scholarly journals Genetic Characteristics of Brook Trout Salvelinus fontinalis (Mitchill, 1848) Broodstocks from Hatcheries in Bosnia and Herzegovina

2020 ◽  
Vol 78 (4) ◽  
pp. 183-194
Author(s):  
Belma Kalamujić Stroil ◽  
Mia Stanić ◽  
Abdurahim Kalajdžić ◽  
Naris Pojskić
Keyword(s):  
Genetic Diversity ◽  
Inbreeding Depression ◽  
Control Region ◽  
Bosnia And Herzegovina ◽  
Brook Trout ◽  
Management Practices ◽  
Salvelinus Fontinalis ◽  
Polymorphic Information Content ◽  
Genetic Characteristics ◽  
Low Genetic Diversity

AbstractThe most commonly farmed fish species in Bosnia and Herzegovina’s aquaculture are from the family Salmonidae, including brook trout Salvelinus fontinalis which is reared both for consumption and stocking purposes. A number of farmers complained about the elevated frequency of anatomical deformities in the smolts and fingerlings of brook trout, decreasing their fitness rate and causing significant financial loss. Since it has been shown that occurrence of deformities is correlated with the low genetic diversity and high inbreeding, this study aimed to assess intra- and interpopulation diversity of Salvelinus fontinalis from different freshwater fish farms in Bosnia and Herzegovina by observing variation in mitochondrial and nuclear genome. Total of 109 samples of brook trout from three hatcheries located at the Neretva River were analyzed for the mitochondrial control region and seven nuclear microsatellite loci. Both PCR-RFLP and sequencing revealed only one haplotype of the control region in all investigated trout. Overall, a low number of genotypes was evident across all the observed loci. Values of genetic diversity and polymorphic information content followed the increase in the number of alleles per locus. In general, values of inbreeding coefficient were generally very high, while the genetic diversity and observed heterozygosity had low rates. The results of our study are congruent with the findings of previous studies in which developmental deformities were concomitant with the low genetic diversity and inbreeding depression. It is, therefore, strongly advised to regularly supplement the broodstock with new, unrelated individuals, as it is of vital importance for sustaining a satisfying level of genetic diversity and preventing inbreeding depression. Additionally, maintaining good management practices regarding the fluctuation of water temperature, exposure to pollution, nutrition, etc., will further contribute to the prevention of this detrimental condition.

scholarly journals Low Genetic Diversity of the Endangered Franciscana (Pontoporia blainvillei) in Its Northernmost, Isolated Population (FMAIa, Espírito Santo, Brazil)

2020 ◽  
Vol 7 ◽  
Author(s):  
Vanessa K. M. de Oliveira ◽  
Drienne M. Faria ◽  
Haydée A. Cunha ◽  
Teresa E. C. dos Santos ◽  
Adriana C. Colosio ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Control Region ◽  
Microsatellite Loci ◽  
Distribution Analysis ◽  
Sample Number ◽  
Espírito Santo ◽  
Low Genetic Diversity ◽  
Southwestern Atlantic Ocean ◽  
Espirito Santo ◽  
Pontoporia Blainvillei

The franciscana, Pontoporia blainvillei, is the most endangered small cetacean in the Southwestern Atlantic Ocean, occurring from Itaúnas, Espírito Santo, Brazil to Chubut province, Argentina. This area is divided into four Franciscana Management Areas (FMA). The northern portion of this species distribution is not continuous and a previous genetic study using mitochondrial DNA (mtDNA) separated it into FMAIa (Espírito Santo state) and FMAIb (North of Rio de Janeiro state). In order to increase the information about this population we expanded the sample number and evaluated mitochondrial and nuclear DNA diversity. Samples of 68 franciscanas found stranded on beaches from 2005 to 2020 were analyzed. Analyses included 350 bp of the mtDNA control region (D-loop) and 12 microsatellite loci. We identified three control region haplotypes in FMAIa, two of them not previously observed in this population, one being a new haplotype. Haplotype and nucleotide diversities were 0.0408 and 0.00012 respectively, the lowest reported for all FMAs analyzed until now. The Neutrality tests were not significant and Mismatch Distribution analysis did not reject the hypothesis of population expansion. One of the microsatellite loci was monomorphic, and for the other loci, two to nine alleles were identified, with expected heterozygosities ranging from 0.306 to 0.801. No substructure was revealed and effective population size (Ne) was estimated in 117.9 individuals. Even with an increased sample size, the high mitochondrial genetic homogeneity suggested for the population in a previous study was confirmed. Among six loci previously analyzed in other franciscana populations, five showed the lowest observed heterozygosities for the Espírito Santo population. The novel microsatellite data also showed low genetic diversity and could not reject the hypothesis of a single, panmitic population along the coast of Espírito Santo. This species has been intensively impacted in the last years by incidental capture during fishing activities and habitat degradation, caused by pollution, coastal development and environmental disasters in FMAIa. Considering that this population is small, isolated, and with low levels of genetic diversity, we reinforce the necessity of different conservation actions, focusing mainly on the reduction of bycatch of this species in the region.

