Co-mapping studies of QTLs for fruit acidity and candidate genes of organic acid metabolism and proton transport in sweet melon (Cucumis melo L.)

Time-Series Transcriptome of Cucumis melo Reveals Extensive Transcriptomic Differences with Different Maturity

As the most important melon cultivar grown in the north-western provinces of China, Hami melon (Cucumis melo) produces large edible fruits that serve as an important dietary component in the world. In general, as a climacteric plant, melon harvested at 60% maturity results in a product with bad quality, while the highest-quality product can be guaranteed when harvesting at 90% maturity. In order to clarify the genetic basis of their distinct profiles of metabolite accumulation, we performed systematic transcriptome analyses between 60% and 90% maturity melons. A total of 36 samples were sequenced and over 1.7 billion reads were generated. Differentially expressed genes in 60% and 90% maturity melons were detected. Hundreds of these genes were functionally enriched in the sucrose and citric acid accumulation process of C. melo. We also detected a number of distinct splicing events between 60% and 90% maturity melons. Many genes associated with sucrose and citric acid accumulation displayed as differentially expressed or differentially spliced between different degrees of maturity of Hami melons, including CmCIN2, CmSPS2, CmBGAL3, and CmSPS2. These results demonstrate that the phenotype pattern differences between 60% and 90% maturity melons may be largely resulted from the significant transcriptome regulation.

Rootstock identity in melon-pumpkin graft combinations determines fruit metabolite profile

Grafting has the potential to improve melon fruit yield and quality, but it is currently held that a lack of compatibility between the rootstock and scion compromises such an effect. To throw light on this subject, we studied melon-pumpkin graft combinations with different levels of compatibility to assess to the effect of the rootstock identity on melon fruit yield and quality, including total fruit ortho-diphenols, total flavonoids, and primary fruit metabolites. Melon cv. 'Kiran' (Ki) was grafted onto three pumpkin rootstocks, 'TZ-148' (TZ), 'Shimshon' (Sh), and '53006' (r53), characterized by high, moderate, and low compatibility, respectively. The non-grafted melon cultivar Ki was used as the control. The incompatible combination Ki/r53 gave the lowest fruit yield and the lowest average fruit weight. In that combination, the content of total ortho-diphenols increased vs. Ki and Ki/TZ and that of total flavonoids decreased vs. Ki/Sh. In addition, concentrations of the amino acids, glutamate, methionine, valine, alanine, glycine, and serine, increased in the pulp of the two compatible combinations, i.e., Ki/TZ and Ki/Sh, suggesting that rootstock identity and compatibility with melon Ki scion modulated amino acid synthesis. Our results show an association between rootstock identity (and level of compatibility with the scion) and an enhancement of fruit nutritional values, i.e., high concentrations of organic acids (determined as citrate, malate, fumarate, and succinate) and soluble carbohydrates (sucrose) were recorded in the pulp of the two compatible combinations, i.e., Ki/TZ and Ki/Sh.

Transcriptome and Resequencing Analyses Provide Insight into Differences in Organic Acid Accumulation in Two Pear Varieties

Fruit acidity is one of the main determinants of fruit flavor and a target trait in fruit breeding. However, the genomic mechanisms governing acidity variation among different pear varieties remain poorly understood. In this study, two pear varieties with contrasting organic acid levels, ‘Dangshansuli’ (low-acidity) and ‘Amute’ (high-acidity), were selected, and a combination of transcriptome and population genomics analyses were applied to characterize their patterns of gene expression and genetic variation. Based on RNA-seq data analysis, differentially expressed genes (DEGs) involved in organic acid metabolism and accumulation were identified. Weighted correlation network analysis (WGCNA) revealed that nine candidate TCA (tricarboxylic acid)-related DEGs and three acid transporter-related DEGs were located in three key modules. The regulatory networks of the above candidate genes were also predicted. By integrating pear resequencing data, two domestication-related genes were found to be upregulated in ‘Amute’, and this trend was further validated for other pear varieties with high levels of organic acid, suggesting distinct selective sweeps during pear dissemination and domestication. Collectively, this study provides insight into organic acid differences related to expression divergence and domestication in two pear varieties, pinpointing several candidate genes for the genetic manipulation of acidity in pears.

