Rowan:Research

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Beth A. Rowan Research

Meiotic Recombination

Introduction

One of the advantages of sexual reproduction is the possibility to generate new combinations of alleles. During meiotic recombination, genetic information is swapped between the maternal and paternal chromosomes. This can lead to the expression of new traits. The positions of these genetic exchanges, known as crossovers, occur on average 1-2 times per chromosome across a diverse range of organisms. However, not all positions along a chromosome have an equal probability of crossing over. The patterns of large and fine scale "hotspots" and coldspots" have been the subject of much research in different biological fields.

I am using the model plant, Arabidopsis thaliana, to investigate the genetic factors that influence the position of crossovers at a genome-wide scale. A crossover is generated when the homologous chromosome is used to repair a double-strand break. Although hundreds of double-strand breaks are purposely initiated by the cells that go on to form gametes during meiosis, the vast majority are repaired using mechanisms that do not result in crossovers.

Understanding Recombination

Through my research, I have developed new approaches to study where and when crossovers occur using next-generation sequencing. The advantage of this approach is that it provides information at high resolution for every position in the genome.

Questions

These are main questions I would like to answer:

• Which proteins promote the formation of crossovers?

• Which proteins restrict the formation of crossovers?

• What are the mechanisms by which these proteins act?

• What are the interactions among proteins that participate in different repair pathways?

• Which of these proteins are conserved or variable across different evolutionary timescales?

and ultimately

• What determines whether a double strand break will be repaired as a crossover or a non-crossover?

Manipulating Recombination

Once I know more about the proteins that are involved in crossovers, I can experimentally manipulate their activity. By employing this strategy, I can seek answers to the following questions:

Questions

General

• Do factors that increase the frequency of crossovers also affect the distributions?
• Can coldspots be converted into hotspots and vice versa?

Mapping traits

Many scientists are interested in understanding which genes produce which traits. If the trait is quantitative (varies continuously in a population), then a technique known as Quantitative Trait Locus (QTL) mapping is employed. This technique takes advantage of recombination to identify which parts of the genome are associated with a given trait.

• Can manipulating recombination enhance QTL mapping?

Crop breeding

Crops have been improved by humans for centuries by taking advantage of recombination and artificial selection. Since recombination does not happen uniformly across the genome, this creates blocks of genes that are inherited together.

• Can altering recombination be used to prevent linked traits from being inherited together?

Evolutionary Implications

Since recombination can create new combinations of alleles, it can produce traits that did not exist in the parental generation. These "new" traits can then be subject to natural selection.

• What affect does altering the recombination rate have on the fitness of populations growing in the field?

Experimental Evolution

Altering recombination rates may also influence the efficiency of natural selection. One way to investigate this would be by using artificial selection to experimentally evolve different traits.

• How does the rate of recombination affect the ability to select for adaptation to stress?

Hybrid Incompatibility

Introduction

When individuals from divergent populations (or species) meet and reproduce, hybrid offspring are formed. Hybridization is quite common in nature and can lead to new phenotypes that are not present in the parental organisms. These phenotypes can respond to natural selection differently, and therefore hybrid organisms can experience a fitness advantage or disadvantage. Plant and livestock breeders have long known that hybridization often leads to growth and yield advantages that have been used to improve our food supply.
However, hybridization can sometimes be detrimental. Interactions among diverged alleles can negatively affect growth and fertility, thereby reducing fitness. In the model plant, Arabidopsis thaliana, about 2-3% of intraspecific crosses between different populations result in aberrant phenotypes in the first generation. This phenomenon, known as hybrid necrosis, arises because the pathogen defense response system is hyperactive, causing reduced growth and cell death. In all cases where the underlying genes are known, at least one of the causal genes is an R-protein (protein responsible for detecting pathogen infection). Thus, interactions among genes from divergent lineages lead to the improper recognition of self as non-self.

Genetic Modifiers

Cases of hybrid necrosis are caused by deleterious interaction among 1-3 loci. Necrosis can be observed when the causal alleles are taken from the parental lines and expressed in a single genetic background. However, the genetic background can also affect the severity of the phenotype conferred by the two causal alleles. This means that there are wild populations of Arabidopsis thaliana that carry natural alleles that modify the phenotypic effects of hybrid necrosis genes.

Questions

• Are natural modifiers common?
• Do they have a general affect on the plant immune system or are they specific to the hybrid necrosis causal alleles?
• What is their normal function?
• How are natural modifiers distributed among populations?

I am using next-generation sequencing to map these modifiers and investigate the answers to the questions above.

Environmental Modifiers

The expression of hybrid necrosis is also influenced by environmental factors. Temperature, for example, is negatively correlated with necrosis, meaning that necrosis is completely absent or extremely attenuated at higher temperatures. The specific temperature at which symptoms completely disappear is different for hybrids with different underlying genetic causes and there is only one case discovered so far that cannot be suppressed at any temperature. The genetic mechanism also determines whether the temperature response will be linear or non-linear.

Questions

• Which genetic factors influence the sensitivity of hybrid necrosis to temperature?
• What other environmental factors influence hybrid necrosis?

Arabidopsis in Argentina

Introduction

Arabidopsis thaliana is native to Europe and Asia, but there are several populations that have been introduced around the world. Most of these introduced populations are found in North America and were brought there in the 19th century. There are very few populations of Arabidopsis in the Southern Hemisphere. Populations of Arabidopsis thaliana in the Patagonia region of Argentina were originally found in the 1960s and new collections were made in recent years.

Questions

• How diverse are the introduced populations in Patagonia?
• Are present-day populations genetically differentiated from the 1960's populations?
• Where did the introduced plants in Patagonia come from?
• What role does genetic diversity play in adapation to a new enivronment?

I am currently investigating the first three of these questions by comparing whole-genome sequencing data of plants from present-day populations to a herbarium specimen from 1967 and to thousands of populations collected worldwide.

Working in Weigel World

The Weigel lab is fun and productive research environment. Scientist working here hail from around the world and work on a diverse range of topics. For more about what we do here, see the following links:
Weigel world website
Weigel world videos

• 2014 Lab overview here
• Detlef Weigel on herbcide resistance here
• Weigel Style here
• What does the plant say? here

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