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The Nordic Gene Bank Information System For Plant Genetic Resources

EPGRIS regional Meeting at Alnarp, August 24
-
25 2001



Dag Terje Endresen






Introduction

The Nordic Gene Bank (NGB) is a regional gene bank for the five Nordic countries: Denmark, Fin
land,
Iceland, Norway and Sweden. The mandate of the gene bank is to preserve material from this geographical
area. Furthermore, the aim is to document, characterise and carry out research and pre
-
breeding projects on
preserved material. NGB is located at
Alnarp, in the south of Sweden, close to the city of Malmö and
Copenhagen.

NGB is organised under and financed by the Nordic Council of Ministers (NMR)The staff members are
engaged on four
-
year contracts with a maximum of 8 years.


History

The Nordic Gene
Bank was founded in 1979 and merged with Internordic Plant Breeding (SNP) in 1993.
During the first years NGB was mainly concerned with collection of wild material and transfer of material
from other Nordic institutions. Routines for seed management and co
nservation was studied and developed.
During the later years of the 1980’s most of the available information on the material was registered in
databases and prepared for publication. During the early 1990’s several projects on description of the
collectio
n was completed and published.


Mandate

The mandate of NGB is to preserve and document Nordic plant genetic resources (PGR) and to support
Nordic plant breeding. The term Nordic material is interpreted as wild material growing in the Nordic
countries, Nord
ic landraces, modern varieties produced in the Nordic countries and other plant material
produced by Nordic scientists or plant breeders. A list of mandate species is maintained by the NGB board.
NGB may in special cases accept short term responsibility fo
r material outside the mandate, for example if
there is material of interest for the Nordic countries which are not preserved elsewhere.


The responsibility for the NGB mandate species is divided into six crop oriented working groups.

Cereals

Fruit and Be
rries

Potatoes

Forage Crops

Vegetables

Root Crops, Oil Plants and Pulses


Ex situ

preservation

Most of the NGB material is preserved
ex situ

as seeds in common household deepfreezers at
-
20

C. The
ex
situ

collection is divided into three separate collectio
ns. The
active collection

is aimed for utilisation
pupose and every accession is stored in small aluminium bags (distribution bags) containing approximately
250 seeds. A larger bulk bag is used for more distribution bags when necessary. The active collecti
on
contains all accessions. The accessions inside our mandate are also stored in The
base collection
is
maintained for
------

and contains all accessions for long term storage, approximately 30000. The base
collection is regularly tested for germination an
d rejuvenation is caried out when the germination drops
below a certain minimum level specified for the species. The
safety collection

is a duplicate of the base
collection and is stored in a coal mine under the permafrost at the Svalbard Islands.


Materia
l in field gene banks

Fruit trees, berries and vegetables are preserved
ex situ

in clonal archives (field gene banks)

The conservation of vegetatively propagated material is a national responsibility, however NGB still has
the responsibility for the docume
ntation.

Potatoes is however an exception. NGB takes full responsibility for the conservation of this material, which
is stored
in vitro

as meristems.


Documentation history

NGB has had a permanent connection to the internet since the late 1994 over a 64 K
bit line. A MS
-
DOS
server was set up at http://www.ngb.se and NGB published documents as WWW, FTP and Wais. In the
summer of 1995 the DOS server was upgraded and Linux installed as operating system. The link was
upgraded to a 2 Mbit line in 1999.

In the 19
80s NGB participated in the development of a software package called BIRS in order to manage
the accession data for minicomputer. When the personal computer came in general use in the 1980s, the
BIRS software was converted to an MS
-
DOS application and used

until early 1990s. NGB also had a
leading role in the Nordic information project ’Nordic biometry project’, 1987
-
1991 resulting in a computer
system with routines for PGR administration for plant breeders. The system was called NOBIS and used by
NGB in th
e early 1990’s.

