scholarly journals Genome-wide insights on gastrointestinal nematode resistance in autochthonous Tunisian sheep

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
A. M. Ahbara ◽  
M. Rouatbi ◽  
M. Gharbi ◽  
M. Rekik ◽  
A. Haile ◽  
...  
Keyword(s):  
Animal Health ◽  
Gastrointestinal Nematode ◽  
Nematode Resistance ◽  
Indigenous Sheep ◽  
Genome Wide ◽  
Population Structure Analysis ◽  
Genetic Mechanisms ◽  
Negative Impacts ◽  
Candidate Regions ◽  
Genomic Regions

AbstractGastrointestinal nematode (GIN) infections have negative impacts on animal health, welfare and production. Information from molecular studies can highlight the underlying genetic mechanisms that enhance host resistance to GIN. However, such information often lacks for traditionally managed indigenous livestock. Here, we analysed 600 K single nucleotide polymorphism genotypes of GIN infected and non-infected traditionally managed autochthonous Tunisian sheep grazing communal natural pastures. Population structure analysis did not find genetic differentiation that is consistent with infection status. However, by contrasting the infected versus non-infected cohorts using ROH, LR-GWAS, FST and XP-EHH, we identified 35 candidate regions that overlapped between at least two methods. Nineteen regions harboured QTLs for parasite resistance, immune capacity and disease susceptibility and, ten regions harboured QTLs for production (growth) and meat and carcass (fatness and anatomy) traits. The analysis also revealed candidate regions spanning genes enhancing innate immune defence (SLC22A4, SLC22A5, IL-4, IL-13), intestinal wound healing/repair (IL-4, VIL1, CXCR1, CXCR2) and GIN expulsion (IL-4, IL-13). Our results suggest that traditionally managed indigenous sheep have evolved multiple strategies that evoke and enhance GIN resistance and developmental stability. They confirm the importance of obtaining information from indigenous sheep to investigate genomic regions of functional significance in understanding the architecture of GIN resistance.

scholarly journals Genome-Wide Variation, Candidate Regions and Genes Associated With Fat Deposition and Tail Morphology in Ethiopian Indigenous Sheep

2019 ◽  
Vol 9 ◽  
Author(s):  
Abulgasim Ahbara ◽  
Hussain Bahbahani ◽  
Faisal Almathen ◽  
Mohammed Al Abri ◽  
Mukhtar Omar Agoub ◽  
...  
Keyword(s):  
Fat Deposition ◽  
Indigenous Sheep ◽  
Genome Wide ◽  
Candidate Regions

scholarly journals Genome-Wide Scan of Gastrointestinal Nematode Resistance in Closed Angus Population Selected for Minimized Influence of MHC

PLoS ONE ◽  
2015 ◽  
Vol 10 (3) ◽  
pp. e0119380 ◽  
Author(s):  
Eui-Soo Kim ◽  
Tad S. Sonstegard ◽  
Marcos V. G. B. da Silva ◽  
Louis C. Gasbarre ◽  
Curtis P. Van Tassell
Keyword(s):  
Gastrointestinal Nematode ◽  
Nematode Resistance ◽  
Genome Wide ◽  
Genome Wide Scan

scholarly journals Genome-wide DNA Variants Identify Genetic Diversity and Population Structure of Leptosphaeria maculans in Western Canada

2020 ◽  
Author(s):  
Qilin Chen ◽  
Gary Peng ◽  
Randy Kutcher ◽  
Fengqun Yu
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genome Wide Association Study ◽  
Leptosphaeria Maculans ◽  
Western Canada ◽  
Effective Management ◽  
Genome Wide ◽  
Population Structure Analysis ◽  
Dna Variants ◽  
Genomic Regions

