Tim Samuels

Oklahoma State University - Stillwater, Stillwater, Oklahoma, United States

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Publications (6)9.81 Total impact

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    ABSTRACT: Switchgrass (Panicum virgatum L.) is a model cellulosic biofuel crop in the United States. Simple sequence repeat (SSR) markers are valuable resources for genetic mapping and molecular breeding. A large number of expressed sequence tags (ESTs) of switchgrass are recently available in our sequencing project. The objectives of this study were to develop new SSR markers from the switchgrass EST sequences and to integrate them into an existing linkage map. More than 750 unique primer pairs (PPs) were designed from 243,600 EST contigs and tested for PCR amplifications, resulting in 538 PPs effectively producing amplicons of expected sizes. Of the effective PPs, 481 amplifying informative bands in NL94 were screened for polymorphisms in a panel consisting of NL94 and its seven first-generation selfed (S1) progeny. This led to the selection of 117 polymorphic EST–SSRs to genotype a mapping population encompassing 139 S1 individuals of NL94. Of 83 markers demonstrating clearly scorable alleles in the mapping population, 79 were integrated into a published linkage map, with three linked to accessory loci and one unlinked. The newly identified EST–SSR loci were distributed in 17 of 18 linkage groups with 27 (32.5 %) exhibiting distorted segregations. The integration of EST–SSRs aided in reducing the average marker interval (cM) to 3.7 from 4.2, and reduced the number of gaps (each[15 cM) to 10 from 23. Developing new EST–SSRs and constructing a higher density linkage map will facilitate quantitative trait locus mapping and provide a firm footing for marker-assisted breeding in switchgrass.
    Molecular Breeding 07/2013; · 3.25 Impact Factor
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    ABSTRACT: Bermudagrass, Cynodon spp, is economically important as a major turf and forage species in the southern United States. However, in transition zones and higher altitude areas, winter survivability is a major concern. Freeze tolerance in bermudagrass is a heritable trait. Limited SSR markers are currently available for bermudagrass research. The objective of this study was to analyze two bermudagrass populations using genomic SSR markers. Within each population they will be further analyzed on the basis of winter survivability by selecting plants that survived the winter and comparing them with the original plants within the given population. Genomic DNA samples were extracted from the bermudagrass genotypes ‘RV’ and ‘YK’. Five libraries were constructed for SSRs enriched for CA-, GA-, ATG-, AAC- and CAG-sequences. A total of 44 non-redundant highly amplified polymorphic markers from all five libraries were used in this study. Results indicate that RV winter survival selection population produced significant different banding patterns that the original population in 86.4% of the SSR markers used. YK data showed a significant difference between winter survival and original population in 36.4% of the SSR markers used. It is interesting to note that RV was significantly different from YK in 34.1% of the markers used. This data suggests the two germplasms used in this study, should be used in breeding new cold tolerant bermudagrass cultivars. 76 Proteomic analysis of Miscanthus sinensis leaves subjected to heat
    01/2013;
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    ABSTRACT: Bermudagrass, Cynodon spp, is economically important as a major turf and forage species in the southern United States. However, in transition zones and higher altitude areas, winter survivability is a major concern. Freeze tolerance in bermudagrass is a heritable trait. Limited SSR markers are currently available for bermudagrass research. The objective of this study was to analyze two bermudagrass populations using genomic SSR markers. Within each population they will be further analyzed on the basis of winter survivability by selecting plants that survived the winter and comparing them with the original plants within the given population. Genomic DNA samples were extracted from the bermudagrass genotypes ‘RV’ and ‘YK’. Five libraries were constructed for SSRs enriched for CA-, GA-, ATG-, AAC- and CAG-sequences. A total of 44 non-redundant highly amplified polymorphic markers from all five libraries were used in this study. Results indicate that RV winter survival selection population produced significant different banding patterns that the original population in 86.4% of the SSR markers used. YK data showed a significant difference between winter survival and original population in 36.4% of the SSR markers used. It is interesting to note that RV was significantly different from YK in 34.1% of the markers used. This data suggests the two germplasms used in this study, should be used in breeding new cold tolerant bermudagrass cultivars.
    Proceedings of the 7th International Symposium on the Molecular Breeding of Forage and Turf MBFT2012 – Salt Lake City, Utah, USA; 06/2012
