Allelic diversity of DQA2 exon 2 gene in Egyptian goat populations

2017 ◽  
Author(s):  
Sahar S. Ahmed ◽  
Salah M. Abdel-Rahman ◽  
Paul J. Grobler ◽  
Antoinette Kotzé
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Allelic Diversity ◽  
Single Strand Conformation Polymorphism ◽  
Immune Gene ◽  
Exon 2 ◽  
Goat Population ◽  
Allele Composition ◽  
The Difference ◽  
Conformation Polymorphism

The study aimed to assess the genetic diversity of 2-decyl-4-quinazolinyl amine exon2 (DQA2 exon2) gene among the Egyptian goat populations from different agro-climatic areas. Data of diseases distribution as well as blood samples were collected. The data collected for diseases distribution showed differences in the types of diseases between the agro-climatic areas. The Single Strand Conformation Polymorphism technique (SSCP) was used to assess the genetic diversity of DQA2 exon2 gene among the goat populations. The results showed that the DQA2 exon2 gene locus displayed 21 alleles with different frequencies in each of goat population. The gene diversity values among the populations ranged from 0.950± 0.022 to 0.887± 0.033. The difference between the most southern population (Aswan) and the remaining populations translate to significant (P less than 0.05) differentiation for only one population pair (Aswan – Baladi, with FST= 0.055; P= 0.001). Scrutiny of allele composition in these two goat populations showed unique alleles in each population (six in Aswan and four in Baladi). The results of the study suggested that the allelic numbers and allelic composition for the DQA2 exon2 gene among the Egyptian goat populations showed diversity in the immune gene due to the different pathogens exposure.

scholarly journals Molecular characterization of wheat (Triticum aestivum L.) genotypes through SSR markers

2012 ◽  
Vol 37 (3) ◽  
pp. 389-398 ◽  
Author(s):  
S Islam ◽  
MS Haque ◽  
RM Emon ◽  
MM Islam ◽  
SN Begum
Keyword(s):  
Genetic Diversity ◽  
Triticum Aestivum ◽  
Genetic Distance ◽  
Microsatellite Markers ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Allelic Diversity ◽  
Triticum Aestivum L ◽  
Allele Number ◽  
Average Gene

A study was undertaken to examine the genetic diversity of 12 wheat (Triticum aestivum L.) genotypes, using 4 simple sequence repeats (SSRs). A total of 10 alleles were found. Allele number per locus ranged from 2 to 4 with an average of 2.5. The polymorphic information content (PIC) values ranged from 0.2755 to 0.5411 with an average of 0.3839. The average gene diversity over all SSR loci for the 12 wheat genotypes was 0.4688, ranging from 0.3299 to 0.6042. Cluster analysis based on microsatellite allelic diversity discriminated the varieties into different clusters. Genetic diversity was the highest between variety Gourab and Akbar as well as Gourab and BAW-1064, showing a genetic distance value of 0.4697. The genetic distance was lowest between Balaka and Aghrani as well as Triticale and BAW-1036. Positive correlations were found between gene diversity, number of alleles, the allele size range and the types of repeat motif of microsatellite markers. It was found from this study that microsatellite markers could characterize and discriminate all of the genotypes. More primers should be used for saturation of different regions in further studies. Bangladesh J. Agril. Res. 37(3): 389-398, September 2012 DOI: http://dx.doi.org/10.3329/bjar.v37i3.12082

A963G single nucleotide variant of BMP15 is not common bio-marker for fecundity in goat

2016 ◽  
Author(s):  
Guang-Xin E ◽  
Yong-Fu Huang ◽  
Jian-Ning He ◽  
Wei-Wei Ni ◽  
Yong-Ju Zhao
Keyword(s):  
Polymerase Chain Reaction ◽  
Single Strand Conformation Polymorphism ◽  
Single Nucleotide Variant ◽  
Chain Reaction ◽  
Single Nucleotide ◽  
Exon 2 ◽  
Morphogenetic Protein ◽  
Polymerase Chain ◽  
Bone Morphogenetic Protein 15 ◽  
Conformation Polymorphism

