scholarly journals Genome analyses revealed genetic admixture and selection signatures in Bos indicus

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
S. P. Dixit ◽  
A. K. Bhatia ◽  
Indrajit Ganguly ◽  
Sanjeev Singh ◽  
Soumya Dash ◽  
...  
Keyword(s):  
Bos Indicus ◽  
Snp Array ◽  
Genomic Diversity ◽  
Genetic Admixture ◽  
Selection Signatures ◽  
Weight Growth ◽  
Glycolysis Regulation ◽  
Shared Ancestry ◽  
Production Body ◽  
Genome Analyses

AbstractThe genomic diversity and relationship among seven diverse cattle breeds viz. Sahiwal, Tharparkar, Gir, Vechur, Ongole, Kangayam and Hariana were investigated in 132 random samples based on high density SNP array comprising > 777 K SNPs. A total of 1993 SNPs (0.25% of the total) having greater power (FST ≥ 0.20) to differentiate these cattle populations were identified, and utilized to partition genome of each animal into a predefined number of clusters. The structure of these cattle indicated shared ancestry of dairy breeds viz. Gir, Tharparkar and Sahiwal. Most of the animals (> 76%) of different populations under study except Vechur clustered into their own group of animals called breed. Vechur population retained highest rate of admixture, consistent with its crossing with other breeds. Ongole, Kangayam and Hariana shared comparatively less of their genome (≤ 15%) with other breeds. The study indicated that all seven breeds evolved from their independent ancestry but there was intermixing of these breeds in the recent past. The selection signatures identified between draft (Kangayam) and dairy breeds included several genes like FAM19A2, RAB31P, BEST3, DGKA, AHCY, PIGU and PFKP which are involved in immune response, metabolic pathway, transportation of glucose and sugars, signaling pathways, cellular processes, cell division and glycolysis regulation, respectively. Moreover, these genomic regions also harbour QTLs affecting milk performance traits. The signatures were also identified even between the dairy breeds. In comparison to large-sized cattle, there were significant differences in the number of QTLs affecting production (body weight, growth rate etc.) and morphological traits (height) in short-statured Vechur breed. The presence of HMGA2 gene in the selection signature on chromosome 5 may explain the variations in stature between these cattle.

scholarly journals Genetic Diversity of Indigenous Pigs from South China Area Revealed by SNP Array

Animals ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 361 ◽  
Author(s):  
Shuqi Diao ◽  
Shuwen Huang ◽  
Zhiting Xu ◽  
Shaopan Ye ◽  
Xiaolong Yuan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Conservation Status ◽  
Snp Array ◽  
Size Analysis ◽  
Selection Signatures ◽  
Effective Population ◽  
Low Genetic Diversity ◽  
Indigenous Pigs

To investigate the genetic diversity, population structure, extent of linkage disequilibrium (LD), effective population size (Ne), and selection signatures in indigenous pigs from Guangdong and Guangxi in China, 226 pigs belonging to ten diverse populations were genotyped using single nucleotide polymorphism (SNP) chips. The genetic divergence between Chinese and Western pigs was determined based on the SNP chip data. Low genetic diversity of Dahuabai (DHB), Luchuan (LC), Lantang (LT), and Meihua (MH) pigs, and introgression of Western pigs into Longlin (LL), MH, and Yuedonghei (YDH) pigs were detected. Analysis of the extent of LD showed that indigenous pigs had low LD when pairwise SNP distance was short and high LD when pairwise SNP distance was long. Effective population size analysis showed a rapid decrease for Chinese indigenous pigs, and some pig populations had a relatively small Ne. This result indicated the loss of genetic diversity in indigenous pigs, and introgression from Western commercial pigs. Selection signatures detected in this study overlapped with meat quality traits, such as drip loss, intramuscular fat content, meat color b*, and average backfat thickness. Our study deepened understanding of the conservation status and domestication of Chinese indigenous pigs.

scholarly journals Assessment of Imputation from Low-Pass Sequencing to Predict Merit of Beef Steers

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1312
Author(s):  
Warren M. Snelling ◽  
Jesse L. Hoff ◽  
Jeremiah H. Li ◽  
Larry A. Kuehn ◽  
Brittney N. Keel ◽  
...  
Keyword(s):  
Genomic Prediction ◽  
Genomic Sequence ◽  
Bos Taurus ◽  
Low Cost ◽  
Bos Indicus ◽  
Snp Array ◽  
Attractive Alternative ◽  
Functional Variant ◽  
Low Pass ◽  
Low Coverage

