De Novo Transcriptome Reconstruction of a Thermo-Sensitive Male Sterility Mutant in Rapeseed (Brassica napus; Brassicaceae)

Premise of the study: SP2S is a spontaneous thermo-sensitive genic male sterility (TGMS) mutation that facilitates two-line hybrid breeding in Brassica napus (Brassicaceae). De novo assembly of the floral bud transcriptome of SP2S can provide a foundation for deciphering the transcriptional regulati...

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Bibliographic Details
Published in:Applications in plant sciences 2017-12, Vol.5 (12), p.n/a
Main Authors: Liu, Xi-Qiong, Yu, Cheng-Yu, Dong, Jun-Gang, Xu, Ai-Xia, Hu, Sheng-Wu
Format: Article
Language:English
Subjects:
Abortion
Brassica napus
Brassicaceae
Cell cycle
Cell division
Gene expression
Gene regulation
Genes
Genetic engineering
GENOMIC RESOURCES ARTICLE
Male sterility
Metabolism
Mutation
Orthology
Plant sciences
RNA polymerase
RNA-seq
Simple sequence repeats
Software
thermo-sensitive genic male sterility
Transcription
transcriptome
Trinity
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Summary:Premise of the study: SP2S is a spontaneous thermo-sensitive genic male sterility (TGMS) mutation that facilitates two-line hybrid breeding in Brassica napus (Brassicaceae). De novo assembly of the floral bud transcriptome of SP2S can provide a foundation for deciphering the transcriptional regulation of SP2S in response to temperature change. Methods: mRNAs of the young floral buds of SP2S and its near-isogenic line SP2F grown under cool (16°C)/warm (22°C) conditions were sequenced on an Illumina Solexa platform, producing 239.7 million short reads with a total length of 19.95 Gbp. Results: The reads were assembled de novo using the Trinity program, resulting in 135,702 transcripts with an average length of 784 bp, an N50 value of 1221 bp, and a total length of 107 Mbp. We identified 24,157 cDNA-derived simple sequence repeats in the assembly. We found 137 and 195 single-nucleotide polymorphisms and 49 and 51 differentially regulated KEGG orthology groups when comparing sample SP2S at 22°C vs. SP2S at 16°C and sample SP2S at 22°C vs. SP2F at 22°C, respectively. Discussion: The numerous differentially expressed genes and the derived single-nucleotide polymorphisms show abnormal transcriptional regulation in the TGMS system. These results outline an intricate transcriptional regulation that occurred in the rapeseed TGMS SP2S when the temperature changed.
ISSN:2168-0450
2168-0450
DOI:10.3732/apps.1700077