Genetic differentiation of wild and cultivated populations: diversity of Coffea canephora Pierre in Uganda

Genome ◽  
2009 ◽  
Vol 52 (7) ◽  
pp. 634-646 ◽  
Author(s):  
P. Musoli ◽  
P. Cubry ◽  
P. Aluka ◽  
C. Billot ◽  
M. Dufour ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Central Africa ◽  
Coffea Canephora ◽  
Genetic Distances ◽  
Perennial Plant ◽  
Expected Heterozygosity ◽  
Population Structuring ◽  
Cultivated Populations ◽  
Large Distribution

Coffea canephora Pierre ex Frohener is a perennial plant originated from Africa. Two main groups, Guinean and Congolese, have already been identified within this species. They correspond to main refugia in western and central Africa. In this paper we present the analysis of a region that has not yet been studied, Uganda. Two wild, one feral (once cultivated but abandoned for many years), and two cultivated populations of C. canephora from Uganda were evaluated using 24 microsatellite markers. Basic diversity, dissimilarity and genetic distances between individuals, genetic differentiation between populations, and structure within populations were analysed. Expected heterozygosity was high for wild compartments (0.48 to 0.54) and for cultivated and feral ones (0.57 to 0.59), with the number of private alleles ranging from 12 for cultivated genotypes to 37 for a wild compartment. The Ugandan samples show significant population structuring. We compared the Ugandan populations with a representative sample of known genetic diversity groups within the species using 18 markers. Coffea canephora of Ugandan origin was found to be genetically different from previously identified diversity groups, implying that it forms another diversity group within the species. Given its large distribution and extremely recent domestication, C. canephora can be used to understand the effect of refugia colonization on genetic diversity.

scholarly journals Genetic analysis of silver-fir populations in the Beskids

2011 ◽  
Vol 72 (2) ◽  
pp. 115-119 ◽  
Author(s):  
Leon Mejnartowicz
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Analysis ◽  
Abies Alba ◽  
Genetic Distances ◽  
Silver Fir ◽  
Geographical Distance ◽  
Polymorphic Loci ◽  
Expected Heterozygosity ◽  
Rare Alleles

Twenty-eight isozymic loci were studied in the Beskid Mts., in four populations of common silver-fir (<em>Abies alba</em>): one in Beskid Makowski (BM) and three populations in Beskid Sądecki (BS). Their genetic variation and diversity were analyzed, and Nei's genetic distances between the populations were calculated. The results show that the geographical distance between the BM population and the three BS populations is reflected in genetic distances. The BM population is clearly distinct from the others. It has the lowest genetic diversity (<em>I</em> = <em>0.42</em>), percentage of polymorphic loci <em>(%PoL </em>= <em>64.29</em>) and number of rare alleles (<em>NoRa </em>= <em>5</em>). Besides, the BM population has the highest observed heterozygosity (<em>Ho </em>= <em>0.291</em>), which exceeds the expected heterozygosity (<em>He </em>= <em>0.254</em>), estimated on the basis of the Hardy-Weinberg Principle. On the contrary, BS populations are in the state of equilibrium, which is manifested, in similar values of <em>He </em>= <em>0.262 </em>and <em>Ho </em>= <em>0.264</em>.

Microsatellites reveal weak genetic differentiation between Rutilus frisii kutum (Kamenskii, 1901) populations south of the Caspian Sea

2011 ◽  
Vol 61 (4) ◽  
pp. 469-483 ◽  
Author(s):  
Mohammad Rezaei ◽  
Bahare Shabanpour ◽  
Ali Shabani ◽  
Hadis Kashiri
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Caspian Sea ◽  
Current Knowledge ◽  
Genetic Management ◽  
The Caspian Sea ◽  
Expected Heterozygosity ◽  
Artificial Breeding ◽  
Genetic Stocks ◽  
Rutilus Frisii Kutum

Abstract Rutilus frisii kutum (Kamenskii, 1901) is one of the most important bony fish inhabiting the Caspian Sea. The Iranian Fisheries Organization produced up to 200 million fry to restock the Caspian Sea population annually. Loss of genetic stocks and gradual depletion of the gene pool are parameters of great concern for the future of the species. In the present study, we used ten microsatellite markers to estimate the level of genetic diversity and compare the degree of genetic differentiation among kutum populations collected from Gharesou, Tajan and Goharbaran rivers in the south of Caspian Sea. The average number of alleles per locus ranged from 4 to 12.33, while the average observed and expected heterozygosity ranged from 0.22 to 1.00 and from 0.69 to 0.88, respectively. Through AMOVA, a low level of variation between regions as well as a large percentage of total variation within population was observed. Current knowledge about artificial breeding suggests that offspring transfer between rivers has probably reduced the natural divergence naturally exists between these pools. These results could be useful for the genetic management of kutum populations.