Decreasing costs are making low coverage sequencing with imputation to a comprehensive reference panel an attractive alternative to obtain functional variant genotypes that can increase the accuracy of genomic prediction. To assess the potential of low-pass sequencing, genomic sequence of 77 steers sequenced to >10X coverage was downsampled to 1X and imputed to a reference of 946 cattle representing multiple Bos taurus and Bos indicus-influenced breeds. Genotypes for nearly 60 million variants detected in the reference were imputed from the downsampled sequence. The imputed genotypes strongly agreed with the SNP array genotypes (r¯=0.99) and the genotypes called from the transcript sequence (r¯=0.97). Effects of BovineSNP50 and GGP-F250 variants on birth weight, postweaning gain, and marbling were solved without the steers’ phenotypes and genotypes, then applied to their genotypes, to predict the molecular breeding values (MBV). The steers’ MBV were similar when using imputed and array genotypes. Replacing array variants with functional sequence variants might allow more robust MBV. Imputation from low coverage sequence offers a viable, low-cost approach to obtain functional variant genotypes that could improve genomic prediction.

scholarly journals Comparative Genome Analyses of Vibrio anguillarum Strains Reveal a Link with Pathogenicity Traits

mSystems ◽  
2017 ◽  
Vol 2 (1) ◽  
Author(s):  
Daniel Castillo ◽  
Paul D. Alvise ◽  
Ruiqi Xu ◽  
Faxing Zhang ◽  
Mathias Middelboe ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Bacterial Species ◽  
Vibrio Anguillarum ◽  
Genomic Diversity ◽  
Comparative Genome ◽  
Accessory Genome ◽  
Pan Genome ◽  
Virulent Strains ◽  
Genome Analyses ◽  
Unique Core

ABSTRACT Comparative genome analysis of strains of a pathogenic bacterial species can be a powerful tool to discover acquisition of mobile genetic elements related to virulence. Here, we compared 28 V. anguillarum strains that differed in virulence in fish larval models. By pan-genome analyses, we found that six of nine highly virulent strains had a unique core and accessory genome. In contrast, V. anguillarum strains that were medium to nonvirulent had low genomic diversity. Integration of genomic and phenotypic features provides insights into the evolution of V. anguillarum and can also be important for survey and diagnostic purposes. Vibrio anguillarum is a marine bacterium that can cause vibriosis in many fish and shellfish species, leading to high mortalities and economic losses in aquaculture. Although putative virulence factors have been identified, the mechanism of pathogenesis of V. anguillarum is not fully understood. Here, we analyzed whole-genome sequences of a collection of V. anguillarum strains and compared them to virulence of the strains as determined in larval challenge assays. Previously identified virulence factors were globally distributed among the strains, with some genetic diversity. However, the pan-genome revealed that six out of nine high-virulence strains possessed a unique accessory genome that was attributed to pathogenic genomic islands, prophage-like elements, virulence factors, and a new set of gene clusters involved in biosynthesis, modification, and transport of polysaccharides. In contrast, V. anguillarum strains that were medium to nonvirulent had a high degree of genomic homogeneity. Finally, we found that a phylogeny based on the core genomes clustered the strains with moderate to no virulence, while six out of nine high-virulence strains represented phylogenetically separate clusters. Hence, we suggest a link between genotype and virulence characteristics of Vibrio anguillarum, which can be used to unravel the molecular evolution of V. anguillarum and can also be important from survey and diagnostic perspectives. IMPORTANCE Comparative genome analysis of strains of a pathogenic bacterial species can be a powerful tool to discover acquisition of mobile genetic elements related to virulence. Here, we compared 28 V. anguillarum strains that differed in virulence in fish larval models. By pan-genome analyses, we found that six of nine highly virulent strains had a unique core and accessory genome. In contrast, V. anguillarum strains that were medium to nonvirulent had low genomic diversity. Integration of genomic and phenotypic features provides insights into the evolution of V. anguillarum and can also be important for survey and diagnostic purposes.

