Genomic analysis reveals selection for Asian genes in European pigs following human-mediated introgression
Bosse, M. ; Megens, H.J.W.C. ; Frantz, L.A.F. ; Madsen, O. ; Paudel, Y. ; Duijvestein, N. ; Crooijmans, R.P.M.A. ; Groenen, M. - \ 2014
Nature Communications 5 (2014). - ISSN 2041-1723 - 8 p.
hydrocarbon dioxin receptor - recent positive selection - haplotype structure - molecular characterization - reproductive traits - domestic pig - wide snp - evolution - models - polymorphisms
The independent domestication of local wild boar populations in Asia and Europe about 10,000 years ago led to distinct European and Asian pig breeds, each with very different phenotypic characteristics. During the Industrial Revolution, Chinese breeds were imported to Europe to improve commercial traits in European breeds. Here we demonstrate the presence of introgressed Asian haplotypes in European domestic pigs and selection signatures on some loci in these regions, using whole genome sequence data. The introgression signatures are widespread and the Asian haplotypes are rarely fixed. The Asian introgressed haplotypes are associated with regions harbouring genes involved in meat quality, development and fertility. We identify Asian-derived non-synonymous mutations in the ¿AHR gene that associate with increased litter size in multiple European commercial lines. These findings demonstrate that increased fertility was an important breeding goal for early nineteenth century pig farmers, and that Asian variants of genes related to this trait were preferentially selected during the development of modern European pig breeds.
Genome-wide association studies for Agronomical Traits in a world wide Spring Barley Collection
Pasam, R.K. ; Sharma, R. ; Malosetti, M. ; Eeuwijk, F.A. van; Haseneyer, G. ; Kilian, B. ; Graner, A. - \ 2012
BMC Plant Biology 12 (2012). - ISSN 1471-2229
multilocus genotype data - hordeum-vulgare l. - linkage disequilibrium - population-structure - complex traits - flowering time - qtl analysis - missing heritability - haplotype structure - genetic diversity
Background Genome-wide association studies (GWAS) based on linkage disequilibrium (LD) provide a promising tool for the detection and fine mapping of quantitative trait loci (QTL) underlying complex agronomic traits. In this study we explored the genetic basis of variation for the traits heading date, plant height, thousand grain weight, starch content and crude protein content in a diverse collection of 224 spring barleys of worldwide origin. The whole panel was genotyped with a customized oligonucleotide pool assay containing 1536 SNPs using Illumina's GoldenGate technology resulting in 957 successful SNPs covering all chromosomes. The morphological trait "row type" (two-rowed spike vs. six-rowed spike) was used to confirm the high level of selectivity and sensitivity of the approach. This study describes the detection of QTL for the above mentioned agronomic traits by GWAS. Results Population structure in the panel was investigated by various methods and six subgroups that are mainly based on their spike morphology and region of origin. We explored the patterns of linkage disequilibrium (LD) among the whole panel for all seven barley chromosomes. Average LD was observed to decay below a critical level (r2-value 0.2) within a map distance of 5-10 cM. Phenotypic variation within the panel was reasonably large for all the traits. The heritabilities calculated for each trait over multi-environment experiments ranged between 0.90-0.95. Different statistical models were tested to control spurious LD caused by population structure and to calculate the P-value of marker-trait associations. Using a mixed linear model with kinship for controlling spurious LD effects, we found a total of 171 significant marker trait associations, which delineate into 107 QTL regions. Across all traits these can be grouped into 57 novel QTL and 50 QTL that are congruent with previously mapped QTL positions. Conclusions Our results demonstrate that the described diverse barley panel can be efficiently used for GWAS of various quantitative traits, provided that population structure is appropriately taken into account. The observed significant marker trait associations provide a refined insight into the genetic architecture of important agronomic traits in barley. However, individual QTL account only for a small portion of phenotypic variation, which may be due to insufficient marker coverage and/or the elimination of rare alleles prior to analysis. The fact that the combined SNP effects fall short of explaining the complete phenotypic variance may support the hypothesis that the expression of a quantitative trait is caused by a large number of very small effects that escape detection. Notwithstanding these limitations, the integration of GWAS with biparental linkage mapping and an ever increasing body of genomic sequence information will facilitate the systematic isolation of agronomically important genes and subsequent analysis of their allelic diversity
Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin
Comodran, J. ; Thomas, W.T.B. ; Eeuwijk, F.A. van; Ceccarelli, S. ; Grando, S. ; Stanca, A.M. ; Pecchioni, N. ; Akar, T. ; Al-Yassin, A. ; Benbelkacem, A. ; Ouabbou, H. ; Bort, J. ; Romagosa, I. ; Hackett, C.A. ; Russel, J.R. - \ 2009
Theoretical and Applied Genetics 119 (2009)1. - ISSN 0040-5752 - p. 175 - 187.
