scholarly journals Double-digest RAD sequencing outperforms microsatellite loci at assigning paternity and estimating relatedness: a proof of concept in a highly promiscuous bird

2017 ◽  
Author(s):  
Derrick J. Thrasher ◽  
Bronwyn G. Butcher ◽  
Leonardo Campagna ◽  
Michael S. Webster ◽  
Irby J. Lovette
Keyword(s):  
Microsatellite Markers ◽  
Restriction Site ◽  
Genetic Relationships ◽  
Bird Species ◽  
Snp Markers ◽  
Rad Sequencing ◽  
Proof Of Concept ◽  
Analysis Pipeline ◽  
Large Numbers ◽  
Field Samples

AbstractInformation on genetic relationships among individuals is essential to many studies of the behavior and ecology of wild organisms. Parentage and relatedness assays based on large numbers of SNP loci hold substantial advantages over the microsatellite markers traditionally used for these purposes. We present a double-digest restriction site-associated DNA sequencing (ddRAD-seq) analysis pipeline that, as such, simultaneously achieves the SNP discovery and genotyping steps and which is optimized to return a statistically powerful set of SNP markers (typically 150-600 after stringent filtering) from large numbers of individuals (up to 240 per run). We explore the tradeoffs inherent in this approach through a set of experiments in a species with a complex social system, the variegated fairy-wren (Malurus lamberti), and further validate it in a phylogenetically broad set of other bird species. Through direct comparisons with a parallel dataset from a robust panel of highly variable microsatellite markers, we show that this ddRAD-seq approach results in substantially improved power to discriminate among potential relatives and considerably more precise estimates of relatedness coefficients. The pipeline is designed to be universally applicable to all bird species (and with minor modifications to many other taxa), to be cost- and time-efficient, and to be replicable across independent runs such that genotype data from different study periods can be combined and analyzed as field samples are accumulated.

scholarly journals Development of SNP markers derived from RAD sequencing for Atlantic salmon (Salmo salar L.) inhabiting the rivers of southern England

2021 ◽  
Author(s):  
R. Andrew King ◽  
Jamie R. Stevens
Keyword(s):  
Atlantic Salmon ◽  
Restriction Site ◽  
Snp Markers ◽  
Rad Sequencing ◽  
Effective Management ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Southern England ◽  
Target Populations ◽  
The Uk

AbstractThe rivers of the Hampshire Basin, southern England contain a genetically unique group of Atlantic salmon that have suffered dramatic declines in numbers over the last 40 years. Knowledge of levels and patterns of genetic diversity is essential for effective management of these vulnerable populations. Using restriction site-associated DNA sequencing (RADseq) data, we describe the development and characterisation of a panel of 94 single nucleotide polymorphism (SNP) loci for salmon from this region and investigate their applicability and variability in both target (i.e. southern English) and non-target populations. The SNP loci will be useful for population genetic and assignment studies on Atlantic salmon within the UK and beyond.

Three hundred years of House Sparrow (Passer domesticus) persecution in Germany

2007 ◽  
Vol 34 (2) ◽  
pp. 307-317 ◽  
Author(s):  
J. SEITZ
Keyword(s):  
Rural Areas ◽  
House Sparrow ◽  
Bird Species ◽  
Passer Domesticus ◽  
Second World War ◽  
Population Increase ◽  
World War ◽  
Large Numbers ◽  
Urban And Rural Areas ◽  
Second World

Modernization of agriculture, economic development and population increase after the end of the Thirty Years' War caused authorities in many parts of Germany to decree the eradication of so-called pest animals, including the House Sparrow. Farmers were given targets, and had to deliver the heads of sparrows in proportion to the size of their farms or pay fines. At the end of the eighteenth century German ornithologists argued against the eradication of the sparrows. During the mid-nineteenth century, C. L. Gloger, the pioneer of bird protection in Germany, emphasized the value of the House Sparrow in controlling insect plagues. Many decrees were abolished because either they had not been obeyed, or had resulted in people protecting sparrows so that they always had enough for their “deliveries”. Surprisingly, various ornithologists, including Ernst Hartert and the most famous German bird conservationist Freiherr Berlepsch, joined in the war against sparrows at the beginning of the twentieth century, because sparrows were regarded as competitors of more useful bird species. After the Second World War, sparrows were poisoned in large numbers. Persecution of sparrows ended in Germany in the 1970s. The long period of persecution had a significant but not long-lasting impact on House Sparrow populations, and therefore cannot be regarded as a factor in the recent decline of this species in urban and rural areas of western and central Europe.

scholarly journals Genetic diversity in table grapes based on RAPD and microsatellite markers