Many new software solutions for relational database management became available and NGB chose the
dBase IV format, which was upgraded to Visual dBase in the middle of the decade and still most of the
seed store databases are managed in this

format. When the Linux server was installed NGB gradually
started using an SQL based database engine with web interface. This is concidered the preferred solution
when developing new application for the information system today. Applications are written i
n various
script languages (PHP, Java, JavaScript, Perl) giving access to the database engine (PostgreSQL) through a
web interface. The web interface is easier to update with altered database structure. Another advantage is
the possibility to work directly

with the data on distance with an active internet connection.

All the server software which NGB uses today is based on free, open
-
source licenses; Linux as operative
system, Samba as file and print server, PostgreSQL as database engine, Apache as web serv
er, Free Wais
for search and indexing engine, Majordomo for the mailing lists and Grass as the GIS tool. A strict policy
on security ia a necessity and therefore a firewall is setup and OpenSSH is used for secure remote login.

The free software solution al
lows for testing new software solutions without wasting budget money and
more budget money is available for upgrading hardware. This is part of NGB’s low cost strategy to present
the NGB solutions as a affordable model for others. NGB is involved in two co
llaboration projects where
the low
-
cost model is used. During 10 years NGB has acted as consultant in the development of the
regional gene bank (SPGRC) in southern Africa (SADC), where specifically the low
-
cost seed handling has
been used. Since 1994 NGB h
as aided in the development of the PGR activities in the Baltic countries
Estonia, Latvia and Lithuania. The low
-
cost documentation model has been implemented with the help of
three technical training courses held at NGB. In addition the low
-
cost documenta
tion model has been
demonstrated at IPGRI in Rome and at a technical course at the VIR institute in St. Petersburg.


Information system today

Today most of the tables in the material databases is handled by the database management system Visual
dBASE. The
content of these tables is every night transferred to the SQL based PostgreSQL management
system and the WAIS indexing system. The information available at the NGB web site is extracted from
the WAIS system. Most of the local information management is carr
ied out directly towards the
PostgreSQL database. An exception is the seed store tables which is still managed by use of a Visual
dBASE application programmed at NGB. Even these tables will probably soon be managed towards the
PostgreSQL database server.

T
he structure of the main tables is given below, but please bear in mind that several modifications on the
structure of the tables is planned. The structure of the NGB information system should generally be
compatible with the Multi
-
Crop passport descriptor
s, and the export to EPGRIS mostly done by translation
of field names.


Material tables

Taxon

Taxon synonyms

Culton

Accession

Passport data

Seed store tables (Batch, Active, Base, Safe)

Germination test results

Evaluations

Material transactions

Regeneratio
n of material


Contacts tables

Institute

Person

Locations



Scientific species names, taxon

In the 1990’s it became evident that it was neccesary to create a separate table for scientific names. The
names used for the same species in the accession table ha
d different spelling and synonyms where used.
This made search by species difficult. The new table was called taxon and the names included has
gradually grown far beyond the NGB mandate. This is partly a result of participation in various Nordic
projects d
ealing with ’additional’ species and agreements with other gene banks on maintainance of
accessions as safety duplicates. The taxon tables (table 1 and table 2) hold administrative data, botanical
data, specific NGB data, data specific for the individual N
ordic countries and some descriptors regarding
use of that particular species.


