Hypothesis testing with the similarity index

Leonard, Anthony; Franson, Susan E.; Hertzberg, Vicki; Smith, Milton T.; Toth, Gregory P.

doi:10.1046/j.1365-294x.1999.00831.x

Cited by 48 publications

(60 citation statements)

References 16 publications

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“…DNA was extracted and PCR conducted as listed above. From these accessions, the within-accession mean genetic diversity values were also estimated from the 33 SSR markers using the similarity index (Dice 1945;Lynch 1990;Leonard et al 1999). The similarity index is defined as: S xy = 2N m /N x ?…”

Section: Subspecies Diversity Analysismentioning

confidence: 99%

“…N y , where N m is the number of marker bands that are shared between individuals x and y, and N x and N y are the total number of bands present in each respective individual. Standard errors of the mean similarity values were computed as per Leonard et al (1999). As the banding patterns of autopolyploid organisms with codominant markers may not express individual's genotypes (Kosman and Leonard 2005), SSR markers were scored as presence/absence binary data.…”

Section: Subspecies Diversity Analysismentioning

confidence: 99%

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Orchardgrass (Dactylis glomerata L.) EST and SSR marker development, annotation, and transferability

et al. 2011

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Orchardgrass, or cocksfoot [Dactylis glomerata (L.)], has been naturalized on nearly every continent and is a commonly used species for forage and hay production. All major cultivated varieties of orchardgrass are autotetraploid, and few tools or information are available for functional and comparative genetic analyses and improvement of the species. To improve the genetic resources for orchardgrass, we have developed an EST library and SSR markers from salt, drought, and cold stressed tissues. The ESTs were bi-directionally sequenced from clones and combined into 17,373 unigenes. Unigenes were annotated based on putative orthology to genes from rice, Triticeae grasses, other Poaceae, Arabidopsis, and the non-redundant database of the NCBI. Of 1,162 SSR markers developed, approximately 80% showed amplification products across a set of orchardgrass germplasm, and 40% across related Festuca and Lolium species. When orchardgrass subspecies were genotyped using 33 SSR markers their within-accession similarity values ranged from 0.44 to 0.71, with Mediterranean accessions having a higher similarity. The total number of genotyped bands was greater for tetraploid accessions compared to diploid accessions. Clustering analysis indicated grouping of Mediterranean subspecies and central Asian subspecies, while the D. glomerata ssp. aschersoniana was closest related to three cultivated varieties.

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Section: Subspecies Diversity Analysismentioning

confidence: 99%

Section: Subspecies Diversity Analysismentioning

confidence: 99%

Orchardgrass (Dactylis glomerata L.) EST and SSR marker development, annotation, and transferability

et al. 2011

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“…Similarly, support for internal clades were determined using 1,000 bootstrap replicates and heuristic, unweighted Wagner parsimony searches with TBR branch swapping and 10 random addition sequences in each bootstrap replicate. The significance of AFLP variation within and among groups was also tested based on comparisons of similarity coefficients as described by Leonard et al (1999) and analysis of molecular variance (AMOVA) as described below.…”

Section: Aflp Analysismentioning

confidence: 99%

Species delimitation tests of endemic Lepidium papilliferum and identification of other possible evolutionarily significant units in the Lepidium montanum complex (Brassicaceae) of western North America

et al. 2009

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Lepidium papilliferum of southwest Idaho was previously treated as an infraspecific variety of Lepidium montanum. Chloroplast (cpDNA) sequences, nuclear ribosomal internal transcribed spacer (ITS) sequences, and AFLPs were used to test species delimitations and other possible evolutionarily significant units (ESU) based on genetic differentiation, isolation by distance (IBD), and genetic admixture among 32 L. montanum and 21 L. papilliferum collections from the western US. The L. papilliferum AFLP genotypes formed a monophyletic clade. However, the AFLP genotypes of L. montanum samples from eight western sites were more similar to L. papilliferum, which together comprise a regionally significant West clade showing significant differentiation from eastern L. montanum collections (East clade). Bayesian analysis of AFLP genotypes detected possible admixture between L. papilliferum and related western L. montanum collections. Neither taxa nor regionally significant AFLP clades displayed reciprocally monophyletic cpDNA or ITS sequences, but the AFLP clades showed stronger cpDNA differentiation and unique ITS alleles. The East and West clades fit models of speciation with relatively strong IBD within groups and weak IBD between groups, based on correlations between the average number of AFLP differences and geographic distances among collection sites, but comparisons between taxa did not fit this model. Conversely, relatively strong partial correlations between AFLP and taxonomic differences, controlling for geography, support taxonomic delimitations. Results suggest that L. papilliferum is a distinct subgroup of L. montanum influenced by speciation. However, gene flow or common ancestry between L. papilliferum and western forms of L. montanum provide a basis for other possible ESUs.

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“…All other genotypes were anticipated to be hybrid-or direct-descendants of these four base populations. Finally, statistical comparisons of genetic diversity within populations were based on the similarity index (S), based on unbiased estimates of the variance for S corrected for covariance [58].…”

Section: Genetic Testing Of Half-sib Hybrid Seedmentioning

confidence: 99%

Development and Testing of Cool-Season Grass Species, Varieties and Hybrids for Biomass Feedstock Production in Western North America

Larson

Pearson²,

Jensen

et al. 2017

Agronomy

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Abstract:Breeding of native cool-season grasses has the potential to improve forage production and expand the range of bioenergy feedstocks throughout western North America. Basin wildrye (Leymus cinereus) and creeping wildrye (Leymus triticoides) rank among the tallest and most rhizomatous grasses of this region, respectively. The objectives of this study were to develop interspecific creeping wildrye (CWR) × basin wildrye (BWR) hybrids and evaluate their biomass yield relative to tetraploid 'Trailhead', octoploid 'Magnar' and interploidy-hybrid 'Continental' BWR cultivars in comparison with other perennial grasses across diverse single-harvest dryland range sites and a two-harvest irrigated production system. Two half-sib hybrid populations were produced by harvesting seed from the tetraploid self-incompatible Acc:641.T CWR genet, which was clonally propagated by rhizomes into isolated hybridization blocks with two tetraploid BWR pollen parents: Acc:636 and 'Trailhead'. Full-sib hybrid seed was also produced from a controlled cross of tetraploid 'Rio' CWR and 'Trailhead' BWR plants. In space-planted range plots, the 'Rio' CWR × 'Trailhead' BWR and Acc:641.T CWR × Acc:636 BWR hybrids displayed high-parent heterosis with 75% and 36% yield advantages, respectively, but the Acc:641.T CWR × 'Trailhead' BWR hybrid yielded significantly less than its BWR high-parent in this evaluation. Half-sib CWR × BWR hybrids of Acc:636 and 'Trailhead' both yielded as good as or better than available BWR cultivars, with yields similar to switchgrass (Panicum virgatum), in the irrigated sward plots. These results elucidate opportunity to harness genetic variation among native grass species for the development of forage and bioenergy feedstocks in western North America.

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Hypothesis testing with the similarity index

Cited by 48 publications

References 16 publications

Orchardgrass (Dactylis glomerata L.) EST and SSR marker development, annotation, and transferability

Orchardgrass (Dactylis glomerata L.) EST and SSR marker development, annotation, and transferability

Species delimitation tests of endemic Lepidium papilliferum and identification of other possible evolutionarily significant units in the Lepidium montanum complex (Brassicaceae) of western North America

Development and Testing of Cool-Season Grass Species, Varieties and Hybrids for Biomass Feedstock Production in Western North America

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