Genomic response to selection for behavior

Rando, Halie Marie

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https://hdl.handle.net/2142/106317 Copy

Description

Title

Genomic response to selection for behavior

Author(s)

Rando, Halie Marie

Issue Date

2019-09-27

Director of Research (if dissertation) or Advisor (if thesis)

Kukekova, Anna V

Doctoral Committee Chair(s)

Kukekova, Anna V

Committee Member(s)

• Carlborg, Örjan
• Bell, Alison M
• Torvik, Vetle I
• Roca, Alfred L

Department of Study

Graduate College Programs

Discipline

Informatics

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

Ph.D.

Degree Level

Dissertation

Keyword(s)

comparative genomics, red fox, social behavior, behavior genetics, North American red fox, fox breeding, farm fox, Vulpes vulpes

Abstract

The red fox (Vulpes vulpes) is a model of significant interest to social behavior genomics because of an experimental breeding project that began in the mid-20th century at the Institute for Cytology and Genetics in Novosibirsk, Russia. In this experiment, foxes acquired from fox farms were bred into two lines: one that displays prosocial, tame behavior and one that is fearfully aggressive towards humans. Today, the two lines exhibit stark behavioral differences known to have a genetic basis. The short time period that has elapsed since the beginning of fox farming (125 years) also renders the fox a potential model for the genomic response to the process of domestication. However, the identification of genes or genetic variants influencing behavior under selective breeding and/or domestication has long been limited by the lack of red fox genomic resources. Although the genome of a male fox was recently sequenced and assembled, this draft assembly is likely to be affected by errors characteristic of assembly from short next-generation sequencing reads. Here, the refinement of the draft genome, the development of red fox genomic resources, and preliminary behavior genetic analyses are described. In chapter 2, the scaffolds (i.e., short sequence fragments) that comprise the draft red fox reference assembly were assembled into 40 fragments on the scale of chromosome arms that constitute the autosomes and X-chromosome. In chapter 3, scaffolds containing Y-chromosome sequence were also identified. Both of these chapters contextualize the red fox chromosomes among those of other carnivores, and chapter 4 describes the application of the Y-chromosome sequence to the confirmation of the farm-bred foxes’ ancestral population. In chapter 5, genome-wide variation in farm-bred foxes and their closest wild relatives is analyzed to identify a dense set of genetic variants and to conduct a preliminary analysis of putative regions under selection during the domestication of red foxes, revealing known and novel candidate genes associated with fox breeding. Finally, chapter 6 describes the high-resolution characterization of variation within and among 83 tame and aggressive individuals and a preliminary analysis to identify regions under selection during selective breeding for tame and aggressive human-directed behavior. The advances in red fox genomic tools described here provide a foundation for the analysis of the red fox’s genetic response to selection for behavior. This work expands on and provides new resources for the study of chromosomal evolution (chapters 2 and 3), population history (chapters 4 and 5), and response to selection for behavior (chapters 5 and 6) in the red fox. This work therefore represents a significant step towards the realization of a red fox model for social behavior genomics that can be used to investigate the genetic architecture of social behavior and to identify loci regulating behavioral variation, with the ultimate goal of identifying loci influencing social behavior and domestication in mammals broadly.

Graduation Semester

2019-12

Type of Resource

text

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http://hdl.handle.net/2142/106317

Copyright and License Information

Copyright 2019 Halie Rando

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