Comparative RNA sequencing based transcriptome profiling of regular bearing and alternate bearing mango (Mangifera indica L.) varieties reveals novel insights into the regulatory mechanisms underlying alternate bearing.

OBJECTIVE: This study is to understand a comprehensive perspective on the molecular mechanisms underlying alternate bearing in mango (Mangifera indica L.) via transcriptome wide gene expression profiling of both regular and irregular mango varieties. RESULTS: Transcriptome data of regular (Neelam) and irregular (Dashehari) mango varieties revealed a total of 42,397 genes. Out of that 12,557 significantly differentially expressed genes were identified, of which 6453 were found to be up-regulated and 6104 were found to be down-regulated genes. Further, many of the common unigenes which were involved in hormonal regulation, metabolic processes, oxidative stress, ion homeostasis, alternate bearing etc. showed significant differences between these two different bearing habit varieties. Pathway analysis showed the highest numbers of differentially expressed genes were related with the metabolic processes (523). A total of 26 alternate bearing genes were identified and principally three genes viz; SPL-like gene (GBVX01015803.1), Rumani GA-20-oxidase-like gene (GBVX01019650.1) and LOC103420644 (GBVX01016070.1) were significantly differentially expressed (at log2FC and pval less than 0.05) while, only single gene (gbGBVW01004309.1) related with flowering was found to be differentially expressed. A total of 15 differentially expressed genes from three important pathways viz; alternate bearing, carbohydrate metabolism and hormone synthesis were validated using Real time PCR and results were at par with in silico analysis. CONCLUSIONS: Deciphering the differentially expressed genes (DEGs) and potential candidate genes associated with alternate bearing, hormone and carbohydrate metabolism pathways will help for illustrating the molecular mechanisms underlying the bearing tendencies in mango.

Edible coatings influence the cold-storage life and quality of 'Santa Rosa' plum (Prunus salicina Lindell).

Plum is a perishable fruit with a very short shelf life of 3-4 days. Several studies have suggested the possible use of edible coatings on maintaining quality and prolonging storage life of fresh horticultural produce. Hence, different edible coatings, namely, lac-based (2:3), Semperfresh™ (1:3) and Niprofresh® (1:5) were selected to observe their efficacy on quality retention of 'Santa Rosa' plums. The effects of these coatings on the physical, physiological and biochemical attributes were studied under cold storage conditions (2 ± 1 °C and 85-90% relative humidity). Our results revealed that all the coatings, especially the lac-based significantly reduced the weight loss and maintained higher firmness throughout the storage period. These surface coatings modified the respiration and ethylene rates of the plums and slowed down their metabolism as shown by the retention of texture of the tissue and delayed colour development. At the end of 35 days of cold storage, lac-based coating helped to retain nearly 55% higher fruit firmness and 21% higher antioxidant activity in fruits as compared to uncoated ones. However, the changes in total anthocyanin content were found to be suppressed by 13% in lac-based coated fruits. Overall, the results suggested that lac-based coating of plum fruits was most effective to extend the storage life of 'Santa Rosa' plums over other coatings and uncoated fruits under low temperature storage conditions.

Postharvest treatment of antioxidant reduces lenticel browning and improves cosmetic appeal of mango (Mangifera indica L.) fruits without impairing quality.

The present study reports the usefulness of ascorbic acid for reducing lenticels browning (LB) in mango, which impairs the cosmetic appeal and thereby the export. Postharvest dip treatment of ascorbic acid at different concentrations (100, 150 and 200 ppm) was given to four varieties of mango (Indian-'Dashehari', 'Langra'; Exotic-'Sensation', 'Eldon'). After treatment, fruits were stored at ambient conditions (35 ± 4 °C and 65 ± 5 % RH) for 10 days. At the end of storage period, observations were recorded on several parameters. Our results revealed that fruits of 'Langra' mango exhibited 100 % LB, followed by 'Dashehari' (52.8 %), 'Sensation' (42.9 %) and 'Eldon' (38.3 %). All concentrations of ascorbic acid reduced the LB to greater extent and improved the cosmetic appeal of fruits of all the varieties significantly over untreated fruits but the best results were obtained with 200 ppm concentration for LB (4.8, 1.6, 3.7, 3.2 %, respectively) and other attributes, non-significantly followed by 150 ppm concentration. All concentrations of ascorbic also reduced the activities of polyphenol oxidase, peroxidase and lipoxigenase enzymes, and also reduced respiration rate and ethylene evolution rate but without impairing eating quality attributes (soluble solids concentrates and total carotenoids). It can be concluded that postharvest dip application of ascorbic acid at 150 ppm reduced LB and improve face value without impairing fruit quality.

