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

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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.

	ABSTRACT

TOP ABSTRACT MATERIALS AND METHODS RESULTS DISCUSSION ACKNOWLEDGEMENTS LITERATURE CITED

 
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.

SNP abundance and LD decay are highly variable in eukaryotic genomes and affected by natural, domestication, and breeding history, mating systems, mutation, migration, genomic rearrangements, recombination, and other factors (CHAPMAN and THOMPSON 2001; HUDSON 2001; BUCKLER and THORNSBERRY 2002; STUMPF 2002; GREENWOOD et al. 2004; RAFALSKI and MORGANTE 2004). Typically, SNPs are less abundant, and LD decays more slowly in autogamous than allogamous species, domesticated than wild genotypes, and inbred than outbred genotypes (CHING et al. 2002; NORDBERG et al. 2002; NORDBERG and TAVARE 2002; FLINT-GARCIA et al. 2003; RAFALSKI and MORGANTE 2004; SHIFMAN et al. 2003; INGVARSSON 2005). For example, SNPs are significantly more frequent in maize (Zea mays L.; 1 SNP/61 bp), a predominantly allogamous species, than soybean (Glycine max L.; 1 SNP/273 bp to 1 SNP/343 bp), a predominantly autogamous species (REMINGTON et al. 2001; TENAILLON et al. 2001, 2002; CHING et al. 2002; ZHU et al. 2003; VAN et al. 2005). Moreover, LD decays more slowly (persists over much longer tracts of DNA) in soybean (>50 kbp) than maize (400–1500 bp). LD decayed more rapidly in exotic outbred germplasm than elite inbred lines in maize, a difference attributed to the effects inbreeding and selection (CHING et al. 2002; RAFALSKI and MORGANTE 2004). The persistence of LD decreases the density of DNA marker loci needed for identifying phenotypic–genotypic associations, but decreases resolution (CARDON and BELL 2001; CARDON and ABECASIS 2003; RAFALSKI and MORGANTE 2004).

Sunflower (Helianthus annuus L.), a predominantly allogamous species, should display patterns of nucleotide diversity and LD similar to maize and other allogamous species. Genetic diversity in modern sunflower cultivars (elite oilseed inbred lines and hybrids) has been shaped by domestication and breeding, as well as the introgression of alleles from wild and exotic germplasm (migration) (CHERES and KNAPP 1998; TANG and KNAPP 2003; HARTER et al. 2004; BURKE et al. 2005). Domestication and breeding create population bottlenecks, decrease genetic diversity, and increase LD, whereas migration increases genetic diversity and decreases LD (CHING et al. 2002; RAFALSKI and MORGANTE 2004). The abundance and distribution of SNPs in elite oilseed inbred line alleles has only been reported for a few genic loci in sunflower (KOLKMAN et al. 2004; HASS et al. 2006; SCHUPPERT et al. 2006; TANG et al. 2006b), and LD has only been surveyed in Native American land races and other exotic cultivars and wild populations (LIU and BURKE 2006). KOLKMAN et al. (2004) found significant differences in SNP frequencies among acetohydroxyacid synthase alleles resequenced from inbred lines and wild populations, a pattern predicted from analyses of SSR diversity (TANG and KNAPP 2003). LIU and BURKE (2006) surveyed nucleotide diversity and LD in nine genic loci in wild populations and exotic germplasm accessions (Native American land races and prehybrid era open-pollinated confectionery and oilseed cultivars); only one elite inbred line allele (HA89) was resequenced. SNPs were twofold more abundant in wild populations (1 SNP/19.9 bp) than exotic germplasm accessions (1 SNP/38.8 bp), exotic alleles harbored half of the nucleotide diversity found in wild alleles, and LD decayed within 200 bp in wild alleles and 1100 bp in exotic alleles. Here, we report SNP frequencies, nucleotide diversity, and LD in elite sunflower inbred lines alleles resequenced from 82 previously mapped restriction fragment length polymorphism (RFLP) marker loci distributed throughout the sunflower genome (2n = 2x = 34) (BERRY et al. 1995; GEDIL et al. 2001; YU et al. 2002, 2003).

