Genetic diversity of avocado from the southern highlands of Tanzania as revealed by microsatellite markers

Abstract Background Avocado is an important cash crop in Tanzania, however its genetic diversity is not thoroughly investigated. This study was undertaken to explore the genetic diversity of avocado in the southern highlands using microsatellite markers. A total of 226 local avocado trees originating from seeds were sampled in eight districts of the Mbeya, Njombe and Songwe regions. Each district was considered as a population. The diversity at 10 microsatellite loci was investigated. Results A total of 167 alleles were detected across the 10 loci with an average of 16.7 ± 1.3 alleles per locus. The average expected and observed heterozygosity were 0.84 ± 0.02 and 0.65 ± 0.04, respectively. All but two loci showed a significant deviation from the Hardy-Weinberg principle. Analysis of molecular variance showed that about 6% of the variation was partitioned among the eight geographic populations. Population FST pairwise comparisons revealed lack of genetic differentiation for the seven of 28 population pairs tested. The principal components analysis (PCA) and hierarchical cluster analysis showed a mixing of avocado trees from different districts. The model-based STRUCTURE subdivided the trees samples into four major genetic clusters. Conclusion High diversity detected in the analysed avocado germplasm implies that this germplasm is a potentially valuable source of variable alleles that might be harnessed for genetic improvement of this crop in Tanzania. The mixing of avocado trees from different districts observed in the PCA and dendrogram points to strong gene flow among the avocado populations, which led to population admixture revealed in the STRUCTURE analysis. However, there is still significant differentiation among the tree populations from different districts that can be utilized in the avocado breeding program.

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Genetic Diversity and Population Structure of Phyllosticta citriasiana in China

Phytopathology ◽

10.1094/phyto-12-18-0451-r ◽

2020 ◽

Author(s):

Yibing Zeng ◽

Tao Xiong ◽

Bei Liu ◽

Elma Carstens ◽

Xiangling Chen ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Mating Type ◽

Tan Spot ◽

Long Distance ◽

High Genetic Diversity ◽

Geographic Population ◽

Sexual And Asexual Reproduction ◽

Geographic Populations ◽

Genetic Clusters

Phyllosticta citriasiana is the causal agent of citrus tan spot, an important pomelo disease in Asia. At present, there is little or no information on the epidemiology or population structure of P. citriasiana. Using simple sequence repeat (SSR) markers, 94 isolates obtained from three pomelo production regions in southern/southeastern China were analyzed. The analyses showed high genetic diversity in each of the three geographic populations. A STRUCTURE analysis revealed two genetic clusters among the 94 isolates, one geographic population was dominated by genotypes in one cluster while the other two geographic populations were dominated by genotypes of the second cluster. P. citriasiana has a heterothallic mating system with two idiomorphs, MAT1-1 and MAT1-2. Analyses using mating type-specific primers revealed that both mating types were present in all three geographic populations, and in all three populations the mating type ratios were in equilibrium. Although the sexual stage of the fungus has not been discovered yet, analyses of allelic associations indicated evidence for sexual and asexual reproduction within and among populations. Despite the observed genetic differentiation among the three geographic populations, evidence for long-distance gene flow was found.

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GENETIC DIVERSITY OF HONEY BEE POPULATIONS IN TURKEY BASED ON MICROSATELLITE MARKERS: A COMPARISON BETWEEN MIGRATORY VERSUS STATIONARY APIARIES AND ISOLATED REGIONS VERSUS REGIONS OPEN TO MIGRATORY BEEKEEPING

10.31237/osf.io/gkusw ◽

2019 ◽

Cited By ~ 1

Author(s):

Mert Kükrer

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Microsatellite Markers ◽

Honey Bee ◽

Honey Bees ◽

Phylogenetic Trees ◽

The Status ◽

Genetic Impact ◽

Geographic Populations ◽

Ecological Importance

The honey bee (Apis mellifera L.) is a globally significant species of apparent economic and ecological importance. Recent reports from Spain, Italy and Greece point to an intense admixture of honey bee populations signified by a loss of population structure. This is mostly attributed to migratory beekeeping practices and replacement of queens or colonies with commercial ones that are usually from non-native races or hybrids of different subspecies. These two practices are also heavily carried out in parts of Turkey where almost three-quarters of the 6 million colonies are transferred seasonally from one region to other.Past research using microsatellite and RAPD markers, mtDNA, allozymes and geometric morphometry revealed the presence of five different subspecies of honey bees (meda, syriaca,caucasica, anatoliaca and an ecotype from Carniolan subspecies group) inTurkey. Here, we carried out an analysis of population structure of Turkish honeybees sampled from six different regions (n = 250) during the period 2010-2012. A total of 29 microsatellite markers were used in four multiplex reactions. The results show that population structure is preserved in general although there are signs of gene flow between the clusters.Overall FST between stationary colonies was calculated as 0,067. For migratory colonies the value was 0,015 and for all the 250 samples the value was 0,047. Four different clusters corresponding to geographical distributions of four subspecies were revealed in structure analysis. The differentiation between the clusters was also apparent in PCA and FCA as well as phylogenetic trees constructed based on genetic distances.The genetic impact of migratory beekeeping was demonstrated for the first time based on a comparison of assignment probabilities of individuals from migratory and stationary colonies to their geographic populations. Another comparison between regions that are either open to migratory beekeeping or closed let us to evaluate the status of isolated regions and showed the importance of establishing such regions. The effects of queen and colony trade were revealed by the presence of introgression from the highly commercial Caucasian bees. Our findings confirm the previously observed high levels geographically structured genetic diversity in honey bees of Turkey and emphasize the need to develop policies to maintain this diversity.

