DOCSLIB.ORG

Expression Levels of LCORL Are Associated with Body Size in Horses

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Expression Levels of LCORL Are Associated with Body Size in Horses Expression Levels of LCORL Are Associated with Body Size in Horses Julia Metzger, Rahel Schrimpf, Ute Philipp, Ottmar Distl* Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Hannover, Germany Abstract Body size is an important characteristic for horses of various breeds and essential for the classification of ponies concerning the limit value of 148 cm (58.27 inches) height at the withers. Genome-wide association analyses revealed the highest associated quantitative trait locus for height at the withers on horse chromosome (ECA) 3 upstream of the candidate gene LCORL. Using 214 Hanoverian horses genotyped on the Illumina equine SNP50 BeadChip and 42 different horse breeds across all size ranges, we confirmed the highly associated single nucleotide polymorphism BIEC2-808543 (2log10P = 8.3) and the adjacent gene LCORL as the most promising candidate for body size. We investigated the relative expression levels of LCORL and its two neighbouring genes NCAPG and DCAF16 using quantitative real-time PCR (RT-qPCR). We could demonstrate a significant association of the relative LCORL expression levels with the size of the horses and the BIEC2- 808543 genotypes within and across horse breeds. In heterozygous C/T-horses expression levels of LCORL were significantly decreased by 40% and in homozygous C/C-horses by 56% relative to the smaller T/T-horses. Bioinformatic analyses indicated that this SNP T.C mutation is disrupting a putative binding site of the transcription factor TFIID which is important for the transcription process of genes involved in skeletal bone development. Thus, our findings suggest that expression levels of LCORL play a key role for body size within and across horse breeds and regulation of the expression of LCORL is associated with genetic variants of BIEC2-808543. This is the first functional study for a body size regulating polymorphism in horses and a further step to unravel the mechanisms for understanding the genetic regulation of body size in horses. Citation: Metzger J, Schrimpf R, Philipp U, Distl O (2013) Expression Levels of LCORL Are Associated with Body Size in Horses. PLoS ONE 8(2): e56497. doi:10.1371/ journal.pone.0056497 Editor: Elissa Z. Cameron, University of Tasmania, Australia Received August 26, 2012; Accepted January 10, 2013; Published February 13, 2013 Copyright: ß 2013 Metzger et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This study was supported by the Mehl-Mu¨lhens Stiftung, Ko¨ln (DI-MM/1-1). The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: [email protected] Introduction advantage and performances are evaluated correspondingly [13,14]. Due to the selection for specific functions, the domestic Body size is an important model trait for studying genetic horse has been modified within breeds into diverse skeletal influences on quantitative traits and has been intensely investigat- morphologic types. The heritability of height at the withers was ed in human and also in domestic animals [1–17]. In human, adult estimated to be medium to high in pony breeds. Particularly, in height is described to be a complex trait influenced by many genes Haflinger and Shetland ponies high heritabilities at 0.79–0.89 and environmental factors [5]. Several genetic variants affecting were found [8–10] while Icelandic and Hanoverian warmblood the adult height have been identified using association analyses showed medium values at 0.5–0.6 [11,12]. The first attempt to [5,6]. identify patterns of skeletal size and shape variation among In horses, body size is an important criterion for the evaluation domestic horses has been made by principal component analyses of different breeds concerning appearance and function and is [15]. Overall body size was used as a principal component crucial for the classification of horses. According to the Fe´de´ration including thirty measurements all over horse’s body like head Equestre Internationale (FEI) veterinary regulations ponies taking length, height at withers, height at croup, chest width and neck part in any FEI competition have to be measured at the highest length. It grouped small ponies together with low scores and large point of the withers. The limit height is in accordance with the draft breeds with high median scores. Light horses showed mid- definition of a pony 148 cm (centimetres) (58.27 inches) without values [15]. Several genome-wide association studies (GWAS) shoes or with competition shoes 149 cm (58.66 inches). If this have been performed for height at withers in horses [1,2,16,17]. height is exceeded the animal is then classified as a horse [7]. In The involvement of LCORL (ligand-dependent nuclear receptor compres- some breeds, the limit values are even lower. The American