Single Nucleotide Polymorphisms and Linkage Disequilibrium in Sunflower

Abstract

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 (u ¼ 0.0094) than wild populations (u ¼ 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.

Contributions of Flowering Time Genes to Sunflower Domestication and Improvement

“…Levels of diversity in the reference genes in wild, landrace, and elite lines were comparable to levels found in previous work (Table 3; Liu and Burke 2006;Kolkman et al 2007;Chapman et al 2008). Also as in previous studies, average pairwise nucleotide diversity (p) and average Watterson's estimator of diversity (u w ) were highest in the wild populations, intermediate in the landraces, and lowest in the elite lines, indicative of genetic bottlenecks at both the domestication and improvement stages (Table 3; Burke et al 2005;Liu and Burke 2006;Chapman et al 2008).…”

“…Linkage disequilibrium (LD) decayed relatively rapidly, r 2 , 0.1 within 2 kb for a sample of elite and landrace lines (Liu and Burke 2006), but LD persisted for much greater distances in a sample of solely elite lines (r 2 0.32 at 5.5 kb and r 2 , 0.1 at 150 kb; Kolkman et al 2007;Fusari et al 2008). LD may persist over even longer distances in regions containing targets of selection.…”

Genetic Variation in the <i>FT1</i> Locus Involved in Reproductive Onset in <i>Populus deltoides</i>

“…For example, a frequency of one SNP for every 100 bp was found in Zea mays (maize) (Rafalski, 2002); one in 77 bp in Gossypium spp. (cotton) (Chuanfu et al, 2008), and one in 45.7 bp in Helianthus annuus (sunflower) (Kolkman et al, 2007). SNP frequency found in Glycine max (soybean) (one in 273 bp) was similar to that in this work (Zhu et al, 2003).…”

A Genomic Scan for Selection Reveals Candidates for Genes Involved in the Evolution of Cultivated Sunflower (Helianthus annuus)

“…As might be expected of an obligate outcrosser, linkage disequilibrium (LD) appears to decay extremely rapidly in wild sunflower, reaching negligible levels within a few hundred base pairs. In the case of cultivated sunflower, nonrandom associations appear to persist for 1 to 2 kb (Liu and Burke, 2006;Kolkman et al, 2007). While selection can have a major effect on the extent of LD in specific genomic regions (Palaisa et al, 2004;Olsen et al, 2006), the apparently rapid decay of LD in sunflower suggests that genes bearing the signature of selection may themselves have been targeted by selection, as opposed to simply marking larger genomic regions containing selectively important genes.…”