	MATERIALS AND METHODS

TOP ABSTRACT MATERIALS AND METHODS RESULTS DISCUSSION ACKNOWLEDGEMENTS LITERATURE CITED

 
Plant materials and allele resequencing:
DNA polymorphisms were surveyed in two wild (ANN1238 and ANN1811) and 10 elite inbred line alleles resequenced from 82 previously mapped RFLP marker loci (ZVG1-ZVG17, ZVG19-ZVG81, ZVG152, and ZVG668) (Tables 1 and 2; supplemental Table 1 at http://www.genetics.org/supplemental/) (BERRY et al. 1994, 1995). We sequenced a single phase known allele/resequenced amplicon (RSA) from each genotype by cloning genomic DNA amplicons and randomly selecting and sequencing a single clone/RSA/genotype; one or two DNA fragments (amplicons) were resequenced per RFLP locus. Leaves were harvested from 10 4- to 6-wk-old plants from each germplasm accession and bulked. Genomic DNA samples were isolated from each bulk using a modified CTAB method (MURRAY and THOMPSON 1980). Of the 82 RFLP probes, 78 were cDNA clones developed from RNAs isolated from etiolated seedlings and 4 were PstI-digested genomic DNA clones (ZVG9, ZVG16, ZVG19, and ZVG51) (BERRY et al. 1994). The probe inserts were sequenced, and BLASTX analyses of the sequences were performed against the National Center for Biotechnology Information (NCBI) Protein Database (http://www.ncbi.nlm.nih.gov) to identify putative functions using a probability threshold of e^–15 (ALTSCHUL et al. 1990; ALTSCHUL and GISH 1996; MCGINNIS and MADDEN 2004). The probe insert sequences were used as templates for designing resequencing primers using Primer3 (http://frodo.wi.mit.edu) and manual selection. Forward and reverse primer sites were chosen as close as possible to opposite ends of the reference allele sequences so as to amplify the longest DNA fragments possible from each locus (supplemental Table 1). Genomic DNA fragments were amplified using long-distance PCR (LD-PCR) (BARNES 1994) in most cases and PCR in a few cases. PCRs and LD-PCRs were performed by adding 30–60 ng of genomic DNA to a 20-µl PCR mix containing 1x buffer, 2 mM MgSO₄, 0.3 mM dNTPs, 0.3 µM of forward and reverse primers, 0.5 U of Platinum Taq DNA Polymerase High Fidelity (Invitrogen, Carlsbad, CA), and dH₂O to a final volume of 20 µl. For LD-PCR, genomic DNAs were amplified using one cycle at 94° for 4 min, followed by 10 cycles at 94° for 10 sec, 58° for 1 min, and 68° for up to 12 min (1 min per kb), 25 cycles at 94° for 10 sec, 58° for 1 min, and 68° for up to 12 min plus 10 sec per cycle, and one cycle at 72° for 20 min; annealing temperatures ranged from 55° to 62°, and extension times ranged from 2 to 12 min. Genomic DNA amplicons were cloned using the Invitrogen TOPO TA-cloning method. We selected and single-pass sequenced a single clone for each genotype by amplicon combination from one or both ends at the University of Nevada, Reno Genomics Center on an Applied Biosystems Prism 3730 DNA Sequencer (Foster City, CA). By sequencing a single cloned amplicon, we acquired a single phase known allele from each genotype.

LD analyses were performed on RSAs >1 kbp in length harboring at least 10 polymorphic sites. The physical distances separating pairs of polymorphic sites between independent RSAs amplified from opposite ends of a locus were estimated from DNA fragment length estimates (supplemental Table 1 at http://www.genetics.org/supplemental/). Using DnaSP, we estimated the minimum number of recombination events (RM) in inbred line alleles using the four-gamete test (HUDSON and KAPLAN 1985), proportion of adjacent polymorphisms in perfect disequilibrium (B) (WALL 1999), and strength of LD between pairs of polymorphic sites (estimated as the squared allele frequency correlation, r²) (WEIR 1996). The decay of LD against physical distance was modeled using nonlinear regression methods described by REMINGTON et al. (2001). Briefly, SAS PROC NLIN (Cary, NC) was used to fit r² estimates (pooled across loci) to a model of the expected level of r² at drift-recombination equilibrium, allowing for a low level of mutation and finite sample size (see Appendix 2 of HILL and WEIR 1988). Although factors such as the nonindependence of linked sites and nonequilibrium populations can reduce the precision of such analyses and introduce bias, they are still useful for investigating the overall rate of decay of LD (see INGVARSSON 2005).

