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ARS Home » Southeast Area » Stoneville, Mississippi » Genomics and Bioinformatics Research » Research » Publications at this Location » Publication #354735

Research Project: Applied Agricultural Genomics and Bioinformatics Research

Location: Genomics and Bioinformatics Research

Title: RNA-Seq Analysis of Floral Bud Response to Freeze Treatments in Southern Highbush Blueberry CV. ‘O’Neal’

item REDPATH, LAUREN - North Carolina State University
item YOW, ASHLEY - North Carolina State University
item ARYAL, RISHI - North Carolina State University
item Hulse-Kemp, Amanda
item FRANKS, ROBERT - North Carolina State University
item WHETTEN, ROSS - North Carolina State University
item ASHRAFI, HAMID - North Carolina State University

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 5/17/2018
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: Blueberry production encompasses wide geographic and climatic ranges, spanning Canada to Mexico. Grown in warmer climates, southern highbush blueberries (SHB) are less cold tolerant and more precocious compared to northern highbush blueberries. The native germplasm of SHB have decreased cold hardiness and chill hour requirement. While these traits expand the seasonal window of blueberry production, SHB are also more suscpeitble spring frosts. Our objective is to determine differentially expressed genes involved in cold tolerance in relation to bud development and recovery from freeze events. Buds of a prominent cultivar in North Carolina, ‘O’Neal’ (SHB), were collected prior to and following budbreak, treated with either freezing (-12 °C) or nonfreezing (+4 °C) conditions, and recovered at +4 °C for varying durations (1-day and 1-week). RNA was extracted and mRNA-Seq libraries were paired-end sequenced. Reads were trimmed and aligned to a transcriptome assembly of ‘O’Neal’. A total of 180,487 contigs were functionally annotated with BLAST2GO (V5) software package. Bioconductor package DeSeq2 was implemented in Trinity (V2.5.1) to identify differentially expressed unigenes between tissue, freeze treatment, and recovery. DESeq2 identified 8,611 DEGs of which 2,482 (43%) had BLAST hits and 1,900 (33%) were annotated. DESeq2 (log2 fold change >|2|; p = 0.05) determined 1,913 DEGs related to tissue, 3,810 DEGs related to temperature, and 4,440 DEGs related to recovery. In a pairwise comparison of DEGs between treatments, there was greater upregulation in tissue post-budbreak compared to tissue prior to budbreak; freeze-treated buds had greater upregulation compared to non-freeze treated buds; and buds with 1-day recovery had greater upregulation compared to those with 1-week recovery. Understanding cold-related DEGs will aid in the development of a marker assisted breeding program for cold resistant high yielding blueberry selections.