Genetic characteristics of broodstock and offspring of the seven-band grouper (Hyporthodus septemfasciatus) using fluorescent-AFLP markers

2016 ◽  
Vol 98 (2) ◽  
pp. 261-267
Author(s):  
Yongshuang Xiao ◽  
Shuguang Guan ◽  
Qinghua Liu ◽  
Hongjun Liu ◽  
Daode Yu ◽  
...  
Keyword(s):  
Diversity Index ◽  
Rocky Reef ◽  
Negative Effects ◽  
Principal Coordinates Analysis ◽  
Genetic Characteristics ◽  
Principal Coordinates ◽  
Sustainable Culture ◽  
Breeding Programmes ◽  
Commercial Breeding ◽  
Rocky Reef Fish

Seven-band grouper (Hyporthodus septemfasciatus) is a commercial rocky reef fish in East Asia that has been regarded as a promising species for aquaculture. To investigate the broodstock contributions to offspring for the sustainability of fry production, 62 individuals ofH. septemfasciatusfrom two broodstocks and one offspring population were analysed using fluorescent-AFLP. A total of 602 bands were amplified and 70.10% of them were polymorphic. The numbers of polymorphic loci were 308 (Pbroodstock I= 55.50%) and 356 (Pbroodstock II= 63.12%) in the two broodstocks, and 294 (Poffspring= 52.88%) in the offspring, respectively. The average values of Shannon diversity index (I) and expected heterozygosity (H) were higher in the broodstock (Ibroodstock I= 0.281,Ibroodstock II= 0.244,Hbroodstock I= 0.185,Hbroodstock II= 0.161) than those in the offspring (Ioffspring= 0.243,Hoffspring= 0.161). AMOVA and FSTanalyses showed that significant genetic differentiation between broodstock and offspring populations, and limited effective broodstock population size has contributed to the offspring. Both STRUCTURE and Principal Coordinates Analysis (PCoA) also showed the three populations composed of two stocks and most offspring individuals (95.0%) only originated from 44.0% of the individuals of broodstock I, which may have negative effects on sustainable fry production. Therefore, genetic variation between broodstock and offspring should be monitored, and large effective size of broodstock should be employed to ensure the success of commercial breeding programmes. Our data provide a useful genetic basis for future planning of sustainable culture and management ofH. septemfasciatus.

scholarly journals Temporal and Spatial Analysis of Forward and Backward Microbial Contamination in a Mars Analog Mission

2021 ◽  
Vol 8 ◽  
Author(s):  
Yael Yair ◽  
Leah Reshef ◽  
Camelia Shopen-Gochev ◽  
Gal Yoffe ◽  
Gil Azulay ◽  
...  
Keyword(s):  
Diversity Index ◽  
Environmental Dna ◽  
Population Diversity ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Mars Analog ◽  
Sequencing Platforms ◽  
Contamination Events

As human exploration missions to Mars are on the horizon, microbial cross-contamination remains a key issue to address. These issues can be approached today using advances in molecular metagenomics methods, which include rapid and sensitive sequencing platforms for characterizing microbial populations. Combined with analog missions, these methods provide powerful tools for assessing the challenges associated with planetary exploration. Here, we designed a protocol to monitor forward and backward contamination events and progression in an 11-days Mars analog mission in the Ramon crater in Israel. Forward contamination soil samples were collected daily from three sites–two sites in close proximity to the habitat and one isolated site. Backward contamination was determined in samples from nitrile gloves of six analog astronauts before and after extravehicular activities Temperature, relative humidity and soil composition data were also collected for all sites. Environmental DNA samples were extracted in the main habitat and 16S (bacterial) and 18S (eukaryotic, fungal) rRNA gene amplicons were sequenced and analyzed to study microbial population diversity and composition. Shannon Diversity index analysis and Principal Coordinates analysis (PCoA) of rRNA genes indicated that differences in the diversity and population composition were significant in sites closer to the habitat when compared to a reference site. These samples also demonstrated the introduction of human-associated taxa to the environment. Backward contamination consisted of bacterial taxa found on gloves upon return from EVA and also detected in soil, altogether 44 genera, indicating backward contamination events. To our knowledge, this is the first protocol to utilize advanced molecular technologies to investigate forward and backward contamination in a Mars analog mission.