AFLP fingerprints of Pyropia yezoensis (Bangiales, Rhodophyta) populations revealed the important effect of farming protocols on genetic diversity

2018 ◽  
Vol 61 (2) ◽  
pp. 141-147 ◽  
Author(s):  
Yuan Cao ◽  
Wen-Jun Wang ◽  
Fu-Li Liu ◽  
Zhou-Rui Liang ◽  
Xiu-Tao Sun ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Selective Breeding ◽  
Agronomic Traits ◽  
Genetic Distances ◽  
Pyropia Yezoensis ◽  
The Other ◽  
High Likelihood ◽  
The Sustainable Development ◽  
Polymorphism Rate ◽  
Cultivated Populations

Abstract Continuous and intensive selective breeding reduces the genetic diversity of cultivated Pyropia stock, thereby increasing its susceptibility to diseases, and hindering the sustainable development of the Pyropia industry. To develop new Pyropia germplasms with desirable agronomic traits, a new Pyropia yezoensis strain, “Huangyou No. 1” was bred from a wild subtidal population. In this study, the genetic diversity of this strain was analyzed using AFLP. Totally, 249 loci were obtained, of which 248 were polymorphic with a polymorphism rate of 99.6%, using seven primer pairs. The intra-population polymorphism rates of the populations Wild 1 and Wild 2 were the highest (47.39% and 59.44%, respectively), while they were relatively low (20.88–24.5%) in the cultivated populations. The genetic distances between the breeding Pyropia populations cultivated in the same aquaculture farm were low. Specifically, the F2 offspring of “Huangyou No. 1” and the control cultivar, cultivated using the “never-drying” protocol, were genetically distant from the other populations, including that from the same seedlings, yet cultivated using the “periodic-drying” protocol. The never-drying cultivation protocol had a high likelihood of influencing genetic diversity of Pyropia yezoensis.

scholarly journals Genetic diversity of wild and cultivated Coffea canephora in northeastern DR Congo and the implications for conservation.

2021 ◽  
Author(s):  
Samuel Vanden Abeele ◽  
Steven B. Janssens ◽  
Justin Asimonyio Anio ◽  
Yves Bawin ◽  
Jonas Depecker ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Coffea Canephora ◽  
Congo Basin ◽  
Ex Situ ◽  
Gene Pools ◽  
Wild Populations ◽  
Genetic Composition ◽  
Robusta Coffee ◽  
Republic Of The Congo

Premise: Many cultivated coffee varieties descend from Coffea canephora, commonly known as Robusta coffee. The Congo Basin has a century long history of Robusta coffee cultivation and breeding, and is hypothesized to be the region of origin of many of the cultivated Robusta varieties. Since little is known about the genetic composition of C. canephora in this region, we assessed the genetic diversity of wild and cultivated C. canephora shrubs in the Democratic Republic of the Congo. Methods: Using 18 microsatellite markers, we studied the genetic composition of wild and backyard-grown C. canephora shrubs in the Tshopo and Ituri provinces, and from the INERA Yangambi Coffee Collection. We assessed genetic clustering patterns, genetic diversity, and genetic differentiation between populations. Key results: Genetic differentiation was relatively strong between wild and cultivated C. canephora shrubs, and both gene pools harbored multiple unique alleles. Strong genetic differentiation was also observed between wild populations. The level of genetic diversity in wild populations was similar to that of the INERA Yangambi Coffee Collection, but local wild genotypes were mostly missing from that collection. Shrubs grown in the backyards were genetically similar to the breeding material from INERA Yangambi. Conclusions: Most C. canephora that is grown in local backyards originated from INERA breeding programs, while a few shrubs were obtained directly from surrounding forests. The INERA Yangambi Coffee Collection could benefit from an enrichment with local wild genotypes, to increase the genetic resources available for breeding purposes, as well as to support ex situ conservation.

