NOMENCLATURE SYSTEM
FOR RICE GENE POOLS, POPULATIONS
AND RECURRENT SELECTION BREEDING
GENERAL USE AND CATALOGUE REGISTRATION
M. ChâteI
E P. Guimarâes
CIRAD-CA
CIAT
1. Introduction
In 1984, a collaborative research project between CIRAD-CA (formerly IRAT) and
EMBRAPA/CNPAF, Brazil, saw the beginning of a rice recurrent selection program. A
few years later, CIAT and IRRI developed rice gene pools for population improvement.
IARCs and NARDs have used this new germplasm in their breeding programs directly
or as male sterile background to introduce new locally adapted germplasm.
Several gene pools and populations are presently used but there is no clear,
standardized nomenclature system. So tracking their backgrounds and selection traits,
and comparing the results of breeding work and strategies, becomes increasingly
difficult. A standardized nomenclature system is needed as the recurrent selection
method becomes more integrated into traditional breeding programs, and as institutions
increase germplasm exchange.
We propose the adoption of a standard nomenclature system and that all information
about gene pools and populations is registered in a catalogue. Each entry is to be fully
described with special emphasis on development, genetic constitution, status of the
germplasm, targeted objective(s) and ecosystems, and main agronomic characteristics.
One of the institutions would be responsible for the catalogue’s coordination and
upkeep.
2. Existing Nomenclatures
We first need to define gene pool and population. This proposal considers gene pool to
be the specific and unique genetic background resulting from combinations of a group
of genotypes. These may be pooled together in similar or different proportions through
crossing, with or without a gene for male sterility. Population is the result of applying any
breeding procedure to these backgrounds. It refers mainly to the enhancement of trait(s)
and the genetic modifications (introducing up to 50% new variability) of the gene pools.
EMBRAPA/CNPAF, CIRAD-CA, IRRI and CIAT have each created and named gene
pools as follows:
CNA-IRAT the gene pools jointly developed in Brazil by EMBRAPA/CNPAF and
CIRAD-CA (formerly IRAT);
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CP the gene pools prepared at IRRI and currently used by CIRAD-CA in Mali (Africa);
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GC the gene pool created by CIAT.
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Each gene pool received a code number for identification, (CP 122, GC 91,
CNA-IRAT 4/0/0). The breeders who developed the gene pools relate these code
numbers to their breeding activities.
In CNA-IRAT’s case, after the standard institutional code (e.g. CNA-IRAT 4 gene pool)
two additional numbers are used, separated by slashes. The first is the number of
selection cycles made in the pool (CNA-IRAT 4/0). The second is the intermating
number applied to the gene pool (CNA-IRAT 4/0/3). So the meaning of CNA-IRAT 4/0/3
is: gene pool CNA-IRAT 4, where there was no selection, but there were 3 cycles of
recombination. A few populations were developed from this gene pool following the
same name pattern. One example is the CNA-IRAT 4/1/3 CIAT received in 1993. The
population came from the CNA-IRAT 4 gene pool after one selection cycle made in the
third intermating cycle.
The CNA-IRAT gene pools were formed using the male sterile gene from IR36, so some
pools have the last number followed by “F” (CNA-IRAT 4/0/iF). In this case, the gene
pool went through one cycle of intermating and the seed increase originated from
heterozygote fertile plants. The same sequence of code numbers applies for the CP
gene pools in Mali. An example is the population CP 1 26/1/1 F: gene pool CP 1 26
goes through one selection cycle and one intermating with seed increase made from
heterozygote fertile plants.
At CIAT, the letters are the initials of the scientists involved in the gene pool
development and the numbers refer to the year when they obtained S0, seeds. So in
1991, Drs. Guimarâes and Correa-Victoria synthesized GC-91.