scholarly journals Genetic Diversity of White Clover (Trifolium Repens L.) from the Urban Area of Rīga Baltā Āboliņa (Trifolium Repens L.) Ģenētiskā Daudzveidība Rīgas Pilsētvidē

2015 ◽  
Vol 69 (3) ◽  
pp. 132-134 ◽  
Author(s):  
Dace Grauda ◽  
Kalvis Avotiņš ◽  
Oksana Fokina ◽  
Agnese Kolodinska-Brantestam ◽  
Isaak Rashal
Keyword(s):  
Urban Environment ◽  
Urban Area ◽  
White Clover ◽  
Trifolium Repens ◽  
Diversity Index ◽  
Genetic Distances ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Plant Groups ◽  
Trifolium Repens L

Abstract White clover (Trifolium repens L.) is well represented in the urban environment and wide areas. The goal of this study was to compare the genetic features and to determine the genetic distances and similarities between some populations of white clover using iPBS (inter primer binding sites) technique in a retrotransposon-based method in samples from ecologically different areas in Latvia. Comparisons were made between three plant groups: urban environment (different areas in Rīga), Latvian countryside territory (four different localities), and the commercial variety ‘Daile’. The Shannon diversity index was not high (0.2974 for Rīga, 0.3079 in countryside territories, and 0.3367 for the variety ‘Daile’), but the polymorphic bands present in all evaluated plant sets were higher than 89%. Using principal coordinates analysis the white clover formed three clusters. One cluster included plants from the variety ‘Daile’. The plants from Rīga urban area and different sites of Latvia formed two clusters.

scholarly journals Genetic Diversity and Association Study of Aromatics in Grapevine

2017 ◽  
Vol 142 (3) ◽  
pp. 225-231 ◽  
Author(s):  
Xiaoxu Yang ◽  
Yinshan Guo ◽  
Junchi Zhu ◽  
Zaozhu Niu ◽  
Guangli Shi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Aroma Compounds ◽  
Species Classification ◽  
Principal Coordinates Analysis ◽  
Phylogenetic Tree Analysis ◽  
Genetic Characteristics ◽  
Principal Coordinates ◽  
Genetic Clusters

Monoterpenoid metabolism and aroma compounds are influenced by genetic characteristics. Linalool, α-terpineol, nerol, and geraniol are primary monoterpenoids that have previously been studied in grape (Vitis vinifera) berries. Previous studies were restricted by the lack of relevant studies investigating population structure and the regulatory mechanism underlying monoterpenoid synthesis. In this study, a total of 1133 alleles were amplified, with each locus having on average 6.06 alleles. We also assessed the genetic variability among the genotypes based on 187 microsatellite primer pairs amplified in 96 grape genotypes. The results of the phylogenetic tree analysis showed that the grapevine accessions grouped into five genetic clusters that largely coincided with the recognized species classification and the result of principal coordinates analysis (PCoA). The molecular characterization of these accessions provides insight into genetic diversity, population structure, and linkage disequilibrium (LD) in grapevines. A total of 51 quantitative trait loci (QTLs) were detected that were significantly associated with linalool, α-terpineol, nerol, and geraniol. We found that Deoxyxylulose phosphate synthase (DXS) was located in the region UDV060 on linkage group (LG) 5, whereas Farnesyl diphosphate synthase (FPPS) and Hydroxymethylbutenyl diphosphate reductase (HDR) were located in the VLG19-I-1 and VLG3-A-1 regions, respectively. These novel QTLs will potentially assist in the screening of aroma compounds in grapevines.

scholarly journals Genetic Diversity in Kenyan Populations of Acacia senegal (L.) Willd. Based on ISSR Markers

2009 ◽  
Vol 58 (1-6) ◽  
pp. 20-28 ◽  
Author(s):  
Chemulanga Josiah Chiveu ◽  
O. G. Dangasuk ◽  
M. E. Omunyin ◽  
F. N. Wachira
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Diversity Index ◽  
Geographic Distance ◽  
Arid Zones ◽  
Economic Traits ◽  
Principal Coordinates Analysis ◽  
Acacia Senegal ◽  
Important Species ◽  
Principal Coordinates