Bone morphogenetic protein 15 (BMP15) is crucial factor for ovulation as well as for increasing litter size. In the present investigation efforts had been carried out to assess the genetic variations in Exon 2 region of BMP15 in goat, using polymerase chain reaction single strand conformation polymorphism (PCR-SSCP) sequencing methods and cooperated frequency distribution to discuss its possibility of related fecundity. Across the 144samples from six breeds were identified in the A963G location of BMP15 using PCR-SSCP and sequences technology. A963A genotype was the most frequent (85.4%) and G963G was the least frequent with a frequency of 4.2% and A963G is 10.4%. It revealed non significant different between high and low fecundity breed. Therefore, this single nucleotide variant is not common Bio-Marker for fecundity in Goat.

scholarly journals Genetic Diversity and Differentiation inPhoma betaePopulations on Table Beet in New York and Washington States

Plant Disease ◽  
2019 ◽  
Vol 103 (7) ◽  
pp. 1487-1497 ◽  
Author(s):  
Lori B. Koenick ◽  
Niloofar Vaghefi ◽  
Noel L. Knight ◽  
Lindsey J. du Toit ◽  
Sarah J. Pethybridge
Keyword(s):  
Genetic Diversity ◽  
New York ◽  
Mating Type ◽  
Gene Diversity ◽  
Management Strategies ◽  
Allelic Diversity ◽  
Genotypic Diversity ◽  
Reproduction Mode ◽  
Inoculum Source ◽  
Seed Crops

Phoma betae is an important seedborne pathogen of table beet worldwide that is capable of causing foliar, root, and damping-off diseases. Ten microsatellite and mating type markers were developed to investigate the genetics of P. betae populations in table beet root crops in New York and in table beet seed crops in Washington, from where table beet seed is predominantly sourced. The markers were used to characterize 175 isolates comprising five P. betae populations (two from New York and three from Washington), and they were highly polymorphic with an allelic range of 4 to 33 and an average of 11.7 alleles per locus. All populations had high genotypic diversity (Simpson’s complement index = 0.857 to 0.924) and moderate allelic diversity (Nei’s unbiased gene diversity = 0.582 to 0.653). Greater differentiation observed between populations from the two states compared with populations within the same state suggested that an external inoculum source, such as windblown ascospores, may be homogenizing the populations. However, most genetic diversity (87%) was among individual isolates within populations (pairwise index of population differentiation = 0.127; P = 0.001), suggesting that local within-field inoculum source(s), such as infested field debris or infected weeds, may also be important in initiating disease outbreaks. Standardized index of association, proportion of compatible pairs of loci, and mating type ratio calculations showed evidence for a mixed reproduction mode in all populations. These findings could be useful in designing more effective management strategies for diseases caused by P. betae in table beet production.

scholarly journals Molecular Genetic Diversity and Population Structure of Ginseng Germplasm in RDA-Genebank: Implications for Breeding and Conservation

Agronomy ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 68 ◽  
Author(s):  
Kyung Jun Lee ◽  
Jung-Ro Lee ◽  
Raveendar Sebastin ◽  
Gyu-Taek Cho ◽  
Do Yoon Hyun
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Gene Diversity ◽  
Research Effort ◽  
Molecular Genetic ◽  
Allelic Diversity ◽  
Perennial Herb ◽  
Molecular Evidence ◽  
Breeding Lines

