scholarly journals Genetic diversity of divergent redclaw crayfish Cherax quadricarinatus (Von Martens, 1868) populations evaluated to initiate a breeding program in Mexico

2021 ◽  
Vol 49 (2) ◽  
pp. 272-279
Author(s):  
Adriana Max-Aguilar ◽  
Humberto Villarreal ◽  
Ignacio Leyva-Valencia ◽  
Rocío Valencia-Valdez ◽  
José Naranjo-Páramo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Decapod Crustacean ◽  
Improvement Program ◽  
Genetic Characteristics ◽  
Cherax Quadricarinatus ◽  
Aquaculture Industry ◽  
Feral Population ◽  
Commercial Farms ◽  
Significant Effort ◽  
Mexican Populations

Cherax quadricarinatus is a decapod crustacean of interest to the aquaculture industry. In Mexico, a significant effort has been made to improve biological requirements, but the genetic characteristics are unknown. We examined the genetic diversity and differentiation in four populations in Mexico (three commercial farms and one feral population), as well as one research line from Argentina, used as reference. To initiate a founder stock in a genetic improvement program, we analyzed five microsatellite markers. The genetic diversity in terms of the number of alleles was low to moderate (2.8-6.2) in Mexican populations than the Argentinean sample (8.8). A pairwise Wright's Fst analysis showed that all populations were significantly different (P < 0.5). Cross-breeding organisms from a different population are suggested to increase genetic variability before initiating a founder stock with higher genetic variation.

scholarly journals Population structure and genetic diversity analysis in Sali (Oryza sativa) rice germplasm of Assam using microsatellite markers

2021 ◽  
Vol 58 (2) ◽  
pp. 279-286
Author(s):  
Sandhani Saikia ◽  
Pratap Jyoti Handique ◽  
Mahendra K Modi
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Genetic Improvement ◽  
Crop Improvement ◽  
Mean Value ◽  
Diversity Analysis ◽  
Rice Cultivars ◽  
Improvement Program ◽  
Information Index ◽  
Improvement Programs

Genetic diversity is the source of novel allelic combinations that can be efficiently utilized in any crop improvement program. To facilitate future crop improvement programs in rice, a study was designed to identify the underlying genetic variations in the Sali rice germplasms of Assam using SSR markers. The 129 SSR markers that were used in the study amplified a total of 765 fragments with an average of 5.93 alleles per locus. The Shannon's Information Index was found to be in the range from 0.533 to 1.786. The Polymorphism Information Content (PIC) fell into the range from 0.304 to 0.691 with a mean value of 0.55. The overall FST value was found to be 0.519 that indicated the presence of genetic differentiation amongst the genotypes used in the study. The Sali population was divided into two clusters. The information obtained from the present study will facilitate the genetic improvement of Sali rice cultivars.

scholarly journals GENETIC DIVERSITY OF MYCOBACTERIUM AVIUM subsp. HOMINISSUIS STRAINS ISOLATED IN ITALY BASED ON VNTR LOCI ANALYSIS

2019 ◽  
Vol 8 (4) ◽  
pp. 441-446
Author(s):  
M. Menichini ◽  
F. Genua ◽  
N. Lari ◽  
L. Rindi
Keyword(s):  
Genetic Diversity ◽  
Mycobacterium Avium ◽  
Allelic Variation ◽  
Local Level ◽  
Geographical Area ◽  
Discriminatory Power ◽  
Mycobacterium Avium Subsp ◽  
Clinical Feature ◽  
Genetic Characteristics ◽  
Vntr Analysis

