from Dave Matthews and Ken Kephart
last update 95.06.14
How to Create Germplasm Records for GrainGenes
The Germplasm class includes cultivars, breeding lines, genetic stocks, wild
accessions, etc. of wheat, barley, oats, rice, maize -- any plant that's in
the database. Pathogens will be put in a different class such as 'Isolate'."
FIELDS AVAILABLE
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Field label Sample Entry Description of field
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Germplasm "Advance CIav3845" Primary name for the
accession. See NAMING
GERMPLASM ACCESSIONS
listed below.
Species "Avena sativa" Name of a Species object.
See discussion on SPECIES
AND SUBSPECIES listed
below.
Subspecies "Triticum turgidum See discussion on
ssp. durum" SPECIES AND SUBSPECIES
listed below.
Donor_species "Aegilops searsii" For addition and
substitution lines,
defines the species of
the progenitor used as
chromosome donor.
Type Cultivar Defines the stock type of
the germplasm record.
Acceptable values include
Cultivar, Substitution,
Amphiploid, Aneuploid,
Deletion, Alien_addition,
Mutation, Marker,
Alloplasmic_line,
Germplasm,
Elite_germplasm,
Synthetic, Isogenic.
Other_name "Rust Proof" Lists additional common
names, experimental
numbers or other synonyms
the germplasm is known by
other than the primary
name.
Collection_and_ID WGRC TA3076 Field requires two values.
Name of a Collection
object (e.g. WGRC)
followed by the
identifier for the
germplasm (e.g. TA3076) in
that particular
collection.
Cross_number CD81653 Accession identifier used
by CIMMYT.
Chromosome_configuration 20''+1'1A See GENETIC STOCKS, below.
Abbreviation CS Official abbreviation of
the germplasm name.
(Pairing_configuration) This old field is now
replaced by Chromosome_
configuration.
Chromosome_number 42tt Usually just an integer.
Female_parent "Era CItr13986" Name of a Germplasm object
used as the cytoplasm
source in developing a
germplasm. Seldom used in
preference to the Pedigree
field.
Male_parent "Justin CItr13462" Name of a Germplasm object
used as the pollen source
in developing a germplasm.
Seldom used in preference
to the Pedigree field.
Pedigree "Era / Justin" Identifies the parents and
crossing sequences used to
produce the cultivar with a
modified version of the
Purdy system. See
PEDIGREE discussion below.
Selection_history L0559-0L-2AP-0AP Identifies the plants
selected at each generation
of selfing since the
original cross.
Market_class "USDA/FGIS Hard Text description of the
Red Spring Wheat" market class based on USDA
Federal Grain Inspection
Service standards.
Trait_score "Dwarf bunt, GRIN" 88 Field requires two values.
Trait and study in which
the germplasm was
evaluated, followed by
numeric score.
Trait_description "Awn-color, GRIN" 2=Blue Alternative to Trait_score,
to be used when the
value is not strictly
numeric.
(Characteristic) "Awn-color: Blue" This field is no longer
used, but exists in older
germplasm records. Usage
replaced by Trait_score
and Trait_description
fields.
(Pathology) "Powdery Mildew" Name of a Pathology object
for a pathology to which
USE OF THIS FIELD IS CURRENTLY DEPRECATED. this germplasm is
resistant.
Rearrangement T13ak Name of a Rearrangement
object, for a translocation
or deletion present in this
stock.
Derived_from Shasta CItr17651 Name of a Germplasm
object, the progenitor of
a mutation, monosomic,
etc., or nuclear
background of an addition
or substitution.
Chromosome_donor Imperial (rye) Name of the Germplasm
providing the new
chromosome for an addition
or substitution.
Developed_by "Arkansas AES" Text citing person or
organization responsible
for development of the
germplasm.
Development_site USA-Wyoming Country and optional
state/province.
Collection_site "Akzaburt; near mountain Text describing where a
Dash-Agl" wild accession was
collected.
Date_of_release <1971 Year, or estimate thereof.
Registration_no CV-755 Crop Science cultivar (CV-)
or germplasm (GP-)
registration number.
Remark "Likes it hot" Free form text providing
any additional information.
Reference CRS-31-491 Name of a Reference object.
Image "Rye chromosomes" Name of an Image object.
Data_source CIMMYT 93.09.21 Field requires two values.
Name of a Colleague
object, followed by the
date on which the
Colleague submitted the
data to GrainGenes, in
yy.mm(.dd) format.
Polymorphism "BCD385 EcoRI" See POLYMORPHISM below.
Coefficient_of_parentage "Shasta CItr17651" 0.6 Field requires two values.
