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Andersson, Leif
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Publications (10 of 185) Show all publications
Negro, S., Imsland, F., Valera, M., Molina, A., Sole, M. & Andersson, L. (2017). Association analysis of KIT, MITF, and PAX3 variants with white markings in Spanish horses. Animal Genetics, 48(3), 349-352.
Open this publication in new window or tab >>Association analysis of KIT, MITF, and PAX3 variants with white markings in Spanish horses
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2017 (English)In: Animal Genetics, ISSN 0268-9146, E-ISSN 1365-2052, Vol. 48, no 3, 349-352 p.Article in journal (Refereed) Published
Abstract [en]

Several variants in the KIT, PAX3 and MITF genes have previously been associated with white markings in horses. In this study, we examined eight variants of these genes in 70 Menorca Purebred horses (PRMe, only black solid-coloured horses) and 70 Spanish Purebred horses (PRE, different coat colour patterns) that were scored for the extent of white markings. A maximum-likelihood chi-square test, logistic regression model and ridge regression analyses showed that a missense mutation (p.Arg682His) in KIT was associated with white facial markings (P<0.05) and with total white markings (P<0.05) in PRMe horses. The relative contribution of this variant to white markings in PRMe horses was estimated at 47.6% (head) and 43.4% (total score). In PRE horses, this variant was also associated with hindlimb scores (P<0.05) with a relative contribution of 41.2%. The g.20147039C>T intronic variant located 29.9kb downstream from the transcription start site of the MITF gene was associated with less white markings on forelimbs (P<0.05) in PRMe horses, with a relative contribution of 63.9%, whereas in PRE horses this variant was associated with white facial markings (P<0.05), with a relative contribution of 63.9%. No significant associations were found for PAX3 variants in these breeds. These results show that KIT and MITF variants are involved in the white marking patterns of both PRMe and PRE horses, providing breeders with an opportunity to use genetic testing to aid in breeding for their desired level of white markings.

Keyword
Menorca Purebred, phenotypic variance, Purebred, SNP, white spotting
National Category
Genetics Medical Biotechnology
Identifiers
urn:nbn:se:uu:diva-322506 (URN)10.1111/age.12528 (DOI)000399953100010 ()28084638 (PubMedID)
Available from: 2017-05-30 Created: 2017-05-30 Last updated: 2017-05-30Bibliographically approved
Bornelöv, S., Seroussi, E., Yosefi, S., Pendavis, K., Burgess, S. C., Grabherr, M., . . . Andersson, L. (2017). Correspondence on Lovell et al.: identification of chicken genes previously assumed to be evolutionarily lost. Genome Biology, 18, Article ID 112.
Open this publication in new window or tab >>Correspondence on Lovell et al.: identification of chicken genes previously assumed to be evolutionarily lost
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2017 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 18, 112Article in journal (Refereed) Published
Abstract [en]

Through RNA-Seq analyses, we identified 137 genes that are missing in chicken, including the long-sought-after nephrin and tumor necrosis factor genes. These genes tended to cluster in GC-rich regions that have poor coverage in genome sequence databases. Hence, the occurrence of syntenic groups of vertebrate genes that have not been observed in Aves does not prove the evolutionary loss of such genes.

National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-327369 (URN)10.1186/s13059-017-1231-1 (DOI)000403239100007 ()28615067 (PubMedID)
Funder
EU, European Research Council
Available from: 2017-08-10 Created: 2017-08-10 Last updated: 2017-08-10Bibliographically approved
Carneiro, M., Hu, D., Archer, J., Feng, C., Afonso, S., Chen, C., . . . Andersson, L. (2017). Dwarfism and Altered Craniofacial Development in Rabbits Is Caused by a 12.1 kb Deletion at the HMGA2 Locus. Genetics, 205(2), 955-965.
Open this publication in new window or tab >>Dwarfism and Altered Craniofacial Development in Rabbits Is Caused by a 12.1 kb Deletion at the HMGA2 Locus
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2017 (English)In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 205, no 2, 955-965 p.Article in journal (Refereed) Published
Abstract [en]

