McAPRR2 : The Key Regulator of Domesticated Pericarp Color in Bitter Gourd

doi:10.21203/rs.3.rs-3241053/v1

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McAPRR2 : The Key Regulator of Domesticated Pericarp Color in Bitter Gourd

https://doi.org/10.21203/rs.3.rs-3241053/v1

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Pericarp color is a crucial commercial trait influencing consumer preferences for bitter gourds. However, until now, the gene responsible for this trait has remained unidentified. In this study, we identified a gene (McAPRR2) controlling pericarp color through a genome-wide association study (GWAS) utilizing the resequencing data of 106 bitter gourd accessions. McAPRR2 exhibits three primary haplotypes: Hap1 is wild type with green pericarp, Hap2 is SA and SEA type with green pericarp, and Hap3 is primarily SEA type with light green pericarp. McAPRR2 haplotype is significantly correlated with both pericarp color and ecological type. Importantly, McAPRR2 with the light green pericarp demonstrated a premature termination due to a 15 bp sequence insertion. The phylogenetic tree clustered according to pericarp color and ecological type, using SNPs located in the McAPRR2 gene and its promoter. High π_wild/SEA and π_SA/SEA values indicate high nucleotide diversity between wild and SEA types and between SA and SEA types in the McAPRR2 gene. The haplotypes, phylogenetic tree, and nucleotide diversity of McAPRR2 suggest that McAPRR2 has undergone domestication selection. This study identifies McAPRR2 as the key gene determining pericarp color in bitter gourds and introduces a novel insight that McAPRR2 is subject to domestication selection.

McAPRR2 regulates green pericarp color in Momordica charantia and pericarp color was under domestication.

Bitter gourd (Momordica charantia), known for its distinctive bitter taste, is a vegetable that widely cultivated in tropical and subtropical Asia. It has been extensively used for health preservation due to its broad pharmacological properties, notably its anti-diabetic, anti-cancer, and anti-HIV effects (Akihisa et al. 2007; Dia and Krishnan 2016; Farooqi et al. 2018; Lee-Huang et al. 1990). Bitter gourd is native to tropical Africa (Schaefer and Renner 2010) and Madagascar (Chomicki et al. 2020). The study about the domestication region of bitter gourd is contentious. Earlier studies reported its domestication in Eastern Asia, possibly eastern India and southern China (Walters and Decker-Walters, 1988; Miniraj at al. 1993). Schaefer and Renner (2010) reported the bitter gourd from tropical Africa dispersed to Asia approximately 19 million years ago. Matsumura et al. (2020) suggest an initial domestication of bitter gourd occurred around 6,000 years ago, followed by the divergence of Southeast Asian cultivars around 800 years ago. According to Cui et al. (2020), M. charantia var. muricata and charantia var. charantia split roughly 1.9 million years ago, while the separation between muricata and charantia happened once again about 6,000 years ago. Based on these parallel studies, Renner (2020) raised a new insight that bitter gourd from Africa expanded to Southeast Asia and was domesticated there (Chomicki et al. 2020; Renner 2020).

Over the course of long-term evolution, plants have undergone domestication and selective breeding to adapt to human needs and environmental changes, leading to significant differences in many aspects between modern cultivated varieties and their wild counterparts. These traits include, but are not limited to, erect plant architecture (Jin et al. 2008), fruit weight (Chakrabarti et al. 2013), seed shattering (Kovach et al. 2007), and pericarp color (Sweeney and McCouch 2007). Several studies indicate that during the process of domestication and selection, the selective forces on certain genes are closely associated with the adaptability of the species to specific geographic locations (Meyer and Purugganan 2013; Olsen and Purugganan 2002). For example, in rice, a red pericarp color is prevalent in wild populations and early landraces, whereas modern cultivars predominantly display a white pericarp color. Similarly, in bitter gourd, individuals from different regions show different pericarp colors; those found in South Asian typically present a green pericarp color, while those predominantly found in Southeast Asia often display a white or light green pericarp color (Dhillon et al., 2016). This indicates that pericarp color may have been subjected to selective pressures during the process of domestication.

