Mutation dynamics of CpG dinucleotides during a recent event of vertebrate diversification
Pértille, Fábio ; Silva, Vinicius da; Johansson, Anna M. ; Lindström, Tom ; Wright, Dominic ; Luiz da Costa Coutinho, Heitor da; Jensen, Per ; Guerrero-Bosagna, Carlos - \ 2019
PRJEB29249 - ERP111539 - genetic variation - DNA methylation - CpG - single nucleotide polymorphisms - copy number variations - germ line - Gallus gallus
Mutation dynamics of CpG dinucleotides during a recent event of vertebrate diversification
Pértille, Fábio ; Silva, Vinicius H. Da; Johansson, Anna M. ; Lindström, Tom ; Wright, Dominic ; Coutinho, Luiz L. ; Jensen, Per ; Guerrero-Bosagna, Carlos - \ 2019
Epigenetics 14 (2019)7. - ISSN 1559-2294 - p. 685 - 707.
copy number variations - CpG - DNA methylation - Gallus gallus - genetic variation - germ line - single nucleotide polymorphisms
DNA methylation in CpGs dinucleotides is associated with high mutability and disappearance of CpG sites during evolution. Although the high mutability of CpGs is thought to be relevant for vertebrate evolution, very little is known on the role of CpG-related mutations in the genomic diversification of vertebrates. Our study analysed genetic differences in chickens, between Red Junglefowl (RJF; the living closest relative to the ancestor of domesticated chickens) and domesticated breeds, to identify genomic dynamics that have occurred during the process of their domestication, focusing particularly on CpG-related mutations. Single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) between RJF and these domesticated breeds were assessed in a reduced fraction of their genome. Additionally, DNA methylation in the same fraction of the genome was measured in the sperm of RJF individuals to identify possible correlations with the mutations found between RJF and the domesticated breeds. Our study shows that although the vast majority of CpG-related mutations found relate to CNVs, CpGs disproportionally associate to SNPs in comparison to CNVs, where they are indeed substantially under-represented. Moreover, CpGs seem to be hotspots of mutations related to speciation. We suggest that, on the one hand, CpG-related mutations in CNV regions would promote genomic ‘flexibility’ in evolution, i.e., the ability of the genome to expand its functional possibilities; on the other hand, CpG-related mutations in SNPs would relate to genomic ‘specificity’ in evolution, thus, representing mutations that would associate with phenotypic traits relevant for speciation.
Integrated linkage map of haliotis midae linnaeus based on microsatellite and SNP markers
Vervalle, Jessica ; Hepple, Juli Ann ; Jansen, Suzaan ; Plessis, Jana Du ; Wang, Peizheng ; Rhode, Clint ; Roodt-Wilding, Rouvay - \ 2013
Journal of Shellfish Research 32 (2013)1. - ISSN 0730-8000 - p. 89 - 103.
abalone - Haliotis midae - linkage map - microsatellites - single nucleotide polymorphisms
The South African abalone Haliotis midae Linnaeus is the most important aquaculture species in South Africa. Marker-assisted selection is envisioned to play an integral part of the genetic improvement program of abalone, and therefore the generation of linkage maps for quantitative trait loci analyses are necessary. This study reports on a first-generation linkage map for H. midae based on microsatellite and single nucleotide polymorphism (SNP) markers. Ten full-sib families were screened with a total of 508 molecular markers derived from genomic and expressed sequence tag sequences. Linkage maps were constructed for each of the families and combined to create an integrated linkage map. The integrated linkage map consists of 186 markers that included 116 microsatellites and 70 SNPs. These markers mapped to 18 linkage groups, which corresponds to the haploid chromosome number of H. midae. The average genome length was estimated at 1,312 cM, displaying an average marker interval of 6.88 cM with 80% genome coverage. The female map is 1.16-fold longer than the male map, indicating differences in recombination rate between the sexes. The association of markers with known genes as well as with transposon elements was also investigated. This study resulted in the first linkage map constructed for any haliotid in which both microsatellite and SNP markers were used, and the results provide a framework for future applications in quantitative trait loci identification.
