Induction and recovery of copy number variation in banana through gamma irradiation and low‐coverage whole‐genome sequencing

Abstract

SummaryTraditional breeding methods are hindered in bananas due to the fact that major cultivars are sterile, parthenocarpic, triploid and thus clonally propagated. This has resulted in a narrow genetic base and limited resilience to biotic and abiotic stresses. Mutagenesis of in vitro propagated bananas is one method to introduce novel alleles and broaden genetic diversity. We previously established a method for the induction and recovery of single nucleotide mutations generated with the chemical mutagen EMS. However, officially released mutant banana varieties have been created using gamma rays, a mutagen that can produce large genomic insertions and deletions (indels). Such dosage mutations may be important for generating observable phenotypes in polyploids. In this study, we establish a low‐coverage whole‐genome sequencing approach in triploid bananas to recover large genomic indels caused by treatment with gamma irradiation. We first evaluated the commercially released mutant cultivar ‘Novaria’ and found that it harbours multiple predicted deletions, ranging from 0.3 to 3.8 million base pairs (Mbp). In total, predicted deletions span 189 coding regions. To evaluate the feasibility of generating and maintaining new mutations, we developed a pipeline for mutagenesis and screening for copy number variation in Cavendish bananas using the cultivar ‘Williams’. Putative mutations were recovered in 70% of lines treated with 20 Gy and 60% of the lines treated with 40 Gy. While deletion events predominate, insertions were identified in 20 Gy‐treated material. Based on these results, we believe this approach can be scaled up to support large breeding projects.

Comparison and Characterization of Mutations Induced by Gamma-Ray and Carbon-Ion Irradiation in Rice (Oryza sativaL.) Using Whole-Genome Resequencing

“…Complex SVs have also been detected in Arabidopsis and rice mutants irradiated by heavy ions and fast neutrons (which are also regarded as high-LET radiation), respectively (Li et al 2016a; Kazama et al 2017) . In contrast, the complex SVs have not been detected in gamma ray-irradiated mutants either in the present study or in previous studies (Naito et al 2005; Morita et al 2009; Henry et al 2015; Datta et al 2018; Li et al 2019). Furthermore, the SVs induced by Ar-ion irradiation have been reported to be more complex than those induced by C-ion irradiation (Kazama et al 2017).…”

Genetic Variability Induced by Gamma Rays and Preliminary Results of Low-Cost TILLING on M2 Generation of Chickpea (Cicer arietinum L.)

“…It remains possible that our population harbors more large variation that cannot be observed by low-cost TILLING. A low-coverage whole genome sequencing approach (LCWGS) can be applied to discover and catalog such variation in plants ( Henry et al, 2015 ; Datta et al, 2018 ). As sequencing prices drop, this approach becomes feasible for more laboratories.…”

DNA Copy Number Variations as Markers of Mutagenic Impact

“…Officially released mutant banana varieties were created using gamma rays. In the study by Datta et al a low-coverage whole-genome sequencing approach was applied in bananas to recover copy number caused by treatment with gamma irradiation [77]. The genome of commercially released mutant cultivar ‘Novaria’ contains multiple predicted large deletions, ranging from 0.3 to 3.8 Mbp spanning 189 coding regions.…”