Single nucleotide polymorphisms (SNPs) are the most common DNA
polymorphisms in plant and animal genomes. SNPs were identified in the allele
sequences of up to 12 sunflower (Helianthus annuus L.) genotypes for a genome-wide
sample of 81 loci originally mapped using restriction fragment length
polymorphism (RFLP) markers. The RFLP loci anchor a dense RFLP linkage
map and second-generation linkage maps constructed using simple sequence
repeats and other high-throughput DNA markers. The goal of this study was to
develop high-throughput SNP markers for the cDNA-RFLP loci for linkage
mapping, diversity analysis, and molecular breeding and genomics research. The
specific objectives were to: (i) develop FP-TDI or fluorescent primer-extension
SNP assays for the cDNA-RFLP loci; (ii) validate the SNP markers by screening
12 sequenced (reference) genotypes; and (iii) assess the utility and polymorphism
rate of the SNP markers across a genetically diverse panel of unsequenced wild
and domesticated sunflower genotypes.
SNP markers were successfully developed for 44 of the targeted 49 cDNA-RFLP
loci. Thirty-one of the SNP markers were further selected for a diversity
analysis across a genetically diverse panel of wild and domesticated sunflower
genotypes. The mean heterozygosity (H) score for the loci was 0.41, which nears
the maximum H score of 0.5 for biallelic markers. SNPs in this study exhibited
polymorphism rates close to those of RFLP and SSR markers in inbred sunflower
lines. / Graduation date: 2004
| Identifer | oai:union.ndltd.org:ORGSU/oai:ir.library.oregonstate.edu:1957/30503 |
| Date | 16 September 2003 |
| Creators | Freeman, Carrie |
| Contributors | Knapp, Steven J. |
| Source Sets | Oregon State University |
| Language | en_US |
| Detected Language | English |
| Type | Thesis/Dissertation |
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