Long-read bitter gourd (Momordica charantia) genome and the genomic architecture of nonclassic domestication

Comparative transcriptomics analysis of tolerant and sensitive genotypes reveals genes involved in the response to cold stress in bitter gourd (Momordica charantia L.)

Bitter gourd is an economically important horticultural crop for its edible and medicinal value. However, the regulatory mechanisms of bitter gourd in response to cold stress are still poorly elucidated. In this study, phytohormone determination and comparative transcriptome analyses in XY (cold-tolerant) and QF (cold-sensitive) after low temperature treatment were conducted. Under cold stress, the endogenous contents of abscisic acid (ABA), jasmonic acid (JA) and salicylic acid (SA) in XY were significantly increased at 24 h after treatment (HAT), indicating that ABA, JA and SA might function in regulating cold resistance. RNA-seq results revealed that more differentially expressed genes were identified at 6 HAT in QF and 24 HAT in XY, respectively. KEGG analysis suggested that the plant hormone signal transduction pathway was significantly enriched in both genotypes at all the time points. In addition, transcription factors showing different expression patterns between XY and QF were identified, including CBF3, ERF2, NAC90, WRKY51 and WRKY70. Weighted gene co-expression network analysis suggested MARK1, ERF17, UGT74E2, GH3.1 and PPR as hub genes. These results will deepen the understanding of molecular mechanism of bitter gourd in response to cold stress and the identified genes may help to facilitate the genetic improvement of cold-resistant cultivars.

Potential locus W and candidate gene McPRR2 associated with pericarp pigment accumulation in bitter gourd (Momordica charantia L.) revealed via BSA-seq analysis

Pericarp color is a prominent agronomic trait that exerts a significant impact on consumer and breeder preferences. Genetic analysis has revealed that the pericarp color of bitter gourd is a quantitative trait. However, the underlying mechanism for this trait in bitter gourd remains largely unknown. In the present study, we employed bulked segregant analysis (BSA) to identify the candidate genes responsible for bitter gourd pericarp color (specifically, dark green versus white) within F2 segregation populations resulting from the crossing of B07 (dark green pericarp) and A06 (white pericarp). Through genomic variation, genetic mapping, and expression analysis, we identified a candidate gene named McPRR2, which was a homolog of Arabidopsis pseudo response regulator 2 (APRR2) encoded by LOC111023472. Sequence alignment of the candidate gene between the two parental lines revealed a 15-bp nucleotide insertion in the coding region of LOC111023472, leading to a premature stop codon and potentially causing a loss-of-function mutation. qRT-PCR analysis demonstrated that the expression of McPRR2 was significantly higher in B07 compared to A06, and it was primarily expressed in the immature fruit pericarp. Moreover, overexpression of McPRR2 in tomato could enhance the green color of immature fruit pericarp by increasing the chlorophyll content. Consequently, McPRR2 emerged as a strong candidate gene regulating the bitter gourd pericarp color by influencing chlorophyll accumulation. Finally, we developed a molecular marker linked to pericarp color, enabling the identification of genotypes in breeding populations. These findings provided valuable insights into the genetic improvement of bitter gourd pericarp color.

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

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 via a genome-wide association study (GWAS) utilizing the resequencing data of 106 bitter gourd accessions. McAPRR2 exhibits three primary haplotypes: Hap1 is a wild type with a green pericarp, Hap2 is a SA (South Asian) and SEA (Southeast Asia) type with a green pericarp, and Hap3 is primarily a SEA type with a light green pericarp. The McAPRR2 haplotype is significantly correlated with both pericarp color and ecological type. Importantly, McAPRR2 with the light green pericarp demonstrated 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 πwild/SEA and πSA/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.

A point mutation in MC06g1112 encoding FLOWERING LOCUS T decreases the first flower node in bitter gourd (Momordica charantia L.)

In Cucurbitaceae crops, the first flower node (FFN) is an important agronomic trait which can impact the onset of maturity, the production of female flowers, and yield. However, the gene responsible for regulating FFN in bitter gourd is unknown. Here, we used a gynoecious line (S156G) with low FFN as the female parent and a monoecious line (K8-201) with high FFN as the male parent to obtain F1 and F2 generations. Genetic analysis indicated that the low FFN trait was incompletely dominant over the high FFN trait. A major quantitative trait locus (QTL)-Mcffn and four minor effect QTLs-Mcffn1.1, Mcffn1.2, Mcffn1.3, and Mcffn1.4 were detected by whole-genome re-sequencing-based QTL mapping in the S156G×K8-201 F2 population (n=234) cultivated in autumn 2019. The Mcffn locus was further supported by molecular marker-based QTL mapping in three S156G×K8-201 F2 populations planted in autumn 2019 (n=234), autumn 2020 (n=192), and spring 2022 (n=205). Then, the Mcffn locus was fine-mapped into a 77.98-kb physical region on pseudochromosome MC06 using a large S156G×K8-201 F2 population (n=2,402). MC06g1112, which is a homolog of FLOWERING LOCUS T (FT), was considered as the most likely Mcffn candidate gene according to both expression and sequence variation analyses between parental lines. A point mutation (C277T) in MC06g1112, which results in a P93S amino acid mutation between parental lines, may be responsible for decreasing FFN in bitter gourd. Our findings provide a helpful resource for the molecular marker-assisted selective breeding of bitter gourd.

