scholarly journals Characterization of 29 polymorphic microsatellite markers developed by genomic screening of Sumatran rhinoceros (Dicerorhinus sumatrensis)

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Jessica R. Brandt ◽  
Sinta H. Saidah ◽  
Kai Zhao ◽  
Yasuko Ishida ◽  
Isabella Apriyana ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Tandem Repeats ◽  
Fecal Samples ◽  
Non Invasive ◽  
Genome Wide ◽  
Genomic Screening ◽  
Illumina Sequence ◽  
Polymorphic Microsatellite ◽  
Almost All ◽  
Conservation Plans

Abstract Objective The Sumatran rhinoceros is critically endangered, with fewer than 100 individuals surviving across its current range. Accurate census estimates of the remaining populations are essential for development and implementation of conservation plans. In order to enable molecular censusing, we here develop microsatellite markers with amplicon sizes of short length, appropriate for non-invasive fecal sampling. Results Due to limited sample quantity and potential lack of genome-wide diversity, Illumina sequence reads were generated from two Sumatran rhinoceros samples. Genomic screening identified reads with short tandem repeats and loci that were polymorphic within the dataset. Twenty-nine novel polymorphic microsatellite markers were characterized (A = 2.4; HO = 0.30). These were sufficient to distinguish among individuals (PID < 0.0001), and to distinguish among siblings (PID(sib) < 0.0001). Among rhinos in Indonesia, almost all markers were established as polymorphic and effective for genotyping DNA from fecal samples. Notably, the markers amplified and displayed microsatellite polymorphisms using DNA extracted from 11 fecal samples collected non-invasively from wild Sumatran rhinoceros. These microsatellite markers provide an important resource for a census and genetic studies of wild Sumatran rhinos.

scholarly journals Development and Integration of Genome-Wide Polymorphic Microsatellite Markers onto a Reference Linkage Map for Constructing a High-Density Genetic Map of Chickpea

PLoS ONE ◽  
2015 ◽  
Vol 10 (5) ◽  
pp. e0125583 ◽  
Author(s):  
Yash Paul Khajuria ◽  
Maneesha S. Saxena ◽  
Rashmi Gaur ◽  
Debasis Chattopadhyay ◽  
Mukesh Jain ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Linkage Map ◽  
Genetic Map ◽  
High Density ◽  
Genome Wide ◽  
Polymorphic Microsatellite

scholarly journals Comparative genome-wide polymorphic microsatellite markers in Antarctic penguins through next generation sequencing

2017 ◽  
Vol 40 (3) ◽  
pp. 676-687 ◽  
Author(s):  
Juliana A. Vianna ◽  
Daly Noll ◽  
Isidora Mura-Jornet ◽  
Paulina Valenzuela-Guerra ◽  
Daniel González-Acuña ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Microsatellite Markers ◽  
Next Generation ◽  
Comparative Genome ◽  
Genome Wide ◽  
Polymorphic Microsatellite ◽  
Generation Sequencing

scholarly journals Development of genome-wide polymorphic microsatellite markers for Trichinella spiralis

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Ting-Ting Li ◽  
Bin Tang ◽  
Xue Bai ◽  
Xue-Lin Wang ◽  
Xue-Nong Luo ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Trichinella Spiralis ◽  
Genome Wide ◽  
Polymorphic Microsatellite

scholarly journals Genome-Wide Analysis of Sex Disparities in the Genetic Architecture of Lung and Colorectal Cancers

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 686
Author(s):  
Alireza Nazarian ◽  
Alexander M. Kulminski
Keyword(s):  
Nucleotide Polymorphisms ◽  
Genetic Associations ◽  
Significance Level ◽  
Association Analyses ◽  
Complex Disorders ◽  
Specific Effects ◽  
Genome Wide ◽  
Genetic Mechanisms ◽  
Sex Disparities ◽  
Almost All

