Genome-wide SNP Genotyping Resolves Signatures of Selection and Tetrasomic Recombination in Peanut

Abstract Background Runs of homozygosity (ROH) have become the state-of-the-art method for analysis of inbreeding in animal populations. Moreover, ROH are suited to detect signatures of selection via ROH islands and are used in other applications, such as genomic prediction and genome-wide association studies (GWAS). Currently, a vast amount of single nucleotide polymorphism (SNP) data is available online, but most of these data have never been used for ROH analysis. Therefore, we performed a ROH analysis on large medium-density SNP datasets in eight animal species (cat, cattle, dog, goat, horse, pig, sheep and water buffalo; 442 different populations) and make these results publicly available. Results The results include an overview of ROH islands per population and a comparison of the incidence of these ROH islands among populations from the same species, which can assist researchers when studying other (livestock) populations or when looking for similar signatures of selection. We were able to confirm many known ROH islands, for example signatures of selection for the myostatin (MSTN) gene in sheep and horses. However, our results also included multiple other ROH islands, which are common to many populations and not identified to date (e.g. on chromosomes D4 and E2 in cats and on chromosome 6 in sheep). Conclusions We are confident that our repository of ROH islands is a valuable reference for future studies. The discovered ROH island regions represent a unique starting point for new studies or can be used as a reference for future studies. Furthermore, we encourage authors to add their population-specific ROH findings to our repository.

Download Full-text

Determination of Genetic Structure and Signatures of Selection in Three Strains of Tanzania Shorthorn Zebu, Boran and Friesian Cattle by Genome-Wide SNP Analyses

PLoS ONE ◽

10.1371/journal.pone.0171088 ◽

2017 ◽

Vol 12 (1) ◽

pp. e0171088 ◽

Cited By ~ 7

Author(s):

George Msalya ◽

Eui-Soo Kim ◽

Emmanuel L. K. Laisser ◽

Maulilio J. Kipanyula ◽

Esron D. Karimuribo ◽

...

Keyword(s):

Genetic Structure ◽

Genome Wide ◽

Signatures Of Selection ◽

Friesian Cattle

Download Full-text

Combination of microRNA expression profiling with genome-wide SNP genotyping to construct a coronary artery disease-related miRNA-miRNA synergistic network

BioScience Trends ◽

10.5582/bst.2014.01031 ◽

2014 ◽

Vol 8 (6) ◽

pp. 297-307 ◽

Cited By ~ 8

Author(s):

Lin Hua ◽

Hong Xia ◽

Ping Zhou ◽

Dongguo Li ◽

Lin Li

Keyword(s):

Coronary Artery Disease ◽

Coronary Artery ◽

Expression Profiling ◽

Snp Genotyping ◽

Microrna Expression ◽

Genome Wide ◽

Artery Disease

Download Full-text

A Whole Genome Re-Sequencing Based GWA Analysis Reveals Candidate Genes Associated with Ivermectin Resistance in Haemonchus contortus

Genes ◽

10.3390/genes11040367 ◽

2020 ◽

Vol 11 (4) ◽

pp. 367 ◽

Cited By ~ 4

Author(s):

Sawar Khan ◽

Ayesha Nisar ◽

Jianqi Yuan ◽

Xiaoping Luo ◽

Xueqin Dou ◽

...

Keyword(s):

Candidate Genes ◽

Haemonchus Contortus ◽

Population Genomics ◽

Small Ruminants ◽

Track Record ◽

Genome Wide ◽

Signatures Of Selection ◽

Parasitic Worms ◽

Important Parasite

The most important and broad-spectrum drug used to control the parasitic worms to date is ivermectin (IVM). Resistance against IVM has emerged in parasites, and preserving its efficacy is now becoming a serious issue. The parasitic nematode Haemonchus contortus (Rudolphi, 1803) is economically an important parasite of small ruminants across the globe, which has a successful track record in IVM resistance. There are growing evidences regarding the multigenic nature of IVM resistance, and although some genes have been proposed as candidates of IVM resistance using lower magnification of genome, the genetic basis of IVM resistance still remains poorly resolved. Using the full magnification of genome, we herein applied a population genomics approach to characterize genome-wide signatures of selection among pooled worms from two susceptible and six ivermectin-resistant isolates of H. contortus, and revealed candidate genes under selection in relation to IVM resistance. These candidates also included a previously known IVM-resistance-associated candidate gene HCON_00148840, glc-3. Finally, an RNA-interference-based functional validation assay revealed the HCON_00143950 as IVM-tolerance-associated gene in H. contortus. The possible role of this gene in IVM resistance could be detoxification of xenobiotic in phase I of xenobiotic metabolism. The results of this study further enhance our understanding on the IVM resistance and continue to provide further evidence in favor of multigenic nature of IVM resistance.

Download Full-text

Genome-wide association study and scan for signatures of selection point to candidate genes for body temperature maintenance under the cold stress in Siberian cattle populations

BMC Genetics ◽

10.1186/s12863-019-0725-0 ◽

2019 ◽

Vol 20 (S1) ◽

Cited By ~ 5

Author(s):

Alexander V. Igoshin ◽

Andrey A. Yurchenko ◽

Nadezhda M. Belonogova ◽

Dmitry V. Petrovsky ◽

Ruslan B. Aitnazarov ◽

...

Keyword(s):

Body Temperature ◽

Cold Stress ◽

Association Study ◽

Candidate Genes ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide ◽

Signatures Of Selection

Download Full-text

GenomegaMap: Within-Species Genome-Wide dN/dS Estimation from over 10,000 Genomes

Molecular Biology and Evolution ◽

10.1093/molbev/msaa069 ◽

2020 ◽

Vol 37 (8) ◽

pp. 2450-2460 ◽

Cited By ~ 3

Author(s):

Daniel J Wilson ◽

Derrick W Crook ◽

Timothy E A Peto ◽

A Sarah Walker ◽

Sarah J Hoosdally ◽

...

Keyword(s):

Protein A ◽

Large Data ◽

Large Data Sets ◽

Data Sets ◽

Protein Coding ◽

Dead Box ◽

Coalescent Simulations ◽

Genome Wide ◽

Signature Of Selection ◽

Signatures Of Selection

Abstract The dN/dS ratio provides evidence of adaptation or functional constraint in protein-coding genes by quantifying the relative excess or deficit of amino acid-replacing versus silent nucleotide variation. Inexpensive sequencing promises a better understanding of parameters, such as dN/dS, but analyzing very large data sets poses a major statistical challenge. Here, I introduce genomegaMap for estimating within-species genome-wide variation in dN/dS, and I apply it to 3,979 genes across 10,209 tuberculosis genomes to characterize the selection pressures shaping this global pathogen. GenomegaMap is a phylogeny-free method that addresses two major problems with existing approaches: 1) It is fast no matter how large the sample size and 2) it is robust to recombination, which causes phylogenetic methods to report artefactual signals of adaptation. GenomegaMap uses population genetics theory to approximate the distribution of allele frequencies under general, parent-dependent mutation models. Coalescent simulations show that substitution parameters are well estimated even when genomegaMap’s simplifying assumption of independence among sites is violated. I demonstrate the ability of genomegaMap to detect genuine signatures of selection at antimicrobial resistance-conferring substitutions in Mycobacterium tuberculosis and describe a novel signature of selection in the cold-shock DEAD-box protein A gene deaD/csdA. The genomegaMap approach helps accelerate the exploitation of big data for gaining new insights into evolution within species.

Download Full-text