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AUTHORS

ABSTRACT

We applied Ethyl methanesulphonate (EMS) to diploid potato by two different mutagenic treatments and screened the resulting populations for novel mutations using high- resolution melting (HRM) analysis. A pollen-treatment with EMS dissolved in a sucrose solution induced mutations at a low frequency. In planta selection of the most vital mutagenized pollen seems to have lowered the mutation density to a frequency that is not suitable for reverse genetics studies. The EMS seed-treatment on the other hand provided a high density of novel mutations. In contrast to most EMS mutagenesis studies, we directly screened the M1 generation of the seed-treated population. The high mutation density of

1/65 kb we found in the seed-treated population makes screening of the M1 generation an

attractive system for obtaining mutations. A large spectrum of 65 novel alleles for six candidate genes involved in starch metabolism was identified in the M1 population. For all

six genes, missense mutations that are predicted to damage protein function were

discovered and for four genes premature stop codon mutations were identified. Genetically stable M2 and M3 plants have been generated for 10 of the most interesting mutations (37%

of the original mutations). The estimated mutation density of M1 mutations that are

transferable to the M2 generation (one “accessible” mutation/118-176 kb) is higher than the

mutation density obtained by M2 screening studies of most other plant species (KUROWSKA

et al. 2011). The results thus demonstrate that M1 screening offers a practical alternative to

the commonly applied M2 screening for the rapid generation of novel genetic variation at a

high density, without too many complications in recovering mutations in the M2

generation.

INTRODUCTION

Commercial potato plants are autotetraploid cultivars resistant to inbreeding and with high levels of heterozygosity and nucleotide diversity (see previous Chapters). Alleles identified by analyzing the natural variation present in a genepool of tetraploid potatoes have been filtered by (natural) selection. Although mutant alleles accumulate in polyploid populations more quickly than in diploids (OTTO 2007) and potato has a high genetic load (VAN ECK et al. 1994),

spontaneous knockout or reduction-of-function mutations are expected to be relatively rare. Chemical mutagenesis with agents such as ethyl methanesulphonate (EMS) is a rapid cost- effective method for generating this kind of new genetic variation and can be used to unravel biological processes and for the alteration of agronomic traits. EMS treatment predominantly induces C-to-T and G-to-A DNA transitions randomly throughout the genome (SEGA 1984). It results in high point mutation densities with only low levels of chromosome breaks that for example cause aneuploidy, reduced fertility, and dominant lethality in atomic bomb and X- Ray irradiation (MOH 1950). In contrast to insertional mutagenesis like T-DNA or

transposon/retrotransposon tagging that generate mostly knockouts, chemical mutagens like EMS can induce a series of alleles for a targeted locus. In addition to loss-of-function alleles, it generates alleles with reduced, enhanced or even novel gene function and thus can provide a range of alternative phenotypes (ALONSO and ECKER 2006). Furthermore, as chemical

Chapter 5 – Introduction

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mutagenesis requires no genetic transformation, it is widely applicable to both model species and crop species. EMS mutagenesis therefore has become the method of choice for many crop improvement and gene function studies and its application in reverse genetics has already been demonstrated for a large number of economically important crops, including rice, barley, wheat, maize, sorghum, soybean, rapeseed, tomato and potato (KUROWSKA et al. 2011).

The method of application of EMS and the genetic structure of the target populations can vary. Typically, EMS mutagenesis is carried out by soaking seed in an EMS solution. Using this method, both parental genomes are targeted. Individuals arising from the mutagenized seeds (the M1 generation) are however chimeric. To avoid the chimeric tissue, commonly the M2

generation of selfed M1 plants is used for mutation screening. The requirement of this second

non-chimeric M2 generation for screening makes it time consuming. Furthermore, since

induced mutations segregate in a M2 population, of each M1 plant multiple M2 family plants,

or seeds, have to be screened in order not to miss the segregating mutation. An alternative mutagenesis method extensively applied in maize is the EMS treatment of pollen. This method is described by Neuffer and Coe (1978) and is based on mixing paraffin-oil diluted EMS with pollen. It has been applied in Eucalyptus (MCMANUS et al. 2006) and been coupled to reverse

genetic screening in maize (TILL et al. 2004). In EMS pollen-treatment, M1 individuals produced

by fertilization with mutagenized pollen have only one mutagenized genome and are non- chimeric. Therefore pollen-treated populations are screened at the M1 generation (TILL et al.

