scholarly journals Haemoglobin polymorphism in atlantic cod(Gadus morhua): Allele frequency variation between yearclasses in a Norwegian fjord stock

1985 ◽  
Vol 39 (1) ◽  
pp. 55-62 ◽  
Author(s):  
J. Mork ◽  
G. Sundnes
Keyword(s):  
Allele Frequency ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Frequency Variation ◽  
Norwegian Fjord ◽  
Allele Frequency Variation

scholarly journals Genetic diversity of ‘Very Important Pharmacogenes’ in two South-Asian populations

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12294
Author(s):  
Neeraj Bharti ◽  
Ruma Banerjee ◽  
Archana Achalere ◽  
Sunitha Manjari Kasibhatla ◽  
Rajendra Joshi
Keyword(s):  
Genetic Diversity ◽  
Allele Frequency ◽  
Population Stratification ◽  
Drug Response ◽  
Fixation Index ◽  
Frequency Variation ◽  
1000 Genomes Project ◽  
1000 Genomes ◽  
Link Type ◽  
Allele Frequency Variation

Objectives Reliable identification of population-specific variants is important for building the single nucleotide polymorphism (SNP) profile. In this study, genomic variation using allele frequency differences of pharmacologically important genes for Gujarati Indians in Houston (GIH) and Indian Telugu in the U.K. (ITU) from the 1000 Genomes Project vis-à-vis global population data was studied to understand its role in drug response. Methods Joint genotyping approach was used to derive variants of GIH and ITU independently. SNPs of both these populations with significant allele frequency variation (minor allele frequency ≥ 0.05) with super-populations from the 1000 Genomes Project and gnomAD based on Chi-square distribution with p-value of ≤ 0.05 and Bonferroni’s multiple adjustment tests were identified. Population stratification and fixation index analysis was carried out to understand genetic differentiation. Functional annotation of variants was carried out using SnpEff, VEP and CADD score. Results Population stratification of VIP genes revealed four clusters viz., single cluster of GIH and ITU, one cluster each of East Asian, European, African populations and Admixed American was found to be admixed. A total of 13 SNPs belonging to ten pharmacogenes were identified to have significant allele frequency variation in both GIH and ITU populations as compared to one or more super-populations. These SNPs belong to VKORC1 (rs17708472, rs2359612, rs8050894) involved in Vitamin K cycle, cytochrome P450 isoforms CYP2C9 (rs1057910), CYP2B6 (rs3211371), CYP2A2 (rs4646425) and CYP2A4 (rs4646440); ATP-binding cassette (ABC) transporter ABCB1 (rs12720067), DPYD1 (rs12119882, rs56160474) involved in pyrimidine metabolism, methyltransferase COMT (rs9332377) and transcriptional factor NR1I2 (rs6785049). SNPs rs1544410 (VDR), rs2725264 (ABCG2), rs5215 and rs5219 (KCNJ11) share high fixation index (≥ 0.5) with either EAS/AFR populations. Missense variants rs1057910 (CYP2C9), rs1801028 (DRD2) and rs1138272 (GSTP1), rs116855232 (NUDT15); intronic variants rs1131341 (NQO1) and rs115349832 (DPYD) are identified to be ‘deleterious’. Conclusions Analysis of SNPs pertaining to pharmacogenes in GIH and ITU populations using population structure, fixation index and allele frequency variation provides a premise for understanding the role of genetic diversity in drug response in Asian Indians.

Historical analysis of Pan I in Atlantic cod (Gadus morhua): temporal stability of allele frequencies in the southeastern part of the species distribution

2007 ◽  
Vol 64 (10) ◽  
pp. 1448-1455 ◽  
Author(s):  
Einar Eg Nielsen ◽  
Brian R MacKenzie ◽  
Eydfinn Magnussen ◽  
Dorte Meldrup
Keyword(s):  
Species Distribution ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Temporal Stability ◽  
Historical Analysis ◽  
Allele Frequencies ◽  
Degraded Dna ◽  
Frequency Variation ◽  
Genetic Stock ◽  
Southeastern Part