Two name variations occur when gene pools or populations are used as male sterile
background to introduce new variability (additional lines are crossed to male sterile
plants of the gene pool or population, their genetic contribution representing at least half
of the new pool):
The germplasm name is maintained; a specific identification is added,
e.g. CNA-IRAT 1 MOl is the first population developed for high altitude areas in
Madagascar (MD). It was derived by introducing 13 locally adapted lines to the CNAIRAT 1 gene pool.
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The name of the original gene pool or population is not present. The new derived
population receives a new name. CNA 1 for example, comes from introducing three
lines into the CNA-IRAT 4/0/SF gene pool by crossing the male sterile plants.
--
The nomenclature used to identify the CNA-IRAT gene pools and populations only gives
the number of selection and recombination cycles employed to improve them. Further
information may be needed to characterize them better.
3.
Standard Nomenclature Proposal
Existing gene pools and populations and new ones need separate consideration.
3.a.
Existing gene pools and populations
Since rice breeders already use the germplasm, changing existing names and codes is
not realistic. We propose keeping these names and codifications registered in the
central catalogue. International Rice Research Notes or Crop Science could publish the
registered population (See Appendix 1).
3.b.New gene pools and populations
The new germplasm may be a truly new gene pool created by an institution. Or it may
be an introduction of improved lines in an existing gene pool or population. There are
several ways this can be done:
Combining a group of genotypes through hand crossing, or by
using the male sterile genes available in their original genetic background.
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Introducing more than 50% of new germplasm, crossing and
backcrossing rice lines with male sterile plants of an already developed gene pool or
population.
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Crossing two or more gene pools or populations.
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Combinations of the previous points or other alternatives.
Germplasm, enhanced for specific trait(s) by using recurrent selection breeding in
existing or new gene pools or populations, is a special case of new populations.
In every instance, the institution that creates, modifies or selects gene pools or
populations will name them using its own criteria. It will register them in the catalogue
with detailed information about the genetic constitution and methodology used. For
exchange and publication purposes, the catalogue nomenclature is the one officially
recognized and used by the breeders.
3.c.System proposed for catalogue nomenclature of gene pools and populations
Prefix For all gene pools and population, we propose to use the prefixes “GP” and “P”
(capital letters), for gene pool and population. The next letters are those of the
institutions, to name their crosses (CT for CIAT, IR for IRRI, ONA for
EMBRAPA/CNPAF, WAB for WARDA etc.). There is no space between any ofthe
letters.
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Numbering The prefix is immediately followed by a dash and a number with no
spaces. This numbering system is consecutive according to the registration catalogue.
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If the CIAT gene pool GC-91 is the first registered in the catalogue, followed by gene
pools or populations from EMBRAPA/CNPAF and WARDA, its official name will be
GPCT-1. The CNA 1 gene pool will be registered as GPCNA-2, the population proposed
by WARDA will appear as PWAB-3. A further, later CIAT gene pool might be GPCT-4,
and so on.
4. Proposal for the identification of the status of gene pool and populations
Population enhancement is a continuous process of evaluation, selection and
recombination. It is important to know the present status of the populations.
Each institution is free to use its own criteria to name the germplasm. But we suggest
the following identification of the working material as a method for breeders to handle
the populations or gene pools during the enhancement process. This is useful when
communicating and exchanging information before registering the germplasm as a new
population.
A full identification gives the number of recombination cycles of the gene pool or
population both before and after selection. It gives the number of selection cycles with
the traits for selection and also names the selection.
Numbers and codes can represent the traits. The official registered name is used. The
number of selection cycles follows, then the trait enhanced by the selection (use IRRI
Standard Evaluation System for Rice acronyms). They are separated by a back slash,
not the slash that is normally used for the identification of crosses. The GC-91 gene
pool, catalogue name GPCT-1, has been selected once for leaf blast. CIAT would
handle the populations as GPCT-1\BI. Numbers in the sequence identify how many
recombination cycles were used after selection, and in which recombination cycle the
selection was applied in the population.
