scholarly journals Estimating genetic diversity and population structure of 22 chicken breeds in Asia using microsatellite markers

2020 ◽  
Vol 33 (12) ◽  
pp. 1896-1904
Author(s):  
Hee-Jong Roh ◽  
Seung-Chang Kim ◽  
Chang-Yeon Cho ◽  
Jinwook Lee ◽  
Dayeon Jeon ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Rhode Island ◽  
Genomic Dna ◽  
Principal Coordinate Analysis ◽  
Conservation Strategies ◽  
White Leghorn ◽  
Asian Countries ◽  
Expected Heterozygosity ◽  
Chicken Breeds

Objective: Estimating the genetic diversity and structures, both within and among chicken breeds, is critical for the identification and conservation of valuable genetic resources. In chickens, microsatellite (MS) marker polymorphisms have previously been widely used to evaluate these distinctions. Our objective was to analyze the genetic diversity and relationships among 22 chicken breeds in Asia based on allelic frequencies.Methods: We used 469 genomic DNA samples from 22 chicken breeds from eight Asian countries (South Korea, KNG, KNB, KNR, KNW, KNY, KNO; Laos, LYO, LCH, LBB, LOU; Indonesia, INK, INS, ING; Vietnam, VTN, VNH; Mongolia, MGN; Kyrgyzstan, KGPS; Nepal, NPS; Sri Lanka, SBC) and three imported breeds (RIR, Rhode Island Red; WLG, White Leghorn; CON, Cornish). Their genetic diversity and phylogenetic relationships were analyzed using 20 MS markers.Results: In total, 193 alleles were observed across all 20 MS markers, and the number of alleles ranged from 3 (MCW0103) to 20 (LEI0192) with a mean of 9.7 overall. The NPS breed had the highest expected heterozygosity (H<sub>exp</sub>, 0.718±0.027) and polymorphism information content (PIC, 0.663±0.030). Additionally, the observed heterozygosity (H<sub>obs</sub>) was highest in LCH (0.690±0.039), whereas WLG showed the lowest H<sub>exp</sub> (0.372±0.055), H<sub>obs</sub> (0.384±0.019), and PIC (0.325±0.049). Nei’s DA genetic distance was the closest between VTN and VNH (0.086), and farthest between KNG and MGN (0.503). Principal coordinate analysis showed similar results to the phylogenetic analysis, and three axes explained 56.2% of the variance (axis 1, 19.17%; 2, 18.92%; 3, 18.11%). STRUCTURE analysis revealed that the 22 chicken breeds should be divided into 20 clusters, based on the highest ΔK value (46.92).Conclusion: This study provides a basis for future genetic variation studies and the development of conservation strategies for 22 chicken breeds in Asia.

scholarly journals Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds

Animals ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1441
Author(s):  
Filippo Cendron ◽  
Francesco Perini ◽  
Salvatore Mastrangelo ◽  
Marco Tolone ◽  
Andrea Criscione ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Conservation Status ◽  
Geographical Area ◽  
Snp Array ◽  
Local Economy ◽  
Conservation Strategies ◽  
Snp Analysis ◽  
Runs Of Homozygosity ◽  
Chicken Breeds

The genomic variability of local Italian chicken breeds, which were monitored under a conservation plan, was studied using single nucleotide polymorphisms (SNPs) to understand their genetic diversity and population structure. A total of 582 samples from 23 local breeds and four commercial stocks were genotyped using the Affymetrix 600 K Chicken SNP Array. In general, the levels of genetic diversity, investigated through different approaches, were lowest in the local chicken breeds compared to those in the commercial stocks. The level of genomic inbreeding, based on runs of homozygosity (FROH), was markedly different among the breeds and ranged from 0.121 (Valdarnese) to 0.607 (Siciliana). In all breeds, short runs of homozygosity (ROH) (<4 Mb in length) were more frequent than long segments. The patterns of genetic differentiation, model-based clustering, and neighbor networks showed that most breeds formed non-overlapping clusters and were clearly separate populations, which indicated the presence of gene flow, especially among breeds that originated from the same geographical area. Four genomic regions were identified as hotspots of autozygosity (islands) among the breeds, where the candidate genes are involved in morphological traits, such as body weight and feed conversion ratio. We conclude that the investigated breeds have conserved authentic genetic patterns, and these results can improve conservation strategies; moreover, the conservation of local breeds may play an important role in the local economy as a source of high-quality products for consumers.

scholarly journals Assessment of Genetic Diversity and Identification of Core Germplasm of Pueraria in Guangxi Using SSR Markers