Pericarp color is primarily determined by the content of chlorophyll, carotene, anthocyanin, and ﬂavonoid in the skin, and the genes regulating the pericarp color have been extensively investigated within the Cucurbitaceae family. In cucumber, the white pericarp trait is regulated by an APRR2 gene (two-component response regulator-like, Csa3G904140), where a single G insertion leads to early translation termination. Meanwhile, the light green pericarp trait is controlled by the Csa6G133820 gene (Liu et al. 2016; Lun et al. 2016). In watermelon, Oren et al. (2019) identified an SNP of G to C mutation in the intron of ClAPRR2 (CICG09G012330) gene leading to premature translation termination in the light green watermelon, while Li et al. (2019) discovered a C to G nonsynonymous SNP mutation in the coding region of ClCG08G017810 (2-phytyl-1,4-beta-naphthoquinone methyltransferase protein) responsible for the pericarp color from dark green to light green. In melon, two studies concluded that the CmAPRR2 (MELO3C003375) controlled a pair of dark and light green pericarp traits. A mutation of C to G in exon 8 or a 13 bp insertion in exon 9 resulted in the termination of the CmAPRR2 translation (Oren et al. 2019; Zhao et al. 2019). In wax gourd, a two-bases (GA) insertion in the coding region of BhAPRR2 (Bch05G003950) leads to a change in pericarp color from white to green (Ma et al. 2021). In bitter gourd, Matsumura et al. (2020) identified the top 15 genes enriched for the uppermost 0.1% SNPs with the highest color association, among which APRR2 was included (Matsumura et al. 2020). Furthermore, McAPRR2 has been reported to regulate green stigma in bitter gourd (Zhan et al. 2023). APRR2 is a transcription factor, and a previous study suggested that it regulates plastid development and maturation in tomato (Pan et al. 2013). Currently, the genes controlling the pericarp color of the bitter gourd remain unknown, and there is a need to identify the key gene that regulates pericarp color.

In this study, we identified the key gene McAPRR2 regulates pericarp color in bitter gourd through a Genome-Wide Association Study (GWAS). Our analysis revealed that a 15 bp sequence insertion in the McAPRR2 gene, causing premature termination of the encoded protein sequence. We identified three haplotypes within McAPRR2, and the haplotype of McAPRR2 was highly correlated with pericarp color and ecological type. Interestingly, this gene was located within a genomic region impacted by domestication. Our findings provide a new insight that pericarp color of the bitter gourd was subjected to domestication, and this discovery will enrich the molecular breeding of bitter gourd.

Resequencing of 106 M. charantia accessions

A total of 106 accessions of M. charantia were used in this study. The resequencing data of sixty accessions were obtained from the NCBI BioProject PRJNA578358 (Matsumura et al. 2020), while the remaining 47 accessions were resequenced in-house (Table S1). Among the 47 accessions, 46 were collected from China. The 47 accessions were germinated at a constant temperature of 30°C and grown in an artificial climate chamber. Genomic DNA was extracted from young leaves using the NuClean Plant Genomic DNA Kit. Paired-end (PE) libraries with an insert size of approximately 350 bp were constructed for each accession, and sequencing was performed on the Novaseq platform with PE 2×150 bp.

The SNP calling and filtering

The raw reads were trimmed for sequence quality and adaptor removal using Trimmomatic with the parameters “SLIDINGWINDOW:4:20 LEADING:3 TRAILING:3 MINLEN:40” (Bolger et al. 2014). The resulting clean reads were aligned to the OHB3-1 V2 genome using the MEM algorithm implemented in the Burrows-Wheeler-Alignment Tool (BWA) (Li et al. 2009). PCR duplicated reads were removed using Picard (https://broadinstitute.github.io/picard/). SNP genotypes were called using the HaplotypeCaller module of the Genome Analysis Toolkit (GATK) and were filtered according to the GATK Best Practices recommendations (McKenna et al. 2010). High-quality (HQ) SNPs were obtained by selecting biallelic SNP sites with a QUAL score >30, a missing rate <10%, and a minor allele frequency (MAF) >5% using vcftools V0.1.15 (Danecek et al. 2011). A total of 3,335,160 SNPs passed the filtering criteria.

Population genetics analyses

The 3,335,160 SNPs were pruned to 68,832 SNPs using the "--indep-pairwise 50 5 0.5" command in Plink V1.07. The pruned SNPs were then used to detect population structure using ADMIXTURE V1.3.0 with K values ranging from 2 to 8 (Alexander et al. 2009; Chang et al. 2015). A subset of 74,616 SNPs located at fourfold-degenerate sites from the HQ SNPs was used to construct a neighbor-joining (NJ) tree in MEGA (Tamura et al. 2021). Principal Component Analysis (PCA) was performed using all 3,335,160 SNPs in EIGENSOFT. Nucleotide diversity (π) and pairwise Fst were calculated in 50 kb windows with 10 kb steps using vcftools (Danecek et al. 2011).