2004). To determine which EMS doses permit efficient mutant generation, protocols describing mutagenic treatment of seed commonly recommend assaying seed mortality or seedling growth in response to treatment (IAEA 1977; MULLARKEY and JONES 2000). When pollen rather than seed is treated, assaying pollen germination reveals which doses do not completely render pollen non-viable, whilst changing pollen behaviour in vitro. This change is important because it indicates that pollen, and therefore M1 seedlings, should carry induced mutations

(MCMANUS et al. 2007).

The efficiency of a mutagenesis approach is defined as “the number of events per genome that are inherited in a population that has been mutagenized under standard conditions” (ALONSO and ECKER 2006). At equal mutation densities per mutagenized genome, only half the number of EMS seed-treated M1 plants have to be screened in order to find a mutation compared to

pollen-treated M1 plants, since in seed-treated EMS populations both parental genomes are

mutagenized and in pollen-treated populations only one. This makes seed-mutagenesis more efficient then pollen-mutagenesis. The number of mutagenized genomes per plant is usually however not considered when calculating mutation densities. Usually, to calculate a mutation density the total number of plants screened is multiplied by the length of the screened DNA target and divided by the number of identified mutations. Calculated in this way, a mutation density of 1 mutation/25 kb in seed-treated hexaploid wheat seems much higher than a mutation density of 1 mutation/40 kb in tetraploid wheat (SLADE et al. 2005). Mutation

densities per mutagenized genome in this example are however very comparable; 1 mutation per respectively 150 kb and 160 kb of mutagenized genome. As an alternative, mutations rates can be calculated as the number of mutations found per 1 kb length screened in 1,000 plants. Also here, the number of mutagenized genomes is not considered but this measurements

gives a clear estimation on how many plants have to be screened to find a number of mutations.

The most established method for the detection of DNA polymorphisms in EMS treated populations is a heteroduplex mismatch cleavage assay based on the endonuclease CEL1 (MCCALLUM et al. 2000). When using restriction-based mutation screening methods, a low level

of natural polymorphisms in the gene of interest is however a requirement for the efficient detection of novel mutations. An alternative technology, High resolution melting (HRM) analysis, derived from the combination of existing techniques of DNA melting analysis with a new generation of fluorescent dyes (WITTWER et al. 2003) could also be used. HRM analysis is

applied to analyse genetic variations including SNPs, length polymorphisms and methylation of DNA in PCR amplicons and has been applied successfully in a number of mutagenesis screens (BOTTICELLA et al. 2011; BUSH and KRYSAN 2010; GADY et al. 2009; ISHIKAWA et al. 2010; REED and WITTWER 2004). The time and costs of HRM are similar to conventional PCR while it avoids the need for post-PCR separation required by many other assays, making it a very efficient method for reverse genetics screens.

The first mutagenesis experiments in potato induced mutations by Röntgen-irradiation, and identified a loss-of-function mutation in the GBSS candidate gene by screening monoploid mini-tubers for absence of amylose starch (HOVENKAMP-HERMELINK et al. 1987). Reverse

genetic mutation screening, where mutations are first identified at the DNA level, so far has only been conducted using an EMS treated dihaploid potato population, screened by direct Sanger sequencing for mutations in the same GBSS gene (MUTH et al. 2008). In reverse genetics

screening, a M1 generation is usually selfed to obtain a M2 generation that harbours

homozygous mutants with potential phenotypes. In diploid potato gametophitic

incompatibility systems are however active that complicate selfing (EIJLANDER et al. 1997). To

obtain a genetically stable M2 generation, Muth et al. (2008) used callus regeneration and

spontaneous chromosome doubling to obtain a tetraploid M1 clone with the mutation of

interest, and crossed this clone with pollen of tetraploid donor plants. The M2 plants were

crossed amongst each other to obtain a homozygous mutant expressing the waxy phenotype of interest. Self-compatible diploid potato clones exist (HOSAKA and HANNEMAN 1998; OLSDER and HERMSEN 1976) and might be useful as alternative to quickly obtain diploid M2 plants

homozygous for the mutation of interest for phenotypic evaluation. These mutants could be incorporated into diploid potato breeding programmes and introduced into tetraploid cultivars by 2n-pollen formation (HUTTEN et al. 1994).

In this chapter we test the efficiency of EMS-mutagenesis by pollen- and seed treatment in diploid potato and the density of genetically stable mutations, accessible in the next generation.

Chapter 5 – Materials and Methods

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MATERIALS AND METHODS