Mitigating postharvest quantitative and qualitative losses in mango fruits through the application of biocontrol agents: An in-vivo and in-vitro assessment.

Mango is a commercial fruit crop of India that suffers huge postharvest losses every year. The application of biocontrol agents (BCAs) bears a vast potential for managing the same, which is yet to be exploited to its fullest extent. Hence, studies were conducted for BCAs application of Debaryomyces hansenii, Bacillus subtilis and Pseudomonas fluorescens strains on mango fruit under in-vitro, in-vivo conditions to know the efficacy of these BCAs on the postharvest pathogen, shelf life and quality retention of mango fruit. The 'poisoned food technique' was attempted for in-vitro studies. For the in-vivo studies, fruit of the commercial cultivar 'Amrapali' were un-inoculated and pre-inoculated with major postharvest pathogens (anthracnose: Colletotrichum gloeosporioides and stem-end rot: Botryodiplodia theobromae) were treated with BCA, followed by ambient storage at (24 ± 4 °C, 75 ± 5 % RH). From the results, it has been observed that under in vitro studies, BCA Debaryomyces hansenii (Strain: KP006) and Bacillus subtilis (Strain: BJ0011) at the treatment level 108 CFU mL-1 while, the Pseudomonas fluorescens at 109 CFU mL-1 (Strain: BE0001) were significantly effective for pathogen inhibition. However, under the in vivo studies, the BCA Debaryomyces hansenii (Strain: KP006) at 108 CFU mL-1 treatment level was found to significantly reduce the pathogen's decay incidence while positively influencing the shelf life and biochemical (quality) attributes. This treatment increased the storage life of mango fruit by more than three days over control fruit. Therefore, BCA Debaryomyces hansenii (Strain: KP006) at 108 CFU mL-1 can be used to control the postharvest pathological loss of mango fruit without affecting its internal quality.

High resolution mapping of QTLs for fruit color and firmness in Amrapali/Sensation mango hybrids.

Introduction: Mango (Mangifera indica L.), acclaimed as the 'king of fruits' in the tropical world, has historical, religious, and economic values. It is grown commercially in more than 100 countries, and fresh mango world trade accounts for ~3,200 million US dollars for the year 2020. Mango is widely cultivated in sub-tropical and tropical regions of the world, with India, China, and Thailand being the top three producers. Mango fruit is adored for its taste, color, flavor, and aroma. Fruit color and firmness are important fruit quality traits for consumer acceptance, but their genetics is poorly understood. Methods: For mapping of fruit color and firmness, mango varieties Amrapali and Sensation, having contrasting fruit quality traits, were crossed for the development of a mapping population. Ninety-two bi-parental progenies obtained from this cross were used for the construction of a high-density linkage map and identification of QTLs. Genotyping was carried out using an 80K SNP chip array. Results and discussion: Initially, we constructed two high-density linkage maps based on the segregation of female and male parents. A female map with 3,213 SNPs and male map with 1,781 SNPs were distributed on 20 linkages groups covering map lengths of 2,844.39 and 2,684.22cM, respectively. Finally, the integrated map was constructed comprised of 4,361 SNP markers distributed on 20 linkage groups, which consisted of the chromosome haploid number in Mangifera indica (n =20). The integrated genetic map covered the entire genome of Mangifera indica cv. Dashehari, with a total genetic distance of 2,982.75 cM and an average distance between markers of 0.68 cM. The length of LGs varied from 85.78 to 218.28 cM, with a mean size of 149.14 cM. Phenotyping for fruit color and firmness traits was done for two consecutive seasons. We identified important consistent QTLs for 12 out of 20 traits, with integrated genetic linkages having significant LOD scores in at least one season. Important consistent QTLs for fruit peel color are located at Chr 3 and 18, and firmness on Chr 11 and 20. The QTLs mapped in this study would be useful in the marker-assisted breeding of mango for improved efficiency.