We investigated temporal genetic differentiation at the pantophysin (Pan I) locus in four Atlantic cod (Gadus morhua) populations from the southeastern part of the species distribution: the Baltic Sea, the North Sea, the Faroe Plateau, and the Faroe Bank. Historical otolith collections enabled investigation of allele frequency variation over time periods up to 69 years employing Pan I primers specifically designed for partially degraded DNA. Small and nonsignificant temporal changes in Pan I allele frequencies were observed in the four populations. Simultaneous microsatellite analysis revealed similar temporal genetic stability with temporal FST values ranging from 0 to 0.006, suggesting limited demographic changes. Sea surface temperature, which has been suggested as the primary driver for the geographical distribution of Pan I alleles in cod, showed no long-term trend although temperature has increased since the mid-1990s. Our study demonstrates that populations in the southeastern part of the species range has been characterized by very high frequencies of the Pan IA allele for many decades, and accordingly, Pan I serves as a reliable marker for genetic stock identification on a macrogeographical scale.

Spatial and temporal microsatellite variation in spawning Atlantic cod, Gadus morhua, around Iceland

2013 ◽  
Vol 70 (8) ◽  
pp. 1151-1158 ◽  
Author(s):  
Guðni Magnús Eiríksson ◽  
Einar Árnason
Keyword(s):  
Allele Frequency ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Genetic Difference ◽  
North Coast ◽  
The South ◽  
Microsatellite Variation ◽  
The North ◽  
Significant Difference ◽  
The Difference

The present study suggests that the observed genetic difference between Atlantic cod, Gadus morhua, off the south and the north coast of Iceland may be caused by natural selection affecting genetic variation at a microsatellite loci (Gmo34). When disregarding this locus from the analysis, no genetic difference was observed between northern and southern Iceland. The methods applied here were very sensitive, and differences as small as FST = 0.0005 are unlikely to go unnoticed. The difference between cod off the south and the north coast of Iceland is thus likely to be smaller than that. Such a small difference is negligible and is not likely to have any biological meaning. Genetic drift was detected by allele frequency comparison among different cohorts (FST = 0.0007, P = 0.0209). A small but significant difference was observed among allele frequency for cod grouped by depth at the south coast of Iceland (FST = 0.0017, P = 0.0002). This difference is very subtle and needs to be interpreted with caution.

scholarly journals Seasonal dynamics of growth and mortality suggest contrasting population structure and ecology for cod, pollack, and saithe in a Norwegian fjord

2012 ◽  
Vol 69 (4) ◽  
pp. 537-546 ◽  
Author(s):  
Mikko Heino ◽  
Terje Svåsand ◽  
Jarle Tryti Nordeide ◽  
Håkon Otterå
Keyword(s):  
Population Structure ◽  
Seasonal Dynamics ◽  
Seasonal Changes ◽  
Gadus Morhua ◽  
Depth Distribution ◽  
Atlantic Cod ◽  
Regular Growth ◽  
Independent Unit ◽  
Norwegian Fjord ◽  
Autumn And Winter

Abstract Heino, M., Svåsand, T., Nordeide, J. T., Otterå, H. 2012. Seasonal dynamics of growth and mortality suggest contrasting population structure and ecology for cod, pollack, and saithe in a Norwegian fjord. – ICES Journal of Marine Science, 69: 537–546. We study the dynamics of Atlantic cod (Gadus morhua L.), pollack (Pollachius pollachius L.), and saithe (Pollachius virens L.) in Masfjorden, a small fjord in western Norway. Annually, cohorts of pollack and cod grow in size and decline in abundance, as expected of closed populations, whereas saithe virtually disappear before maturity. Seasonally, in contrast, the dynamics of cod and pollack differ. Pollack shows a regular growth pattern, with most of the growth taking place in summer. Its abundance-at-age shows strong seasonal variations, with a marked increase from spring to summer followed by a decline through autumn and winter. These patterns relate partly to seasonal changes in depth distribution and catchability. Combined with the observation that spawning-stage pollack are abundant in spring, we interpret these patterns to suggest that pollack in Masfjorden represent a dynamically independent unit. Seasonal changes in abundance are less marked for cod, and seasonal changes in depth distribution seem insignificant. However, cod shows an unusual pattern in length at age, with no apparent growth in summer and fast growth in autumn. These patterns suggest that the population structure of cod may be more open than that of pollack and may involve mixing of more than one population component.

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