Semester

Summer

Date of Graduation

2023

Document Type

Dissertation

Degree Type

PhD

College

Eberly College of Arts and Sciences

Department

Biology

Committee Chair

Jennifer Hawkins

Committee Member

Vagner Benedito

Committee Member

Jonathan Cumming

Committee Member

Jennifer Gallagher

Committee Member

Stephanie Young

Abstract

Meiotic recombination plays a vital role in shaping genome evolution by introducing genetic diversity necessary for natural selection. Recombination rates exhibit extensive variation within and between species, occurring in specific regions known as hotspots and coldspots along individual chromosomes. Maize, with its well-characterized genome, provides an excellent model for studying the nonrandom pattern of meiotic recombination. While retrotransposon activity contributes to significant intergenic variation in maize inbred lines, the genic space remains conserved in terms of gene order and sequence. To investigate recombination activity in the Bz1/Sh1 region, the maize haplotypes W22 and B73, which share genetic backgrounds but differ in the presence or absence of large indels, were utilized. Previous research revealed significant differences in allelic expression for genes neighboring known recombination hotspots in maize hybrids of diverse genotypes. Notably, considerable expression variation was observed near sesquiterpene cyclase (STC), tac6058058 (gene of unknown function), and an upstream region containing a putative transcription factor (PTF) and accumulated photosystem (Apo2). In Chapter 3, a PCR-based method was developed to amplify unique polymorphisms specific to each parental line, enabling the bin mapping of recombination rates across the region. Remarkably, recombination hotspots near differentially expressed genes were identified, despite disparities in genome structure and content at these locations. Furthermore, an unidentified hotspot within this region was characterized, with the highest frequency hotspot being adjacent to the lowest frequency coldspot, both situated in an area devoid of TE insertions and methylation. Previous research by Hawkins et al. (2014) has demonstrated extensive allelic variation in gene expression within this region, influenced by cis-regulatory factors. Specifically, eight genes exhibited differential allelic expression across multiple tissues. Notably, genes showing significant allelic expression divergence were located in recombination hotspots, while genes with lower divergence were found in recombination coldspots. Despite the evident impact of cis-regulatory variation on gene expression, the role of recombination in shaping this diversity remains poorly understood. This dissertation aimed to uncover the allelic expression of four genes in the Bz1/Sh1 region in recombinant individuals by amplifying parent-specific SNPs and sequencing the resulting amplicons using Illumina MiSeq technology. It was revealed that recombination events occurring in cis-regulatory regions can induce changes in gene expression patterns, leading to tissue-specific allelic variation within the same species. This variation may be attributed to the swapping of promoters. These findings offer valuable insights into the intricate regulatory mechanisms governing gene expression in maize hybrids and parental inbred lines, furthering our understanding in this field. Additionally, long non coding RNAs (lncRNA) have been shown to play a role in shaping the recombination landscape in various organisms. The final chapter investigates the relationship between recombination frequency across the maize genome and the number of lncRNAs found in recombination hotspots. Findings suggest an inverse relationship between recombination frequency and the number of lncRNAs found in recombination hotspots.

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