sor-like protein) in height at withers has been primarily shown in a Miniature Horse Association requires a limit height at the last GWAS in Hanoverian stallions [16]. A highly significant QTL on hairs of the mane of 86.4 cm (34 inches). For breeders, body size horse chromosome (ECA) 3 in the region of LCORL was detected of horses is an essential parameter to improve marketability, for conformation traits like head, neck, frame and development function and performance. The important effect of size for [17]. In Franches-Montagnes horses, quantitative trait loci (QTL) competitive jumping ability in ponies was suggested [8]. Generally, on ECA3 and 9 were significantly associated with withers height. larger animals within each height class possess competitive Both associated SNPs were located in large intergenic regions [1]. PLOS ONE | www.plosone.org 1 February 2013 | Volume 8 | Issue 2 | e56497 LCORL Expression Associated with Equine Body Size Figure 1. Genome-wide association analysis shows a highly significant peak on equine chromosome (ECA) 3 in Hanoverian. (A) Manhattan-plot of the 2log10P-values from genome-wide association analysis (MLM) of body size in Hanoverian warmblood horses. The highest peak is located at 105 Mb on ECA3. (B) Q-Q plot of observed versus expected 2log10P-values from a genome- wide association study (GWAS) in Hanoverian warmblood horses. The expected distribution (solid line) and the observed 2log10P-values plotted against the expected 2log10P-values (black dots) are shown. The peak value (BIEC2-808543) is located on horse chromosome 3 at 105.55 Mb. doi:10.1371/journal.pone.0056497.g001 In thoroughbred horses, the same locus on ECA3 was found as strongest statistical effect was detected for the SNP ADI- highly associated with body size. A scan of 48 horses from 16 POQ:g.1596G.A, possibly influencing the anchoring of the different breeds revealed that four loci on ECA3, 6, 9 and 11 transcription pre-initiation transcription factor IID (TFIID) complex explain 83% of the variance for size. The highest associated SNP and therefore affecting the stability of the initiation complex [18]. was located near the candidate gene LCORL and this finding was Analyses of TFIID in mice resulted in dwarf phenotypes with an in line with the other analyses for withers height in horses about 50% reduced body weight. According to its multiple [2,16,17]. In human, the candidate gene LCORL has been molecular functions, TFIID is considered as a central component discussed to be involved in trunk and hip axis length [6]. GWAS of the transcription apparatus [19]. Furthermore, analyses showed in cattle for growth traits such as birth weight, body length, carcass a correlation between body weight, withers height and further size weight and longissimus muscle area, revealed an association in the measurements [20]. region of NCAPG (non-SMC condensing I complex subunit) and LCORL. In thoroughbred horses, a mass to height at the withers ratio Coding regions of the candidate genes were sequenced and was used to test the influence of the MSTN (myostatin) gene revealed further associated markers [4]. In Angus cattle, g.66493737C.T genotypes on body mass. Sprinters are proposed polymorphisms in the candidate genes adiponectin (ADIPOQ) and to be generally shorter animals with greater muscle mass [21,22]. somatostatin (SST) were tested for growth and carcass traits. The PLOS ONE | www.plosone.org 2 February 2013 | Volume 8 | Issue 2 | e56497 LCORL Expression Associated with Equine Body Size The objective of our study was to investigate the role of the heavier horses predominantly showed the genotype C/C (Table candidate gene LCORL and its flanking polymorphisms with the S1). Heterozygous horses in pony breeds showed relatively high development of body size in horses. First, we validated the withers height values and those stallions served breeders to pass on association of the genomic region around LCORL in Hanoverian larger height at the wither to the offspring. The results show that warmblood horses as well as substantiated the association of this this SNP proved to be a highly predictive marker of genetic locus with body size in a large number of horse breeds with potential for body size. extreme size and then we sequenced genomic and copy DNA of LCORL for polymorphism detection. In order to show a functional Candidate region analysis relationship of LCORL with body size and the associated SNP Bioinformatic sequence analysis of the genomic region of the upstream of LCORL, we employed expression analyses for LCORL highly associated SNP (BIEC2-808543) using Patch 1.0 and and its two adjacent genes for horses with differing height at SIGNAL SCAN showed that the polymorphism was located in a withers within and across breeds. putative DNA consensus sequence element, the transcription factor binding site of TFIID, which influences the transcription by Results RNA polymerase II [23,24].
