scholarly journals Development and Characterization of Microsatellite Markers for a Little Bluestem Collection

2015 ◽  
Vol 140 (1) ◽  
pp. 78-87 ◽  
Author(s):  
Karen Harris-Shultz ◽  
Melanie Harrison ◽  
Phillip A. Wadl ◽  
Robert N. Trigiano ◽  
Timothy Rinehart
Keyword(s):  
Microsatellite Markers ◽  
Ploidy Level ◽  
High Throughput Sequencing ◽  
Genomic Library ◽  
Long Terminal Repeat Retrotransposons ◽  
Schizachyrium Scoparium ◽  
Little Bluestem ◽  
Sequence Identifier ◽  
Primer Sets ◽  
Successful Amplification

Little bluestem (Schizachyrium scoparium) is a perennial bunchgrass that is native to North American prairies and woodlands from southern Canada to northern Mexico. Originally used as a forage grass, little bluestem is now listed as a major U.S. native, ornamental grass. With the widespread planting of only a few cultivars, we aimed to assess the ploidy level and genetic diversity among some popular cultivars and accessions in the U.S. Department of Agriculture National Plant Germplasm System collection. Ten microsatellite markers, with successful amplification, were developed by using sequences available in Genbank and additional simple sequence repeat (SSR) markers were generated by using ion torrent sequencing of a genomic library created from the cultivar The Blues. A total of 2812 primer sets was designed from high-throughput sequencing, 100 primer pairs were selected, and 82 of these primers successfully amplified DNA from the Schizachyrium accessions. Only 35 primer pairs, generating 102 scored fragments, were polymorphic among S. scoparium accessions. Twenty-two primer pairs generated more than four fragments per accession. The use of a repetitive sequence identifier found that of 117 examined sequences, only nine sequences did not have similarity to DNA transposons, retrotransposons, viruses, or satellite sequences. The most frequently identified fragments were the long terminal repeat retrotransposons Gypsy (177 fragments) and Copia (98 fragments) and the DNA transposon EnSpm (60 fragments). Using the software program Structure, cluster analysis of the SSR data for S. scoparium revealed four groups. The lowest genetic similarity between little bluestem samples was 86%, which was surprising as a high degree of morphological variation is seen in this species. Furthermore, no variation in ploidy level was seen among little bluestem samples. These microsatellite markers are the first sequence-specific markers designed for little bluestem and can serve as a resource for future genetic studies.

Successful development of microsatellite markers in a challenging species: the horizontal borer Austroplatypus incompertus (Coleoptera: Curculionidae)

2011 ◽  
Vol 101 (5) ◽  
pp. 551-555 ◽  
Author(s):  
S. Smith ◽  
T. Joss ◽  
A. Stow
Keyword(s):  
Microsatellite Markers ◽  
High Throughput ◽  
Evolutionary Biology ◽  
High Throughput Sequencing ◽  
Genomic Library ◽  
454 Sequencing ◽  
Cost Effective ◽  
Microsatellite Isolation ◽  
Potential Benefits ◽  
Neutral Markers

AbstractThe analysis of microsatellite loci has allowed significant advances in evolutionary biology and pest management. However, until very recently, the potential benefits have been compromised by the high costs of developing these neutral markers. High-throughput sequencing provides a solution to this problem. We describe the development of 13 microsatellite markers for the eusocial ambrosia beetle, Austroplatypus incompertus, a significant pest of forests in southeast Australia. The frequency of microsatellite repeats in the genome of A. incompertus was determined to be low, and previous attempts at microsatellite isolation using a traditional genomic library were problematic. Here, we utilised two protocols, microsatellite-enriched genomic library construction and high-throughput 454 sequencing and characterised 13 loci which were polymorphic among 32 individuals. Numbers of alleles per locus ranged from 2 to 17, and observed and expected heterozygosities from 0.344 to 0.767 and from 0.507 to 0.860, respectively. These microsatellites have the resolution required to analyse fine-scale colony and population genetic structure. Our work demonstrates the utility of next-generation 454 sequencing as a method for rapid and cost-effective acquisition of microsatellites where other techniques have failed, or for taxa where marker development has historically been both complicated and expensive.

