Procedures for listing loci and alleles of ruminants: 1991 proposals

The following procedures for listing loci in ruminants were proposed at the 1991 1st Workshop on Genetic Nomenclature of Farm Ruminants organised by COGNOSAG (Committee on Genetic Nomenclature of Sheep and Goats): identification of locus, genomic location, gene effect classification (24 entries), summary of alleles and, for each allele, after identification, phenotypic effect, inheritance and breeds implied. This


INTRODUCTION
The definition of guidelines for gene nomenclature of sheep and goats was prepared during COGNOSAG Workshops (Committee on Genetic Nomenclature of Sheep and Goats) in 1987 and 1989 (Alexieva et al, 1989a(Alexieva et al, , 1990. At the 1991 Workshop, entitled First Workshop on Genetic Nomenclature of Farm Ruminants, these guidelines were reviewed so that they would be suitable for all ruminants (Andresen et al, 1991).
Besides these guidelines COGNOSAG started to elaborate the general procedure of listing loci and alleles of sheep and goats during the 1987 Workshop (Alexieva et al, 1989b). This document was revised almost without change during the Workshop at Eugene (Oregon) in 1989, and, at the above-mentioned 1991 Workshop, these procedures were again reviewed and are given in the present article. The purpose is to make them suitable for all ruminants in order to prepare a first edition of MIS, MIG and MIC catalogues (mendelian inheritance in sheep, goats and cattle respectively) and also to be used in future data banking.

OBJECTIVES
The objectives are to use the guidelines for gene nomenclature elaborated during the above-quoted 1991 Workshop (Andresen et al, 1991) to produce a list of loci and alleles for cattle, sheep and goats, and to assess the contribution made by each reference to knowledge of the inheritance of the allele.
The list and assessment are such that they can be fully checked by other workers, and can be added to or amended as necessary.

CATEGORIES OF LOCI AND HEADINGS
Within each of the species -cattle, sheep and goats -loci are classified into 4 categories, namely: Genomic location This will be specified by selecting one of the following descriptors: i) undefined, where the genomic location has not been reported; ii) sex chromosomes or autosome, when there is evidence implicating either the X/Y chromosomes or the autosomes but insufficient evidence to go beyond this; iii) the chromosome number, arm or region, as defined by ISCNDA 1989ISCNDA rules (1990 and/or earlier reports of the Committee for Standardisation of the Karyotypes of Domestic Animals (Reading Conference, 1980;Long, 1985). If only chromosome number but no further information on the regional localisation of a locus is known, this will be indicated as eg &dquo;Chr 7&dquo; or &dquo;Chr 8&dquo;. Designating chromosome arms as either & d q u o ; p & d q u o ; or & d q u o ; q & d q u o ; will only be appropriate for the sheep autosomes, chromosome numbers 1-3, the cattle X-chromosome and the Y-chromosome in all ruminants; iv) the syntenic group will be designated by the symbol &dquo;U&dquo; followed by an Arabic number, eg U1, U2, etc... Such designations will be most frequently made from studies involving somatic cell hybrids in which the identification of ruminants chromosomes retained by the hybrid cells has not been reported; v) the linkage group will be designated by the symbol &dquo;LG&dquo; followed by an Arabic number, eg LG1, LG2, etc...; or, vi) mitochondrial, where it is known that the locus is not located on the nuclear genome, but is present on the mitochondrial genome.
In most cases, it will be sufficient to select only one of those descriptors. However, there may be instances in which it is informative to specify 2 such descriptors, eg linkage groups, as well as the chromosome number.
Reference: a short reference comprising the name(s) of the authors and year will be given to support the genomic location of each locus. Status: P or C. The &dquo;P&dquo; is to be allocated when there is only a single report of the location of a locus indicating that its location is &dquo;provisional&dquo;. The &dquo;C&dquo; will be awarded when the location of a locus has been &dquo;confirmed&dquo;.

Gene effect classification
Each locus is classified into one or more of the following classes: 1. Coat colour 2. Skin, fibres, hooves and horns and function 3. Skeletal system (including legs and tail) and function (including locomotion) 4. Appendages (including outer ears and wattles) 5. Nervous system (including brain, inner ear and eye) and function 6. Endocrine system (including dwarfism and obesity) and function 7. Reproductive system (including fertility, gametes, zygotes, embryos and fetuses) and function 8. Circulatory system and function 9. Digestive system (including metabolism) and function 10. Muscle and function 11. Urinary system and function 12. Respiratory system and function 13. Mammary glands and lactation  (table) Name and symbol: the names and symbol are given as set out in the COGNOSAG Guidelines for Gene Nomenclature in Ruminants 1991 (Andresen et al, 1991). The alleles are listed in order of dominance, where known, the dominant allele being at the top.
Status: the evidence presented for each allele is assessed as follows, unless otherwise indicated in the introduction to a category listing: -the evidence is such that the existence of the allele as being the cause of the effect is established beyond reasonable doubt. Segregation data which demonstrate this must be given. Evidence for the allele is unequivocal; -the evidence is such that the allele is most probably the cause of the effect, but the possibility of other causes has not been reasonably excluded. Reports in this category would include those with extensive population studies or those with segregation data consistent with the existence of the allele, but for which the evidence is not unequivocal.
the essence of an allele is postulated to explain the phenotype described: A brief description is given of the effects of the allele. The effects are those observed in the genetic background of the breed or strain of cattle, sheep or goats with which the authors worked, or on the wild type. The effects of the allele are described from the phenotypes of animals homozygous for the allele in question whenever possible.

Inheritance
Comments are made on the pattern of inheritancepossibly including some of the following terms: -pleiotropy, polygenic (quantitative), genetic background, epistasis; -incomplete penetrance, variable expressivity, threshold character; -dominant, co-dominant, recessive. Status: an assessment of the evidence presented for each allele is made as described above.

Breeds
The breeds mentioned in the references quoted for each allele are given. As a precaution against unwarranted extrapolation or inference, breeds not quoted in references are not listed.