RAPD markers as predictors of infectious hypodermal and hematopoietic necrosis virus (IHHNV) resistance in shrimp (Litopenaeus stylirostris)

Genome ◽  
2002 ◽  
Vol 45 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Suzanne E Hizer ◽  
Arun K Dhar ◽  
Kurt R Klimpel ◽  
Denise K Garcia
Keyword(s):  
Viral Load ◽  
Quantitative Pcr ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Regression Tree ◽  
Classification And Regression Tree ◽  
Necrosis Virus ◽  
Real Time Quantitative Pcr ◽  
In The Wild ◽  
Two Populations

Random amplified polymorphic DNA (RAPD) fingerprints of two shrimp populations (Litopenaeus stylirostris) were compared to find genetic marker(s) that may be associated with infectious hypodermal and hematopoietic necrosis virus (IHHNV) resistance or susceptibility. Of the 100 10-mer random primers and 100 intersimple-sequence repeat (ISSR) primers screened, five provided markers specific to the Super Shrimp population and three provided markers specific to the wild caught population. The two populations were further characterized for relative viral load (reported as cycle threshold, CT) using real-time quantitative PCR with primers specific to the IHHNV genome. The β-actin gene was amplified to serve as a control for normalization of the IHHNV viral load. The mean viral load was significantly lower (CT = 34.58; equivalent to 3.3 × 101 copies of IHHNV genome/ng DNA) in Super Shrimp than in the wild caught population (CT = 23.49; equivalent to 4.2 × 104 copies/ng DNA; P < 0.001; CT values are inversely related to viral load). A preliminary prediction model was created with Classification and Regression Tree (CART) software (Salford Systems, San Diego, Calif.), where the resultant decision tree uses the presence or absence of seven RAPD markers as predictors of the relative viral load.Key words: RAPD, quantitative PCR, Litopenaeus stylirostris, shrimp, genetic markers.

scholarly journals Real-Time Quantitative PCR Assay for Monitoring of Nervous Necrosis Virus Infection in Grouper Aquaculture

2011 ◽  
Vol 49 (3) ◽  
pp. 1090-1096 ◽  
Author(s):  
H.-C. Kuo ◽  
T.-Y. Wang ◽  
P.-P. Chen ◽  
Y.-M. Chen ◽  
H.-C. Chuang ◽  
...  
Keyword(s):  
Virus Infection ◽  
Real Time ◽  
Quantitative Pcr ◽  
Nervous Necrosis Virus ◽  
Necrosis Virus ◽  
Pcr Assay ◽  
Real Time Quantitative Pcr ◽  
Quantitative Pcr Assay

Molecular Differentiation Within and Between Eucalyptus risdonii, E. amygdalina and Their Hybrids Using RAPD Markers

1996 ◽  
Vol 44 (5) ◽  
pp. 559 ◽  
Author(s):  
MM Sale ◽  
BM Potts ◽  
AK West ◽  
JB Reid
Keyword(s):  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Genetic Isolation ◽  
Population Differences ◽  
Genetic Affinity ◽  
Hybrid Swarm ◽  
Leaf Phenotype ◽  
Morphological Differences ◽  
Two Populations ◽  
Advanced Generation

Random amplified polymorphic DNA (RAPD) studies of a natural hybrid swarm between Eucalyptus amygdalina Labill. and E. risdonii Hook.f. and nearby allopatric stands revealed that, despite clear morphological differences, all bands were shared between species. However, frequency differences revealed genetic divergence between species, populations within species, and individuals within populations. Variation was greatest between individuals within populations and lowest between species. For both species, the direction of variation which distinguished the two populations was in a different direction to that which separated the two species, suggesting population differences were not due to introgression but were the result of genetic isolation and/or strong localised selection. Several morphologically typical individuals with intermediate RAPD profiles were detected in the hybrid swarm and nearby allopatric samples of both species, suggesting that some cryptic introgression may be occurring. Controlled F1 crosses generally had closer genetic affinity to E. risdonii, raising the possibility that some parents used may have been advanced generation hybrids. While natural hybrids selected for their intermediate leaf phenotype were usually also intermediate between the two species using RAPD markers, some deviated markedly toward E. risdonii. The study suggests that morphological appearance does not necessarily reflect genetic (RAPD) status and in some cases detectable RAPD differences between spatially close populations of the same species may be as great or greater than the differences between species.

scholarly journals Quantitative Trait Loci (QTL) Analysis of Canning Quality Traits in Kidney Bean (Phaseolus vulgaris L.)

