ÖC

Örjan Carlborg

Uppsala University

Author Statistics

Papers

Citation

H-Index

i-10 index

Research Trends

Author Order

Document Type

Co-Authors

P.B. Siegel

Virginia Tech

Leif Andersson

Uppsala University

Christa F. Honaker

Virginia Tech

Yanjun Zan

Chinese Academy of Agricultural Sciences

François Besnier

Norwegian Institute of Marine Research

Xia Shen

University of Edinburgh

Mats E. Pettersson

Blekinge Institute of Technology

Lars Rönnegård

University of New England

Zheya Sheng

Huazhong Agricultural University

Simon K. G. Forsberg

Uppsala University

Cooperative Institutions

Uppsala University

Swedish University of Agricultural Sciences

Science for Life Laboratory

Karolinska Institutet

China Agricultural University

University of Copenhagen

Howard Hughes Medical Institute

Institute of Cytology and Genetics

Max Planck Institute for Evolutionary Anthropology

Genomics (United Kingdom)

Author Statistics

Papers

Citation

H-Index

i-10 index

Research Field

Strong signatures of selection in the domestic pig genome

Proceedings of the National Academy of Sciences (2012)

Carl‐Johan Rubin Hendrik‐Jan Megens Álvaro Martínez Barrio Khurram Maqbool Shumaila Sayyab

Domestication of wild boar ( Sus scrofa ) and subsequent selection have resulted in dramatic phenotypic changes in domestic pigs for a number of traits, including behavior, body composition, reproduction, and coat color. Here we have used whole-genome resequencing to reveal some of the loci that underlie phenotypic evolution in European domestic pigs. Selective sweep analyses revealed strong signatures of selection at three loci harboring quantitative trait loci that explain a considerable part of one of the most characteristic morphological changes in the domestic pig—the elongation of the back and an increased number of vertebrae. The three loci were associated with the NR6A1, PLAG1 , and LCORL genes. The latter two have repeatedly been associated with loci controlling stature in other domestic animals and in humans. Most European domestic pigs are homozygous for the same haplotype at these three loci. We found an excess of derived nonsynonymous substitutions in domestic pigs, most likely reflecting both positive selection and relaxed purifying selection after domestication. Our analysis of structural variation revealed four duplications at the KIT locus that were exclusively present in white or white-spotted pigs, carrying the Dominant white , Patch , or Belt alleles. This discovery illustrates how structural changes have contributed to rapid phenotypic evolution in domestic animals and how alleles in domestic animals may evolve by the accumulation of multiple causative mutations as a response to strong directional selection.

Coat

Nonsynonymous substitution

Domestic pig

Selective sweep

Phenotypic trait

Directional selection

Negative selection

10.1073/pnas.1217149109

Cite

Citations (586)

How To Perform Meaningful Estimates of Genetic Effects

PLoS Genetics (2008)

José M. Álvarez-Castro Arnaud Le Rouzic Örjan Carlborg

Although the genotype-phenotype map plays a central role both in Quantitative and Evolutionary Genetics, the formalization of a completely general and satisfactory model of genetic effects, particularly accounting for epistasis, remains a theoretical challenge. Here, we use a two-locus genetic system in simulated populations with epistasis to show the convenience of using a recently developed model, NOIA, to perform estimates of genetic effects and the decomposition of the genetic variance that are orthogonal even under deviations from the Hardy-Weinberg proportions. We develop the theory for how to use this model in interval mapping of quantitative trait loci using Halley-Knott regressions, and we analyze a real data set to illustrate the advantage of using this approach in practice. In this example, we show that departures from the Hardy-Weinberg proportions that are expected by sampling alone substantially alter the orthogonal estimates of genetic effects when other statistical models, like F2 or G2A, are used instead of NOIA. Finally, for the first time from real data, we provide estimates of functional genetic effects as sets of effects of natural allele substitutions in a particular genotype, which enriches the debate on the interpretation of genetic effects as implemented both in functional and in statistical models. We also discuss further implementations leading to a completely general genotype-phenotype map.

