DNA diversity in prairie cordgrass (Spartina pectinata Link) populations indigenous to the United States

Graves, Hannah Elizabeth

Permalink

https://hdl.handle.net/2142/89022 Copy

Description

Title

DNA diversity in prairie cordgrass (Spartina pectinata Link) populations indigenous to the United States

Author(s)

Graves, Hannah Elizabeth

Issue Date

2015-12-03

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

• Lee, DK
• Rayburn, A. Lane

Department of Study

Crop Sciences

Discipline

Crop Sciences

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

M.S.

Degree Level

Thesis

Keyword(s)

• prairie cordgrass
• single nucleotide polymorphism (SNP)
• Spartina
• polymorphism
• transcriptome
• cpDNA
• polyploid

Abstract

Plant diversity, more specifically genetic diversity, is important for the environment and essential as an economic and social resource. Genetic variation assessment has allowed for contributions to many fields, and enables plant breeders to select plant varieties that are more suited to the current needs of the diverse agriculture system. Breeders can also monitor genetic diversity and select better crop varieties using polymorphisms in DNA. Prairie cordgrass (Spartina pectinata Link) has many uses such as conservation and wildlife habitat, and is currently being developed as a bioenergy crop. This species is a C4, rhizotomous, perennial grass, native to the North American Prairie. In order to utilize this species one must understand the genetic diversity found within and among native populations. Chloroplast DNA and nuclear DNA analysis provides a basic understanding into the amount of genetic variation present in this species. In this study, two highly polymorphic chloroplast regions were sequenced across 16 natural populations, in addition SNP markers were developed and tested on 38 natural populations of prairie cordgrass. Most of the variation (SNPs and indels) found in chloroplast DNA were observed in the octoploid cytotype with a few variants observed in the tetraploid cytotype, and no variants observed in the hexaploid cytotype. To delve into nuclear polymorphisms, SNP markers were developed from a complied transcriptome and were used validated putative SNPs. Also, the SNPs ability to distinguish true crosses and selfs during a breeding program was assessed. Variation identified in the nuclear transcriptome occurred equally between octoploid and tetraploid populations with less variation observed in the hexaploid population. In addition, χ2 analysis was performed on an F1 population and determined that the individuals followed normal Mendelian inheritance patterns and could not be rejected for the markers chosen. This information is needed to open up the ability to understand genetic diversity of this species and for use in the development of a molecular based breeding program.

Graduation Semester

2015-12

Type of Resource

text

Permalink

http://hdl.handle.net/2142/89022

Copyright and License Information

Copyright 2015 Hannah Graves

Owning Collections