Investigation of genetic diversity and selection signatures in Czech cattle genetic resources revealed by genome-wide analysis

2022 ◽  
pp. 104825
Author(s):  
Jitka Kyselová ◽  
Artur Gurgul ◽  
Igor Jasielczuk ◽  
Monika Bugno-Poniewierska ◽  
Věra Mátlová ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Resources ◽  
Selection Signatures ◽  
Genome Wide Analysis ◽  
Genome Wide

Genome-wide analysis of genetic diversity and selection signatures in three Indian sheep breeds

2021 ◽  
Vol 243 ◽  
pp. 104367
Author(s):  
K.A. Saravanan ◽  
Manjit Panigrahi ◽  
Harshit Kumar ◽  
Bharat Bhushan ◽  
Triveni Dutt ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Selection Signatures ◽  
Genome Wide Analysis ◽  
Sheep Breeds ◽  
Genome Wide ◽  
Indian Sheep

Genome-wide analysis of deletions in maize population reveals abundant genetic diversity and functional impact

2021 ◽  
Author(s):  
Xiao Zhang ◽  
Yonghui Zhu ◽  
Karl A. G. Kremling ◽  
M. Cinta Romay ◽  
Robert Bukowski ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Functional Impact ◽  
Genome Wide Analysis ◽  
Maize Population ◽  
Genome Wide

scholarly journals Genome-wide scans for detecting the selection signature of the Jeju-island native pig in Korea

2020 ◽  
Vol 33 (4) ◽  
pp. 539-546
Author(s):  
Young-Sup Lee ◽  
Donghyun Shin ◽  
Kyeong-Hye Won ◽  
Dae Cheol Kim ◽  
Sang Chul Lee ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
Population Differentiation ◽  
Cellular Response ◽  
Jeju Island ◽  
Selection Signatures ◽  
Selection Signature ◽  
Genome Wide ◽  
Yorkshire Pigs ◽  
Gene Ontologies

Objective: The Jeju native pig (JNP) found on the Jeju Island of Korea is a unique black pig known for high-quality meat. To investigate the genetic uniqueness of JNP, we analyzed the selection signature of the JNP in comparison to commercial pigs such as Berkshire and Yorkshire pigs.Methods: We surveyed the genetic diversity to identify the genetic stability of the JNP, using the linkage disequilibrium method. A selective sweep of the JNP was performed to identify the selection signatures. To do so, the population differentiation measure, Weir-Cockerham’s F<sub>st</sub> was utilized. This statistic directly measures the population differentiation at the variant level. Additionally, we investigated the gene ontologies (GOs) and genetic features.Results: Compared to the Berkshire and Yorkshire pigs, the JNP had lower genetic diversity in terms of linkage disequilibrium decays. We summarized the selection signatures of the JNP as GO. In the JNP and Berkshire pigs, the most enriched GO terms were epithelium development and neuron-related. Considering the JNP and Yorkshire pigs, cellular response to oxygen-containing compound and generation of neurons were the most enriched GO.Conclusion: The selection signatures of the JNP were identified through the population differentiation statistic. The genes with possible selection signatures are expected to play a role in JNP’s unique pork quality.

scholarly journals Comparative Genomic Analysis Provides Insights into the Evolution and Genetic Diversity of Community-Genotype Sequence Type 72 Staphylococcus aureus Isolates

mSystems ◽  
2021 ◽  
Author(s):  
Wangxiao Zhou ◽  
Ye Jin ◽  
Yanzi Zhou ◽  
Yuan Wang ◽  
Luying Xiong ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Staphylococcus Aureus ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Sequence Type ◽  
Comparative Genomic ◽  
Health Issues ◽  
Content Type ◽  
Genome Wide Analysis ◽  
Genome Wide

Understanding the evolution and dissemination of community-genotype ST72 Staphylococcus aureus isolates is important, as isolates of this lineage have rapidly spread into hospital settings and caused serious health issues. In this study, we first carried out genome-wide analysis of 107 global ST72 isolates to characterize the evolution and genetic diversity of the ST72 lineage.

scholarly journals A Genome-Wide Analysis of Populations from European Russia Reveals a New Pole of Genetic Diversity in Northern Europe