Abstract Background: Leptosphaeria maculans is a serious concern for canola production in Canada. For effective management, knowledge of the pathogen’s genetic variability and population structure is a prerequisite. Despite some information on race dynamics of the western Canadian L. maculans population in recent years, genetic diversity based on a large number of genome-wide DNA variants has not been investigated.Results: From 1,590 L. maculans isolates collected from 23 field sites in three provinces: Manitoba, Saskatchewan and Alberta, Canada, in the years 2007-2008 and 2012-2014, 150 representative isolates were selected and whole-genome sequenced, and 31,870 polymorphic DNA variants (SNPs and InDels) were used to study L. maculans genetic diversity and population structure. Cluster analysis showed that the genetic diversity levels and isolate groupings varied with the number and genomic regions of the variants involved; isolates collected in 2012-2014 were more genetically diverse than those collected in 2007-2008 when genome-wide variants were considered. The genome wide association study (GWAS) detected variants in egn4_Lema_T86290 (AvrLm4-7), egn4_Lema_T86300 and egn4_Lema_T86310 associated with the year of collection, but no variants was found to be associated with the province or specific location from which the isolates were collected. Population structure analysis indicated the presence of three distinct sub-populations in western Canada. While isolates from Saskatchewan were mainly of one sub-population (sub-pop1), the Alberta isolates comprised two sub-populations (sub-pop1 and sub-pop2), and all the 3 subpopulations were found in Manitoba.Conclusion: The genetic diversity of the western Canadian L. maculans population varied among provinces. It was highly admixed in Manitoba, followed by that in Alberta. The Saskatchewan population had the lowest genetic diversity. Significant genome variation between 2007-2008 and 2012-2014 occurred in the genes egn4_Lema_T86290 (AvrLm4-7), egn4_Lema_T86300 and egn4_Lema_T86310), with AvrLm4-7 becoming much more common in the L. maculans population in the later period.

scholarly journals Genome‐wide association study to identify genetic loci associated with gastrointestinal nematode resistance in Katahdin sheep

2020 ◽  
Vol 51 (2) ◽  
pp. 330-335 ◽  
Author(s):  
G. M. Becker ◽  
K. M. Davenport ◽  
J. M. Burke ◽  
R. M. Lewis ◽  
J. E. Miller ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Gastrointestinal Nematode ◽  
Nematode Resistance ◽  
Genome Wide Association ◽  
Genetic Loci ◽  
Genome Wide

scholarly journals Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle

2021 ◽  
Vol 12 ◽  
Author(s):  
Slim Ben-Jemaa ◽  
Gabriele Senczuk ◽  
Elena Ciani ◽  
Roberta Ciampolini ◽  
Gennaro Catillo ◽  
...  
Keyword(s):  
Muscle Development ◽  
Single Nucleotide Polymorphism Array ◽  
Reference Population ◽  
Selection Signatures ◽  
Genomic Signatures ◽  
Genome Wide ◽  
Parasite Infections ◽  
Breeding Schemes ◽  
Candidate Regions ◽  
Genomic Regions

The Maremmana cattle is an ancient Podolian-derived Italian breed raised in semi-wild conditions with distinctive morphological and adaptive traits. The aim of this study was to detect potential selection signatures in Maremmana using medium-density single nucleotide polymorphism array. Putative selection signatures were investigated combining three statistical approaches designed to quantify the excess of haplotype homozygosity either within (integrated haplotype score, iHS) or among pairs of populations (Rsb and XP-EHH), and contrasting the Maremmana with a single reference population composed of a pool of seven Podolian-derived Italian breeds. Overall, the three haplotype-based analyses revealed selection signatures distributed over 19 genomic regions. Of these, six relevant candidate regions were identified by at least two approaches. We found genomic signatures of selective sweeps spanning genes related to mitochondrial function, muscle development, growth, and meat traits (SCIN, THSD7A, ETV1, UCHL1, and MYOD1), which reflects the different breeding schemes between Maremmana (semi-wild conditions) and the other Podolian-derived Italian breeds (semi-extensive). We also identified several genes linked to Maremmana adaptation to the environment of the western-central part of Italy, known to be hyperendemic for malaria and other tick-borne diseases. These include several chemokine (C-C motif) ligand genes crucially involved in both innate and adaptive immune responses to intracellular parasite infections and other genes playing key roles in pulmonary disease (HEATR9, MMP28, and ASIC2) or strongly associated with malaria resistance/susceptibility (AP2B1). Our results provide a glimpse into diverse selection signatures in Maremmana cattle and can be used to enhance our understanding of the genomic basis of environmental adaptation in cattle.