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    ABSTRACT: Switchgrass (Panicum virgatum) has been identified as a promising cellulosic biofuel crop in the United States. Construction of a genetic linkage map is fundamental for switchgrass molecular breeding and the elucidation of its genetic mechanisms for economically important traits. In this study, a novel population consisting of 139 selfed progeny of a northern lowland genotype, NL 94 LYE 16X13, was used to construct a linkage map. A total of 2493 simple sequence repeat markers were screened for polymorphism. Of 506 polymorphic loci, 80.8% showed a goodness-of-fit of 1:2:1 segregation ratio. Among 469 linked loci on the framework map, 241 coupling vs. 228 repulsion phase linkages were detected that conformed to a 1:1 ratio, confirming disomic inheritance. A total of 499 loci were mapped to 18 linkage groups (LG), of which the cumulative length was 2085.2 cM, with an average marker interval of 4.2 cM. Nine homeologous LG pairs were identified based on multi-allele markers and comparative genomic analysis. Two clusters of segregation-distorted loci were identified on LG 5b and 9b, respectively. Comparative analysis indicated a one-to-one relationship between nine switchgrass homeologous groups and nine foxtail millet (Setaria italica) chromosomes, suggesting strong homology between the two species. The linkage map derived from selfing a heterozygous parent, instead of two separate maps usually constructed for a cross-fertilized species, provides a new genetic framework to facilitate genomics research, quantitative trait locus (QTL) mapping, and marker-assisted breeding.
    G3-Genes Genomes Genetics 03/2012; 2(3):357-70. · 1.79 Impact Factor
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    ABSTRACT: 2103 RESEARCH B ermudagrass (Cynodon spp.) is economically the most important and extensively used warm-season turfgrass in the southern United States and in many other countries with warmer climates. Most of the commercialized turf bermudagrass cultivars have been vegetatively propagated, although private companies have dem-onstrated increased interest in the development of seeded cultivars (Taliaferro, 2003). Vegetatively propagated bermudagrass cultivars provide extremely beautiful and uniform turf for golf courses, sports fi elds, commercial grounds, and residential lawns (Hanna and Anderson, 2008). Clonal bermudagrass cultivars are easily asexually propagated by means of their stolons, shoots, and rhi-zomes through transport and installation of sod, plugs, and sprigs. Commercial sod production of clonal bermudagrass cultivars is large and widespread in the USA. Turf bermudagrass cultivars are diff erent in turf quality, adaptation, management requirement, and cost of sod production. Selection of the cultivar with the best fi t for a specifi c scenario is important so as to increase the likelihood ABSTRACT Accurate identifi cation of bermudagrass (Cyn-odon spp.) cultivars is necessary to ensure the purity of the cultivars produced by sod farmers, to protect the intellectual property of cultivar devel-opers, and to assure cultivar purity for the benefi t of turfgrass consumers. Vegetatively propagated turf bermudagrass cultivars have been exten-sively used in the turf industry not only in the USA but also in many other countries. Accordingly, the objectives of the study were to examine simple sequence repeat (SSR) markers for their ability to distinguish commonly grown clonal turf ber-mudagrass cultivars, which were derived through crosses and mutations, from each other and their respective parent cultivars and to develop a set of SSR markers for accurate identifi cation of com-mercially used clonal cultivars. Thirty-two clonal turf bermudagrass genotypes comprising 29 commercially released cultivars and 3 Oklahoma State University experimental lines were assessed by 11 microsatellite markers. A total of 141 DNA fragments were generated for the 11 primer pairs in the 32 bermudagrass genotypes, with an aver-age of 12.8 bands per primer pair. Forty-four frag-ments were cultivar specifi c. The SSR markers successfully identifi ed 22 cultivars when mutant cultivars had the same banding patterns as the 2 parent cultivars, 'Tifgreen' and 'Tifway'. It was concluded from the study that the SSR markers are highly polymorphic and can be utilized as a reliable tool for accurate cultivar identifi cation in nonmutated bermudagrass.
    Crop Science 09/2010; 50:2103-2111. · 1.51 Impact Factor
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    ABSTRACT: Bermudagrass (Cynodon spp.) is extensively cultivated for forage and turf in the the southern United States and in parts of Asia, Africa, southern Europe, Australia and South America. However, few simple sequence repeat (SSR) markers are available for bermudagrass genetics research. Accordingly, the objective of this study was to develop SSR markers in bermudagrass by transferring sorghum genomic SSR primers and by exploring bermudagrass expressed sequence tags (ESTs) from the National Center for Biotechnology Information (NCBI) database. The transferability of 354 tested sorghum SSRs was 57% to C. transvaalensis T577 (2n=2x=18), 27% to C. dactylon Tifton 10 (2n=6x=54) and 22% to Zebra (2n=4x=36). Among the transferred SSRs, 65 primer pairs generated reproducible SSR bands across the three genotypes. From 20,237 Cynodon ESTs at NCBI, 303 designed SSR primer pairs amplified target bands in at least one of C. dactylon var. aridus (2n=2x=18), C. transvaalensis T577, C. dactylon cv. Tifton 10, and C. dactylon var. dactylon Zebra. Of the effective EST SSRs, 230 primer pairs produced reproducible bands in all four genotypes. The study demonstrated that EST sequences and sorghum SSR primers are useful sources for the development of SSR markers for bermudagrass. The developed SSR markers will make a valuable contribution to the molecular identification of commercial cultivars, construction of genetic maps, and marker-assisted breeding in bermudagrass. KeywordsSimple sequence repeat (SSR)– Cynodon –Bermudagrass–Molecular marker–Expressed sequence tag (EST)
    Molecular Breeding 29(1):23-30. · 3.25 Impact Factor