Induction and recovery of copy number variation in banana through gamma irradiation and low-coverage whole-genome sequencing.
Induction and recovery of copy number variation in banana through gamma irradiation and low-coverage whole-genome sequencing.
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DOI：
10.1111/pbi.12901
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发表时间：
2018-02-24
影响因子：
13.8
通讯作者：
Till BJ
中科院分区：
文献类型：
--
作者：
Datta S;Jankowicz-Cieslak J;Nielen S;Ingelbrecht I;Till BJ
传统的育种方法在香蕉中受到阻碍，因为主要栽培品种是不育的、单性结实的、三倍体的，因此是克隆繁殖的。这导致遗传基础狭窄，对生物和非生物压力的恢复能力有限。香蕉离体繁殖的诱变是引入新等位基因和扩大遗传多样性的一种方法。我们以前建立了一种方法，用于诱导和恢复由化学诱变剂EMS产生的单核苷酸突变。然而，官方发布的突变香蕉品种是使用伽马射线创造的，伽马射线是一种诱变剂，可以产生大的基因组插入和缺失（indels）。这种剂量突变对于在多倍体中产生可观察到的表型可能是重要的。在这项研究中，我们在三倍体香蕉中建立了一种低覆盖率的全基因组测序方法，以恢复由伽马辐照处理引起的大基因组插入缺失。我们首先评估了商业上发布的突变体品种'Novaria'，发现它含有多个预测的缺失，范围从0.3到3.8百万个碱基对（Mbp）。总的来说，预测的缺失跨越189个编码区。为了评估产生和维持新突变的可行性，我们开发了一种使用栽培品种'Williams'在卡文迪什香蕉中诱变和筛选拷贝数变异的管道。假定的突变在20戈伊处理的70%的株系和40戈伊处理的60%的株系中恢复。虽然缺失事件占主导地位，但在20戈伊处理的材料中发现了插入。基于这些结果，我们相信这种方法可以扩大规模，以支持大型育种项目。
Traditional 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.
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影响因子：
4.6
作者：
Casanova-Sáez R;Candela H;Micol JL
通讯作者：
Micol JL
DOI：
10.1073/pnas.0909218106
发表时间：
2009-12-08
影响因子：
11.1
作者：
Fulcher, Nick;Sablowski, Robert
通讯作者：
Sablowski, Robert
影响因子：
12.3
作者：
Kader, Tanjina;Goode, David L.;Gorringe, Kylie L.
通讯作者：
Gorringe, Kylie L.
影响因子：
3.3
作者：
Hribova, Eva;Holusova, Katerina;Vrana, Jan
通讯作者：
Vrana, Jan
影响因子：
64.8
作者：
D'Hont, Angelique;Denoeud, France;Wincker, Patrick
通讯作者：
Wincker, Patrick