Animal Science Publications Animal Science 2011 Standard Genetic Nomenglature of the Pig, with Glossaries Zhiliang Hu Iowa State University, [email protected] Carissa A. Park Iowa State University, [email protected] James M. Reecy Iowa State University, [email protected] Follow this and additional works at: http://lib.dr.iastate.edu/ans_pubs Part of the Agriculture Commons, Animal Sciences Commons, and the Genetics Commons The ompc lete bibliographic information for this item can be found at http://lib.dr.iastate.edu/ ans_pubs/172. For information on how to cite this item, please visit http://lib.dr.iastate.edu/ howtocite.html. This Article is brought to you for free and open access by the Animal Science at Iowa State University Digital Repository. It has been accepted for inclusion in Animal Science Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Standard Genetic Nomenglature of the Pig, with Glossaries Abstract Genetics includes the study of genotypes, phenotypes and the mechanisms of genetic control between them. Genetic terms describe the processes, genes and traits with which genetic phenomena are described and examined. The eg netic process terminologies are thoroughly discussed in the previous chapters. Therefore, in this chapter, we will only list the terms for genetic processes and concepts in Appendix I (a general genetic glossary), and concentrate the discussion on pig gene and trait terminologies (Appendix 10; a glossary for pig diseases and defects is also included (Appendix III). Disciplines Agriculture | Animal Sciences | Genetics Comments This chapter is from The Genetics of the Pig, 2nd ed., chapter 19 (2011): 473. Posted with permission. This article is available at Iowa State University Digital Repository: http://lib.dr.iastate.edu/ans_pubs/172 Zhi-Liang Hu, Carissa A. Park and James M. Reecy Iowa State University, USA Introduction 473 Locus and Gene Names and Symbols 474 Locus name and symbol 474 Allele name and symbol 475 Genotype terminology 475 Trait and Phenotype Terminology 475 Pig traits and trait ontology 475 Trait nomenclature recommendations 479 Phenotype nomenclature recommendations 480 Future Prospects 480 Acknowledgements 480 References 481 Appendix I Genetic Glossary 482 Appendix II Pig Trait Glossary 487 Appendix III Pig Disease and Defect Glossary 492 Introduction production and genetic improvement indus­ tries. This issue becomes even more evident in Genetics includes the study of genotypes, phe­ the post-genomics era, owing to the rapid notypes and the mechanisms of genetic con­ accumulation of large quantities of genetic and trol between them. Genetic terms describe the phenotypic data, and the use of computer processes, genes and traits with which genetic software to manage such data. This imposes a phenomena are described and examined. The challenge for the precise definition and inter­ genetic process terminologies are thoroughly pretation of gene and trait terms. discussed in the previous chapters. Therefore, For example, Myostatin (gene MSTN) is in this chapter, we will only list the terms for also known as Growth and Differentiation genetic processes and concepts in Appendix I Factor 8 (gene GDF8) (one can also find inap­ (a general genetic glossary), and concentrate propriate abbreviations such as GDF-8 in the the discussion on pig gene and trait terminolo­ literature) and is referred to as the 'muscle gies (Appendix 10; a glossary for pig diseases hypertrophy" locus in cattle. While all these and defects is also included (Appendix III). names are interchangeably used in the litera­ A standardized genetic nomenclature is ture, it gets more complicated when one con­ vital . for unambiguous concept description, siders paralogous gene duplications across efficient genetic data management and effec­ species, which led Rodgers et a/. (2007) to tive communications among not only scien­ propose MSTN-1 and MSTN-2 as names. tists, but also those who are involved in the pig Unfortunately, this naming scheme does not ©CAB International 2011. The Genetics of the Pig, 2nd Edn (eds M.F. Rothschild and A. Ruvinsky) 473 follow Human Gene Nomenclature Committee synonymous with a gene, refers to a position in (HGNC) guidelines, which would indicate that the genome that can be identified by a marker. they should be named MSTNl and MSTN2. A 'chromosome region' is defined as a genomic In terms of traits, an example that would region that has been associated with a particu­ benefit from consistent nomenclature is the lar syndrome or phenotype. longissimus dorsi muscle area, which is also Gene names and symbols will follow the referred to as the loin eye area (LEA), loin mus­ human gene when 1:1 orthology is known. Gene cle area (LMA), meat area (MLD), ribeye area names should be short and specific and convey (REA), etc. Each of these is known by different the character or function of the gene. Gene individuals as the default name for the trait. names will be written using American spelling Complexity is