Identifying Native Prairie Grass Seedlings

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 450e-451
Author(s):  
Virginia A. Gaynor ◽  
Mary Hockenberry Meyer
Keyword(s):  
Panicum Virgatum ◽  
Schizachyrium Scoparium ◽  
Sorghastrum Nutans ◽  
Native Prairie ◽  
Switch Grass ◽  
Little Bluestem ◽  
Prairie Grass ◽  
Central United States ◽  
Prairie Restorations ◽  
Sideoats Grama

There is great interest in prairie gardens and prairie restorations in the central United States. Small prairie gardens are often established with plugs, but most restorationists and landscape contractors use seed for large plantings. If initial establishment is poor, restorations are often interseeded the second or third season. However, to evaluate early establishment and determine if interseeding is necessary, contractors must be able to identify native grasses in the seedling and juvenile stages. In this study we investigated vegetative characteristics of native prairie grass seedlings. Seven species of native prairie grass were grown in the greenhouse: Andropogon gerardii (big bluestem), Sorghastrum nutans (Indian grass), Panicum virgatum (switch grass), Schizachyrium scoparium (little bluestem), Bouteloua curtipendula (sideoats grama), Elymus canadensis (Canada wildrye), and Bromus kalmii (Kalmís brome). Every 2 to 3 weeks after germination, seedlings were photographed, pressed, and mounted. Additional photographs were taken through the dissecting scope at key stages of development. Ligules and auricles were found to be useful in distinguishing species, and our close-up photographs highlight these structures. Hairiness and color were variable within a species and could not be used reliably in identification. A seedling identification key will be presented for the species studied.

scholarly journals Polymorphic DNA microsatellite markers for forensic individual identification and parentage analyses of seven threatened species of parrots (family Psittacidae)

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2416 ◽  
Author(s):  
Catherine Jan ◽  
Luca Fumagalli
Keyword(s):  
Microsatellite Markers ◽  
Threatened Species ◽  
Captive Breeding ◽  
Genomic Library ◽  
Habitat Destruction ◽  
Individual Identification ◽  
Illegal Trade ◽  
The Mean ◽  
Dna Microsatellite ◽  
Dna Microsatellite Markers

The parrot family represents one of the bird group with the largest number of endangered species, as a result of habitat destruction and illegal trade. This illicit traffic involves the smuggling of eggs and animals, and the laundering through captive breeding facilities of wild-caught animals. Despite the huge potential of wildlife DNA forensics to determine with conclusive evidence illegal trade, current usage of DNA profiling approaches in parrots has been limited by the lack of suitable molecular markers specifically developed for the focal species and by low cross-species polymorphism. In this study, we isolated DNA microsatellite markers in seven parrot species threatened with extinction (Amazona brasiliensis,A. oratrix,A. pretrei,A. rhodocorytha,Anodorhynchus leari,Ara rubrogenysandPrimolius couloni). From an enriched genomic library followed by 454 pyrosequencing, we characterized a total of 106 polymorphic microsatellite markers (mostly tetranucleotides) in the seven species and tested them across an average number of 19 individuals per species. The mean number of alleles per species and across loci varied from 6.4 to 8.3, with the mean observed heterozygosities ranging from 0.65 to 0.84. Identity and parentage exclusion probabilities were highly discriminatory. The high variability displayed by these microsatellite loci demonstrates their potential utility to perform individual genotyping and parentage analyses, in order to develop a DNA testing framework to determine illegal traffic in these threatened species.

