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

Abstract

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.

Comparative analysis of the complete plastid genomes of Mangifera species and gene transfer between plastid and mitochondrial genomes

“…Mango is a tall, evergreen tree belonging to the genus Mangifera of the Anacardiaceae family. It is an important tropical fruit ( Iquebal et al, 2017 ; Lora & Hormaza, 2018 ) that originates in tropical and subtropical regions in Southeast Asia ( Dutta et al, 2013 ; Sherman et al, 2015 ). Owing to its wide range of cultivation ( Bajpai et al, 2016 ), high nutrient value, pleasing appearance, and unique flavor ( Surapaneni et al, 2013 ), it is widely loved by consumers and has the reputation of being known as the “King of Tropical Fruits” ( Khan, Ali & Khan, 2015 ).…”

Cyanide produced with ethylene by ACS and its incomplete detoxification by β-CAS in mango inflorescence leads to malformation

“…Mk, Rk and Ln cultivars showed different flowering (December to January) and fruit maturity (May to July) time 91 . These cultivars are diversely related each other in a study on nucleotide polymorphisms (SNPs) 92 . The genetic background of these cultivars described earlier showed that Rk cultivar grouped in phylogenetic cluster 5 of structure sub-population I, while Ln and Mk cultivars are grouped in phylogenetic cluster 7 of structure sub-population II 93 .…”

Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops

“…One way to reduce the complexity in GBS is RAD-Seq (restriction-site associated DNA sequencing). Using this technique, 1.25 million SNPs were discovered in a panel of 84 mango varieties and used for development of the genomic resource MiSNPDb [ 21 ]. SNPs are also commonly mined from expressed sequence tag (EST) or transcriptome gene sequences.…”