Influence of small-scale habitat patchiness on the genetic diversity of the Korean endemic species Saussurea chabyoungsanica (Asteraceae)

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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Primer Binding Site (PBS) Profiling of Genetic Diversity of Natural Populations of Endemic Species Allium ledebourianum Schult.

BioTech ◽

10.3390/biotech10040023 ◽

2021 ◽

Vol 10 (4) ◽

pp. 23

Author(s):

Oxana Khapilina ◽

Ainur Turzhanova ◽

Alevtina Danilova ◽

Asem Tumenbayeva ◽

Vladislav Shevtsov ◽

...

Keyword(s):

Genetic Diversity ◽

Endemic Species ◽

Biological Diversity ◽

Natural Populations ◽

Subsequent Development ◽

Dna Profiling ◽

Primer Binding Site ◽

Anthropogenic Factors ◽

Habitat Specificity ◽

Interspersed Repeats

Endemic species are especially vulnerable to biodiversity loss caused by isolation or habitat specificity, small population size, and anthropogenic factors. Endemic species biodiversity analysis has a critically important global value for the development of conservation strategies. The rare onion Allium ledebourianum is a narrow-lined endemic species, with natural populations located in the extreme climatic conditions of the Kazakh Altai. A. ledebourianum populations are decreasing everywhere due to anthropogenic impact, and therefore, this species requires preservation and protection. Conservation of this rare species is associated with monitoring studies to investigate the genetic diversity of natural populations. Fundamental components of eukaryote genome include multiple classes of interspersed repeats. Various PCR-based DNA fingerprinting methods are used to detect chromosomal changes related to recombination processes of these interspersed elements. These methods are based on interspersed repeat sequences and are an effective approach for assessing the biological diversity of plants and their variability. We applied DNA profiling approaches based on conservative sequences of interspersed repeats to assess the genetic diversity of natural A. ledebourianum populations located in the territory of Kazakhstan Altai. The analysis of natural A. ledebourianum populations, carried out using the DNA profiling approach, allowed the effective differentiation of the populations and assessment of their genetic diversity. We used conservative sequences of tRNA primer binding sites (PBS) of the long-terminal repeat (LTR) retrotransposons as PCR primers. Amplification using the three most effective PBS primers generated 628 PCR amplicons, with an average of 209 amplicons. The average polymorphism level varied from 34% to 40% for all studied samples. Resolution analysis of the PBS primers showed all of them to have high or medium polymorphism levels, which varied from 0.763 to 0.965. Results of the molecular analysis of variance showed that the general biodiversity of A. ledebourianum populations is due to interpopulation (67%) and intrapopulation (33%) differences. The revealed genetic diversity was higher in the most distant population of A. ledebourianum LD64, located on the Sarymsakty ridge of Southern Altai. This is the first genetic diversity study of the endemic species A. ledebourianum using DNA profiling approaches. This work allowed us to collect new genetic data on the structure of A. ledebourianum populations in the Altai for subsequent development of preservation strategies to enhance the reproduction of this relict species. The results will be useful for the conservation and exploitation of this species, serving as the basis for further studies of its evolution and ecology.

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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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Comparative Population Genetics of Two Korean Aedes Mosquito Species with Vector Potential based on Mitochondrial DNA

10.21203/rs.3.rs-261518/v1 ◽

2021 ◽

Author(s):

Jiyeong Shin ◽

Jongwoo Jung

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Vector Control ◽

Endemic Species ◽

Korean Peninsula ◽

Mismatch Distribution ◽

Mosquito Species ◽

Mitochondrial Genes ◽

Rapid Expansion ◽

Number Of Individuals

Abstract Background: Mosquitoes of the genus Aedes are important invasive species contributing to the spread of chikungunya, dengue fever, yellow fever, Zika virus, and other dangerous vector-borne diseases. Aedes albopictus is native to southeast Asia with rapid expansion due to human activity, showing a wide distribution in the Korean peninsula. Aedes flavopictus is considered to be native to East Asia with a broad distribution in the region, including in the Korean peninsula. Gaining a better understanding of the genetic diversity of these species is critical for establishing strategies for disease prevention and vector control. Methods: We obtained DNA from 148 specimens of Ae. albopictus and 166 specimens of Ae. flavopictus in Korea, and amplified two mitochondrial genes (COI and ND5) to compare the genetic diversity and structure of the two species.Results: We obtained a 658-bp sequence of COI and a 423-bp sequence of ND5 from the two mosquito species. We found low diversity and an insignificant population genetic structure in Ae. albopictus, and high diversity and an insignificant structure in Ae. flavopictus for these two mitochondrial genes. Ae. albopictus had less haplotypes with respect to the number of individuals, and a slight mismatch distribution was confirmed. By contrast, Ae. flavopictus had a large number of haplotypes compared with the number of individuals, and a large unimodal-type mismatch distribution was confirmed. Although the genetic structure of both species was insignificant, Ae. flavopictus exhibited higher genetic diversity than Ae. albopictus.Conclusions: Ae. albopictus appears to be an introduced species, whereas Ae. flavopictus is an endemic species to the Korean peninsula, and the difference in genetic diversity between the two species is related to their adaptability and introduction history. As an endemic species, Ae. flavopictus is likely to have a larger population size than expected. Further studies on the genetic structure and diversity of these two mosquito species will provide useful data for vector control.

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