Almost all complex disorders have manifested epidemiological and clinical sex disparities which might partially arise from sex-specific genetic mechanisms. Addressing such differences can be important from a precision medicine perspective which aims to make medical interventions more personalized and effective. We investigated sex-specific genetic associations with colorectal (CRCa) and lung (LCa) cancers using genome-wide single-nucleotide polymorphisms (SNPs) data from three independent datasets. The genome-wide association analyses revealed that 33 SNPs were associated with CRCa/LCa at P < 5.0 × 10−6 neither males or females. Of these, 26 SNPs had sex-specific effects as their effect sizes were statistically different between the two sexes at a Bonferroni-adjusted significance level of 0.0015. None had proxy SNPs within their ±1 Mb regions and the closest genes to 32 SNPs were not previously associated with the corresponding cancers. The pathway enrichment analyses demonstrated the associations of 35 pathways with CRCa or LCa which were mostly implicated in immune system responses, cell cycle, and chromosome stability. The significant pathways were mostly enriched in either males or females. Our findings provided novel insights into the potential sex-specific genetic heterogeneity of CRCa and LCa at SNP and pathway levels.

Genetic Enhancement in Mungbean (Vigna radiata) as Revealed by Genome-Wide Mapped Microsatellite Markers

2021 ◽  
Author(s):  
Aditya Pratap ◽  
Chandra Mohan Singh ◽  
Sanjeev Gupta ◽  
Ajeet Kumar Gupta ◽  
Revanappa S. Birader ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Vigna Radiata ◽  
Genetic Enhancement ◽  
Genome Wide

Development of polymorphic microsatellite markers for the Tertiary relict tree species Taiwania cryptomerioides (Cupressaceae) in East Asia

2021 ◽  
Vol 48 (3) ◽  
pp. 3031-3036
Author(s):  
Mengyun Qin ◽  
Ningning Zhang ◽  
Shixin Zhu ◽  
Caipeng Yue ◽  
Jinyong Huang ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
East Asia ◽  
Tree Species ◽  
Polymorphic Microsatellite ◽  
Taiwania Cryptomerioides

Genetic characterization of novel polymorphic microsatellite markers for Epilobium nankotaizanense (Onagraceae), an endemic and threatened herb in Taiwan

2021 ◽  
pp. 1-4
Author(s):  
Yu-Wei Tseng ◽  
Chi-Chun Huang ◽  
Chih-Chiang Wang ◽  
Chiuan-Yu Li ◽  
Kuo-Hsiang Hung
Keyword(s):  
Microsatellite Markers ◽  
Natural Populations ◽  
Conservation Strategy ◽  
Sequencing Data ◽  
Germplasm Collections ◽  
The Family ◽  
Conservation Genetic ◽  
Population Sizes ◽  
Polymorphic Microsatellite

Abstract Epilobium belongs to the family Onagraceae, which consists of approximately 200 species distributed worldwide, and some species have been used as medicinal plants. Epilobium nankotaizanense is an endemic and endangered herb that grows in the high mountains in Taiwan at an elevation of more than 3300 m. Alpine herbs are severely threatened by climate change, which leads to a reduction in their habitats and population sizes. However, only a few studies have addressed genetic diversity and population genetics. In the present study, we developed a new set of microsatellite markers for E. nankotaizanense using high-throughput genome sequencing data. Twenty polymorphic microsatellite markers were developed and tested on 30 individuals collected from three natural populations. These loci were successfully amplified, and polymorphisms were observed in E. nankotaizanense. The number of alleles per locus (A) ranged from 2.000 to 3.000, and the observed (Ho) and expected (He) heterozygosities ranged from 0.000 to 0.929 and from 0.034 to 0.631, respectively. The developed polymorphic microsatellite markers will be useful in future conservation genetic studies of E. nankotaizanense as well as for developing an effective conservation strategy for this species and facilitating germplasm collections and sustainable utilization of other Epilobium species.

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