	RESULTS

TOP ABSTRACT MATERIALS AND METHODS RESULTS DISCUSSION ACKNOWLEDGEMENTS LITERATURE CITED

 
Allele resequencing and putative functions of the resequenced loci:
The inserts of 4 genomic DNA and 78 cDNA clones previously used as RFLP probes (BERRY et al. 1994, 1995; GEDIL et al. 2001) were sequenced and ranged in length from 97 to 3025 bp (supplemental Table 1 at http://www.genetics.org/supplemental/; GenBank accession nos. EF469860–EF469941). The putative functions of 48 of the 82 loci were inferred from BLASTX searches (Table 1). For the other 34 loci, BLASTX searches either failed to identify proteins (probabilities were >e^–15) or identified unknown proteins.

The 82 RFLP markers were known to be low-copy and polymorphic among elite inbred lines (BERRY et al. 1994, 1995). The primer pairs selected for allele resequencing produced amplicons ranging in length from 97 to 10,000 bp across loci (Figure 1; supplemental Table 1 at http://www.genetics.org/supplemental/). Of the 82 primer pairs, 77 produced paralog-specific amplicons and 31 of the 77 spanned introns, INDELs, or both (amplicon lengths are shown in supplemental Table 1). By sequencing cloned amplicons, a single phase-known allele was resequenced from each genotype (Table 2). Collectively, 1312 RSAs and 129 DNA sequence alignments were produced for 81 of the 82 loci; allele sequences could not be produced for the ZVG46 locus (GenBank accession nos. EF469941–EF462190; allele sequence alignments are displayed in supplemental Figure 1). Nucleotide polymorphisms were surveyed in 84 to 100 DNA sequences/genotype and 49.4 kbp of DNA sequence/genotype (Table 3). Nucleotide diversity analyses were performed on 107 DNA sequence alignments comprised of 6 to 10 inbred line allele sequences each from 71 of the 81 resequenced loci. The other 22 DNA sequence alignments were either comprised of 6 or fewer inbred line allele sequences, paralogous RSAs, or both specific and nonspecific RSAs.

View larger version (24K): [in this window] [in a new window] [Download PPT slide]   FIGURE 1.— Genomic DNA fragments for two genic loci (ZVG68 and ZVG75) amplified from 10 elite inbred lines and two wild populations (ANN1811 and AN1238).

The mean number of segregating sites was = 0.0094, and the mean number of pairwise sequence differences was = 0.0107 among RSAs (Table 3). Nucleotide diversity was twofold greater in noncoding than coding sequences, sixfold greater for SNPs ( = 0.0092) than INDELs ( = 0.0016), and greatest in introns ( = 0.01480). Nonsynonymous substitutions (_nonsyn = 0.0028) were sixfold less prevalent than synonymous substitutions (_syn = 0.0176), suggesting variability among loci has primarily been produced by purifying selection (Figure 2; Table 3). _nonsyn ranged from 0.0 to 0.055, and _syn ranged from 0.0 to 0.109 among RSAs (nucleotide diversity statistics for individual RSAs are shown in supplemental Table 2 at http://www.genetics.org/supplemental/). Only two RSAs had _nonsyn/_syn ratios >1.0 (_nonsyn/_syn = 1.12 for ZVG47 and 1.10 for ZVG80-R) (supplemental Table 2).

View larger version (6K): [in this window] [in a new window] [Download PPT slide]   FIGURE 2.— Nucleotide diversities for synonymous (syn) and nonsynonymous (nonsyn) SNPs among sunflower 10 inbred line alleles (107 RSAs), resequenced from 71 genic loci distributed among the 17 linkage groups of sunflower (2n = 2x = 34).

View larger version (48K): [in this window] [in a new window] [Download PPT slide]   FIGURE 3.— silent and haplotype diversity statistics among 10 inbred line and two wild alleles amplified from 71 genic loci (107 RSAs) distributed among the 17 linkage groups of sunflower (2n = 2x = 34). Loci are displayed in the order found on each linkage group from 1 (top) to 17 (bottom).

View larger version (28K): [in this window] [in a new window] [Download PPT slide]   FIGURE 4.— SNP allele frequency (least common allele) and heterozygosity distributions for 1078 SNPs identified in 10 inbred line alleles resequenced from 71 genic loci (107 RSAs).

