Agronomy and Horticulture, Department of


First Advisor

David Hyten

Date of this Version



A DISSERTATION Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Doctor of Philosophy, Major: Agronomy (Plant Breeding and Genetics), Under the Supervision of Professor David L. Hyten. Lincoln, Nebraska: June, 2022

Copyright © 2022 Samantha J. McConaughy


Recombination allows for the exchange of genetic material between two parents which plant breeders exploit to make new and improved varieties. This recombination is not distributed evenly across the chromosome. In crops, it mostly occurs in the euchromatic regions of the genome and even then, recombination is focused into recombination hotspots flanked by recombination cold spots. Understanding the distribution of these hotspots along with the sequence motifs associated with them may lead to methods that enable breeders to better exploit recombination in breeding.

In chapter 1 background information on recombination, recombination hotspots detection methods, landscape of recombination (describe recombination patterns along the genome), and environmental influence on recombination hotspot locations are outlined. In chapter 2 recombination hotspots were mapped in two-biparental soybean [Glycine max (L.) Merr.] recombinant inbred line (RIL) populations, Williams crossed by Essex (WE) and Williams 82 crossed by PI479752 (WP). These populations consist of 922 RIL(WE) and 1,086 RIL (WP) and were genotyped with 50,000 SNP markers using the SoySNP50k Illumina Infinium assay. In chapter 3 the location of recombination hotspots in the USDA Soybean Germplasm Collection in three populations: wild (806), landraces (5396), and North American cultivars (563) are reported. Genotyping was conducted using the SoySNP50k Illumina Infinium assay. Germplasm hotspot locations were compared to results in chapter 2, two-biparental soybean recombinant inbred line (RIL) populations. In chapter 2 and 3 statistical tests were conducted for genome features association with hotspot locations based on logistical regression, discovered nucleotide motifs surrounding hotspot regions across the genome.

Advisor: David L. Hyten