Brettanomyces bruxellensis wine isolates show high geographical dispersal and long remanence in cellars

AbstractBrettanomyces bruxellensis is the main wine spoiler yeast all over the world, yet the structuration of the populations associated with winemaking remains elusive. In this work, we considered 1411 wine isolates from 21 countries that were genotyped using twelve microsatellite markers. We confirmed that B. bruxellensis isolates from wine environments show high genetic diversity, with 58 and 42% of triploid and diploid individuals respectively distributed in 5 main genetic groups. The distribution in the genetic groups varied greatly depending on the country and/or the wine-producing region. However, the two wine triploid groups showing sulfite resistance/tolerance were identified in almost all regions/countries. Genetically identical isolates were also identified. The analysis of these clone groups revealed that a given genotype could be isolated repeatedly in the same winery over decades, demonstrating unsuspected remanence ability. Besides cellar residency, a great geographic dispersal was also evidenced, with some genotypes isolated in wines from different continents. Finally, the study of old isolates and/or isolates from old vintages revealed that only the diploid groups were identified prior 1990 vintages. The triploid groups were identified in subsequent vintages, and their proportion has increased steadily these last decades, suggesting adaptation to winemaking practices such as sulfite use. A possible evolutionary scenario explaining these results is discussed.

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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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High Genetic Diversity but Absence of Population Structure in Local Chickens of Sri Lanka Inferred by Microsatellite Markers

Frontiers in Genetics ◽

10.3389/fgene.2021.723706 ◽

2021 ◽

Vol 12 ◽

Author(s):

Amali Malshani Samaraweera ◽

Ranga Liyanage ◽

Mohamed Nawaz Ibrahim ◽

Ally Mwai Okeyo ◽

Jianlin Han ◽

...

Keyword(s):

Genetic Diversity ◽

Sri Lanka ◽

Microsatellite Markers ◽

Allelic Diversity ◽

Genetic Distances ◽

Population Substructure ◽

High Genetic Diversity ◽

Naked Neck ◽

Local Chicken ◽

Local Chickens

Local chicken populations belonging to five villages in two geographically separated provinces of Sri Lanka were analyzed using 20 microsatellite markers to determine the genetic diversity of local chickens. Population genetic parameters were estimated separately for five populations based on geographic locations and for eight populations based on phenotypes, such as naked neck, long legged, crested or crown, frizzle feathered, Giriraj, commercial layer, crossbreds, and non-descript chicken. The analysis revealed that there was a high genetic diversity among local chickens with high number of unique alleles, mean number of alleles per locus (MNA), and total number of alleles per locus per population. A total of 185 microsatellite alleles were detected in 192 samples, indicating a high allelic diversity. The MNA ranged from 8.10 (non-descript village chicken) to 3.50 (Giriraj) among phenotypes and from 7.30 (Tabbowa) to 6.50 (Labunoruwa) among village populations. In phenotypic groups, positive inbreeding coefficient (FIS) values indicated the existence of population substructure with evidence of inbreeding. In commercial layers, a high expected heterozygosity He = 0.640 ± 0.042) and a negative FIS were observed. The positive FIS and high He estimates observed in village populations were due to the heterogeneity of samples, owing to free mating facilitated by communal feeding patterns. Highly admixed nature of phenotypes was explained as a result of rearing many phenotypes by households (58%) and interactions of chickens among neighboring households (53%). A weak substructure was evident due to the mating system, which disregarded the phenotypes. Based on genetic distances, crown chickens had the highest distance to other phenotypes, while the highest similarity was observed between non-descript village chickens and naked neck birds. The finding confirms the genetic wealth conserved within the populations as a result of the breeding system commonly practiced by chicken owners. Thus, the existing local chicken populations should be considered as a harbor of gene pool, which can be readily utilized in developing locally adapted and improved chicken breeds in the future.