multilocus genotype data - ssp-spontaneum - haplotype structure - powdery mildew - barley - genome - resistance - loci - polymorphism - cultivars
Population structure and genome-wide linkage disequilibrium (LD) were investigated in 192 Hordeum vulgare accessions providing a comprehensive coverage of past and present barley breeding in the Mediterranean basin, using 50 nuclear microsatellite and 1,130 DArT® markers. Both clustering and principal coordinate analyses clearly sub-divided the sample into five distinct groups centred on key ancestors and regions of origin of the germplasm. For given genetic distances, large variation in LD values was observed, ranging from closely linked markers completely at equilibrium to marker pairs at 50 cM separation still showing significant LD. Mean LD values across the whole population sample decayed below r 2 of 0.15 after 3.2 cM. By assaying 1,130 genome-wide DArT® markers, we demonstrated that, after accounting for population substructure, current genome coverage of 1 marker per 1.5 cM except for chromosome 4H with 1 marker per 3.62 cM is sufficient for whole genome association scans. We show, by identifying associations with powdery mildew that map in genomic regions known to have resistance loci, that associations can be detected in strongly stratified samples provided population structure is effectively controlled in the analysis. The population we describe is, therefore, shown to be a valuable resource, which can be used in basic and applied research in barley
Association mapping of quality traits in potato (Solanum tuberosum L.)
hoop, B.B. D'; Paulo, M.J. ; Mank, R. ; Eck, H.J. van; Eeuwijk, F.A. van - \ 2008
Euphytica 161 (2008)1-2. - ISSN 0014-2336 - p. 47 - 60.
late blight resistance - phytophthora-infestans mont. - spring barley cultivars - linkage disequilibrium - diploid potato - population-structure - genetic-linkage - arabidopsis-thaliana - haplotype structure - tetraploid potato
In this paper, we describe the assessment of linkage disequilibrium and its decay in a collection of potato cultivars. In addition, we report on a simple regression based association mapping approach and its results to quality traits in potato. We selected 221 tetraploid potato cultivars and progenitor lines, representing the global diversity in potato, with emphasis on genetic variation for agro-morphological and quality traits. Phenotypic data for these agro-morphological and quality traits were obtained from recent trials performed by five breeding companies. The collection was genotyped with 250 AFLP® markers from five primer combinations. The genetic position of a subset of the markers could be inferred from an ultra dense potato map. Decay of linkage disequilibrium was estimated by calculating the squared correlation between pairs of markers using marker band intensities. Marker-trait associations were investigated by fitting single marker regression models for phenotypic traits on marker band intensities with and without correction for population structure. The paper illustrates the potential of association mapping in tetraploid potato, because existing phenotypic data, a modest number of AFLP markers, and a relatively simple statistical analysis, allowed identifying interesting associations.
Genetic resources, genome mapping and evolutionary genomics of the pig (Sus scrofa)
Chen, K. ; Baxter, T. ; Muir, W.M. ; Groenen, M.A.M. ; Schook, L.B. - \ 2007
International Journal of Biological Sciences 3 (2007)3. - ISSN 1449-2288 - p. 153 - 165.
mitochondrial-dna sequence - increased ovulation rate - radiation hybrid panel - pre-messenger-rna - microsatellite markers - natural-selection - phylogenetic-relationships - chromosome evolution - haplotype structure - mammalian genomes
The pig, a representative of the artiodactyla clade, is one of the first animals domesticated, and has become an important agriculture animal as one of the major human nutritional sources of animal based protein. The pig is also a valuable biomedical model organism for human health. The pig's importance to human health and nutrition is reflected in the decision to sequence its genome (3X). As an animal species with its wild ancestors present in the world, the pig provides a unique opportunity for tracing mammalian evolutionary history and defining signatures of selection resulting from both domestication and natural selection. Completion of the pig genome sequencing project will have significant impacts on both agriculture and human health. Following the pig whole genome sequence drafts, along with large-scale polymorphism data, it will be possible to conduct genome sweeps using association mapping, and identify signatures of selection. Here, we provide a description of the pig genome sequencing project and perspectives on utilizing genomic technologies to exploit pig genome evolution and the molecular basis for phenotypic traits for improving pig production and health.