further increased by variation in and contain only Latin letters or a combination of anatomical locations, physiological stages and Latin letters and Arabic numerals. The first letter methods used to measure a given trait. This may of a gene symbol should be the same as for the seem manageable at first, but once one starts to gene name. The symbol will consist of upper­ compare data across different labs, publications case Latin letters and possibly Arabic numerals. or species, it quickly becomes very confusing. Gene symbols must be unique. While we may not want to dictate to the The locus name should be in capitalized community how genetic terms are defined, Latin letters or a combination of Latin letters there are good reasons why all researchers and Arabic numerals. If the locus name is two need to adopt standardized genetic nomencla­ or more words, each word after the first word tures. The emergence of the use of ontologies should be in capital Latin characters. The locus in biological research has contributed a new symbol should consist of as few Latin letters as way to effectively use, standardize and manage possible or a combination of Latin letters and genetics terms. The Gene Ontology (GO) con­ Arabic numerals. The characters of a symbol sortium has provided a good example (The should always be capital Latin characters, and Gene Ontology Consortium, 2000). When should begin with the initial letter of the name genomics information must be transferred of the locus. If the locus name is two or more across species to perpetuate genetic discover­ words, then the initial letters should be used in ies, the role of a standardized genetic nomen­ the locus symbol. The locus name and symbol clature becomes even more important. should be printed in italics wherever possible; The goal of this chapter is to help estab­ otherwise they should be underlined. lish guidelines for nomenclature, with the hope When assigning gene nomenclature, the that it will facilitate the comparison of results gene name and symbol should be assigned between experiments and, most importantly, based on existing HGNC nomenclature where prevent confusion. possible (e.g. 1:1 for swine:human orthologues). Ensembl (a joint project between EMBL-EBI (European Molecular Biology Laboratory­ Locus and Gene Names and Symbols European Bioinformatics Institute) and the Wellcome Trust Sanger Institute to develop a Locus name and symbol software system that produces and maintains automatic annotation on selected eukaryotic These guidelines for gene nomenclature are genomes) has used the new EPO (Enredo, adapted and abbreviated from the HGNC Guide­ Pecan, Ortheus) pipeline (Paten et a/., 2008) lines (http://www.genenames.org/guidelines. for whole genome alignment of the swine html). genome. Initial efforts to provide information A 'gene' is a functional hereditary unit about genes predicted during the swine genome that occupies a fixed location on a chromo­ sequencing effort assigned standardized nomen­ some, has a specific influence on phenotype, clature based on human gene nomenclature for and is capable of mutation to various allelic 2798 swine genes (http://www.ensembl.org/ forms. In the absence of demonstrated function Sus_scrofa/lnfo/StatsTable). a gene may be characterized by sequence, tran­ There are two categories of novel swine scription or homology. A 'locus', which is not genes: (i) novel genes predicted by bioinformatic gene prediction programs; and (ii) novel swine SNP occurs outside an identified gene, the genes that were studied before the completion SNP locus can be designated using the dbSNP _ of the swine genome. In cases where no strict id as the locus symbol, and the nucleotide allelic 1:1 human orthologue exists that has been variants are then superscripted as alleles (e.g. assigned nomenclature, the LOC# or Ensembl rs123456T). ID should be used as a temporary gene symbol. The allele symbol should always be written In order to assign a name to a novel gene, it will with the locus symbol. Specifically, the allele need to be manually curated and assigned a symbol is written as a superscript following the unique name, following HGNC guidelines. locus symbol. For example, an SNP allele can be designated based on its dbSNP_id, followed by a hyphen and the specific nucleotide, as in Allele name and symbol MSTN•1234567 r. The allele symbol should be printed immediately adjacent to the locus sym­ These guidelines for allele nomenclature are bol, with no gaps. The allele name and symbol adapted from Young (1998) and mouse should be printed in italics whenever possible, genome nomenclature guidelines (http://www. or otherwise be underlined. informatics.jax.org/mgihome/nomen/gene. shtml), in accordance with HGNC guidelines. The allele names should be as brief as pos­ Genotype terminology sible, yet still convey the variation associated with the allele. Alleles do not have to be named, The genotype of an individual should be shown If allele is but should be given symbols.