High-Throughput Sequencing for Life-History Sorting and for Bridging Reference Sequences in Marine Gerromorpha (Insecta: Heteroptera)

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Jia Jin Marc Chang ◽  
Yin Cheong Aden Ip ◽  
Lanna Cheng ◽  
Ismael Kunning ◽  
Ralph R Mana ◽  
...  
Keyword(s):  
Life History ◽  
High Throughput Sequencing ◽  
Association Studies ◽  
Morphological Characters ◽  
Adult Males ◽  
Accurate Identification ◽  
Life History Stages ◽  
Coi Sequences ◽  
Primer Sets ◽  
Insect Taxonomy

Abstract Accurate identification and association of larval specimens with adults is a major challenge in insect taxonomy. Fortunately, it is now possible for nonexperts to sort collections of bulk samples with DNA barcodes rapidly and cost-effectively. We demonstrate this process using nanopore barcoding of 757 marine insects (Insecta: Gerromorpha), of which 81% were nymphs and many samples did not have co-occurring adult males for specific identification. We successfully associated 738 specimens (97%) to nine gerromorphan species, which would have been impossible to identify using morphological characters alone. This improved ability to incorporate information from all life-history stages has led to greater precision of species distributional ranges—knowledge that will be crucial for a more complete understanding of marine insects. We also highlighted two distinct, nonoverlapping Gerromorpha COI sequence databases on GenBank—a consequence of using two different primer sets to amplify different regions of COI. This issue inevitably hinders species identification with DNA-based methods, particularly for poorly represented groups such as marine insects. We bridged these databases by analyzing full-length COI sequences. We believe this will inspire future studies to incorporate DNA-based methods for more adult–larval association studies and for enhancing existing genetic resources, especially in understudied groups.

scholarly journals DNA metabarcoding of insects and allies: an evaluation of primers and pipelines

2015 ◽  
Vol 105 (6) ◽  
pp. 717-727 ◽  
Author(s):  
G.-J. Brandon-Mong ◽  
H.-M. Gan ◽  
K.-W. Sing ◽  
P.-S. Lee ◽  
P.-E. Lim ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Illumina Miseq ◽  
Ease Of Use ◽  
Malaise Trap ◽  
Detection Rates ◽  
Operational Taxonomic Units ◽  
Arthropod Species ◽  
Primer Sets ◽  
Arthropod Biodiversity

AbstractMetabarcoding, the coupling of DNA-based species identification and high-throughput sequencing, offers enormous promise for arthropod biodiversity studies but factors such as cost, speed and ease-of-use of bioinformatic pipelines, crucial for making the leapt from demonstration studies to a real-world application, have not yet been adequately addressed. Here, four published and one newly designed primer sets were tested across a diverse set of 80 arthropod species, representing 11 orders, to establish optimal protocols for Illumina-based metabarcoding of tropical Malaise trap samples. Two primer sets which showed the highest amplification success with individual specimen polymerase chain reaction (PCR, 98%) were used for bulk PCR and Illumina MiSeq sequencing. The sequencing outputs were subjected to both manual and simple metagenomics quality control and filtering pipelines. We obtained acceptable detection rates after bulk PCR and high-throughput sequencing (80–90% of input species) but analyses were complicated by putative heteroplasmic sequences and contamination. The manual pipeline produced similar or better outputs to the simple metagenomics pipeline (1.4 compared with 0.5 expected:unexpected Operational Taxonomic Units). Our study suggests that metabarcoding is slowly becoming as cheap, fast and easy as conventional DNA barcoding, and that Malaise trap metabarcoding may soon fulfill its potential, providing a thermometer for biodiversity.

scholarly journals Seed Preferences of Wintering Henslow's Sparrows

The Condor ◽  
2007 ◽  
Vol 109 (3) ◽  
pp. 595-604
Author(s):  
Jennifer K. Dimiceli ◽  
Philip C. Stouffer ◽  
Erik I. Johnson ◽  
Claudia Leonardi ◽  
Edgar B. Moser
Keyword(s):  
Pinus Palustris ◽  
Active Management ◽  
Schizachyrium Scoparium ◽  
Bird Abundance ◽  
Characteristic Structure ◽  
Little Bluestem ◽  
Species Of Conservation Concern ◽  
Ammodramus Henslowii ◽  
Pine Savannas ◽  
Henslow's Sparrow