Integrated Secondary Metabolomic and Antioxidant Ability Analysis Reveals the Accumulation Patterns of Metabolites in Momordica charantia L. of Different Cultivars

Bitter gourd (Momordica charantia L.) contains rich bioactive ingredients and secondary metabolites; hence, it has been used as medicine and food product. This study systematically quantified the nutrient contents, the total content of phenolic acids (TPC), flavonoids (TFC), and triterpenoids (TTC) in seven different cultivars of bitter gourd. This study also estimated the organic acid content and antioxidative capacity of different cultivars of bitter gourd. Although the TPC, TFC, TTC, organic acid content, and antioxidative activity differed significantly among different cultivars of bitter gourd, significant correlations were also observed in the obtained data. In the metabolomics analysis, 370 secondary metabolites were identified in seven cultivars of bitter gourd; flavonoids and phenolic acids were significantly more. Differentially accumulated metabolites identified in this study were mainly associated with secondary metabolic pathways, including pathways of flavonoid, flavonol, isoflavonoid, flavone, folate, and phenylpropanoid biosyntheses. A number of metabolites (n = 27) were significantly correlated (positive or negative) with antioxidative capacity (r ≥ 0.7 and p < 0.05). The outcomes suggest that bitter gourd contains a plethora of bioactive compounds; hence, bitter gourd may potentially be applied in developing novel molecules of medicinal importance.

Map-based cloning of the APRR2 gene controlling green stigma in bitter gourd (Momordica charantia)

Bitter gourd is an economically important vegetable and medicinal crop distinguished by its bitter fruits. Its stigma color is widely used to assess the distinctiveness, uniformity, and stability of bitter gourd varieties. However, limited researches have been dedicated to genetic basis of its stigma color. In this study, we employed bulked segregant analysis (BSA) sequencing to identify a single dominant locus McSTC1 located on pseudochromosome 6 through genetic mapping of an F₂ population (n =241) derived from the cross between green and yellow stigma parental lines. An F₂-derived F₃ segregation population (n = 847) was further adopted for fine mapping, which delimited the McSTC1 locus to a 13.87 kb region containing one predicted gene McAPRR2 (Mc06g1638), a homolog of the Arabidopsis two-component response regulator-like gene AtAPRR2. Sequence alignment analysis of McAPRR2 revealed that a 15 bp insertion at exon 9 results in a truncated GLK domain of its encoded protein, which existed in 19 bitter gourd varieties with yellow stigma. A genome-wide synteny search of the bitter gourd McAPRR2 genes in Cucurbitaceae family revealed its close relationship with other cucurbits APRR2 genes that are corresponding to white or light green fruit skin. Our findings provide insights into the molecular marker-assisted breeding of bitter gourd stigma color and the mechanism of gene regulation for stigma color.

Lateral Root Initiation in Cucumber (Cucumis sativus): What Does the Expression Pattern of Rapid Alkalinization Factor 34 (RALF34) Tell Us?

In Arabidopsis, the small signaling peptide (peptide hormone) RALF34 is involved in the gene regulatory network of lateral root initiation. In this study, we aimed to understand the nature of the signals induced by RALF34 in the non-model plant cucumber (Cucumis sativus), where lateral root primordia are induced in the apical meristem of the parental root. The RALF family members of cucumber were identified using phylogenetic analysis. The sequence of events involved in the initiation and development of lateral root primordia in cucumber was examined in detail. To elucidate the role of the small signaling peptide CsRALF34 and its receptor CsTHESEUS1 in the initial stages of lateral root formation in the parental root meristem in cucumber, we studied the expression patterns of both genes, as well as the localization and transport of the CsRALF34 peptide. CsRALF34 is expressed in all plant organs. CsRALF34 seems to differ from AtRALF34 in that its expression is not regulated by auxin. The expression of AtRALF34, as well as CsRALF34, is regulated in part by ethylene. CsTHESEUS1 is expressed constitutively in cucumber root tissues. Our data suggest that CsRALF34 acts in a non-cell-autonomous manner and is not involved in lateral root initiation in cucumber.