Amenability of an Agrobacterium tumefaciens-mediated shoot apical meristem-targeted in planta transformation strategy in Mango (Mangifera indica L.).

Mango (Mangifera indica L.) is one of the most popular tropical fruits in the world owing to its rich taste, flavor, color, production volume and diverse end usage. Conventional mango breeding practices are unable to withstand the demand for improved varieties as it is time consuming and requires heavy investment. However, problems associated with traditional plant breeding can be curtailed through genetic transformation. Nevertheless, major limitation of transgenic development has been its recalcitrant nature toward tissue culture practices involving latent microbial infection, phenol exudation, etc. This opens wide scope for tissue culture-independent in planta transformation approaches These strategies have proved to be easy to execute and cost effective in producing large number of transformants. One such apical meristem targeted in planta approach was successfully exploited to demonstrate its utility in transforming a tree species. Mango variety Amrapali was transformed with two visual marker gene vectors GFP::hptII in pCAMBIA1302 and GUS::nptII in pCAMBIA2301 individually, to demonstrate its amenability. Preliminary confirmations identified 65.0% of GFP and 57.14% of GUS plants to be transformed. Further, molecular characterization of these primary transformants demonstrated transgene integration at genomic and transcript level in some of the plants. This established protocol holds good for functional gene validation and knock in/out studies and aid in mango improvement programs.

Hydrocolloid edible coatings extend shelf life, reduce postharvest decay, and maintain keeping quality of mango fruits (Mangifera indica L.) under ambient storage.

Mango fruit exhibit high postharvest losses due to physiological, biochemical, and pathological deterioration during storage. Edible coatings such as hydrocolloids (HC) bear promising potential for fruit quality preservation at ambient storage due to its triple action (physiological, biochemical and pathological) on fruit and thus widely researched in recent years. This study demonstrates the influence of health and eco-safe hydrocolloid edible coatings such as "Carboxymethyl cellulose" (CMC) (1%), "Guar gum" (1.5%), "Gum Arabica" (10%), and "Xanthan gum" (0.3%) as dip treatment to enhance the postharvest quality and storage life of mangoes at ambient storage (25 ± 4°C and 65 ± 5% RH). "Xanthan gum" (0.3%) treatment exhibited the highest efficacy in reducing the decay loss by more than threefold and physiological loss by twofold over control fruit. It lowered the physiological and fruit softening enzyme activities (PG, PME, and LOX), while maintaining the biochemicals. Moreover, it maintained both internal as well as external (consumer preference) quality of fruit and extended 6 days shelf life on the physiological loss standard basis (≤10%) than that of the control. The results recommend the application of "Xanthan gum" (0.3%) as an efficacious ecological, sustainable, and health-friendly surface edible coating for quality preservation and storage period extension of mango fruit under ambient storage. PRACTICAL APPLICATIONS: The selected hydrocolloid edible coatings dip treatment showed promising potential in controlling the physiological, biochemical, and pathological deterioration of mango fruit stored under ambient condition. The selected treatments extended the shelf life without diminishing fruit quality. However, among the attempted HC treatments, the "Xanthan gum" (0.3%) (XG) coating displayed the excellent results. It added the storage life of mango fruit by 6 days over the control. XG treated fruit displayed the excellent results in terms of storage period extension, quality retention, consumer preference, and control over the fruit decay and softening enzymes activities. Postharvest preservation of mango fruit using HC is nonchemical, cost-effective approach which is GRAS (generally recognized as safe), health, and eco safe.

Assessing the genetic diversity of guava germplasm characterized by morpho-biochemical traits.