2002 ◽  
Vol 127 (4) ◽  
pp. 608-615 ◽  
Author(s):  
Maria-Carmela T. Posa-Macalincag ◽  
George L. Hosfield ◽  
Kenneth F. Grafton ◽  
Mark A. Uebersax ◽  
James D. Kelly
Keyword(s):  
Phaseolus Vulgaris ◽  
Linkage Group ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Recombinant Inbred Lines ◽  
Kidney Bean ◽  
Major Genes ◽  
The Core ◽  
Two Populations ◽  
Canning Quality

Canning quality of dry bean (Phaseolus vulgaris L.), of which the degree of splitting (SPLT) and overall appearance (APP) of canned beans are major components, is a complex trait that exhibits quantitative inheritance. The objectives of this study were to identify major genes that affect APP and SPLT in kidney bean, and map the location of these loci to the integrated core map of common bean. The analysis was performed using random amplified polymorphic DNA (RAPD) markers and two populations of kidney bean, consisting of 75 and 73 recombinant inbred lines (RILs), respectively. The two populations—`Montcalm' × `California Dark Red Kidney 82' and `Montcalm' × `California Early Light Red Kidney'—were planted in six year-location combinations in Michigan, Minnesota and North Dakota from 1996 to 1999. Correlations between APP and SPLT were high (0.91 to 0.97). Heritability estimates for APP and SPLT ranged from 0.83 to 0.85 in the two populations. Major genes for these traits were identified on two linkage groups. The first QTL, associated with seven RAPD markers, was putatively mapped to the B8 linkage group of the core bean linkage map. Desirable canning quality appeared to be derived from Montcalm at this locus. The second QTL, associated with four markers, appeared to be derived from the California parents. The second linkage group was not assigned to a linkage group in the core map. Population and environment-specificity were observed for the markers identified.

scholarly journals Genetic diversity of two Brazilian populations of the Pampas deer (Ozotoceros bezoarticus, Linnaeus 1758)

2007 ◽  
Vol 67 (4 suppl) ◽  
pp. 805-811 ◽  
Author(s):  
FP. Rodrigues ◽  
JF. Garcia ◽  
PRR. Ramos ◽  
J. Bortolozzi ◽  
JMB. Duarte
Keyword(s):  
Genetic Variation ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Habitat Destruction ◽  
Population Divergence ◽  
Dispersal Patterns ◽  
Mammal Species ◽  
Management Guidelines ◽  
Ozotoceros Bezoarticus ◽  
Two Populations

The Pampas deer (Ozotoceros bezoarticus) is one of the most endangered Neotropical cervid with populations that have been drastically reduced to small and isolated ones, mainly because of its habitat destruction. Random amplified polymorphic DNA (RAPD) markers were used to analyze population divergence and genetic variation within and between two populations corresponding to distinct subspecies. The RAPD markers displayed substantial genetic variation with all animals possessing unique RAPD phenotypes over 105 polymorphic bands produced by 15 primers. An analysis of molecular variance (AMOVA) and a neighbor-joining cluster analysis were performed to assess levels of differentiation between populations. No differentiation was recorded and about 96.0% (P < 0.00001) of the total variance was attributable to variation within populations. This result is quite distinct from data obtained by the analysis of the mtDNA control region, and is discussed on the basis of genetic differences between the different markers and the male-biased dispersal patterns generally observed in the mammal species. The data presented herein are potentially useful for future taxonomic and genetic studies in this species, for the monitoring of the genetic variation observed within these populations, and for the development of management guidelines for its conservation.

scholarly journals Intra and inter populational genetic variability in Maytenus ilicifolia Mart. ex Reiss. 1861, through RAPD markers

2007 ◽  
Vol 67 (4 suppl) ◽  
pp. 957-961 ◽  
Author(s):  
AJ. Mossi ◽  
RL. Cansian ◽  
O. Leontiev-Orlov ◽  
EM. Zanin ◽  
CH. Oliveira ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Dna Markers ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Folk Medicine ◽  
And Cluster Analysis ◽  
Genetic Pool ◽  
Maytenus Ilicifolia ◽  
Two Populations ◽  
Anthropic Action

Maytenus ilicifolia is a medicinal plant largely used in the South Brazilian folk medicine. The aim of this study was to quantify the intra and inter populational genetic variability in three populations of M. ilicifolia, focusing on the genetic conservation of this species, which has been threatened by anthropic action. RAPD (Random Amplified Polymorphic DNA) markers were used to analyze 30 plants of each of the three populations collected in the Alto Uruguai Gaúcho region. Fourteen selected primers generated a total of 158 bands, 71.5% of which were polymorphic. The comparison of Jaccard’s distances showed that the intra populational variation was higher than the inter populational variability, and cluster analysis allowed the separation of the three populations. Just 7.6% of the bands were specific of at least two populations. Data indicate that the analyzed M. ilicifolia populations represent a single genetic pool, and therefore any of the population thoroughly can represent the overall genetic variability of the species in the sampled region.

scholarly journals Understanding Determinants of Racial and Ethnic Disparities in Viral Load Suppression

2016 ◽  
Vol 16 (1) ◽  
pp. 23-29 ◽  
Author(s):  
Daniel J. Feller ◽  
Bruce D. Agins
Keyword(s):  
Viral Load ◽  
Explanatory Power ◽  
New York State ◽  
Ethnic Disparities ◽  
Regression Tree ◽  
Classification And Regression Tree ◽  
People Living With Hiv ◽  
Racial And Ethnic Disparities ◽  
Viral Load Suppression ◽  
Behavioral Determinants

