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11 results for “simple sequence repeat”
Data from: Comparative population genetic analysis of bocaccio rockfish Sebastes paucispinis using anonymous and gene-associated simple sequence repeat loci
Comparative population genetic analyses of traditional and emergent molecular markers aid in determining appropriate use of new technologies. The bocaccio rockfish Sebastes paucispinis is a high-gene-flow marine species off the west coast of North America that experienced strong population decline over the past three decades. We used 18 anonymous and 13 gene associated simple sequence repeat loci (EST-SSRs) to characterize range-wide population structure with temporal replicates. No FST-outliers were detected using the LOSITAN program, suggesting that neither balancing nor divergent selection affected the loci surveyed. Consistent hierarchical structuring of populations by geography or year class was not detected regardless of marker class. The EST-SSRs were less variable than the anonymous SSRs, but no correlation between FST and variation or marker class was observed. General Linear Model analysis showed that low EST-SSR variation was attributable to low mean repeat number. Comparative genomic analysis with Gasterosteus aculeatus, Takifugu rubripes, and Oryzias latipes showed consistently lower repeat number in EST-SSRs than SSR loci that were not in ESTs. Purifying selection likely imposed functional constraints on EST-SSRs resulting in low repeat numbers that affected diversity estimates, but did not affect the observed pattern of population structure.
Unravelling the genetic diversity of water yam (Dioscorea alata L.) accessions from Tanzania using simple sequence repeat (SSR) markers
<p><span>Water yam</span><span> (<em>Dioscorea alata</em></span><span> L.) is among the most cultivated species used as a source of food and income for small-scale farmers in Tanzania. However, little is documented about <em>Dioscorea</em> species available in Tanzania, including their genetic diversity. This study used ten polymorphic microsatellite markers to determine the genetic diversity and relationship of 63 <em>D. alata</em> accessions from six major producing regions. Results revealed a polymorphic information content (PIC) of 0.63, while the number of alleles per locus ranged from 4 to 12 with a mean of 7.60. The expected heterozygosity ranged from 0.17 to 0.74, with a mean of 0.49, which suggests moderate genetic diversity of <em>D. alata</em> accessions. Kagera region had the highest mean number of (1.5) private alleles. Analysis of molecular variance revealed that 91% of the variation was attributed to within-population while among-population contributed 9% of the total variation. The highest Nei's genetic distance (0.65) was for accessions sampled from Arusha and Mtwara regions. Principal coordinate analysis and cluster analysis using Unweighted Paired Group Method using Arithmetic (UPGMA) grouped <em>D. alata</em> accessions into two major clusters regardless of geographical origin and local names. The Bayesian structure analysis confirmed the two clusters obtained in UPGMA and revealed an admixture of <em>D. alata</em> accessions in all six regions suggesting farmers' extensive exchange of planting materials. These results are helpful in the selection of <em>D. alata</em> accessions for breeding programs in Tanzania.</span></p>
Data from: Comparative population genetic analysis of bocaccio rockfish Sebastes paucispinis using anonymous and gene-associated simple sequence repeat loci
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Unravelling the genetic diversity of water yam (Dioscorea alata L.) accessions from Tanzania using simple sequence repeat (SSR) markers
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Spatial and temporal genetic variation in Ethiopian barley (Hordeum vulgare L.) landraces as revealed by simple sequence repeat (SSR) markers
<p>Ethiopia is a center of diversity for barley (<i>Hordeum vulgare </i>L.) and it is grown across different agro-ecologies of the country. Unraveling population structure and gene flow status on temporal scales assists an evaluation of the consequences of physical, demographic as well as overall environmental changes on the stability and persistence of populations. Here, we examine spatial and temporal genetic variation within and among barley landrace samples collected over a period of four decades (1976-2017), using simple sequence repeat (SSR) markers. Our objective was to evaluate spatial and temporal changes in barley population connectivity associated with the closure of geographic origin and time periods. Low to strong genetic diversity was observed among the landraces and STRUCTURE, Neighbour joining tree and Discriminant Analysis of Principal Component analysis revealed three clusters. The cluster analysis revealed a close relationship between landraces along geographic proximity with genetic distance increases along with geographic distance. The grouping of landraces based on altitudinal classes was influenced by geographic proximity. From AMOVA year categories, it was observed