Load more

Recommended publications
  • Genome-Wide Association Study of Body Weight
    Genome-wide association study of body weight in Australian Merino sheep reveals an orthologous region on OAR6 to human and bovine genomic regions affecting height and weight Hawlader A. Al-Mamun, Paul Kwan, Samuel A. Clark, Mohammad H. Ferdosi, Ross Tellam, Cedric Gondro To cite this version: Hawlader A. Al-Mamun, Paul Kwan, Samuel A. Clark, Mohammad H. Ferdosi, Ross Tellam, et al.. Genome-wide association study of body weight in Australian Merino sheep reveals an orthologous region on OAR6 to human and bovine genomic regions affecting height and weight. Genetics Selection Evolution, 2015, 47 (1), pp.66. 10.1186/s12711-015-0142-4. hal-01341302 HAL Id: hal-01341302 https://hal.archives-ouvertes.fr/hal-01341302 Submitted on 4 Jul 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. et al. Genetics Selection Evolution Al-Mamun (2015) 47:66 Genetics DOI 10.1186/s12711-015-0142-4 Selection Evolution RESEARCH ARTICLE Open Access Genome-wide association study of body weight in Australian Merino sheep reveals an orthologous region on OAR6 to human and bovine genomic regions affecting height and weight Hawlader A. Al-Mamun1,2, Paul Kwan2, Samuel A.
    [Show full text]
  • Genetic Architecture of Quantitative Traits in Beef Cattle Revealed by Genome Wide Association Studies of Imputed Whole Genome S
    Zhang et al. BMC Genomics (2020) 21:36 https://doi.org/10.1186/s12864-019-6362-1 RESEARCH ARTICLE Open Access Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: I: feed efficiency and component traits Feng Zhang1,2,3,4, Yining Wang1,2, Robert Mukiibi2, Liuhong Chen1,2, Michael Vinsky1, Graham Plastow2, John Basarab5, Paul Stothard2 and Changxi Li1,2* Abstract Background: Genome wide association studies (GWAS) on residual feed intake (RFI) and its component traits including daily dry matter intake (DMI), average daily gain (ADG), and metabolic body weight (MWT) were conducted in a population of 7573 animals from multiple beef cattle breeds based on 7,853,211 imputed whole genome sequence variants. The GWAS results were used to elucidate genetic architectures of the feed efficiency related traits in beef cattle. Results: The DNA variant allele substitution effects approximated a bell-shaped distribution for all the traits while the distribution of additive genetic variances explained by single DNA variants followed a scaled inverse chi- squared distribution to a greater extent. With a threshold of P-value < 1.00E-05, 16, 72, 88, and 116 lead DNA variants on multiple chromosomes were significantly associated with RFI, DMI, ADG, and MWT, respectively. In addition, lead DNA variants with potentially large pleiotropic effects on DMI, ADG, and MWT were found on chromosomes 6, 14 and 20. On average, missense, 3’UTR, 5’UTR, and other regulatory region variants exhibited larger allele substitution effects in comparison to other functional classes. Intergenic and intron variants captured smaller proportions of additive genetic variance per DNA variant.
