Small-Scale Fragmentation Effects on Local Genetic Diversity in Two Phyllostomid Bats with Different Dispersal Abilities in Panama

The geographical pattern of genetic diversity was investigated in the endemic Sicilian pond turtle Emys trinacris across its entire distribution range, using 16 microsatellite loci. Overall, 245 specimens of E. trinacris were studied, showing high polymorphic microsatellite loci, with allele numbers ranging from 7 to 30. STRUCTURE and GENELAND analyses showed a noteworthy, geographically based structuring of the studied populations in five well-characterized clusters, supported by a moderate degree of genetic diversity (FST values between 0.075 and 0.160). Possible explanations for the genetic fragmentation observed are provided, where both natural and human-mediated habitat fragmentation of the Sicilian wetlands played a major role in this process. Finally, some conservation and management suggestions aimed at preventing the loss of genetic variability of the species are briefly reported, stressing the importance of considering the five detected clusters as independent Management Units.

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Genetic diversity and population structure of Escherichia coli from neighboring small-scale dairy farms

The Journal of Microbiology ◽

10.1007/s12275-011-0461-2 ◽

2011 ◽

Vol 49 (5) ◽

pp. 693-702 ◽

Cited By ~ 8

Author(s):

Jesús Andrei Rosales-Castillo ◽

Ma. Soledad Vázquez-Garcidueñas ◽

Hugo Álvarez-Hernández ◽

Omar Chassin-Noria ◽

Alba Irene Varela-Murillo ◽

...

Keyword(s):

Escherichia Coli ◽

Genetic Diversity ◽

Population Structure ◽

Dairy Farms ◽

Small Scale ◽

Small Scale Dairy

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Statistical analysis in support of maintaining a healthy traditional Siamese cat population

Genetics Selection Evolution ◽

10.1186/s12711-020-00596-w ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Arthur M. A. Pistorius ◽

Ineke Blokker

Keyword(s):

Genetic Diversity ◽

Cluster Analysis ◽

Companion Animals ◽

Hereditary Diseases ◽

Small Scale ◽

Genetic Traits ◽

Inbreeding Coefficients ◽

A Value ◽

Siamese Cat ◽

Line Breeding

Abstract Background For many years, breeders of companion animals have applied inbreeding or line breeding to transfer desirable genetic traits from parents to their offspring. Simultaneously, this resulted in a considerable spread of hereditary diseases and phenomena associated with inbreeding depression. Results Our cluster analysis of kinship and inbreeding coefficients suggests that the Thai or traditional Siamese cat could be considered as a subpopulation of the Siamese cat, which shares common ancestors, although they are considered as separate breeds. In addition, model-based cluster analysis could detect regional differences between Thai subpopulations. We show that by applying optimal contribution selection and simultaneously limiting the contributions by other breeds, the genetic diversity within subpopulations can be improved. Conclusion In principle, the European mainland Thai cat population can achieve a genetic diversity of about 26 founder genome equivalents, a value that could potentially sustain a genetically diverse population. However, reaching such a target will be difficult in the absence of a supervised breeding program. Suboptimal solutions can be obtained by minimisation of kinships within regional subpopulations. Exchanging animals between different regions on a small scale might be already quite useful to reduce the kinship, by achieving a potential diversity of 23 founder genome equivalents. However, contributions by other breeds should be minimised to preserve the original Siamese gene pool.

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Organoleptic, Sensory and Biochemical Traits of Arabica Coffee and their Arabusta Hybrids

10.5772/intechopen.95520 ◽

2021 ◽

Author(s):

Kahiu Ngugi ◽

Jane Jerono Cheserek ◽

Chrispine Ogutu Omondi

Keyword(s):

Experimental Data ◽

Genetic Diversity ◽

Genetic Variation ◽

Coffea Arabica ◽

Small Scale ◽

Arabica Coffee ◽

Biochemical Compounds ◽

Small Scale Farmers ◽

Organoleptic Traits ◽

Cup Quality

Coffee as a cash crop, reduces food insecurity by providing regular incomes and is a major foreign exchange earner in more than fifty tropical countries where it is grown either as Arabica (Coffea arabica) or Robust (Coffea canepora). In Kenya which grow some Robusta but mostly Arabica coffee, the production has been declining, mainly because world coffee prices have plummeted to about 5 USD for a 650Kg of un-hulled beans per acre. The only way world prices are likely to increase and benefit the small-scale farmers, is by improving the cup quality and enabling these countries to sell their coffee in specialty markets. This review, underscores the importance of analyzing and estimating organoleptic, sensory and biochemical compounds diversity in Arabica coffee, since these are the factors that determine cup quality. In an attempt to do so, the chapter presents experimental data that analyzed various sensory and organoleptic traits of Arabica coffee and their Arabusta hybrids that proves that tremendous genetic diversity exists in coffee genotypes grown in Kenya and it is possible to utilize this genetic variation to improve cup quality.