The dwarf phenotype characterizes the smallest of rabbit breeds and is governed largely by the effects of a single dwarfing allele with an incompletely dominant effect on growth. Dwarf rabbits typically weigh under 1 kg and have altered craniofacial morphology. The dwarf allele is recessive lethal and dwarf homozygotes die within a few days of birth. The dwarf phenotype is expressed in heterozygous individuals and rabbits from dwarf breeds homozygous for the wild-type allele are normal, although smaller when compared to other breeds. Here, we show that the dwarf allele constitutes a similar to 12.1 kb deletion overlapping the promoter region and first three exons of the HMGA2 gene leading to inactivation of this gene. HMGA2 has been frequently associated with variation in body size across species. Homozygotes for null alleles are viable in mice but not in rabbits and probably not in humans. RNA-sequencing analysis of rabbit embryos showed that very few genes (4-29 genes) were differentially expressed among the three HMGA2/dwarf genotypes, suggesting that dwarfism and inviability in rabbits are caused by modest changes in gene expression. Our results show that HMGA2 is critical for normal expression of IGF2BP2, which encodes an RNA-binding protein. Finally, we report a catalog of regions of elevated genetic differentiation between dwarf and normal-size rabbits, including LCORL-NCAPG, STC2, HOXD cluster, and IGF2BP2. Levels and patterns of genetic diversity at the LCORL-NCAPG locus further suggest that small size in dwarf breeds was enhanced by crosses with wild rabbits. Overall, our results imply that small size in dwarf rabbits results from a large effect, loss-of-function (LOF) mutation in HMGA2 combined with polygenic selection.

Place, publisher, year, edition, pages
GENETICS SOCIETY AMERICA, 2017
Keyword
whole-genome sequencing, RNA-seq, body size, IGF2BP2, mtDNA
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-320763 (URN)10.1534/genetics.116.196667 (DOI)000394144900034 ()27986804 (PubMedID)
Funder
EU, European Research Council, 286431
Available from: 2017-04-25 Created: 2017-04-25 Last updated: 2017-04-25Bibliographically approved
Hill, G. E., Lopes, R. J., Johnson, J. D., Toomey, M. B., Ferreira, M., Melo-Ferreira, J., . . . Hill, G. (2017). Genetic Basis for Red Coloration in Birds. Paper presented at Annual Meeting of the Society-for-Integrative-and-Comparative-Biology (SICB), JAN 04-08, 2017, New Orleans, LA. Integrative and Comparative Biology, 57, E292-E292.
Open this publication in new window or tab >>Genetic Basis for Red Coloration in Birds
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2017 (English)In: Integrative and Comparative Biology, ISSN 1540-7063, E-ISSN 1557-7023, Vol. 57, E292-E292 p.Article in journal, Meeting abstract (Other academic) Published
Place, publisher, year, edition, pages
OXFORD UNIV PRESS INC, 2017
National Category
Zoology
Identifiers
urn:nbn:se:uu:diva-328837 (URN)000398668701418 ()
Conference
Annual Meeting of the Society-for-Integrative-and-Comparative-Biology (SICB), JAN 04-08, 2017, New Orleans, LA
Available from: 2017-10-30 Created: 2017-10-30 Last updated: 2017-10-30Bibliographically approved
Fegraeus, K. J., Lawrence, C., Petäjistö, K., Johansson, M. K., Wiklund, M., Olsson, C., . . . Velie, B. D. (2017). Lack of significant associations with early career performance suggest no link between the DMRT3 "Gait Keeper" mutation and precocity in Coldblooded trotters. PLoS ONE, 12(5), Article ID e0177351.
Open this publication in new window or tab >>Lack of significant associations with early career performance suggest no link between the DMRT3 "Gait Keeper" mutation and precocity in Coldblooded trotters
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2017 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, no 5, e0177351Article in journal (Refereed) Published
Abstract [en]

