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Title: Development of single nucleotide polymorphism (SNP) markers from the mango (Mangiferaindica) transcriptome for mapping and estimation of genetic diversity

Author
item Kuhn, David
item DILLON, NATALIE - Department Of Agriculture - Australia
item INNES, DAVID - Department Of Agriculture - Australia
item WU, LE-SHIN - National Center For Genome Research
item MOCKAITIS, KEITHANNE - Indiana University

Submitted to: Acta Horticulturae
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/14/2015
Publication Date: 7/11/2016
Citation: Kuhn, D.N., Dillon, N.L., Innes, D.J., Wu, L., Mockaitis, K. 2016. Development of single nucleotide polymorphism (SNP) markers from the mango (Mangiferaindica) transcriptome for mapping and estimation of genetic diversity. Acta Hortic. 1111, 315-322 DOI: 10.17660/ActaHortic.2016.1111.45.http://dx.doi.org/10.17660/ActaHortic.2016.1111.45

Interpretive Summary: Mango (Mangifera indica) is an economically important tree fruit crop grown in the tropics and subtropics. India is the largest producer, Mexico is the largest exporter, and the United States is the largest importer of mango. Commercial mangos originated in Southeast Asia, and mango was only brought to Florida, US, in the late 19th century. However, 'Tommy Atkins', a selection of a 'Haden' cross in Florida, is an important part of the worldwide mango trade. Creating new mango cultivars with improved flavor, nutriceuticals, shelf life and marketability is the goal of breeding programs in Australia, Brazil, China, India, Indonesia, Israel, Mexico, Pakistan and Thailand, among others. A better understanding of the genetic diversity of germplasm available for breeding, and a genetic map to allow marker assisted selection, are needed to support these breeding programs. We have identified ~400,000 single-nucleotide polymorphism (SNP) markers for mango. We have designed assays for 960 of these SNPs. Results of SNP genotyping of mapping populations and germplasm collections are important to scientists and breeders worldwide and will lead to the identification of new, improved cultivars of mango for distribution to growers.

Technical Abstract: The development of resources for genomic studies in Mangifera indica (mango) will allow marker-assisted selection and identification of genetically diverse germplasm, greatly aiding mango breeding programs. We report here a first step in developing such resources, our identification of thousands unambiguous molecular markers that can be easily assayed across genotypes of the species. With origin centered in Southeast Asia, mangos are grown throughout the tropics and subtropics as a nutritious fruit that exhibits remarkable intraspecific phenotypic diversity. With the goal of building a high density genetic map, we have undertaken discovery of sequence variation in expressed genes across a broad range of mango cultivars. A transcriptome sequence reference was built de novo from extensive sequencing and assembly of RNA from cultivar 'Tommy Atkins'. Single nucleotide polymorphisms (SNPs) in protein coding transcripts were determined from alignment of RNA reads from 24 mango cultivars of diverse origins: 'Amin Abrahimpur' (India), 'Aroemanis' (Indonesia), 'Burma' (Burma), 'CAC' (Hawaii), 'Duncan' (Florida), 'Edward' (Florida), 'Everbearing' (Florida), 'Gary' (Florida), 'Hodson' (Florida), 'Itamaraca' (Brazil), 'Jakarata' (Florida), 'Long' (Jamaica), 'M. Casturi Purple' (Borneo), 'Malindi' (Kenya), 'Mulgoba' (India), 'Neelum' (India), 'Peach' (unknown), 'Prieto' (Cuba), 'Sandersha' (India), 'Tete Nene' (Puerto Rico), 'Thai Everbearing' (Thailand), 'Toledo' (Cuba), 'Tommy Atkins' (Florida) and 'Turpentine' (West Indies). SNPs in a selected subset of protein coding transcripts are currently being converted into Fluidigm assays for genotyping of mapping populations and germplasm collections. Using an alternate approach, SNPs (144) discovered by sequencing of candidate genes in 'Kensington Pride' have already been converted and used for genotyping.