Genetic diversity and structure in a collection of tulip cultivars assessed by SNP markers
Tang, N. ; Shahin, A. ; Bijman, P.J.J. ; Liu, J. ; Tuyl, J.M. van; Arens, P. - \ 2013
Scientia Horticulturae 161 (2013). - ISSN 0304-4238 - p. 286 - 292.
single nucleotide polymorphisms - population-structure - genome - identification - conservation - liliaceae - program - power
Although tulip is one of the most important bulbous crops worldwide, the genetic background of most cultivars is unclear at present. The purposes of this study are to investigate genetic diversity and to identify the genetic structure and relationships among tulip cultivars. A total of 236 polymorphic single nucleotide polymorphisms (SNPs) were obtained from 'Kees Nelis' and 'Cantata', from which 121 SNPs with a minor allele frequency above 0.1 were selected for genetic analysis. The total observed heterozygosity (Ho) among the 72 accessions was 0.35, Ho of cultivar groups ranged from 0.22 (Tulipa fosteriana) to 0.43 (Tulipa gesneriana x T. fosteriana hybrids). Rather small genetic distances were found among T. gesneriana cultivar groups which are defined according to flowering time and morphology. In both PCoA (principle coordinate analysis) and STRUCTURE analysis, the 72 accessions were separated into three clusters (F-ST =0.208, P
Genetic relationships in an international collection of Puccinia horiana isolates based on newly identified molecular markers and demonstration of recombination
Backer, M. de; Bonants, P.J.M. ; Pedley, K.F. ; Maes, M. ; Roldan-Ruiz, I. ; Bockstaele, E. van; Heungens, K. ; Lee, T.A.J. van der - \ 2013
Phytopathology 103 (2013)11. - ISSN 0031-949X - p. 1169 - 1179.
chrysanthemum white rust - multilocus genotype data - single nucleotide polymorphisms - whole genome amplification - f-sp tritici - parentage analysis - computer-program - x morifolium - resistance - pathogens
The obligate biotrophic pathogen Puccinia horiana is the causal agent of chrysanthemum white rust. Although P. horiana is a quarantine organism, it has been able to spread to most chrysanthemum-producing regions in the world since the 1960s; however, the transfer routes are largely obscure. An extremely low level of allelic diversity was observed in a geographically diverse set of eight isolates using complexity reduction of polymorphic sequences (CRoPS) technology. Only 184 of the 16,196 contigs (1.1%) showed one or more single-nucleotide polymorphisms (SNPs). Thirty-two SNPs and one simple-sequence repeat were translated into molecular markers and used to genotype 45 isolates originating from North and South America, Asia, and Europe. In most cases, phylogenetic clustering was related to geographic origin, indicating local establishment. The European isolates mostly grouped in two major populations that may relate to the two historic introductions previously reported. However, evidence of recent geographic transfer was also observed, including transfer events between Europe and South America and between Southeast Asia and Europe. In contrast with the presumed clonal propagation of this microcyclic rust, strong indications of marker recombination were observed, presumably as a result of anastomosis, karyogamy, and somatic meiosis. Recombination and transfer also explain the geographic dispersal of specific markers. A near-to-significant correlation between the genotypic data and previously obtained pathotype data was observed and one marker was associated with the most virulent pathotype group. In combination with a fast SNP detection method, the markers presented here will be helpful tools to further elucidate the transfer pathways and local survival of this pathogen
Whole-genome regression and prediction methods applied to plant and animal breeding
Los Campos, G. De; Hickey, J.M. ; Pong-Wong, R. ; Daetwyler, H.D. ; Calus, M.P.L. - \ 2013
Genetics 193 (2013)2. - ISSN 0016-6731 - p. 327 - 345.
marker-assisted selection - quantitative trait locus - genetic-relationship information - single nucleotide polymorphisms - linear unbiased prediction - dense molecular markers - dairy-cattle - variable selection - reference population - beef-cattle
Genomic-enabled prediction is becoming increasingly important in animal and plant breeding, and is also receiving attention in human genetics. Deriving accurate predictions of complex traits requires implementing whole-genome regression (WGR) models where phenotypes are regressed on thousands of markers concurrently. Following the groundbreaking contribution of MEUWISSEN et al. (2001) several methods have been proposed and evaluated, and genome-enabled selection (GS) is being implemented in several plant and animal breeding programs. The list of methods is long, and the relationships between the available methods have not been fully addressed. In this article we provide an overview of available methods for implementing parametric WGR models, discuss selected topics which emerge in the application of these methods and present a general discussion of lessons learnt from simulation and empirical data analysis in the last decade
Genome-wide association study to identify chromosomal regions associated with antibody response to Mycobacterium avium subspecies paratuberculosis in milk of Dutch Holstein-Friesians
Hulzen, K.J.E. van; Schopen, G.C.B. ; Arendonk, J.A.M. van; Nielen, M. ; Koets, A.P. ; Schrooten, C. ; Heuven, H.C.M. - \ 2012
Journal of Dairy Science 95 (2012)5. - ISSN 0022-0302 - p. 2740 - 2748.