Analysis of the Complete Mitochondrial Genome of the Bitter Gourd (Momordica charantia)

Bitter gourd (Momordica charantia L.) is a significant vegetable. Although it has a special bitter taste, it is still popular with the public. The industrialization of bitter gourd could be hampered by a lack of genetic resources. The bitter gourd's mitochondrial and chloroplast genomes have not been extensively studied. In the present study, the mitochondrial genome of bitter gourd was sequenced and assembled, and its substructure was investigated. The mitochondrial genome of bitter gourd is 331,440 bp with 24 unique core genes, 16 variable genes, 3 rRNAs, and 23 tRNAs. We identified 134 SSRs and 15 tandem repeats in the entire mitochondrial genome of bitter gourd. Moreover, 402 pairs of repeats with a length greater than or equal to 30 were observed in total. The longest palindromic repeat was 523 bp, and the longest forward repeat was 342 bp. We found 20 homologous DNA fragments in bitter gourd, and the summary insert length was 19,427 bp, accounting for 5.86% of the mitochondrial genome. We predicted a total of 447 potential RNA editing sites in 39 unique PCGs and also discovered that the ccmFN gene has been edited the most often, at 38 times. This study provides a basis for a better understanding and analysis of differences in the evolution and inheritance patterns of cucurbit mitochondrial genomes.

Identification of clade-wide putative cis-regulatory elements from conserved non-coding sequences in Cucurbitaceae genomes

Cis-regulatory elements regulate gene expression and play an essential role in the development and physiology of organisms. Many conserved non-coding sequences (CNSs) function as cis-regulatory elements. They control the development of various lineages. However, predicting clade-wide cis-regulatory elements across several closely related species remains challenging. Based on the relationship between CNSs and cis-regulatory elements, we present a computational approach that predicts the clade-wide putative cis-regulatory elements in 12 Cucurbitaceae genomes. Using 12-way whole-genome alignment, we first obtained 632 112 CNSs in Cucurbitaceae. Next, we identified 16 552 Cucurbitaceae-wide cis-regulatory elements based on collinearity among all 12 Cucurbitaceae plants. Furthermore, we predicted 3 271 potential regulatory pairs in the cucumber genome, of which 98 were verified using integrative RNA sequencing and ChIP sequencing datasets from samples collected during various fruit development stages. The CNSs, Cucurbitaceae-wide cis-regulatory elements, and their target genes are accessible at http://cmb.bnu.edu.cn/cisRCNEs_cucurbit/. These elements are valuable resources for functionally annotating CNSs and their regulatory roles in Cucurbitaceae genomes.

Fine-mapping and candidate gene analysis of the Mcgy1 locus responsible for gynoecy in bitter gourd (Momordica spp.)

The Mcgy1 locus responsible for gynoecy was fine-mapped into a 296.94-kb region, in which four single-nucleotide variations and six genes adjacent to them might be associate with sex differentiation in bitter gourd. Gynoecy plays an important role in high-efficiency hybrid seed production, and gynoecious plants are excellent materials for dissecting sex differentiation in Cucurbitaceae crop species, including bitter gourd. However, the gene responsible for gynoecy in bitter gourd is unknown. Here, we first identified a gynoecy locus designated Mcgy1 using the F₂ population (n = 291) crossed from the gynoecious line S156G and the monoecious line K8-201 via bulked segregant analysis with whole-genome resequencing (BSA-seq) and molecular marker linkage analysis. Then, a large S156G × K8-201 F₂ population (n = 5,656) was used for fine-mapping to delimit the Mcgy1 locus into a 296.94-kb physical region on pseudochromosome MC01, where included 33 annotated genes different from any homologous gynoecy genes previously reported in Cucurbitaceae species. Within this region, four underlying single-nucleotide variations (SNVs) that might cause gynoecy were identified by multiple genomic sequence variation analysis, and their six neighbouring genes were considered as potential candidate genes for Mcgy1. Of these, only MC01g1681 showed a significant differential expression at two-leaf developmental stage between S156G and its monoecious near-isogenic line S156 based on RNA sequencing (RNA-seq) and qRT-PCR analyses. In addition, transcriptome analysis revealed 21 key differentially expressed genes (DEGs) and possible regulatory pathways of the formation of gynoecy in bitter gourd. Our findings provide a new clue for researching on gynoecious plants in Cucurbitaceae species and a theoretical basis for breeding gynoecious bitter gourd lines by the use of molecular markers-assisted selection.

Molecular mapping of genomic regions and identification of possible candidate genes associated with gynoecious sex expression in bitter gourd