2021 ◽  
Author(s):  
Xiao-Hong Shang ◽  
Yun Zhou ◽  
Liang Xiao ◽  
Ying Wang ◽  
Wen-Dan Zeng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Core Collection ◽  
Principal Coordinate Analysis ◽  
Germplasm Resources ◽  
Theoretical Support ◽  
Expected Heterozygosity ◽  
Core Germplasm ◽  
The Mean ◽  
Being There ◽  
Simple Sequence

Abstract Pueraria is not only one of the most important commercial crops, but a health supplement for human being. There are abundant Pueraria germplasm resources and a large planting scale in Guangxi. However, the genetic diversity and core germplasm of the Pueraria species in Guangxi are rarely understood. In this study, 272 individuals of Pueraria species in Guangxi combined with 23 pairs of simple sequence repeat primers were used to evaluate the genetic diversity and construct core germplasm. Ultimately, 118 alleles were identified and 112 alleles were polymorphic; the mean expected heterozygosity per locus is 0.1841, and the mean gene flow Nm is 1.7690. 272 individuals were divided into two main clusters, which is consistent with the results based on principal coordinate analysis and STRUCTURE cluster analysis. We proposed a core collection of 20 Pueraria accessions capturing 105 alleles. There was a non-significant relationship between genetic distance and geographical distance. The results could provide theoretical support for the scientific conversation of Pueraria genetic resources, which can serve as the basis for the breeding program of Pueraria.

Genetic Diversity of Cambuci (Campomanesia Phaea) Revealed by Microsatellite Markers

2021 ◽  
Author(s):  
Rafael Oliveira Moreira ◽  
Eduardo de Andrade Bressan ◽  
Horst Bremer Neto ◽  
Angelo Pedro Jacomino ◽  
Antonio Figueira ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Microsatellite Markers ◽  
Native Species ◽  
Genetic Parameters ◽  
Genomic Library ◽  
Conservation Strategies ◽  
Paulo State ◽  
Allele Number ◽  
Expected Heterozygosity

Abstract Campomanesia phaea (Myrtaceae), known as cambuci, is a native species from the Brazilian Atlantic Forest with great potential to be developed as a new fruit crop. Microsatellite markers were developed for cambuci to characterize the genetic diversity and to investigate the genetic structure of a group of accessions originally collected at the presumed center of diversity of the species. The work involved the collection of 145 accessions from five regional groups (Juquitiba, Paraibuna, Mogi das Cruzes, Ribeirão Pires, and Salesópolis) in São Paulo state, Brazil. Fourteen loci were identified in an enriched genomic library developed from one of these accessions. Six out of 14 loci revealed to be polymorphic, disclosing 26 alleles. Based on the allele frequencies, the calculated genetic parameters of the five groups indicated an average allele number per loci (A) of 3.83, with the expected heterozygosity (He) of 0.57 and the observed heterozygosity (Ho) of 0.54. The analysis of the genetic structure indicated that most of the genetic diversity is found within each population (HS = 0.57), whereas the genetic diversity among populations was low (GST = 0.19). The genetic diversity parameter of Nei was considered low for the cambuci analyzed populations, with no evidence of inbreeding. Based on Darwin analysis, we chose 18 accessions from the five regional populations to compose a core collection that includes most of the genetic diversity found in this study. Our findings may contribute to define better conservation strategies and genetic breeding approaches for this native species in Brazil.

scholarly journals Genetic diversity and structure of native maize races from Northwestern Mexico

2017 ◽  
Vol 52 (11) ◽  
pp. 1023-1032 ◽  
Author(s):  
Isrrael Vega-Alvarez ◽  
Amalio Santacruz-Varela ◽  
Mario Rocandio-Rodríguez ◽  
Leobigildo Córdova-Téllez ◽  
Higinio López-Sánchez ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Zea Mays ◽  
Bayesian Model ◽  
Population Distribution ◽  
Principal Coordinate Analysis ◽  
Expected Heterozygosity ◽  
Genetic Diversity And Structure ◽  
Broad Variation ◽  
Northwestern Mexico ◽  
Probabilistic Value

Abstract: The objective of this work was to evaluate the genetic diversity of nine maize races (Zea mays ssp. mays) from Northwestern Mexico and one population of teosinte of the Balsas race (Zea mays ssp. parviglumis). A total of 649 alleles were identified, with an average of 20.9 alleles per locus using 31 microsatellite loci; 84.3% of them were polymorphic loci with a 0.49 expected heterozygosity. Graphic representation of principal coordinate analysis (PCoA) showed broad variation and population distribution. The highest probabilistic value obtained with the ΔK criterion confirmed the existence of five population groups clustered by the Bayesian model. This grouping coincided with the population distribution observed in the PCoA graph. Maize races examined retain broad genetic diversity among and within the evaluated populations.

scholarly journals Genetic diversity of pituitary transcription factor 1 (PIT 1) gene in Nigerian local and exotic chicken

