scholarly journals Next Generation Sequencing-Based Molecular Marker Development: A Case Study in Betula Alnoides

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 2963 ◽  
Author(s):  
Jing Tan ◽  
Jun-Jie Guo ◽  
Ming-Yu Yin ◽  
Huan Wang ◽  
Wen-Pan Dong ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Molecular Marker ◽  
Ssr Markers ◽  
Southern China ◽  
Diversity Index ◽  
Next Generation ◽  
Wiener Diversity Index ◽  
Nucleotide Repeats ◽  
Betula Alnoides ◽  
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.

scholarly journals Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants

Molecules ◽  
2018 ◽  
Vol 23 (2) ◽  
pp. 399 ◽  
Author(s):  
Sima Taheri ◽  
Thohirah Lee Abdullah ◽  
Mohd Yusop ◽  
Mohamed Hanafi ◽  
Mahbod Sahebi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Ssr Markers ◽  
Next Generation ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data ◽  
Generation Sequencing

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

Genes ◽  
2017 ◽  
Vol 8 (10) ◽  
pp. 238 ◽  
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

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

Molecules ◽  
2013 ◽  
Vol 18 (7) ◽  
pp. 8376-8392 ◽  
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

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

2013 ◽  
Vol 40 (12) ◽  
pp. 6855-6862 ◽  
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

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

Molecules ◽  
2016 ◽  
Vol 21 (1) ◽  
pp. 67 ◽  
Author(s):  
Chiuan-Yu Li ◽  
Tzen-Yuh Chiang ◽  
Yu-Chung Chiang ◽  
Hsin-Mei Hsu ◽  
Xue-Jun Ge ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Ssr Markers ◽  
Next Generation ◽  
Generation Sequencing

Development of soybean aphid genomic SSR markers using next generation sequencing

Genome ◽  
2011 ◽  
Vol 54 (5) ◽  
pp. 360-367 ◽  
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.

scholarly journals Combined use of gap-PCR and next-generation sequencing improves thalassaemia carrier screening among premarital adults in China

2020 ◽  
Vol 73 (8) ◽  
pp. 488-492 ◽  
Author(s):  
Jianghong Zhao ◽  
Jia Li ◽  
Qiaohong Lai ◽  
Yanping Yu
Keyword(s):  
Next Generation Sequencing ◽  
Southern China ◽  
Cost Effective ◽  
Carrier Screening ◽  
Lower Sensitivity ◽  
Carrier Rate ◽  
Next Generation ◽  
Cost Effective Method ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

AimsThalassaemia is one of the most common genetics disorders in the world, especially in southern China. The aim of the present study was to investigate the feasibility of combining the gap-PCR and next-generation sequencing (NGS) for thalassaemia carrier screening in the Chinese population.MethodsBlood samples were obtained from 944 prepregnancy couples; thalassaemia carrier screening was performed by using a routine haematological method and a combination of gap-PCR and NGS method.ResultsWe found that the α thalassaemia carrier rate was 11% (207/1888); the β thalassaemia carrier rate was 3.7% (70/1888); the composite α thalassaemia and β thalassaemia carrier rate was 0.4% (8/1888). We also identified seven novel mutations, including HBA1: c.412A>G, −50 (G>A), HBB: c.*+129T>A, HBB: c.-64G>C, HBB: c.-180G>C, HBB: c.*+5G>A and HBB: c.-113A>G. By comparing the combined gap-PCR and NGS method, the MCV+MCH and HbA2 detection strategy showed a lower sensitivity of 61.05% (105/172) and a higher missed diagnosis ratio of 38.95% (67/172) for α thalassaemia mutations. The sensitivity was improved with the MCV+MCH and HbA2 detection screen when compared with MCV+MCH detection for β thalassaemia (98.51% vs 85.90%).ConclusionsOur study suggests the combined gap-PCR and NGS method is a cost-effective method for the thalassaemia carrier screening, particularly for the α thalassaemia mutation carriers.

scholarly journals Characterization of 23 Polymorphic SSR Markers in Salix humboldtiana (Salicaceae) Using Next-Generation Sequencing and Cross-Amplification from Related Species

2015 ◽  
Vol 3 (4) ◽  
pp. 1400120 ◽  
Author(s):  
Jorge A. Bozzi ◽  
Sascha Liepelt ◽  
Sebastian Ohneiser ◽  
Leonardo A. Gallo ◽  
Paula Marchelli ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Ssr Markers ◽  
Related Species ◽  
Next Generation ◽  
Cross Amplification ◽  
Generation Sequencing

Development of genome-wide SSR markers in rapeseed by next generation sequencing

Gene ◽  
2021 ◽  
pp. 145798
Author(s):  
Ji-feng Zhu ◽  
Jun-ying Zhang ◽  
Mei-yan Jiang ◽  
Wei-rong Wang ◽  
Jian-xia Jiang ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Ssr Markers ◽  
Next Generation ◽  
Genome Wide ◽  
Generation Sequencing
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