View larger version (20K): [in this window] [in a new window] [Download PPT slide]   FIGURE 5.— Percentage of unique haplotypes identified among inbred line and wild alleles resequenced from 71 genic loci (107 RSAs).

View larger version (13K): [in this window] [in a new window] [Download PPT slide]   FIGURE 6.— Squared allele frequency correlations (r2) as a function of physical distance (bp) among polymorphic sites identified in alleles resequenced from 10 inbred lines. The predicted decline in LD (solid line) was found by nonlinear regression of r2 on bp using the mutation-recombination-drift model of HILL and WEIR (1988). See text for details.

	DISCUSSION

TOP ABSTRACT MATERIALS AND METHODS RESULTS DISCUSSION ACKNOWLEDGEMENTS LITERATURE CITED

The germplasm underlying modern oilseed sunflower cultivars was not founded by direct selection in primitive and early OP cultivars alone, but through breeding in elite and exotic germplasm (CHERES and KNAPP 1998). Although the early history of sunflower breeding is incomplete, our data support the notion that genetic diversity in modern cultivars has been supplemented by the introgression of wild and exotic alleles. Because the sunflower domestication syndrome is complex, the number of loci under selection in wide hybrids in contemporary oilseed sunflower breeding programs is predicted to be large; at least 14 of the 17 chromosomes are known to harbor phenotypic and quantitative trait loci for domestication and confectionery traits and should be under strong selection in oilseed sunflower breeding programs (BURKE et al. 2002, 2005; GANDHI et al. 2005; TANG et al. 2006a). The introgression of wild alleles into modern oilseed sunflower inbred lines has produced a patchwork of elite and wild alleles. Unique haplotypes were found in one or more inbred lines for several of the loci sampled (Figure 5; supplemental Figure 1 at http://www.genetics.org/supplemental/). As noted earlier, sampling may partly underlie differences between the present analysis and the work of LIU and BURKE (2006). Here, we resequenced alleles from a sample of 81 previously mapped genic loci and performed analyses on 107 fragments amplified from 71 loci (BERRY et al. 1995; GEDIL et al. 2001), whereas LIU and BURKE (2006) resequenced alleles from a random sample of nine genic loci. Moreover, because RFLP markers for the former were known to be polymorphic among oilseed inbred lines (BERRY et al. 1994, 1995), the resequenced loci could be more polymorphic, as a whole, than a random sample of loci. As a point of comparison, SSRs revealed greater diversity in land races than oilseed inbred lines (TANG and KNAPP 2003; HARTER et al. 2004).

Nucleotide diversity in autogamous and allogamous plant species:
Nucleotide diversity in sunflower is slightly lower than maize (REMINGTON et al. 2001; TENAILLON et al. 2001, 2002; CHING et al. 2002; LIU and BURKE 2006; BUCKLER et al. 2006), two- to fivefold greater than other domesticated grasses (BUCKLER et al. 2001), eight- to 10-fold greater than soybean (ZHU et al. 2003; VAN et al. 2005), and several-fold greater than other autogamous plant species (KANAZIN et al. 2002; GARRIS et al. 2003; HAMBLIN et al. 2004). Observed SNP frequencies seem to be comparable in sunflower and maize inbred lines. SNP frequencies were 1/32 bp in noncoding and 1/63 bp in coding sequences in sunflower inbred lines (Table 3) and 1/31 bp in noncoding and 1/124 bp in coding sequences in maize inbred lines (CHING et al. 2002). SNP frequencies, however, are sensitive to the number of genotypes sampled (larger samples have a greater likelihood of capturing rare SNPs), and the studies referenced above differed widely in terms of sampling strategies. However, because is roughly proportional to heterozygosity, the expected number of nucleotide differences between a randomly selected pair of alleles can be estimated. For sunflower, a randomly selected pair of elite alleles is expected to differ at 1 out of every 106 nucleotides (i.e., 1/0.0094 = 106.4), whereas corn is expected to differ at 1 out of every 105 nucleotides (TENAILLON et al. 2001), and soybean is expected to differ at 1 out of every 1,030 nucleotides (ZHU et al. 2003). Hence, SNP frequencies seem to be sufficient in the modern sunflower cultivars for the development of SNP genotyping assays for most loci and for very high density genetic mapping using highly parallel SNP genotyping methods (BOREVITZ et al. 2003; HAZEN and KAY 2003; WINZELER et al. 2003; WERNER et al. 2005; GUNDERSON et al. 2006; SYVANEN 2001, 2005).