Genome-wide association (GWAS) of pericarp color

Pericarp color was categorized into five groups: dark green, green, medium green, light green, and white. The phenotypic data were collected and evaluated three times in Tongzhou, Beijing, yielding highly consistent results. GWAS was performed using a total of 3,335,160 SNPs that passed the filtering criteria: biallelic SNP sites, QUAL >30, missing rate <10%, and MAF >5%. PCA was employed to correct for population stratification, and GWAS analyses were conducted using the GLM algorithm in TASSEL (Bradbury et al. 2007).

The genetic analysis of McAPRR2 gene

The McAPRR2 haplotype was determined using the Haploview software based on seven highly related SNPs in the McAPRR2 promoter region, as well as two functional mutations in the coding sequence (CDS) of McAPRR2 (Barrett et al. 2005). A phylogenetic tree was constructed in MEGA using 74 SNPs located in the promoter and gene region of McAPRR2 (Tamura et al. 2021). The π of the wild, SA, and SEA groups was calculated in 10 kb windows with 2 kb steps using vcftools (Danecek et al. 2011). The APRR2 protein sequence, previously reported to regulate pericarp color within the Cucurbitaceae family, was used in a multiple sequence alignment performed with DNAMAN.

RT-qPCR analysis of McAPRR2

Pericarp tissues from samples with different haplotypes were used for qRT-PCR analysis. RNA was isolated from the pericarp at 10 days post-pollination using the Plant Total RNA Extraction Kit (Vazyme, RC411) according to the manufacturer's instructions. The McAPRR2 CDS with three haplotypes were amplified from the total RNA using the primers listed in Table S4. First-strand cDNA was synthesized using the First Strand cDNA Synthesis Kit (Vazyme, R223), with 1 μg of total RNA. The qRT-PCR reaction was performed in a total volume of 10 μl, consisting of 1 μl of cDNA template, 0.2 μl of each primer (10 μM), 5 μl of TB Green Premix Ex Taq (2×, TaKaRa, RR460), and 3.6 μl of RNase-free water. The PCR conditions were as follows: initial denaturation at 95℃ for 30 s; followed by 40 cycles of denaturation at 95℃ for 5 s and annealing/extension at 60℃ for 34 s; then a final melting curve step of 95℃ for 15 s, 60℃ for 1 min, and 95℃ for 15 s. qRT-PCR was conducted on the LightCycler 480 System (Roche Diagnostics). The relative expression levels were computed using the comparative Ct method (2^-ΔΔCt) (Livak and Schmittgen 2001). The primers employed for qRT-PCR are listed in Table S4.

Analysis and Quantification of chlorophyll and carotenoid contents

The sample used for pigment content measurement was the same as that used for qRT-PCR. The chlorophyll and carotenoid contents of the pericarp were determined using the method described in the previous study (Ma et al. 2021).

Genetic characteristics of 106 bitter gourd accessions

A total of 47 M. charantia accessions were collected from China, with one exception. The resequencing of these accessions produced 222.90 Gb of clean data, corresponding to a genomic coverage ranging from approximately 13.12× (KG19) to 19.07× (KG21) (Table S1). For comparative purposes with individuals from distinct geographical regions, an additional 60 M. charantia accessions were downloaded from the NCBI database. Therefore, this study included a total of 66 accessions from Southeast Asia (SEA), 24 from South Asia (SA), 16 from Taiwan (TAI) and Thailand (THAI), along with one outgroup (Fig. 1). By mapping the clean reads onto the OHB3-1 reference genome, this study identified a final set of 3,335,160 high-quality SNPs based on the resequencing of 106 accessions.

To infer the genetic structure of the 106 bitter gourd accessions, ADMIXTURE analysis, phylogenetic tree construction, and principal component analysis (PCA) were employed. Interestingly, our bitter gourd accessions formed groups distinct from the previously published TAI, THAI, SA, and SEA (Matsumura et al. 2020). The 106 accessions in this study clustered into four distinct groups: wild type from TAI and THAI, SA, SEA1, and SEA2 (Fig. 2A, B, Table S1). The SEA group initially diverged from the others when K = 2, subsequently, the SA group separated from the wild type when K = 3. When K = 4, SEA split into SEA1 and SEA2, reported for the first time here. Accordingly, the ADMIXTURE models with K = 4 yielded the lowest cross-validation errors (Fig. 2A). The neighbor-joining (NJ) tree and PCA were also largely consistent with the ADMIXTURE analysis (Figs. 2C, D). PC1 and PC2 explained 70.46% and 8.40% of the variation, respectively. Eight individuals were found to be admixtures among wild, SA and SEA for max Q < 0.70, while 15 were admixtures between SEA1 and SEA2 (Figs. 2B, C, and D, Table S1).

