotide mutation as red-fleshed watermelon accessions. The mutation of G^676th to T^676th altered the 226th amino acid from valine (Val) to phenylalanine (Phe), whereas the mutation of G^1,305th to C^1,305th altered the 435th amino acid from lysine (Lys) to asparagine (Asp). This finding indicated that the ClLCYB protein may have the same function in COS and PI 192938. The lycopene content in the mature flesh of the two parental lines was quite low compared with that in a red-fleshed variety identified in our previous study (Fang et al., 2020). The expression level of ClNCED-7 in both parental lines showed an increasing trend over time after pollination, and COS presented a significantly higher expression level than PI 192938, except at 26 DAP.

The sequence variations in genes encoding enzymes at each step of the carotenoid pathway were also analyzed between COS and PI 192938 using resequencing data. Three SNPs were found in the coding region of ClZDS in PI 192938 compared with that in COS, and two of these SNPs led to amino acid substitutions. Mutation of the 161st base (G→A) resulted in a change in the 54th amino acid from serine (Ser) to asparagine (Asp), and mutation of the 480th amino acid (G→T) resulted in a change in the 160th amino acid from lysine (Lys) to asparagine (Asp). Only one nonsynonymous residue was detected in ClCRTISO, and mutation of the 526th base (T→C) changed the 176th amino acid from tyrosine (Tyr) to histidine (His). No variations were detected in the coding region of ClPDS or ClNCED-7.

According to the above-described results, we speculated the cause of the high β-carotene content shown in Fig. 7. High expression of ClPsy1 in PI 192938 contributed to increased phytoene accumulation, and the abundance of phytoene may upregulate the expression of ClPDS, ClZDS and ClCRTISO at each step of the carotenoid metabolism pathway to result in the synthesis of higher amounts of zeta-carotene and tetra-cis-lycopene in PI 192938. Tetra-cis-lycopene could be isomerized through ClCRTISO to generate lycopene, which is the carotenoid upstream of β-carotene. The same genotype of the ClLCYB protein may have a similar cyclization effect in PI 192938 and COS, and nearly all lycopene can be cyclized into β-carotene. High expression of ClCHYB increased violaxanthin accumulation, whereas low expression of ClNCED-7 may prevent β-carotene metabolism in PI 192938. These factors may be the main reasons for the high accumulation of violaxanthin and β-carotene in PI 192938 and thus its orange flesh color.

Various patterns of ClPsy1 regulation may exist among different watermelon accessions

The first committed and rate-controlling step is mediated by the phytoene synthase (Psy) protein, which catalyzes the conversion of two molecules of GGPP to phytoene (colorless) as the first carotenoid (Cazzonelli and Pogson, 2010; Welsch et al., 2010; Giuliano et al., 2017). As an important gene in the carotenoid metabolic pathway, Psy1 has been reported to function in carrot (Maass et al., 2009 and Massimo et al., 2016), banana (Paul et al., 2017), citrus (Lu et al., 2018), tomato (Xiong et al., 2019) and pepper (Jeong et al., 2019). Compared with white and bitter wild-type watermelon, modern cultivated watermelon (C. lanatus) exhibits various flesh colors. ClPsy1, located in a selective chromosome segment, may play an important role in watermelon flesh color formation during the domestication process (Guo et al., 2020). In this study, the sequence variations in both coding and promoter regions were analyzed in 26 watermelon accessions belonging to three subspecies with different flesh colors. No representative mutations were found between the C. mucosospermus and C. lanatus groups. However, multiple variations were detected in the C. amarus group compared with the C. mucosospermus and C. lanatus groups. A low gene expression level of ClPsy1 was also found in C. amarus (such as PI 296341-FR, Guo et al., 2015). SNP^9,448,438 was detected only in the C. amarus group, but whether this SNP mutation alerts ClPsy1 function needs further verification. Based on published RNA-seq data or previous research, white-fleshed C. mucosospermus (such as PI 186490, Fang et al., 2020 and Wang et al., 2021) showed a significantly lower expression level than colored cultivated watermelon varieties, although the former presented the same genotype in coding and promoter regions as the colored accessions. This feature may be regulated by TFs or epigenetic factors, but further research is needed. Compared with other watermelon accessions, two SNP mutations in cis-acting element sites were only found in COS. Further qRT-PCR results implied that these two SNP mutations may be the main reason for the low ClPsy1 expression level.

