Originally published as Genetics Published Articles Ahead of Print on July 29, 2007.

Genetics, Vol. 177, 457-468, September 2007, Copyright © 2007
doi:10.1534/genetics.107.074054

Single Nucleotide Polymorphisms and Linkage Disequilibrium in Sunflower

Judith M. Kolkman^*,1, Simon T. Berry, Alberto J. Leon, Mary B. Slabaugh^*, Shunxue Tang^*,, Wenxiang Gao, David K. Shintani^**, John M. Burke and Steven J. Knapp^*,,2

^* Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon 97331, Advanta Seeds UK, Norfolk, PE31 8LS, United Kingdom, Advanta Semillas, Balcarce Research Station, Argentina, Center for Applied Genetic Technologies, The University of Georgia, Athens, Georgia 30602, ^** Department of Biochemistry and Molecular Biology, The University of Nevada, Reno, Nevada 89557 and Department of Plant Biology, The University of Georgia, Athens, Georgia 30602

² Corresponding author: Center for Applied Genetic Technologies, 111 Riverbend Road, The University of Georgia, Athens, GA 30602.
E-mail: sjknapp{at}uga.edu.

Genetic diversity in modern sunflower (Helianthus annuus L.) cultivars (elite oilseed inbred lines) has been shaped by domestication and breeding bottlenecks and wild and exotic allele introgression^–the former narrowing and the latter broadening genetic diversity. To assess single nucleotide polymorphism (SNP) frequencies, nucleotide diversity, and linkage disequilibrium (LD) in modern cultivars, alleles were resequenced from 81 genic loci distributed throughout the sunflower genome. DNA polymorphisms were abundant; 1078 SNPs (1/45.7 bp) and 178 insertions-deletions (INDELs) (1/277.0 bp) were identified in 49.4 kbp of DNA/genotype. SNPs were twofold more frequent in noncoding (1/32.1 bp) than coding (1/62.8 bp) sequences. Nucleotide diversity was only slightly lower in inbred lines ( = 0.0094) than wild populations ( = 0.0128). Mean haplotype diversity was 0.74. When extraploted across the genome (3500 Mbp), sunflower was predicted to harbor at least 76.4 million common SNPs among modern cultivar alleles. LD decayed more slowly in inbred lines than wild populations (mean LD declined to 0.32 by 5.5 kbp in the former, the maximum physical distance surveyed), a difference attributed to domestication and breeding bottlenecks. SNP frequencies and LD decay are sufficient in modern sunflower cultivars for very high-density genetic mapping and high-resolution association mapping.

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