Table 1, Scientific names, taxon table

field descriptive name

field name

fiber derived

FIBUSE

working group code

WGRCDE

taxon responsibility

TAXRSP

taxon name

TAX
NAM

taxon number

TAXNUM

cork derived

CRKUSE

secondary metabolites derived

SMTUSE

fresh usage

FRSUSG

food usage

FOOUSG

forage usage

FORUSG

fodder usage

FODUSG

industrial usage

INDUSG

genus name

GENNAM

spice usage

SPIUSG

medic
al usage

MEDUSG

drug usage

DRUUSG

poison usage

POIUSG

perfume usage

PERUSG

dye usage

DYEUSG

ornamental usage

ORNUSG

environmental usage

ENVUSG

fertilizer usage

FERUSG

energy usage

ENEUSG

species name

SPENAM

object usage

OBJUS
G

Nordic gene bank type

NGBTYP

Nordic gene bank responsibility

NGBRSP

Swedish taxon name

SWETAXNAM

German taxon name

DEUTAXNAM

Nordic gene bank activity

NGBACT

Nordic gene bank preservation
recommendation

NGBRCO

Nordic gene bank budget

NGBBUD

thousand grain weight

THGWEI

minimum germination percent

MINGRMPCT

Danish taxon name

DNKTAXNAM

family number

FAMNUM

Finnish taxon name

FINTAXNAM

Icelandic taxon name

ISLTAXNAM

Norwegian taxon name

NORTAXNAM

British taxon name


GBETAXNAM

French taxon name

FRATAXNAM

Portuguese taxon name

PRTTAXNAM

family name

FAMNAM

wild culture type

WILCLT

reservate culture type

RESCLT

weed culture type

WEECLT

sub name

SUBNAM

author name

AUTNAM

current author name

CUR
AUTNAM

previous author name

PREAUTNAM

taxon pedigree

TAXPED

chromosome number

CHRNUM

life form

LIFFRM

breeding system

BRDSYS

taxon origin

TAXORI

forest culture type

FORCLT

landscape culture type

LANCLT

agriculture culture type

AG
RCLT

orchard culture type

ORCCLT

horticulture culture type

HORCLT

greenhouse culture type

GRNCLT

indoor culture type

INDCLT

in vitro

culture type

VITCLT

rhizome used

RHIUSE

stem used

STEUSE

shoot (stem+leaves) used

SHOUSE

cortex u
sed

CORUSE

leaf used

LEAUSE

flower used

FLWUSE

fruit used

FRUUSE

grin taxon number

GRITAXNUM

seed used

SEEUSE

pollen used

POLUSE

resin used

RSNUSE

sap used

SAPUSE

sugar derived

SUGUSE

starch derived

STAUSE

oil derived

OILU
SE

protein derived

PROUSE

data source

DTASRC

cellulose derived

CELUSE

vitamins derived

VITUSE

minerals derived

MINUSE

wood derived

WOOUSE



Table 2, taxonomic synonyms

field descriptive name

field name

grin taxon number

TAXNO

val
id grin taxon number

VALIDTAXNO

grin taxon name

TAXON

grin taxon author

TAXAUTHOR

grin synonym taxon name

SYNTAXNAM

Nordic gene bank valid grin taxon name

NGBVALTAX

taxon number

TAXNUM



Culton table

In addition to the taxon table, NGB ha
s a level below the systematic species in order to group accessions by
commercial and primitive cultivars, landraces, different kinds of breeding material, wild material and
others. This level is called culton (table 3). Each culton is linked to a species
in the taxon table.


Table 3, culton table

field descriptive name

field name

culton name

CULNAM

approval year

APPYEA

release year

RELYEA

breeding method

BREMET

breeding free pollination

BREFRE

breeding line selection

BRELIN

breeding m
ass selection

BREMAS

breeding cross

BRECRO

breeding back
-
cross

BREBCR

breeding mutation

BREMUT

mixed taxon name

MIXTAXNAM

breeding polyploiditation

BREPLO

breeding transgenic

BRETRA

culton pedigree text

CULPEDTXT

culton reference te
xt

CULREFTXT

culton description

CULDES

culton source

CULSRC

marketing year

MARYEA

withdrawal year

WITYEA

origin data

ORIDTA

original record numbers

ORCNUM

additive data

ADDDTA

old variety
-
type number

OVNUM

sub type

SUBTYP

bree
der institute acronym

BREINSACR

breeder person name

BREPERNAM

taxon number

TAXNUM

breeder country

BRECOU

breeder taxon name

BRETAXNAM

breeder culton name

BRECULNAM

culton type

CULTYP

culton number

CULNUM



Accessions

The accession t
able (table 4) contain information about the accessions in the NGB seed store. Work is
carried out to include accessions kept as clones
in vitro

(potato) or in clonal archives (fruit trees, berries and
vegetables).