Enzyme activity is also an important factor affecting ClPsy1 gene function in carotenoid accumulation. The reduction in total carotenoids was consistent with the requirement of galactolipids for PSY protein activity in etiolated seedlings of Arabidopsis mutants (Fujii et al., 2018). In loquat (Eriobotrya japonica Lindl.), a mutant EjPSY2Ad lacking the C-terminal region (694-bp segment) in the fifth exon and thus no corresponding catalytic activity resulted in the absence of carotenoids and thus an inability to form white flesh (Fu et al., 2014). The aspartic acid-rich region (DXXXD) is an important functional domain of the PSY protein (Zhai et al., 2016). We also compared the mutation locations among watermelon accessions with different flesh colors, but none of the SNPs were located in this domain region. Among the varieties belonging to the C. mucosospermus and C. lanatus groups, SNP^9,448,870 was also not correlated with flesh color in the natural watermelon panel. These two lines of evidence may imply that the function of ClPsy1 in flesh color formation is dependent on expression rather than a difference in enzymatic activity. These results showed that the expression pattern of ClPsy1 was regulated in different ways in different watermelon subspecies.

Regulatory factors in carotenoid accumulation and flesh color formation

The function of Psy is affected by many regulatory factors at both the transcriptional and protein translation levels. In tomato, ripening inhibitors (RINs), through their interaction with the SlPsy1 promoter, have been shown to regulate fruit carotenoid concentrations (Martel et al., 2011). B-box zinc-finger transcription factor (SlBBX20) can activate the expression of SlPsy1, leading to dark-green fruits and leaves and higher levels of carotenoids, by directly binding to a G-box motif in its promoter (Xiong et al., 2019). A transcriptomic analysis of AdMYB7-infiltrated N. benthamiana leaves showed upregulation of NbPSY (Ampomah-Dwamena et al., 2019). The overexpression of CsMADS6 in citrus calli can increase the carotenoid content by directly binding to the CsPSY, CsPDS and CsCCD1 promoters (Lu et al., 2018). Two ClMYB and one ClMYC2 TFs exhibited expression trends similar to that of ClPsy1 in COS and PI 192938 and were thus hypothesized to be regulatory factors of ClPsy1. Compared with the Arabidopsis genome, AtMYB21/AtMYB3, AtMYB24, AtMYB57, AtMYB48 and AtMYB59 showed high identity in conserved domains with the two ClMYBs (Cla97C10G196920 and Cla97C02G046390), whereas bHLH-MYC/R2R3-MYB and AtMYC2 showed the highest homology to ClMYC2 (Cla97C06G112130). With the exception of the two mutation sites, some other MYB- and MYC2-binding sites were located in the promoter regions of COS and PI 192938, which could partly explain why obvious expression levels of Cla97C10G196920, Cla97C02G046390 and Cla97C06G112130 in COS could be detected at 26 DAP, even though the binding sites participate in the variation.