Abstract Acacia senegal (L.) Willd is an African arid and semi arid zones, leguminous multipurpose tree species belonging to the subfamily Mimosoideae, family Fabaceae and subgenus Aculeiferum, highly valued for gum arabic production. Patterns of genetic diversity of this important species in Kenya have not been studied for efficiency of germplasm utilization, conservation and improvement. Four natural populations of A. senegal in Kenya (Bulla Sambul, Kutulo, Wamba and Meisori) were analyzed to estimate genetic variation among and within populations, by use of ISSR (Inter-simple sequence repeat) markers. Using five primers, 17 polymorphic loci were observed, ranging in size from 564bp to 983bp. A high mean total genetic diversity index for the species was observed (H= 0.27). The principal coordinates analysis (PCoA) of the 95 samples from the four populations showed that about 40.75% of the total variation was described by the first two axes with much overlap among populations; hence populations were not defined on the basis of geographic distance. Much of the genetic variation resided within the populations based on the coefficient of gene differentiation (Gst = 0.0573) and Analysis of Molecular Variance (AMOVA) (95%). It was therefore recommended that selection for the desired important economic traits for improvement and conservation should emphasize on individual trees within populations rather than among populations, and also ensure a comprehensive coverage of the entire ecological amplitude of the populations.

scholarly journals Genotyping of Two Mediterranean Trout Populations in Central-Southern Italy for Conservation Purposes Using a Rainbow-Trout-Derived SNP Array

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1803
Author(s):  
Valentino Palombo ◽  
Elena De Zio ◽  
Giovanna Salvatore ◽  
Stefano Esposito ◽  
Nicolaia Iaffaldano ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Genetic Structure ◽  
Fishery Management ◽  
Snp Array ◽  
Fine Scale ◽  
Principal Coordinates Analysis ◽  
Data Set ◽  
Management Actions ◽  
Principal Coordinates ◽  
Mediterranean Trout

Mediterranean trout is a freshwater fish of particular interest with economic significance for fishery management, aquaculture and conservation biology. Unfortunately, native trout populations’ abundance is significantly threatened by anthropogenic disturbance. The introduction of commercial hatchery strains for recreation activities has compromised the genetic integrity status of native populations. This work assessed the fine-scale genetic structure of Mediterranean trout in the two main rivers of Molise region (Italy) to support conservation actions. In total, 288 specimens were caught in 28 different sites (14 per basins) and genotyped using the Affymetrix 57 K rainbow-trout-derived SNP array. Population differentiation was analyzed using pairwise weighted FST and overall F-statistic estimated by locus-by-locus analysis of molecular variance. Furthermore, an SNP data set was processed through principal coordinates analysis, discriminant analysis of principal components and admixture Bayesian clustering analysis. Firstly, our results demonstrated that rainbow trout SNP array can be successfully used for Mediterranean trout genotyping. In fact, despite an overwhelming number of loci that resulted as monomorphic in our populations, it must be emphasized that the resulted number of polymorphic loci (i.e., ~900 SNPs) has been sufficient to reveal a fine-scale genetic structure in the investigated populations, which is useful in supporting conservation and management actions. In particular, our findings allowed us to select candidate sites for the collection of adults, needed for the production of genetically pure juvenile trout, and sites to carry out the eradication of alien trout and successive re-introduction of native trout.

scholarly journals Tree Species Diversity and Composition of Miombo Woodlands in South-Central Angola: A Chronosequence of Forest Recovery after Shifting Cultivation

2017 ◽  
Vol 2017 ◽  
pp. 1-13 ◽  
Author(s):  
Francisco M. P. Gonçalves ◽  
Rasmus Revermann ◽  
Amândio L. Gomes ◽  
Marcos P. M. Aidar ◽  
Manfred Finckh ◽  
...  
Keyword(s):  
Shifting Cultivation ◽  
Stand Structure ◽  
Woody Species ◽  
Distinct Group ◽  
Forest Recovery ◽  
Miombo Woodlands ◽  
Principal Coordinates Analysis ◽  
South Central ◽  
Principal Coordinates ◽  
Management Plans