    [Show full text]
  • LCORL (NM 153686) Human Tagged ORF Clone Product Data
    OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for RC207306L4 LCORL (NM_153686) Human Tagged ORF Clone Product data: Product Type: Expression Plasmids Product Name: LCORL (NM_153686) Human Tagged ORF Clone Tag: mGFP Symbol: LCORL Synonyms: MLR1 Vector: pLenti-C-mGFP-P2A-Puro (PS100093) E. coli Selection: Chloramphenicol (34 ug/mL) Cell Selection: Puromycin ORF Nucleotide The ORF insert of this clone is exactly the same as(RC207306). Sequence: Restriction Sites: SgfI-MluI Cloning Scheme: ACCN: NM_153686 ORF Size: 954 bp This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 2 LCORL (NM_153686) Human Tagged ORF Clone – RC207306L4 OTI Disclaimer: The molecular sequence of this clone aligns with the gene accession number as a point of reference only. However, individual transcript sequences of the same gene can differ through naturally occurring variations (e.g. polymorphisms), each with its own valid existence. This clone is substantially in agreement with the reference, but a complete review of all prevailing variants is recommended prior to use. More info OTI Annotation: This clone was engineered to express the complete ORF with an expression tag. Expression varies depending on the nature of the gene. RefSeq: NM_153686.4, NP_710153.2 RefSeq Size: 3577 bp RefSeq ORF: 957 bp Locus ID: 254251 UniProt ID: Q8N3X6, B4DSW0 Domains: HTH_psq Protein Families: Transcription Factors MW: 35.4 kDa Gene Summary: This gene encodes a transcription factor that appears to function in spermatogenesis.
    [Show full text]
  • High-Resolution Analysis of Selection Sweeps Identified Between Fine
    Gutiérrez‑Gil et al. Genet Sel Evol (2017) 49:81 DOI 10.1186/s12711-017-0354-x Genetics Selection Evolution RESEARCH ARTICLE Open Access High‑resolution analysis of selection sweeps identifed between fne‑wool Merino and coarse‑wool Churra sheep breeds Beatriz Gutiérrez‑Gil1* , Cristina Esteban‑Blanco1,2, Pamela Wiener3, Praveen Krishna Chitneedi1, Aroa Suarez‑Vega1 and Juan‑Jose Arranz1 Abstract Background: With the aim of identifying selection signals in three Merino sheep lines that are highly specialized for fne wool production (Australian Industry Merino, Australian Merino and Australian Poll Merino) and considering that these lines have been subjected to selection not only for wool traits but also for growth and carcass traits and parasite resistance, we contrasted the OvineSNP50 BeadChip (50 K-chip) pooled genotypes of these Merino lines with the genotypes of a coarse-wool breed, phylogenetically related breed, Spanish Churra dairy sheep. Genome re-sequenc‑ ing datasets of the two breeds were analyzed to further explore the genetic variation of the regions initially identifed as putative selection signals. Results: Based on the 50 K-chip genotypes, we used the overlapping selection signals (SS) identifed by four selec‑ tion sweep mapping analyses (that detect genetic diferentiation, reduced heterozygosity and patterns of haplotype diversity) to defne 18 convergence candidate regions (CCR), fve associated with positive selection in Australian Merino and the remainder indicating positive selection in Churra. Subsequent analysis of whole-genome sequences from 15 Churra and 13 Merino samples identifed 142,400 genetic variants (139,745 bi-allelic SNPs and 2655 indels) within the 18 defned CCR. Annotation of 1291 variants that were signifcantly associated with breed identity between Churra and Merino samples identifed 257 intragenic variants that caused 296 functional annotation variants, 275 of which were located across 31 coding genes.