Racial and ethnic disparities in viral load suppression (VLS) have been well documented among people living with HIV (PLWH). The authors hypothesized that a contemporary analytic technique could reveal factors underlying these disparities and provide more explanatory power than broad stereotypes. Classification and regression tree analysis was used to detect factors associated with VLS among 11 419 adult PLWH receiving treatment from 186 New York State HIV clinics in 2013. A total of 8885 (77.8%) patients were virally suppressed. The algorithm identified 8 mutually exclusive subgroups characterized by age, housing stability, drug use, and insurance status but neither race nor ethnicity. Our findings suggest that racial and ethnic disparities in VLS exist but likely reflect underlying social and behavioral determinants of health.

Understanding the viral load during the synthesis and after rebinding of virus imprinted particles via real-time quantitative PCR

The Analyst ◽  
2018 ◽  
Vol 143 (11) ◽  
pp. 2616-2622 ◽  
Author(s):  
M. Gast ◽  
S. Kühner ◽  
H. Sobek ◽  
B. Mizaikoff
Keyword(s):  
Viral Load ◽  
Real Time ◽  
Quantitative Pcr ◽  
Real Time Quantitative Pcr

In the present study, virus imprinted particles have been synthesized for recognizing and specifically binding viruses.

scholarly journals Integration of Genetic Linkage Maps of BC1 and F1 Populations of the Intergeneric Cross of Citrus grandis × Poncirus trifoliata Using RAPD Markers

HortScience ◽  
1996 ◽  
Vol 31 (4) ◽  
pp. 616a-616 ◽  
Author(s):  
Courtney A. Weber ◽  
Gloria A. Moore
Keyword(s):  
Cold Tolerance ◽  
Genetic Linkage ◽  
Rapd Markers ◽  
Genetic Linkage Map ◽  
Random Amplified Polymorphic Dna ◽  
Poncirus Trifoliata ◽  
Intergeneric Cross ◽  
Bulk Segregation Analysis ◽  
Two Populations

A greater saturation of the previously constructed genetic linkage map of Citrus is important in the long term goal of mapping quantitative trait loci (QTL) such as those controlling cold and salt tolerance. Segregation for cold tolerance appears to be greatly enhanced in the intergeneric F1 population of Citrus grandis × Poncirus trifoliata as compared to the BC1 population previously used for mapping due to the higher percentage of P. trifoliata genes present. This is not unexpected since P. trifoliata is the source of cold tolerance in this cross and is a highly heterozygous species. An integration of the maps of the two populations using about 50 random amplified polymorphic DNA (RAPD) markers common to the two populations is possible using the JoinMap computer program. This will allow the placing of approximately 100 new polymorphic RAPD markers from the F1 population identified by screening from 42 random oligonucleotide primers onto the Citrus map. This saturated map will be used to locate QTL following bulk segregation analysis of cold tolerance in the F1 population.

scholarly journals Mapping the Root-Knot Nematode Resistance Gene (Rk) in Tobacco with RAPD Markers

Plant Disease ◽  
1998 ◽  
Vol 82 (12) ◽  
pp. 1319-1322 ◽  
Author(s):  
H.-Y. Yi ◽  
R. C. Rufty ◽  
E. A. Wernsman ◽  
M. C. Conkling
Keyword(s):  
Meloidogyne Incognita ◽  
Rapd Markers ◽  
Rapd Analysis ◽  
Random Amplified Polymorphic Dna ◽  
Nematode Resistance ◽  
Root Knot Nematode ◽  
Burley Tobacco ◽  
Nematode Resistance Gene ◽  
Two Populations ◽  
Low Rate

Random amplified polymorphic DNA (RAPD) analysis was conducted to map the Rk gene in tobacco which conditions resistance to races 1 and 3 of the root-knot nematode, Meloidogyne incognita. Resistant burley tobacco genotype NC 528, containing the Rk gene, and the susceptible cultivar Ky 14 were screened with 1,500 random decamers. A low rate of genetic polymor-phism (<10%) was detected among these lines. Two populations (F1 and F3) of maternally de-rived doubled haploid (MDH) lines of burley tobacco, developed from the cross NC 528 × Ky 14, were used to map the Rk gene. NC 528, Ky 14, three Rk-resistant (Rk-R) DNA bulks, andthree Rk-susceptible (Rk-S) bulks generated from F1-derived MDH individuals were screenedwith the primers that amplified bands polymorphic between Rk-R and Rk-S lines. A total of 67 F1MDH lines and 59 F3MDH lines were screened with the primers that amplified bands polymorphic between Rk-R bulks and Rk-S bulks to confirm linkage between candidate markers and the Rk gene. Sixteen RAPD markers were positioned at six loci in a map 24.1 centimorgans long. Six RAPD markers, including one identified in the F3MDH population, were mapped at the Rk locus.

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