Genome-wide nucleotide diversity (π) for each group was calculated using 3,335,160 SNPs. The wild group displayed a significantly higher π (2.61×10^-3) than the total cultivated bitter gourd groups (0.9×10^-3). Among the cultivated groups, the SA group exhibited the highest π (1.28×10^-3), while the SEA2 group showed the lowest (0.37×10^-3) (Fig. S1A). Additionally, the π was relatively consistent across the 11 chromosomes in the wild group, SEA1, and SEA2, except for Chr4 of the SA group, which exhibited higher diversity (Fig. S1B). Evaluations of the fixation index value (Fst) revealed that SEA1 and SEA2 displayed higher differentiation from the wild group than the SA group (Table S2). SEA1 only weakly differentiated from SEA2, while differentiation between SEA and the SA group was moderate.

Genome-wide association of pericarp color in bitter gourd

Significant variation in pericarp color was observed among the 106 bitter gourd accessions from different genetic groups. The wild group typically showed green or dark green pericarp, whereas the cultivated group exhibited a wide array of green shades (Table S1). Specifically, 83.33% of individuals from the SA group displayed medium to dark green pericarp, while 71.21% of individuals from the SEA group exhibited light green or white pericarp (Fig. 3B).

A genome-wide association study (GWAS) for pericarp color was conducted using the SNP variations derived from the resequencing of 106 accessions. The GWAS analysis revealed a single peak across the 11 chromosomes (Fig. 3A). We identified 41 significantly associated SNPs in Chr6 for pericarp color at the threshold of –log(p) = 10, thereby narrowing down the region to 17.3 kb (Fig. 3AB, Table S3). The quantile-quantile plot demonstrated a deviation of observed values from the expected X=Y line, verifying the reliability of the identified significant association SNPs (Fig. S2). Within the candidate region, only one gene, designated as evm.TU.chr6.3557, was located in the OHB3-1 V2 genome. This gene (McAPRR2) encodes a two-component response regulator-like protein APRR2, which has previously been reported to be involved in regulating pericarp color in Cucurbitaceae (Liu et al. 2016; Ma et al. 2021; Oren et al. 2019; Zhao et al. 2019).

The haplotype of McAPRR2

Seven SNPs on the promoter of McAPRR2, one nonsynonymous mutation on exon9, and one InDel on exon10 were found to be significantly associated with pericarp color (–log(p)>10) (Fig. 3C). Linkage disequilibrium (LD) analysis of McAPRR2 revealed a strong LD block between InDel4422 and other significant variants (Fig. 3C). Using these significant variants, a haplotype analysis was conducted on 106 bitter gourd accessions. After excluding missing data and heterozygous loci, haplotypes were finally assigned for 86 bitter gourd accessions. These 86 accessions were divided into three haplotypes, namely Hap1, Hap2, and Hap3 (Fig. 3D). Hap1, consisting 14 accessions, exclusively exhibited a green pericarp phenotype and originated entirely from the wild group. Hap2, which included 28 accessions, presented a uniformly green pericarp phenotype, with 75% of samples from the SA group and 25% from the SEA group. Hap3 contained 44 accessions, 95.45% of which displayed a light green pericarp phenotype, primarily originating from the SEA group. Interestingly, one wild type in Hap3 may be the original source of Hap3. Taken together, these findings suggest that the McAPRR2 haplotype is strongly correlated with pericarp color and geographical location.

The expression pattern of McAPRR2 and pigment content in pericarp color

The expression pattern of McAPRR2 and pigment content of the three haplotypes were analyzed. McAPRR2 expression of in Hap1 and Hap2 was higher than that in Hap3, with dark green pericarp showing significantly higher McAPRR2 expression compared to green and light green pericarp (Fig. 4A). Additionally, the samples used for analyzing haplotype expression were also used for pigment content assessment. The contents of chlorophyll a, chlorophyll b, and carotenoids in Hap1 were higher than those in Hap2 and Hap3, with Hap2 displaying higher pigment content than Hap3 (Fig. 4B). Dark green pericarp exhibited higher pigment content than the other pericarp types. The relationship between McAPRR2 expression and the levels of chlorophyll a, chlorophyll b, and carotenoids was analyzed, revealing a positive correlation with a coefficient exceeding 0.94 (Fig. 4C).