The Swedish-Norwegian Coldblooded trotter (CBT) is a local breed in Sweden and Norway mainly used for harness racing. Previous studies have shown that a mutation from cytosine (C) to adenine (A) in the doublesex and mab-3 related transcription factor 3 (DMRT3) gene has a major impact on harness racing performance of different breeds. An association of the DMRT3 mutation with early career performance has also been suggested. The aim of the current study was to investigate this proposed association in a randomly selected group of CBTs. 769 CBTs (485 raced, 284 unraced) were genotyped for the DMRT3 mutation. The association with racing performance was investigated for 13 performance traits and three different age intervals: 3 years, 3 to 6 years, and 7 to 10 years of age, using the statistical software R. Each performance trait was analyzed for association with DMRT3 using linear models. The results suggest no association of the DMRT3 mutation with precocity (i.e. performance at 3 years of age). Only two traits (race time and number of disqualifications) were significantly different between the genotypes, with AA horses having the fastest times and CC horses having the highest number of disqualifications at 3 years of age. The frequency of the AA genotype was significantly lower in the raced CBT sample compared with the unraced sample and less than 50% of the AA horses participated in a race. For the age intervals 3 to 6 and 7 to 10 years the AA horses also failed to demonstrate significantly better performance than the other genotypes. Although suggested as the most favorable genotype for racing performance in Standardbreds and Finnhorses across all ages, the AA genotype does not appear to be associated with superior performance, early or late, in the racing career of CBTs.

Place, publisher, year, edition, pages
PUBLIC LIBRARY SCIENCE, 2017
National Category
Veterinary Science
Identifiers
urn:nbn:se:uu:diva-325333 (URN)10.1371/journal.pone.0177351 (DOI)000401314100066 ()
Funder
Swedish Research Council, 621-2012-4666Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning, 221-2013-1661
Available from: 2017-06-30 Created: 2017-06-30 Last updated: 2017-11-29Bibliographically approved
Seroussi, E., Pitel, F., Leroux, S., Morisson, M., Bornelöv, S., Miyara, S., . . . Friedman-Einat, M. (2017). Mapping of leptin and its syntenic genes to chicken chromosome 1p. BMC Genetics, 18, Article ID 77.
Open this publication in new window or tab >>Mapping of leptin and its syntenic genes to chicken chromosome 1p
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2017 (English)In: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156, Vol. 18, 77Article in journal (Refereed) Published
Abstract [en]

Background: Misidentification of the chicken leptin gene has hampered research of leptin signaling in this species for almost two decades. Recently, the genuine leptin gene with a GC-rich (similar to 70%) repetitive-sequence content was identified in the chicken genome but without indicating its genomic position. This suggests that such GC-rich sequences are difficult to sequence and therefore substantial regions are missing from the current chicken genome assembly.

Results: A radiation hybrid panel of chicken-hamster Wg3hCl2 cells was used to map the genome location of the chicken leptin gene. Contrary to our expectations, based on comparative genome mapping and sequence characteristics, the chicken leptin was not located on a microchromosome, which are known to contain GC-rich and repetitive regions, but at the distal tip of the largest chromosome (1p). Following conserved synteny with other vertebrates, we also mapped five additional genes to this genomic region (ARF5, SND1, LRRC4, RBM28, and FLNC), bridging the genomic gap in the current Galgal5 build for this chromosome region. All of the short scaffolds containing these genes were found to consist of GC-rich (54 to 65%) sequences comparing to the average GC-content of 40% on chromosome 1. In this syntenic group, the RNA-binding protein 28 (RBM28) was in closest proximity to leptin. We deduced the full-length of the RBM28 cDNA sequence and profiled its expression patterns detecting a negative correlation (R = -0.7) between the expression of leptin and of RBM28 across tissues that expressed at least one of the genes above the average level. This observation suggested a local regulatory interaction between these genes. In adipose tissues, we observed a significant increase in RBM28 mRNA expression in breeds with lean phenotypes.

Conclusion: Mapping chicken leptin together with a cluster of five syntenic genes provided the final proof for its identification as the true chicken ortholog. The high GC-content observed for the chicken leptin syntenic group suggests that other similar clusters of genes in GC-rich genomic regions are missing from the current genome assembly (Galgal5), which should be resolved in future assemblies of the chicken genome.

