Biomedical subjects

Steven J Knapp

Publications and source records attributed to Steven J Knapp.

17 recordsLinked to original sources

PubMed2026

Scalable medium-density genotyping platforms for cultivar identification, pedigree authentication, marker-assisted and genomic selection, and other applications in strawberry.

A broad spectrum of high-density genotyping approaches, including single-nucleotide polymorphism (SNP) arrays, genotyping-by-sequencing, and whole-genome reduced-representation sequencing, have been shown to perform well in strawberry (Fragaria × ananassa), despite the inherent complexity of the octoploid genome. While these approaches are effective, their routine deployment in breeding programs can be constrained by cost, computational requirements, and workflow complexity. In parallel, many breeding programs continue to rely on locus-specific assays for marker-assisted selection, resulting in fragmented and inefficient genotyping strategies. Here, we describe medium-density amplicon-based genotyping platforms for strawberry designed to provide cost-effective, turnkey solutions that integrate markers used for marker-assisted selection with genome-wide markers suitable for genomic prediction in a single laboratory assay. These platforms were developed by targeting 1,650 or 4,811 target SNPs via amplicon sequencing, and are interoperable with existing high-density genotyping resources, including a widely used 50K SNP array, thereby facilitating data integration across platforms. We benchmarked their performance relative to the 50K SNP array across breeding-relevant applications, including identity and purity testing, pedigree authentication, marker-assisted selection, and genomic selection, and further evaluated the feasibility of genotype imputation to enhance genome-wide information content. Across analyses, the 1,650- and 4,811-amplicon platforms produced results comparable to higher-density platforms while substantially reducing genotyping cost and analytical overhead. This work demonstrates that targeted amplicon-based genotyping can support efficient, scalable, and integrated genome-informed breeding, enabling the routine application of both marker-assisted and genomic selection within strawberry breeding workflows. Open-source R workflows are provided to support streamlined analyses in breeding contexts.

Fragaria↗

PubMed2007

Using variable rate models to identify genes under selection in sequence pairs: their validity and limitations for EST sequences.

Using likelihood-based variable selection models, we determined if positive selection was acting on 523 EST sequence pairs from two lineages of sunflower and lettuce. Variable rate models are generally not used for comparisons of sequence pairs due to the limited information and the inaccuracy of estimates of specific substitution rates. However, previous studies have shown that the likelihood ratio test (LRT) is reliable for detecting positive selection, even with low numbers of sequences. These analyses identified 56 genes that show a signature of selection, of which 75% were not identified by simpler models that average selection across codons. Subsequent mapping studies in sunflower show four of five of the positively selected genes identified by these methods mapped to domestication QTLs. We discuss the validity and limitations of using variable rate models for comparisons of sequence pairs, as well as the limitations of using ESTs for identification of positively selected genes.

Base Pairing↗

PubMed2006

Identification and comparison of natural rubber from two Lactuca species.

Renewed interest in the identification of alternative sources of natural rubber to Hevea brasiliensis has focused on the Compositae family. In our search for Compositae models for rubber synthesis, we extracted latex from stems of two lettuce species: Lactuca serriola, prickly lettuce, and Lactuca sativa cv. Salinas, crisphead lettuce. Both species contained cis-1,4-polyisoprene rubber in the dichloromethane-soluble portions of their latex, and sesquiterpene lactones in their acetone-soluble portions. The rubber from both species and their progeny had molecular weights in excess of 1,000,000g/mol, and polydispersity values of 1.1. Rubber transferase activity was detected across a range of farnesyl diphosphate initiator concentrations, with decreased activity as initiator concentrations exceeded putative saturation. These results add lettuce to the short list of plant species that produce high molecular weight rubber in their latex. Due to the genomic and agronomic resources available in lettuce species, they provide the opportunity for further dissection of natural rubber biosynthesis in plants.

Lactones↗

PubMed2006

Ty3/gypsy-like retrotransposon knockout of a 2-methyl-6-phytyl-1,4-benzoquinone methyltransferase is non-lethal, uncovers a cryptic paralogous mutation, and produces novel tocopherol (vitamin E) profiles in sunflower.