Bitter gourd is an important vegetable crop grown throughout the tropics mainly because of its high nutritional value. Sex expression and identification of gynoecious trait in cucurbitaceous vegetable crops has facilitated the hybrid breeding programme in a great way to improve productivity. In bitter gourd, gynoecious sex expression is poorly reported and detailed molecular pathways involve yet to be studied. The present experiment was conducted to study the inheritance, identify the genomic regions associated with gynoecious sex expression and to reveal possible candidate genes through QTL-seq. Segregation for the gynoecious and monoecious sex forms in the F₂ progenies indicated single recessive gene controlling gynoecious sex expression in the genotype, PVGy-201. Gynoecious parent, PVGy-201, Monoecious parent, Pusa Do Mausami (PDM), and two contrasting bulks were constituted for deep-sequencing. A total of 10.56, 23.11, 15.07, and 19.38 Gb of clean reads from PVGy-201, PDM, gynoecious bulk and monoecious bulks were generated. Based on the ΔSNP index, 1.31 Mb regions on the chromosome 1 was identified to be associated with gynoecious sex expression in bitter gourd. In the QTL region 293,467 PVGy-201 unique variants, including SNPs and indels, were identified. In the identified QTL region, a total of 1019 homozygous variants were identified between PVGy1 and PDM genomes and 71 among them were non-synonymous variants (SNPS and INDELs), out of which 11 variants (7 INDELs, 4 SNPs) were classified as high impact variants with frame shift/stop gain effect. In total twelve genes associated with male and female gametophyte development were identified in the QTL-region. Ethylene-responsive transcription factor 12, Auxin response factor 6, Copper-transporting ATPase RAN1, CBL-interacting serine/threonine-protein kinase 23, ABC transporter C family member 2, DEAD-box ATP-dependent RNA helicase 1 isoform X2, Polygalacturonase QRT3-like isoform X2, Protein CHROMATIN REMODELING 4 were identified with possible role in gynoecious sex expression. Promoter region variation in 8 among the 12 genes indicated their role in determining gynoecious sex expression in bitter gourd genotype, DBGy-1. The findings in the study provides insight about sex expression in bitter gourd and will facilitate fine mapping and more precise identification of candidate genes through their functional validation.

Candidate gene based SSR and SNP markers for gynoecy in bitter gourd (Momordica charantia L.)

BACKGROUND

Even though the bitter gourd hybrids are shown to have significant heterosis for many of the economic traits, processes such as manual bagging and hand pollination make the hybrid seed production labour-intensive. Use of gynoecious line as female parent makes hybrid seed production more economical. This work was performed with the objective to identify the candidate gene based molecular markers for gynoecy in bitter gourd.

METHODS AND RESULTS

Seven putative genes for flowering and sex expression, isolated from the monoecious (MC-136) and gynoecious (KAU-MCGy-101) bitter gourd accessions, were sequence characterized. MADS-box transcription factor genes AG6 and McAG2 had nucleotide polymorphisms at five sites each and were potential candidates for marker development. An In/Del polymorphism of 48 bp ([TC]₂₄) in AG6 gene was used to develop an SSR marker and a transition mutation of [A/G] in this gene was used to develop a set of SNP markers. These markers have developed distinct polymorphism between the monoecious and gynoecious genotypes and were found suited for the marker assisted selection.

CONCLUSIONS

MADS box transcription factor genes AG6 and McAG2 are identified as candidates for sex expression in bitter gourd. Based on the InDels and transition in the intronic region of AG6, SSR marker BGAG6 and an SNP marker set segregating with the sex forms were developed. The markers have been validated using four other monoecious lines and are routinely used in our bitter gourd hybrid seed production programmes.

Chromosome-Level Genome Assembly of Herpetospermum pedunculosum (Cucurbitaceae)

This study presents a chromosome-level reference genome assembly of a traditional Tibetan medicinal plant, Herpetospermum pedunculosum belonging to the Cucurbitaceae family. Following a combined PacBio high-fidelity sequencing and Hi-C analysis, a final H. pedunculosum genome assembly, 804.11 Mb in length was obtained, 90.45% of which was anchored into ten pseudochromosomes with a contig N50 of 24.39 Mb. In addition, 579.55 Mb repetitive sequences and 23,924 high-confidence protein-coding genes were annotated. Phylogenetic analysis revealed that H. pedunculosum was sister to a clade formed by cucumber, zucchini, and wax gourd. Further whole-genome duplication analysis revealed no recent polyploidization event in the H. pedunculosum genome. The high-quality H. pedunculosum genome presented here will be highly useful in investigating the molecular mechanisms underlying the biosynthesis of its active compounds and adaptation strategies to the extreme environment. It will also provide great insights into comparative genomic studies of Cucurbitaceae and flowering plants.

CuGenDBv2: an updated database for cucurbit genomics

The Cucurbitaceae (cucurbit) family consists of about 1,000 species in 95 genera, including many economically important and popular fruit and vegetable crops. During the past several years, reference genomes have been generated for >20 cucurbit species, and variome and transcriptome profiling data have been rapidly accumulated for cucurbits. To efficiently mine, analyze and disseminate these large-scale datasets, we have developed an updated version of Cucurbit Genomics Database. The updated database, CuGenDBv2 (http://cucurbitgenomics.org/v2), currently hosts 34 reference genomes from 27 cucurbit species/subspecies belonging to 10 different genera. Protein-coding genes from these genomes have been comprehensively annotated by comparing their protein sequences to various public protein and domain databases. A novel 'Genotype' module has been implemented to facilitate mining and analysis of the functionally annotated variome data including SNPs and small indels from large-scale genome sequencing projects. An updated 'Expression' module has been developed to provide a comprehensive gene expression atlas for cucurbits. Furthermore, synteny blocks between any two and within each of the 34 genomes, representing a total of 595 pair-wise genome comparisons, have been identified and can be explored and visualized in the database.