scholarly journals Conservation genomics of an Australian orchid complex with implications for the taxonomic and conservation status of Corybas dowlingii

2020 ◽  
Author(s):  
Natascha D. Wagner ◽  
Mark A. Clements ◽  
Lalita Simpson ◽  
Katharina Nargar
Keyword(s):  
Species Complex ◽  
Conservation Status ◽  
Taxonomic Status ◽  
Genomic Diversity ◽  
Hybrid Origin ◽  
Genetic Admixture ◽  
Conservation Genomics ◽  
Closely Related Species ◽  
Genomic Signatures ◽  
Genetic Position

AbstractThis study assessed genomic diversity in an Australian species complex in the helmet orchids to clarify taxonomic delimitation and conservation status of the threatened species Corybas dowlingii, a narrow endemic from southeast Australia. Taxonomic delimitation between the three closely related species C. aconitiflorus, C. barbarae, and C. dowlingii has been mainly based on floral traits which exhibit varying degrees of overlap, rendering species delimitation in the complex difficult. Genomic data for the species complex was generated using double-digest restriction-site associated DNA (ddRAD) sequencing. Maximum likelihood, NeighborNet, and Bayesian structure analyses showed genetic differentiation within the species complex and retrieved genomic signatures consistent with hybridisation and introgression between C. aconitiflorus and C. barbarae, and an intermediate genetic position of C. dowlingii indicating a hybrid origin of the species. The genetic structure analysis showed varying levels of genetic admixture for several C. aconitiflorus, C. barbarae, and C. dowlingii samples, thus further corroborating the presence of hybridisation and introgression within the species complex. The taxonomic status of C. dowlingii D.L.Jones was revised to C. × dowlingii D.L.Jones stat. nov. to reflect its hybrid origin. The conservation status of C. × dowlingii was assessed based on key ecological and ethical aspects, and recommendations made regarding its conservation status in Australian conservation legislation.

scholarly journals Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array

Animals ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 3469
Author(s):  
Jun Ma ◽  
Xue Gao ◽  
Junya Li ◽  
Huijiang Gao ◽  
Zezhao Wang ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
Muscle Growth ◽  
Snp Array ◽  
Cattle Breed ◽  
Principal Component ◽  
Composite Likelihood ◽  
Mechanism Analysis ◽  
Economic Traits ◽  
Selection Signatures ◽  
Genetic Features

Huaxi cattle, a specialized beef cattle breed in China, has the characteristics of fast growth, high slaughter rate, and net meat rate, good reproductive performance, strong stress resistance, and wide adaptability. In this study, we evaluated the genetic diversity, population structure, and genetic relationships of Huaxi cattle and its ancestor populations at the genome-wide level, as well as detecting the selection signatures of Huaxi cattle. Principal component analysis (PCA) and phylogenetic analysis revealed that Huaxi cattle were obviously separated from other cattle populations. The admixture analysis showed that Huaxi cattle has distinct genetic structures among all populations at K = 4. It can be concluded that Huaxi cattle has formed its own unique genetic features. Using integrated haplotype score (iHS) and composite likelihood ratio (CLR) methods, we identified 143 and 199 potentially selected genes in Huaxi cattle, respectively, among which nine selected genes (KCNK1, PDLIM5, CPXM2, CAPN14, MIR2285D, MYOF, PKDCC, FOXN3, and EHD3) related to ion binding, muscle growth and differentiation, and immunity were detected by both methods. Our study sheds light on the unique genetic feature and phylogenetic relationship of Huaxi cattle, provides a basis for the genetic mechanism analysis of important economic traits, and guides further intensive breeding improvement of Huaxi cattle.

scholarly journals Genome-wide local ancestry and direct evidence for mitonuclear co-adaptation in African hybrid cattle populations (Bos taurus/indicus)

2021 ◽  
Author(s):  
James A. Ward ◽  
Gillian P. McHugo ◽  
Michael J. Dover ◽  
Thomas J. Hall ◽  
Said Ismael Ng’ang’a ◽  
...  
Keyword(s):  
Bos Taurus ◽  
Phenotypic Diversity ◽  
Bos Indicus ◽  
Snp Array ◽  
Human Migration ◽  
Nuclear Genes ◽  
Local Ancestry ◽  
African Cattle ◽  
Mitochondrial Haplotypes ◽  
Wide Range