Abstract.Background.Mycobacterium avium subsp. hominissuis (MAH) is an important pathogen responsible for most of the human-associated nontuberculous mycobacteria infections. Over the past few decades the incidence of MAH infections is increasing in Italy, as in many countries worldwide. The present study is aimed to elucidate the genetic characteristics of MAH strains isolated from human patients using VNTR typing and to show the genetic relatedness among them.Methods.The genetic diversity of 108 human isolates of MAH was determined by VNTR analysis targeting 8 loci, coded 32, 292, X3, 25, 3, 7, 10 and 47.Results.The VNTR analysis revealed 25 distinct VNTR patterns; of these, 13 patterns were unique, while 12 patterns were shared by 2 or more isolates, thus yielding 12 clusters including a total of 95 isolates. The discriminatory power of our VNTR analysis yielded an HGDI of 0.990, indicating that VNTR typing has an excellent discriminatory power. No association of a particular VNTR pattern with a particular clinical feature, such as the disseminated, pulmonary or extrapulmonary type of infection, was observed. Minimum spanning tree analysis showed that 21 VNTR patterns, occurring either as clustered or unique isolates, differed from the nearest one for one allelic variation.Conclusions.The results obtained through the VNTR analysis showed that most MAH strains displayed a close genetic relationship. This high phylogenetic proximity of the VNTR loci over a long time period supports the concept that the MAH genotype is highly homogeneous in our geographical area, suggesting the hypothesis of the presence of possible sources of infection and transmission pathways at the local level.

scholarly journals Whole-Genome Analysis of Coxsackievirus B3 Reflects Its Genetic Diversity in China and Worldwide

2021 ◽  
Author(s):  
Qian Yang ◽  
Dongmei Yan ◽  
Yang Song ◽  
Shuangli Zhu ◽  
Yun He ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Foot And Mouth Disease ◽  
Coxsackievirus B3 ◽  
Whole Genome ◽  
Nucleotide Substitution Rate ◽  
Whole Genome Analysis ◽  
Genetic Characteristics ◽  
Heavy Burden ◽  
Group D

Abstract Background Coxsackievirus B3 (CVB3) has emerged as an active pathogen in myocarditis, aseptic meningitis, hand, foot, and mouth disease (HFMD), and pancreatitis, and is a heavy burden on public health. However, CVB3 has not been systematically analyzed with regard to whole-genome diversity and recombination. Therefore, this study was undertaken to systematically examine the genetic characteristics of CVB3 based on its whole genome. Methods We combined CVB3 isolates from our national HFMD surveillance and global sequences retrieved from GenBank. Phylogenetic analysis was performed to examine the whole genome variety and recombination forms of CVB3 in China and worldwide. Results Phylogenetic analysis showed that CVB3 strains isolated worldwide could be classified into groups A–E based on the sequence of the entire VP1 region. The predominant CVB3 strains in China belonged to group D, whereas group E CVB3 might be circulated globally compared to other groups. The average nucleotide substitution rate in the P1 region of CVB3 was 4.82 × 10−3 substitutions/site/year. Myocarditis was more common with group A. Groups C and D presented more cases of acute flaccid paralysis, and group D may be more likely to cause HFMD. Multiple recombination events were detected among CVB3 variants, and there were twenty-three recombinant lineages of CVB3 circulating worldwide. Conclusions Overall, this study provides full-length genomic sequences of CVB3 isolates with a wide geographic distribution over a long-term time scale in China, which will be helpful for understanding the evolution of this pathogen. Simultaneously, continuous surveillance of CVB3 is indispensable to determine its genetic diversity in China as well as worldwide.

Genetic structure and variability in Pinusstrobus in Quebec

1994 ◽  
Vol 24 (8) ◽  
pp. 1726-1733 ◽  
Author(s):  
J. Beaulieu ◽  
J.-P. Simon
Keyword(s):  
Genetic Diversity ◽  
Statistical Tests ◽  
Natural Populations ◽  
Genetic Distances ◽  
White Pine ◽  
Eastern White Pine ◽  
Improvement Program ◽  
Bonferroni Procedure ◽  
Natural Range ◽  
Very High