Amid environmental crises, a galloping population, and changing food habits, increasing fruit production with nutritional quality is a global challenge. To address this, there is a necessity to exploit the germplasm accessions in order to develop high-yielding varieties/hybrids with good adaptability and high quality fruit under changing environmental and biological conditions. In the study, a total of 33 morpho-biochemical traits enabled an assessment of the genetic variability, diversity, and structure in a collection of 28 diverse germplasm lines of guava. Results showed that highly significant genetic variability existed in the studied traits in the guava germplasm. The coefficient of variation values for the qualitative and quantitative traits varied from 23.5-72.36 to 1.39-58.62%, respectively. Germplasm Thai, Lucknow-49, Punjab Pink, Psidium friedrichsthalianum, and Shweta had the highest fruit weight (359.32 g), ascorbic acid content (197.27 mg/100 g fruit), total phenolic content (186.93 mg GAE/100 g), titratable acidity (0.69 percent), and antioxidant capacity (44.49 µmolTrolox/g), respectively. Fruit weight was positively correlated with ascorbic acid content; however, titratable acidity was negatively correlated with fruit weight. The principal component analysis (PCA) was 84.2% and 93.3% for qualitative and quantitative traits, respectively. Furthermore, K-mean clustering was executed; the population was grouped into three clusters for both traits. Additionally, the dendrogram using agglomerative hierarchical clustering (AHC), where all the germplasm were grouped into four clusters, revealed that among the clusters, clusters III and IV were highly divergent. The high variability, diversity, and structure could be utilized for the breeding programme of guava and also explored for molecular analysis using next-generation technology to enhance the guava yield and nutrition properties and also develop the climate resilient technology to fulfill the existing demand gap and nutrition availability, which could not only mitigate the nutrition requirement but also enhance the easy availability of fruits year-round.

MiSNPDb: a web-based genomic resources of tropical ecology fruit mango (Mangifera indica L.) for phylogeography and varietal differentiation.

Mango is one of the most important fruits of tropical ecological region of the world, well known for its nutritive value, aroma and taste. Its world production is >45MT worth >200 billion US dollars. Genomic resources are required for improvement in productivity and management of mango germplasm. There is no web-based genomic resources available for mango. Hence rapid and cost-effective high throughput putative marker discovery is required to develop such resources. RAD-based marker discovery can cater this urgent need till whole genome sequence of mango becomes available. Using a panel of 84 mango varieties, a total of 28.6 Gb data was generated by ddRAD-Seq approach on Illumina HiSeq 2000 platform. A total of 1.25 million SNPs were discovered. Phylogenetic tree using 749 common SNPs across these varieties revealed three major lineages which was compared with geographical locations. A web genomic resources MiSNPDb, available at http://webtom.cabgrid.res.in/mangosnps/ is based on 3-tier architecture, developed using PHP, MySQL and Javascript. This web genomic resources can be of immense use in the development of high density linkage map, QTL discovery, varietal differentiation, traceability, genome finishing and SNP chip development for future GWAS in genomic selection program. We report here world's first web-based genomic resources for genetic improvement and germplasm management of mango.

Leaf Transcriptome Sequencing for Identifying Genic-SSR Markers and SNP Heterozygosity in Crossbred Mango Variety 'Amrapali' (Mangifera indica L.).

Mango (Mangifera indica L.) is called "king of fruits" due to its sweetness, richness of taste, diversity, large production volume and a variety of end usage. Despite its huge economic importance genomic resources in mango are scarce and genetics of useful horticultural traits are poorly understood. Here we generated deep coverage leaf RNA sequence data for mango parental varieties 'Neelam', 'Dashehari' and their hybrid 'Amrapali' using next generation sequencing technologies. De-novo sequence assembly generated 27,528, 20,771 and 35,182 transcripts for the three genotypes, respectively. The transcripts were further assembled into a non-redundant set of 70,057 unigenes that were used for SSR and SNP identification and annotation. Total 5,465 SSR loci were identified in 4,912 unigenes with 288 type I SSR (n ≥ 20 bp). One hundred type I SSR markers were randomly selected of which 43 yielded PCR amplicons of expected size in the first round of validation and were designated as validated genic-SSR markers. Further, 22,306 SNPs were identified by aligning high quality sequence reads of the three mango varieties to the reference unigene set, revealing significantly enhanced SNP heterozygosity in the hybrid Amrapali. The present study on leaf RNA sequencing of mango varieties and their hybrid provides useful genomic resource for genetic improvement of mango.