2011 ◽  
Vol 46 (9) ◽  
pp. 1035-1044 ◽  
Author(s):  
Patrícia Coelho de Souza Leão ◽  
Sérgio Yoshimitsu Motoike
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Genetic Relationships ◽  
Similarity Index ◽  
Genetic Distances ◽  
Table Grape ◽  
Group Method ◽  
Molecular Characteristics ◽  
Table Grapes ◽  
Pair Group

The objective of this work was to analyze the genetic diversity of 47 table grape accessions, from the grapevine germplasm bank of Embrapa Semiárido, using 20 RAPD and seven microsatellite markers. Genetic distances between pairs of accessions were obtained based on Jaccard's similarity index for RAPD data and on the arithmetic complement of the weighted index for microsatellite data. The groups were formed according to the Tocher's cluster analysis and to the unweighted pair‑group method with arithmetic mean (UPGMA). The microsatellite markers were more efficient than the RAPD ones in the identification of genetic relationships. Information on the genetic distance, based on molecular characteristics and coupled with the cultivar agronomic performance, allowed for the recommendation of parents for crossings, in order to obtain superior hybrids in segregating populations for the table grape breeding program of Embrapa Semiárido.

scholarly journals Investigation of Genetic Relationships within Miscanthus using SNP Markers Identified using SLAF-Seq

2021 ◽  
Author(s):  
ZHIYONG Chen ◽  
Yancen He ◽  
Yasir Iqbal ◽  
Yanlan Shi ◽  
Hongmei Huang ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Genetic Relationships ◽  
Female Parent ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Sequencing Method ◽  
Specific Locus

Abstract Background: Miscanthus, which is a leading dedicated-energy grass in Europe and in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is difficult to investigate phylogenetic relationships and the evolution of gene function in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent (M. lutarioriparius), 30 candidate male parents (M. lutarioriparius, M. sinensis, and M. sacchariflorus), and 19 offspring. We used high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms.Results: We identified 800,081 SLAF tags, of which 160,368 were polymorphic. Each tag was 264–364 bp long. The obtained SNPs were used to investigate genetic relationships within Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs, and found that the germplasms fell into two clades: one clade of M. sinensis only and one clade that included the offspring, M. lutarioriparius, and M. sacchariflorus. Genetic cluster analysis indicated that M. lutarioriparius germplasm C3 was the most likely male parent of the offspring.Conclusions: As a high-throughput sequencing method, SLAF-seq can be used to identify informative SNPs in Miscanthus germplasms and to rapidly characterize genetic relationships within this genus. Our results will support the development of breeding programs utilizing Miscanthus cultivars with elite biomass- or fiber-production potential.

Conservation of the Swift Parrot Lathamus discolor ? management lessons for a threatened migratory species

2007 ◽  
Vol 13 (2) ◽  
pp. 111 ◽  
Author(s):  
Debbie Saunders ◽  
Raymond Brereton ◽  
Chris Tzaros ◽  
Mark Holdsworth ◽  
Rob Price
Keyword(s):  
Site Fidelity ◽  
Bird Species ◽  
Migratory Bird ◽  
Small Population ◽  
Assessment Process ◽  
Migratory Species ◽  
Conservation Assessment ◽  
Broad Distribution ◽  
Large Numbers

Conserving habitat for wide-ranging fauna species provides a challenge because impacts on these species tend to be dismissed based on the assumption that there is sufficient habitat in other areas of its range. This incremental loss of habitat is a serious conservation issue for a diversity of bird species. As knowledge of wide-ranging and migratory bird species increases, it often becomes evident that they select specific sites on a regular basis (i.e., the species exhibit site fidelity). Gaining a better understanding of site fidelity and selective habitat use for wide-ranging species is clearly important, but also extremely challenging. In this paper, challenges associated with conservation of the migratory and wide-ranging Swift Parrot Lathamus discolor are discussed as an example of how a recovery programme has aimed to address such conservation and management challenges. Despite the small population size (less than 2 500 birds), broad distribution (1 250 000 km2) and often cryptic nature, the implementation of the national recovery programme has been successful in the identification and protection of important habitats. This has been made possible by involving large numbers of volunteers who collect long-term sighting and habitat data over large areas, together with more detailed ecological research. This information is then used to inform the conservation assessment process and to improve habitat conservation throughout the range of the species.