Table 4, accession table

field descript
ive name

field name

accession responsibility

ACCRSP

accession number

ACCNUM

duplicate accession number

DUPACCNUM

accession name

ACCNAM

origin country

ORICOU

accession breeder pedigree

ACCBREPED

accession breeding free pollination

ACCB
REFRE

culton type

CULTYP

accession breeding mass selection

ACCBREMAS

accession breeding line selection

ACCBRELIN

accession breeding cross

ACCBRECRO

accession breeding back
-
cross

ACCBREBCR

accession breeding mutation

ACCBREMUT

accession
breeding polyploiditation

ACCBREPLO

accession breeding transgenic

ACCBRETRA

accession reference acronym

ACCREFACR

old variety
-
type number

OVNUM

accession type

ACC_TYPE

gene bank institute acronym

GBKINSACR

mixed taxon number

MIXTAXNUM

mixed taxon name

MIXTAXNAM

taxon number

TAXNUM

accession sub type

ACCSUBTYP

additive data

ADDDTA

accession remarks

ACCREM

donor country

DONCOU

donor institute acronym

DONINSACR

donor person number

DONPERNUM

donor person acronym

DON
PERACR

donor taxon name

DONTAXNAM

culton number

CULNUM

donor accession name

DONACCNAM

donor accession number

DONACCNUM

other accession number

OTHACCNUM

collector institute acronym

COLINSACR

collector person number

COLPERNUM

collector

person acronym

COLPERACR

collector accession number

COLACCNUM

breeder institute acronym

BREINSACR



Passport

The passport table (table 5) contains information about the collection place (for the collected accessions).


Table 5, accession passport

data

field descriptive name

field name

mixed taxon name

MIXTAXNAM

collector sub type

COLSUBTYP

location institute name

LOCINSNAM

location person name

LOCPERNAM

location accession name

LOCACCNAM

location county name

LOCCNTNAM

location

commune name

LOCCOMNAM

location village name

LOCVILNAM

location area name

LOCARENAM

location collector place

LOCCOLPLA

location latitude

LOCLATTUD

location longitude

LOCLONTUD

location altitude

LOCALTTUD

site aspect direction

SITASPDI
R

site slope percent

SITSLOPCT

site landform
-

physiography

SITLNDFRM

site general habitat

SITGNRHAB

site special habitat

SITSPCHAB

donor accession number

DONACCNUM

site culture type habitat

SITCLTHAB

site land
-
use

SITLNDUSE

native n
ame

NATNAM

genetic origin

GEN_ORIG

collector composite

COLL_COMP

Nordic forage database number

NFDB_NO

origin data

ORIDTA

accession source

ACCSRC

collector date

COLDAT

collector accession number

COLACCNUM

collector person acronym

C
OLPERACR

collector person name

COLPERNAM

collector taxon name

COLTAXNAM

origin country / location country acronym

ORICOU

batch number

BATNUM

collector accession name

COLACCNAM

accession number

ACCNUM

accession type

ACCTYP



Batch tab
le

When the seeds of an stored accession are loosing viability or the number of seeds are decreasing,
regeneration or multiplication is carried out. Even though NGB takes careful steps to maintain the
accession, the new seeds will differ from the original
seeds because of alien pollen, selection or other
evolutionary forces. The seed samples from different regenerations and multiplications are for this reason,
registered and kept as individual batch samples (table 6).


Table 6, batch, accession sample

fiel
d descriptive name

field name

donor acronym

DONACR

harvest year

HARYEA

accession number

ACCNUM

batch number

BATNUM

received date

RECDAT

TEMP

TEMP

pedigree number

PEDNUM

generation number

GENNUM

donor accession number

DONACCNUM

last batch

LSTBAT



Seed storage tables

The active and base collection is kept in household deep freezers at Alnarp and the safety base collection is
kept in a coal mine at Svalbard. The location of an accession sample (batch) is registered in the tabl
es
‘active’ (table 7), ‘base’ (table 8) and ‘safe’ (table 8). The stored seeds are regularly tested for germination
and the result registered in the ‘gtest’ table (table 10).



