Characterization of Single Nucleotide Polymorphism Marker in the Chinese Giant Salamander Andrias davidianus

Background: Chinese giant salamander Andrias davidianus is called “baby fish” in China. Due to its palatability and nutritional value, it was widely cultured in China. The current study was to evaluate the genetic diversity of the farmed A. davidianus. Methods: 30 salamanders were collected from farm and DNA was extracted. Thirty contigs potentially containing SNPs were selected from the previously developed RAD-seq library. The primer was designed and PCR was performed, than the products was sequenced from different direction. At last the sequences were analyzed using the vector NTI 10.Result: 5824bp high-quality sequences embodied in 16 contigs were sequenced and eighty SNP loci were identified which each SNP locus exhibited bi-alleles. The effective allele number from 1.03 to 2.00 and the minor allele frequency was 0.017 to 0.500. The expected heterozygosity was from 0.0333 to 0.5091 and the observed heterozygosity was 0.0333 to 1.0000. Sixty-six of the 80 loci significantly deviated from the Hardy-Weinberg equilibrium (P less than 0.05). The results provide useful genomic resources to evaluate the genetic diversity of A. davidianus for conservation and aquaculture.

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Development and characterization of 33 SNP markers in a critically endangered Hynobius amjiensis using ddRAD sequencing

10.21203/rs.3.rs-804020/v1 ◽

2021 ◽

Author(s):

Xia Kan ◽

Guoliang Wang ◽

Lili Zhang ◽

Xin Zhao ◽

Shuangshuang Shan ◽

...

Keyword(s):

Restriction Site ◽

Snp Markers ◽

Inbreeding Coefficient ◽

Critically Endangered ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Critically Endangered Species ◽

Expected Heterozygosity ◽

Genetic Assessment

Abstract Hynobius amjiensis was considered as one of the 29 most threatened amphibian in China. To effectively conserve, manage and recover the population of this critically endangered species, 33 single nucleotide polymorphism (SNP) markers were developed using double digest restriction-site associated DNA (ddRAD) sequencing. The minor allele frequency per locus ranged from 0.0161 to 0.5000. The observed heterozygosity and expected heterozygosity varied from 0.0323 to 0.6667 (average 0.3303) and from 0.0317 to 0.5000 (average 0.2772), respectively. The inbreeding coefficient value ranged between − 0.3315 and 0.0000. No significant deviation from Hardy-Weinberg equlibrium (P > 0.05) were found in all loci. These novel SNPs will be helpful for the population genetic assessment and conservation of H. amjiensis.

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Development And Identification of 131 SNP Markers In Sthenoteuthis Pteropus (Steenstrup)

10.21203/rs.3.rs-1147398/v1 ◽

2021 ◽

Author(s):

Yan Zhao ◽

Congcong Wang ◽

Bilin Liu ◽

Gang Li ◽

Hao Xu

Keyword(s):

Molecular Markers ◽

Snp Markers ◽

Scientific Management ◽

Sustainable Utilization ◽

Bonferroni Correction ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Polymorphic Snps ◽

Expected Heterozygosity ◽

Hardy Weinberg Equilibrium

Abstract The orangeback flying squid, Sthenoteuthis pteropus, is a species of significant potential value that is widely distributed in the tropical and temperate waters of the Atlantic Ocean. There have been no reports of the population genetics and effective molecular markers for this species due to a lack of reliable information regarding its genetic structure and its many individual differences, as well as its complex and changeable life history. Therefore, the development of auxiliary molecular markers would contribute to the development, sustainable utilization, and protection of the species. In this study, 131 novel single nucleotide polymorphism (SNP) markers were developed by double digest restriction-site associated DNA sequencing (dd-RAD). The observed heterozygosity (Ho) and expected heterozygosity (He) ranged from 0.00 to 0.80 and 0.18 to 0.50, respectively. The polymorphism information content (PIC) value ranged from 0.18 to 0.50. None of the marker locations significantly deviated from the Hardy-Weinberg equilibrium (p >0.05) after a Bonferroni correction. These polymorphic SNPs will be important in the further analysis of the population heredity of S. pteropus and its scientific management.