The m (Tph(1)) mutation partially disrupts the synthesis of alpha-tocopherol (vitamin E) in sunflower (Helianthus annuus L.) seeds and was predicted to disrupt a methyltransferase activity necessary for the synthesis of alpha- and gamma-tocopherol. We identified and isolated two 2-methyl-6-phytyl-1,4-benzoquinone/2-methyl-6-solanyl-1,4-benzoquinone methyltransferase (MPBQ/MSBQ-MT) paralogs from sunflower (MT-1 and MT-2), resequenced MT-1 and MT-2 alleles from wildtype (m(+) m(+)) and mutant (m m) inbred lines, identified m as a non-lethal knockout mutation of MT-1 caused by the insertion of a 5.2 kb Ty3/gypsy-like retrotransposon in exon 1, and uncovered a cryptic codominant mutation (d) in a wildtype x mutant F(2) population predicted to be segregating for the m mutation only. MT-1 and m cosegregated and mapped to linkage group 1 and MT-1 was not transcribed in mutant homozygotes (m m). The m locus was epistatic to the d locus--the d locus had no effect in m(+) m(+) and m(+) m individuals, but significantly increased beta-tocopherol percentages in m m individuals. MT-2 and d cosegregated, MT-2 alleles isolated from mutant homozygotes (d d) carried a 30 bp insertion at the start of the 5'-UTR, and MT-2 was more strongly transcribed in seeds and leaves of wildtype (d(+) d(+)) than mutant (d d) homozygotes (transcripts were 2.2- to 5.0-fold more abundant in the former than the latter). The double mutant (m m d d) was non-lethal and produced 24-45% alpha- and 55-74% beta-tocopherol (the wildtype produced 96% alpha- and 4% beta-tocopherol). MT-2 compensated for the loss of the MT-1 function, and the MT-2 mutation profoundly affected the synthesis of tocopherols without adversely affecting the synthesis of plastoquinone crucial for normal plant growth and development.

Chromosome Segregation↗

PubMed2006

Three non-allelic epistatically interacting methyltransferase mutations produce novel tocopherol (vitamin E) profiles in sunflower.

Wildtype sunflower (Helianthus annuus L.) seeds are a rich source of alpha-tocopherol (vitamin E). The g = Tph(2) mutation disrupts the synthesis of alpha-tocopherol, enhances the synthesis of gamma-tocopherol, and was predicted to knock out a gamma-tocopherol methyltransferase (gamma-TMT) necessary for the synthesis of alpha-tocopherol in sunflower seeds--wildtype (g(+) g(+)) lines accumulated > 90% alpha-tocopherol, whereas mutant (g g) lines accumulated > 90% gamma-tocopherol. We identified and isolated two gamma-TMT paralogs (gamma-TMT-1 and gamma-TMT-2). Both mapped to linkage group 8, cosegregated with the g locus, and were transcribed in developing seeds of wildtype lines. The g mutation greatly decreased gamma-TMT-1 transcription, caused alternative splicing of gamma-TMT-1, disrupted gamma-TMT-2 transcription, and knocked out one of two transcription initiation sites identified in the wildtype; gamma-TMT transcription was 36 to 51-fold greater in developing seeds of wildtype (g(+) g(+)) than mutant (g g) lines. F(2) populations (B109 x LG24 and R112 x LG24) developed for mapping the g locus segregated for a previously unidentified locus (d). B109, R112, and LG24 were homozygous for a null mutation (m = Tph(1)) in MT-1, one of two 2-methyl-6-phytyl-1,4-benzoquinone/2-methyl-6-solanyl-1,4-benzoquinone methyltransferase (MPBQ/MSBQ-MT) paralogs identified in sunflower. The d mutations segregating in B109 x LG24 and R112 x LG24 were allelic to a cryptic mutation identified in the other MPBQ/MSBQ-MT paralog (MT-2) and disrupted the synthesis of alpha- and gamma-tocopherol in F(2) progeny carrying m or g mutations--m m g(+) g(+) d d homozygotes accumulated 41.5% alpha- and 58.5% beta-T, whereas m m g g d d homozygotes accumulated 58.1% gamma- and 41.9% delta-T. MT-2 cosegregated with d and mapped to linkage group 4. Hence, novel tocopherol profiles are produced in sunflower seed oil by three non-allelic epistatically interacting methyltransferase mutations.

