Procedures for listing loci and alleles of ruminants: 1991 proposals

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Procedures for listing loci and alleles of ruminants: 1991

proposals

E Andresen, T Broad, L Di Stasio, Chs Dolling, D Hill, K Huston, B Larsen,

Jj Lauvergne, H Levéziel, X Malher, et al.

To cite this version:

Letter to

the Editor

Procedures

for

_listing

loci

and

alleles of ruminants:

1991

_proposals

E

Andresen

T Broad

L

Di Stasio

CHS

_Dolling

D Hill

K Huston

B Larsen

JJ

_Lauvergne

H Levéziel

9

X Malher

P Millar

AL Rae

C

Renieri

EM

Tucker

1

!

Division

_of

Animal

_{Genetics, Department of}

Animal Science and

Health,

Biilowsvej 13,

1870

_{Frederiksberg C, Denmark;}

2

DSIR

_Grassland,

Palmerston

North,

New

Zealand ;

3

Dipartimento

di Scienxe

Zootechnice,

Via

Genova,

6, 10126

Turin, Italy;

4

Box

_74,

Mc Laren

_Vale,

SA

_{5171, Australia;}

!

University of

Otago,

Department

of Biochemistry,

Box

_{56, Dunedin,}

New

_Zealand;

6

1689

Arthur

_{Drive, Wooster,}

OH

_{!,!, 691,}

_USA;

!

National Institute

_of

Animal

_{Science, Department}

_of

Animal

_Physiology

and

_{Biochemistry,}

PO Box 39, 8830

_{Tjele, Denmark;}

8

Laboratoire de

_{Génétique Factorielle, Département}

de

_Génétique

Animale de

_l’INRA,

CRJ,

78 352

_{Jouy-en-Josas,}

_C!dex;

!

Laboratoire de

_{Genetique Biochimique, Department}

de

_Génétique

Animale de

_l’INRA,

CRJ,

78 352

_{Jouy-en-Josas,}

_Cedex;

10

_Ecole

Nationale V6t6rinaire de

_{Nantes, D6partement}

des Productions

_Animales,

BP

_{527, 4}

₄

₀₂₆

Nantes

_{C6dex, France;}

11 _Britbred

Ltd,

12A Riselaw

_{Crescent, Edinburgh,}

EHIO

_{6HL, UK;}

12

16,

Wallace

_Place,

Palmerston

North,

New

Zealand;

13

Istituto di Produzioni

Animali,

Via San Constanzo

4,

06100

Perugia, Italy;

14

AFRC,

Institute

_{of Physiology}

and Genetics

_Research,

Babraham, Cambridge

CB2

4AT,

UK

(Received

27

_{February 1992; accepted}

31 March

₁₉₉₂₎

Summary - 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

*

set of

_procedures

is intended for the first edition of the

_MIS,

MIG and MIC

_catalogues

(mendelian

inheritance in

_sheep,

_goats and

_cattle,

_{respectively)}

and is a basis for future data

_banking.

ruminants

_/

loci

_/

listing procedures

/

nomenclature

R.ésumé - Procédures de listage des loci et allèles des ruminants 1991. Au cours du premier Atelier de Nomenclature

_Génétique

des Ruminants de Ferme

_organisé

par le COGOVICA

_(Comité

de Nomenclature

_Génétique

des Ovins et

_Caprins)

en

_1991,

les

procédures

suivantes de

_listage

des loci chez les Ruminants ont été

_{proposées: identification}

du

_locus,

localisation sur le

_{génome, effet}

du

_gène

_{(24 entrées),}

tableau des allèles _{et, pour}

chaque allèle,

outre

_{l’identification, l’effet phénotypique,}

l’hérédité et les races concernées.

Conçue

pour être utilisée dans la

première

édition des

_{catalogues MIS,}

MIG et MIC

(Mendelian

Inheritance in

_Sheep,

Goats and Cattle

_resp),

cette

grille

peut servir de base pour une

_{future banque}

de données.

ruminants

_/

loci

_/

procédures de listage

/

nomenclature

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,}

_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,

CATEGORIES OF LOCI AND HEADINGS

Within each of the

species -

cattle,

sheep

and

_{goats -}

loci are classified into

4

_{categories, namely:}

1. Coat colour

2. Visible traits other than coat colour

3.

Blood,

milk and other

_body

fluids

4. Other

_genetic

_systems

_{( eg}

molecular

_markers)

Loci and alleles are listed within each of the above

_categories.

The information

available on each

_locus

and on each allele should be

_given

under the

following

basic

set of

_headings:

Locus Name

Symbol

Other names

Genomic location

_(with

references and

_status)

Gene effect classification

Summary

of alleles

_(name,

_symbol,

_status,

_references)

Comments on the locus

References for the locus Allele Name

Symbol

Phenotypic

effect of allele Inheritance

Status Breeds

Comments on the allele

References for the allele

Then,

as an

_option,

at the end of the

_listing

of all loci and alleles in a

_category:

Bibliography.

LOCUS DESCRIPTION

_(DETAILS)

Name, symbol,

other names

Names and

_symbols

are defined as set out in the COGNOSAG Guidelines for Gene

Nomenclature in Ruminants 1991

_(Andresen

et

_al,

_1991).

The &dquo;other names&dquo; for loci include those which have been used in the literature

other than the names

designated

_by

COGNOSAG.