AbstractDomestic cattle have a key economic role in African societies, providing an important source of mobile wealth through supply of meat, milk, cowhide, fuel, transport, and traction. The phenotypic diversity of African cattle reflects adaptation to a wide range of agroecological conditions and complex patterns of admixture between the humpless Bos taurus (taurine) and humped Bos indicus (zebu) subspecies, which share a common ancestor 150-500 thousand years ago. Human migration and trade from Asia have left a peak of zebu nuclear ancestry in East Africa and most cattle populations across the continent have a hybrid genetic composition. Notwithstanding this, all African cattle possess taurine mitochondrial haplotypes, even populations with significant zebu nuclear ancestry. In this regard, the efficient functioning of the mitochondrion relies on a network of biochemical interactions between the products of 37 mitochondrial genes and more than one thousand nuclear genes; therefore, admixed African cattle represent ideal populations for evaluating mitonuclear interactions and mismatch between the nuclear and mitochondrial genomes. Using high-density SNP array data from 18 different cattle populations, including ten African admixed breeds, we find strong evidence for mitonuclear coevolution in hybrid African cattle with significant retention of Bos taurus alleles at mitochondrially-targeted nuclear genes, particularly those genes with products that directly interact with mtDNA-encoded protein subunits in OXPHOS and ribosomal complexes, or that have functions in mtDNA replication. We also show that subspecific local ancestry varies substantially across the genomes of admixed populations, with a marked signal of taurine ancestry at the major histocompatibility (MHC) gene cluster, which likely reflects adaptation to infectious disease challenges facing African livestock. Our results demonstrate that African admixed cattle represent an excellent comparative model for studying the phenotypic consequences of mitonuclear mismatch and genomic introgression in humans and other large mammals.

scholarly journals SNP panels for the estimation of dairy breed proportion and parentage assignment in African crossbred dairy cattle

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Netsanet Z. Gebrehiwot ◽  
Eva M. Strucken ◽  
Karen Marshall ◽  
Hassan Aliloo ◽  
John P. Gibson
Keyword(s):  
Allele Frequency ◽  
Bos Taurus ◽  
Low Cost ◽  
Bos Indicus ◽  
High Density ◽  
Indigenous Populations ◽  
Genetic Admixture ◽  
Genotype Data ◽  
Parentage Assignment ◽  
Snp Panels

Abstract Background Understanding the relationship between genetic admixture and phenotypic performance is crucial for the optimization of crossbreeding programs. The use of small sets of informative ancestry markers can be a cost-effective option for the estimation of breed composition and for parentage assignment in situations where pedigree recording is difficult. The objectives of this study were to develop small single nucleotide polymorphism (SNP) panels that can accurately estimate the total dairy proportion and assign parentage in both West and East African crossbred dairy cows. Methods Medium- and high-density SNP genotype data (Illumina BovineSNP50 and BovineHD Beadchip) for 4231 animals sampled from African crossbreds, African Bos taurus, European Bos taurus, Bos indicus, and African indigenous populations were used. For estimating breed composition, the absolute differences in allele frequency were calculated between pure ancestral breeds to identify SNPs with the highest discriminating power, and different combinations of SNPs weighted by ancestral origin were tested against estimates based on all available SNPs. For parentage assignment, informative SNPs were selected based on the highest minor allele frequency (MAF) in African crossbred populations assuming two Scenarios: (1) parents were selected among all the animals with known genotypes, and (2) parents were selected only among the animals known to be a parent of at least one progeny. Results For the medium-density genotype data, SNPs selected for the largest differences in allele frequency between West African indigenous and European Bos taurus breeds performed best for most African crossbred populations and achieved a prediction accuracy (r2) for breed composition of 0.926 to 0.961 with 200 SNPs. For the high-density dataset, a panel with 70% of the SNPs selected on their largest difference in allele frequency between African and European Bos taurus performed best or very near best across all crossbred populations with r2 ranging from 0.978 to 0.984 with 200 SNPs. In all African crossbred populations, unambiguous parentage assignment was possible with ≥ 300 SNPs for the majority of the panels for Scenario 1 and ≥ 200 SNPs for Scenario 2. Conclusions The identified low-cost SNP assays could overcome incomplete or inaccurate pedigree records in African smallholder systems and allow effective breeding decisions to produce progeny of desired breed composition.

