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doi:10.1534/genetics.107.074054
A more recent version of this article appeared on September 1, 2007.
REGULAR RESEARCH PAPERS |
Single Nucleotide Polymorphisms and Linkage Disequilibrium in Sunflower
Judith M. Kolkman 1, Simon T. Berry 2, Alberto J. Leon 3, Mary B. Slabaugh 4, Shunxue Tang 5, Wenxiang Gao 5, David K. Shintani 6, John M. Burke 5 and Steven J. Knapp 5*
1 Cornell University
2 Advanta Seeds UK
3 Advanta Semillas
4 Oregon State University
5 The University of Georgia
6 The University of Nevada, Reno
* To whom correspondence should be addressed. E-mail: sjknapp{at}uga.edu.
Submitted on March 31, 2007
Revised on July 13, 2007
Accepted on 13 July 2007
Genetic diversity in modern sunflower (Helianthus annuus L.) cultivars (oilseed inbred lines) has been shaped by domestication and breeding bottlenecks and wild allele introgression--the former narrowing and the latter broadening genetic diversity. To assess nucleotide diversity and linkage disequilibrium (LD) in elite inbred lines of sunflower, we resequenced 107 independent amplicons from 71 genic loci distributed throughout the genome. DNA polymorphisms were abundant--1,078 single nucleotide polymorphisms (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 two-fold more frequent in non-coding (1/32.1 bp) than coding (1/62.8 bp) sequences. Nucleotide diversity was only slightly lower in inbred lines (q = 0.0094) than previously found in wild populations (q = 0.0128). The mean haplotype diversity was 0.74 among inbred lines. From these data, the 3,500 Mbp sunflower genome is predicted to harbor at least 76.3 million common SNPs among elite inbred lines. Linkage disequilibrium (LD) decayed much more slowly in inbred lines than previously found in wild biotypes (mean LD declined to 0.32 by 5.5 kbp in the former, the maximum physical distance surveyed). The persistence of LD over longer physical distances in elite than wild alleles is presumably a consequence of domestication and breeding bottlenecks. SNP frequencies and LD decay are thus sufficient in modern sunflower cultivars for high-density genetic mapping and high-resolution association mapping.
Key Words: Asteraceae, Compositae, Helianthus, association mapping, nucleotide diversity
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