Alleles↗

PubMed2005

Quantitative trait loci associated with seed and seedling traits in Lactuca.

Seed and seedling traits related to germination and stand establishment are important in the production of cultivated lettuce (Lactuca sativa L.). Six seed and seedling traits segregating in a L. sativa cv. Salinas x L. serriola recombinant inbred line population consisting of 103 F8 families revealed a total of 17 significant quantitative trait loci (QTL) resulting from three seed production environments. Significant QTL were identified for germination in darkness, germination at 25 and 35 degrees C, median maximum temperature of germination, hypocotyl length at 72 h post-imbibition, and plant (seedling) quality. Some QTL for germination and early seedling growth characteristics were co-located, suggestive of pleiotropic loci regulating these traits. A single QTL (Htg6.1) described 25 and 23% of the total phenotypic variation for high temperature germination in California- and Netherlands-grown populations, respectively, and was significant between 33 and 37 degrees C. Additionally, Htg6.1 showed significant epistatic interactions with other Htg QTL and a consistent effect across all the three seed production environments. L. serriola alleles increased germination at these QTL. The estimate of narrow-sense heritability (h2) of Htg6.1 was 0.84, indicating potential for L. serriola as a source of germination thermotolerance for lettuce introgression programs.

Breeding↗

PubMed2005

The self-incompatibility locus (S) and quantitative trait loci for self-pollination and seed dormancy in sunflower.

Wild populations of common sunflower (Helianthus annuus L.) are self-incompatible and have deep seed dormancy, whereas modern cultivars, inbreds, and hybrids are self-compatible and partially-to-strongly self-pollinated, and have shallow seed dormancy. Self-pollination (SP) and seed dormancy are genetically complex traits, the number of self-compatibility (S) loci has been disputed, and none of the putative S loci have been genetically mapped in sunflower. We genetically mapped quantitative trait loci (QTL) for self-incompatibility (SI), SP, and seed dormancy in a backcross population produced from a cross between an elite, self-pollinated, nondormant inbred line (NMS373) and a wild, self-incompatible, dormant population (ANN1811). A population consisting of 212 BC(1) progeny was subsequently produced by backcrossing a single hybrid individual to NMS373. BC(1) progeny produced 0-838 seeds per primary capitula when naturally selfed and 0-518 seeds per secondary capitula when manually selfed and segregated for a single S locus. The S locus mapped to linkage group 17 and was tightly linked to a cluster of previously identified QTL for several domestication and postdomestication traits. Two synergistically interacting QTL were identified for SP among self-compatible (ss) BC(1) progeny (R(2)=34.6%). NMS373 homozygotes produced 271.5 more seeds per secondary capitulum than heterozygotes. Germination percentages of seeds after-ripened for 4 weeks ranged from 0% to 100% among self-compatible BC(1)S(1) families. Three QTL for seed dormancy were identified (R(2)=38.3%). QTL effects were in the predicted direction (wild alleles decreased self-pollination and seed germination). The present analysis differentiated between loci governing SI and SP and identified DNA markers for bypassing SI and seed dormancy in elite x wild crosses through marker-assisted selection.

Chromosome Mapping↗

PubMed2005

Genetic consequences of selection during the evolution of cultivated sunflower.

We mapped quantitative trait loci (QTL) controlling differences in seed oil content and composition between cultivated and wild sunflower and used the results, along with those of a previous study of domestication-related QTL, to guide a genome-wide analysis of genetic variation for evidence of past selection. The effects of the seed oil QTL were almost exclusively in the expected direction with respect to the parental phenotypes. A major, oil-related QTL cluster mapped near a cluster of domestication-related QTL on linkage group six (LG06), the majority of which have previously been shown to have effects that are inconsistent with the parental phenotypes. To test the hypothesis that this region was the target of a past selective sweep, perhaps resulting in the fixation of the antagonistic domestication-related QTL, we analyzed simple sequence repeat (SSR) diversity from 102 markers dispersed throughout the sunflower genome. Our results indicate that LG06 was most likely the target of multiple selective sweeps during the postdomestication era. Strong directional selection in concert with genetic hitchhiking therefore offers a possible explanation for the occurrence of numerous domestication-related QTL with apparently maladaptive phenotypic effects.