scholarly journals Genome-Wide Analysis Revealed Homozygosity and Demographic History of Five Chinese Sheep Breeds Adapted to Different Environments

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1480
Author(s):  
Adam Abied ◽  
Lei Xu ◽  
Bahlibi W. Sahlu ◽  
Feng Xing ◽  
Abulgasim Ahbara ◽  
...  
Keyword(s):  
Demographic History ◽  
Adaptive Immune Response ◽  
Conservation Strategies ◽  
Distribution Analysis ◽  
Runs Of Homozygosity ◽  
Sheep Breeds ◽  
Indigenous Sheep ◽  
Genome Wide ◽  
History Of ◽  
Genomic Regions

Homozygosity of long sequence genotypes are a result of parents transmitting identical haplotypes, which can be used to estimate their auto-zygosity. Therefore, we used high-density SNP Chip data to characterize the auto-zygosity of each breed according to the occurrence and distribution of runs of homozygosity (ROH). Subsequently, we identified the genomic regions with high runs of homozygosity frequencies within individuals of each breed. We selected 96 sheep samples from five local Chinese sheep breeds belonging to different geographical locations. We identified 3046 ROHs within the study breed individuals, among which the longer segments (>1–5 Mb) were dominant. On average, ROH segments covered about 12% of the genomes; the coverage rate of OAR20 was the lowest and that of OAR2 was the highest. The distribution analysis of runs of homozygosity showed that the detected ROH mainly distributed between >26 and 28 Mb. The Hetian and Hu sheep showed the lowest ROH distribution. The estimation of homozygosity level reflects the history of modern and ancient inbreeding, which may affect the genomes of Chinese indigenous sheep breeds and indicate that some animals have experienced recent self-pollination events (Yabuyi, Karakul and Wadi). In these sheep breeds, the genomic regions were assumed to be under selection signatures frequently in line with long ROH. These regions included candidate genes associated with disease resistance traits (5S_rRNA), the innate and adaptive immune response (HERC2 and CYFIP1), digestion and metabolism (CENPJ), growth (SPP1), body size and developments (GJB2 and GJA3). This study highlighted new insights into the ROH patterns and provides a basis for future breeding and conservation strategies of Chinese sheep breeds.

scholarly journals Metabolome Genome-Wide Association Study Identifies 74 Novel Genomic Regions Influencing Plasma Metabolites Levels

Metabolites ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 61
Author(s):  
Pirro G. Hysi ◽  
Massimo Mangino ◽  
Paraskevi Christofidou ◽  
Mario Falchi ◽  
Edward D. Karoly ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Plasma Metabolites ◽  
Physiological Processes ◽  
Genome Wide ◽  
A Genome ◽  
Genetic Mechanisms ◽  
Health And Disease ◽  
Genomic Regions

Metabolites are small products of metabolism that provide a snapshot of the wellbeing of an organism and the mechanisms that control key physiological processes involved in health and disease. Here we report the results of a genome-wide association study of 722 circulating metabolite levels in 8809 subjects of European origin, providing both breadth and depth. These analyses identified 202 unique genomic regions whose variations are associated with the circulating levels of 478 different metabolites. Replication with a subset of 208 metabolites that were available in an independent dataset for a cohort of 1768 European subjects confirmed the robust associations, including 74 novel genomic regions not associated with any metabolites in previous works. This study enhances our knowledge of genetic mechanisms controlling human metabolism. Our findings have major potential for identifying novel targets and developing new therapeutic strategies.