The level of genetic diversity of natural populations of eastern white pine (Pinusstrobus L.) from Quebec was estimated from allozyme variants of 18 loci coding 12 enzyme systems. On average, a white pine population was polymorphic at 50.6% of loci, had 1.96 alleles and 1.22 effective alleles per locus, and observed and expected heterozygosities of 0.176 and 0.180, respectively. The level of genetic diversity was lower in the populations of the St. Lawrence lowlands than in those of western Quebec. This observation will help in guiding the selection program of the eastern white pine improvement program under way in Quebec. Genetic differentiation among sampled populations was weak and accounted for only 2% of the total diversity. The estimate of gene flow was very high, resulting in low values for genetic distances among populations. Only one locus showed a heterogeneity of allelic frequencies among populations after the Bonferroni procedure was applied for simultaneous statistical tests. A cluster analysis based on genetic distances among populations revealed that the Anticosti and Abitibi populations, located at the limit of the natural range of white pine, were similar to populations from regions that were geographically the most distant.

scholarly journals Genetic characteristics of broodstock collected from four Norwegian coastal cod (Gadus morhua) populations

2006 ◽  
Vol 63 (2) ◽  
pp. 209-215 ◽  
Author(s):  
G. Dahle ◽  
K.E. Jørstad ◽  
H.E. Rusaas ◽  
H. Otterå
Keyword(s):  
Gadus Morhua ◽  
White Muscle ◽  
Atlantic Cod ◽  
Genetic Differences ◽  
Offspring Performance ◽  
Genetic Characteristics ◽  
Aquaculture Industry ◽  
Initial Selection ◽  
Selection Of ◽  
Spawning Sites

Abstract The aquaculture industry in Norway is now focused on developing economically viable farming based on the Atlantic cod, Gadus morhua. Extensive research has been carried out on this species for the past two decades, much of it in connection with stock enhancement. Until now, most of the intensive cage culture has been based on wild broodstock. However, a future cod aquaculture industry must be based on a domesticated broodstock, and the initial selection of wild cod becomes an important issue. Genetic differentiation between coastal cod populations in Norway has been reported, and it is of interest to evaluate offspring from some of these populations under farmed conditions. Live mature cod were collected at four selected spawning sites along the Norwegian coast (Porsangerfjord, Tysfjord, Herøy/Helgeland, and Øygarden). The fish were transported to Parisvatnet, a cod aquaculture facility west of Bergen, where they were kept in net pens. Individual tagging and extensive sampling (blood, white muscle, and fin clips) for genetic characterization were carried out. Each potential broodstock fish was genotyped at the haemoglobin and pantophysin I loci in addition to five allozyme (LDH-3∗, GPD∗, IDH-2∗, PGM∗, PGI-1∗) and ten microsatellite loci (Gmo2, Gmo3, Gmo8, Gmo19, Gmo34, Gmo35, Gmo36, Gmo37, Gmo132, Tch11). Comparison of allele frequencies revealed significant genetic differences among some of the coastal cod samples, and offspring performance of the broodstock is now being compared under farmed conditions. The overall test revealed significant genetic differences among the coastal broodstocks, with the HbI, PanI and the microsatellite Gmo132 loci being most informative.

scholarly journals Genetic Diversity Among Ethiopian Coffee (Coffea Arabica L.) Collections Available In Indian Gene Bank Using Sequence Related Amplified Polymorphism Markers

2014 ◽  
Vol 70 (1) ◽  
pp. 29-40 ◽  
Author(s):  
Manoj Kumar Mishra ◽  
Sandhyarani Nishani ◽  
Madhura Gowda ◽  
Dandamudi Padmajyothi ◽  
Narayana Suresh ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Coffea Arabica ◽  
Clustering Algorithm ◽  
Germplasm Conservation ◽  
Gene Bank ◽  
Resolving Power ◽  
Srap Marker ◽  
Improvement Program ◽  
Arabica Coffee ◽  
Rare Alleles

