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Title:Linkage mapping in prairie cordgrass (Spartina pectinata Link) using genotyping-by-sequencing markers
Author(s):Crawford, Joseph D
Advisor(s):Voigt, Thomas; Lee, DoKyoung
Contributor(s):Brown, Patrick J.
Department / Program:Crop Sciences
Discipline:Crop Sciences
Degree Granting Institution:University of Illinois at Urbana-Champaign
Degree:M.S.
Genre:Thesis
Subject(s):Prairie Cordgrass
Spartina pectinata
linkage mapping
genotyping-by-sequencing
disomic inheritance
polysomic inheritance
genetic mapping
high density linkage map
allopolyploid
autopolyploid
biomass
bioenergy
bioenergy feedstocks
perennial grasses
dedicated energy crops
Abstract:Global climate change from anthropogenic carbon emissions can be mitigated through the development of bioenergy systems. Bioenergy feedstocks tolerant of marginal land can reduce the tension between bioenergy production and food production. Prairie cordgrass (Spartina pectinata Link) is tolerant of poorly drained soils, saline soils, and low temperature. Prairie cordgrass (Spartina pectinata) is a polyploid Chloridoid grass with tetraploid (2n=4X=40), hexaploid (2n=6X=60), and octaploid (2n=8X=80) cytotypes, and is a potential dedicated energy crop with promising yields in marginal environments. Breeding efforts in prairie cordgrass are currently hampered by the lack of a linkage map, the lack of a Chloridoid reference genome, and by lack of information on inheritance patterns (disomic versus polysomic). Genotyping-by-sequencing (GBS) was applied to a population of 85 progeny from a reciprocal cross of heterozygous tetraploid parents. A total of 26,418 SNPs were discovered, with a distribution of allele frequencies suggesting disomic inheritance. A filtered set of 3,034 single-dose, high-coverage SNPs was used for pseudo-testcross mapping, resulting in two parental maps of 20 linkage groups containing 1,522 and 1,016 SNPs and a nearly 1:1 ratio of coupling to repulsion phase linkages, again suggesting disomic inheritance. Genomic contigs from tef (Eragrostis tef (Zucc.) Trotter), another Chloridoid grass, were used as a bridge to associate short prairie cordgrass reads with unique positions in the sorghum genome, providing a first glimpse into synteny between Chloridoids and other grasses. Genotyping-by-sequencing enabled rapid generation of a linkage map that will aid in future breeding and genomics efforts in prairie cordgrass.
Issue Date:2015-07-24
Type:Thesis
URI:http://hdl.handle.net/2142/88128
Rights Information:Copyright 2015 Joseph Crawford
Date Available in IDEALS:2015-09-29
Date Deposited:August 201


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