Transcriptomic sequence variation analysis reveals unique markers, chromosomal deletions, and chimerism in tissue culture-derived fusarium wilt tropical race 4 tolerant cultivars of Giant Cavendish banana

Selection of tissue culture-derived variants of Giant Cavendish banana (Musa acuminata) by the Taiwan Banana Research Institute (TBRI) has resulted in several cultivars tolerant to fusarium wilt tropical race 4, which is threatening global banana production. However, sequence variation in these tissue culture-derived and propagated somaclonal variants has not been characterized, thus hampering the development of molecular markers. To address this issue we profiled the transcriptomes of two tolerant somaclonal variants, Tai-Chiao No. 5 (TC5) and Tai-Chiao No. 7 (TC7), and their susceptible progenitor Pei-Chiao (PC) to investigate sequence variation among them and develop markers of high specificity.Transcriptome-wide analysis of sequence variants indicates a highly heterozygous triploid genome for the three cultivars. Compared to the PC transcriptome, the TC5 and TC7 transcriptomes showed loss and alteration of heterozygosity in some chromosomal regions, which appeared to be the consequence of single-copy chromosomal deletions. Nevertheless, the loss of heterozygosity was not universally detected in every TC7 sample and tissue we assayed. Even different tissues derived from a single TC7 plant displayed varied degrees of allele ratio at the same site, suggesting chimerism. A group of single nucleotide variants (SNVs) specific to TC5 or TC7 were recovered from the analysis of transcriptome data and validated by Sanger sequencing of DNA from independent samples. Several SNVs were further converted into cleaved amplified polymorphic sequence (CAPS) or derived CAPS markers that could identify TC5 and TC7 among 13 Cavendish cultivars that were collected locally and 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 variation can uncover chromosomal deletions and chimerism in banana somaclonal variants. The approaches used in this study could also be applicable to somaclonal variants of other banana cultivars or vegetatively propagated crops which will yield tools and knowledge useful for protection of plant breeders rights and germplasm management.