single nucleotide polymorphisms - estimated breeding values - quantitative trait loci - genetic-variation - johnes-disease - linkage disequilibrium - short-communication - us holsteins - infection - cattle
Heritability of susceptibility to Johne's disease in cattle has been shown to vary from 0.041 to 0.159. Although the presence of genetic variation involved in susceptibility to Johne's disease has been demonstrated, the understanding of genes contributing to the genetic variance is far from complete. The objective of this study was to contribute to further understanding of genetic variation involved in susceptibility to Johne's disease by identifying associated chromosomal regions using a genome-wide association approach. Log-transformed ELISA test results of 265,290 individual Holstein-Friesian cows from 3,927 herds from the Netherlands were analyzed to obtain sire estimated breeding values for Mycobacterium avium subspecies paratuberculosis (MAP)-specific antibody response in milk using a sire-maternal grandsire model with fixed effects for parity, year of birth, lactation stage, and herd; a covariate for milk yield on test day; and random effects for sire, maternal grandsire, and error. For 192 sires with estimated breeding values with a minimum reliability of 70%, single nucleotide polymorphism (SNP) typing was conducted by a multiple SNP analysis with a random polygenic effect fitting 37,869 SNP simultaneously. Five SNP associated with MAP-specific antibody response in milk were identified distributed over 4 chromosomal regions (chromosome 4, 15, 18, and 28). Thirteen putative SNP associated with MAP-specific antibody response in milk were identified distributed over 10 chromosomes (chromosome 4, 14, 16, 18, 19, 20, 21, 26, 27, and 29). This knowledge contributes to the current understanding of genetic variation involved in Johne's disease susceptibility and facilitates control of Johne's disease and improvement of health status by breeding.
Genome-wide associations for feed utilisation complex in primiparous Holstein–Friesian dairy cows from experimental research herds in four European countries
Veerkamp, R.F. ; Coffey, M.P. ; Berry, D.P. ; Haas, Y. de; Strandberg, E. ; Bovenhuis, H. ; Calus, M.P.L. ; Wall, E. - \ 2012
Animal 6 (2012)11. - ISSN 1751-7311 - p. 1738 - 1749.
body condition score - single nucleotide polymorphisms - leptin gene polymorphisms - growth-hormone-receptor - milk-production traits - dry-matter intake - energy-balance - performance traits - live weight - food-intake
Genome-wide association studies for difficult-to-measure traits are generally limited by the sample size with accurate phenotypic data. The objective of this study was to utilise data on primiparous Holstein–Friesian cows from experimental farms in Ireland, the United Kingdom, the Netherlands and Sweden to identify genomic regions associated with the feed utilisation complex: fat and protein corrected milk yield (FPCM), dry matter intake (DMI), body condition score (BCS) and live-weight (LW). Phenotypic data and 37 590 single nucleotide polymorphisms (SNPs) were available on up to 1629 animals. Genetic parameters of the traits were estimated using a linear animal model with pedigree information, and univariate genome-wide association analyses were undertaken using Bayesian stochastic search variable selection performed using Gibbs sampling. The variation in the phenotypes explained by the SNPs on each chromosome was related to the size of the chromosome and was relatively consistent for each trait with the possible exceptions of BTA4 for BCS, BTA7, BTA13, BTA14, BTA18 for LW and BTA27 for DMI. For LW, BCS, DMI and FPCM, 266, 178, 206 and 254 SNPs had a Bayes factor >3, respectively. Olfactory genes and genes involved in the sensory smell process were overrepresented in a 500 kbp window around the significant SNPs. Potential candidate genes were involved with functions linked to insulin, epidermal growth factor and tryptophan