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ARS Home » Midwest Area » Madison, Wisconsin » Vegetable Crops Research » Research » Publications at this Location » Publication #322701

Research Project: Genetic Enhancement of Allium, Cucumis, and Daucus Germplasm

Location: Vegetable Crops Research

Title: Single nucleotide polymorphisms and indel markers from the transcriptome of garlic

Author
item Havey, Michael
item AHN, YUL-KYUN - National Institute Of Horticultural & Herbal Science (NIHHS)

Submitted to: Journal of the American Society for Horticultural Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/30/2015
Publication Date: 1/5/2016
Publication URL: http://handle.nal.usda.gov/10113/61989
Citation: Havey, M.J., Ahn, Y. 2016. Single nucleotide polymorphisms and indel markers from the transcriptome of garlic. Journal of the American Society for Horticultural Science. 141(1):62-65.

Interpretive Summary: Garlic is cultivated world-wide and widely appreciated for its culinary uses. In spite of primarily being asexually propagated, garlic shows great diversity for adaptation to diverse production environments and bulb phenotypes. In this study, we undertook transcriptome sequencing from a single garlic plant in order to identify molecular markers in expressed regions of the garlic genome. Garlic sequences were assembled and selected if they were similar to monomorphic sequences from a doubled haploid of onion. Single nucleotide polymorphisms and insertion-deletion (indel) events were identified in 4,355 independent garlic assemblies. A sample of the indels was verified using the original cDNA library and genomics DNAs from diverse garlics, and segregation confirmed using sexual progenies of garlic. These molecular markers from the garlic transcriptome should be useful for garlic germplasm curators, researchers, and producers for estimation of genetic diversity, identification and removal of duplicate accessions from germplasm collections, and the development of a detailed genetic map of this important vegetable crop.

Technical Abstract: Garlic (Allium sativum L.) is cultivated world-wide and widely appreciated for its culinary uses. In spite of primarily being asexually propagated, garlic shows great diversity for adaptation to diverse production environments and bulb phenotypes. Anonymous molecular markers have been used to assess the genetic diversity among garlics. In this study, we undertook transcriptome sequencing from a single garlic plant in order to identify molecular markers in expressed regions of the garlic genome. Garlic sequences were assembled and selected if they were similar to monomorphic sequences from a doubled haploid of onion. Single nucleotide polymorphisms and insertion-deletion (indel) events were identified in 4,355 independent garlic assemblies. A sample of the indels was verified using the original cDNA library and genomics DNAs from diverse garlics, and segregation confirmed by sexual progenies of garlic. These molecular markers from the garlic transcriptome should be useful for estimates of genetic diversity, identification and removal of duplicate accessions from germplasm collections, and the development of a detailed genetic map of this important vegetable crop.