Epistasis

genetic model

Quantitative Genetics

Trait

Genetic data

10.1371/journal.pgen.1000062

Cite

Citations (39)

Researching on the fine structure and admixture of the worldwide chicken population reveal connections between populations and important events in breeding history

Evolutionary Applications (2021)

Ying Guo Jen‐Hsiang Ou Yanjun Zan Yuzhe Wang Huifang Li

Here, we have evaluated the general genomic structure and diversity and studied the divergence resulting from selection and historical admixture events for a collection of worldwide chicken breeds. In total, 636 genomes (43 populations) were sequenced from chickens of American, Chinese, Indonesian, and European origin. Evaluated populations included wild junglefowl, rural indigenous chickens, breeds that have been widely used to improve modern western poultry populations and current commercial stocks bred for efficient meat and egg production. In-depth characterizations of the genome structure and genomic relationships among these populations were performed, and population admixture events were investigated. In addition, the genomic architectures of several domestication traits and central documented events in the recent breeding history were explored. Our results provide detailed insights into the contributions from population admixture events described in the historical literature to the genomic variation in the domestic chicken. In particular, we find that the genomes of modern chicken stocks used for meat production both in eastern (Asia) and western (Europe/US) agriculture are dominated by contributions from heavy Asian breeds. Further, by exploring the link between genomic selective divergence and pigmentation, connections to functional genes feather coloring were confirmed.

Population genomics

Demographic history

Genetic admixture

10.1111/eva.13241

Cite

Citations (24)

Genetic Regulation of Transcriptional Variation in NaturalArabidopsis thalianaAccessions

G3 Genes Genomes Genetics (2016)

Yanjun Zan Xia Shen Simon K. G. Forsberg Örjan Carlborg

An increased knowledge of the genetic regulation of expression in Arabidopsis thaliana is likely to provide important insights about the basis of the plant's extensive phenotypic variation. Here, we reanalyzed two publicly available datasets with genome-wide data on genetic and transcript variation in large collections of natural A. thaliana accessions. Transcripts from more than half of all genes were detected in the leaves of all accessions, and from nearly all annotated genes in at least one accession. Thousands of genes had high transcript levels in some accessions, but no transcripts at all in others, and this pattern was correlated with the genome-wide genotype. In total, 2669 eQTL were mapped in the largest population, and 717 of them were replicated in the other population. A total of 646 cis-eQTL-regulated genes that lacked detectable transcripts in some accessions was found, and for 159 of these we identified one, or several, common structural variants in the populations that were shown to be likely contributors to the lack of detectable RNA transcripts for these genes. This study thus provides new insights into the overall genetic regulation of global gene expression diversity in the leaf of natural A. thaliana accessions. Further, it also shows that strong cis-acting polymorphisms, many of which are likely to be structural variations, make important contributions to the transcriptional variation in the worldwide A. thaliana population.

10.1534/g3.116.030874

Cite

Citations (25)

Statistical Epistasis Is a Generic Feature of Gene Regulatory Networks

Genetics (2006)

Arne B. Gjuvsland Ben J. Hayes Stig W. Omholt Örjan Carlborg

Functional dependencies between genes are a defining characteristic of gene networks underlying quantitative traits. However, recent studies show that the proportion of the genetic variation that can be attributed to statistical epistasis varies from almost zero to very high. It is thus of fundamental as well as instrumental importance to better understand whether different functional dependency patterns among polymorphic genes give rise to distinct statistical interaction patterns or not. Here we address this issue by combining a quantitative genetic model approach with genotype-phenotype models capable of translating allelic variation and regulatory principles into phenotypic variation at the level of gene expression. We show that gene regulatory networks with and without feedback motifs can exhibit a wide range of possible statistical genetic architectures with regard to both type of effect explaining phenotypic variance and number of apparent loci underlying the observed phenotypic effect. Although all motifs are capable of harboring significant interactions, positive feedback gives rise to higher amounts and more types of statistical epistasis. The results also suggest that the inclusion of statistical interaction terms in genetic models will increase the chance to detect additional QTL as well as functional dependencies between genetic loci over a broad range of regulatory regimes. This article illustrates how statistical genetic methods can fruitfully be combined with nonlinear systems dynamics to elucidate biological issues beyond reach of each methodology in isolation.