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Genetic Diversity Among Old Local Grape Cultivars in South of Syria

International Journal of Environment ◽

10.3126/ije.v8i2.25507 ◽

2019 ◽

Vol 8 (2) ◽

pp. 43-54

Author(s):

Bayan M. Muzher ◽

Ola T. Al-Halabi

Keyword(s):

Genetic Diversity ◽

Genetic Similarity ◽

Morphological Traits ◽

Principal Component ◽

Hierarchical Cluster ◽

The Other ◽

Jaccard Coefficient ◽

Eigen Values ◽

Grape Cultivars ◽

High Diversity

This investigation was carried out in Sweida governorate of Syria from 2014 to 2015. The purpose of this investigation was to estimate the genetic diversity among 17 old local grape cultivars using morphological traits and SSR molecular markers. Principal Component Analysis (PCA) of morphological traits revealed that four main components were accountable for 50.34 % of variance, with Eigen values of 16.77%, 13.31%, 10.59% and 9.67%, respectively. While distribution of cultivars was found significantly dependent of first and second components, which separated Aswad Sharar and Derbly cultivars rather than other studied cultivars. Hierarchical cluster of morphological traits showed high diversity among studied cultivars. On the other hand, molecular characterization was conducted using eight informative SSR primer pairs, polymorphism was detected by seven SSR's primers. As a result, 18 polymorphic alleles were revealed with a polymorphism percentage of 100%, which reflected the genetic variation among studied cultivars. Genetic similarity was achieved, where 0.875 was the highest between Zeiny and Khedry cultivars, while the other two cultivars Ebeidy and AhmarMokamaa showed the lowest genetic similarity as 0.077. Cluster analysis of SSR markers grouped the studied cultivars into three clusters as per Jaccard coefficient. The first cluster grouped Ebeidy, Aswad Helwany and Derbly cultivars together, the second cluster contained two cultivars Beiady and Alb Atair, while the third cluster contained the remaining cultivars. Consequently, the results showed high diversity among studied cultivars, and some morphological traits were useful for cultivar discrimination.

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GENETIC DIFFERENTIATION OF SPRUCE POPULATIONS IN NORTHWEST RUSSIA REVEALED WITH MICROSATELLITE MARKERS

Ecological genetics ◽

10.17816/ecogen10240-49 ◽

2012 ◽

Vol 10 (2) ◽

pp. 40-49

Author(s):

Elena K Potokina ◽

Larisa V Orlova ◽

Maria S Vishnevskaya ◽

Ekaterina A Alekseeva ◽

Alexander F Potokin ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

Microsatellite Markers ◽

The Other ◽

The South ◽

The North ◽

Ssr Analysis ◽

Genetic Clusters

Analysis of genetic diversity of spruce populations in northwest Russia using microsatellite markers revealed two moderately distinctive genetic clusters. One of them combined trees that were determined by morphological featuers as P. abies. The other cluster included trees identified as P. obovata and P. fennica. The SSR analysis does not support taxonomical independence of the hybrid-derived species P. fennica. Occurrence of P. abies genotypes revealed by SSR analysis significantly decreases from the south to the north.

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Genetic diversity based on microsatellite markers in five Nile tilapia strains

Biodiversity Science ◽

10.3724/sp.j.1003.2009.08266 ◽

2009 ◽

Vol 17 (1) ◽

pp. 82 ◽

Cited By ~ 2

Author(s):

Liang Hongwei ◽

Li Zhong ◽

Luo Xiangzhong ◽

Wang Changzhong ◽

Hu Guangfu ◽

...

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Nile Tilapia

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Genetic Diversity of Enteric Viruses in Children under Five Years Old in Gabon

Viruses ◽

10.3390/v13040545 ◽

2021 ◽

Vol 13 (4) ◽

pp. 545

Author(s):

Gédéon Prince Manouana ◽

Paul Alvyn Nguema-Moure ◽

Mirabeau Mbong Ngwese ◽

C.-Thomas Bock ◽

Peter G. Kremsner ◽

...