Name of a Germplasm
object, followed by a
numeric COP score from
0.0 to 1.0.
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Notes:
The words "Name of an object" used above mean "GrainGenes ID of a database
record of the indicated class". For example, whereas "Avena sativa L." is the
name of a species in a loose sense, it is not the name of a Species object in
the GrainGenes database and would be incorrect here, because the GrainGenes ID
for this species is "Avena sativa".
All text values containing embedded blanks must be bracketed by quotation
marks (").
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EXAMPLES SYNTAX NOTES
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Germplasm : "Chinese Spring CItr14108" Must include the " : ".
Species "Triticum aestivum"
Subspecies "Triticum aestivum ssp. aestivum"
Abbreviation CS If the value of a field does not
Development_site China contain any blank spaces, the
Date_of_release 1932 quotes (") are optional.
Data_source CIMMYT 93.09
Data_source "Kephart, Kenneth D." 94.02.09 If a field has multiple values,
list them one below the other.
Germplasm : "Chinese Spring-Thatcher Tetrasomic Substitution 6D TH (6D CS)"
Species "Triticum aestivum"
Type "Substitution"
Type "Aneuploid"
Abbreviation "CS-TH TS6D"
Chromosome_number 44
Chromosome_configuration "20''+1''''6D TH(6D CS)"
Derived_from "Chinese Spring CItr 14108"
Chromosome_donor "Thatcher CItr10003"
Development_site "USDA-ARS, Columbia, MO"
Collection_and_ID "USDA-ARS, Columbia, MO"
Data_source "Raupp, W. John" 94.11.15
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NAMING GERMPLASM ACCESSIONS
---------------------------
Each Germplasm in the database is known by a single primary name, which is one
of its common names if it has any, followed by its accession number in some
recognized germplasm collection. If information must be added to GrainGenes
about a Germplasm for which only a common name is known, the identifier should
be the common name followed by the name of the crop.
Examples: "Astro CIav9160", "Lamar (oat)"
What is the "common" name? Sometimes more than one exists. GRIN, for
example, has six categories of names: 1) Varietal, 2) Local, 3)
Institution, 4) Common, 5) Donor and 6) Other. In exporting GRIN data to
GrainGenes, we have used the lowest-numbered category for which a name is
given. If additional names are given, they are placed in the Other_name
field.
There are several trivial aspects of Germplasm names -- punctuation, blanks,
etc. -- that tend to be used inconsistently. Here are some of the conventions
that are followed in GrainGenes to prevent such naming inconsistencies. When
in doubt, send email to kephart.
"CI" Numbers: Use the complete "Cereal Investigations" prefix for the correct
crop species and do not embed a blank between prefix and accession number.
All wheat accessions identified by a "CI" number use the prefix "CItr" (e.g.
"CItr1353", not "CI 1353" or "CItr 1353"). Other CI prefixes for small grains
include "CIho" (barley), "CIav" (oat) and "CIse" (rye)
"PI" Numbers: Do not embed a blank between the "PI" prefix and accession
number (e.g. "PI38347", not "PI 38347").
CIMMYT Cross ID - Selection ID numbers: "CID-SID: 541-6"
Abbreviations of US states: Do follow with a blank. "MO 11769", not
"MO11769".
"RL" and similar accession numbers: Do not embed a blank between prefix and
accession number (e.g. "RL6002", not "RL 6002").
SPECIES AND SUBSPECIES
----------------------
All primary Germplasm records should have a value in the Species field. An
optional Subspecies field is also available; it should contain the full
species and subspecies name. Examples:
Germplasm : "Advance CIav3845"
Species "Avena sativa"
Germplasm : TA1
Species "Triticum timopheevii"
Subspecies "Triticum timopheevii ssp. araraticum"
Note also that the authority is not included as part of either the Species
or the Subspecies value. This information is in the GrainGenes record for
the Species itself.
GENETIC STOCKS
--------------
The conventions for naming wheat genetic stocks, for formulating their
official abbreviations, and for certain fields like Chromosome_configuration
are described in WJ Raupp, B Friebe and BS Gill, "Suggested guidelines for
the nomenclature and abbreviation of the genetic stocks of wheat, Triticum
aestivum L. em Thell., and its relatives", http://wheat.pw.usda.gov/
ggpages/GeneticStockNaming.html.
PEDIGREES
---------
The pedigree identifies the parents and crossing sequences used to produce the
cultivar. The method used to illustrate pedigrees is a slightly modified
version of the system proposed by Purdy et al. in 1969 (see Crop Sci. 8:405-
406). Use of abbreviations has been minimized. Crosses are symbolized by
combinations of slash marks ("/") with female and male parents listed to left
and right side, respectively. Numbers indicate the order in which crosses
were made:
/ = primary cross
/2/ = secondary cross
/3/ = tertiary cross
/X/ = Xth level cross, etc.