Geographic

terms are used to describe loci or alleles found in different

parts

of

the world if:

- alleles with similar effects have been identified in different

regions;

- tests for allelism have not been carried

- additional

description

is needed to

_prevent

confusion in the term used to

designate

locus or allele.

The loci are considered as

_being

_separate

until tests for allelism have been carried

out.

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 1989 rules

(1990) and/or

earlier

_reports

of the Committee for Standardisation of the

Karyo-types

of Domestic Animals

_(Reading

_{Conference, 1980; Long,}

_1985).

If

_only

chro-mosome 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

chromo-some arms as either

_{&dquo;p&dquo;}

or

_{&dquo;q&dquo;}

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

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 14.

_Lethal,

sublethal and subvital factors

15. Plasma enzymes

16. Plasma

_proteins

other than enzymes

17.

_Erythrocyte

enzymes

18.

_Erythrocyte

proteins

and

_{transport systems}

other than _enzymes 19.

_{Erythrocyte antigens}

20.

_{Lymphocyte antigens}

21. Milk

_proteins

22.

_Leucocyte

_enzymes

23.

_{Leucocyte proteins}

other than _enzymes 24. Resistance to assault

Disease Toxins

Other 25. DNA sequences

Summary

of alleles

_(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:

References

(in

the

_table):

the references for alleles are

presented

with the name of

the author and year.

Comments on the locus

Comments may include historical definition of the effects of the locus or of the

breeds which _express the

_locus,

and

_descriptions

of

_cattle,

_sheep

and

_goats

with different

_genetic

_backgrounds.

The nature of the evidence for the existence of the

locus may be discussed.

Homology

of the locus with loci in other

_species,

where

known,

is indicated.

References for the locus

References for the locus _may be listed here or in a

_bibliography

at the end of the

category.

They

are

_given

in

_alphabetical

order of the name of the first

_author,

and

are not numbered.

All references for any

category

should be either in this format:

Adalsteinsson

_S,

Basrur PK

₍₁₉₈₄₎

Inheritance of

_spina

bifida in Icelandic lambs. J Hered

75,

378-382

or in this format:

Adalsteinsson

_S,

Basrur PK

₍₁₉₈₄₎

J Hered

_75,

378-382

ALLELE DESCRIPTION

_(DETAILS)

Phenotypic

effect

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 inheritance -

_{possibly 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

Comments

Comments _may include the historical definition of the effects of the allele in the breeds which carry the

allele,

and

descriptions

of

cattle,

sheep

and

goats

with different

_genetic

_background.

The nature of the evidence for the existence of the allele may be discussed.

References for the allele

References _{for the allele may be listed here} or in a

bibliography

at the end of the

category.

They

should all be in one of the forms

exemplified

above

(see

_References

for

the

_locus).

REFERENCES

Alexieva

_SA,

Aliev

_G,

Bourzat

_D,

Denis

_B,

_{Dolling CHS, Lauvergne}

_JJ,

Lundie

RS,

Millar

_P,

Rachovski

_ML,

Rae

_AL,

Renieri

_{C, Sponenberg}

DP,

Tucker EM

₍₁₉₉₀₎

Gene nomenclature in

_sheep

and

_goats,

_1989,

In:

_{Loci for}

Coat Colour in

_Sheep

and

Coats

_(JJ

_Lauvergne,

_ed)

_COGNOSAG,

Clamart

Alexieva

_SA,

Denis

_B,

_{Dolling CHS, Lauvergne}

_JJ,

Lundie

_RS,

Millar

_P,

Rae

AL,

Renieri

_C,

_Sponenberg

_DP,

Tucker EM

₍₁₉₈₉₎

Gene nomenclature in

_sheep

and

_goats

1987. In: Proc COGNOSAG

_Workshop

_{1987 (JJ}

_Lauvergne,

_ed)

Bureau

Ressources

_G6n6tiques,

_Paris,

17-21

Alexieva

SA,

Denis

_B,

_Dolling

_{CHS, Lauvergne JJ,}

Lundie

_RS,

Millar

_P,

Rae

AL,

Renieri

_C,

_Sponenberg

_DP,

Tucker EM

_(1989b)

General

_procedures

for

_listing

loci and alleles of

_sheep

and

_goats

1987. In: Proc COGNOSAG

_Workshop

1987

(JJ

Lauvergne,

ed)

Bureau Ressources

_G6n6tiques,

Paris,

23-32

Andresen

_E,

Broad

_T,

Di Stasio

L,

Dolling CHS,

Hill

_D,

Huston

K,

Larsen

_B,

Lauvergne

JJ,

Lev6ziel

_H,

Malher

_X,

Millar

_P,

Rae

AL,

Renieri

C,

Tucker EM

(1991)

Guidelines for _{gene nomenclature} in ruminants 1991. Genet Sel Evol

23,

461-466

ISAG Nomenclature Standardisation

_Workshop

₍₁₉₈₅₎

Anim Blood

_Groups

Biochem

Genet

16,

249-252

ISCNDA

_(1989,

₁₉₉₀₎

International

_System

for

_Cytogenetic

Nomenclature of

Do-mestic

Animals

_(D

Di

_Bernardino,

H

_Hayes,

R

_Fries,

S

_Long,

_eds)

_Cytogenet

Cell Genet

_53,

65-79

Long

S

₍₁₉₈₅₎

Standard nomenclature for the G-band

_karyotype

of the domestic

sheep

(Ovis aries).

Hereditas

103,

165-170

Reading

Conference

₍₁₉₈₀₎

Proc 1st Int Conf Standard Banded

_Karyotypes