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Two Paralogous Genes Encoding Auxin Efflux Carrier Differentially Expressed in Bitter Gourd (Momordica charantia).

ABSTRACT: The phytohormone auxin regulates various developmental programs in plants, including cell growth, cell division and cell differentiation. The auxin efflux carriers are essential for the auxin transport. To show an involvement of auxin transporters in the coordination of fruit development in bitter gourd, a juicy fruit, we isolated novel cDNAs (referred as McPIN) encoding putative auxin efflux carriers, including McPIN1, McPIN2 (allele of McPIN1) and McPIN3, from developing fruits of bitter gourd. Both McPIN1 and McPIN3 genes possess six exons and five introns. Hydropathy analysis revealed that both polypeptides have two hydrophobic regions with five transmembrane segments and a predominantly hydrophilic core. Phylogenetic analyses revealed that McPIN1 shared the highest homology to the group of Arabidopsis, cucumber and tomato PIN1, while McPIN3 belonged to another group, including Arabidopsis and tomato PIN3 as well as PIN4. This suggests different roles for McPIN1 and McPIN3 in auxin transport involved in the fruit development of bitter gourd. Maximum mRNA levels for both genes were detected in staminate and pistillate flowers. McPIN1 is expressed in a particular period of early fruit development but McPIN3 continues to be expressed until the last stage of fruit ripening. Moreover, these two genes are auxin-inducible and qualified as early auxin-response genes. Their expression patterns suggest that these two auxin transporter genes play a pivotal role in fruit setting and development.

SUBMITTER: Li YL

PROVIDER: S-EPMC5713312 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Genome-Wide Analysis of Simple Sequence Repeats in Bitter Gourd (Momordica charantia).

Project description:Bitter gourd (Momordica charantia) is widely cultivated as a vegetable and medicinal herb in many Asian and African countries. After the sequencing of the cucumber (Cucumis sativus), watermelon (Citrullus lanatus), and melon (Cucumis melo) genomes, bitter gourd became the fourth cucurbit species whose whole genome was sequenced. However, a comprehensive analysis of simple sequence repeats (SSRs) in bitter gourd, including a comparison with the three aforementioned cucurbit species has not yet been published. Here, we identified a total of 188,091 and 167,160 SSR motifs in the genomes of the bitter gourd lines 'Dali-11' and 'OHB3-1,' respectively. Subsequently, the SSR content, motif lengths, and classified motif types were characterized for the bitter gourd genomes and compared among all the cucurbit genomes. Lastly, a large set of 138,727 unique in silico SSR primer pairs were designed for bitter gourd. Among these, 71 primers were selected, all of which successfully amplified SSRs from the two bitter gourd lines 'Dali-11' and 'K44'. To further examine the utilization of unique SSR primers, 21 SSR markers were used to genotype a collection of 211 bitter gourd lines from all over the world. A model-based clustering method and phylogenetic analysis indicated a clear separation among the geographic groups. The genomic SSR markers developed in this study have considerable potential value in advancing bitter gourd research.

| S-EPMC5479929 | biostudies-literature

Fluorimetric studies of the binding of Momordica charantia (bitter gourd) lectin with ligands.

Project description:The association constants for the binding of a series of ligands with a galactose-specific lectin from Momordica charantia (bitter gourd) has been determined through the ligand-induced quenching of protein fluorescence. Analysis of the iodide quenching suggested that there is a slight increase in the accessibility of tryptophan residues of the lectin on binding lactose.

| S-EPMC1162892 | biostudies-other

Mapping of the gynoecy in bitter gourd (Momordica charantia) using RAD-seq analysis.

Project description:Momordica charantia is a monoecious plant of the Cucurbitaceae family that has both male and female unisexual flowers. Its unique gynoecious line, OHB61-5, is essential as a maternal parent in the production of F1 cultivars. To identify the DNA markers for this gynoecy, a RAD-seq (restriction-associated DNA tag sequencing) analysis was employed to reveal genome-wide DNA polymorphisms and to genotype the F2 progeny from a cross between OHB61-5 and a monoecious line. Based on a RAD-seq analysis of F2 individuals, a linkage map was constructed using 552 co-dominant markers. In addition, after analyzing the pooled genomic DNA from monoecious or gynoecious F2 plants, several SNP loci that are genetically linked to gynoecy were identified. GTFL-1, the closest SNP locus to the putative gynoecious locus, was converted to a conventional DNA marker using invader assay technology, which is applicable to the marker-assisted selection of gynoecy in M. charantia breeding.

| S-EPMC3907450 | biostudies-literature

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

Project description:The genetic architecture of quantitative traits is determined by both Mendelian and polygenic factors, yet classic examples of plant domestication focused on selective sweep of newly mutated Mendelian genes. Here we report the chromosome-level genome assembly and the genomic investigation of a nonclassic domestication example, bitter gourd (Momordica charantia), an important Asian vegetable and medicinal plant of the family Cucurbitaceae. Population resequencing revealed the divergence between wild and South Asian cultivars about 6,000 y ago, followed by the separation of the Southeast Asian cultivars about 800 y ago, with the latter exhibiting more extreme trait divergence from wild progenitors and stronger signs of selection on fruit traits. Unlike some crops where the largest phenotypic changes and traces of selection happened between wild and cultivar groups, in bitter gourd large differences exist between two regional cultivar groups, likely reflecting the distinct consumer preferences in different countries. Despite breeding efforts toward increasing female flower proportion, a gynoecy locus exhibits complex patterns of balanced polymorphism among haplogroups, with potential signs of selective sweep within haplogroups likely reflecting artificial selection and introgression from cultivars back to wild accessions. Our study highlights the importance to investigate such nonclassic example of domestication showing signs of balancing selection and polygenic trait architecture in addition to classic selective sweep in Mendelian factors.

| S-EPMC7321978 | biostudies-literature

Analysis of the Complete Mitochondrial Genome of the Bitter Gourd (<i>Momordica charantia</i>).