The MYB TF family is very large and functionally diverse in plants. MYB members have been reported to participate in carotenoid metabolism. Chili pepper fruits synthesize and accumulate carotenoid pigments, which are responsible for the yellow, orange and red colors. CaCCS (capsanthin-capsorubin synthase), CaBCH (β-carotene hydroxylase), and CaPSY were clustered with six MYB-related genes (CaDIV1, CaDIV3, CaMYBR13, CaTRF2, CaMYBC1, and CaPHR9) and an atypical MYB (CaMYB5R) based on a coexpression analysis (Arce-Rodriguez et al., 2021). The R2R3-MYB transcription factor CrMYB68 directly regulates the α- and β-branches in the carotenoid pathway in Citrus reticulata. Reduced expression of CrBCH2 and CrNCED5 is responsible for the delay in α- and β-carotene synthesis. The expression of these genes is negatively correlated with the expression of CrMYB68 in green fruit (Feng et al., 2017). A coexpression network and transient expression analysis suggested a potential direct link between flavonoid and carotenoid biosynthesis pathway genes (PSY, ZDS and CYP97C) through MYB TF regulation in Primula vulgaris (Li et al., 2020). SlMYB72 directly binds to the SlPSY, SlZISO, and SlLCYB genes and regulates carotenoid biosynthesis in tomato. The downregulation of SlMYB72 decreases the lycopene content and promotes β-carotene production and chromoplast development (Wu et al., 2020). CpMYB1 (MYB44-like) and CpMYB2 are transcriptional repressors that can bind to the CpPDS2, CpPDS4, and CpCHY-b promoters and suppress the activities of these genes in papaya (Fu et al., 2020).

In Medicago truncatula, an R2R3-MYB protein (WHITE PETAL1, WP1) functions as a transcriptional activator that modulates floral carotenoid pigmentation by directly regulating the expression of multiple carotenoid biosynthesis-related genes (Meng et al., 2019). The silencing of strigolactone (SL, carotenoid-derived phytohormone) biosynthesis-related genes results in the upregulation of MYC2 (Xu et al., 2019). To date, the regulation of flesh color by MYB or MYC2 TFs in watermelon has not been studied. The binding effect and regulatory mechanism of Cla97C10G196920, Cla97C02G046390 and Cla97C06G112130 need further verification and research.

The Or gene (encoding a plastid-targeted protein containing a cysteine-rich zinc finger domain) is also another important gene for golden trait formation. In melon (Tzuri et al., 2015) and cauliflower (Li et al., 2001), the Or gene reportedly regulates β-carotene accumulation based on forward genetic research. CmOr exerts only a slight effect on CmPsy1 expression but strongly affects the CmPsy1 protein levels and enzymatic activity in melon (Chayut et al., 2017). In Arabidopsis and sweet potato, the PSY protein is affected by OR/OR-like proteins (Zhou et al., 2015; Park et al., 2016). The AtOR protein enhances AtPSY protein stability and increases the enzymatically active proportion of AtPSY in Atclpc1 in Arabidopsis (Welsch et al., 2018).

Molecular breeding suggestions for golden-fleshed watermelon

This study provides the first report of the gf gene in watermelon. Although the Psy gene reportedly functions in gf trait formation in some plants, genetic evidence remains lacking. According to the results, abundant ClPsy1 transcripts may lead to a rich β-carotene content in PI 192938. Red-colored flesh always has a higher ClPsy1 expression level than flesh with other colors (Wang et al., 2016), starting at the color turning stage and ending at the mature stage. Interestingly, the ClPsy1 content in the red-fleshed watermelon accession LSW-177 was higher than that in PI 192938 (Fang et al., 2020), but the β-carotene content in LSW-177 flesh was significantly lower than that in mature PI 192938 flesh (2.605±0.375 versus 16.133±0.952 μg/g), whereas the lycopene content in LSW-177 was significantly higher than that in PI 192938 (1.523±0.199 versus 25.950±0.390 μg/g). This finding indicated that the high expression of ClPsy1 was not the only main reason for β-carotene accumulation. The upstream gene of β-carotene is ClLCYB, which encodes a cyclase that can catalyze the conversion from lycopene to β-carotene. The downregulation of ClLCYB causes lycopene accumulation, whereas the overexpression of ClLCYB in the red-fleshed line causes the flesh color to change to orange (β-carotene) (Zhang et al., 2020). Among watermelon accessions, two nonsynonymous SNP sites generate three haplotypes (ClLCYB^red, ClLCYB^white, and ClLCYB^yellow). COS and PI 192938 contained the same haplotype of ClLCYB^yellow, which indicated that the ClLCYB protein had the same function in the two lines. In PI 192938, nearly all lycopene was cyclized into β-carotene to form a gold flesh. This finding may indicate that ClLCYB is also an important gene for β-carotene accumulation and partly explains the accumulation of β-carotene observed in LSW-177, COS and PI 192938.