Epistasis

Genetic architecture

Gene regulatory network

10.1534/genetics.106.058859

Cite

Citations (109)

Simultaneous mapping of epistatic QTL in chickens reveals clusters of QTL pairs with similar genetic effects on growth

Genetics Research (2004)

Örjan Carlborg P.M. Hocking David W. Burt Chris Haley

We used simultaneous mapping of interacting quantitative trait locus (QTL) pairs to study various growth traits in a chicken F2 intercross. The method was shown to increase the number of detected QTLs by 30% compared with a traditional method detecting QTLs by their marginal genetic effects. Epistasis was shown to be an important contributor to the genetic variance of growth, with the largest impact on early growth (before 6 weeks of age). There is also evidence for a discrete set of interacting loci involved in early growth, supporting the previous findings of different genetic regulation of early and late growth in chicken. The genotype–phenotype relationship was evaluated for all interacting QTL pairs and 17 of the 21 evaluated QTL pairs could be assigned to one of four clusters in which the pairs in a cluster have very similar genetic effects on growth. The genetic effects of the pairs indicate commonly occurring dominance-by-dominance, heterosis and multiplicative interactions. The results from this study clearly illustrate the increase in power obtained by using this novel method for simultaneous detection of epistatic QTL, and also how visualization of genotype–phenotype relationships for epistatic QTL pairs provides new insights to biological mechanisms underlying complex traits.

Epistasis

Family-based QTL mapping

Dominance (genetics)

Genetic architecture

10.1017/s0016672304006779

Cite

Citations (97)

cnF2freq: Efficient Determination of Genotype and Haplotype Probabilities in Outbred Populations Using Markov Models

Lecture notes in computer science (2009)

Carl Nettelblad Sverker Holmgren Lucy Crooks Örjan Carlborg

10.1007/978-3-642-00727-9_29

Cite

Citations (19)

Epistatic regulation of behavioural and morphological traits in the zebrafish (Danio rerio)

Behavior Genetics (2006)

I. A. Wright Roger K. Butlin Örjan Carlborg

Epistasis

Genetic architecture

Danio

10.1007/s10519-006-9080-9

Cite

Citations (41)

SNP detection and prediction of variability between chicken lines using genome resequencing of DNA pools

BMC Genomics (2010)

Stefan L. Marklund Örjan Carlborg

Next-generation sequencing technologies are widely used for detection of millions of Single Nucleotide Polymorphisms (SNPs) and also provide a means of assessing their variation. This information is useful for composing subsets of highly informative SNPs for region-specific or genome-wide analysis and to identify mutations regulating phenotypic differences within or between populations. In this study, we investigated the sensitivity of SNP detection and introduced the flanking SNPs value (FSV) as a novel measure for predicting SNP-variability using ~5X genome resequencing with ABI SOLID and DNA pools from two chicken lines divergently selected for juvenile bodyweight. Genotyping with a 60 K SNP chip revealed polymorphisms within or between two divergently selected chicken lines for 31 363 SNPs, 48% of which were also detected using resequencing of DNA pools. SNP detection using resequencing was more powerful for positions with larger differences in allele frequency between the lines. About 50% of the SNPs with non-reference allele frequencies in the range 0.5-0.6 and 67% of those with frequencies > 0.9 could be detected. On average, ~3.7 SNPs/kb were detected by resequencing, with about 5% lower density on microchromosomes than on macrochromosomes. There was a positive correlation between the observed between-line SNP variation from the 60 K chip analysis and our proposed FSV score computed from the genome resequencing data. The strongest correlations on macrochromosomes and microchromosomes were observed when the FSV was calculated with total flanking regions of 62 kb (correlation 0.55) and 38 kb (correlation 0.45), respectively. Genome resequencing with limited coverage (~5X) using pooled DNA samples and three non-reference reads as a threshold for SNP detection, identified 50 - 67% of the 60 K SNPs with a non-reference allele frequency larger than 0.5. The SNP density was around 5% lower on the microchromosomes, most likely because of their higher gene content. Our proposed method to estimate the SNP variation (FSV) uses additional sequence information to better predict SNP informativity. The FSV scores showed higher correlations for SNPs with a larger difference in allele frequency between the populations. The correlation was strongest on macrochromosomes, probably due to a lower recombination rate.

SNP genotyping

Microchromosome

SNP

SNP array

Tag SNP

10.1186/1471-2164-11-665

Cite

Citations (20)

Major Growth QTLs in Fowl Are Related to Fearful Behavior: Possible Genetic Links Between Fear Responses and Production Traits in a Red Junglefowl × White Leghorn Intercross

Behavior Genetics (2003)

Karin E. Schütz Susanne Kerje Lina Jacobsson Björn Forkman Örjan Carlborg

10.1023/b:bege.0000009481.98336.fc

Cite

Citations (140)