Project description: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.

| S-EPMC10143269 | biostudies-literature

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

Project description: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.

| S-EPMC7893057 | biostudies-literature

Effect of seed hydro-priming durations on germination and seedling growth of bitter gourd (Momordica charantia).

Project description:The yield and quality of an annual crop are highly dependent on uniform and rapid germination of the seeds. In case of bitter gourd (Momordica charantia), the germination and field emergence is always a problem as seeds have thick and hard seed coat. Pre-sowing hydro-priming is one of the most suitable, affordable, easily available, and cost-effective techniques in breaking down seed dormancy to enhance germination. Hence, a field experiment was conducted in Surkhet district of Nepal 2020 to assess the effect of different hydro-priming duration on germination and seedling growth of bitter gourd. The experiment was laid out in single factor Randomized Complete Block Design (RCBD) with four replications and seven treatments including different hydro-priming durations (T0: control, T1: 6 hours, T2: 12 hours, T3: 18 hours, T4: 24 hours, T5: 36 hours and T6: 48 hours) of bitter gourd seeds of Palee variety, the most popular variety among the farmers. The highest water uptake and germination were found in 48 hours of seed hydro-primed seeds whereas the lowest water uptake and germination were observed on non-primed seeds. Similarly, the tallest seedling, most vigorous seedling in terms of seedling vigour index I and II was observed in 48 hours hydro-primed seeds followed by 36 hours of seed hydro-priming and shortest seedling and the least vigorous seedling in control. Thus 48 hours of seed hydro-priming was found to be effective for increasing germination and seedling growth in bitter gourd, which needs to be further investigated under large, open-field conditions with different varieties.

| S-EPMC8341585 | biostudies-literature

A RAD-Based Genetic Map for Anchoring Scaffold Sequences and Identifying QTLs in Bitter Gourd (Momordica charantia).

Project description:Genetic mapping is a basic tool necessary for anchoring assembled scaffold sequences and for identifying QTLs controlling important traits. Though bitter gourd (Momordica charantia) is both consumed and used as a medicinal, research on its genomics and genetic mapping is severely limited. Here, we report the construction of a restriction site associated DNA (RAD)-based genetic map for bitter gourd using an F2 mapping population comprising 423 individuals derived from two cultivated inbred lines, the gynoecious line 'K44' and the monoecious line 'Dali-11.' This map comprised 1,009 SNP markers and spanned a total genetic distance of 2,203.95 cM across the 11 linkage groups. It anchored a total of 113 assembled scaffolds that covered about 251.32 Mb (85.48%) of the 294.01 Mb assembled genome. In addition, three horticulturally important traits including sex expression, fruit epidermal structure, and immature fruit color were evaluated using a combination of qualitative and quantitative data. As a result, we identified three QTL/gene loci responsible for these traits in three environments. The QTL/gene gy/fffn/ffn, controlling sex expression involved in gynoecy, first female flower node, and female flower number was detected in the reported region. Particularly, two QTLs/genes, Fwa/Wr and w, were found to be responsible for fruit epidermal structure and white immature fruit color, respectively. This RAD-based genetic map promotes the assembly of the bitter gourd genome and the identified genetic loci will accelerate the cloning of relevant genes in the future.

| S-EPMC5906717 | biostudies-literature

Map-based cloning of the APRR2 gene controlling green stigma in bitter gourd (<i>Momordica charantia</i>).

Project description: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.

| S-EPMC10208069 | biostudies-literature

Development and validation of genome-wide InDel markers with high levels of polymorphism in bitter gourd (Momordica charantia).

Project description:BackgroundThe preferred choice for molecular marker development is identifying existing variation in populations through DNA sequencing. With the genome resources currently available for bitter gourd (Momordica charantia), it is now possible to detect genome-wide insertion-deletion (InDel) polymorphisms among bitter gourd populations, which guides the efficient development of InDel markers.ResultsHere, using bioinformatics technology, we detected 389,487 InDels from 61 Chinese bitter gourd accessions with an average density of approximately 1298 InDels/Mb. Then we developed a total of 2502 unique InDel primer pairs with a polymorphism information content (PIC) ≥0.6 distributed across the whole genome. Amplification of InDels in two bitter gourd lines '47-2-1-1-3' and '04-17,' indicated that the InDel markers were reliable and accurate. To highlight their utilization, the InDel markers were employed to construct a genetic map using 113 '47-2-1-1-3' × '04-17' F2 individuals. This InDel genetic map of bitter gourd consisted of 164 new InDel markers distributed on 15 linkage groups with a coverage of approximately half of the genome.ConclusionsThis is the first report on the development of genome-wide InDel markers for bitter gourd. The validation of the amplification and genetic map construction suggests that these unique InDel markers may enhance the efficiency of genetic studies and marker-assisted selection for bitter gourd.

| S-EPMC7968231 | biostudies-literature

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