Abstract The South-Western highlands of Ethiopia are considered to be the centre of origin and diversity of the arabica coffee, Coffea arabica. More than 80 accessions of arabica coffee collected from Ethiopia are available in Indian gene bank. However, the genetic diversity of these accessions is not studied in detail. In the present study, genetic diversity analysis of 48 accessions collected from eight provinces of Ethiopia was carried out using Sequence-related amplified Polymorphism (SRAP) marker. Among the thirty two SRAP primer combinations tested, 14 primer pairs were polymorphic and generated 203 distinct fragments. The number of fragments ranged from 7 to 21 with a mean of 14.5 fragments per primer combination. Of the total 203 amplified fragments, 182 (89.65%) were polymorphic and the percent of polymorphism ranged from 53.84% to a maximum of 100% using different primers. The average resolving power (Rp) and average polymorphism information content (PIC) of the 14 SRAP primer combinations was 14.31 and 0.648 respectively. A total of 13 rare alleles were obtained from SRAP assays, of which six rare alleles were obtained from the accessions collected from Shoa province. The UPGMA clustering algorithm from SRAP analysis grouped the 48 coffee accessions into two major clusters. The accessions collected from particular province clustered together which could be attributed to the substantial gene flow between adjacent population and the influence of geographical origin on genetic diversity. The study demonstrated the existence of substantial genetic variation in Ethiopian germplasm which could be utilized in coffee germplasm conservation and improvement program.

scholarly journals Evolution and Genetic Diversity of Porcine Circovirus 3 in China

Viruses ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 786 ◽  
Author(s):  
Ye Chen ◽  
Quanming Xu ◽  
Hong Chen ◽  
Xian Luo ◽  
Qi Wu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Eastern China ◽  
Porcine Circovirus ◽  
Recent Common Ancestor ◽  
Fujian Province ◽  
Tissue Samples ◽  
Genetic Characteristics ◽  
Most Recent Common Ancestor ◽  
Porcine Circovirus 3 ◽  
High Degree

The identification of a new circovirus (Porcine Circovirus 3, PCV3) has raised concern because its impact on swine health is not fully known. In Fujian Province in eastern China, even its circulating status and genetic characteristics are unclear. Here, we tested 127 tissue samples from swine from Fujian Province that presented respiratory symptoms. All of the PCV3 positive samples were negative for many other pathogens involved in respiratory diseases like PCV2, PRRSV, and CSFV, suggesting that PCV3 is potentially pathogenic. From phylogenetic analysis, PCV3 strains are divided into two main clades and five sub-clades; PCV3a-1, PCV3a-2, PCV3a-3, PCV3b-1, and PCV3b-2. Our identified strains belong to genotypes PCV3a-1, PCV3a-2, PCV3a-3, and PCV3b-2, indicating a high degree of genetic diversity of PCV3 in Fujian province until 2019. Interestingly, we found the time of the most recent common ancestor (tMRCA) of PCV3 was dated to the 1950s, and PCV3 has a similar evolutionary rate as PCV2 (the main epidemic genotypes PCV2b and PCV2d). In addition, positive selection sites N56D/S and S77T/N on the capsid gene are located on the PCV3 antigen epitope, indicating that PCV3 is gradually adaptive in swine. In summary, our results provide important insights into the epidemiology of PCV3.

scholarly journals Genetic Diversity of Upland Rice Germplasm in Malaysia Based on Quantitative Traits

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
M. Sohrabi ◽  
M. Y. Rafii ◽  
M. M. Hanafi ◽  
A. Siti Nor Akmar ◽  
M. A. Latif
Keyword(s):  
Genetic Diversity ◽  
Growth Traits ◽  
Upland Rice ◽  
Flag Leaf ◽  
Crop Improvement ◽  
Leaf Length ◽  
Width Ratio ◽  
Improvement Program ◽  
Days To Flowering ◽  
Flag Leaf Length