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Genetic Diversity and Population Structure of Metaphire vulgaris Based on the Mitochondrial COI Gene and Microsatellites

Frontiers in Genetics ◽

10.3389/fgene.2021.686246 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yu Fang ◽

Jie Chen ◽

Honghua Ruan ◽

Nan Xu ◽

Ziting Que ◽

...

Keyword(s):

Genetic Diversity ◽

Coi Gene ◽

Small Scale ◽

The Novel ◽

Mitochondrial Coi ◽

Allele Number ◽

Medicinal Value ◽

Mitochondrial Coi Gene ◽

Data Content ◽

Genetic Structures

The earthworm species Metaphire vulgaris (a member of the Clitellata class) is widely distributed across China, and has important ecological functions and medicinal value. However, investigations into its genetic diversity and differentiation are scarce. Consequently, we evaluated the genetic diversity of five populations of M. vulgaris (GM, HD, NYYZ, QDDY, and QDY) in Yancheng, China via the mitochondrial COI gene and the novel microsatellites developed there. A total of nine haplotypes were obtained by sequencing the mitochondrial COI gene, among which NYYZ and QDDY populations had the greatest number of haplotypes (nh = 5). Further, the nucleotide diversity ranged from 0.00437 to 0.1243. The neighbor-joining trees and the TCS network of haplotypes indicated that earthworm populations within close geographical range were not genetically isolated at these small scale distances. Results of the identification of microsatellite molecular markers revealed that the allele number in 12 microsatellite loci ranged from 4 to 13. The observed heterozygosity ranged from 0.151 to 0.644, whereas the expected heterozygosity ranged from 0.213 to 0.847. The polymorphism data content of most sites was >0.5, which indicated that the designed sites had high polymorphism. Structural analysis results indicated that GM, HD, and NYYZ had similar genetic structures across the five populations. The Nei’s genetic distance between HD and NYYZ populations was the smallest (Ds = 0.0624), whereas that between HD and QDY populations was the largest (Ds = 0.2364). The UPGMA tree showed that HD were initially grouped with NYYZ, followed by GM, and then with QDDY. Furthermore, cross-species amplification tests were conducted for Metaphire guillelmi, which indicated that the presented markers were usable for this species. This study comprised a preliminary study on the genetic diversity of M. vulgaris, which provides basic data for future investigations into this species.

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Implications of farmers’ seed exchanges for on-farm conservation of quinoa, as revealed by its genetic diversity in Chile

The Journal of Agricultural Science ◽

10.1017/s0021859612000056 ◽

2012 ◽

Vol 150 (6) ◽

pp. 702-716 ◽

Cited By ~ 37

Author(s):

F. F. FUENTES ◽

D. BAZILE ◽

A. BHARGAVA ◽

E. A. MARTÍNEZ

Keyword(s):

Genetic Diversity ◽

Genetic Erosion ◽

Agricultural Practices ◽

Urban Systems ◽

Small Scale ◽

South American ◽

Exchange Networks ◽

On Farm Conservation ◽

Genetic Structure And Diversity ◽

On Farm

SUMMARYQuinoa cultivation in Chile presents an ancient and active complex of geographic, climatic, social and cultural interactions that has determined its current biodiversity in the three main growing zones (north, central and south). Importantly, these interactions involve the participation of farmers, whose activities are at the base of seed exchange networks due to their knowledge andin situconservation of genetic diversity. The present study reports how a better understanding of farmers’ seed exchanges and local production practices could impact the genetic structure and diversity of quinoa at national scale in Chile. Using field interviews and characterization of 20 microsatellite genetic markers in a multi-origin set of 34 quinoa accessions representative of Chile and the South American region, the phenetic analysis of germplasm was consistent with the current classification of quinoa ecotypes present in Chile and Andean zone. This allowed the identification of five populations, which were represented by quinoa of Salares (northern Chile), Coastal/Lowlands (central and southern Chile), Highlands (Peru, Bolivia and Argentina) and Inter-Andean Valleys (Ecuador and Colombia). The highly informative quality of the markers used revealed a wide genetic diversity among main growing areas in Chile, which correlated well with natural geographical–edaphic–climatic and social–linguistic context to the expansion of quinoa biodiversity. Additionally, in addition to ancient seed exchanges, this process is still governed by the diverse agricultural practices of Andean farmers. Genetic erosion is considered an imminent risk due to small-scale farming, where the influence of increased migration of people to urban systems and export-driven changes to the agro-ecosystems may further reduce the diversity of quinoa plants in cultivation.