    [Show full text]
  • Supplementary Information – Postema Et Al., the Genetics of Situs Inversus Totalis Without Primary Ciliary Dyskinesia
    1 Supplementary information – Postema et al., The genetics of situs inversus totalis without primary ciliary dyskinesia Table of Contents: Supplementary Methods 2 Supplementary Results 5 Supplementary References 6 Supplementary Tables and Figures Table S1. Subject characteristics 9 Table S2. Inbreeding coefficients per subject 10 Figure S1. Multidimensional scaling to capture overall genomic diversity 11 among the 30 study samples Table S3. Significantly enriched gene-sets under a recessive mutation model 12 Table S4. Broader list of candidate genes, and the sources that led to their 13 inclusion Table S5. Potential recessive and X-linked mutations in the unsolved cases 15 Table S6. Potential mutations in the unsolved cases, dominant model 22 2 1.0 Supplementary Methods 1.1 Participants Fifteen people with radiologically documented SIT, including nine without PCD and six with Kartagener syndrome, and 15 healthy controls matched for age, sex, education and handedness, were recruited from Ghent University Hospital and Middelheim Hospital Antwerp. Details about the recruitment and selection procedure have been described elsewhere (1). Briefly, among the 15 people with radiologically documented SIT, those who had symptoms reminiscent of PCD, or who were formally diagnosed with PCD according to their medical record, were categorized as having Kartagener syndrome. Those who had no reported symptoms or formal diagnosis of PCD were assigned to the non-PCD SIT group. Handedness was assessed using the Edinburgh Handedness Inventory (EHI) (2). Tables 1 and S1 give overviews of the participants and their characteristics. Note that one non-PCD SIT subject reported being forced to switch from left- to right-handedness in childhood, in which case five out of nine of the non-PCD SIT cases are naturally left-handed (Table 1, Table S1).
    [Show full text]
  • A Genome-Wide Association Study for Body Weight in Japanese Thoroughbred Racehorses Clarifies Candidate Regions on Chromosomes 3, 9, 15, and 18
    —Full Paper— A genome-wide association study for body weight in Japanese Thoroughbred racehorses clarifies candidate regions on chromosomes 3, 9, 15, and 18 Teruaki TOZAKI1*, Mio KIKUCHI1, Hironaga KAKOI1, Kei-ichi HIROTA1 and Shun-ichi NAGATA1 1Genetic Analysis Department, Laboratory of Racing Chemistry, Tochigi 320-0851, Japan Body weight is an important trait to confirm growth and development in humans and animals. In Thoroughbred racehorses, it is measured in the postnatal, training, and racing periods to evaluate growth and training degrees. The body weight of mature Thoroughbred J. Equine Sci. racehorses generally ranges from 400 to 600 kg, and this broad range is likely influenced Vol. 28, No. 4 by environmental and genetic factors. Therefore, a genome-wide association study pp. 127–134, 2017 (GWAS) using the Equine SNP70 BeadChip was performed to identify the genomic regions associated with body weight in Japanese Thoroughbred racehorses using 851 individuals. The average body weight of these horses was 473.9 kg (standard deviation: 28.0) at the age of 3, and GWAS identified statistically significant SNPs on chromosomes 3 (BIEC2_808466, P=2.32E-14), 9 (BIEC2_1105503, P=1.03E-7), 15 (BIEC2_322669, P=9.50E-6), and 18 (BIEC2_417274, P=1.44E-14), which were associated with body weight as a quantitative trait. The genomic regions on chromosomes 3, 9, 15, and 18 included ligand-dependent nuclear receptor compressor-like protein (LCORL), zinc finger and AT hook domain containing (ZFAT), tribbles pseudokinase 2 (TRIB2), and myostatin (MSTN), respectively, as candidate genes. LCORL and ZFAT are associated with withers height in horses, whereas MSTN affects muscle mass.