scholarly journals Genetic diversity of different breeds of Kazakh sheep using microsatellite analysis

2019 ◽  
Vol 62 (1) ◽  
pp. 305-312
Author(s):  
Kairat Dossybayev ◽  
Zarina Orazymbetova ◽  
Aizhan Mussayeva ◽  
Naruya Saitou ◽  
Rakhymbek Zhapbasov ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distance ◽  
Microsatellite Loci ◽  
Allelic Diversity ◽  
Genetic Distances ◽  
Sheep Breed ◽  
Expected Heterozygosity ◽  
The Mean ◽  
High Level ◽  
Short Tandem

Abstract. A total of 75 individuals from five sheep populations in Kazakhstan were investigated based on 12 STR (short tandem repeat, also known as microsatellite) markers in order to study their genetic structure and phylogenetic relationship based on genetic distances. These sheep had a high level of genetic diversity. In total, 163 alleles were found in all the populations using 12 microsatellite loci. The mean number of alleles, effective number of alleles, and polymorphism information content (PIC) values per loci were 13.4, 5.9, and 0.78, respectively. Comparing the allelic diversity between the populations, the highest genetic diversity was observed in the Edilbay-1 sheep breed (8.333±0.644), and the lowest parameter was for Kazakh Arkhar-Merino (7.083±0.633). In all populations, there is a deficiency of heterozygosity. The largest genetic diversity was found in loci INRA023 and CSRD247 with 16 alleles, and the smallest polymorphism was noted for the locus D5S2 with 8 alleles. The level of observed heterozygosity was in the range 0.678±0.051 for Kazakh Arkhar-Merino and 0.767±0.047 for Kazakh fat-tailed coarse wool. The expected heterozygosity level range was from 0.702±0.033 for Kazakh Arkhar-Merino to 0.777±0.023 for Edilbay-1. When 12 microsatellite loci are compared, the OarFCB20 locus showed the highest level of genetic variability. Excess of heterozygosity was observed at three loci; MAF065, McM042, and OarFCB20. The highest genetic distance was observed between Kazakh Arkhar-Merino and Edilbay-1, whereas the genetic distance between Edilbay-1 and Edilbay-2 is the smallest using Nei's standard genetic distance. The Edilbay-1 sheep breed possesses the largest genetic diversity among these five populations.

scholarly journals Genetic diversity in global chicken breeds as a function of genetic distance to the wild populations

2020 ◽  
Author(s):  
Dorcus Kholofelo Malomane ◽  
Steffen Weigend ◽  
Armin Otto Schmitt ◽  
Annett Weigend ◽  
Christian Reimer ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Genetic Distance ◽  
Isolation By Distance ◽  
Genetic Distances ◽  
Founder Population ◽  
Wild Populations ◽  
Metabolic Processes ◽  
Evolutionary Forces ◽  
The Relationship

AbstractMigration of populations from their founder population is expected to cause a reduction in genetic diversity and facilitates population differentiation between the populations and their founder population as predicted by the theory of genetic isolation by distance. Consistent with that, a model of expansion from a single founder predicts that patterns of genetic diversity in populations can be well explained by their geographic expansion from the founders, which is correlated to the genetic differentiation. To investigate this in the chicken, we have estimated the relationship between the genetic diversity in 172 domesticated chicken populations and their genetic distances to wild populations. We have found a strong inverse relationship whereby 87.5% of the variation in the overall genetic diversity of domesticated chicken can be explained by the genetic distance to the wild populations. We also investigated if different types of SNPs and genes present similar patterns of genetic diversity as the overall genome. Among different SNP classes, the non-synonymous ones were the most deviating from the overall genome. However, the genetic distances to wild populations still explained more variation in domesticated chicken diversity in all SNP classes ranging from 81.7 to 88.7%. The genetic diversity seemed to change at a faster rate within the chicken in genes that are associated with transmembrane transport, protein transport and protein metabolic processes, and lipid metabolic processes. In general, such genes are flexible to be manipulated according to the population needs. On the other hand, genes which the genetic diversity hardly changes despite the genetic distance to the wild populations are associated with major functions e.g. brain development. Therefore, changes in the genes may be detrimental to the chickens. These results contribute to the knowledge of different evolutionary patterns of different functional genomic regions in the chicken.Author summaryThe chicken was first domesticated about 6000 B.C. in Asia from the jungle fowl. Following domestication, chickens were taken to different parts of the world mainly by humans. Evolutionary forces such as selection and genetic drift have shaped diversification within the chicken species. In addition, new breeds or strains have been developed from crossbreeding programs facilitated by man. These events, together with other breeding practices, have led to genomic alterations causing genetic differentiation between the domesticated chickens and their ancestral/wild population as well as manipulation of the genetic diversity within the domesticated chickens. We investigated the relationship between 172 domesticated chicken populations from different selection, breeding and management backgrounds and their genetic distance to the wild type chickens. We found that the genetic diversity within the populations decreases with the increasing genetic distances to the wild types. Human manipulation of chicken genetic diversity has more effect on the genetic differentiation than simple geographic separations (through migrations) do. We further found that some genes associated with vital functions show evolutionary constraints or persistent selection across the populations and do not comply with this relationship i.e. the genetic diversity within the populations is constant despite the change in the genetic distance to the wild types.