Keyword(s):

Genetic Diversity ◽

Preventive Measures ◽

Phylogenetic Analyses ◽

Enteric Viruses ◽

Study Cohort ◽

Viral Agent ◽

A Genome ◽

Stool Samples ◽

Pcr Techniques ◽

High Diversity

Enteric viruses are the leading cause of diarrhea in children globally. Identifying viral agents and understanding their genetic diversity could help to develop effective preventive measures. This study aimed to determine the detection rate and genetic diversity of four enteric viruses in Gabonese children aged below five years. Stool samples from children <5 years with (n = 177) and without (n = 67) diarrhea were collected from April 2018 to November 2019. Norovirus, astrovirus, sapovirus, and aichivirus A were identified using PCR techniques followed by sequencing and phylogenetic analyses. At least one viral agent was identified in 23.2% and 14.9% of the symptomatic and asymptomatic participants, respectively. Norovirus (14.7%) and astrovirus (7.3%) were the most prevalent in children with diarrhea, whereas in the healthy group norovirus (9%) followed by the first reported aichivirus A in Gabon (6%) were predominant. The predominant norovirus genogroup was GII, consisting mostly of genotype GII.P31-GII.4 Sydney. Phylogenetic analysis of the 3CD region of the aichivirus A genome revealed the presence of two genotypes (A and C) in the study cohort. Astrovirus and sapovirus showed a high diversity, with five different astrovirus genotypes and four sapovirus genotypes, respectively. Our findings give new insights into the circulation and genetic diversity of enteric viruses in Gabonese children.

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Sarcoptic mange in wild ruminants in Spain: solving the epidemiological enigma using microsatellite markers

Parasites & Vectors ◽

10.1186/s13071-021-04673-x ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Barbara Moroni ◽

Samer Angelone ◽

Jesús M. Pérez ◽

Anna Rita Molinar Min ◽

Mario Pasquetti ◽

...

Keyword(s):

Microsatellite Markers ◽

Sarcoptes Scabiei ◽

Host Population ◽

Sarcoptic Mange ◽

Wild Ruminant ◽

Capra Pyrenaica ◽

Wild Ruminants ◽

In The Wild ◽

Genetic Clusters ◽

Genetic Strains

Abstract Background In Spain, sarcoptic mange was first described in native wildlife in 1987 in Cazorla Natural Park, causing the death of nearly 95% of the local native population of Iberian ibex (Capra pyrenaica). Since then, additional outbreaks have been identified in several populations of ibex and other wild ungulate species throughout the country. Although the first epizootic outbreak in wildlife was attributed to the introduction of an infected herd of domestic goats, the origin and the cause of its persistence remain unclear. The main aims of this study are to understand (i) the number of Sarcoptes scabiei “strains” circulating in wild ruminant populations in Spain, and (ii) the molecular epidemiological relationships between S. scabiei and its hosts. Methods Ten Sarcoptes microsatellite markers were used to characterize the genetic structure of 266 mites obtained from skin scrapings of 121 mangy wild ruminants between 2011 and 2019 from 11 areas in Spain. Results Seventy-three different alleles and 37 private alleles were detected. The results of this study show the existence of three genetic strains of S. scabiei in the wild ruminant populations investigated. While two genetic clusters of S. scabiei were host- and geography-related, one cluster included multi-host mites deriving from geographically distant populations. Conclusions The molecular epidemiological study of S. scabiei in wild ruminants in Spain indicates that the spreading and persistence of the parasite may be conditioned by host species community composition and the permissiveness of each host population/community to the circulation of individual “strains,” among other factors. Wildlife–livestock interactions and the role of human-driven introduction or trade of wild and domestic animals should be better investigated to prevent further spread of sarcoptic mange in as yet unaffected natural areas of the Iberian Peninsula.

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Unveiling a unique genetic diversity of cultivated Coffea arabica L. in its main domestication center: Yemen

Genetic Resources and Crop Evolution ◽

10.1007/s10722-021-01139-y ◽

2021 ◽

Author(s):

C. Montagnon ◽

A. Mahyoub ◽

W. Solano ◽

F. Sheibani

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Coffea Arabica ◽

Genetic Improvement ◽

The World ◽

Genetic Clusters ◽

Domestication Process ◽

Almost All ◽

Coffea Arabica L ◽

Cup Quality

AbstractWhilst it is established that almost all cultivated coffee (Coffea arabica L.) varieties originated in Yemen after some coffee seeds were introduced into Yemen from neighboring Ethiopia, the actual coffee genetic diversity in Yemen and its significance to the coffee world had never been explored. We observed five genetic clusters. The first cluster, which we named the Ethiopian-Only (EO) cluster, was made up exclusively of the Ethiopian accessions. This cluster was clearly separated from the Yemen and cultivated varieties clusters, hence confirming the genetic distance between wild Ethiopian accessions and coffee cultivated varieties around the world. The second cluster, which we named the SL-17 cluster, was a small cluster of cultivated worldwide varieties and included no Yemen samples. Two other clusters were made up of worldwide varieties and Yemen samples. We named these the Yemen Typica-Bourbon cluster and the Yemen SL-34 cluster. Finally, we observed one cluster that was unique to Yemen and was not related to any known cultivated varieties and not even to any known Ethiopian accession: we name this cluster the New-Yemen cluster. We discuss the consequences of these findings and their potential to pave the way for further comprehensive genetic improvement projects for the identification of major resilience/adaptation and cup quality genes that have been shaped through the domestication process of C. arabica.

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