PLoS ONE ◽  
2013 ◽  
Vol 8 (3) ◽  
pp. e58552 ◽  
Author(s):  
Andrey V. Khrunin ◽  
Denis V. Khokhrin ◽  
Irina N. Filippova ◽  
Tõnu Esko ◽  
Mari Nelis ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
European Russia ◽  
Northern Europe ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome

Berbers and Arabs: Tracing the genetic diversity and history of Southern Tunisia through genome wide analysis

2020 ◽  
Vol 173 (4) ◽  
pp. 697-708
Author(s):  
Paolo Anagnostou ◽  
Valentina Dominici ◽  
Cinzia Battaggia ◽  
Nouri Boukhchim ◽  
Jaâfar Ben Nasr ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genome Wide Analysis ◽  
Southern Tunisia ◽  
Genome Wide ◽  
History Of

Identification of putative markers of triclabendazole resistance by a genome-wide analysis of genetically recombinant Fasciola hepatica

Parasitology ◽  
2013 ◽  
Vol 140 (12) ◽  
pp. 1523-1533 ◽  
Author(s):  
J. HODGKINSON ◽  
K. CWIKLINSKI ◽  
N. J. BEESLEY ◽  
S. PATERSON ◽  
D. J. L. WILLIAMS
Keyword(s):  
Genetic Resources ◽  
Fasciola Hepatica ◽  
Genome Wide Analysis ◽  
Extensive Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Genetic Mechanisms ◽  
Triclabendazole Resistance

SUMMARYDespite years of investigation into triclabendazole (TCBZ) resistance in Fasciola hepatica, the genetic mechanisms responsible remain unknown. Extensive analysis of multiple triclabendazole-susceptible and -resistant isolates using a combination of experimental in vivo and in vitro approaches has been carried out, yet few, if any, genes have been demonstrated experimentally to be associated with resistance phenotypes in the field. In this review we summarize the current understanding of TCBZ resistance from the approaches employed to date. We report the current genomic and genetic resources for F. hepatica that are available to facilitate novel functional genomics and genetic experiments for this parasite in the future. Finally, we describe our own non-biased approach to mapping the major genetic loci involved in conferring TCBZ resistance in F. hepatica.

scholarly journals Selective signatures and high genome-wide diversity in traditional Brazilian manioc (Manihot esculenta Crantz) varieties

2021 ◽  
Author(s):  
Alessandro Alves-Pereira ◽  
Maria Imaculada Zucchi ◽  
Charles R. Clement ◽  
João Paulo Gomes Viana ◽  
José Baldin Pinheiro ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Resources ◽  
Manihot Esculenta ◽  
Evolutionary Dynamics ◽  
Raw Material ◽  
Nucleotide Polymorphisms ◽  
Manihot Esculenta Crantz ◽  
Genome Wide ◽  
Neutral Genetic Diversity ◽  
Effective Use

Knowledge about crops' genetic diversity is essential to promote effective use and conservation of their genetic resources, because genetic diversity enables farmers to adapt their crops to specific needs and is the raw material for breeding efforts. Currently, manioc (Manihot esculenta ssp. esculenta) is one of the most important food crops in the world and has the potential to help achieve food security in the context of on-going climate changes. In this study we assessed the patterns of genome-wide diversity of traditional Brazilian manioc varieties conserved in the gene bank of the Luiz de Queiroz College of Agriculture, University of São Paulo. We used single nucleotide polymorphisms to evaluate the organization of genetic diversity and to identify selective signatures contrasting varieties from different biomes with samples of manioc's wild relative M. esculenta ssp. flabellifolia. We identified signatures of selection putatively associated with resistance genes, plant development and response to abiotic stresses. This presumed adaptive variation might have been important for the initial domestication and for the crop's diversification in response to cultivation in different environments. The neutral variation revealed high levels of genetic diversity within groups of varieties from different biomes and low to moderate genetic divergence among biomes. These results reflect the complexity of manioc's biology and its evolutionary dynamics under traditional cultivation. Our results exemplify how the smallholder practices contribute to the conservation of manioc's genetic resources, maintaining variation of potential adaptive significance and high levels of neutral genetic diversity.

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