Genetic differentiation of mainland-island sheep of Greece: Implications for identifying candidate genes for long-term local adaptation

Kominakis, A.; Tarsani, Eirini; Hager-Theodorides, Ariadne L.; Mastranestasis, Ioannis; Gkelia, D.; Hadjigeorgiou, I.

doi:10.1371/journal.pone.0257461

Cited by 13 publications

(6 citation statements)

References 61 publications

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“…Finally, nucleotide diversity (π) and fixation index ( F ST ) within and between AD and CD pigs were calculated by VCFtools ( 35 ) software. As individual π and F ST values may be subjected by genotyping and missing errors in chip data, consistent with previous literature ( 36 , 37 ), we estimated these statistics using a 500-kb sliding window.…”

Section: Methodsmentioning

confidence: 63%

Runs of Homozygosity Uncover Potential Functional-Altering Mutation Associated With Body Weight and Length in Two Duroc Pig Lines

Wang

Ruan

et al. 2022

Front. Vet. Sci.

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Runs of homozygosity (ROH) are widely used to investigate genetic diversity, demographic history, and positive selection signatures of livestock. Commercial breeds provide excellent materials to reveal the landscape of ROH shaped during the intense selection process. Here, we used the GeneSeek Porcine 50K single-nucleotide polymorphism (SNP) Chip data of 3,770 American Duroc (AD) and 2,096 Canadian Duroc (CD) pigs to analyze the genome-wide ROH. First, we showed that AD had a moderate genetic differentiation with CD pigs, and AD had more abundant genetic diversity and significantly lower level of inbreeding than CD pigs. In addition, sows had larger levels of homozygosity than boars in AD pigs. These differences may be caused by differences in the selective intensity. Next, ROH hotspots revealed that many candidate genes are putatively under selection for growth, sperm, and muscle development in two lines. Population-specific ROHs inferred that AD pigs may have a special selection for female reproduction, while CD pigs may have a special selection for immunity. Moreover, in the overlapping ROH hotspots of two Duroc populations, we observed a missense mutation (rs81216249) located in the growth and fat deposition-related supergene (ARSB-DMGDH-BHMT) region. The derived allele of this variant originated from European pigs and was nearly fixed in Duroc pigs. Further selective sweep and association analyses indicated that this supergene was subjected to strong selection and probably contributed to the improvement of body weight and length in Duroc pigs. These findings will enhance our understanding of ROH patterns in different Duroc lines and provide promising trait-related genes and a functional-altering marker that can be used for genetic improvement of pigs.

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Section: Methodsmentioning

confidence: 63%

Runs of Homozygosity Uncover Potential Functional-Altering Mutation Associated With Body Weight and Length in Two Duroc Pig Lines

Wang

Ruan

et al. 2022

Front. Vet. Sci.

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“…We know that the parameter ±500 kb, used for gene annotation based on the SNP position, is arbitrarily defined. For example, ±250 kb [50][51][52] and ±800 kb [53] have also been used for gene annotation in other studies. Therefore, we focused on the FNTB and CHURC1 genes, where some significantly associated SNPs were located.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Study of Body Conformation Traits in Tashi Goats (Capra hircus)

Yang,

Zhou,

Tan

et al. 2024

Animals

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Identifying genetic markers of economically valuable traits has practical benefits for the meat goat industry. To better understand the genomic variations influencing body conformation traits, a genome-wide association study was performed on Tashi goats, an indigenous Chinese goat breed. A total of 155 Tashi goats were phenotyped for eight body conformation traits: body height, body length, chest depth, chest width, chest girth, rump width, rump height, and cannon bone circumference. Then, 100 Tashi goats were randomly selected for whole-genome sequencing and genotyped. We obtained 1676.4 Gb of raw data with an average sequencing depth of 6.2X. Clean reads were aligned to the ARS1.2 reference genome, and 11,257,923 single nucleotide polymorphisms (SNPs) were identified. The structure analysis showed that these Tashi goats were almost not genetically related. The 109, 20, 52, 14, 62, 51, 70, and 7 SNPs were significantly associated with body height, body length, chest depth, chest width, chest girth, rump width, rump height, and cannon bone circumference. Within the ±500 kb region of significant SNPs, 183 genes were annotated. The most significantly enriched KEGG pathway was “olfactory transduction”, and the most significantly enriched gene ontology (GO) terms were “cellular process”, “cellular anatomical entity”, and “molecular transducer activity”. Interestingly, we found several SNPs on chromosomes 10 and 11 that have been identified multiple times for all eight body conformation traits located in two fragments (114 kb and 1.03 Mb). In chr.10:25988403-26102739, the six SNPs were tightly linked, the TACTAG genotype was the highest at 91.8%, and the FNTB (Farnesyltransferase, CAAX Box Beta) and CHURC1 (Churchill Domain Containing 1) genes were located. In chr.11:88216493-89250659, ten SNPs were identified with several dependent linkage disequilibrium (LD) blocks, and seven related genes were annotated, but no significant SNP was located in them. Our results provide valuable biological information for improving growth performance with practical applications for genomic selection in goats.

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“…However, one of the copies is truncated and does not contain a copy of the CHRNB1 gene (Supplementary Figure S7B). CHRNB1 has been linked to body size traits in sheep (95,96). ( 96) also linked its expression level to BMI in humans.…”

Section: Differential Copy Number Genes In Blue Whale Compared To Vaq...mentioning

confidence: 99%

A high-quality blue whale genome, segmental duplications, and historical demography

Bukhman

Morin

Meyer

et al. 2022

Preprint

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BackgroundThe blue whale, Balaenoptera musculus , is the largest animal known to have ever existed. Body size is tightly coupled to cell metabolism and environmental adaptations. A high-quality genome assembly of this magnificent animal will aid our understanding of body size regulation and related biological processes.ResultsWe report a reference-quality, long read based assembly of the blue whale genome. We sequenced genomic DNA using PacBio long-read, Illumina short-read, and 10X Genomics synthetic long-read technologies. We also obtained long-range mapping information using Bionano optical mapping and Dovetail Hi-C. Additionally, we sequenced the transcriptome of blue whale fibroblasts using Illumina RNA-seq and PacBio Iso-seq technologies. We also measured genome size using a flow cytometry technique. We report on: (1) comparison of alternative long-read and short-read-based assemblies; (2) segmental duplications within the blue whale genome, which have resulted in dramatic amplifications of several genes; (3) sites in IGF1 gene correlated to body size in cetaceans; and (4) heterozygosity and historical demography of Pacific and Atlantic blue whale populations.ConclusionsThis is one of the first high-quality reference genomes of a cetacean and the first baleen whale sequenced using a long-read technology. A high quality, annotated blue whale genome will serve as an important resource for biology, evolution, and conservation research.

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Genetic differentiation of mainland-island sheep of Greece: Implications for identifying candidate genes for long-term local adaptation

Cited by 13 publications

References 61 publications

Runs of Homozygosity Uncover Potential Functional-Altering Mutation Associated With Body Weight and Length in Two Duroc Pig Lines

Runs of Homozygosity Uncover Potential Functional-Altering Mutation Associated With Body Weight and Length in Two Duroc Pig Lines

Genome-Wide Association Study of Body Conformation Traits in Tashi Goats (Capra hircus)

A high-quality blue whale genome, segmental duplications, and historical demography

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