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Genetic Diversity and Structure of Latvian Tilia cordata Populations

Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences. ◽

10.2478/prolas-2021-0039 ◽

2021 ◽

Vol 75 (4) ◽

pp. 261-267

Author(s):

Dainis Edgars Ruņģis ◽

Baiba Krivmane

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Vegetative Reproduction ◽

Growth Conditions ◽

Climatic Conditions ◽

Tilia Cordata ◽

High Genetic Diversity ◽

Genetic Diversity And Structure ◽

Broadleaf Tree ◽

Broadleaf Species

Abstract Changing climatic conditions are transforming the ecological and silvicultural roles of broadleaf tree species in northern Europe. Small-leaved lime (Tilia cordata Mill.) is distributed throughout most of Europe, and is a common broadleaf species in Latvia. This species can tolerate a broad range of environmental and ecological conditions, including temperature, water availability, and soil types. The aim of this study was to assess the genetic diversity and differentiation of Latvian T. cordata populations using nuclear microsatellite markers developed for Tilia platyphyllos. After testing of 15 microsatellite markers, Latvian T. cordata samples were genotyped at 14 micro-satellite loci. Latvian T. cordata populations had high genetic diversity, and were not overly isolated from each other, with moderate gene flow between populations. No highly differentiated populations were identified. Vegetative reproduction was identified in most analysed populations, and almost one-third of analysed individuals are of clonal origin. T. cordata has high timber production potential under the current climatic and growth conditions in Latvia, and therefore this species has potential for use in forestry, as well as playing a significant role in maintaining biodiversity and other ecosystem services.

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High genetic diversity and low differentiation in mud crab (Scylla paramamosain) along the southeastern coast of China revealed by microsatellite markers

Journal of Experimental Biology ◽

10.1242/jeb.071654 ◽

2012 ◽

Vol 215 (17) ◽

pp. 3120-3125 ◽

Cited By ~ 12

Author(s):

H. Ma ◽

H. Cui ◽

C. Ma ◽

L. Ma

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Scylla Paramamosain ◽

Mud Crab ◽

High Genetic Diversity ◽

Southeastern Coast

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Genetic Diversity of Rice vampireweed (Rhamphicarpa fistulosa) Populations in Rainfed Lowland Rice in West Africa

Weed Science ◽

10.1614/ws-d-15-00143.1 ◽

2016 ◽

Vol 64 (3) ◽

pp. 430-440

Author(s):

Norliette Zossou ◽

Hubert Adoukonèou-Sagbadja ◽

Daniel Fonceka ◽

Lamine Baba-Moussa ◽

Mbaye Sall ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

Lowland Rice ◽

Rice Grain ◽

High Genetic Diversity ◽

Genetic Groups ◽

Rainfed Lowland ◽

Rice Genotypes ◽

The Relationship ◽

Aflp Technique

Rice vampireweed belongs to the Orobanchaceae and is found in Africa and Australia. It is a hemiparasitic weed of lowland rice genotypes and causes losses of 40 to 100% of rice grain yield. Our study addressed the genetic diversity of rice vampireweed in Benin and Senegal. The specific objectives of this research were to study the genetic diversity of rice vampireweed accessions in Benin and Senegal and the relationship between the different genotypes of rice vampireweed through agroecological areas. To achieve these objectives, the genetic diversity of rice vampireweed accessions using the AFLP technique was studied. Based on our results, dendrogram classification has distinguished four different genetic groups. The populations of Benin and Senegal are genetically diverse. Substantial genetic differentiation (GST) exists among agroecological areas within Benin and Senegal (GST = 0.17). The high genetic diversity of rice vampireweed in Benin and Senegal presents a challenge for the development of resistant rice germplasm.

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Molecular Assessment of Genetic Diversity among Egyptian Landraces of Wheat (Triticum aestivum L.) Using Microsatellite Markers

Asian Journal of Biochemistry, Genetics and Molecular Biology ◽

10.9734/ajbgmb/2020/v3i430094 ◽

2020 ◽

pp. 46-58 ◽

Cited By ~ 1

Author(s):

Ahmed Medhat Mohamed Al-Naggar ◽

Mohamed Abd El-Maboud Abd El-Shafi ◽

Mohamed Helmy El-Shal ◽

Ali Hassan Anany

Keyword(s):