Telomere-to-telomere genome assembly of bitter melon (Momordica charantia L. var. abbreviata Ser.) reveals fruit development, composition and ripening genetic characteristics

Momordica charantia L. var. abbreviata Ser. (Mca), known as bitter gourd or bitter melon, is a Momordica variety with medicinal value and belongs to the Cucurbitaceae family. In view of the lack of genomic information on bitter gourd and other Momordica species and to promote Mca genomic research, we assembled a 295.6-Mb telomere-to-telomere (T2T) high-quality Mca genome with six gap-free chromosomes after Hi-C correction. This genome is anchored to 11 chromosomes, which is consistent with the karyotype information, and comprises 98 contigs (N50 of 25.4 Mb) and 95 scaffolds (N50 of 25.4 Mb). The Mca genome harbors 19 895 protein-coding genes, of which 45.59% constitute predicted repeat sequences. Synteny analysis revealed variations involved in fruit quality during the divergence of bitter gourd. In addition, assay for transposase-accessible chromatin by high-throughput sequencing and metabolic analysis showed that momordicosides and other substances are characteristic of Mca fruit pulp. A combined transcriptomic and metabolomic analysis revealed the mechanisms of pigment accumulation and cucurbitacin biosynthesis in Mca fruit peels, providing fundamental molecular information for further research on Mca fruit ripening. This report provides a new genetic resource for Momordica genomic studies and contributes additional insights into Cucurbitaceae phylogeny.

Transcriptome analysis provides insights into lignin synthesis and MAPK signaling pathway that strengthen the resistance of bitter gourd (Momordica charantia) to Fusarium wilt

Fusarium wilt is a typical soil-borne disease caused by Fusarium oxysporum f. sp. momordicae (FOM) in bitter gourd. In this study, by comparing sequencing data at multiple time points and considering the difference between resistant (R) and susceptible (S) varieties, differentially expressed genes were screened out. Short time-series expression miner analysis revealed the upregulated expression trend of genes, which were enriched in phenylpropanoid biosynthesis, plant-pathogen interaction, and mitogen-activated protein kinase signaling pathway. Further, observation of the microstructure revealed that the R variety may form tyloses earlier than the S variety to prevent mycelium diffusion from the xylem vessel. After Fusarium wilt infection, the enzymatic activities of superoxide dismutase, peroxidase, phenylalanine ammonia lyase, and catalaseas well as levels of superoxide anion and malondialdehyde were increased in the R variety higher than those in the S variety. This study provides a reference to elucidate the disease resistance mechanism of bitter gourd.

The Current Developments in Medicinal Plant Genomics Enabled the Diversification of Secondary Metabolites' Biosynthesis

Medicinal plants produce important substrates for their adaptation and defenses against environmental factors and, at the same time, are used for traditional medicine and industrial additives. Plants have relatively little in the way of secondary metabolites via biosynthesis. Recently, the whole-genome sequencing of medicinal plants and the identification of secondary metabolite production were revolutionized by the rapid development and cheap cost of sequencing technology. Advances in functional genomics, such as transcriptomics, proteomics, and metabolomics, pave the way for discoveries in secondary metabolites and related key genes. The multi-omics approaches can offer tremendous insight into the variety, distribution, and development of biosynthetic gene clusters (BGCs). Although many reviews have reported on the plant and medicinal plant genome, chemistry, and pharmacology, there is no review giving a comprehensive report about the medicinal plant genome and multi-omics approaches to study the biosynthesis pathway of secondary metabolites. Here, we introduce the medicinal plant genome and the application of multi-omics tools for identifying genes related to the biosynthesis pathway of secondary metabolites. Moreover, we explore comparative genomics and polyploidy for gene family analysis in medicinal plants. This study promotes medicinal plant genomics, which contributes to the biosynthesis and screening of plant substrates and plant-based drugs and prompts the research efficiency of traditional medicine.

Epidermal Patterning Factor 2-like (McEPFL2): A Putative Candidate for the Continuous Ridge (cr) Fruit Skin Locus in Bitter Gourd (Momordica charantia L.)