Table 7, active collection at Alnarp

field descriptive name

field name

batc
h number

BATNUM

accession number

ACCNUM

distribution bag

DISBAG

bulk bag

BULBAG

bulk weight

BULWGT

cabinet number

CABNUM

storage date active

STADAT

cardboard box number

CARNUM



Table 8, base collection at Alnarp

field descriptive
name

field name

storage base date

STBDAT

bottle number

BOTNUM

bottle weight

BOTWGT

box number

BOXNUM

cardboard box number

CARNUM

accession number

ACCNUM

batch number

BATNUM



Table 9, safe, safety base collection at Svalbard

field
descriptive name

field name

close date

CLSDAT

storage safe date

STSDAT

safe box number

SBXNUM

batch number

BATNUM

accession number

ACCNUM



Table 10, gtest, germination test data

field descriptive name

field name

batch number

BATNUM

accession number

ACCNUM

germination percent

GRMPCT

test date

TSTDAT

seeds

SEENUM

hard seeds

HRDNUM

abnormal seeds

ABNNUM

dead seeds

DEANUM

test number

TSTNUM

last test

LSTTST

donor acronym

DONACR

harvest year

HARYEA

field

number

FLDNUM

normal seeds

NRMNUM



Evaluation data

NGB endeavour to have a well documented collection. Evaluation data has recently been organised in the
‘accobs’ table (table 11) using a model through inspiration from the GRIN databases.


Table 11
, evaluation data

field descriptive name

field name

record

recnum

accession number

obsaccnum

batch number

obsbatnum

record in project table

prorecnum

obsdscnum

obsdscnum

observation site number

obssitnum

observation date

accobsdat

observed value

accobsval

obsrptcnt

obsrptcnt

institute acronym

gbkinsacr



Material transactions

Most seed requests result in material transactions. The essential data regarding the transaction is registered
in the ‘tra’ table (table 12 and table
13). Also seeds received from collections or other sources are registered
in this table as well as seeds sent to and comming from regeneration or multiplication.


Table 12, material transactions

field descriptive name

field name

TraNum

tranum

Transa
ction date

tradat

Transaction direction

tradir

Person number

trapernum

Institute number

trainsnum

Staff person number

stfpernum

Request flag

trareqflg

Regeneration flag

trafieflg

MTA flag

tramtaflg

Material for evaluation

traevlflg


Crop name

tracrp

Remarks

trarem

Action taken

reqacttak

Request received date

reqrcvdat

Person name

fiepernam

Project number

trapronum

Role code

trarolcod

Cereals wg

trawg1flg

Fruit and berries wg

trawg2flg

Potato wg

trawg3flg


Forage wg

trawg4flg

Vegetables wg

trawg5flg

Root crops, oil plants and pulses wg

trawg6flg

Project code

traprocod

Characterisation flag

trachrflg



Table 13, transaction details

field descriptive name

field name

Sample number

smpnum

Transaction number

smptranum

Accession number

smpaccnum

Batch number

smpbatnum

Distribution bags sent

smpdbg

Weight sent

smpwgt

Remarks

smprem

Expected recieve date

exprcvdat

Marking deleted records

delflg



Regeneration and multi
plication agreements

The agreements regarding seed regeneration and multiplication are organised in a separate database table
(accreg) table 14.


Table 14, seed regeneration agreements

field descriptive name

field name

Record

recnum

Project code

fi
eprocod

Project number

fiepronum

Transaction number

fietranum

Sent sample number

sndsmpnum

Accession number

fieaccnum

Low germination reason for regeneration

grmcauflg

Low seed amount reason for
regeneration

amtcauflg

Agreed returned se
ed amount

agrseeamt

Agreed germination percent

agrgrmpct

Agreed number of returned plants

agrplanum

Sowing date

fiesowdat

Sowing season

fiesowsea

Agreed return date

agrretdat

Agreed return season

agrretsea

Agreed costs

agrcosamt

Agr
eed costs curency

agrcoscur

Agreed costs financed by

agrcosfin

Received sample

rcvsmpnum

Cultivation method

fiecltcod

Isolation method

fieisncod

Remarks

fieremtxt

Agreed returned seed amount (weight)

agrseewgt

Harvest method (bulk, sin
gle)

fieharcod

Cereal wg

fiecerflg

Fruit and berries wg

fiefruflg

Potato wg

fiepotflg

Forage wg

fieforflg

Vegetables wg

fievegflg

Root, oil, fibre crops & pulses wg

fierotflg



Contact information

The NGB keeps data on contacts in a p
erson table (table 15) and an institute table (table 16).