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An evaluation of small-scale genetic diversity and the mating system in Zostera noltii on an intertidal sandflat in the Wadden Sea

Annals of Botany ◽

10.1093/aob/mcq214 ◽

2010 ◽

Vol 107 (1) ◽

pp. 127-134 ◽

Cited By ~ 28

Author(s):

Andreas M. Zipperle ◽

James A. Coyer ◽

Karsten Reise ◽

Wytze T. Stam ◽

Jeanine L. Olsen

Keyword(s):

Genetic Diversity ◽

Mating System ◽

Wadden Sea ◽

Small Scale ◽

Zostera Noltii ◽

Intertidal Sandflat

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Small-scale patterns in snowmelt timing affect gene flow and the distribution of genetic diversity in the alpine dwarf shrub Salix herbacea

Heredity ◽

10.1038/hdy.2014.19 ◽

2014 ◽

Vol 113 (3) ◽

pp. 233-239 ◽

Cited By ~ 32

Author(s):

A J Cortés ◽

S Waeber ◽

C Lexer ◽

J Sedlacek ◽

J A Wheeler ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Dwarf Shrub ◽

Small Scale ◽

Salix Herbacea

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Life histories predict genetic diversity and population structure within three species of Octopus targeted by small-scale fisheries in Northwest Mexico

10.7287/peerj.preprints.3016 ◽

2017 ◽

Author(s):

José F Domínguez-Contreras ◽

Adrian Munguia-Vega ◽

Bertha P Ceballos-Vázquez ◽

Marcial Arellano-Martínez ◽

Francisco J García-Rodríguez ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Population Size ◽

Effective Population Size ◽

Gulf Of California ◽

Life Histories ◽

Local Population ◽

Small Scale ◽

Effective Population ◽

Northwest Mexico

The fishery for octopus in Northwest Mexico has increased to over 2,000 tons annually, but to date the specific composition of the catch has been ignored. With at least three main species with varying life histories targeted by artisanal fisheries in the region, lack of information about the distribution of each species and metapopulation size and structure could impede effective fisheries management to avoid overexploitation. Here we tested if different life histories in three species of octopus help to predict observed patterns of genetic diversity, population dynamics, structure and connectivity that could be relevant to the sustainable management of the fishery. We sequenced two mitochondrial genes and genotyped seven nuclear microsatellite loci to identify the distribution of each species in 20 locations from the Gulf of California and the Pacific coast of the Baja California peninsula. We tested four a priori hypothesis derived from population genetic theory based on differences in the fecundity and dispersal potential for each species. We found that the species with low fecundity and without a planktonic larval stage (Octopus bimaculoides) had lower average effective population size and genetic diversity, but higher levels of kinship, population structure, and richness of private alleles, suggesting limited dispersal and high local recruitment. In contrast, two species with higher fecundity and planktonic larvae (O. bimaculatus, O. hubbsorum) showed higher effective population size and genetic diversity, and overall lower kinship and population structure, supporting higher levels of gene flow over a larger geographical scale. Even among the latter, there were differences in the calculated parameters possibly associated with increased connectivity in the species with the longest planktonic larval duration (O. bimaculatus). We consider that O. bimaculoides could be more susceptible to over exploitation of small, isolated populations that could have longer recovery times, and suggest that management should take place within each local population. For the two species with pelagic larvae, management should consider metapopulation structure over larger geographic scales and the directionality and magnitude of larval dispersal between localities driven by ocean currents. The distribution of each species and variations in their reproductive timing should also be considered when establishing marine reserves or seasonal fishing closures.

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Direct cryopreservation of poultry/avian embryonic reproductive cells: A low-tech, cost-effective and efficient method for safeguarding genetic diversity

10.1101/2021.09.28.462137 ◽

2021 ◽

Author(s):

Tuanjun Hu ◽

Lorna Taylor ◽

Adrian Sherman ◽

Christian Keambou Tiambo ◽

Steven J Kemp ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Resources ◽

Production Systems ◽

Smallholder Farmers ◽

Effective Means ◽

Cost Effective ◽

Reproductive Technologies ◽

Small Scale ◽

Scale Production ◽

Climate Resilience

Chickens are an important resource for smallholder farmers who raise locally adapted, genetically distinct breeds for eggs and meat. The development of efficient reproductive technologies to conserve and regenerate chicken breeds safeguards existing biodiversity and secures poultry genetic resources for climate resilience, biosecurity, and future food production. The majority of the over 1600 breeds of chicken are raised in low and lower to middle income countries (LMICs) under resource limited, small scale production systems, which necessitates a low tech, cost effective means of conserving diversity is needed. Here, we validate a simple biobanking technique using cryopreserved embryonic chicken gonads. The gonads are quickly isolated, visually sexed, pooled by sex, and cryopreserved. Subsequently, the stored material is thawed and dissociated before injection into sterile host chicken embryos. By using pooled GFP and RFP-labelled donor gonadal cells and Sire Dam Surrogate (SDS) mating, we demonstrate that chicks deriving entirely from male and female donor germ cells are hatched. This technology will enable ongoing efforts to conserve chicken genetic diversity for both commercial and small holder farmers, and to preserve existing genetic resources at poultry research facilities.

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