scholarly journals Uncovering Sub-Structure and Genomic Profiles in Across-Countries Subpopulations of Angus Cattle

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Diercles Francisco Cardoso ◽  
Gerardo Alves Fernandes Júnior ◽  
Daiane Cristina Becker Scalez ◽  
Anderson Antonio Carvalho Alves ◽  
Ana Fabrícia Braga Magalhães ◽  
...  
Keyword(s):  
Growth Traits ◽  
Genomic Analysis ◽  
Principal Component ◽  
Divergent Selection ◽  
Genomic Diversity ◽  
Population Subdivision ◽  
Selection Signatures ◽  
Inbreeding Coefficients ◽  
Angus Cattle ◽  
Genomic Regions

Abstract Highlighting genomic profiles for geographically distinct subpopulations of the same breed may provide insights into adaptation mechanisms to different environments, reveal genomic regions divergently selected, and offer initial guidance to joint genomic analysis. Here, we characterized similarities and differences between the genomic patterns of Angus subpopulations, born and raised in Canada (N = 382) and Brazil (N = 566). Furthermore, we systematically scanned for selection signatures based on the detection of autozygosity islands common between the two subpopulations, and signals of divergent selection, via FST and varLD tests. The principal component analysis revealed a sub-structure with a close connection between the two subpopulations. The averages of genomic relationships, inbreeding coefficients, and linkage disequilibrium at varying genomic distances were rather similar across them, suggesting non-accentuated differences in overall genomic diversity. Autozygosity islands revealed selection signatures common to both subpopulations at chromosomes 13 (63.77–65.25 Mb) and 14 (22.81–23.57 Mb), which are notably known regions affecting growth traits. Nevertheless, further autozygosity islands along with FST and varLD tests unravel particular sites with accentuated population subdivision at BTAs 7 and 18 overlapping with known QTL and candidate genes of reproductive performance, thermoregulation, and resistance to infectious diseases. Our findings indicate overall genomic similarity between Angus subpopulations, with noticeable signals of divergent selection in genomic regions associated with the adaptation in different environments.

scholarly journals The Tangent copy-number inference pipeline for cancer genome analyses

2019 ◽  
Author(s):  
Barbara Tabak ◽  
Gordon Saksena ◽  
Coyin Oh ◽  
Galen F. Gao ◽  
Barbara Hill Meyers ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Copy Number ◽  
Signal To Noise Ratio ◽  
Snp Array ◽  
Cancer Genome ◽  
The Cancer Genome Atlas ◽  
Sequencing Data ◽  
Array Data ◽  
Link Type ◽  
Genome Analyses

AbstractMotivationSomatic copy-number alterations (SCNAs) play an important role in cancer development. Systematic noise in sequencing and array data present a significant challenge to the inference of SCNAs for cancer genome analyses. As part of The Cancer Genome Atlas (TCGA), the Broad Institute Genome Characterization Center developed the Tangent copy-number inference pipeline to generate copy-number profiles using single-nucleotide polymorphism (SNP) array and whole-exome sequencing (WES) data from over 10,000 pairs of tumors and matched normal samples. Here, we describe the Tangent pipeline, which begins with DNA sequencing data in the form of .bam files or raw SNP array probe-level intensity data, and ends with segmented copy-number calls to facilitate the identification of novel genes potentially targeted by SCNAs. We also describe a modification of Tangent, Pseudo-Tangent, which enables denoising through comparisons between tumor profiles when few normal samples are available.ResultsTangent Normalization offers substantial signal-to-noise ratio (SNR) improvements compared to conventional normalization methods in both SNP array and WES analyses. The improvement in SNRs is achieved primarily through noise reduction with minimal effect on signal. Pseudo-Tangent also reduces noise when few normal samples are available. Tangent and Pseudo-Tangent are broadly applicable and enable more accurate inference of SCNAs from DNA sequencing and array data.Availability and ImplementationTangent is available at https://github.com/coyin/tangent and as a Docker image (https://hub.docker.com/r/coyin/tangent). Tangent is also the normalization method for the Copy Number pipeline in Genome Analysis Toolkit 4 (GATK4)[email protected], [email protected], [email protected]

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