Genetic Diversity ◽

Triticum Aestivum ◽

Microsatellite Markers ◽

Ssr Markers ◽

Triticum Aestivum L ◽

Genetic Progress ◽

High Genetic Diversity ◽

Breeding Programs ◽

High Polymorphism Information Content ◽

Wheat Landraces

To increase the genetic progress in wheat (Triticum aestivum L.) yield, breeders search for germplasm of high genetic diversity, one of them is the landraces. The present study aimed at evaluating genetic diversity of 20 Egyptian wheat landraces and two cultivars using microsatellite markers (SSRs). Ten SSR markers amplified a total of 27 alleles in the set of 22 wheat accessions, of which 23 alleles (85.2%) were polymorphic. The majority of the markers showed high polymorphism information content (PIC) values (0.67-0.94), indicating the diverse nature of the wheat accessions and/or highly informative SSR markers used in this study. The genotyping data of the SSR markers were used to assess genetic variation in the wheat accessions by dendrogram. The highest genetic distance was found between G21 (Sakha 64; an Egyptian cultivar) and the landrace accession No. 9120 (G11). These two genotypes could be used as parents in a hybridization program followed by selection in the segregating generations, to identify some transgressive segregates of higher grain yield than both parents. The clustering assigned the wheat genotypes into four groups based on SSR markers. The results showed that the studied SSR markers, provided sufficient polymorphism and reproducible fingerprinting profiles for evaluating genetic diversity of wheat landraces. The analyzed wheat landraces showed a good level of genetic diversity at the molecular level. Molecular variation evaluated in this study of wheat landraces can be useful in traditional and molecular breeding programs.

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Indigenous rice of Northeast India harbor rich genetic diversity as measured by SSR markers and Zn/Fe content

10.21203/rs.2.13868/v1 ◽

2019 ◽

Author(s):

Vanlalsanga No Surname ◽

Sagolshem Priyokumar Singh ◽

Yengkhom Tunginba Singh

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Microsatellite Markers ◽

Oryza Sativa L ◽

Northeast India ◽

Rice Cultivars ◽

High Genetic Diversity ◽

Fe Content ◽

Ne India ◽

Improvement Programs

Abstract Background Rice (Oryza sativa L.) is one of the most important crops of the world and a major staple food for half of the World’s human population. The Northeastern (NE) region of India lies in the Indo-Burma biodiversity hotspot and about 45% of the total flora of the country is found in the region. Local rice cultivars from different states of NE India were analyzed for genetic diversity and population structure using microsatellite markers, and their zinc and iron content. Results A total of 149 bands were detected using twenty-two microsatellite markers comprising both random and trait-linked markers, showing 100% polymorphism and high value of expected heterozygosity (0.6311) and the polymorphism information content (0.5895). Nali Dhan cultivar of Arunachal Pradesh possessed the highest genetic diversity (0.3545) among studied populations while Moirangphou Khonganbi of Manipur exhibited the lowest genetic diversity (0.0343). The model-based population structure revealed that all the studied 65 rice cultivars were grouped into two clusters. Cluster I was represented by 36 cultivars and cluster II by 29 cultivars. Badalsali cultivar of Assam possessed the highest Zn content (75.8 μg/g) and Kapongla from Manipur possessed the lowest (17.98 μg/g). The highest and the lowest Fe content was found in Fazu (215.62 μg/g) and Idaw (11.42 μg/g) of Mizoram. Conclusion The result suggested rice cultivars of NE India possessing high genetic diversity (Nali Dhan), high Zn (Badalsali) and Fe (Fazu) content can be useful as a source of germplasm for future rice improvement programs.

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Genetic diversity of Ukrainian local pig breeds based on microsatellite markers

Regulatory Mechanisms in Biosystems ◽

10.15421/021826 ◽

2018 ◽

Vol 9 (2) ◽

pp. 177-182 ◽

Cited By ~ 3

Author(s):