The 15 bp insertion in McAPRR2 alters its function

Sequencing of the McAPRR2 CDS from the three haplotypes confirmed the existence of SNP3742 and InDel4422 (Fig. 5AB). Notably, InDel4422, a 15 bp insertion (TCCTAACTGATAATC) in exon 10 of McAPRR2, leads to a premature termination in the protein encoded by Hap3, inducing a shift in pericarp color from green to light green.

The conserved domains of McAPRR2 were predicted using InterPro, identifying the Response Regulatory Domain and the Myb Domain. The Response Regulatory Domain is located before the Myb Domain (Fig. S3). InDel4422 is not located within either domain, thus its mutation does not impact the function of the two domains in McAPRR2. APRR2 has been previously reported to significantly influence the pericarp color of watermelon, cucumber, melon, and wax gourd (Oren et al. 2019; Liu et al. 2016; Ma et al. 2021). In this study, we conducted a multiple sequence alignment of the APRR2 protein sequence. The mutation sites of these APRR2 proteins are located after the Myb Domain, suggesting they do not affect the function of the two domains, with the exception of the mutation sites in white wax gourd, which are found before the Myb Domain (Fig. S3).

McAPRR2 was under domestication in bitter gourd

McAPRR2 haplotype is significantly correlated with both pericarp color and ecological type. Hap1 was strictly associated with wild types exhibiting green pericarp, while Hap2 corresponded to SA and SEA types with green pericarp. Hap3 was mainly related to SEA types, distinguished by a light green pericarp. The insertion of a 15 bp sequence in Hap3 altered the function of McAPRR2, leading to a modification in pericarp color. These findings suggest that McAPRR2 was potentially subjected to selection during domestication. To investigate whether McAPRR2 was subject to domestication selection, we analyzed the phylogenetic tree and nucleotide diversity of this gene. Using 74 SNPs located in the McAPRR2 gene region and its promoter, a phylogenetic tree was constructed. We observed that the tree generally clustered according to pericarp color and genetic group. Green pericarp types were clustered together, as were light green pericarp types. Wild types were clustered together, while SA and a subset of green pericarp SEA types formed another group, and SEA types were gathered in yet another cluster. The nucleotide diversity in the McAPRR2 gene showed that the π_wild/SA value was the lowest, indicating low nucleotide diversity between these two groups on the McAPRR2 gene. High π_wild/SEA and π_SA/SEA values indicate high nucleotide diversity between wild and SEA types and between SA and SEA types on the McAPRR2 gene. The loss of genome-wide genetic diversity in modern crops is a typical characteristic of plant domestication. In conjunction with haplotype and pericarp color phenotypes, we concluded that pericarp color underwent domestication in the SEA region, leading to the formation of the light green pericarp phenotype.

In our current study, we resequenced 47 accessions, and incorporated the resequencing data of an additional 60 accessions as reported by Matsumura et al. (2020). We identified a significant 17.3 kb region that is highly associated with pericarp color through GWAS, which has been extensively utilized in many plants and has proven to be an effective method for identifying crucial genes for various traits (Guo et al. 2019; Huang et al. 2010; Li et al. 2018; Zhao et al. 2019). Interestingly, McAPRR2 was the only gene located in this significant region. In bitter gourd, Matsumura et al. (2020) identified the top 15 genes that were enriched for the top 0.1% of SNPs with the highest color association, and APRR2 was among these genes. APRR2 was the second-to-last gene associated with pericarp color, and they failed to identify the key gene regulating pericarp color due to an inadequate sample size for the GWAS. Additionally, McAPRR2 has been reported to regulate green stigma in bitter gourd (Zhan et al. 2023). Taken together with our study, McAPRR2 regulates pericarp color and stigma color in bitter gourd, which is consist with CsAPRR2 in cucumber that CsAPRR2 regulates pericarp color, stem, leaf, and flower (Liu et al. 2016). Furthermore, we identified a 15 bp insertion in exon 10 of McAPRR2, leading to a premature termination in the protein encoded by McAPRR2, which is associated with a light green pericarp (Fig. 5). This finding is consistent with studies in Cucurbitaceae crops where the premature termination of the APRR2 protein also controls pericarp color, further reinforcing the role of McAPRR2 in regulating pericarp color in our study (Liu et al. 2016; Ma et al. 2021; Oren et al. 2019; Zhao et al. 2019).