Biological Evolution↗

PubMed2005

Extensive chromosomal repatterning and the evolution of sterility barriers in hybrid sunflower species.

New species may arise via hybridization and without a change in ploidy. This process, termed homoploid hybrid speciation, is theoretically difficult because it requires the development of reproductive barriers in sympatry or parapatry. Theory suggests that isolation may arise through rapid karyotypic evolution and/or ecological divergence of hybrid neospecies. Here, we investigate the role of karyotypic change in homoploid hybrid speciation by generating detailed genetic linkage maps for three hybrid sunflower species, Helianthus anomalus, H. deserticola, and H. paradoxus, and comparing these maps to those previously generated for the parental species, H. annuus and H. petiolaris. We also conduct a quantitative trait locus (QTL) analysis of pollen fertility in a BC2 population between the parental species and assess levels of pollen and seed fertility in all cross-combinations of the hybrid and parental species. The three hybrid species are massively divergent from their parental species in karyotype; gene order differences were observed for between 9 and 11 linkage groups (of 17 total), depending on the comparison. About one-third of the karyoypic differences arose through the sorting of chromosomal rearrangements that differentiate the parental species, but the remainder appear to have arisen de novo (six breakages/six fusions in H. anomalus, four breakages/three fusions in H. deserticola, and five breakages/five fusions in H. paradoxus). QTL analyses indicate that the karyotypic differences contribute to reproductive isolation. Nine of 11 pollen viability QTL occur on rearranged chromosomes and all but one map close to a rearrangement breakpoint. Finally, pollen and seed fertility estimates for F1's between the hybrid and parental species fall below 11%, which is sufficient for evolutionary independence of the hybrid neospecies.

Chromosome Mapping↗

PubMed2004

Chemical composition of caneberry (Rubus spp.) seeds and oils and their antioxidant potential.

Caneberries (Rubus spp. L.) are grown primarily throughout the Pacific Northwestern United States and Canada. Processing of caneberry fruit typically removes the seed, and the development of a value-added use of seeds could expand the market for caneberries and the profit margins for growers. An initial step toward the use of the seeds is a characterization of seed and oil. Our investigation has described compositional characteristics for seeds of five commonly grown caneberry species: red raspberry, black raspberry, boysenberry, Marion blackberry, and evergreen blackberry. Seeds from all five species had 6-7% protein and 11-18% oil. The oils contained 53-63% linoleic acid, 15-31% linolenic acid, and 3-8% saturated fatty acids. The two smaller seeded raspberry species had higher percentages of oil, the lowest amounts of saturated fatty acid, and the highest amounts of linolenic acid. Antioxidant capacities were detected both for whole seeds and for cold-pressed oils but did not correlate to total phenolics or tocopherols. Ellagitannins and free ellagic acid were the main phenolics detected in all five caneberry species and were approximately 3-fold more abundant in the blackberries and the boysenberry than in the raspberries.

Amino Acids↗

PubMed2004

Acetohydroxyacid synthase mutations conferring resistance to imidazolinone or sulfonylurea herbicides in sunflower.

