Single nucleotide polymorphisms and linkage disequilibrium in sunflower
Judith M Kolkman1, Simon T Berry, Alberto J Leon
1Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon 97331, USA.
Genetics
|July 31, 2007
Summary
Modern sunflower genetic diversity, shaped by breeding, shows abundant single nucleotide polymorphisms (SNPs) and insertions-deletions (INDELs). High SNP frequencies and linkage disequilibrium in cultivars support high-density genetic mapping.
Area of Science:
- Plant Genetics
- Crop Breeding
- Genomics
Background:
- Domestication and breeding bottlenecks narrowed genetic diversity in modern sunflower (Helianthus annuus L.) cultivars.
- Introgression of wild and exotic alleles broadened genetic diversity.
Purpose of the Study:
- To assess single nucleotide polymorphism (SNP) frequencies, nucleotide diversity, and linkage disequilibrium (LD) in modern sunflower cultivars.
- To evaluate the potential for high-density genetic and association mapping in elite oilseed inbred lines.
Main Methods:
- Resequencing of alleles from 81 genic loci across the sunflower genome.
- Identification and analysis of single nucleotide polymorphisms (SNPs) and insertions-deletions (INDELs).
- Calculation of nucleotide diversity and linkage disequilibrium (LD) decay.
Main Results:
- Abundant DNA polymorphisms were identified: 1078 SNPs (1/45.7 bp) and 178 INDELs (1/277.0 bp) in 49.4 kbp.
- SNPs were more frequent in noncoding (1/32.1 bp) than coding (1/62.8 bp) sequences.
- Nucleotide diversity in inbred lines (0.0094) was only slightly lower than in wild populations (0.0128).
- Linkage disequilibrium decayed more slowly in inbred lines than wild populations.
Conclusions:
- Modern sunflower cultivars harbor substantial genetic variation, including millions of common SNPs.
- SNP frequencies and LD patterns are suitable for high-density genetic mapping and high-resolution association mapping.
- Understanding genetic diversity is crucial for improving elite oilseed sunflower breeding.
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