中央研究院 資訊科學研究所

Selection of tissue culture-derived somaclonal variants of Giant Cavendish banana (Musa acuminata) by the Taiwan Banana Research Institute (TBRI) has resulted in several cultivars tolerant to Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), which is threatening global banana production. However, sequence variation in these somaclonal variants has not been characterized. We profiled the transcriptomes of three TBRI Foc TR4 tolerant cultivars: ‘Tai-Chiao No. 5’ (TC5), ‘Tai-Chiao No. 7’(TC7), and ‘Formosana’ (FM), and their susceptible progenitor ‘Pei-Chiao’ (PC) to investigate sequence variation among them and develop cultivar-specific markers. Compared to the PC transcriptome, the transcriptomes of TC5, TC7 and FM showed loss and alteration of heterozygosity in some chromosomal regions, which appeared to be the consequence of single-copy chromosomal deletions. Moreover, different tissues of a single TC7 plant displayed varying degrees of allele ratio in one of these regions, suggesting chimerism. A group of single nucleotide variants (SNVs) specific to one cultivar were recovered from the analysis of transcriptome data and validated by Sanger sequencing of DNA. Several SNVs were further converted into cleaved amplified polymorphic sequence (CAPS) or derived CAPS markers that could identify the three Foc TR4 tolerant cultivars among 13 Cavendish cultivars that were cultivated locally or worldwide. This work demonstrates that reliable SNV markers of tissue culture-derived and propagated banana cultivars of a triploid genome can be developed from transcriptome data. Moreover, analysis of sequence heterozygosity can uncover chromosomal deletions and chimerism in banana somaclonal variants.

Dr. Ho-Ming Chen is an Associate Research Fellow of the Agricultural Biotechnology Research Center, Academia Sinica. Dr. Chen received her Ph.D. in Molecular and Biological Agricultural Sciences from the Taiwan International Graduate Program provided by Academia Sinica and National Chung Hsing University in 2009 with emphasis on plant microRNA and small RNA data analysis. Her current research focuses on the discovery of post-transcriptional gene regulations in plant defense pathways for developing approaches for crop improvement. Her research interests also include applications of bioinformatics and next-generation sequencing technologies to diverse questions in RNA biology and plant translational research.