The study was carried out in the Cusseque area of the Municipality of Chitembo in south-central Angola. Our objectives were to assess the floristic diversity, the species composition, and stand structure of Miombo woodlands during regeneration after shifting cultivation. A total of 40 plots of 1000 m2were surveyed and analyzed, corresponding to mature forests/woodlands and three fallow types of different age. The analyses were based on plot inventories of all trees with DBH ≥ 5 cm. A total of 51 woody species, 38 genera, and 19 families were recorded. The dominant family was Fabaceae, with subfamily Caesalpinioideae being very abundant. Shannon Diversity and Evenness were highest in mature forests and young fallows, while the mature forest stands showed the highest species richness. A Principal Coordinates Analysis (PCoA) showed many species shared between the intermediate fallow types, but only few species were shared with young fallows. Mature forests formed a clearly distinct group. This study shows potential pathways of forest recovery in terms of faster regeneration after agricultural abandonment and, thus, the results presented here can be used in future conservation and management plans in order to reduce the pressure on mature forests.

scholarly journals Unraveling city-specific signature and identifying sample origin locations for the data from CAMDA MetaSUB challenge

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Runzhi Zhang ◽  
Alejandro R. Walker ◽  
Susmita Datta
Keyword(s):  
Machine Learning ◽  
Error Rates ◽  
Average Error ◽  
Importance Score ◽  
Learning Methods ◽  
Principal Coordinates Analysis ◽  
Principal Coordinates ◽  
Total Variability ◽  
The Common ◽  
Feature Selecting

Abstract Background Composition of microbial communities can be location-specific, and the different abundance of taxon within location could help us to unravel city-specific signature and predict the sample origin locations accurately. In this study, the whole genome shotgun (WGS) metagenomics data from samples across 16 cities around the world and samples from another 8 cities were provided as the main and mystery datasets respectively as the part of the CAMDA 2019 MetaSUB “Forensic Challenge”. The feature selecting, normalization, three methods of machine learning, PCoA (Principal Coordinates Analysis) and ANCOM (Analysis of composition of microbiomes) were conducted for both the main and mystery datasets. Results Features selecting, combined with the machines learning methods, revealed that the combination of the common features was effective for predicting the origin of the samples. The average error rates of 11.93 and 30.37% of three machine learning methods were obtained for main and mystery datasets respectively. Using the samples from main dataset to predict the labels of samples from mystery dataset, nearly 89.98% of the test samples could be correctly labeled as “mystery” samples. PCoA showed that nearly 60% of the total variability of the data could be explained by the first two PCoA axes. Although many cities overlapped, the separation of some cities was found in PCoA. The results of ANCOM, combined with importance score from the Random Forest, indicated that the common “family”, “order” of the main-dataset and the common “order” of the mystery dataset provided the most efficient information for prediction respectively. Conclusions The results of the classification suggested that the composition of the microbiomes was distinctive across the cities, which could be used to identify the sample origins. This was also supported by the results from ANCOM and importance score from the RF. In addition, the accuracy of the prediction could be improved by more samples and better sequencing depth.

Genetic analysis of a heritage variety collection

2018 ◽  
Vol 17 (03) ◽  
pp. 232-244 ◽  
Author(s):  
J. M. Preston ◽  
B. V. Ford-Lloyd ◽  
L. M. J. Smith ◽  
R. Sherman ◽  
N. Munro ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Group Method ◽  
Niche Markets ◽  
Principal Coordinates Analysis ◽  
Pair Group ◽  
Landrace Diversity ◽  
Principal Coordinates ◽  
Length Polymorphisms ◽  
Seed Saving ◽  
History Of

AbstractLandraces (including heritage varieties) are an important agrobiodiversity resource offering considerable value as a buffer against crop failures, as a crop for niche markets, and as a source of diversity for crop genetic improvement activities underpinning future food security. Home gardens are reservoirs of landrace diversity, but some of the accessions held in them are vulnerable or threatened with extinction. Those associated with seed saving networks have added security, for example, ca. 800 varieties are stored in the Heritage Seed Library (HSL) of Garden Organic, UK. In this study, Amplified Fragment Length Polymorphisms-based genetic analysis of accessions held in the HSL was used to (a) demonstrate the range of diversity in the collection, (b) characterize accessions to aid collection management and (c) promote broader use of the collection. In total, 171 accessions were included from six crops: Vicia faba L., Pisum sativum L., Daucus carota L., Cucumis sativus L., Lactuca sativa L. and Brassica oleracea L. var. acephala (DC.) Metzq. Average expected heterozygosity ranged from 0.18 to 0.28 in D. carota; 0.02–0.18 in P. sativum; 0.05–0.18 in L. sativa; 0.15–0.26 in B. oleracea var. acephala; 0.15–0.37 in C. sativus and 0.07–0.36 in V. faba. Genetic diversity and Fst values generally reflected the breeding system and cultivation history of the different crops. Comparisons of the diversity found in heritage varieties with that found in commercial varieties did not show a consistent pattern. Principal coordinates analysis and Unweighted Pair Group Method with Arithmetic Mean cluster analysis were used to identify four potential duplicate accession pairs.

