Isolation and characterization of 10 SSR markers of Momordica charantia (Cucurbitaceae)

Metabolome Revealed the Potential Mechanism of Fusarium Wilt Resistance in Bitter Gourd (Momordica charantia) Based on Liquid Chromatography with Mass Spectrometry

Fusarium wilt fungus infection of bitter gourd, a major melon vegetable crop, results in massive yield reduction. Through extensive testing, some Fusarium wilt-resistant bitter melon varieties have been produced, but the molecular mechanism of their resistance to the fungus remains unknown. Importantly, after bitter melon plants are infected with Fusarium oxysporum f. sp. momordicae (FOM), apart from altering their gene expression levels, numerous metabolites are produced because of the interaction with the fungus. In the current study, an untargeted metabolomics analysis was performed to investigate the metabolic difference between resistant and susceptible bitter gourd varieties at various timepoints postinoculation with FOM based on liquid chromatography with mass spectrometry. A total of 1,595 positive ion mode and 922 negative ion mode metabolites were identified. Between the resistant and susceptible bitter gourd varieties, 213 unique differentially abundant metabolites (DAMs) were identified, and they were mainly enriched in the alpha-linolenic acid metabolism pathway. By comparing the postinoculation with preinoculation timepoints in the resistant and susceptible bitter gourd varieties, 93 and 159 DAMs were identified, respectively. These DAMs were mainly related to beta-alanine metabolism, among others. Multiple metabolites in the biosynthesis of the phenylpropanoid pathway showed greater variability in the susceptible than the resistant varieties, which may be related to senescence and mortality in the susceptible variety. These results provide new insights into the understanding of metabolite changes after FOM infection and a theoretical foundation for the elucidation of the bitter gourd disease resistance mechanism.

Genetic Diversity and Population Structure Analyses in Bitter Gourd (Momordica charantia L.) Based on Agro-Morphological and Microsatellite Markers

Bitter gourd (Momordica charantia L.) is an important vine crop of the Cucurbitaceae family and is well known for its high nutritional and medicinal values. However, the genetic variation remains largely unknown. Herein, 96 diverse bitter gourd genotypes were undertaken for diversity analysis using 10 quantitative traits, and 82 simple sequence repeat (SSR) markers. Out of 82 SSRs, 33 were polymorphic and the mean polymorphism information content (PIC) value was 0.38. Marker, JY-003 revealed a maximum (0.81) PIC value and, the number of alleles per locus ranged from 2 to 7 (average 3.46). The value of gene diversity showed the presence of a significant level of polymorphism among these genotypes. The unweighted pair group method (UPGMA) cluster analysis grouped the genotypes into two major clusters of which Cluster I comprised mostly small and medium-fruited genotypes of both M. charantia var. charantia and M. charantia var. muricata, whereas Cluster II included mostly long and extra-long fruited genotypes. Furthermore, these genotypes were divided into six distinct groups based on population structure analysis. The diversity analysis based on 10 quantitative traits revealed that earliness and high-yielding ability were exhibited by the predominantly gynoecious line DBGS-21-06 followed by DBGS-48-00. The principal component analysis (PCA) revealed that the first two components exhibited more than 50% of the total genetic variation. The present study deciphered a higher magnitude of agro-morphological and genetic diversity in 96 bitter gourd genotypes. Therefore, trait-specific genotypes identified in this study could be utilized in breeding programmes directed towards the development of improved cultivars and hybrids of bitter gourd.

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.

Analysis of Genetic Diversity and Population Structure in Bitter Gourd (Momordica charantia L.) Using Morphological and SSR Markers

The present investigation was carried out using 51 diverse bitter gourd accessions as material for studying genetic diversity and relatedness using morphological and SSR markers. A wide variation was observed for morphological traits like the number of days to the first female flower anthesis (37.33–60.67), the number of days to the first fruit harvest (47.67–72.00), the number of fruits/plant (12.00–46.67), fruit length (5.00–22.23 cm), fruit diameter (1.05–6.38 cm), average fruit weight (20.71–77.67 g) and yield per plant (513.3–1976 g). Cluster analysis for 10 quantitative traits grouped the 51 accessions into 6 clusters. Out of 61 SSR primers screened, 30 were polymorphic and highly informative as a means to differentiate these accessions. Based on genotyping, a high level of genetic diversity was observed, with a total of 99 alleles. The polymorphic information content (PIC) values ranged from 0.038 for marker BG_SSR-8 to 0.721 for S-24, with an average of 0.429. The numbers of alleles ranged from 2 to 5, with an average of 3.3 alleles per locus. Gene diversity ranged from 0.04 for BG_SSR-8 to 0.76 for S-24, showing a wide variation among 51 accessions. The UPGMA cluster analysis grouped these accessions into 3 major clusters. Cluster I comprised 4 small, fruited accessions that are commercially cultivated in central and eastern India. Cluster II comprised 35 medium- to long-sized fruited accessions, which made up an abundant and diverse group. Cluster III comprised 11 long and extra-long fruited accessions. The polymorphic SSR markers of the study will be highly useful in genetic fingerprinting and mapping, and for association analysis in Momordica regarding several economic traits.