Genetic diversity is prerequisite for any crop improvement program as it helps in the development of superior recombinants. Fifty Malaysian upland rice accessions were evaluated for 12 growth traits, yield and yield components. All of the traits were significant and highly significant among the accessions. The higher magnitudes of genotypic and phenotypic coefficients of variation were recorded for flag leaf length-to-width ratio, spikelet fertility, and days to flowering. High heritability along with high genetic advance was registered for yield of plant, days to flowering, and flag leaf length-to-width ratio suggesting preponderance of additive gene action in the gene expression of these characters. Plant height showed highly significant positive correlation with most of the traits. According to UPGMA cluster analysis all accessions were clustered into six groups. Twelve morphological traits provided around 77% of total variation among the accessions.

scholarly journals Molecular Epidemiology of Rabies in Wild Canidae in Tunisia

Viruses ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2473
Author(s):  
Zied Bouslama ◽  
Habib Kharmachi ◽  
Nourhene Basdouri ◽  
Jihen Ben Salem ◽  
Samia Ben Maiez ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Wild Animals ◽  
Genetic Characteristics ◽  
Bayesian Phylogenetic Analysis ◽  
Viral Sequencing ◽  
Virus Isolates ◽  
Virus Strains ◽  
Natural Barrier

Rabies is a viral zoonosis that is transmissible to humans via domestic and wild animals. There are two epidemiological cycles for rabies, the urban and the sylvatic cycles. In an attempt to study the epidemiological role of wild canidae in rabies transmission, the present study aimed to analyze the genetic characteristics of virus isolates and confirm prior suggestions that rabies is maintained through a dog reservoir in Tunisia. Virus strains isolated from wild canidae were subject to viral sequencing, and Bayesian phylogenetic analysis was performed using Beast2 software. Essentially, the virus strains isolated from wild canidae belonged to the Africa-1 clade, which clearly diverges from fox-related strains. Our study also demonstrated that genetic characteristics of the virus isolates were not as distinct as could be expected if a wild reservoir had already existed. On the contrary, the geographic landscape is responsible for the genetic diversity of the virus. The landscape itself could have also acted as a natural barrier to the spread of the virus.

scholarly journals Genetic characteristics of yellow seabream Acanthopagrus latus (Houttuyn, 1782) (Teleostei: Sparidae) after stock enhancement in southeastern China coastal waters

2021 ◽  
Author(s):  
Puqing Song ◽  
Cheng Liu ◽  
Zizi Cai ◽  
Shigang Liu ◽  
Jiali Xiang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Coastal Waters ◽  
Population Expansion ◽  
Future Research ◽  
Beibu Gulf ◽  
High Genetic Diversity ◽  
Phylogenetic Structure ◽  
Genetic Characteristics ◽  
Nucleotide Mismatch ◽  
Baseline Information

Yellowfin seabream is an important economic fish that is widely distributed in the East and South China seas. Many attempts to enhance stocks of yellowfin seabream have occurred in China, but a lack of genetic information for this species after stock release represents an obstacle to its management and conservation. To provide scientific guidance for sustainable germplasm resource development, we sequence the mitochondrial DNA (mtDNA) control region (CR) of 123 yellowfin seabream from 6 sample populations (Xiamen, Dongshan I, Dongshan II, Yangjiang, Fangchenggang, and Beibu Gulf). Populations of both wild and cultured yellowfin seabream have high genetic diversity, which we relate to their breeding habits and growth rate. A neighbor-joining tree of CR haplotypes reveals no specific phylogenetic structure corresponding to location of fish capture. Both neutral test and nucleotide mismatch distribution analyses suggest that yellowfin seabream have experienced population expansion events. Pleistocene glacial periods and recent stock releases have played important roles in the formation of present-day phylogeographical patterns. Our study provides baseline information which will assist future research on genetic structure, genetic diversity, and historical demography of yellowfin seabream after stock release in southeast China coastal waters. The use of exotic seeds should be avoided in stock breeding and release, and relevant follow-up surveys and genetic monitoring should be undertaken to clarify the genetic impact of exotic seed use on wild populations.

Sign in / Sign up

Export Citation Format

Share Document