In tomato, the accumulation of tetra-cis-lycopene (the upstream carotenoid of lycopene) can also lead to the formation of orange flesh by SlCRTISO (Jayaraj et al., 2021, Dahan-Meir et al., 2018). In watermelon, the genotype of ClCRTISO also cosegregates with an orange flesh color (Jin et al., 2019). Visual observation alone does not allow differentiation of the two types of carotenoids. Although they have the same color, tetra-cis-lycopene is not converted into the precursor of vitamin A without β-cyclization. The golden trait not only focuses on flesh color but also considers the physiological function of carotenoids. For the gf trait, the MAS process depends only on the expression level and the genotype of ClPsy1, and visual observation is not sufficient or accurate. The genotypes of ClPsy1, ClCRTISO and ClLCYB should also be considered at the same time to confirm the carotenoid composition.

“Push” and “block” are the two main strategies for gf trait molecular breeding and biofortification (Watkins et al., 2020). The “push” strategy involves enhancing the metabolic flux of carotenoids synthesized upstream of β-carotene and is regarded as the most effective method. The overexpression of Psy or 1-deoxy-D-xylulose-5-phosphate synthase (DXS) increases the synthetic amounts of total carotenoids or β-carotene. Cassava (Welsch et al., 2010), rice (Bai et al., 2016), wheat (Wang et al., 2014), potato (Mortimer et al., 2016) and banana (Paul et al., 2017) show up to 100- to 1,000-fold higher contents of total carotenoids. Silencing the expression of genes downstream of β-carotene to prevent the degradation of target products is another strategy for regulating the gf trait, and this method is called “block”. In potato, the inhibition of zeaxanthin epoxidase (ZEP), lycopene epsilon-cyclase (LCYE) and carotene hydroxylase (CHY) could lead to approximately 10-fold increases in the zeaxanthin and β-carotene contents (Pons et al., 2014). “Push” and “Block” have always been used together to obtain better results: the overexpression of CrtB (a homologous gene of Psy in bacteria) accompanied by the silencing of CHY could produce a large amount of β-carotene in the endosperm of wheat (Zeng et al., 2015). Significantly high accumulation of zeaxanthin could be induced by the overexpression of Psy1 and the silencing of LCYE in the maize endosperm (Farre et al., 2016).

Acknowledgments This work was supported by funding from the University Nursing Program for Young Scholars with Creative Talents in Heilongjiang Province [Grant# UNPYSCT-201816].

Author contribution statement Shi Liu designed the experiment, analyzed the data and wrote the manuscript. Zhongqi Gao performed the major experiments with the help of Shi Liu. Xuezheng Wang and Feishi Luan revised the manuscript. Zuyun Dai, Zhongzhou Yang, Qian Zhang provided part of materials used in this study and participated in phenotypic data collection. Shi Liu and Zhongqi Gao contributed equally to this work. Feishi Luan, Xuezheng Wang and Shi Liu were as the co-corresponding authors.

Data availability All data pertinent to the reported work have been provided in the manuscript or in the supplemental online materials.

Conflict of interest The authors declare that there is no conflict of interest.

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Table 1. Segregation of golden flesh color in six generations from COS × PI 192938 cross over 2 years
Populations	Plants	Orange	Non-orange	Expected segregation ratio	P value of Chisquare tests
PI 192938	15	15	0	N/A	N/A
COS	15	0	15	N/A	N/A
F₁	15	0	15	N/A	N/A
2018 F₂	84	17	67	1:3	0.313
2019 F₂	279	74	205	1:3	0.557
2019 BC₁P₁	37	0	37	0:1	0.513
2019 BC₁P₂	84	39	45	1:1	0.563
N/A: Not Applicable

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Nucleotide Variation In The Phytoene Synthase (ClPsy1) Gene Contributes To Golden Flesh In Watermelon (Citrullus Lanatus L.)

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