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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Research Unit » Research » Publications at this Location » Publication #307210
Title: Next-Generation Sequencing of Elite Berry Germplasm and Data Analysis Using a Bioinformatics Pipeline for Virus Detection and Discovery

Author
item HO, THIEN - University Of Arkansas
item Martin, Robert
item TZANETAKIS, IOANNIS - University Of Arkansas

Submitted to: Methods in Molecular Biology
Publication Type: Book / Chapter
Publication Acceptance Date: 10/3/2014
Publication Date: 5/15/2015
Publication URL: http://10.1007/978-1-4939-2620-6_22
Citation: Ho, T., Martin, R.R., Tzanetakis, I.E. 2015. Next-Generation Sequencing of Elite Berry Germplasm and Data Analysis Using a Bioinformatics Pipeline for Virus Detection and Discovery. Methods in Molecular Biology. 1302:301-313.

Interpretive Summary: Berry crops (members of the genera Fragaria, Ribes, Rubus, Sambucus and Vaccinium) are known hosts for more than 70 viruses and new ones are identified frequently. In modern berry cultivars, viruses tend to be asymptomatic in single infections and symptoms only develop after plants accumulate multiple viruses. Most certification programs are based on visual observations. Infected, asymptomatic material may be propagated in the nursery system and shipped to farms where plants acquire additional viruses and develop symptoms. This practice may result in disease epidemics with great impact to growers and the natural ecosystem. In this chapter we present work that allows for the detection of both known and new viruses in elite germplasm, having the potential to greatly reduce virus dispersal associated with movement of plants for planting.

Technical Abstract: Berry crops (members of the genera Fragaria, Ribes, Rubus, Sambucus and Vaccinium) are known hosts for more than 70 viruses and new ones are identified frequently. In modern berry cultivars, viruses tend to be asymptomatic in single infections and symptoms only develop after plants accumulate multiple viruses. Most certification programs are based on visual observations. Infected, asymptomatic material may be propagated in the nursery system and shipped to farms where plants acquire additional viruses and develop symptoms. This practice may result in disease epidemics with great impact to growers and the natural ecosystem. In this chapter we present work that allows for the detection of both known and new viruses in elite germplasm, having the potential to greatly reduce virus dispersal associated with movement of plants for planting.