Allelic diversity of simple sequence repeats among elite inbred lines of cultivated sunflower

Abstract

Simple sequence repeat (SSR) markers were developed for cultivated sunflower (Helianthus annuus L.) from the DNA sequences of 970 clones isolated from genomic DNA libraries enriched for (CA)n,, (CT)n, (CAA)n, (CATA)n, or (GATA)n. The clones harbored 632 SSRs, of which 259 were unique. SSR markers were developed for 130 unique SSRs by designing and testing primers for 171 unique SSRs. Of the total, 74 SSR markers were polymorphic when screened for length polymorphisms among 16 elite inbred lines. The mean number of alleles per locus was 3.7 for dinucleotide, 3.6 for trinucleotide, and 9.5 for tetranucleotide repeats and the mean polymorphic information content (PIC) scores were 0.53 for dinucleotide, 0.53 for trinucleotide, and 0.83 for tetranucleotide repeats. Cluster analyses uncovered patterns of genetic diversity concordant with patterns produced by RFLP fingerprinting. SSRs were found to be slightly more polymorphic than RFLPs. Several individual SSRs were significantly more polymorphic than RFLP and other DNA markers in sunflower (20% of the polymorphic SSR markers had PIC scores ranging from 0.70 to 0.93). The newly developed SSRs greatly increase the supply of sequence-based DNA markers for DNA fingerprinting, genetic mapping, and molecular breeding in sunflower; however, several hundred additional SSR markers are needed to routinely construct complete genetic maps and saturate the genome.

Single Nucleotide Polymorphisms and Linkage Disequilibrium in Sunflower

“…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 3 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 Yu et al 2002Yu et al , 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).…”

“…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(Tenaillon et al , 2002Yu et al 2002Yu et al , 2003Liu 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 Tang and Knapp 2003;Kolkman et al 2004;Liu and Burke 2006).…”

“…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 ¼ 2x ¼ 34) (Berry et al 1995;Gedil et al 2001;Yu et al 2002Yu et al , 2003.…”

Genetic Consequences of Selection During the Evolution of Cultivated Sunflower

“…To test for the signature of selection on LG06, we analyzed patterns of SSR variation across the sunflower genome using the software package POPGENE (version 1.31;Yehet al 1999). This analysis was based on genotypic data from a total of 102 single-locus, codominant SSR loci (supplemental Table 1S at http:/ /www.genetics.org/supplemental/) that were run on a panel consisting of one individual from each of 15 wild sunflower populations, 13 Native American landraces and openpollinated, primitive cultivars (hereafter referred to as the ''exotic'' lines), and 16 highly improved, elite oilseed inbred lines (supplemental Table 2S at http:/ /www.genetics.org/ supplemental/; see Knapp 2003 andYu et al 2002 for additional details regarding both the markers employed and the individuals surveyed). The number of markers per linkage group ranged from three to eight, with a total of eight loci (ORS57, ORS339, ORS349, ORS381, ORS608, ORS678, ORS1193, and HT769) residing on LG06 (Burke et al , 2004Tang et al 2002;Yu et al 2003).…”

Development of microsatellite markers in Cannabis Sativa for fingerprinting and genetic relatedness analyses

“…Microsatellite markers have shown high levels of polymorphism in many plant species including rice [96], tropical trees [97], Hop [95], oat [98], maize [99], wheat [100], sunflower [101], and many more. To discriminate between different cultivars of C. sativa and to potentially associate the samples of clonal origin using microsatellites, the selected STR loci would need to be highly polymorphic.…”