Development of novel microsatellite markers using RAD sequencing technology for diversity assessment of rambutan (Nephelium lappaceum L.) germplasm

This study reports the development, characterization, and cross-species transferability of 20 genomic microsatellite markers for Aronia melanocarpa, an important nutraceutical fruit crop. The markers were developed with Illumina paired-end genomic sequencing technology using DNA from Professor Ed cultivar that was originally collected from the wild in New Hampshire. The markers were highly polymorphic and transferable to Aronia arbutifolia and Aronia prunifolia genomes. The average number of alleles per locus was 9.1, 4.5, and 5.6 for A. melanocarpa, A. arbutifolia, and A. prunifolia, respectively. The polymorphism information content (PIC) of loci ranged from 0.38 to 0.95 for all taxa, with an average of 0.80, 0.68, and 0.87 for A. melanocarpa, A. arbutifolia, and A. prunifolia, respectively. This is the first study to develop microsatellite markers in the Aronia genus. These markers will be very useful in studying the genetic diversity and population structure of wild Aronia and expediting the breeding efforts of this emerging fruit crop through marker-assisted selection.

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Development of 14 microsatellite markers in the Queensland koala (Phascolarctos cinereus adustus) using next generation sequencing technology

Conservation Genetics Resources ◽

10.1007/s12686-013-0115-2 ◽

2014 ◽

Vol 6 (2) ◽

pp. 429-431 ◽

Cited By ~ 13

Author(s):

Christina T. Ruiz-Rodriguez ◽

Yasuko Ishida ◽

Alex D. Greenwood ◽

Alfred L. Roca

Keyword(s):

Next Generation Sequencing ◽

Microsatellite Markers ◽

Next Generation ◽

Sequencing Technology ◽

Phascolarctos Cinereus ◽

Next Generation Sequencing Technology ◽

Generation Sequencing Technology ◽

Generation Sequencing

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

10.1101/169144 ◽

2017 ◽

Cited By ~ 2

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.

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Rapid development of polymorphic microsatellite markers for the Amur sturgeon (Acipenser schrenckii) using next-generation sequencing technology

Genetics and Molecular Research ◽

10.4238/2015.july.14.16 ◽

2015 ◽

Vol 14 (3) ◽

pp. 7910-7913 ◽

Cited By ~ 1

Author(s):

L.M. Li ◽

L. Wei ◽

H.Y. Jiang ◽

Y. Zhang ◽

X.J. Zhang ◽

...

Keyword(s):

Next Generation Sequencing ◽

Microsatellite Markers ◽

Rapid Development ◽

Next Generation ◽

Sequencing Technology ◽

Next Generation Sequencing Technology ◽

Generation Sequencing Technology ◽

Amur Sturgeon ◽

Polymorphic Microsatellite ◽

Generation Sequencing

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Development and characterization of 29 polymorphic microsatellite loci of Megalobrama pellegrini by next-generation sequencing technology and cross-species amplification in related species

10.7287/peerj.preprints.2490 ◽

2016 ◽

Author(s):

Wen Song ◽

Dongmei Zhu ◽

Yefeng Lv ◽

Weimin Wang

Keyword(s):

Microsatellite Markers ◽

Microsatellite Loci ◽

Related Species ◽

Polymorphic Information Content ◽

Sequencing Technology ◽

Next Generation Sequencing Technology ◽

Expected Heterozygosity ◽

Polymorphic Microsatellite ◽

Generation Sequencing

Megalobrama pellegrini is one of the economically important freshwater fish in China. Here, we developed 29 polymorphic microsatellite loci of M. pellegrini. The number of alleles (Na), effective number of alleles (Ne), observed heterozygosity (HO), expected heterozygosity (HE) and polymorphic information content (PIC) ranged from 3 to 11 (mean±SD 5.4828±1.9571), 2.8708 to 9.6257 (mean±SD 5.0865±1.6681), 0.4333 to 0.9333 (mean±SD 0.7874±0.1213), 0.6627 to 0.9113 (mean±SD 0.7946±0.0751) and 0.5785 to 0.8868 (mean±SD 0.7439±0.0950), respectively. Cross-species amplification was successful at most loci for related species such as M. amblycephala, M. hoffmanni, M. skolkovii and Parabramis pekinensis. The transferability rate of the 29 polymorphic microsatellite markers in M. amblycephala, M. hoffmanni, M. skolkovii and P. pekinensis were 96.55%, 86.21%, 86.21% and 75.86%, respectively. These polymorphic microsatellites are not only useful in genetic study and conservation of M. pellegrini, but also an effective tool for identifying the related species. We could use 5 microsatellite markers (HHF-63, HHF-104, HHF-113, HHF-148, HHF-163) to distinguish the 5 species.

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