A System for Dosage-Based Functional Genomics in Poplar

Henry, Isabelle; Zinkgraf, Matthew S.; Groover, Andrew; Comai, Luca

doi:10.1105/tpc.15.00349

Cited by 79 publications

(101 citation statements)

References 74 publications

(79 reference statements)

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“…However, the predominance of SBS mutations over Indels does not necessarily reflect that more single nucleotide damages were produced than DSBs, because a large proportion of Indel mutations could be lethal or could not be passed down into their progeny due to somatic and haplontic competition (Prina et al, 2012). Henry et al (2015) failed to detect SBS mutations in the five poplar plants with relatively high sequencing depth (<14.5×). They attributed the non-finding of SBS mutation, which was different from previous reports on this subject, to the differences of materials used.…”

Section: Type Of γ Irradiation-induced Mutationsmentioning

confidence: 97%

“…Our analysis of their data also suggested that the non-finding is highly likely to be false negative due to the tremendous amount of heterozygous loci present in every poplar plant, which is estimated to be several orders of magnitude more than the number of mutations induced by γ irradiation. As direct evidence, they reported a 7% Indel mutation frequency in nonirradiated control plants (see Table 1 of Henry et al (2015)); seemingly such Indels are more likely to be from heterozygous sites rather than mutations generated spontaneously in a single generation.…”

Section: Type Of γ Irradiation-induced Mutationsmentioning

confidence: 97%

“…Recently, NGS techniques were also used to study the frequency and type of spontaneous (Ossowski et al, 2010) and induced mutations, i.e. fast neutron mutagenesis in Arabidopsis (Belfield et al, 2012), ethyl methanesulfonate in lotus (Mohd-Yusoff et al, 2015), and γ irradiation in poplar (Henry et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

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Frequency and type of inheritable mutations induced by γ rays in rice as revealed by whole genome sequencing

Zheng

Hairui

et al. 2016

J. Zhejiang Univ. Sci. B

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Mutation breeding is based on the induction of genetic variations; hence knowledge of the frequency and type of induced mutations is of paramount importance for the design and implementation of a mutation breeding program. Although γ ray irradiation has been widely used since the 1960s in the breeding of about 200 economically important plant species, molecular elucidation of its genetic effects has so far been achieved largely by analysis of target genes or genomic regions. In the present study, the whole genomes of six γ-irradiated M 2 rice plants were sequenced; a total of 144-188 million high-quality (Q>20) reads were generated for each M 2 plant, resulting in genome coverage of >45 times for each plant. Single base substitution (SBS) and short insertion/deletion (Indel) mutations were detected at the average frequency of 7.5×10 −6 -9.8×10 −6 in the six M 2 rice plants (SBS being about 4 times more frequent than Indels). Structural and copy number variations, though less frequent than SBS and Indel, were also identified and validated. The mutations were scattered in all genomic regions across 12 rice chromosomes without apparent hotspots. The present study is the first genome-wide single-nucleotide resolution study on the feature and frequency of γ irradiation-induced mutations in a seed propagated crop; the findings are of practical importance for mutation breeding of rice and other crop species.

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Section: Type Of γ Irradiation-induced Mutationsmentioning

confidence: 97%

Section: Type Of γ Irradiation-induced Mutationsmentioning

confidence: 97%

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Frequency and type of inheritable mutations induced by γ rays in rice as revealed by whole genome sequencing

Zheng

Hairui

et al. 2016

J. Zhejiang Univ. Sci. B

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“…For example, using exome capture sequencing in maize, Jia reported the recovery of a 6203‐bp deletion linked to opaque kernel phenotype (Jia et al ., ). In poplar, treatment of pollen with gamma irradiation resulted in indels varying between whole chromosomes to small fragments (Henry et al ., ). This work further showed that large genomic indels could be effectively recovered using low‐coverage whole‐genome sequencing (LC WGS), making mutation discovery more cost‐effective and data analyses more streamlined.…”

Section: Introductionmentioning

confidence: 99%

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

Datta

Jankowicz-Cieślak

Nielen

et al. 2018

Plant Biotechnology Journal

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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.

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“…Discovery of large genomic indels via sequencing may also prove more efficient as lower depth of coverage is needed for accurate variant calling compared to SNPs, and therefore more samples can be screened per run. This approach has been used to catalogue gamma-induced mutations created through irradiation of pollen from poplar (Henry et al 2015). Continued improvement in sequencing technologies suggests that cloning both SNP and large indel mutations will become more common in the near future.…”

Section: Cloning Mutant Alleles Causative For Improved Traitsmentioning

confidence: 99%

Mutagenesis for Crop Breeding and Functional Genomics

Jankowicz-Cieślak

Chikelu

Till

2016

Biotechnologies for Plant Mutation Breeding

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Genetic variation is a source of phenotypic diversity and is a major driver of evolutionary diversification. Heritable variation was observed and used thousands of years ago in the domestication of plants and animals. The mechanisms that govern the inheritance of traits were later described by Mendel. In the early decades of the twentieth century, scientists showed that the relatively slow rate of natural mutation could be increased by several orders of magnitude by treating Drosophila and cereals with X-rays. What is striking about these achievements is that they came in advance of experimental evidence that DNA is the heritable material. This highlights one major advantage of induced mutations for crop breeding: prior knowledge of genes or gene function is not required to successfully create plants with improved traits and to release new varieties. Indeed, mutation induction has been an important tool for crop breeding since the release of the first mutant variety of tobacco in the 1930s. In addition to plant mutation breeding, induced mutations have been used extensively for functional genomics in model organisms and crops. Novel reverse-genetic strategies, such as Targeting Induced Local Lesions IN Genomes (TILLING), are being used for the production of stable genetic stocks of mutant plant populations such as Arabidopsis, barley, soybean, tomato and wheat. These can be kept for many years and screened repeatedly for different traits. Robust and efficient methods are required for the seamless integration of induced mutations in breeding and functional genomics studies. This chapter provides an overview of the principles and methodologies that underpin the set of protocols and guidelines for the use of induced mutations to improve crops.

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A System for Dosage-Based Functional Genomics in Poplar

Cited by 79 publications

References 74 publications

Frequency and type of inheritable mutations induced by γ rays in rice as revealed by whole genome sequencing

Frequency and type of inheritable mutations induced by γ rays in rice as revealed by whole genome sequencing

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

Mutagenesis for Crop Breeding and Functional Genomics

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