    [Show full text]
  • Sheep Genome Functional Annotation Reveals Proximal Regulatory Elements Contributed to the Evolution of Modern Breeds
    ARTICLE DOI: 10.1038/s41467-017-02809-1 OPEN Sheep genome functional annotation reveals proximal regulatory elements contributed to the evolution of modern breeds Marina Naval-Sanchez1, Quan Nguyen1, Sean McWilliam1, Laercio R. Porto-Neto1, Ross Tellam1, Tony Vuocolo1, Antonio Reverter1, Miguel Perez-Enciso 2,3, Rudiger Brauning4, Shannon Clarke4, Alan McCulloch4, Wahid Zamani5, Saeid Naderi 6, Hamid Reza Rezaei7, Francois Pompanon 8, Pierre Taberlet8, Kim C. Worley9, Richard A. Gibbs9, Donna M. Muzny9, Shalini N. Jhangiani9, Noelle Cockett10, Hans Daetwyler11,12 & James Kijas1 1234567890():,; Domestication fundamentally reshaped animal morphology, physiology and behaviour, offering the opportunity to investigate the molecular processes driving evolutionary change. Here we assess sheep domestication and artificial selection by comparing genome sequence from 43 modern breeds (Ovis aries) and their Asian mouflon ancestor (O. orientalis)to identify selection sweeps. Next, we provide a comparative functional annotation of the sheep genome, validated using experimental ChIP-Seq of sheep tissue. Using these annotations, we evaluate the impact of selection and domestication on regulatory sequences and find that sweeps are significantly enriched for protein coding genes, proximal regulatory elements of genes and genome features associated with active transcription. Finally, we find individual sites displaying strong allele frequency divergence are enriched for the same regulatory features. Our data demonstrate that remodelling of gene expression is likely to have been one of the evolutionary forces that drove phenotypic diversification of this common livestock species. 1 CSIRO Agriculture and Food, 306 Carmody Road, St. Lucia 4067 QLD, Australia. 2 Centre for Research in Agricultural Genomics (CRAG), Bellaterra 08193, Spain. 3 ICREA, Carrer de Lluís Companys 23, Barcelona 08010, Spain.
    [Show full text]
  • NCAPG Dynamically Coordinates the Myogenesis of Fetal Bovine Tissue by Adjusting Chromatin Accessibility
    International Journal of Molecular Sciences Article NCAPG Dynamically Coordinates the Myogenesis of Fetal Bovine Tissue by Adjusting Chromatin Accessibility 1,2, 1, 3 4 1 1 1 Xin Hu y, Yishen Xing y, Xing Fu , Qiyuan Yang , Ling Ren , Yahui Wang , Qian Li , Junya Li 1,* and Lupei Zhang 1,* 1 Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; [email protected] (X.H.); [email protected] (Y.X.); [email protected] (L.R.); [email protected] (Y.W.); [email protected] (Q.L.) 2 Molecular and Cellular Biology, Gembloux Agro-Bio Tech, University of Liège, 5030 Gembloux, Belgium 3 School of Animal Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA; [email protected] 4 Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA; [email protected] * Correspondence: [email protected] (L.Z.); [email protected] (J.L.) These authors contributed equally to this work. y Received: 29 January 2020; Accepted: 11 February 2020; Published: 13 February 2020 Abstract: NCAPG is a subunit of condensin I that plays a crucial role in chromatin condensation during mitosis. NCAPG has been demonstrated to be associated with farm animal growth traits. However, its role in regulating myoblast differentiation is still unclear. We used myoblasts derived from fetal bovine tissue as an in vitro model and found that NCAPG was expressed during myogenic differentiation in the cytoplasm and nucleus. Silencing NCAPG prolonged the mitosis and impaired the differentiation due to increased myoblast apoptosis.