Table 15, contact institutes (instab)

field descriptive name

field name

Valid institute number

dupinsnum

Institute acronym

insacr

Institute fao code

inscod

Institute name (1)

enginsna
m1

Local institute name (1)

locinsnam1

Local institute name (2)

locinsnam2

Local institute name (3)

locinsnam3

Swedish institute name (1)

sweinsnam1

Swedish institute name (2)

sweinsnam2

Swedish institute name (3)

sweinsnam3

Box adress

insboxadr

Town name

instwnnam

Country acronum

inscouacr

Country name

inscounam

Telex phone number

instlxpho

Email

insemaurl

Fax phone number

insfaxpho

Visiting adress

insvisadr

Longitud

inslontud

Lattitud

inslattud

Altitud

in
salttud

Role codes

insrolcod

Genebank flag

insgbkbin

Breeder flag

insbrebin

Donor flag

insdonbin

Collector flag

inscolbin

To receive Nordic NGB publications

inspbnbin

To receive international NGB
publications

inspbibin

To recieve gen
vägar

insgnvbin

Clonal archive flag

insclobin

Horticultural network partner flag

inshcnbin

Request flag

insreqbin

Additional data

insadddta

Longitud (float)

inslonflt

Lattitud (float)

inslatflt

Institute name (2)

enginsnam2

Voice ph
one number

insvoipho

Web
-
url

inswwwurl

Institute name (3)

enginsnam3

InsNum

insnum



Table 16, contact persons (pertab)

field descriptive name

field name

Valid person number

duppernum

First name

fstnam

Last name

lstnam

Box adress

perboxadr

Country acronym

percouacr

Country name

percounam

Fax phone number

perfaxpho

Other phone number

peraddpho

Email

peremaurl

Web
-
url

perwwwurl

Role codes

perrolcod

Additional data

peradddta

Title

engpertit

Title (swedish)


swepertit

Title (local language)

locpertit

Cereals working group member

perwg1bin

Fruit and berries working group member

perwg2bin

Potatoes working group member

perwg3bin

Forage working group member

perwg4bin

Vegetables working group mem
ber

perwg5bin

Root, oil, fibre crops & pulses working
group member

perwg6bin

Member of working group 7

perwg7bin

Member of working group 8

perwg8bin

Board member

perboabin

Chairperson (board)

perchabin

Working group member

permembin

St
aff

perstfbin

HCN partner

perhcnbin

Request flag

perreqbin

Mobile phone number

permobpho

Work phone number

perwrkpho

Street adress

perstradr

PerNum

pernum

InsNum

insnum

Town name

pertwnnam

Nationality (country acronym)

pernatacr


Person acronym

peracr

Voice phone number

pervoipho



Locations

The NGB stores some information on relevant geographical locations in a location table (table 17). The
table is used for several GIS presentations at the web server.


Table 17, loctab,

location table

field descriptive name

field name

Location name

locnam

Longitud (float)

lonflt

Lattitud (float)

latflt

Altitud (feet)

altfee

Country acronym

couacr

Zip code

zipcod

Location number (key)

locnum

comlocnum

comlocnum




References:

The information is collected from the NGB annual reports and the publication ’Nordic Gene Bank 1979


1999’. In particular the two references given below has been very helpful.


Hulden, Morten, 1995, NGB's Information system. In: Verksamhet
sberättelse 1995. Nordic Gene Bank
Publications 31. ISSN 1100
-
3456. [In Swedish]


Hulden, Morten, 1999, Development of the Information System at the NGB 1989
-
1999. In: Nordic Gene
Bank 1979
-
1999. Nordic Gene Bank Publications 35. ISSN 1100
-
3456.