Cross-Species, Amplifiable EST-SSR Markers for Amentotaxus Species Obtained by Next-Generation Sequencing

Betula alnoides is a fast-growing valuable indigenous tree species with multiple uses in the tropical and warm subtropical regions in South-East Asia and southern China. It has been proved to be tetraploid in most parts of its distribution in China. In the present study, next generation sequencing (NGS) technology was applied to develop numerous SSR markers for B. alnoides, and 64,376 contig sequences of 106,452 clean reads containing 164,357 candidate SSR loci were obtained. Among the derived SSR repeats, mono-nucleotide was the main type (77.05%), followed by di- (10.18%), tetra- (6.12%), tri- (3.56%), penta- (2.14%) and hexa-nucleotide (0.95%). The short nucleotide sequence repeats accounted for 90.79%. Among the 291 repeat motifs, AG/CT (46.33%) and AT/AT (44.15%) were the most common di-nucleotide repeats, while AAT/ATT (48.98%) was the most common tri-nucleotide repeats. A total of 2549 primer sets were designed from the identified putative SSR regions of which 900 were randomly selected for evaluation of amplification successfulness and detection of polymorphism if amplified successfully. Three hundred and ten polymorphic markers were obtained through testing with 24 individuals from B. alnoides natural forest in Jingxi County, Guangxi, China. The number of alleles (NA) of each marker ranged from 2 to 19 with a mean of 5.14. The observed (HO) and expected (HE) heterozygosities varied from 0.04 to 1.00 and 0.04 to 0.92 with their means being 0.64 and 0.57, respectively. Shannon-Wiener diversity index (I) ranged from 0.10 to 2.68 with a mean of 1.12. Cross-species transferability was further examined for 96 pairs of SSR primers randomly selected, and it was found that 48.96–84.38% of the primer pairs could successfully amplify each of six related Betula species. The obtained SSR markers can be used to study population genetics and molecular marker assisted breeding, particularly genome-wide association study of these species in the future.

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Development of Genome-Wide SSR Markers from Angelica gigas Nakai Using Next Generation Sequencing

Genes ◽

10.3390/genes8100238 ◽

2017 ◽

Vol 8 (10) ◽

pp. 238 ◽

Cited By ~ 5

Author(s):

Jinsu Gil ◽

Yurry Um ◽

Serim Kim ◽

Ok Kim ◽

Sung Koo ◽

...

Keyword(s):

Next Generation Sequencing ◽

Ssr Markers ◽

Next Generation ◽

Angelica Gigas ◽

Angelica Gigas Nakai ◽

Genome Wide ◽

Generation Sequencing

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Development of 65 Novel Polymorphic cDNA-SSR Markers in Common Vetch (Vicia sativa subsp. sativa) Using Next Generation Sequencing

Molecules ◽

10.3390/molecules18078376 ◽

2013 ◽

Vol 18 (7) ◽

pp. 8376-8392 ◽

Cited By ~ 27

Author(s):

Jong-Wook Chung ◽

Tae-Sung Kim ◽

Sundan Suresh ◽

Sok-Young Lee ◽

Gyu-Taek Cho

Keyword(s):

Next Generation Sequencing ◽

Ssr Markers ◽

Vicia Sativa ◽

Next Generation ◽

Common Vetch ◽

Generation Sequencing

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Development of SSR markers by next-generation sequencing of Korean landraces of chamoe (Cucumis melo var. makuwa)

Molecular Biology Reports ◽

10.1007/s11033-013-2803-0 ◽

2013 ◽

Vol 40 (12) ◽

pp. 6855-6862 ◽

Cited By ~ 7

Author(s):

Inkyu Park ◽

Jungeun Kim ◽

Jeongyeo Lee ◽

Sewon Kim ◽

Okhee Cho ◽

...

Keyword(s):

Next Generation Sequencing ◽

Ssr Markers ◽

Cucumis Melo ◽

Next Generation ◽

Generation Sequencing

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Development of soybean aphid genomic SSR markers using next generation sequencing

Genome ◽

10.1139/g11-002 ◽

2011 ◽

Vol 54 (5) ◽

pp. 360-367 ◽

Cited By ~ 18

Author(s):

Tae-Hwan Jun ◽

Andrew P. Michel ◽

M.A. Rouf Mian

Keyword(s):

Molecular Markers ◽

Next Generation Sequencing ◽

Ssr Markers ◽

The United States ◽

Soybean Aphid ◽

Genomic Sequences ◽

Next Generation ◽

Soybean Aphids ◽

Genomic Ssr ◽

Generation Sequencing

Simple sequence repeats (SSRs) or microsatellites are very useful molecular markers, owing to their locus-specific codominant and multiallelic nature, high abundance in the genome, and high rates of transferability across species. The soybean aphid ( Aphis glycines Matsumura) has become the most damaging insect pest of soybean ( Glycine max (L.) Merr.) in North America, since it was first found in the Midwest of the United States in 2000. Biotypes of the soybean aphid capable of colonizing newly developed aphid-resistant soybean cultivars have been recently discovered. Genetic resources, including molecular markers, to study soybean aphids are severely lacking. Recently developed next generation sequencing platforms offer opportunities for high-throughput and inexpensive genome sequencing and rapid marker development. The objectives of this study were (i) to develop and characterize genomic SSR markers from soybean aphid genomic sequences generated by next generation sequencing technology and (ii) to evaluate the utility of the SSRs for genetic diversity or relationship analyses. In total 128 SSR primer pairs were designed from sequences generated by Illumina GAII from a reduced representation library of A. glycines. Nearly 94% (120) of the primer pairs amplified SSR alleles of expected size and 24 SSR loci were polymorphic among three aphid samples from three populations. The polymorphic SSRs were successfully used to differentiate among 24 soybean aphids from Ohio and South Dakota. Sequencing of PCR products of two SSR markers from four aphid samples revealed that the allelic polymorphism was due to variation in the SSR repeats among the aphids. These markers should be particularly useful for genetic differentiation among aphids collected from soybean fields at different localities and regions. These SSR markers provide the soybean aphid research community with the first set of PCR-based codominant markers developed from the genomic sequences of A. glycines.

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