    [Show full text]
  • Plant & Animal Genome V
    January 9-13, 2016 PLANT & ANIMAL GENOME XXIV Town & Country Hotel THE INTERNATIONAL CONFERENCE San Diego, CA ON THE STATUS OF PLANT & ANIMAL GENOME RESEARCH FINAL PROGRAM & EXHIBIT GUIDE Organizing Committee Chairman: Stephen R. Heller, NIST (USA) Ī PLANT COORGANIZERS Juan F. Medrano, University of California, Dave Clements, Johns Hopkins University, Davis, USA USA Huaijun Zhou, University of California, Catherine Feuillet, Bayer CropScience, USA Davis, USA J. Perry Gustafson, University of Missouri, (Retired ), USA Ī ABSTRACT & WEBSITE Jerome P. Miksche, Emeritus Director, COORDINATORS USDA, Plant Genome Program, USA David Grant, USDA/ARS/CICGR, USA Graham Moore, John Innes Centre, UK Gerard Lazo, USDA/ARS/WRRC, USA Susan R. Wessler, University of California, Victoria Carollo Blake, USA Riverside, USA Rod A. Wing, University of Arizona, USA; Ī TRAVEL GRANTS COORDINATOR International Rice Research Institute, Tom Blake, Professor Emeritus, Philippines Montana State University, USA Ī ANIMAL COORGANIZERS Ī SPECIAL DUTY COORDINATORS Daniel Ciobanu, University of Nebraska – Hans Cheng, USDA/ARS, USA Lincoln, USA Max Rothschild, Iowa State University, USA Kwan-Suk Kim, Chungbuk National University, South Korea Sponsors and Supporters ORGANIZER Scherago International Ī USDA, Agricultural Research Service 111 Town Square Place Ī USDA, National Agricultural Library Suite 1208 USDA, National Institute of Food and Agriculture Ī Jersey City, NJ 07310 Ī John Innes Centre Phone: (201) 653-4777 Fax: (201) 653-5705 Cover artwork provided by Applied Biosystems. Originally developed for the company’s “Genetic Harvest” Agriculture Seminars, this image Email: [email protected] represents the importance of molecular genetic approaches in plant and animal research. Website: www.intlpag.org About Frasergen Frasergen is an innovative leader in cutting-edge bioinformatics and overseas in high-throughput genome sequencing, big genome data genomics.
    [Show full text]
  • 393LN V 393P 344SQ V 393P Probe Set Entrez Gene
    393LN v 393P 344SQ v 393P Entrez fold fold probe set Gene Gene Symbol Gene cluster Gene Title p-value change p-value change chemokine (C-C motif) ligand 21b /// chemokine (C-C motif) ligand 21a /// chemokine (C-C motif) ligand 21c 1419426_s_at 18829 /// Ccl21b /// Ccl2 1 - up 393 LN only (leucine) 0.0047 9.199837 0.45212 6.847887 nuclear factor of activated T-cells, cytoplasmic, calcineurin- 1447085_s_at 18018 Nfatc1 1 - up 393 LN only dependent 1 0.009048 12.065 0.13718 4.81 RIKEN cDNA 1453647_at 78668 9530059J11Rik1 - up 393 LN only 9530059J11 gene 0.002208 5.482897 0.27642 3.45171 transient receptor potential cation channel, subfamily 1457164_at 277328 Trpa1 1 - up 393 LN only A, member 1 0.000111 9.180344 0.01771 3.048114 regulating synaptic membrane 1422809_at 116838 Rims2 1 - up 393 LN only exocytosis 2 0.001891 8.560424 0.13159 2.980501 glial cell line derived neurotrophic factor family receptor alpha 1433716_x_at 14586 Gfra2 1 - up 393 LN only 2 0.006868 30.88736 0.01066 2.811211 1446936_at --- --- 1 - up 393 LN only --- 0.007695 6.373955 0.11733 2.480287 zinc finger protein 1438742_at 320683 Zfp629 1 - up 393 LN only 629 0.002644 5.231855 0.38124 2.377016 phospholipase A2, 1426019_at 18786 Plaa 1 - up 393 LN only activating protein 0.008657 6.2364 0.12336 2.262117 1445314_at 14009 Etv1 1 - up 393 LN only ets variant gene 1 0.007224 3.643646 0.36434 2.01989 ciliary rootlet coiled- 1427338_at 230872 Crocc 1 - up 393 LN only coil, rootletin 0.002482 7.783242 0.49977 1.794171 expressed sequence 1436585_at 99463 BB182297 1 - up 393
    [Show full text]
  • A Genome-Wide Scan for Diversifying Selection Signatures in Selected Horse Breeds