that within population genetic diversity much higher than between population genetic diversity and that the temporal differentiation is considerably smaller. The low to strong genetic differentiation between landraces from various geographic origins could be attributed to gene flow across the region as a consequence of seed exchange among farmers. Nevertheless, we found some connectivity between changes in population dynamics as well as contemporary gene flow. The results demonstrate that this set of SSRs was highly informative and was useful in generating a meaningful classification of barley germplasms. Furthermore, our data also suggest that landraces are a source of valuable germplasm for sustainable agriculture in the context of future climate change, and that <i>in-situ</i> conservation strategies based on farmers use can conserve the genetic identity of landraces while allowing adaptation to local-environments.</p>
Spatial and temporal genetic variation in Ethiopian barley (Hordeum vulgare L.) landraces as revealed by simple sequence repeat (SSR) markers
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Computational prediction of miRNAs and their targets in Phaseolus vulgaris using simple sequence repeat signatures
GEO Series GSE68305. Phaseolus vulgaris. 1 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Screening for simple sequences repeat markers in Hemileia vastatrix
<p><span><span><span><span><span><span><span><span><span><span><span><i>Hemileia vastatrix</i> is the most important fungal pathogen affecting <i>Coffea arabica</i> and has invaded nearly every coffee-growing region in the world and the causal agent of recurrent disease epidemics. The development of resistant varieties of coffee against <i>H. vastatrix</i> requires fundamental understanding of the biology of the fungus. However, the complete life cycle of <i>H. vastatrix</i> remains unknown and conflicting studies exist as to whether the fungus is capable of sexual reproduction or not. Here we used population genetics of <i>H. vastatrix </i>to determine the reproductive mode of the fungus across most of its current geographic range. The genetic relationships among <i>H. vastatrix</i> isolates were determined using eight simple sequence repeat markers (SSRs) developed for this study. The analyses of the standardized index of association (rbarD = 0.114 - 0.557, p = 0.001), Hardy Weinberg equilibrium (p ≤ 0.05), and clonal richness (0 - 0.19) all strongly support asexual reproduction of <i>H. vastatrix</i> in all sampled areas. Similarly, the Minimum Spanning Network reinforces the interpretation of clonal reproduction in the global <i>H. vastatrix</i> population. These findings may have profound implications for resistance breeding and other programs against <i>H. vastatrix</i>.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Genetic diversity and population structure of Urochloa grass accessions from Tanzania using simple sequence repeat (SSR) markers
Urochloa (syn.—Brachiaria s.s.) is one of the most important tropical forages that transformed livestock industries in Australia and South America. Farmers in Africa are increasingly interested in growing Urochloa to support the burgeoning livestock business, but the lack of cultivars adapted to African environments has been a major challenge. Therefore, this study examines genetic diversity of Tanzanian Urochloa accessions to provide essential information for establishing a Urochloa breeding program in Africa. A total of 36 historical Urochloa accessions initially collected from Tanzania in 1985 were analyzed for genetic variation using 24 SSR markers along with six South American commercial cultivars. These markers detected 407 alleles in the 36 Tanzania accessions and 6 commercial cultivars. Markers were highly informative with an average polymorphic information content of 0.79. The analysis of molecular variance revealed high genetic variation within individual accessions in a species (92%), fixation index of 0.05 and gene flow estimate of 4.77 showed a low genetic differentiation and a high level of gene flow among populations. An unweighted neighbor-joining tree grouped the 36 accessions and six commercial cultivars into three main clusters. The clustering of test accessions did not follow geographical origin. Similarly, population structure analysis grouped the 42 tested genotypes into three major gene pools. The results showed the Urochloa brizantha (A. Rich.) Stapf population has the highest genetic diversity (I = 0.94) with high utility in the Urochloa breeding and conservation program. As the Urochloa accessions analyzed in this study represented only 3 of 31 regions of Tanzania, further collection and characterization of materials from wider geographical areas are necessary to comprehend the whole Urochloa diversity in Tanzania.
Data from: Genetic diversity and population structure of Urochloa grass accessions from Tanzania using simple sequence repeat (SSR) markers
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Screening for simple sequences repeat markers in Hemileia vastatrix
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