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.

Phytochemistry, Pharmacological Activities, Toxicity and Clinical Application of Momordica cochinchinensis

Momordica cochinchinensis (Lour.) Spreng (M. cochinchinensis) is a deciduous vine that grows in Southeast Asia. It is known as gac in Vietnam and as Red Melon in English. Gac is reputed to be extremely benificial for health and has been widely used as food and folk medicine in Southeast Asia. In China, the seed of M. cochinchinensis (Chinese name: Mu biezi) is used as traditional Chinese medicine (TCM) for the treatment of various diseases. More than 60 chemical constituents have been isolated from M. cochinchinensis. Modern pharmacological studies and clinical practice demonstrate that some chemical constituents of M. cochinchinensis possess wide pharmacological activities, such as anti-tumor, anti-oxidation, anti-inflammatory, etc. This paper reviews the phytochemistry, pharmacological activities, toxicity, and clinical application of M. cochinchinensis, aiming to bring new insights into further research and application of this ancient herb.

Mapping and QTL Analysis of Gynoecy and Earliness in Bitter Gourd (Momordica charantia L.) Using Genotyping-by-Sequencing (GBS) Technology

A high-density, high-resolution genetic map was constructed for bitter gourd (Momordica charantia L.). A total of 2013 high quality SNP markers binned to 20 linkage groups (LG) spanning a cumulative distance of 2329.2 cM were developed. Each LG ranging from 185.2 cM (LG-12) to 46.2 cM (LG-17) and average LG span of 116.46 cM. The number of SNP markers mapped in each LG varied from 23 markers in LG-20 to 146 markers in LG-1 with an average of 100.65 SNPs per LG. The average distance between markers was 1.16 cM across 20 LGs and average distance between the markers ranged from 0.70 (LG-4) to 2.92 (LG-20). A total of 22 QTLs for four traits (gynoecy, sex ratio, node and days at first female flower appearance) were identified and mapped on 20 LGs. The gynoecious (gy-1) locus is flanked by markers TP_54865 and TP_54890 on LG 12 at a distance of 3.04 cM to TP_54890 and the major QTLs identified for the earliness traits will be extremely useful in marker development and MAS for rapid development of various gynoecious lines with different genetic background of best combiner for development of early and high yielding hybrids in bitter gourd.

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

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.

De Novo Assembly of Bitter Gourd Transcriptomes: Gene Expression and Sequence Variations in Gynoecious and Monoecious Lines

Bitter gourd (Momordica charantia L.) is a nutritious vegetable crop of Asian origin, used as a medicinal herb in Indian and Chinese traditional medicine. Molecular breeding in bitter gourd is in its infancy, due to limited molecular resources, particularly on functional markers for traits such as gynoecy. We performed de novo transcriptome sequencing of bitter gourd using Illumina next-generation sequencer, from root, flower buds, stem and leaf samples of gynoecious line (Gy323) and a monoecious line (DRAR1). A total of 65,540 transcripts for Gy323 and 61,490 for DRAR1 were obtained. Comparisons revealed SNP and SSR variations between these lines and, identification of gene classes. Based on available transcripts we identified 80 WRKY transcription factors, several reported in responses to biotic and abiotic stresses; 56 ARF genes which play a pivotal role in auxin-regulated gene expression and development. The data presented will be useful in both functions studies and breeding programs in bitter gourd.

Development of novel simple sequence repeat markers in bitter gourd (Momordica charantia L.) through enriched genomic libraries and their utilization in analysis of genetic diversity and cross-species transferability

Microsatellite or simple sequence repeat (SSR) markers are the preferred markers for genetic analyses of crop plants. The availability of a limited number of such markers in bitter gourd (Momordica charantia L.) necessitates the development and characterization of more SSR markers. These were developed from genomic libraries enriched for three dinucleotide, five trinucleotide, and two tetranucleotide core repeat motifs. Employing the strategy of polymerase chain reaction-based screening, the number of clones to be sequenced was reduced by 81 % and 93.7 % of the sequenced clones contained in microsatellite repeats. Unique primer-pairs were designed for 160 microsatellite loci, and amplicons of expected length were obtained for 151 loci (94.4 %). Evaluation of diversity in 54 bitter gourd accessions at 51 loci indicated that 20 % of the loci were polymorphic with the polymorphic information content values ranging from 0.13 to 0.77. Fifteen Indian varieties were clearly distinguished indicative of the usefulness of the developed markers. Markers at 40 loci (78.4 %) were transferable to six species, viz. Momordica cymbalaria, Momordica subangulata subsp. renigera, Momordica balsamina, Momordica dioca, Momordica cochinchinesis, and Momordica sahyadrica. The microsatellite markers reported will be useful in various genetic and molecular genetic studies in bitter gourd, a cucurbit of immense nutritive, medicinal, and economic importance.

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

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.