scholarly journals Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiaoting Xia ◽  
Shunjin Zhang ◽  
Huaju Zhang ◽  
Zijing Zhang ◽  
Ningbo Chen ◽  
...  
Keyword(s):  
Population Structure ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
System Response ◽  
Whole Genome ◽  
Population Structure Analysis ◽  
Native Cattle ◽  
Genomic Regions

Abstract Background Native cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. Jiaxian Red, a Chinese native cattle breed, is reported to have originated from crossbreeding between taurine and indicine cattle; their history as a draft and meat animal dates back at least 30 years. Using whole-genome sequencing (WGS) data of 30 animals from the core breeding farm, we investigated the genetic diversity, population structure and genomic regions under selection of Jiaxian Red cattle. Furthermore, we used 131 published genomes of world-wide cattle to characterize the genomic variation of Jiaxian Red cattle. Results The population structure analysis revealed that Jiaxian Red cattle harboured the ancestry with East Asian taurine (0.493), Chinese indicine (0.379), European taurine (0.095) and Indian indicine (0.033). Three methods (nucleotide diversity, linkage disequilibrium decay and runs of homozygosity) implied the relatively high genomic diversity in Jiaxian Red cattle. We used θπ, CLR, FST and XP-EHH methods to look for the candidate signatures of positive selection in Jiaxian Red cattle. A total number of 171 (θπ and CLR) and 17 (FST and XP-EHH) shared genes were identified using different detection strategies. Functional annotation analysis revealed that these genes are potentially responsible for growth and feed efficiency (CCSER1), meat quality traits (ROCK2, PPP1R12A, CYB5R4, EYA3, PHACTR1), fertility (RFX4, SRD5A2) and immune system response (SLAMF1, CD84 and SLAMF6). Conclusion We provide a comprehensive overview of sequence variations in Jiaxian Red cattle genomes. Selection signatures were detected in genomic regions that are possibly related to economically important traits in Jiaxian Red cattle. We observed a high level of genomic diversity and low inbreeding in Jiaxian Red cattle. These results provide a basis for further resource protection and breeding improvement of this breed.

scholarly journals Genome-Wide Analysis of Sex Disparities in the Genetic Architecture of Lung and Colorectal Cancers

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 686
Author(s):  
Alireza Nazarian ◽  
Alexander M. Kulminski
Keyword(s):  
Nucleotide Polymorphisms ◽  
Genetic Associations ◽  
Significance Level ◽  
Association Analyses ◽  
Complex Disorders ◽  
Specific Effects ◽  
Genome Wide ◽  
Genetic Mechanisms ◽  
Sex Disparities ◽  
Almost All

Almost all complex disorders have manifested epidemiological and clinical sex disparities which might partially arise from sex-specific genetic mechanisms. Addressing such differences can be important from a precision medicine perspective which aims to make medical interventions more personalized and effective. We investigated sex-specific genetic associations with colorectal (CRCa) and lung (LCa) cancers using genome-wide single-nucleotide polymorphisms (SNPs) data from three independent datasets. The genome-wide association analyses revealed that 33 SNPs were associated with CRCa/LCa at P < 5.0 × 10−6 neither males or females. Of these, 26 SNPs had sex-specific effects as their effect sizes were statistically different between the two sexes at a Bonferroni-adjusted significance level of 0.0015. None had proxy SNPs within their ±1 Mb regions and the closest genes to 32 SNPs were not previously associated with the corresponding cancers. The pathway enrichment analyses demonstrated the associations of 35 pathways with CRCa or LCa which were mostly implicated in immune system responses, cell cycle, and chromosome stability. The significant pathways were mostly enriched in either males or females. Our findings provided novel insights into the potential sex-specific genetic heterogeneity of CRCa and LCa at SNP and pathway levels.

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