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Isolation and Characterization of 17 Polymorphic Microsatellite Loci for Musella lasiocarpa (Musaceae)

HortScience ◽

10.21273/hortsci.44.7.2041 ◽

2009 ◽

Vol 44 (7) ◽

pp. 2041-2042 ◽

Cited By ~ 2

Author(s):

Chun-yan Yang ◽

Yuan Huang ◽

Chunlin Long

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Southwest China ◽

Microsatellite Primers ◽

Genetic Population ◽

Allele Number ◽

Isolation And Characterization ◽

Hardy Weinberg Equilibrium ◽

Polymorphic Microsatellite

Seventeen microsatellite markers were isolated from 24 wild individuals collected from three populations of Musella lasiocarpa (Franch.) C. Y. Wu ex H. W. Li, a plant endemic to southwest China. The average allele number of these markers was 3.6 per locus, ranging from two to seven. The expected (He) and observed (Ho) heterozygosities varied from 0.4672 to 0.8183 and from 0.0417 to 1, respectively. Eleven loci were significantly deviated from Hardy-Weinberg equilibrium as a result of the heterozygote deficiency. These microsatellite primers will be used for studying genetic population structure and genetic diversity of M. lasiocarpa.

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Development of 30 SNP Markers for the Daphnia Magna based on Restriction Site-associated DNA Sequencing (RAD-seq)

10.21203/rs.3.rs-162999/v1 ◽

2021 ◽

Author(s):

Shengman Zhang ◽

Wenhui He ◽

Haisu Zheng ◽

Yiran Xiong ◽

Meng Tan ◽

...

Keyword(s):

Dna Sequencing ◽

Daphnia Magna ◽

Restriction Site ◽

Snp Markers ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Genetics Research ◽

Expected Heterozygosity ◽

Water Ecosystem ◽

Hardy Weinberg Equilibrium

Abstract Daphnia magna belongs to the Cladocera and plays an important role in the water ecosystem. With the intensification of water pollution, the wild population of D. magna has declined rapidly in recent years, and insufficient molecular markers have limited effective research and conservation of this species. In this research, 30 novel single nucleotide polymorphism (SNP) markers were developed in a cultivar of Daphnia magna and 12 wild Daphnia magna using restriction site-associated DNA sequencing (RAD-seq). The minor allele frequency, observed heterozygosity, and expected heterozygosity ranged from 0.115 to 0.721, 0.073 to 0.800, and 0.077 to 0.520, respectively. The PIC ranged from 0.071 to 0.403. Six loci showed significant deviations from the Hardy-Weinberg equilibrium after Bonferroni correction (p < 0.05).These newly developed polymorphic SNP markers for D. magna are of great significance in terms of the genetic breeding of D. magna, identification of wild and artificially domesticated species and conservation genetics research.

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Sex-biased dispersal of greater long-tailed hamster (Tscherskia triton) revealed by microsatellites

Canadian Journal of Zoology ◽

10.1139/z05-060 ◽

2005 ◽

Vol 83 (6) ◽

pp. 773-779 ◽

Cited By ~ 15

Author(s):

Mingjing Song ◽

Zhibin Zhang ◽

Karsten Neumann ◽

Rolf Gattermann

Keyword(s):

Genetic Diversity ◽

Allelic Richness ◽

Allelic Diversity ◽

Hebei Province ◽

Effective Number ◽

Republic Of China ◽

Allele Number ◽

Expected Heterozygosity ◽

Hardy Weinberg Equilibrium ◽

Polymorphic Microsatellite

For 2 consecutive years we studied the effect of dispersal on the genetic diversity of greater long-tailed hamsters (Tscherskia triton (de Winton, 1899)) in farmland habitat, Hebei Province, People's Republic of China. Level of genetic diversity was estimated by analyzing six highly polymorphic microsatellite loci in terms of mean d2, allele number, allelic diversity, effective number of alleles, allelic richness, average observed heterozygosity, and expected heterozygosity. The genetic diversity in populations from both two sites and 2 years indicated that the males contained higher levels of genetic diversity than the females, which supported our prediction that male-biased dispersal increased population genetic diversity. We also found significant departures from HardyWeinberg equilibrium and a reduction in genetic diversity in samples from a partially isolated site, which was probably due to genetic drift, inbreeding, or a combination of these factors.

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A comparison of genetic diversity between wild and cultured populations of the Chinese giant salamander,Andrias davidianus, based on microsa-tellite analyses

Biodiversity Science ◽

10.3724/sp.j.1003.2008.08105 ◽

2008 ◽

Vol 16 (6) ◽

pp. 533

Author(s):

Meng Yan ◽

Yang Yanqing ◽

Zhang Yan ◽

Xiao Hanbing

Keyword(s):

Genetic Diversity ◽

Andrias Davidianus ◽

Chinese Giant Salamander

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Genetic Diversity of Purple Passion Fruit, Passiflora edulis f. edulis, Based on Single-Nucleotide Polymorphism Markers Discovered through Genotyping by Sequencing

Diversity ◽

10.3390/d13040144 ◽

2021 ◽

Vol 13 (4) ◽

pp. 144

Author(s):