Wild biotypes of cultivated sunflower ( Helianthus annuus L.) are weeds in corn ( Zea mays L.), soybean ( Glycine max L.), and other crops in North America, and are commonly controlled by applying acetohydroxyacid synthase (AHAS)-inhibiting herbicides. Biotypes resistant to two classes of AHAS-inhibiting herbicides-imidazolinones (IMIs) or sulfonylureas (SUs)-have been discovered in wild sunflower populations (ANN-PUR and ANN-KAN) treated with imazethapyr or chlorsulfuron, respectively. The goals of the present study were to isolate AHAS genes from sunflower, identify mutations in AHAS genes conferring herbicide resistance in ANN-PUR and ANN-KAN, and develop tools for marker-assisted selection (MAS) of herbicide resistance genes in sunflower. Three AHAS genes ( AHAS1, AHAS2, and AHAS3) were identified, cloned, and sequenced from herbicide-resistant (mutant) and -susceptible (wild type) genotypes. We identified 48 single-nucleotide polymorphisms (SNPs) in AHAS1, a single six-base pair insertion-deletion in AHAS2, and a single SNP in AHAS3. No DNA polymorphisms were found in AHAS2 among elite inbred lines. AHAS1 from imazethapyr-resistant inbreds harbored a C-to-T mutation in codon 205 ( Arabidopsis thaliana codon nomenclature), conferring resistance to IMI herbicides, whereas AHAS1 from chlorsulfuron-resistant inbreds harbored a C-to-T mutation in codon 197, conferring resistance to SU herbicides. SNP and single-strand conformational polymorphism markers for AHAS1, AHAS2, and AHAS3 were developed and genetically mapped. AHAS1, AHAS2, and AHAS3 mapped to linkage groups 2 ( AHAS3), 6 ( AHAS2), and 9 ( AHAS1). The C/T SNP in codon 205 of AHAS1 cosegregated with a partially dominant gene for resistance to IMI herbicides in two mutant x wild-type populations. The molecular breeding tools described herein create the basis for rapidly identifying new mutations in AHAS and performing MAS for herbicide resistance genes in sunflower.

Acetolactate Synthase↗

PubMed2004

Comparative mapping and rapid karyotypic evolution in the genus helianthus.

Comparative genetic linkage maps provide a powerful tool for the study of karyotypic evolution. We constructed a joint SSR/RAPD genetic linkage map of the Helianthus petiolaris genome and used it, along with an integrated SSR genetic linkage map derived from four independent H. annuus mapping populations, to examine the evolution of genome structure between these two annual sunflower species. The results of this work indicate the presence of 27 colinear segments resulting from a minimum of eight translocations and three inversions. These 11 rearrangements are more than previously suspected on the basis of either cytological or genetic map-based analyses. Taken together, these rearrangements required a minimum of 20 chromosomal breakages/fusions. On the basis of estimates of the time since divergence of these two species (750,000-1,000,000 years), this translates into an estimated rate of 5.5-7.3 chromosomal rearrangements per million years of evolution, the highest rate reported for any taxonomic group to date.

Biological Evolution↗

PubMed2003

PCR-multiplexes for a genome-wide framework of simple sequence repeat marker loci in cultivated sunflower.

Simple sequence repeat (SSR) and other DNA sequence-tagged site markers can be genotyped more rapidly and cost efficiently by simultaneously amplifying multiple loci (multiplex PCR). The development of PCR-multiplexes for a nearly genome-wide framework of 78 SSR marker loci in cultivated sunflower ( Helianthus annuus L.) is described herein. The most outstanding single-locus SSR markers in the public collection (300 out of 1,089) were identified and screened for polymorphisms among 24 elite inbred lines, preparatory to selecting SSR markers for testing in multiplex PCRs. The selected SSR markers produced robust PCR products, amplified a single locus each, were polymorphic among elite inbred lines (minimum, mean and maximum heterozygosities were 0.08, 0.53 and 0.85, respectively), and supply a dense genome-wide framework of predominantly or completely codominant, single-locus DNA markers for molecular breeding and genomics research in sunflower. Thirteen six-locus multiplex PCRs were developed for 78 SSR marker loci strategically positioned throughout the sunflower genome (three to five per linkage group) by identifying compatible SSR primer combinations and optimizing multiplex PCR protocols. The multiplexed SSR markers, when coupled with 17 complementary SSR marker loci, create a 'standard genotyping' set ideal for first-pass scans of the genome, as are often needed when screening bulked-segregant DNA samples or mapping phenotypic trait loci. The minimum, mean and maximum heterozygosities of the multiplexed SSR markers were 0.38, 0.62 and 0.83, respectively. The PCR-multiplexes increase genotyping throughput, reduce reagent costs, and are ideal for repetitive genotyping applications where common sets of SSR marker loci are required or advantageous.

Chromosome Mapping↗

PubMed2003

Haplotyping and mapping a large cluster of downy mildew resistance gene candidates in sunflower using multilocus intron fragment length polymorphisms.

