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Genome-based Biotechnologies in Aquaculture









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    Article
    Genome-Wide Association Scan Suggests Basis for Microtia in Awassi Sheep 2016
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    Microtia, the underdevelopment of the pinna, the structural part of the outer ear, has been observed in many species,including humans, mice, dogs and various livestock. Microtia is relatively prevalent in sheep, observed in multiple breeds including some entire populations, but its genetic basis has not been described. The Awassi sheep, a breed native to Southwest Asia, carries this phenotype and was targeted for molecular characterization via a genome-wide association study . DNA samples wer e collected from sheep flocks in Jordan, within the native range of the Awassi. Samples from eight affected and twelve normal individuals were genotyped with the Illumina OvineSNP50 ® chip. Haplotype-based analyses failed to identify any major runs of homozygosity associated with the trait. In contrast, a single-locus genome-wide association analysis revealed a solitary statistically significant association (P= 0.012, genome wide) with a single-nucleotide polymorphism at base-pair 34,647,4 99 on OAR23. This marker is adjacent to the gene encoding transcription factor GATA-6, which has been shown to play a critical role in many developmental processes, including chondrogenesis. The lack of extended homozygosity in this region suggests a fairly ancient mutation, and the time of occurrence was estimated to be approximately 860 generations ago. This result suggests that many of the sheep breeds showing this phenotype may share the causative mutation, especially within the sub- group of fat-tailed, wool sheep.
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    A Silver Lining of the Pandemic: Whole-Genome Sequencing and Food Safety
    The benefits of whole-genome sequencing are far ranging
    2021
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    With the coronavirus disease 2019 (COVID-19) pandemic, whole-genome sequencing (WGS) has proven once again to be an efficient tool for outbreak investigations. The first sequence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was published on January 10, 2020.1 WGS was continuously used to investigate the virus’s genetic variants and their spread, to understand the impacts of mutations, and to monitor emerging lineages.2 The sequenced data and relevant information have been made available on open-source platforms, leading to scientific collaboration and accelerating research on the virus. A prominent example of such collaboration is the “Nextstrain” project3 with its online platform, which has enabled scientists to upload real-time data and facilitated further scientific analyses. While interpretations of the information on such platforms may have been used for decision making,4 one of the most redeeming values of the open platform is that it connects scientists to the general public, as this is a scientific communication tool with effective visuals.5 This confirms the importance of securing an enabling environment for global WGS data sharing, which was discussed extensively at a meeting convened by the Food and Agriculture Organization of the United Nations (FAO) in 2016.6 The scope of the meeting was on WGS applications, particularly for food safety management, which deals with various types of pathogenic microbes.
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    A disjunctive marginal edge of evergreen broad-leaved oak (quercus gilva) in East Asia: the high genetic distinctiveness and unusual diversity of Jeju island populations and insight into a massive, independent postglacial colonization
    XV World Forestry Congress, 2-6 May 2022
    2022
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    Jeju Island is located at a marginal edge of the distributional range of East Asian evergreen broad-leaved forests. The low genetic diversity of such edge populations is predicted to have resulted from genetic drift and reduced gene flow when compared to core populations. To test this hypothesis, we examined the levels of genetic diversity of marginal-edge populations of Quercus gilva, restricted to a few habitats on Jeju Island, and compared them with the southern Kyushu populations. We also evaluated their evolutionary potential and conservation value. The genetic diversity and structure were analyzed using 40 polymorphic microsatellite markers developed in this study. Ecological Niche Modeling (ENM) has been employed to develop our insights, which can be inferred from historical distribution changes. Contrary to our expectations, we detected a similar level of genetic diversity in the Jeju populations, comparable to that of the southern Kyushu populations, which have been regarded as long-term glacial refugia with a high genetic variability of East Asian evergreen trees. We found no signatures of recent bottlenecks in the Jeju populations. The results of STRUCTURE, neighbor-joining phylogeny, and Principal Coordinate Analysis (PCoA) with a significant barrier clearly demonstrated that the Jeju and Kyushu regions are genetically distinct. However, ENM showed that the probability value for the distribution of the trees on Jeju Island during the Last Glacial Maximum (LGM) converge was zero. In consideration of these results, we hypothesize that independent massive postglacial colonization from a separate large genetic source, other than Kyushu, could have led to the current genetic diversity of Jeju Island. Therefore, we suggest that the Jeju populations deserve to be separately managed and designated as a level of management unit (MU). These findings improve our understanding of the paleovegetation of East Asian evergreen forests, and the microevolution of oaks . Keywords: marginal edge; Quercus gilva; genetic diversity; massive colonization; Jeju Island; conservation ID: 3612841

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