Origin, Diversity and Genome Sequence of Mango (Mangifera indica L.)

Abstract

Mango (Mangifera indica L.) is known as the 'king of fruits' for its rich taste, flavor, color, production volume and diverse end usage. It belongs to plant family Anacardiaceae and has a small genome size of 439 Mb (2n = 40). Ancient literature indicates origin of cultivated mango in India. Although wild species of genus Mangifera are distributed throughout South and South-East Asia, recovery of Paleocene mango leaf fossils near Damalgiri, West Garo Hills, Meghalaya point to the origin of genus in peninsular India before joining of the Indian and Asian continental plates. India produces more than fifty percent of the world's mango and grows more than thousand varieties. Despite its huge economic significance genomic resources for mango are limited and genetics of useful horticultural traits are poorly understood. Here we present a brief account of our recent efforts to generate genomic resources for mango and its use in the analysis of genetic diversity and population structure of mango cultivars. Sequencing of leaf RNA from mango cultivars 'Neelam', 'Dashehari' and their hybrid 'Amrapali' revealed substantially higher level of heterozygosity in 'Amrapali' over its parents and helped develop genic simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. Sequencing of double digested restriction-site-associated genomic DNA (ddRAD) of 84 diverse mango cultivars identified 1.67 million high quality SNPs and two major sub-populations. We have assembled 323 Mb of the highly heterozygous 'Amrapali' genome using long sequence reads of PacBio single molecule real time (SMRT) sequencing chemistry and predicted 43,247 protein coding genes. We identified in the mango genome 122,332 SSR loci and developed 8,451 Type1 SSR and 835 HSSR markers for high level of polymorphism. Among the published genomes, mango showed highest similarity with sweet orange (Citrus sinensis). These genomic resources will fast track the mango varietal improvement for high productivity, disease resistance and superior end use quality.

Population genomic analysis of mango (Mangifera indica) suggests a complex history of domestication

“…One possibility for the observed differences in gene diversity between studies is that low sequence coverage and low tolerance for missing data at the interspecific level in the present study produced a dataset of highly conserved genomic regions, which are inherently less diverse (Huang & Knowles, ). As we progress toward a high‐quality sequence of the mango genome (Singh, ; D. Kuhn, pers. comm.)…”

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

“…Andhra Pradesh, Uttar Pradesh, Bihar, Karnataka, Maharashtra, West Bengal and Gujarat together contribute about 82% of the total mango production in India [ 4 ]. More than 1,000 varieties of mango exist in India today, which contribute 39.5% of the total fruit production in the country [ 5 – 6 ]. There are 25 major commercial cultivars of mango some of which are highly preferred in the International market.…”

De novo transcriptome assembly and annotation for gene discovery in avocado, macadamia and mango

“…However, this genome assembly comprises 79% of the estimated macadamia genome size 11,12 . A draft mango genome was published in 2016, although it is not yet be publicly available 13 . We believe that our de novo transcriptome assemblies derived from normalized RNA-Seq libraries are complimentary to these resources as they accentuate rare/low abundance transcripts.…”