Bitter gourd (Momordica charantia L.) is an economically important vegetable and medicinal crop in many Asian countries. Limited work has been conducted in understanding the genetic basis of horticulturally important traits in bitter gourd. Bitter gourd is consumed primarily for its young, immature fruit, and fruit appearance plays an important role in market acceptability. One such trait is the ridges on the fruit skin. In the present study, molecular mapping of a locus underlying fruit ridge continuity was conducted. Genetic analysis in segregating populations, derived from the crosses between two inbred lines Y1 with continuous ridges (CR) and Z-1-4 with discontinuous ridges (DCR), suggested that CR was controlled by a single recessive gene (cr). High-throughput genome sequencing of CR and DCR bulks combined with high-resolution genetic mapping in an F2 population delimited cr into a 108 kb region with 16 predicted genes. Sequence variation analysis and expression profiling supported the epidermal patterning factor 2-like (McEPFL2) gene as the best candidate of the cr locus. A 1 bp deletion in the first exon of McEPFL2 in Y1 which would result in a truncated McEPFL2 protein may be the causal polymorphism for the phenotypic difference between Y1 and Z-1-4. The association of this 1 bp deletion with CR was further supported by gDNA sequencing of McEPFL2 among 31 bitter gourd accessions. This work provides a foundation for understanding the genetic and molecular control of fruit epidermal pattering and development, which also facilitates marker-assisted selection in bitter melon breeding.

MC03g0810, an Important Candidate Gene Controlling Black Seed Coat Color in Bitter Gourd (Momordica spp.)

Seed coat color is one of the most intuitive phenotypes in bitter gourd (Momordica spp.). Although the inheritance of the seed coat color has been reported, the gene responsible for it is still unknown. This study used two sets of parents, representing, respectively, the intersubspecific and intraspecific materials of bitter gourd, and their respective F₁ and F₂ progenies for genetic analysis and primary mapping of the seed coat color. A large F_2:3 population comprising 2,975 seedlings from intraspecific hybridization was used to fine-map the seed coat color gene. The results inferred that a single gene, named McSC1, controlled the seed coat color and that the black color was dominant over the yellow color. The McSC1 locus was mapped to a region with a physical length of ∼7.8 Mb and 42.7 kb on pseudochromosome 3 via bulked segregant analysis with whole-genome resequencing (BSA-seq) and linkage analysis, respectively. Subsequently, the McSC1 locus was further fine-mapped to a 13.2-kb region containing only one candidate gene, MC03g0810, encoding a polyphenol oxidase (PPO). Additionally, the variations of MC03g0810 in the 89 bitter gourd germplasms showed a complete correlation with the seed coat color. Expression and PPO activity analyses showed a positive correlation between the expression level of MC03g0810 and its product PPO and the seed coat color. Therefore, MC03g0810 was proposed as the causal gene of McSC1. Our results provide an important reference for molecular marker-assisted breeding based on the seed coat color and uncover molecular mechanisms of the seed coat color formation in bitter gourd.

A critical review on cytogenetics of Cucurbitaceae with updates on Indian taxa

The cytogenetic relationships in the species of Cucurbitaceae are becoming immensely important to answer questions pertaining to genome evolution. Here, a simplified and updated data resource on cytogenetics of Cucurbitaceae is presented on the basis of foundational parameters (basic, zygotic and gametic chromosome numbers, ploidy, genome size, karyotype) and molecular cytogenetics. We have revised and collated our own findings on seven agriculturally important Indian cucurbit species in a comparative account with the globally published reports. Chromosome count (of around 19% species) shows nearly three-fold differences while genome size (of nearly 5% species) shows 5.84-fold differences across the species. There is no significant correlation between chromosome numbers and nuclear genome sizes. The possible trend of evolution is discussed here based on molecular cytogenetics data, especially the types and distribution of nucleolus organizer regions (NORs). The review supersedes the scopes of general chromosome databases and invites scopes for continuous updates. The offline resource serves as an exclusive toolkit for research and breeding communities across the globe and also opens scope for future establishment of web-database on Cucurbitaceae cytogenetics.

Cucurbitaceae genome evolution, gene function and molecular breeding

The Cucurbitaceae is one of the most genetically diverse plant families in the world. Many of them are important vegetables or medicinal plants and are widely distributed worldwide. The rapid development of sequencing technologies and bioinformatic algorithms has enabled the generation of genome sequences of numerous important Cucurbitaceae species. This has greatly facilitated research on gene identification, genome evolution, genetic variation and molecular breeding of cucurbit crops. So far, genome sequences of 18 different cucurbit species belonging to tribes Benincaseae, Cucurbiteae, Sicyoeae, Momordiceae and Siraitieae have been deciphered. This review summarizes the genome sequence information, evolutionary relationship, and functional genes associated with important agronomic traits (e.g., fruit quality). The progress of molecular breeding in cucurbit crops and prospects for future applications of Cucurbitaceae genome information are also discussed.