Ginseng (Panax ginseng C.A. Meyer), commonly known as Korean or Asian ginseng, is a perennial herb native to Korea and China. There has been limited research effort to analyze the genetic diversity and population structure of ginseng germplasm because of its growth habits. In the present study, genetic diversity and population structure of ginseng germplasm conserved in the National Agrobiodiversity Center (NAC) of South Korea were analyzed to provide basic data for future preservation and breeding of ginseng genetic resources. Seventeen simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 1109 ginseng accessions. Among 1109 ginseng accessions, 1042 (94.0%) accessions were landraces and 66 (6.0%) accessions were breeding lines (61 accessions, 5.5%) or cultivars (5 accessions, 0.5%). SSR markers revealed 56 different alleles with an average of 3.29 alleles per locus. The average gene diversity was 0.49. Analysis of molecular variance showed that 91% of allelic diversity was attributed to individual accessions within clusters while only 9% was distributed among clusters. Using discriminant analysis of principal components, 12 clusters were detected in 1109 ginseng accessions. The results of this study provide molecular evidence for the narrow genetic base of ginseng germplasm in NAC. For the broad understanding and efficient use of ginseng germplasm, it is necessary to analyze functional factors and to evaluate morphological traits.

Genetic diversity in a remnant population of lake trout (Salvelinus namaycush)

2009 ◽  
Vol 87 (7) ◽  
pp. 642-647 ◽  
Author(s):  
Tina M.J. Giroux ◽  
Douglas P. Chivers ◽  
Michael J. Fitzsimmons ◽  
Neil B. Chilton
Keyword(s):  
Genetic Diversity ◽  
National Park ◽  
Sequence Variation ◽  
Lake Trout ◽  
Single Strand Conformation Polymorphism ◽  
Salvelinus Namaycush ◽  
Nucleotide Variation ◽  
Prince Albert National Park ◽  
Conformation Polymorphism ◽  
Remnant Population

Genetic diversity of the remnant population of lake trout ( Salvelinus namaycush (Walbaum in Artedi, 1792)) in Crean Lake was compared with that for two other populations in the Prince Albert National Park (PANP) using single-strand conformation polymorphism (SSCP) and DNA sequencing analyses of two mtDNA genes. Although there was no sequence variation among individuals for nad5, six different nad2 haplotypes were detected. The Crean Lake population had the least number of haplotypes and lowest nucleotide variation. Also, one common nad2 haplotype in Crean Lake was not detected in the other populations. The results suggest that introductions of lake trout from Wassegam Lake into Crean Lake were unsuccessful with respect to the establishment and (or) reproduction of the stocked fish. Conservation of the remnant population of lake trout in Crean Lake is important because it is genetically distinct from other populations within PANP and in adjacent areas.

scholarly journals Genetic Diversity of Aromatic Rice Germplasm Revealed By SSR Markers

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Saba Jasim Aljumaili ◽  
M. Y. Rafii ◽  
M. A. Latif ◽  
Siti Zaharah Sakimin ◽  
Ibrahim Wasiu Arolu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Diversity Index ◽  
Gene Diversity ◽  
Allelic Diversity ◽  
Peninsular Malaysia ◽  
Breeding Program ◽  
Aromatic Rice ◽  
Information Index ◽  
Rice Germplasm

Aromatic rice cultivars constitute a small but special group of rice and are considered the best in terms of quality and aroma. Aroma is one of the most significant quality traits of rice, and variety with aroma has a higher price in the market. This research was carried out to study the genetic diversity among the 50 aromatic rice accessions from three regions (Peninsular Malaysia, Sabah, and Sarawak) with 3 released varieties as a control using the 32 simple sequence repeat (SSR) markers. The objectives of this research were to quantify the genetic divergence of aromatic rice accessions using SSR markers and to identify the potential accessions for introgression into the existing rice breeding program. Genetic diversity index among the three populations such as Shannon information index (I) ranged from 0.25 in control to 0.98 in Sabah population. The mean numbers of effective alleles and Shannon’s information index were 0.36 and 64.90%, respectively. Similarly, the allelic diversity was very high with mean expected heterozygosity (He) of 0.60 and mean Nei’s gene diversity index of 0.36. The dendrogram based on UPGMA and Nei’s genetic distance classified the 53 rice accessions into 10 clusters. Analysis of molecular variance (AMOVA) revealed that 89% of the total variation observed in this germplasm came from within the populations, while 11% of the variation emanated among the populations. These results reflect the high genetic differentiation existing in this aromatic rice germplasm. Using all these criteria and indices, seven accessions (Acc9993, Acc6288, Acc6893, Acc7580, Acc6009, Acc9956, and Acc11816) from three populations have been identified and selected for further evaluation before introgression into the existing breeding program and for future aromatic rice varietal development.

