Development of polymorphic microsatellites for genetic studies of white scar oyster (Crassostrea belcheri) using paired-end shotgun sequencing

AbstractMicrosatellites (simple sequence repeats, SSRs) are co-dominant nuclear markers that are widely used in population genetic studies. Population genetic parameters from different studies might be significantly influenced by differences in marker number. In our study, 265 sequences with polymorphic microsatellites were obtained from SLAF-seq data. Then, subpopulations containing different numbers (5, 6, 7,…, 15, 20, 25, 30, 35, 40) of markers were genotyped 10 times to investigate the impact of marker numbers on population genetic diversity results. Our results show that genotyping with less than 11 or 12 microsatellite markers lead to significant deviations in the population genetic diversity or genetic structure results. In order to provide markers for population genetic and conservation studies for Rhododendron, 26 SSR primers were designed and validated in three species.

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Isolation and characterization of polymorphic microsatellites in the Tibetan cypress Cupressus gigantea using paired-end Illumina shotgun sequencing

Conservation Genetics Resources ◽

10.1007/s12686-014-0222-8 ◽

2014 ◽

Vol 6 (3) ◽

pp. 795-797 ◽

Cited By ~ 3

Author(s):

Shaoke Li ◽

Zengqiang Qian ◽

Yaru Fu ◽

Weilie Zheng ◽

Huie Li

Keyword(s):

Shotgun Sequencing ◽

Isolation And Characterization ◽

Polymorphic Microsatellites

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Development of Genomic Resources From Crossostephium Chinense (Asteraceae) Based on Genome Skimming Data

10.21203/rs.3.rs-280353/v1 ◽

2021 ◽

Author(s):

Luxian Liu ◽

Shook Ling Low ◽

Yu Feng ◽

Binjie Ge ◽

Kamil Konowalik ◽

...

Keyword(s):

Population Genetics ◽

Genetic Background ◽

Ornamental Plant ◽

Chinese Medicinal Herb ◽

Genetic Studies ◽

Genomic Resources ◽

Expected Heterozygosity ◽

Polymorphic Microsatellites ◽

Chloroplast Genomes ◽

Genome Skimming

Abstract Crossostephium chinense is a traditional Chinese medicinal herb and it is often cultivated as an ornamental plant. Previous studies on this species mainly focused on its chemical composition and it was represented rarely and marginally in genetic studies, which limited knowledge about its genetic background, and thus genomic resources remain scarce. To develop both chloroplast and nuclear polymorphic microsatellites for C. chinense, potential microsatellites were screened from genome skimming data of two individuals of C. chinense. Sixty-four and 63 cpSSR markers were identified from two chloroplast genomes of C. chinense. This study performed for the first-ever study on employment of genome skimming data and CandiSSR, consequently a total of 133 polymorphic nSSRs were developed. Ten nSSRs were randomly selected to test their transferability across 35 individuals from three populations of C. chinense, and 20 individuals each of Artemisia stolonifera and A. argyi. Cross-amplifications were successful done for C. chinense, and were partially successful amplified for both Artemisia species. The number of alleles varied from two to nine. The observed heterozygosity and expected heterozygosity per locus ranged from 0.000 to 0.286 and from 0.029 to 0.755, respectively. These genomic resources will be valuable for population genetics and conservation studies in C. chinense and Artemisia.

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Two highly polymorphic microsatellites within the porcine ryanodine receptor 3 gene (RYR3)

Animal Genetics ◽

10.1046/j.1365-2052.1999.00445-5.x ◽

1999 ◽

Vol 30 (4) ◽

pp. 321-322 ◽

Cited By ~ 1

Author(s):

T. Leeb ◽

A. Giese ◽

I. Pfeiffer ◽

B. Brenig

Keyword(s):

Ryanodine Receptor ◽

Polymorphic Microsatellites

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Polymorphic microsatellites associated with the equine CKM and CMA1 genes

Animal Genetics ◽

10.1046/j.1365-2052.2000.00577.x ◽

2000 ◽

Vol 31 (2) ◽

pp. 141-141 ◽

Cited By ~ 1

Author(s):

A R Caetano ◽

J D Murray ◽

A T Bowling

Keyword(s):

Polymorphic Microsatellites

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Characterization of polymorphic microsatellites from current and historic populations of North American pocket gophers (Geomyidae: Thomomys)

Molecular Ecology ◽

10.1046/j.1365-294x.1999.00655.x ◽

1999 ◽

Vol 8 (6) ◽

pp. 1075 ◽

Cited By ~ 14

Author(s):

Steinberg Eleanor K.

Keyword(s):

North American ◽

Pocket Gophers ◽

Polymorphic Microsatellites

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Moving beyond the “LDL hypothesis”

VASA ◽

10.1024/0301-1526/a000451 ◽

2015 ◽

Vol 44 (5) ◽

pp. 333-340 ◽

Cited By ~ 7

Author(s):

Christian Werner ◽

Ulrich Laufs

Keyword(s):

Ldl Cholesterol ◽

Causal Relation ◽

Low Density Lipoprotein ◽

Density Lipoprotein ◽

Clinical Trial Data ◽

Randomised Clinical Trial ◽

Trial Data ◽

Low Density Lipoprotein Cholesterol ◽

Genetic Studies ◽

Statin Drug

Abstract. Summary: The term “LDL hypothesis” is frequently used to describe the association of low-density lipoprotein cholesterol (LDL-cholesterol, LDL-C) and cardiovascular (CV) events. Recent data from genetic studies prove a causal relation between serum LDL-C and CV events. These data are in agreement with mechanistic molecular studies and epidemiology. New randomised clinical trial data show that LDL-C lowering with statins and a non-statin drug, ezetimibe, reduces CV events. We therefore believe that the “LDL-hypothesis” has been proven; the term appears to be outdated and should be replaced by “LDL causality”.

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