Higher numbers indicate more recent crosses in the sequence. The most recent
or final cross used to create a cultivar is indicated by the highest number
within the pedigree. For example, the pedigree of "Scout" hard red winter
wheat is:
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Example 1: Comparison of Purdy pedigree nomenclature to a tree
diagram of the pedigree of Scout hard red winter wheat.
Scout = Nebred /2/ Hope / Turkey Red /3/ Cheyenne / Ponca
OR
Hope Turkey Red
|______ / _____|
|
|
Nebred "?"
|_____ /2/ _____|
| Cheyenne Ponca
| |______ / ____|
| |
| |
"?" "?"
|___________ /3/ __________|
|
|
Scout
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In narrative terms, an unidentified progeny of a primary cross between "Hope"
hard red spring wheat and "Turkey Red" hard red winter wheat was selected and
crossed to "Nebred" hard red winter wheat. One of the progeny selected from
the "Nebred/2/Hope/Turkey Red" sequence of crosses was crossed to another
unidentified progeny derived by crossing "Cheyenne" and "Ponca" hard red
winter wheats. The cultivar Scout was selected from progeny resulting from
the final or "/3/" cross. Specific generations and selection techniques
involved are not indicated, but may be obtained from the referenced
literature.
Single slash marks are also used where the parents are known, but the exact
sequence of a series of crosses is unknown. Backcrossing sequences are
indicated by use of an asterisk ("*") preceded or followed by a number to
indicate the total number of crosses made with the recurrent parent (see
Examples 2 and 3). Left and right parentheses are used to bracket both the
pedigree and designation of breeding lines contained within a cultivar's
pedigree (see Example 4). Commas are used to separate breeding line pedigrees
from designations within the parentheses.
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Example 2: Pedigree with three backcrosses of female recurrent parent
for TAM 107 hard red winter wheat.
TAM 107 = TAM 105*4 / Amigo
OR
TAM 105 Amigo
|____ / ____|
|
TAM 105 |
1st backcross> |____ *2 / ____|
|
TAM 105 |
2nd backcross> |____ *3 / ____|
|
TAM 105 |
3rd backcross> |_____ *4 / _____|
|
|
TAM 107
Example 3: Pedigree with three backcrosses of male recurrent parent
for Blueboy II soft red winter wheat.
Blueboy II = Agent / Tascosa /2/ 4*Blueboy
OR
Agent Tascosa
|____ / ____|
|
| Blueboy
|____ /2/ ____|
|
| Blueboy
1st backcross> |____ /2/ 2* ____|
|
| Blueboy
2nd backcross> |____ /2/ 3* ____|
|
| Blueboy
3rd backcross> |____ /2/ 4* ____|
|
|
Blueboy II
Example 4: Use of parentheses to delineate breeding line used in the
pedigree of Pitic 62 hard red spring wheat.
Pitic 62 = Yaktana 54 /2/ (Sel. 26-1c, Norin 10 / Brevor)
^
Indicates Sel. 26-1c as the male
parent of the highest order cross for
Pitic 62, with its own pedigree of
"Norin 10 / Brevor".
OR
Norin 10 Brevor
|________ / ______|
|
|
Yaktana 54 Sel. 26-1c
|__________ /2/ _________|
|
|
Pitic 62
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Narratives providing more detailed information are used where necessary for
clarification. Pedigrees of cultivars screened from another cultivar are
listed as "pure line selections". Pedigrees of cultivars phenotypically
selected from mixtures or out-crosses in commercial fields are listed as
"farmer selections" with the original source material identified wherever
possible.
POLYMORPHISMS
-------------
The Polymorphism field can accept just the Name of a Polymorphism record (e.g.
"BCD385 EcoRI"). Alternatively this name can be followed by additional
information about what fragments of this polymorphism are present or absent in
this Germplasm. This is done by adding the word "Present" or "Absent",
followed by a list of fragments/molecules. Example:
Germplasm : "Advance CIav3845"
Polymorphism "BCD385 EcoRI" Present 14.9 13.4
Polymorphism "BCD385 EcoRI" Absent 17.2 12.4 4.6
Polymorphism "BCD719 EcoRI" Present 6.6 4.4
Polymorphism "BCD719 EcoRI" Absent 14.5
The fragments may be designated by their sizes in kb, as here, but any text
string is allowed. Thus isozyme or protein polymorphisms could also be
described in this field.