SNP abundance in sunflower and other plant genomes:
The genic loci we sampled supply an estimate of the number of common SNPs in the sunflower genome. With 3500 Mbp of DNA in the nuclear genome (BAACK et al. 2005) and 1078 SNPs in the 49.4 kbp sample of DNA surveyed in the present study (Table 3), modern sunflower cultivars are predicted to harbor at least 76.4 million SNPs (3,500,000,000 bp/49,400 bp x 1078 SNPs). When translated into genetic distance, modern cultivars are predicted to harbor at least 54,571 SNPs/cM, assuming 1400 cM in the sunflower genome (TANG et al. 2002; YU et al. 2002, 2003). These estimates assume the loci sampled are typical of DNA as a whole in sunflower and do not account for rare SNPs below the threshold of detection in our study (f_r < 0.125). If the inbred lines we selected under represent allelic diversity in modern cultivars, and the protein coding loci we selected are less polymorphic than noncoding DNA in sunflower, the number of common SNPs will be >76.4 million. Conversely, if the loci selected for resequencing are more polymorphic than the balance of the genome, 76.4 million may overestimate the number of common SNPs in modern cultivars. Cultivated soybean, which is significantly less polymorphic than cultivated sunflower, is predicted to harbor 4–5 million SNPs in 1115 Mbp of DNA (ZHU et al. 2003; YOON et al. 2007), whereas maize inbred lines, with 114 SNPs in 6935 bp of DNA (CHING et al. 2002), is predicted to harbor 41 million SNPs in 2500 Mbp of DNA. The number of SNPs in sunflower, per Mbp of DNA (21,800/Mbp), is estimated to be five- to sixfold greater than soybean (3587–4484/Mbp) and 1.3-fold greater than maize (16,400/Mbp). Hence, the predicted number of SNPs in cultivated and wild sunflower is on par with the most polymorphic plant species surveyed so far (BUCKLER et al. 2001; REMINGTON et al. 2001; TENAILLON et al. 2001, 2002; CHING et al. 2002; KANAZIN et al. 2002; GARRIS et al. 2003; HAMBLIN et al. 2004; ZHU et al. 2003; BUCKLER et al. 2006; LIU and BURKE 2006; VAN et al. 2005).

Nucleotide and haplotype diversity within and between heterotic groups:
Two wild alleles (ANN1238 and ANN1811) were resequenced to supply a benchmark for assessing differences in haplotype structure, SNP frequencies, and nucleotide and haplotype diversities between elite and wild sunflower alleles. Similar to maize (CHING et al. 2002), we identified a small number of distinct haplotypes (one to nine) among inbred line alleles, where intralocus SNPs comprising haplotypes were in LD (supplemental Figure 1 at http://www.genetics.org/supplemental/). Selection for seed yield and hybrid seed production traits has created broad female (B) and male (R) heterotic groups in sunflower (BERRY et al. 1994; GENTZBITTEL et al. 1994; HONGTRAKUL et al. 1997; CHERES and KNAPP 1998). Significant genetic diversity has apparently been preserved in a small number of highly divergent B- and R-line haplotypes in sunflower, where haplotype divergence is greater between than within heterotic groups (supplemental Figure 1). While heterotic groups seem to be much less sharply differentiated in sunflower than maize, patterns of genetic diversity and haplotype divergence seem to be similar within and between heterotic groups in both species (TENAILLON et al. 2001, 2002; YU et al. 2002, 2003; LIU et al. 2003; REIF et al. 2003; JUNG et al. 2004; CHING et al. 2002). By contrast, haplotypes seem to be unstructured in the wild progenitor of maize (WHITE and DOEBLEY 1999; LIU et al. 2003) and wild sunflower (SLABAUGH et al. 2003; TANG and KNAPP 2003; KOLKMAN et al. 2004; LIU and BURKE 2006). While we only sampled two wild alleles/locus, wild haplotypes for two-thirds of the loci were unique (Figure 5; supplemental Figure 1).