Genome-wide mining of potentially-hypervariable microsatellites and validation of markers in Momordica charantia L

Relatively large number of bitter melon microsatellite markers have been reported; however, only few resulted in successful PCR amplification and a small fraction shown polymorphisms. This limited chance of recovering polymorphic markers makes the primer screening a cost-demanding process. To test the hypothesis that microsatellites with longer motifs as well as shorter motifs repeated substantially shall have better prospects to be polymorphic, we performed a genome-wide microsatellite mining. We selected a sample of genome-wide microsatellites with prescribed motif lengths or satisfying a target repeat number, which were considered potentially-hyper variable, for primer designing and validation. Seventy five microsatellites satisfying these criteria were identified, of which 69 were validated through successful PCR amplification. Among them, 40 (53.33% of the markers identified) were polymorphic. This result showed a significantly higher success compared to our initial results of 51 (20.64%) polymorphic markers out of the 188 amplified when 247 previously reported markers were screened. The screening of two cultivars revealed that markers were efficient to identify up to three alleles. The characterization of these 69 new markers with 247 markers previously reported showed that di-nucleotide motifs were most abundant, followed by tri- and tetra-nucleotide motifs. TC motif markers were most polymorphic (12.08%) followed by AG and CT motifs (both 9.89%). Similarly, AGA (6.59%) and TATT (3.29%) were most polymorphic among the tri- and tetra-nucleotide motifs. These 69 hypervariable microsatellite markers along with 188 markers initially validated in this study shall be useful for phylogenetic analyses, studies of linkage, QTL, and association mapping in bitter melon.

The ecological, genetic and genomic architecture of local adaptation and population differentiation in Boechera stricta

Differential local adaptation restricts gene flow between populations inhabiting distinct environments, resulting in isolation by adaptation. In addition to the statistical inferences of genotype-environment associations, an integrative approach is needed to investigate the effect of local adaptation on population divergence at the ecological, genetic and genomic scale. Here, we combine reciprocal transplant, genome-environment association and QTL mapping to investigate local adaptation in Boechera stricta (Drummond's rockcress). With reciprocal transplant experiment, we found local genetic groups exhibit phenotypic characteristics corresponding to the distinct selection forces from different water availability. At the genetic level, the local allele of a major fitness QTL confers higher and sturdier flowering stalks, maximizing the fecundity fitness component under sufficient water supply, and its genetic variation is associated with precipitation across the landscape. At the genomewide scale, we further showed that multiple loci associated with precipitation are highly differentiated between genetic groups, suggesting that local adaptation has a widespread effect on reducing gene flow. This study provides one of the few comprehensive examples demonstrating how local adaptation facilitates population divergence at the trait, gene and genome level.

Building a cluster of NLR genes conferring resistance to pests and pathogens: the story of the Vat gene cluster in cucurbits

Most molecularly characterized plant resistance genes (R genes) belong to the nucleotide-binding-site-leucine-rich-repeat (NLR) receptor family and are prone to duplication and transposition with high sequence diversity. In this family, the Vat gene in melon is one of the few R genes known for conferring resistance to insect, i.e., Aphis gossypii, but it has been misassembled and/or mispredicted in the whole genomes of Cucurbits. We examined 14 genomic regions (about 400 kb) derived from long-read assemblies spanning Vat-related genes in Cucumis melo, Cucumis sativus, Citrullus lanatus, Benincasa hispida, Cucurbita argyrosperma, and Momordica charantia. We built the phylogeny of those genes. Investigating the paleohistory of the Vat gene cluster, we revealed a step by step process beginning from a common ancestry in cucurbits older than 50 my. We highlighted Vat exclusively in the Cucumis genera, which diverged about 20 my ago. We then focused on melon, evaluating a minimum duplication rate of Vat in 80 wild and cultivated melon lines using generalist primers; our results suggested that duplication started before melon domestication. The phylogeny of 44 Vat-CDS obtained from 21 melon lines revealed gain and loss of leucine-rich-repeat domains along diversification. Altogether, we revealed the high putative recognition scale offered in melon based on a combination of SNPs, number of leucine-rich-repeat domains within each homolog and number of homologs within each cluster that might jointly confer resistance to a large pest and pathogen spectrum. Based on our findings, we propose possible avenues for breeding programs.

Genetic analysis and QTL mapping of yield and fruit traits in bitter gourd (Momordica charantia L.)

Bitter gourd (Momordica charantia L.) is an economically important vegetable crop grown in tropical parts of the world. In this study, a high-density linkage map of M. charantia was constructed through genotyping-by-sequencing (GBS) technology using F2:3 mapping population generated from the cross DBGy-201 × Pusa Do Mausami. About 2013 high-quality SNPs were assigned on a total of 20 linkage groups (LGs) spanning over 2329.2 CM with an average genetic distance of 1.16 CM. QTL analysis was performed for six major yield-contributing traits such as fruit length, fruit diameter, fruit weight, fruit flesh thickness, number of fruits per plant and yield per plant. These six quantitative traits were mapped with 19 QTLs (9 QTLs with LOD > 3) using composite interval mapping (CIM). Among 19 QTLs, 12 QTLs derived from 'Pusa Do Mausami' revealed a negative additive effect when its allele increased trait score whereas 7 QTLs derived from 'DBGy-201' revealed a positive additive effect when its allele trait score increased. The phenotypic variation (R2%) elucidated by these QTLs ranged from 0.09% (fruit flesh thickness) on LG 14 to 32.65% (fruit diameter) on LG 16 and a total of six major QTLs detected. Most QTLs detected in the present study were located relatively very close, maybe due to the high correlation among the traits. This information will serve as a significant basis for marker-assisted selection and molecular breeding in bitter gourd crop improvement.