Nohra Castillo Rodríguez ◽

Xingbo Wu ◽

María Isabel Chacón ◽

Luz Marina Melgarejo ◽

Matthew Wohlgemuth Blair

Keyword(s):

Genetic Diversity ◽

Single Nucleotide Polymorphism ◽

Genotyping By Sequencing ◽

Passion Fruit ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Passiflora Edulis ◽

Tropical Fruit ◽

Commercial Cultivars ◽

Purple Passion Fruit

Orphan crops, which include many of the tropical fruit species used in the juice industry, lack genomic resources and breeding efforts. Typical of this dilemma is the lack of commercial cultivars of purple passion fruit, Passiflora edulis f. edulis, and of information on the genetic resources of its substantial semiwild gene pool. In this study, we develop single-nucleotide polymorphism (SNP) markers for the species and show that the genetic diversity of this fruit crop has been reduced because of selection for cultivated genotypes compared to the semiwild landraces in its center of diversity. A specific objective of the present study was to determine the genetic diversity of cultivars, genebank accession, and landraces through genotyping by sequencing (GBS) and to conduct molecular evaluation of a broad collection for the species P. edulis from a source country, Colombia. We included control genotypes of yellow passion fruit, P. edulis f. flavicarpa. The goal was to evaluate differences between fruit types and compare landraces and genebank accessions from in situ accessions collected from farmers. In total, 3820 SNPs were identified as informative for this diversity study. However, the majority distinguished yellow and purple passion fruit, with 966 SNPs useful in purple passion fruits alone. In the population structure analysis, purple passion fruits were very distinct from the yellow ones. The results for purple passion fruits alone showed reduced diversity for the commercial cultivars while highlighting the higher diversity found among landraces from wild or semi-wild conditions. These landraces had higher heterozygosity, polymorphism, and overall genetic diversity. The implications for genetics and breeding as well as evolution and ecology of purple passion fruits based on the extant landrace diversity are discussed with consideration of manual or pollinator-assisted hybridization of this species.

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Development of a core set of single nucleotide polymorphism markers for genetic diversity analysis and cultivar fingerprinting in cowpea

Legume Science ◽

10.1002/leg3.93 ◽

2021 ◽

Author(s):

Xinyi Wu ◽

Baogen Wang ◽

Suqi Wu ◽

Sujuan Li ◽

Yan Zhang ◽

...

Keyword(s):

Genetic Diversity ◽

Single Nucleotide Polymorphism ◽

Diversity Analysis ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Genetic Diversity Analysis ◽

Core Set

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Assessment of diversity in tropical soybean (Glycine max (L.) Merr.) varieties and elite breeding lines using single nucleotide polymorphism markers

Plant Genetic Resources ◽

10.1017/s1479262121000034 ◽

2021 ◽

Vol 19 (1) ◽

pp. 20-28

Author(s):

Abush Tesfaye Abebe ◽

Adesike Oladoyin Kolawole ◽

Nnanna Unachukwu ◽

Godfree Chigeza ◽

Hailu Tefera ◽

...

Keyword(s):

Genetic Diversity ◽

Single Nucleotide Polymorphism ◽

Glycine Max ◽

Snp Markers ◽

Fixation Index ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Breeding Lines ◽

Soybean Germplasm ◽

Elite Breeding Lines

AbstractSoybean (Glycine max (L.) Merr.) is an important legume crop with high commercial value widely cultivated globally. Thus, the genetic characterization of the existing soybean germplasm will provide useful information for enhanced conservation, improvement and future utilization. This study aimed to assess the extent of genetic diversity of soybean elite breeding lines and varieties developed by the soybean breeding programme of the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria. The genetic diversity of 65 soybean genotypes was studied using single-nucleotide polymorphism (SNP) markers. The result revealed that 2446 alleles were detected, and the indicators for allelic richness and diversity had good differentiating power in assessing the diversity of the genotypes. The three complementary approaches used in the study grouped the germplasm into three major clusters based on genetic relatedness. The analysis of molecular variance revealed that 71% (P < 0.001) variation was due to among individual genotypes, while 11% (P < 0.001) was ascribed to differences among the three clusters, and the fixation index (FST) was 0.11 for the SNP loci, signifying moderate genetic differentiation among the genotypes. The identified private alleles indicate that the soybean germplasm contains diverse variability that is yet to be exploited. The SNP markers revealed high diversity in the studied germplasm and found to be efficient for assessing genetic diversity in the crop. These results provide valuable information that might be utilized for assessing the genetic variability of soybean and other legume crops germplasm by breeding programmes.

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