Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.
Mol Genet Genomics. 2019 Oct;294(5):1183-1197. doi: 10.1007/s00438-019-01571-x. Epub 2019 May 9.
Uniquely, oat, among cereals, accumulates an appreciable amount of oil in the endosperm together with starch. Oat is also recognized for its soluble fibers in the form of β-glucans. Despite high and increasing interest in oat yield and quality, the genetic and molecular understanding of oat grain development is still very limited. Transcription factors (TFs) are important regulatory components for plant development, product quality and yield. This study aimed to develop a workflow to determine seed tissue specificity of transcripts encoding transcription factors to reveal differential expression of potential importance for storage compound deposition and quality characters in oat. We created a workflow through the de novo assembly of sequenced seed endosperm and embryo, and publicly available oat seed RNAseq dataset, later followed by TF identification. RNAseq data were assembled into 33,878 transcripts with approximately 90% completeness. A total of 3875 putative TF encoding transcripts were identified from the oat hybrid assemblies. Members of the B3, bHLH, bZIP, C3H, ERF, NAC, MYB and WRKY families were the most abundant TF transcripts. A total of 514 transcripts which were differentially expressed between embryo and endosperm were identified with a threshold of 16-fold expression difference. Among those, 36 TF transcript homologs, belonging to 7 TF families, could be identified through similarity search in wheat embryo and endosperm EST libraries of NCBI Unigene database, and almost all the closest homologs were specifically expressed in seed when explored in WheatExp database. We verified our findings by cloning, sequencing and finally confirming differential expression of two TF encoding transcripts in oat seed embryo and endosperm. The developed workflow for identifying tissue-specific transcription factors allows further functional characterization of specific genes to increase our understanding of grain filling and quality.
与其他谷物不同，燕麦在胚乳中积累了大量的淀粉和油脂。燕麦还以其形式存在的可溶性纤维β-葡聚糖而闻名。尽管人们对燕麦的产量和质量越来越感兴趣，但对燕麦籽粒发育的遗传和分子认识仍然非常有限。转录因子（TFs）是植物发育、产品质量和产量的重要调控成分。本研究旨在开发一种工作流程，以确定编码转录因子的转录本在种子组织中的特异性，从而揭示对燕麦中贮藏化合物沉积和品质特征具有潜在重要意义的差异表达。我们通过对测序的种子胚乳和胚胎进行从头组装，以及公开的燕麦种子 RNAseq 数据集，后来又进行了 TF 鉴定，创建了一个工作流程。RNAseq 数据组装成 33878 个转录本，完整性约为 90%。从燕麦杂种组装中总共鉴定出 3875 个推测的 TF 编码转录本。B3、bHLH、bZIP、C3H、ERF、NAC、MYB 和 WRKY 家族的成员是最丰富的 TF 转录本。总共鉴定出 514 个在胚和胚乳之间差异表达的转录本，阈值为 16 倍表达差异。其中，通过在 NCBI Unigene 数据库的小麦胚和胚乳 EST 文库中进行相似性搜索，在 36 个 TF 转录本同源物中可以鉴定出属于 7 个 TF 家族的 36 个 TF 转录本同源物，并且当在 WheatExp 数据库中进行探索时，几乎所有最近的同源物都特异性地在种子中表达。我们通过克隆、测序并最终确认两个 TF 编码转录本在燕麦种子胚和胚乳中的差异表达来验证我们的发现。开发的用于鉴定组织特异性转录因子的工作流程允许对特定基因进行进一步的功能表征，以增加我们对谷物灌浆和品质的理解。