scholarly journals Usefulness of a Locus LE21085 in the Genetic Differentiation of Tomato Varieties

2017 ◽  
Vol 9 (2) ◽  
pp. 209-213
Author(s):  
Elizabeta MISKSOKA-MILEVSKA ◽  
Zoran T. POPOVSKI ◽  
Tome NESTOROVSKI
Keyword(s):  
Genetic Diversity ◽  
Lycopersicon Esculentum ◽  
Genetic Differentiation ◽  
Allele Frequency ◽  
Base Pair ◽  
Microsatellite Loci ◽  
Individual Genome ◽  
Microsatellites Markers ◽  
Expected Heterozygosity ◽  
Polymorphic Microsatellite

The microsatellites are specific for each individual genome or species. In order to evaluate the genetic diversity and the relationships within the genus Lycopersicon, microsatellites markers were used. The main objective of this study was to determine the usefulness of the locus LE21085 in the genetic differentiation among six morphologically different tomato varieties of Lycopersicon esculentum Mill. (var. grandifolium subsp. cultum; var. cerasiforme - red and yellow, var. pruniforme, var. pyriforme subsp. subspontaneum and var. racemigerum subsp. spontaneum). For the microsatellites locus LE21085 were detected two alleles in all estimated tomato varieties, that differed by one base pair (122 and 123 bp). The biggest allele frequency was found for the allelic variant of 122 bp, and its values were: 0.8462 for L. esculentum subsp. subspontaneum var. cerasiforme (red), 0.6923 for L. esculentum subsp. subspontaneum var. cerasiforme (yellow), 0.5769 for L. esculentum subsp. cultum var. grandifolium, 0.6923 for L. esculentum subsp. subspontaneum var. pruniforme, 0.6154 for L. esculentum subsp. subspontaneum var. pyriforme and 0.8077 for L. esculentum subsp. spontaneum var. racemigerum. The average of observed heterozygosity for the locus LE21085 (Ho = 0.5641) was higher than average expected heterozygosity (He = 0.4158). The average PIC value for the locus LE21085 was 0.3294 and it was classified as a modest informative markers. From the obtained results it can be concluded that locus LE21085 could be used in genetic differentiation of tomato varieties, but in combination with other polymorphic microsatellite loci.

scholarly journals Genetic Diversity and Differentiation of Relict Plant Liriodendron Populations Based on 29 Novel EST-SSR Markers

Forests ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 334 ◽  
Author(s):  
Xiaofei Long ◽  
Yuhao Weng ◽  
Siqin Liu ◽  
Zhaodong Hao ◽  
Yu Sheng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Ssr Markers ◽  
Eastern China ◽  
Genetic Distances ◽  
Breeding Strategy ◽  
Western China ◽  
The Usa ◽  
Ssr Loci ◽  
Liriodendron Chinense

