Articles
Development of a robust RNA extraction protocol for black raspberry
Article number
1277_16
Pages
113 – 120
Language
English
Abstract
Black raspberry (Rubus occidentalis) is a US Pacific Northwest specialty crop prized for its unique flavor profile and nutritional attributes.
Market expansion depends on production, which is currently hindered by aphid-vectored viruses, such as Black raspberry necrosis virus. In order to enable dissection of genetic loci controlling aphid resistance, a reliable RNA extraction protocol was necessary to process leaf samples with a range of maturities.
We developed and optimized an RNA extraction protocol we refer to as the modified chloroform (MC) method for black raspberry intended for Pacific Biosciences Iso-Seq analysis.
Using this method, we were able to produce high quality RNA from mature leaves.
Going forward, we will use RNA for identification and fine mapping of quantitative trait loci (QTL) in the black raspberry genome that correlates with the aphid resistance phenotype.
Market expansion depends on production, which is currently hindered by aphid-vectored viruses, such as Black raspberry necrosis virus. In order to enable dissection of genetic loci controlling aphid resistance, a reliable RNA extraction protocol was necessary to process leaf samples with a range of maturities.
We developed and optimized an RNA extraction protocol we refer to as the modified chloroform (MC) method for black raspberry intended for Pacific Biosciences Iso-Seq analysis.
Using this method, we were able to produce high quality RNA from mature leaves.
Going forward, we will use RNA for identification and fine mapping of quantitative trait loci (QTL) in the black raspberry genome that correlates with the aphid resistance phenotype.
Authors
C. Mulch, N.V. Bassil, C.E. Finn, M. Dossett, K.J. Vining
Keywords
quantitative trait loci (QTL), Iso-Seq, aphid resistance, Rubus occidentalis
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