Heterozygosity and haplotype diversity:
SNPs and other biallelic DNA markers are, as a whole, less informative than mulitallelic RFLP and SSR markers; however, when multiple SNPs in haplotype blocks are genotyped, the informativeness of SNP haplotypes should be comparable to RFLP and SSR markers (CHING et al. 2002). The inbred lines selected for allele resequencing (Table 2) were predicted from pedigree and RFLP, AFLP, and SSR marker diversity analyses to broadly sample genetic diversity, capture a significant percentage of the nucleotide diversity in elite inbred lines, and to be minimally redundant (BERRY et al. 1994; GENTZBITTEL et al. 1994; CHERES and KNAPP 1998; GEDIL et al. 2001; YU et al. 2002, 2003; TANG and KNAPP 2003). SNP heterozygosities and haplotype diversities were therefore expected to be greater among the resequenced inbred line alleles than among a random sample of inbred line alleles (Figures 3 and 4; supplemental Figure 1 at http://www.genetics.org/supplemental/). The probability of observing RFLP or SSR polymorphisms between two inbred lines (h_p) has been in the 0.32–0.53 range in several inbred line surveys in sunflower (BERRY et al. 1994; GENTZBITTEL et al. 1994; YU et al. 2002a,b; TANG and KNAPP 2003). The probability of observing different SNP haplotypes (p_s) between two inbred lines was 0.57 in the present study and thus slightly greater than h_p for RFLP and SSR markers (supplemental Figure 1). The difference could be an artifact of sampling differences; we selected inbred lines to minimize redundancy and maximize uniqueness, whereas several inbred lines within heterotic groups were sampled in previous RFLP and SSR diversity surveys, thereby increasing redundancy and decreasing heterozygosity. With deeper sampling, haplotype diversity should decrease, whereas the number of haplotypes should not substantially increase (CHING et al. 2002; ZHU et al. 2003; VAN et al. 2005); deeper sampling is predicted to identify less common alleles introgressed into elite inbred lines from exotic germplasm sources.

LD:
The rate of decay of LD affects the resolution of association mapping analyses and the density of DNA markers needed for identifying phenotype–genotype associations (JORDE 1995, 2000; BUCKLER and THORNSBERRY 2002; NORDBORG et al. 2002; CHING et al. 2002; RAFALSKI and MORGANTE 2004; BUCKLER et al. 2006). The rapid decay of LD in wild sunflower and maize alleles (CHING et al. 2002; LIU and BURKE 2006) facilitates very high-resolution association mapping; however, concomitantly high DNA marker densities are needed for discovering associations (RISCH 2000; CARDON and BELL 2001; JOHNSON et al. 2001; STUMPF 2002; GREENWOOD et al. 2004; WEIGEL and NORDBORG 2005; KIM et al. 2006). Lower DNA marker densities are needed for association mapping in species where LD persists over greater physical distances, although resolution decreases (CARDON and ABECASIS 2003). Our results indicate that LD persists over longer tracts of DNA in inbred lines than primitive and early open-pollinated cultivars and wild populations in sunflower (LIU and BURKE 2006). LD decayed to r² = 0.1 by 200 bp in wild populations and 1100 bp in OP cultivars (LIU and BURKE 2006), but only decayed to 0.32 by 5500 bp in inbred lines in our study, the longest physical distance surveyed (Figure 6); analyses of longer tracts of DNA are needed to more thoroughly assess LD decay in inbred lines. While there was significant LD variability among loci, the slower decay in sunflower inbred lines can be attributed to population bottlenecks produced by inbreeding and artificial selection, a common phenomenon in domesticated species where intense selection has been practiced for many generations (BUCKLER et al. 2001; CHING et al. 2002; DOEBLEY et al. 2006). Whether analyses are done in domesticated or wild germplasm, very high DNA marker densities are needed for association mapping in sunflower, a species with ample diversity to support such analyses.

	ACKNOWLEDGEMENTS

TOP ABSTRACT MATERIALS AND METHODS RESULTS DISCUSSION ACKNOWLEDGEMENTS LITERATURE CITED

 
This research was supported by grants from the United States Department of Agriculture National Research Initiative Plant Genome Program (no. 2000-04292), the National Science Foundation Plant Genome Program (no. 0421630), and Advanta Semillas.

	FOOTNOTES

 
Sequence data from this article have been deposited with EMBL/GenBank Data Libraries under accession nos. EF469860-EF469941 and EF460879-EF462190.

¹ Present address: Department of Plant Pathology, Cornell University, Ithaca, NY 14853.

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TOP ABSTRACT MATERIALS AND METHODS RESULTS DISCUSSION ACKNOWLEDGEMENTS LITERATURE CITED

 

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