scholarly journals Keragaman Genetik Kukang Jawa (Nycticebus javanicus) Menggunakan Control Region (D-loop) DNA Mitokondria (mtDNA) (GENETIC DIVERSITY ON JAVAN SLOW LORIS (NYCTICEBUS JAVANICUS) USING OF CONTROL REGION (D-LOOP) mtDNA)

2019 ◽  
Vol 20 (3) ◽  
pp. 360
Author(s):  
Wirdateti Wirdateti ◽  
Hayati Aziza ◽  
Handayani Handayani
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Control Region ◽  
West Java ◽  
Slow Loris ◽  
Genetic Population ◽  
Central Java ◽  
Low Genetic Diversity ◽  
The Status ◽  
D Loop

Javan slow loris (Nycticebus javanicus)  one of the species of the genus Nycticebus is endemic in Java.  Their distribution region  is in West Java and Banten, and also reported to be found in Central Java and East Java, although very rarely.  Status of the species is Critically Endangered due to high levels of poaching, habitat loss and habitat fragmentation, so that the necessary conservation in order to increase the population. For conservation management it is necessary to know the status of genetic resources that play of  role in breeding, then this research is to explore the genetic population of the Javan slow loris  from some locations in West Java. The research objective was to assess the diversity of their current population of Java loris through the control region (D-loop) of mitochondrial DNA (mtDNA). A total of 23 individuals samples from Gunung Halimun Park, Tasikmalaya, Garut, Ciamis, Jember and confiscated at the Rehabilitation Center IAR Bogor were used in this stydy. Specific primers of D-loop are used for loris with a length of 296 bp sequence. The result showed there are only five different sites and formed six haplotypes, each haplotypes only 1-3 nucleotides different. Low genetic diversity is shown as much as 42.96% of individuals show the same sequence or genetic distance (d) = 0 that indicate was monomorf population from different population. The genetic distance of the entire population was 0.003 ± 0:01 (0.3%).

scholarly journals Low Genetic Diversity in Turkish Populations of Wels Catfish Silurus glanis L., 1758 (Siluridae, Pisces) Revealed by Mitochondrial Control Region Sequences

2020 ◽  
Vol 20 (10) ◽  
pp. 767-776
Author(s):  
Yusuf Bektas ◽  
Ismail Aksu ◽  
Gokhan Kalayci ◽  
Davut Turan
Keyword(s):  
Genetic Diversity ◽  
Control Region ◽  
Mismatch Distribution ◽  
Phylogenetic Trees ◽  
Goodness Of Fit ◽  
Haplotype Diversity ◽  
Mitochondrial Control Region ◽  
Haplotype Network ◽  
Silurus Glanis ◽  
Low Genetic Diversity

This study aimed to investigate the genetic diversity and population structure of Wels catfish Silurus glanis L. 1758 in Turkey using squences of the mitochondrial DNA control region The 887-bp fragment of D-loop was aligned for 112 S. glanis individuals from ten wild populations in Turkey, defined by 29 polymorphic sites comprising 16 haplotypes. The low haplotype diversity and nucleotide diversity within each population ranged from 0.000 to 0.378 and from 0.0000 to 0.0045, respectively. Analysis of molecular variance showed significant genetic differentiation among ten populations (FST =0.940; P<0.01). AMOVA revealed that the most of genetic variation was found between Thrace and Anatolia clades (74,07 %). The phylogenetic trees and haplotype network topologies were consistent with the results of AMOVA analysis. The non-significant negative Tajima's D (-0.875 P<0.05) and Fu's Fs (-0.381, P<0.02) values and mismatch distribution for S. glanis populations indicated no evidence for changes in population size. Furthermore, goodness-of-fit of the observed versus the theoretical mismatch distribution tested the sum of squared deviation (SSD; 0.00308, P>0.05), Harpending’s raggedness index (Hri; 0,300, P>0.05) and Ramos-Onsins & Rozas (R2; 0,0771, P>0.05), supporting population neutrality.