2020 ◽  
Vol 47 (1) ◽  
pp. 12-18
Author(s):  
B. O. Agaviezor ◽  
C. S. Chukwuemeka
Keyword(s):  
Genetic Diversity ◽  
Transcription Factor ◽  
Genetic Distance ◽  
Genomic Dna ◽  
Evolutionary Divergence ◽  
Breeding Programs ◽  
Naked Neck ◽  
Chicken Breeds ◽  
Transcription Factor 1 ◽  
Segregating Sites

This study was carried out to investigate the genetic diversity of PIT1 gene in Nigerian local and exotic chicken breeds. Genomic DNA was extracted from the blood of Isa brown, Shika brown and Naked neck chickens which was used to amplify the PIT1 gene and later sequenced. Sequences were aligned and analyzed using Mega 6.0 and DNASp. The results revealed that Naked neck had 181 monomorphic sites and the least was observed in Isa brown (34). However, Isa brown had the highest number of polymorphic site (181) and the least was observed in Shika brown. Singleton variable sites also varied across breeds. Number of segregating sites was highest in Isa brown (174). The highest number of haplotypes was observed in Isa brown (11). Highest number of indel sites were observed in Isa brown (46) chickens. The highest estimates of average evolutionary divergence over sequence pairs within chicken breeds was observed in Isa brown (0.766) and the least in Shika brown (0.15). The highest genetic distance is between Isa brown and Naked neck and the least between Naked neck and Shika brown. The result obtained from this study revealed a clearer understanding of the genetic diversity in PIT1 gene across the different breeds. This information can be harnessed for better policies for conservation and breeding programs.

Single Nucleotide Polymorphisms (SNPs), Phylogeny and Spatiotemporal analysis of pro gene in HIV samples from Pakistan

2021 ◽  
Vol 15 (8) ◽  
pp. 1910-1913
Author(s):  
Sana Shabir ◽  
Hira Tiwana ◽  
Khaver Ali ◽  
Sana Riaz ◽  
Mehboob Ahmed ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
South Asian ◽  
Treatment Options ◽  
Hiv Protease ◽  
Hiv Positive ◽  
Protease Gene ◽  
Asian Countries ◽  
China And India ◽  
Keywords Hiv

Background: The increase in incidence of HIV infection with limited treatment options has enhanced the morbidity and mortality in South Asian countries. The mutations, geographical and genetic diversity in Pro gene in HIV positive patients from other South Asian countries can be helpful for treatment options. Aim: To identify mutations and genetic diversity in Pro gene in HIV positive patients in Pakistan and compare the sequences to neighbouring countries China and India. Methods: The HIV protease gene or pro-gene sequence were retrieved from NCBI. The sequence were studied from Pakistan, China and India were analysed for their linkage and genetic mutations through bioinformatics tools, MEGAX and CLUSTALW Results: The phylogenetic analysis of samples for maximum likelihood and mutation from South Asian countries Pakistan, China and India individually displayed variation in sequences of HIV pro gene in all these isolates. Whereas Pakistani isolates have more genetic similarities with the isolates from China than India. Conclusion: The phylogeny analysis depicts there is gradual evolution in viral types and possible entry is through the neighbouring transmission might have been through social connections. The mutations studies provides bases for the novel targets for the drug design and development against HIV. Keywords: HIV, Protease gene, MEGA, Phylogenetic analysis, Pakistan

scholarly journals Molecular Characterization of Vitex agnus-castus L. (Verbenaceae) Populations Grown in Aydin, Turkey

2019 ◽  
Vol 11 (2) ◽  
pp. 218-221
Author(s):  
Emre SEVİNDİK ◽  
Serkan CANER ◽  
Mahmut COŞKUN
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Genomic Dna ◽  
Rapd Markers ◽  
Genetic Relationships ◽  
Genetic Distances ◽  
Purple Flower ◽  
A Value ◽  
Pink Flower ◽  
Agnus Castus

In this study, we performed a genetic diversity analysis using RAPD markers for some Vitex agnus-castus populations grown in Aydin, Turkey. Total genomic DNA isolation from the leaves of Vitex agnus-castus was performed using a commercial kit. Seven RAPD primers (OPA-02, OPA-05, OPA-13, OPA-15, OPA-16, OPA-18, OPA-20) were used to determine genetic diversity among populations. Polymerase Chain Reaction (PCR) was performed with all genomic DNA samples and primers. PCR products were run in agarose gel electrophoresis and visualized under UV light. The amplified products were scored as bands (1) and no bands (0) for all gel images and their matrix files were generated. A total of 36 characters were obtained from the primers. Phylogenetic relationships and genetic distances between the cultivars were calculated by using the PAUP* (Phylogenetic Analysis Using Parsimony and other methods) program. According to PAUP analysis, the closest genetic distances were between Çine pink flower and Çakmar purple flower, and Çakmar pink flower and Çakmar purple flower populations with a value of 0.05556; and the greatest genetic distance was between Çakmar pink flower and Köşk purple flower populations with a value of 0.36111. In the phylogenetic analysis obtained using UPGMA algorithms, the phylogenetic tree consisted of four groups. The results suggest that RAPD markers are useful tools for determining genetic relationships among Vitex agnus-castus genotypes.

