No 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.

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.

-Genetic transformation of guava (Psidium guajavaL

No 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.

No abstract

In citrus, development of new hybrids is difficult due to failure of the germination of zygotic embryos. Hence, this study was conducted to standardize embryo age and media for maximizing the germination and subsequent seedling growth in sour orange × Sacaton citrumelo crosses followed by the identification of simple sequence repeats (SSR) markers for distinguishing the hybrids. A factorial experiment in complete randomized design was conducted with two each embryo age (110–120 and 130–140 days after pollination) and culture media (G‐B5 supplemented with 1.5 mg/L GA3 plus malt extract and G‐B5 plus malt extract) for in vitro embryo culture of sour orange × Sacaton citrumelo progenies. Older embryos germinated well in both media, though highest on M1 medium (100%). In fact, M1 medium gave higher plantlet survival in both age groups. The seedling growth of older embryos had highest root length (37.80 mm) and shoot length (24.20 mm) in M1 medium at 60 days after inoculation (DAI). Three SSR markers (TAA45, CAC15 and CAC39) showed polymorphism between female and male parents and were able to identify their hybrids.