Identification of SNP markers for inferring phylogeny in temperate bamboos ( P oaceae: B ambusoideae) using RAD sequencing

2013 ◽  
Vol 13 (5) ◽  
pp. 938-945 ◽  
Author(s):  
X. Q. Wang ◽  
L. Zhao ◽  
D. A. R. Eaton ◽  
D. Z. Li ◽  
Z. H. Guo
Keyword(s):  
Snp Markers ◽  
Rad Sequencing

scholarly journals An optimized approach for local de novo assembly of overlapping paired-end RAD reads from multiple individuals

2018 ◽  
Vol 5 (2) ◽  
pp. 171589 ◽  
Author(s):  
Yu-Long Li ◽  
Dong-Xiu Xue ◽  
Bai-Dong Zhang ◽  
Jin-Xian Liu
Keyword(s):  
Data Reduction ◽  
De Novo Assembly ◽  
Genetic Variance ◽  
Restriction Site ◽  
De Novo ◽  
Optimal Number ◽  
Rad Sequencing ◽  
Conservation Genomics ◽  
Model Species

Restriction site-associated DNA (RAD) sequencing is revolutionizing studies in ecological, evolutionary and conservation genomics. However, the assembly of paired-end RAD reads with random-sheared ends is still challenging, especially for non-model species with high genetic variance. Here, we present an efficient optimized approach with a pipeline software, RADassembler, which makes full use of paired-end RAD reads with random-sheared ends from multiple individuals to assemble RAD contigs. RADassembler integrates the algorithms for choosing the optimal number of mismatches within and across individuals at the clustering stage, and then uses a two-step assembly approach at the assembly stage. RADassembler also uses data reduction and parallelization strategies to promote efficiency. Compared to other tools, both the assembly results based on simulation and real RAD datasets demonstrated that RADassembler could always assemble the appropriate number of contigs with high qualities, and more read pairs were properly mapped to the assembled contigs. This approach provides an optimal tool for dealing with the complexity in the assembly of paired-end RAD reads with random-sheared ends for non-model species in ecological, evolutionary and conservation studies. RADassembler is available at https://github.com/lyl8086/RADscripts.

scholarly journals  Genetic diversity of Czech apple cultivars inferred from microsatellite markers analysis

2012 ◽  
Vol 39 (No. 4) ◽  
pp. 149-157 ◽  
Author(s):  
J. Patzak ◽  
F. Paprštein ◽  
A. Henychová ◽  
J. Sedlák
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Simple Sequence Repeat ◽  
Cultivar Identification ◽  
Genetic Relationships ◽  
Similarity Coefficient ◽  
Collection Management ◽  
Apple Cultivars ◽  
Repeat Primer ◽  
Simple Sequence

Genetic diversity and genetic relationships of Czech apple cultivars were evaluated. Trees of 33 Czech apple cultivars and 97 reference foreign cultivars were analysed using the set of 10 SSR (simple sequence repeat) primer pairs. The total of 89 polymorphic alleles were amplified, while the number of alleles per locus ranged from 4 to 14. The SSR dendrogram, based on the Jaccard’s similarity coefficient, divided apple cultivars into three major groups: Cox’s Orange Pippin, McIntosh and Golden Delicious ancestries. The clustering highly depended on pedigree and origin of apple cultivars. Spontaneous mutated cultivars were identical with their progenitors. We proved that microsatellite markers were useful for evaluation of genetic resources, collection management and cultivar identification.  

scholarly journals Species-Specific Marker Discovery in Tilapia

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Mochamad Syaifudin ◽  
Michaël Bekaert ◽  
John B. Taggart ◽  
Kerry L. Bartie ◽  
Stefanie Wehner ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Restriction Site ◽  
De Novo ◽  
Snp Markers ◽  
Specific Marker ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Species Analysis ◽  
Species Specific ◽  
Marker Discovery

Abstract Tilapias (family Cichlidae) are of importance in aquaculture and fisheries. Hybridisation and introgression are common within tilapia genera but are difficult to analyse due to limited numbers of species-specific genetic markers. We tested the potential of double digested restriction-site associated DNA (ddRAD) sequencing for discovering single nucleotide polymorphism (SNP) markers to distinguish between 10 tilapia species. Analysis of ddRAD data revealed 1,371 shared SNPs in the de novo-based analysis and 1,204 SNPs in the reference-based analysis. Phylogenetic trees based on these two analyses were very similar. A total of 57 species-specific SNP markers were found among the samples analysed of the 10 tilapia species. Another set of 62 species-specific SNP markers was identified from a subset of four species which have often been involved in hybridisation in aquaculture: 13 for Oreochromis niloticus, 23 for O. aureus, 12 for O. mossambicus and 14 for O. u. hornorum. A panel of 24 SNPs was selected to distinguish among these four species and validated using 91 individuals. Larger numbers of SNP markers were found that could distinguish between the pairs of species within this subset. This technique offers potential for the investigation of hybridisation and introgression among tilapia species in aquaculture and in wild populations.

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