Abstract Abstract. The Henslow's Sparrow (Ammodramus henslowii), a species of conservation concern, winters primarily in longleaf pine (Pinus palustris) forest ecosystems in the southeastern U.S. These pine savannas have been reduced to 5% of their former range, with remaining patches requiring active management with fire to maintain characteristic structure and plant diversity. Wintering Henslow's Sparrow abundance tracks growing-season fires; bird abundance peaks in the winter following burning, then declines in subsequent winters. Fire also determines dominant plant species, suggesting that Henslow's Sparrows may respond to abundance of preferred seeds. To determine diet preferences of Henslow's Sparrows, we tested seeds from eight species of native plants from southeastern Louisiana pine savannas, including species common in the first winter after burning (‘fire grasses’) and species that increase in abundance in the second and subsequent winters after burning. Seed consumption by individual birds differed considerably, suggesting that Henslow's Sparrows forage on a variety of resources in the highly diverse savannas. Henslow's Sparrows preferred fire grasses, especially Muhlenbergia expansa (cutover muhly). They also preferred Dichanthelium angustifolium (needleleaf rosette grass), a species more common in the second year after burning, but consumed relatively little of the sedges Rhynchospora plumosa (plumed beaksedge) and R. gracilenta (slender beaksedge), species common in the second winter after fire. Birds consumed almost none of the ubiquitous grass Schizachyrium scoparium (little bluestem). These results suggest that preferred seeds may include those that are most common in the first winter after burning, but that some suitable seeds are available for at least another winter.

scholarly journals Development of Pineapple Microsatellite Markers and Germplasm Genetic Diversity Analysis

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Suping Feng ◽  
Helin Tong ◽  
You Chen ◽  
Jingyi Wang ◽  
Yeyuan Chen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Genomic Library ◽  
Trinucleotide Repeats ◽  
The Other ◽  
Diversity Analysis ◽  
Dominant Type ◽  
Genetic Diversity Analysis ◽  
Ssr Loci ◽  
Ssr Development

Two methods were used to develop pineapple microsatellite markers. Genomic library-based SSR development: using selectively amplified microsatellite assay, 86 sequences were generated from pineapple genomic library. 91 (96.8%) of the 94 Simple Sequence Repeat (SSR) loci were dinucleotide repeats (39 AC/GT repeats and 52 GA/TC repeats, accounting for 42.9% and 57.1%, resp.), and the other three were mononucleotide repeats. Thirty-six pairs of SSR primers were designed; 24 of them generated clear bands of expected sizes, and 13 of them showed polymorphism. EST-based SSR development: 5659 pineapple EST sequences obtained from NCBI were analyzed; among 1397 nonredundant EST sequences, 843 were found containing 1110 SSR loci (217 of them contained more than one SSR locus). Frequency of SSRs in pineapple EST sequences is 1SSR/3.73 kb, and 44 types were found. Mononucleotide, dinucleotide, and trinucleotide repeats dominate, accounting for 95.6% in total. AG/CT and AGC/GCT were the dominant type of dinucleotide and trinucleotide repeats, accounting for 83.5% and 24.1%, respectively. Thirty pairs of primers were designed for each of randomly selected 30 sequences; 26 of them generated clear and reproducible bands, and 22 of them showed polymorphism. Eighteen pairs of primers obtained by the one or the other of the two methods above that showed polymorphism were selected to carry out germplasm genetic diversity analysis for 48 breeds of pineapple; similarity coefficients of these breeds were between 0.59 and 1.00, and they can be divided into four groups accordingly. Amplification products of five SSR markers were extracted and sequenced, corresponding repeat loci were found and locus mutations are mainly in copy number of repeats and base mutations in the flanking region.

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