Genetic diversity of mungbean (Vigna radiata L.) germplasm in Indonesia

2014 ◽  
Vol 12 (S1) ◽  
pp. S91-S94 ◽  
Author(s):  
Puji Lestari ◽  
Sue Kyung Kim ◽  
Reflinur ◽  
Yang Jae Kang ◽  
Nurwita Dewi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Vigna Radiata ◽  
Diversity Index ◽  
Polymorphic Information Content ◽  
Conservation Strategy ◽  
Low Genetic Diversity ◽  
Breeding Programmes ◽  
The Mean ◽  
Simple Sequence

Despite widespread mungbean [Vigna radiata (L.) Wilczek] consumption in Indonesia, few molecular studies have been carried out on accessions and available data are minimal. In this study, we used 30 newly developed simple sequence repeat (SSR) markers designed from the mapped sequence scaffolds of the Korean Sunhwanokdu and Gyeonggijaerae 5 mungbean genomes. These markers were used to examine loci in 83 mungbean accessions collected from diverse geographical areas in Indonesia. A total of 107 alleles were detected among the accessions with 29 polymorphic markers. However, the mean of polymorphic information content (0.33) value and diversity index (0.38) value was indicative of low genetic diversity in this germplasm. The mungbean population structure was not clearly differentiated and the number of subpopulations was unclear. Neighbour-joining tree analysis revealed that the genetic cluster did not reflect the geographical origin of the accessions. Interestingly, the most agriculturally improved varieties were genetically similar to some landraces from one of the main mungbean-producing regions. These newly developed SSR markers could be useful for detecting genetic variability as a basis for establishing a conservation strategy for mungbean germplasm with the aim of enhancing Indonesian breeding programmes.

scholarly journals Characterization and Genetic Diversity of Taif Chicken Ecotype Using Dense Microsatellites Panel

2021 ◽  
Vol 14 (4) ◽  
pp. 1962-1967
Author(s):  
Ayman Sabry
Keyword(s):  
Genetic Diversity ◽  
Polymorphic Information Content ◽  
Inbreeding Coefficient ◽  
Comprehensive Investigation ◽  
Low Genetic Diversity ◽  
Expected Heterozygosity ◽  
Native Chicken ◽  
High Level ◽  
Weinberg Expectation ◽  
Dense Panel

The current study is the first comprehensive investigation to address the native chicken ecotypes of the Taif region to unravel the genetic diversity using a dense panel of 40 microsatellites (SSR). Blood samples were collected from 25 hens randomly sampled from a village farm at Taif governorate. A total of 147 alleles were detected, with an average of 3.7 alleles per locus. The overall mean of polymorphic information content (PIC) was 0.43. The average observed heterozygosity (Hobs) of 0.28 was lower than the expected heterozygosity (Hexp) of 0.48. Out of 40l ocionly11 loci showed insignificant deviation from Hardy Weinberg expectation. The ecotypes showed low genetic diversity (HS = 0.65) and a high level of inbreeding (FIS= 0.75). The high FIS is indicative of the endangerment potentiality of this ecotype. Nine SSR showed an inbreeding coefficient of one. The significant estimate of the inbreeding coefficient of the present study calls for an immediate breeding plan to preserve such endangered ecotypes. Results of the present study will provide an initial guide to design further investigations for the development of sustainable genetic improvement and conservation programs for the Taif ecotype genetic resources.

scholarly journals Assessment of genetic diversity in Moroccan sesame (Sesamum indicum) using ISSR molecular markers

OCL ◽  
2021 ◽  
Vol 28 ◽  
pp. 3
Author(s):  
Meriem El Harfi ◽  
Jamal Charafi ◽  
Karim Houmanat ◽  
Hafida Hanine ◽  
Abdelghani Nabloussi
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Polymorphic Information Content ◽  
Issr Markers ◽  
Sesamum Indicum ◽  
Simple Method ◽  
Low Genetic Diversity ◽  
Simple Repeats ◽  
New Germplasm ◽  
Issr Primers

There is a need for sesame (Sesamum indicum L.) breeding in Morocco to release performant and adapted varieties, which requires a large genetic variability in the germplasm to be used. In this context, genetic diversity of sesame populations from different locations in Tadla area was investigated using ISSR (Inter Sequence Simple Repeats) markers as a simple method to reveal polymorphism among them. A total of 130 individuals representing 31 populations were sampled. Twenty-four ISSR primers were used for analysis of individuals representing the 31 different sesame populations grown in different agroclimatic zones of Tadla, accounting for 90% of sesame cultivation area in Morocco. Indeed, seven primers showed legible and reproducible genomic profiles with an interesting number of bands. A total of 57 bands were obtained with ISSR primers, of which 47 were polymorphic. PIC (Polymorphic Information Content) ranged from 0.002 to 0.350, showing that ISSR markers are informative and relevant for discriminating the populations evaluated. The similarity coefficient of ISSR data ranged from 0.509 to 1, with an average of 0.870. The results obtained showed that Moroccan sesame populations are characterized by a low genetic diversity, suggesting a genetic proximity among them. Therefore, new germplasm should be either introduced from diverse geographical origins or created through mutagenesis breeding in order to broaden the existing genetic variability.

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