Sensory, physicochemical and volatile compound analysis of short and long shelf-life melon (Cucumis melo L.) genotypes at harvest and after postharvest storage

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Maturity at harvest and after storage plus genotype impact melon fruit flavor.

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Volatiles increased in storage for all melon genotypes with esters being dominant.

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Short shelf-life melons associated with esters, sulphur compounds and a terpenoid.

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Long shelf-life melons related with green/grassy aroma/flavor, firmness, aldehydes.

Flavor is a key attribute defining melon fruit quality and driving consumer preferences. We characterized and compared fruit ripening patterns (ethylene, respiration), physicochemical properties (rind/flesh color, firmness, soluble solids, acidity), aroma volatiles, and flavor-related sensory attributes in seven melon genotypes differing in shelf life capacity. Fruits were evaluated at optimal maturity and after storage for six days at 5 °C plus one day at room temperature. Total volatile content increased after storage in all genotypes, with esters being dominant. Shorter shelf-life genotypes, displaying a sharper climacteric phase, correlated with fruity/floral/sweet flavor-related descriptors, and with esters, sulfur-containing compounds and a terpenoid. Longer shelf-life types were associated with firmness, green and grassy aroma/flavor and aldehydes. Multivariate regression identified key volatiles that predict flavor sensory perception, which could accelerate breeding of longer shelf-life melons with improved flavor characteristics.

Mapping the Flavor Contributing Traits on "Fengwei Melon" (Cucumis melo L.) Chromosomes Using Parent Resequencing and Super Bulked-Segregant Analysis

We used a next-generation high-throughput sequencing platform to resequence the Xinguowei and Shouxing melon cultivars, the parents of Fengwei melon. We found 84% of the reads (under a coverage rate of “13×”) placed on the reference genome DHL92. There were 2,550,000 single-nucleotide polymorphisms and 140,000 structural variations in the two genomes. We also identified 1,290 polymorphic genes between Xinguowei and Shouxing. We combined specific length amplified fragment sequencing (SLAF-seq) and bulked-segregant analysis (super-BSA) to analyze the two parents and the F₂ extreme phenotypes. This combined method yielded 12,438,270 reads, 46,087 SLAF tags, and 4,480 polymorphic markers (average depth of 161.81×). There were six sweet trait-related regions containing 13 differential SLAF markers, and 23 sour trait-related regions containing 48 differential SLAF markers. We further fine-mapped the sweet trait to the genomic regions on chromosomes 6, 10, 11, and 12. Correspondingly, we mapped the sour trait-related genomic regions to chromosomes 2, 3, 4, 5, 9, and 12. Finally, we positioned nine of the 61 differential markers in the sweet and sour trait candidate regions on the parental genome. These markers corresponded to one sweet and eight sour trait-related genes. Our study provides a basis for marker-assisted breeding of desirable sweet and sour traits in Fengwei melons.

Genomics-based strategies for the use of natural variation in the improvement of crop metabolism

Next-generation genomics holds great potential in the study of plant phenotypic variation. With several crop reference genomes now available, the affordable costs of de novo genome assembly or target resequencing offer the opportunity to mine the enormous amount of genetic diversity hidden in crop wild relatives. Wide introgressions from these wild ancestors species or land races represent a possible strategy to improve cultivated varieties. In this review, we discuss the mechanisms underlying metabolic diversity within plant species and the possible strategies (and barriers) to introgress novel metabolic traits into cultivated varieties. We show how deep genomic surveys uncover various types of structural variants from extended gene pools of major crops and highlight how this variation may be used for the improvement of crop metabolism.

Transcriptome profiling of Cucumis melo fruit development and ripening

Hami melon (Cucumis melo) is the most important melon crop grown in the north-western provinces of China. In order to elucidate the genetic and molecular basis of developmental changes related to size, flesh, sugar and sour content, we performed a transcriptome profiling of its fruit development. Over 155 000 000 clean reads were mapped to MELONOMICS genome, yielding a total of 23 299 expressed genes. Of these, 554 genes were specifically expressed in flowers, and 3260 genes in fruit flesh tissues. The 7892 differentially expressed genes (DEGs) were related to fruit development and mediated diverse metabolic processes and pathways; 83 DEGs and 13 DEGs were possibly associated with sucrose and citric acid accumulation, respectively. The quantitative real-time PCR results showed that six out of eight selected candidate genes displayed expression trends similar to our DEGs. This study profiled the gene expression related to different growing stages of flower and fruit at the whole transcriptome level to provide an insight into the regulatory mechanism underlying Hami melon fruit development.