Downy mildew (Plasmopara halstedii (Farl.) Berlese et de Toni) is a serious foliar pathogen of cultivated sunflower (Helianthus annuus L.). Genetic resistance is conditioned by several linked downy mildew resistance gene specificities in the HaRGC1 cluster of TIR-NBS-LRR resistance gene candidates (RGCs) on linkage group 8. The complexity and diversity of the HaRGC1 cluster was assessed by multilocus intron fragment length polymorphism (IFLP) genotyping using a single pair of primers flanking a hypervariable intron located between the TIR and NBS domains. Two to 23 bands were amplified per germplasm accession. The size of the included intron ranged from 89 to 858 nucleotides. Forty-eight unique markers were distinguished among 24 elite inbred lines, six partially isogenic inbred lines, nine open-pollinated populations, four Native American land races, and 20 wild H. annuus populations. Nine haplotypes (based on 24 RGCs) were identified among elite inbred lines and were correlated with known downy mildew resistance specificities. Sixteen out of 39 RGCs identified in wild H. annuus populations were not observed in elite germplasm. Five partially isogenic downy mildew resistant lines developed from wild H. annuus and H. praecox donors carried eight RGCs not found in other elite inbred lines. Twenty-four HaRGC1 loci were mapped to a 2-4 cM segment of linkage group 8. The multilocus IFLP marker and duplicated, hypervariable microsatellite markers tightly linked to the HaRGC1 cluster are powerful tools for distinguishing downy mildew resistance gene specificities and identifying and introgressing new downy mildew resistance gene specificities from wild sunflowers.

Journal Article↗

PubMed2002

Microsatellites uncover extraordinary diversity in native American land races and wild populations of cultivated sunflower.

The contemporary oilseed sunflower (Helianthus annuus L.) gene pool is a product of multiple breeding and domestication bottlenecks. Despite substantial phenotypic diversity, modest differences in molecular genetic diversity have been uncovered in anciently and recently domesticated sunflowers. The paucity of molecular marker polymorphisms in early analyses led to the hypothesis of a single domestication origin. Phylogenetic analyses were performed on 47 domesticated and wild germplasm accessions using 122 microsatellite loci distributed throughout the sunflower genome. Extraordinary allelic diversity was found in the Native American land races and wild populations, and progressively less allelic diversity was found in germplasm produced by successive cycles of domestication and breeding. Of 1,341 microsatellite alleles, 489 were unique to land races, exotic domesticates and wild populations, whereas only 15 were unique to elite inbred lines. The number of taxon-specific alleles was 35-fold greater among wild populations (26.27) than elite inbred lines (0.75). Microsatellite genotyping uncovered the possibility of multiple domestication origins. Land races domesticated by Native Americans of the southwestern US (Hopi and Havasupai) formed a clade independent of land races domesticated by Native Americans of the Great Plains and eastern US (Arikara and Seneca). Predictably, domestication and breeding have ratcheted genetic diversity down in sunflower. The contemporary oilseed sunflower gene pool, while not imperiled, could profit from an infusion of novel alleles from the reservoir of latent genetic diversity present in wild populations and Native American land races.

Alleles↗

PubMed2002

Genetic analysis of sunflower domestication.

Quantitative trait loci (QTL) controlling phenotypic differences between cultivated sunflower and its wild progenitor were investigated in an F(3) mapping population. Composite interval mapping revealed the presence of 78 QTL affecting the 18 quantitative traits of interest, with 2-10 QTL per trait. Each QTL explained 3.0-68.0% of the phenotypic variance, although only 4 (corresponding to 3 of 18 traits) had effects >25%. Overall, 51 of the 78 QTL produced phenotypic effects in the expected direction, and for 13 of 18 traits the majority of QTL had the expected effect. Despite being distributed across 15 of the 17 linkage groups, there was a substantial amount of clustering among QTL controlling different traits. In several cases, regions influencing multiple traits harbored QTL with antagonistic effects, producing a cultivar-like phenotype for some traits and a wild-like phenotype for others. On the basis of the directionality of QTL, strong directional selection for increased achene size appears to have played a central role in sunflower domestication. None of the other traits show similar evidence of selection. The occurrence of numerous wild alleles with cultivar-like effects, combined with the lack of major QTL, suggests that sunflower was readily domesticated.

Chromosome Mapping↗

PubMed2002

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

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.

DNA Primers↗