The genetic structure and the conservation of the five natural populations of Pinusradiata

1988 ◽  
Vol 18 (5) ◽  
pp. 506-514 ◽  
Author(s):  
G. F. Moran ◽  
J. C. Bell ◽  
K.G. Eldridge
Keyword(s):  
Genetic Diversity ◽  
Natural Populations ◽  
Allozyme Variation ◽  
Conservation Strategies ◽  
Mainland Population ◽  
Island Populations ◽  
Expected Heterozygosity ◽  
Environmental Criteria ◽  
Total Genetic Diversity ◽  
Allozyme Loci

Pinusradiata is restricted to three mainland coastal populations in California and two island populations off Baja California, Mexico. In this study each population was divided into two geographic stands based on natural disjunctions within populations. In addition to the division mentioned above, each mainland population was also divided into a number of ecological stands based on ecological and environmental criteria. Genetic variation was measured by analysing 31 allozyme loci electrophoretically using germinated seed from 272 families across all stands and populations. Moderate levels of allozyme variation were found as shown by population averages for mean number of alleles per locus (1.79), percent polymorphic loci (46.4%, 0.99 criterion), and expected heterozygosity (0.098). In fact, the overall genetic diversity in P. radiata (HT = 0.117) is low compared with that of other conifers. In comparison with populations, the levels of allozyme variation in both ecological and geographic stands were slightly lower (means across ecological stands: A = 1.56, P = 39.3%, and He = 0.095). Of the total genetic diversity in P. radiata, 16.2% could be apportioned between populations, a high proportion for a conifer. In contrast, only 2.0 and 1.3% of the genetic diversity on average within mainland populations was between ecological and geographic stands, respectively. These results indicate a low level of genetic differentiation within populations, at least based on the ecological or geographic criteria used in this study. The implications and usefulness of these findings for the development of insitu conservation strategies are discussed.

scholarly journals Assessment of genetic diversity among Egyptian and Saudi chicken ecotypes and local Egyptian chicken breeds using microsatellite markers

2021 ◽  
Vol 42 (1) ◽  
pp. 33-39
Author(s):  
A. Sabry ◽  
◽  
S. Ramadan ◽  
M.M. Hassan ◽  
A.A. Mohamed ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Saudi Arabia ◽  
Microsatellite Markers ◽  
Rhode Island ◽  
Polymorphic Information Content ◽  
Genetic Distances ◽  
Native Chicken ◽  
Hardy Weinberg Equilibrium ◽  
Chicken Breeds ◽  
Endangered Status

Aim: To assess genetic diversity of two chicken ecotypes from Egypt and Saudi Arabia and compare these ecotypes to six local Egyptian and two exotic pure chicken breeds using 14 microsatellite markers. Methodology: Dataset consisted of two subsets. First subset represented two ecotypes from Saudi Arabia and Egypt. Second dataset consisted birds six Egyptian native chicken strains: Fayoumi (FAY), Dandarawy (DAN), Baladi (BAL), Sinai (Sini), El-Salam (Els) and Golden Montazah (GG), and two commercial strains: White Leghorn (WL) and Rhode Island Red (RIR). fourteen microsatellites markers were utilized to assess DNA polymorphism. Data analyses of the results were carried out using R statistical environment. Results: The obtained results indicated that number of alleles per locus averaged 11.4 ± 5.0. Polymorphic information content was informative (> 50%) for the local breeds, but not for two ecotypes. The observed and expected heterozygosity averaged 0.46 and 0.75, both ecotypes had the lowest estimates. All breeds showed significant deviation from Hardy–Weinberg equilibrium expectation. The average population differentiation index (FST) was 0.143, overall heterozygosity deficiency (FIT) was 0.156, and global inbreeding of individuals within breeds (FIS) was 0.319. Interpretation: This study revealed that both Egyptian and Saudi ecotypes have an endangered status. Lower genetic distances and lower FST values were reported for the Egyptian indigenous breeds. Phylogenetic and principle components showed that both ecotypes were genetically closer to each other when compared with other breeds. It also showed that the Dandarawy native Egyptian chicken breed was genetically the closest breed to both the Egyptian and Saudi ecotypes. Key words: Chicken, Ecotypes, Genetic diversity, Microsatellites, Phylogenetics

Sign in / Sign up

Export Citation Format

Share Document