scholarly journals Detection of Genetic Diversity in Four Candidate Genes by Polymerase Chain Reaction-Single Strand Conformation Polymorphism (PCR-SSCP) Analysis of Goats in Sri Lanka

2016 ◽  
Vol 4 (1) ◽  
pp. 133-138
Author(s):  
H.B.P.C. Ariyarathne ◽  
LGS Lokugalappatti ◽  
H.B.S. Ariyaratne ◽  
D.M.S. Munasinghe
Keyword(s):  
Genetic Diversity ◽  
Polymerase Chain Reaction ◽  
Candidate Genes ◽  
Single Strand Conformation Polymorphism ◽  
Single Strand ◽  
Sri Lankan ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Phenotypic Groups ◽  
Conformation Polymorphism

Genetic diversity of Sri Lankan goats (Capra hircus) was evaluated using Polymerase Chain Reaction-Single Strand Conformation Polymorphism (PCR-SSCP) method to detect polymophism in four candidate genes (LALBA, k-CSN3, GnRHR and BMP4) in a sample of 219 goats representing three phenotypic groups. All studied loci were polymorphic, having three morphs for BMP4, LALBA and two morphs for k-CSN3 and GnRHR in the study population. A significant difference between genotypic frequencies for BMP4 and GnRHR genes was found while PIC criterion revealed an intermediate polymorphism for all analyzed phenotypic groups except for k-CSN3 and GnRHR genes. Cross-bred animals for BMP4 gene and nondescript animals for LALBA gene were comparatively more polymorphic according to the effective allele number criterion. This study provides insight into the genetic diversity of Sri Lankan goats, which can be utilized to develop single nucleotide polymorphism markers to be used in association studies, and marker assisted selection.Int J Appl Sci Biotechnol, Vol 4(1): 133-138

scholarly journals SSR allelic diversity in relation to morphological traits and resistance to grain mould in sorghum

2010 ◽  
Vol 61 (3) ◽  
pp. 230 ◽  
Author(s):  
Rajan Sharma ◽  
S. P. Deshpande ◽  
S. Senthilvel ◽  
V. P. Rao ◽  
V. Rajaram ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Morphological Traits ◽  
Ssr Marker ◽  
Allelic Variation ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Allelic Diversity ◽  
Average Score ◽  
Marker Loci

Allelic variation at 46 simple sequence repeat (SSR) marker loci well distributed across the sorghum genome was used to assess genetic diversity among 92 sorghum lines, 74 resistant and 18 susceptible to grain mould. Of the 46 SSR markers, 44 were polymorphic, with the number of alleles ranging from 2 to 20 with an average of 7.55 alleles per locus. Genetic diversity among the sorghum lines was high as indicated by polymorphic information content (PIC) and gene diversity values. PIC values of polymorphic SSR markers ranged from 0.16 to 0.90, with an average of 0.54. Gene diversity among the sorghum lines varied from 0.16 to 0.91, with an average score of 0.58 per SSR marker. AMOVA indicated that 12% of the total variation observed among the sorghum lines was accounted for between grain mould resistant and susceptible types. Diversity based on six morphological traits and grain mould scores indicated major roles of panicle type and glumes coverage, followed by grain colour, in clustering of the lines. Seven grain mould resistant/susceptible pairs with dissimilarity indices >0.50, but with similar flowering time, plant height, and panicle type/inflorescence within each pair, were selected for use in developing recombinant inbred line mapping populations to identify genomic regions (and quantitative trait loci) associated with sorghum grain mould resistance.

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