RNA-Seq 揭示了与红麻（Nee）高纤维品质相关的差异表达基因。

RNA-Seq Reveals Differentially Expressed Genes Associated with High Fiber Quality in Abaca ( Nee).

机构信息

Philippine Genome Center for Agriculture, University of the Philippines Los Baños, Laguna 4031, Philippines.

Plant Physiology Laboratory, Institute of Plant Breeding (IPB), College of Agriculture and Food Science, University of the Philippines Los Baños, Laguna 4031, Philippines.

出版信息

Genes (Basel). 2022 Mar 15;13(3):519. doi: 10.3390/genes13030519.

DOI:10.3390/genes13030519

PMID:35328071

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8953247/

Abstract

Despite the importance of and current demand for abaca ( Nee) fiber, there has been limited study that capitalizes on RNA-seq to identify candidate genes associated with high fiber quality and bunchy top virus (AbBTV) resistance. Three varieties (Abuab, Inosa, and Tangongon), one wild banana variety ( Colla) Pacol, and two developed backcrosses (Abuab × Pacol BC and BC) were grown at the Institute of Plant Breeding (IPB), Laguna, Philippines. The pseudostems of 3-month-old suckers of each genotype were sampled for RNA-seq. Datasets were analyzed for differential expression (DE) implementing various model frameworks, including pairwise, genotypic and non-DE models. Results indicate that Abuab and BC induce the highest proportion (70%) of abaca-specific genes. Gene ontology (GO) enrichment analysis showed several genes associated with cellulose synthase activity, callose synthase, ß-glucosidase activity, glucan biosynthetic process, etc. KEGG pathway analysis showed several genes encoding for enzymes involved in the lignin biosynthetic pathway. Analysis using genotypic DE (GDE) between abaca bunchy top virus (AbBTV)-resistant and -susceptible groups revealed genes such as pathogenesis-related protein and NBS-LRR. As the genotypes were not infected with the pathogen, these genes are yet to be confirmed for their roles in disease resistance and are an interesting subject for further investigation.

摘要

尽管蕉麻（Nee）纤维具有重要性和当前需求，但利用 RNA-seq 来鉴定与高纤维质量和束顶病毒（AbBTV）抗性相关的候选基因的研究有限。三种品种（Abuab、Inosa 和 Tangongon）、一种野生香蕉品种（Colla）Pacol 和两个开发的回交系（Abuab×Pacol BC 和 BC）在菲律宾拉古纳的植物育种研究所（IPB）种植。每个基因型 3 个月大的吸芽假茎被取样进行 RNA-seq。通过各种模型框架（包括成对、基因型和非 DE 模型）分析数据集以进行差异表达（DE）。结果表明，Abuab 和 BC 诱导了最高比例（70%）的蕉麻特异性基因。基因本体论（GO）富集分析显示了与纤维素合酶活性、几丁质合酶、ß-葡萄糖苷酶活性、葡聚糖生物合成过程等相关的几个基因。KEGG 途径分析显示了几个编码参与木质素生物合成途径的酶的基因。使用基因型差异表达（GDE）分析抗和易感蕉麻束顶病毒（AbBTV）的基因型之间的差异，发现了与病程相关蛋白和 NBS-LRR 相关的基因。由于这些基因型未感染病原体，这些基因的抗病作用仍有待证实，这是进一步研究的一个有趣课题。