S. S. Kramarenko ◽

S. I. Lugovoy ◽

V. R. Kharzinova ◽

V. Y. Lykhach ◽

A. S. Kramarenko ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variability ◽

Microsatellite Markers ◽

Pig Breeds ◽

Genetic Groups ◽

The Mean ◽

Living Material ◽

The Individual ◽

High Degree ◽

Private Alleles

Preserving the current diversity of the living material on Earth is fundamental for the survival of future generations . A study was conducted to investigate the genetic diversity of Ukrainian local pig breeds. A total of 350 pigs representing five local pig breeds from Ukraine (Mirgorod – MIR, Poltava Meat – PM, Ukrainian Meat – UM, Ukrainian White Steppe – UWS and Ukrainian Spotted Steppe – USS) and one commercial breed (Duroc, DUR) were sampled. Twelve microsatellite loci (SW24, S0155, SW72, SW951, S0386, S0355, SW240, SW857, S0101, SW936, SW911 and S0228) were selected and belong to the list of microsatellite markers recommended by ISAG. The results indicate that there exists, in general, a high degree of genetic variability within the five Ukrainian local pig breeds. However, the genetic variability in the MIR and PM breeds was significantly lower (mean Na = 2.92–3.92; Ho = 0.382–0.411; FIS = 0.178–0.184) than in the other three Ukrainian local pig breeds – UM, UWS and USS (mean Na = 5.00–8.42; Ho = 0.549–0.668; FIS = 0.027–0.066). Thirty-four private alleles were identified among the six analyzed genetic groups which were distributed between 11 of the 12 loci. A high number of alleles typical for the breed (private alleles) was observed in Duroc pigs – 9 alleles did not occur in Ukrainian local pig breeds. The HWE test showed that all of the polymorphic loci deviated from HWE (P < 0.05) in at least one population. Loci S0355 (5), S0386 (4) and SW24 (4) presented a higher number of populations in imbalance. The mean FST showed that approximately 77.8% of the genetic variation was within-population and 12.2% was across the populations. The five Ukrainian local breeds were classified into two major groups, according to the phylogenetic tree, which was based on standard genetic distance. Overall, we found that 92.6% of the individual pigs were correctly assigned (324 out of 350) to the respective breed of origin, which is likely a consequence of the well-defined breed structure. Probabilities from the allocation test of individuals for the six pig genetic groups were estimated with Structure Harvester. In cluster 1 the highest grouping probabilities were found for the MIR (0.917) and PM (0.750) breeds. Local breeds UM (0.824) and USS (0.772) were grouped in cluster 2. Cluster 3 was related to the local pig breed USW (0.873). Cluster 4 presented high allocation probabilities for the commercial pig breed Duroc (0.924). The obtained results are important for the future conservation of Ukrainian local pig breeds.

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Genetic Diversity and Structure in RegionalCercospora beticolaPopulations fromBeta vulgarissubsp.vulgarisSuggest Two Clusters of Separate Origin

Phytopathology ◽

10.1094/phyto-07-18-0264-r ◽

2019 ◽

Vol 109 (7) ◽

pp. 1280-1292 ◽

Cited By ~ 4

Author(s):

Noel L. Knight ◽

Niloofar Vaghefi ◽

Julie R. Kikkert ◽

Melvin D. Bolton ◽

Gary A. Secor ◽

...

Keyword(s):

Genetic Diversity ◽

New York ◽

Genotypic Diversity ◽

Population Divergence ◽

Cercospora Leaf Spot ◽

High Genetic Diversity ◽

Genetic Diversity And Structure ◽

The World ◽

Population Origin ◽

Geographic Regions

Cercospora leaf spot, caused by Cercospora beticola, is a highly destructive disease of Beta vulgaris subsp. vulgaris worldwide. C. beticola populations are usually characterized by high genetic diversity, but little is known of the relationships among populations from different production regions around the world. This information would be informative of population origin and potential pathways for pathogen movement. For the current study, the genetic diversity, differentiation, and relationships among 948 C. beticola isolates in 28 populations across eight geographic regions were investigated using 12 microsatellite markers. Genotypic diversity, as measured by Simpson’s complement index, ranged from 0.18 to 1.00, while pairwise index of differentiation values ranged from 0.02 to 0.42, with the greatest differentiation detected between two New York populations. In these populations, evidence for recent expansion was detected. Assessment of population structure identified two major clusters: the first associated with New York, and the second with Canada, Chile, Eurasia, Hawaii, Michigan, North Dakota, and one population from New York. Inferences of gene flow among these regions suggested that the source for one cluster likely is Eurasia, whereas the source for the other cluster is not known. These results suggest a shared origin of C. beticola populations across regions, except for part of New York, where population divergence has occurred. These findings support the hypothesis that dispersal of C. beticola occurs over long distances.

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