Quantitative Trait Loci Mapping for Earliness, Fruit, and Seed Related Traits Using High Density Genotyping-by-Sequencing-Based Genetic Map in Bitter Gourd (Momordica charantia L.)

Bitter gourd (Momordica charantia L.) is an important vegetable crop having numerous medicinal properties. Earliness and yield related traits are main aims of bitter gourd breeding program. High resolution quantitative trait loci (QTLs) mapping can help in understanding the molecular basis of phenotypic variation of these traits and thus facilitate marker-assisted breeding. The aim of present study was to identify genetic loci controlling earliness, fruit, and seed related traits. To achieve this, genotyping-by-sequencing (GBS) approach was used to genotype 101 individuals of F₄ population derived from a cross between an elite cultivar Punjab-14 and PAUBG-6. This population was phenotyped under net-house conditions for three years 2018, 2019, and 2021. The linkage map consisting of 15 linkage groups comprising 3,144 single nucleotide polymorphism (SNP) markers was used to detect the QTLs for nine traits. A total of 50 QTLs for these traits were detected which were distributed on 11 chromosomes. The QTLs explained 5.09-29.82% of the phenotypic variance. The highest logarithm of the odds (LOD) score for a single QTL was 8.68 and the lowest was 2.50. For the earliness related traits, a total of 22 QTLs were detected. For the fruit related traits, a total of 16 QTLs and for seed related traits, a total of 12 QTLs were detected. Out of 50 QTLs, 20 QTLs were considered as frequent QTLs (FQ-QTLs). The information generated in this study is very useful in the future for fine-mapping and marker-assisted selection for these traits in bitter gourd improvement program.

Review on the Development and Applications of Medicinal Plant Genomes

With the development of sequencing technology, the research on medicinal plants is no longer limited to the aspects of chemistry, pharmacology, and pharmacodynamics, but reveals them from the genetic level. As the price of next-generation sequencing technology becomes affordable, and the long-read sequencing technology is established, the medicinal plant genomes with large sizes have been sequenced and assembled more easily. Although the review of plant genomes has been reported several times, there is no review giving a systematic and comprehensive introduction about the development and application of medicinal plant genomes that have been reported until now. Here, we provide a historical perspective on the current situation of genomes in medicinal plant biology, highlight the use of the rapidly developing sequencing technologies, and conduct a comprehensive summary on how the genomes apply to solve the practical problems in medicinal plants, like genomics-assisted herb breeding, evolution history revelation, herbal synthetic biology study, and geoherbal research, which are important for effective utilization, rational use and sustainable protection of medicinal plants.

High-Density GBS-Based Genetic Linkage Map Construction and QTL Identification Associated With Yellow Mosaic Disease Resistance in Bitter Gourd (Momordica charantia L.)

Yellow mosaic disease (YMD) in bitter gourd (Momordica charantia) is a devastating disease that seriously affects its yield. Although there is currently no effective method to control the disease, breeding of resistant varieties is the most effective and economic option. Moreover, quantitative trait locus (QTL) associated with resistance to YMD has not yet been reported. With the objective of mapping YMD resistance in bitter gourd, the susceptible parent "Punjab-14" and the resistant parent "PAUBG-6" were crossed to obtain F₄ mapping population comprising 101 individuals. In the present study, the genotyping by sequencing (GBS) approach was used to develop the genetic linkage map. The map contained 3,144 single nucleotide polymorphism (SNP) markers, consisted of 15 linkage groups, and it spanned 2415.2 cM with an average marker distance of 0.7 cM. By adopting the artificial and field inoculation techniques, F_4:5 individuals were phenotyped for disease resistance in Nethouse (2019), Rainy (2019), and Spring season (2020). The QTL analysis using the genetic map and phenotyping data identified three QTLs qYMD.pau_3.1, qYMD.pau_4.1, and qYMD.pau_5.1 on chromosome 3, 4, and 5 respectively. Among these, qYMD.pau_3.1, qYMD.pau_4.1 QTLs were identified during the rainy season, explaining the 13.5 and 21.6% phenotypic variance respectively, whereas, during the spring season, qYMD.pau_4.1 and qYMD.pau_5.1 QTLs were observed with 17.5 and 22.1% phenotypic variance respectively. Only one QTL qYMD.pau_5.1 was identified for disease resistance under nethouse conditions with 15.6% phenotypic variance. To our knowledge, this is the first report on the identification of QTLs associated with YMD resistance in bitter gourd using SNP markers. The information generated in this study is very useful in the future for fine-mapping and marker-assisted selection for disease resistance.