Systems approach for exploring the intricate associations between sweetness, color and aroma in melon fruits

BACKGROUND

Melon (Cucumis melo) fruits exhibit phenotypic diversity in several key quality determinants such as taste, color and aroma. Sucrose, carotenoids and volatiles are recognized as the key compounds shaping the above corresponding traits yet the full network of biochemical events underlying their synthesis have not been comprehensively described. To delineate the cellular processes shaping fruit quality phenotypes, a population of recombinant inbred lines (RIL) was used as a source of phenotypic and genotypic variations. In parallel, ripe fruits were analyzed for both the quantified level of 77 metabolic traits directly associated with fruit quality and for RNA-seq based expression profiles generated for 27,000 unigenes. First, we explored inter-metabolite association patterns; then, we described metabolites versus gene association patterns; finally, we used the correlation-based associations for predicting uncharacterized synthesis pathways.

RESULTS

Based on metabolite versus metabolite and metabolite versus gene association patterns, we divided metabolites into two key groups: a group including ethylene and aroma determining volatiles whose accumulation patterns are correlated with the expression of genes involved in the glycolysis and TCA cycle pathways; and a group including sucrose and color determining carotenoids whose accumulation levels are correlated with the expression of genes associated with plastid formation.

CONCLUSIONS

The study integrates multiple processes into a genome scale perspective of cellular activity. This lays a foundation for deciphering the role of gene markers associated with the determination of fruit quality traits.

Construction of a high-density genetic map and QTLs mapping for sugars and acids in grape berries

BACKGROUND

QTLs controlling individual sugars and acids (fructose, glucose, malic acid and tartaric acid) in grape berries have not yet been identified. The present study aimed to construct a high-density, high-quality genetic map of a winemaking grape cross with a complex parentage (V. vinifera × V. amurensis) × ((V. labrusca × V. riparia) × V. vinifera), using next-generation restriction site-associated DNA sequencing, and then to identify loci related to phenotypic variability over three years.

RESULTS

In total, 1 826 SNP-based markers were developed. Of these, 621 markers were assembled into 19 linkage groups (LGs) for the maternal map, 696 for the paternal map, and 1 254 for the integrated map. Markers showed good linear agreement on most chromosomes between our genetic maps and the previously published V. vinifera reference sequence. However marker order was different in some chromosome regions, indicating both conservation and variation within the genome. Despite the identification of a range of QTLs controlling the traits of interest, these QTLs explained a relatively small percentage of the observed phenotypic variance. Although they exhibited a large degree of instability from year to year, QTLs were identified for all traits but tartaric acid and titratable acidity in the three years of the study; however only the QTLs for malic acid and β ratio (tartaric acid-to-malic acid ratio) were stable in two years. QTLs related to sugars were located within ten LGs (01, 02, 03, 04, 07, 09, 11, 14, 17, 18), and those related to acids within three LGs (06, 13, 18). Overlapping QTLs in LG14 were observed for fructose, glucose and total sugar. Malic acid, total acid and β ratio each had several QTLs in LG18, and malic acid also had a QTL in LG06. A set of 10 genes underlying these QTLs may be involved in determining the malic acid content of berries.

CONCLUSION

The genetic map constructed in this study is potentially a high-density, high-quality map, which could be used for QTL detection, genome comparison, and sequence assembly. It may also serve to broaden our understanding of the grape genome.

Coupled carbon, sulfur and nitrogen cycles of mixotrophic growth of Pseudomonas sp. C27 under denitrifying sulfide removal conditions

Pseudomonas sp. C27 is a facultative autotrophic bacterium (FAB) that can effectively conduct mixotrophic denitrifying sulfide removal (DSR) reactions using organic matters and sulfide as electron donors. Quantitative proteomics analysis of C27 using isobaric tag for relative and absolute quantitation (iTRAQ) and bioinformatics techniques identified 1916 unique proteins, based on which a novel pathway utilizing couple carbon, sulfide and nitrogen cycles for mixotrophic growth of C27. DSR experiments at different C/N ratios confirmed the presence of the new pathway. This novel pathway may be of great significance for C27-alike strains to conduct sulfide and nitrate removals in biological treatments.