Color is a significant trait in plants, and numerous studies have reported that the color of various plant species has undergone domestication and selection processes, such as the berry color of grape (Dong et al. 2023), pericarp color (Sweeney and McCouch 2007), and seed color of grain (Stetter et al. 2019). Bitter gourd, primarily cultivated in Asia, serves dual roles as both a vegetable and a significant medicinal crop. However, its limited demand has resulted in a slower rate of domestication compared to other cucurbit crops. The domestication of bitter gourd appears to be a complex process, with particular human preferences varying across different cultures. South Asians, for example, favor highly bitter, smaller fruits (although larger than their wild counterparts) with spiny, dark green features. In contrast, Southeast Asians prefer less bitter fruits with light green (or white) and smooth skin (Dhillon et al. 2016). In this study of 106 bitter gourd accessions, wild types were green or dark green, SA types were mainly dark green, and SEA types were predominantly light green or white. The distribution of bitter gourd pericarp color evidently correlates with geographical location (Fig. 1). Existing research suggests that selection pressures during the course of domestication and subsequent selection processes are associated with adaptations to specific geographical locations (Meyer and Purugganan 2013). Therefore, it is plausible that McAPRR2 has been under domestication and selection pressures. The haplotypes of McAPRR2 display a high correlation with both pericarp color and ecological type (Fig. 3D). The phylogenetic tree of McAPRR2 clustered according to pericarp color and ecological type (Fig. 6A). Moreover, the nucleotide diversity of McAPRR2 exhibits a gradual decline among the wild, SA, and SEA groups (Fig. 6B). These results collectively suggest that the pericarp color of bitter gourd primarily underwent domestication selection.

To date, despite several studies reporting on the evolution of bitter gourd, these findings remain inconsistent, leaving the evolutionary history of bitter gourd inadequately elucidated. It is unequivocally established that bitter gourd originated in Africa (Schaefer and Renner, 2010), and was domesticated in Asia (Walters and Decker-Walters,1988; Miniraj at al. 1993). Cui et al. (2020) proposed that the bitter gourd was domesticated in South Asia (SA). In contrast, Matsumura et al. (2020) reported that the signals of selection between wild and Southeast Asia (SEA) types predominantly arose from the selection during the SA–SEA divergence stage, rather than the result of a gradual and accumulative evolution from wild to SA to SEA. Renner (2020), integrating insights from two parallel studies, proposed that the bitter gourd expanded from Africa to Southeast Asia underwent domestication there (Chomicki et al. 2020; Renner 2020). The domestication selection of bitter gourd pericarp color is associated with consumer preferences, individuals in the SEA region tend to favor a lighter green pericarp color (Dhillon et al. 2016). Considering the results of our study, we conclude that the pericarp color of bitter gourd underwent domestication in the SEA region, a finding that aligns with Renner's report. Future studies should include a broader range of accessions from varied geographical locations to more effectively elucidate the history of bitter gourd domestication.

Supplementary Information The online version contains supplementary material available at XX.

Acknowledgments

Author contribution statement CLW, SWT and JJY conceived and designed the research. JJY and XFZ performed the research, XFZ participated in data analysis. JJY wrote the manuscript. All authors have read and agreed to the published version of the manuscript.

Funding This work was supported by the Beijing Academy of Agricultural and Forestry Sciences (Grant Nos. KJCX20230301, KYCX202304, JKZX202207, and KJCX20230126) and National Natural Science Foundation of China (Grant No. 32002060).

Data availability The raw data has been uploaded to the GSA (https://bigd.big.ac.cn/gsa/) under the accession number CRA011965.

Conflict of interest The authors declare no confict of interest.

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McAPRR2 : The Key Regulator of Domesticated Pericarp Color in Bitter Gourd

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Abstract

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Key Message

Introduction

Material and method

Resequencing of 106 M. charantia accessions

The SNP calling and filtering

Population genetics analyses

Genome-wide association (GWAS) of pericarp color

The genetic analysis of McAPRR2 gene

RT-qPCR analysis of McAPRR2

Analysis and Quantification of chlorophyll and carotenoid contents

Results

Genetic characteristics of 106 bitter gourd accessions

Genome-wide association of pericarp color in bitter gourd

The haplotype of McAPRR2

The expression pattern of McAPRR2 and pigment content in pericarp color

The 15 bp insertion in McAPRR2 alters its function

McAPRR2 was under domestication in bitter gourd

Discussion

Declarations

References

Supplementary Figure

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