Surviving relict populations of species that were more widespread in ancient times can teach us a lot, such as evolution and genetic differentiation. One such relict plant is Liriodendron, of which populations remain in China (L. chinense (Hemsl.) Sarg.) and the USA (L. tulipifera L.). Studying the genetic structure of these populations would give insight into the genetic differentiation and the breeding strategy. In this work, we developed and characterized 29 novel simple sequence repeat (SSR) markers based on expressed sequence tags (ESTs) from hybrid Liriodendron (Liriodendron chinense × tulipifera) callus. In total, 29 SSRs with perfect primer-designed were used to assess genetic diversity and differentiation. The set of polymorphic EST-SSR loci was identified in 48 Liriodendron individuals, represented by 35 individuals sampled from 14 provenances of L. chinense and 13 individuals sampled from 5 provenances of L. tulipifera. Our results indicated that L. chinense populations possess slightly higher genetic diversity than L. tulipifera populations. Based on genetic distances, 48 Liriodendron individuals clustered into three groups (the eastern China L. chinense, the western China L. chinense and L. tulipifera), although the STRUCTURE analysis of the Liriodendron populations revealed just two clear genetic clusters (L. chinense and L. tulipifera). Among these 29 novel markers, ESSR119 showed an obvious species-specific characteristic which can be very useful in marker-assisted selection (MAS). In general, all these EST-SSR markers may have agronomic potential and constitute a basis for future studies on the identification, innovation, and even preservation of Liriodendron germplasms.

scholarly journals Combining Quantitative Data on Growth, Wood Density and Other Traits with SSR Markers to Evaluate Genetic Diversity and Structure in a Planted Population of Eucalyptus camaldulensis Dehn.

Forests ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1090
Author(s):  
Xiuhua Shang ◽  
Roger J. Arnold ◽  
Zhihua Wu ◽  
Peijian Zhang ◽  
Guo Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Ssr Markers ◽  
Quantitative Trait ◽  
Eucalyptus Camaldulensis ◽  
Genetic Distances ◽  
Bark Thickness ◽  
Seed Sources ◽  
Pilodyn Penetration ◽  
Ssr Loci

Eucalyptus camaldulensis Dehn. is one of the most morphologically and genetically variable Eucalyptus species. Growth, Leptocybe invasa Fisher & La Salle susceptibility, pilodyn penetration and other traits up to age 36 months were assessed in a seed source/family trial in China comprising 112 seedlots representing five natural stand and six exotic seed sources. Genetic diversity and population structure of this trial population were also analyzed using 48 simple sequence repeat (SSR) markers. The key objective was to examine whether the genomic data could provide value over information obtained from just quantitative trait data. Significant genetic variation was found among seed sources and among families within seed sources for most quantitative traits. The ratio of variance among seed sources to variance among families within seed sources, based on variances estimated from quantitative trait data, varied from 0.1% (height at 9 months) up to 75.2% (bark thickness). Equivalent ratios estimated from the AMOVA on SSR loci data were similar for height (ages 24 and 36 months) and also pilodyn penetration at 36 months, but not for 9-month height or 36-month bark thickness. From 48 SSR loci examined, the genetic differentiation coefficient (among seed sources) was 0.086, indicating low genetic differentiation among seed sources. While overall genetic diversity in the trial population examined was high, the levels within the different seed sources varied markedly. Prior to this study, genetic distances among families from the three exotic seed sources (from domesticated Indian populations) in the trial, along with their genetic distances from, and relatedness to, families from five natural stand seed sources (Australian) in the trial were unknown. The SSR loci data removed uncertainties and revealed that the exotic sources increased the breadth of genetic origins represented in the trial population—information that could not have been obtained from just the quantitative trait data.

Genetic diversity among four short stature cattle populations of India

2008 ◽  
Vol 43 ◽  
pp. 15-23
Author(s):  
M.S. Tantia ◽  
R.K. Vijh ◽  
B. Mishra ◽  
S.T. Bharani Kumar
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Differentiation ◽  
Short Stature ◽  
Correspondence Analysis ◽  
Microsatellite Loci ◽  
South India ◽  
Relative Magnitude ◽  
Expected Heterozygosity ◽  
The Mean

SummaryThe genetic diversity, genetic differentiation and relationship between four short stature cattle populations of south India - Punganur, Iduki, Kasargod and Vatakara - was studied, using 24 microsatellite loci. A total of 164 alleles were observed. The mean number of alleles per locus was 6.58 with mean observed and expected heterozygosity values of 0.70 and 0.75 respectively. The relative magnitude of gene differentiation (FST) was 6% and was significant except between the Iduki and Kasargod populations. The negative FIS values obtained for the majority of loci indicated a lack of population structure in the four populations. Both phylogenetic and correspondence analysis exhibited a closeness between Iduki and Kasargod animals. The results indicated that all four populations were outbred and Kasargod and Iduki animals should be considered as one even though these are reared for different purposes.

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