    RESEARCH ARTICLE A genome-wide scan for diversifying selection signatures in selected horse breeds 1 1 1 1 Artur GurgulID *, Igor Jasielczuk , Ewelina Semik-Gurgul , Klaudia Pawlina-TyszkoID , 2 1 3 Monika Stefaniuk-SzmukierID , Tomasz Szmatoøa , Grażyna Polak , Iwona Tomczyk- Wrona3, Monika Bugno-Poniewierska1,4 1 Department of Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland, 2 Department of Horse Breeding, University of Agriculture in KrakoÂw, al. KrakoÂw, Poland, 3 Department of Horse Breeding, National Research Institute of Animal Production, Balice, Poland, 4 Institute of Veterinary a1111111111 Sciences, University of Agriculture in Krakow, al. KrakoÂw, Poland a1111111111 * [email protected] a1111111111 a1111111111 a1111111111 Abstract The genetic differentiation of the current horse population was evolutionarily created by nat- ural or artificial selection which shaped the genomes of individual breeds in several unique OPEN ACCESS ways. The availability of high throughput genotyping methods created the opportunity to Citation: Gurgul A, Jasielczuk I, Semik-Gurgul E, study this genetic variation on a genome-wide level allowing detection of genome regions Pawlina-Tyszko K, Stefaniuk-Szmukier M, Szmatoøa divergently selected between separate breeds as well as among different horse types shar- T, et al. (2019) A genome-wide scan for ing similar phenotypic features. In this study, we used the population differentiation index diversifying selection signatures in selected horse breeds. PLoS ONE 14(1): e0210751. https://doi. (FST) that is generally used for measuring locus-specific allele frequencies variation org/10.1371/journal.pone.0210751 between populations, to detect selection signatures among six horse breeds maintained in Editor: Juan J Loor, University of Illinois, UNITED Poland.
    [Show full text]
  • The Functional Consequences of Variation in Transcription Factor Binding
    The Functional Consequences of Variation in Transcription Factor Binding Darren A. Cusanovich1, Bryan Pavlovic1, 2, Jonathan K. Pritchard1, 2,3, Yoav Gilad1 1Department of Human Genetics and 2Howard Hughes Medical Institute, University of Chicago, Chicago, IL, 60637, USA 3Departments of Genetics and Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA, 94305, USA Email addresses: DAC: [email protected]; JKP: [email protected]; YG: [email protected] Corresponding authors: DAC, JKP, and YG 1 Abstract One goal of human genetics is to understand how the information for precise and dynamic gene expression programs is encoded in the genome. The interactions of transcription factors (TFs) with DNA regulatory elements clearly play an important role in determining gene expression outputs, yet the regulatory logic underlying functional transcription factor binding is poorly understood. Many studies have focused on characterizing the genomic locations of TF binding, yet it is unclear to what extent TF binding at any specific locus has functional consequences with respect to gene expression output. To evaluate the context of functional TF binding we knocked down 59 TFs and chromatin modifiers in one HapMap lymphoblastoid cell line. We then identified genes whose expression was affected by the knockdowns. We intersected the gene expression data with transcription factor binding data (based on ChIP-seq and DNase-seq) within 10 kb of the transcription start sites of expressed genes. This combination of data allowed us to infer functional TF binding. On average, 14.7% of genes bound by a factor were differentially expressed following the knockdown of that factor, suggesting that most interactions between TF and chromatin do not result in measurable changes in gene expression levels of putative target genes.
    [Show full text]