Place, publisher, year, edition, pages
BIOMED CENTRAL LTD, 2017
Keyword
Chicken leptin, Syntenic clusters, chicken RBM28, GC-rich, chicken chromosome 1
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-334316 (URN)10.1186/s12863-017-0543-1 (DOI)000407949700002 ()28793857 (PubMedID)
Available from: 2017-11-23 Created: 2017-11-23 Last updated: 2017-11-29Bibliographically approved
Feng, C., Pettersson, M., Lamichhaney, S., Rubin, C.-J., Rafati, N., Casini, M., . . . Andersson, L. (2017). Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate. eLIFE, 6, Article ID e23907.
Open this publication in new window or tab >>Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate
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2017 (English)In: eLIFE, E-ISSN 2050-084X, Vol. 6, e23907Article in journal (Refereed) Published
Abstract [en]

The Atlantic herring is one of the most abundant vertebrates on earth but its nucleotide diversity is moderate (pi = 0.3%), only three-fold higher than in human. Here, we present a pedigree-based estimation of the mutation rate in this species. Based on whole-genome sequencing of four parents and 12 offspring, the estimated mutation rate is 2.0 x 10(-9) per base per generation. We observed a high degree of parental mosaicism indicating that a large fraction of these de novo mutations occurred during early germ cell development. The estimated mutation rate the lowest among vertebrates analyzed to date - partially explains the discrepancy between the rather low nucleotide diversity in herring and its huge census population size. But a species like the herring will never reach its expected nucleotide diversity because of fluctuations in population size over the millions of years it takes to build up high nucleotide diversity.

Place, publisher, year, edition, pages
ELIFE SCIENCES PUBLICATIONS LTD, 2017
National Category
Biological Sciences
Identifiers
urn:nbn:se:uu:diva-333409 (URN)10.7554/eLife.23907 (DOI)000406099100001 ()
Funder
EU, European Research Council, Bateson
Available from: 2017-11-15 Created: 2017-11-15 Last updated: 2017-11-29Bibliographically approved
Lamichhaney, S., Fuentes-Pardo, A. P., Rafati, N., Ryman, N., McCracken, G. R., Bourne, C., . . . Andersson, L. (2017). Parallel adaptive evolution of geographically distant herring populations on both sides of the North Atlantic Ocean. Proceedings of the National Academy of Sciences of the United States of America, 114(17), E3452-E3461.
Open this publication in new window or tab >>Parallel adaptive evolution of geographically distant herring populations on both sides of the North Atlantic Ocean
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2017 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 114, no 17, E3452-E3461 p.Article in journal (Refereed) Published
Abstract [en]

Atlantic herring is an excellent species for studying the genetic basis of adaptation in geographically distant populations because of its characteristically large population sizes and low genetic drift. In this study we compared whole-genome resequencing data of Atlantic herring populations from both sides of the Atlantic Ocean. An important finding was the very low degree of genetic differentiation among geographically distant populations (fixation index = 0.026), suggesting lack of reproductive isolation across the ocean. This feature of the Atlantic herring facilitates the detection of genetic factors affecting adaptation because of the sharp contrast between loci showing genetic differentiation resulting from natural selection and the low background noise resulting from genetic drift. We show that genetic factors associated with timing of reproduction are shared between genetically distinct and geographically distant populations. The genes for thyroid-stimulating hormone receptor (TSHR), the SOX11 transcription factor (SOX11), calmodulin (CALM), and estrogen receptor 2 (ESR2A), all with a significant role in reproductive biology, were among the loci that showed the most consistent association with spawning time throughout the species range. In fact, the same two SNPs located at the 5' end of TSHR showed the most significant association with spawning time in both the east and west Atlantic. We also identified unexpected haplotype sharing between spring-spawning oceanic herring and autumn-spawning populations across the Atlantic Ocean and the Baltic Sea. The genomic regions showing this pattern are unlikely to control spawning time but may be involved in adaptation to ecological factor(s) shared among these populations.

Place, publisher, year, edition, pages
NATL ACAD SCIENCES, 2017
Keyword
genetic adaptation, Atlantic herring, parallel evolution, reproductive strategies, whole-genome resequencing
National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-322174 (URN)10.1073/pnas.1617728114 (DOI)000399995600010 ()28389569 (PubMedID)
Funder
Swedish Research Council, 80576801 70374401 RGPIN-2014-04696Swedish Research Council Formas
Available from: 2017-05-17 Created: 2017-05-17 Last updated: 2017-05-17Bibliographically approved
Thalmann, D. S., Ring, H., Sundström, E., Cao, X., Larsson, M., Kerje, S., . . . Andersson, L. (2017). The evolution of Sex-linked barring alleles in chickens involves both regulatory and coding changes in CDKN2A. PLoS Genetics, 13(4), Article ID e1006665.
Open this publication in new window or tab >>The evolution of Sex-linked barring alleles in chickens involves both regulatory and coding changes in CDKN2A
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2017 (English)In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 13, no 4, e1006665Article in journal (Refereed) Published
Abstract [en]

