Transcriptome based genetic resources from Rabbiteye and Southern Highbush blueberries

Abstract

BACKGROUND: Blueberry is among the fastest growing fruit crops in the world, which is beneficial to human health and attracts extensive interests. In contrast to its rapid development and utilization, availability of molecular and genetic resources for blueberries are still scarce. OBJECTIVE: In present report, transcriptomic profiling of four widely cultivated varieties of Rabbiteye and Southern Highbush blueberries were characterized to assist the breeding programs. METHODS: Both de novo and reference-based assembly were conducted to generate the genetic resources that can be used in the further functional and breeding studies. RESULTS: De novo and reference-based assembly found average 136,350 and 158,123 non-redundant transcripts, respectively. Average 57,668 de novo assembled transcripts can be functionally annotated by homology search with different databases. We further detected 6,268 polymorphic simple sequence repeats, 566,913 high-quality single nucleotide polymorphisms and 88,662 insertion and deletions among the four varieties with comparison to a recently released reference genome of blueberry. Differentially expressed genes analysis showed that varieties of same species show less differences within species but larger differences between species. CONCLUSIONS: These comprehensive and high-quality genetic resources will contribute to a wide range of genetics and molecular breeding studies in blueberries.