Conservation genetics of the endangered Spotted Turtle (Clemmys guttata) illustrate the risks of “bottleneck tests”

2014 ◽  
Vol 92 (2) ◽  
pp. 149-162 ◽  
Author(s):  
Christina M. Davy ◽  
Robert W. Murphy
Keyword(s):  
Population Genetics ◽  
Freshwater Turtles ◽  
Population Declines ◽  
Isolated Populations ◽  
Principal Coordinates Analysis ◽  
Turtle Species ◽  
Principal Coordinates ◽  
Clemmys Guttata ◽  
Spotted Turtle ◽  
Cast Doubt

Studies of population genetics in turtles have suggested that turtles do not experience genetic impacts of bottlenecks as strongly as expected. However, recent studies cast doubt on two commonly used tests implemented in the program BOTTLENECK, suggesting that these findings should be re-evaluated. The Spotted Turtle (Clemmys guttata (Schneider, 1792)) is endangered both globally and within Canada, but genetic data required to develop effective recovery strategies are unavailable. Here, we conducted the first study of population genetic structure in C. guttata. We then used multiple small populations of C. guttata as replicates to test whether the commonly used program BOTTLENECK could detect the genetic signature of bottlenecks in our study populations, which are all thought to have experienced significant declines in the past 2–3 generations (75 years). Turtles (n = 256) were genotyped at 11 microsatellite loci. A suite of Bayesian population genetics analyses and a principal coordinates analysis identified a minimum of 6 distinct genetic populations and a maximum of 10 differentiated subpopulations across the sampled Canadian range of C. guttata, which corresponded to demographically independent units. BOTTLENECK failed to detect population declines. A literature review found that bottleneck tests in 17 of 18 previous genetic studies of tortoises and freshwater turtles were based on suboptimal sampling, potentially confounding their results. High retention of genetic diversity (allelic richness and heterozygosity) in isolated populations of C. guttata and other turtle species is encouraging for species recovery, but conclusions about the prevalence of genetic bottlenecks in such populations should be re-examined.

Use of multivariate methods in forest research site selection

1991 ◽  
Vol 21 (11) ◽  
pp. 1573-1580 ◽  
Author(s):  
Andrew J. Burton ◽  
Carl W. Ramm ◽  
Kurt S. Pregitzer ◽  
David D. Reed
Keyword(s):  
Site Selection ◽  
Large Scale ◽  
Multivariate Methods ◽  
Data Bases ◽  
Principal Coordinates Analysis ◽  
Research Site ◽  
Principal Coordinates ◽  
Alternative Sites ◽  
Existing Data ◽  
Selection Of

In large-scale gradient studies, selection of the best research sites is critical but time-consuming and costly. Multivariate methods can be used to quickly identify suitable sites from existing data bases. Based on a study of acid deposition in the Great Lakes region (the Michigan Gradient Study), we illustrate the use of multivariate methods in screening potential research sites for similarity. Sites were examined using cluster analysis, principal coordinates analysis, and correspondence analysis. The graphical displays generated by the multivariate methods were used to identify similar sites across the gradient. A list of 31 potential sites was reduced to 5 similar research sites and several alternative sites. The results of the multivariate methods compared well with more traditional methods of research site selection but allowed for multiple comparisons of many potential sites using a variety of data from existing data bases. By eliminating sites that are unacceptable with respect to available data, the multivariate methods reduce the number of sites that require field visitation prior to final site verification. This process represents a substantial savings in time and effort when dealing with a long list of potential research sites.

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