Sex-linked barring is a fascinating plumage pattern in chickens recently shown to be associated with two non-coding and two missense mutations affecting the ARF transcript at the CDKN2A tumor suppressor locus. It however remained a mystery whether all four mutations are indeed causative and how they contribute to the barring phenotype. Here, we show that Sex-linked barring is genetically heterogeneous, and that the mutations form three functionally different variant alleles. The B0 allele carries only the two non-coding changes and is associated with the most dilute barring pattern, whereas the B1 and B2 alleles carry both the two non-coding changes and one each of the two missense mutations causing the Sex-linked barring and Sex-linked dilution phenotypes, respectively. The data are consistent with evolution of alleles where the non-coding changes occurred first followed by the two missense mutations that resulted in a phenotype more appealing to humans. We show that one or both of the non-coding changes are cis-regulatory mutations causing a higher CDKN2A expression, whereas the missense mutations reduce the ability of ARF to interact with MDM2. Caspase assays for all genotypes revealed no apoptotic events and our results are consistent with a recent study indicating that the loss of melanocyte progenitors in Sex-linked barring in chicken is caused by premature differentiation and not apoptosis. Our results show that CDKN2A is a major locus driving the differentiation of avian melanocytes in a temporal and spatial manner.

Place, publisher, year, edition, pages
PUBLIC LIBRARY SCIENCE, 2017
Keyword
ARF TUMOR-SUPPRESSOR; GENE-EXPRESSION; LOCUS; MUTATIONS; INK4A/ARF; MELANOMA; GENOME; SENESCENCE; NICHE; CELLS
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-327066 (URN)10.1371/journal.pgen.1006665 (DOI)000402549200008 ()
Available from: 2017-08-01 Created: 2017-08-01 Last updated: 2018-01-03Bibliographically approved
Staiger, E. A., Almén, M. S., Promerova, M., Brooks, S., Cothran, E. G., Imsland, F., . . . Andersson, L. (2017). The evolutionary history of the DMRT3 'Gait keeper' haplotype. Animal Genetics, 48(5), 551-559.
Open this publication in new window or tab >>The evolutionary history of the DMRT3 'Gait keeper' haplotype
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2017 (English)In: Animal Genetics, ISSN 0268-9146, E-ISSN 1365-2052, Vol. 48, no 5, 551-559 p.Article in journal (Refereed) Published
Abstract [en]

A previous study revealed a strong association between the DMRT3:Ser301STOP mutation in horses and alternate gaits as well as performance in harness racing. Several follow-up studies have confirmed a high frequency of the mutation in gaited horse breeds and an effect on gait quality. The aim of this study was to determine when and where the mutation arose, to identify additional potential causal mutations and to determine the coalescence time for contemporary haplotypes carrying the stop mutation. We utilized sequences from 89 horses representing 26 breeds to identify 102 SNPs encompassing the DMRT3 gene that are in strong linkage disequilibrium with the stop mutation. These 102 SNPs were genotyped in an additional 382 horses representing 72 breeds, and we identified 14 unique haplotypes. The results provided conclusive evidence that DMRT3: Ser301STOP is causal, as no other sequence polymorphisms showed an equally strong association to locomotion traits. The low sequence diversity among mutant chromosomes demonstrated that they must have diverged from a common ancestral sequence within the last 10 000 years. Thus, the mutation occurred either just before domestication or more likely some time after domestication and then spread across the world as a result of selection on locomotion traits.

Place, publisher, year, edition, pages
WILEY, 2017
Keyword
domestication, donkey, horse, locomotion, Przewalski's horse
National Category
Veterinary Science
Identifiers
urn:nbn:se:uu:diva-335121 (URN)10.1111/age.12580 (DOI)000410617400006 ()28741731 (PubMedID)
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council Formas
Available from: 2017-12-04 Created: 2017-12-04 Last updated: 2017-12-04Bibliographically approved
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