Sorghum is an important crop widely used for food, feed, and fuel. Transcriptome-wide studies of 3′ untranslated regions (3′UTR) using regular RNA-seq remain scarce in sorghum, while transcriptomes have been characterized extensively using Illumina short-read sequencing platforms for many sorghum varieties under various conditions or developmental contexts. 3′UTR is a critical regulatory component of genes, controlling the translation, transport, and stability of messenger RNAs. In the present study, we profiled the alternative 3′UTRs at the transcriptome level in three genetically related but phenotypically contrasting lines of sorghum: Rio, BTx406, and R9188. A total of 1,197 transcripts with alternative 3′UTRs were detected using RNA-seq data. Their categorization identified 612 high-confidence alternative 3′UTRs. Importantly, the high-confidence alternative 3′UTR genes significantly overlapped with the genesets that are associated with RNA N⁶-methyladenosine (m⁶A) modification, suggesting a clear indication between alternative 3′UTR and m⁶A methylation in sorghum. Moreover, taking advantage of sorghum genetics, we provided evidence of genotype specificity of alternative 3′UTR usage. In summary, our work exemplifies a transcriptome-wide profiling of alternative 3′UTRs using regular RNA-seq data in non-model crops and gains insights into alternative 3′UTRs and their genotype specificity.

高粱是重要的农作物，广泛用于食品，饲料和燃料。高粱中对使用常规RNA-seq进行3'非翻译区（3'UTR）的转录组范围的研究仍然很少，而在不同条件或发展背景下，使用Illumina短读测序平台对许多高粱品种进行了广泛的转录组表征。3'UTR是基因的关键调控成分，控制信使RNA的翻译，转运和稳定性。在本研究中，我们在三种与遗传相关但在表型上相反的高粱品系：Rio，BTx406和R9188中，在转录组水平上分析了备选3'UTR。使用RNA-seq数据共检测到1,197个具有替代3'UTR的转录本。他们的分类确定了612个高可信度替代3'UTR。重要的，^6-甲基腺苷（m ⁶ A）修饰，表明在高粱中替代3'UTR和m ⁶ A甲基化之间有明确指示。此外，利用高粱遗传学，我们提供了替代3'UTR使用的基因型特异性的证据。总而言之，我们的工作使用非模型作物中的常规RNA-seq数据，举例说明了替代3'UTR的转录组范围内的谱分析，并深入了解了替代3'UTR及其基因型特异性。