Continuing the previous example, during this planting semester, CIAT’s GPCT-1\BI
population would be named GPCT-1\BI\1\1, because the gene pool GPCT-1 was
selected for leaf blast in the first cycle of recombination, then recombined once. In a
hypothetical example, GPCT-4\0\0\0 means the gene pool produced by CIAT, fourth
registered in the catalogue, with no cycle of recombination or selection. After being
worked, it becomes GPCT-4\NBI\0\4, which means that a selection for neck blast, with
no recombination cycle, was made in the fourth cycle of recombination of the GPCT-4
gene pool. GPCT-4\NBI\3\4 means three cycles of recombination after a selection for
neck blast made in the fourth cycle of recombination of the original gene pool.
In most cases, selection is made for more than a single character. In such situations,
the germplasm identification must give the acronyms of the traits. For example, if a
population is enhanced for leaf blast and brown spot at the same time, the identification
would be GPCT-4\BI,BS\2\4.
Identification of a population enhanced for a certain trait in one season, and for another
in the next, would be GPCT-4\BI\3\4,BS\0 the separated trait acronyms indicating
enhancement in different seasons.
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In the case of several selections for the same trait, we recommend identification as in
the following example. Consider a CNA gene pool with four recombinations GPCNA4\0\0\4 submitted once to selection for neck blast and recombined twice GPCNA4\NBI\2\4. It is selected for the same trait the next season, then recombined five times.
The identification would be GPCNA-4\NBI\2\4,NBI\5.
When the germplasm has been sufficiently enhanced for the trait(s) under selection, the
breeder can register it, following the same rules for including a new population in the
catalogue. For example, GPCT-4\NB1\3\4 becomes PCT-10, the simpler catalogue
nomenclature, the number referring to the registration. Once accustomed to the system,
we can retrace all information on the enhancement of the germplasm.
5. Selection of Elite Lines
Two cases of extraction of elite lines are considered; extraction using gene pools or
enhanced populations, and extraction obtained from different cycles of
selection/recombination during the improvement process of the germplasm. The
nomenclature is based on that proposed by WARDA for traditional line development
and accepted by participants of the First International Upland Breeders Workshop held
at CIRAD-CA, Montpellier-France, September 6-10, 1993.
5.a. Gene pool or enhanced populations
Nomenclature of elite lines selected from gene pools or populations should indicate the
germplasm used to develop the line and the institution(s) involved in the process. We
symbol to separate the name of gene pool population from the
propose using a
assigned pedigree. Here are three examples:
“ “
GPWAB-3>78-4-3-2-1
This is an elite line extracted by WARDA within a gene pool they have registered.
PCT-5 >WAB-4-3-2-1
This is an elite line extracted by WARDA within a population developed by CIAT.
PIR-7>23-1-WAB-3-4-CNA-4-B
The population PIR-7 is produced by IRRI, within which IRRI made selection of elite
line during two generations. WARDA received the line PIR-7>23-1 and selected during
two more generations. Finally the line PIR.-7>23-1-WAB-3-4 was sent to
EMBRAPA/CNPAF and selected for one more generation. Then the seeds were
harvested in bulk.
5 .b. Different cycles of Selection/Recombination (working material)
PWAB-7\GQ\2\3> 79-7-4-2
A WARDA population is under selection to enhance grain quality. The institution
extracts elite lines from the third cycle of recombination of the population PWAB-7,
selects once for grain quality and then recombines twice.
6. Further Considerations
6.a. Seed exchange and conservation
Each institution will have seeds of its registered gene pools or populations (breeders
seed) for exchange. When answering a seed request, the catalogue information should
also be included.
A minimum of 2000 seeds should be sent to the institution responsible for the
catalogue, with the request for registration. Each institution will be in charge of keeping
its gene pools and populations under medium-term conservation. A sample should be
sent to IRRI for long-term conservation. Each institution would have to inform potential
users in advance of its intention to discard a population no longer in use, and send the
remaining seed to IRRI for long term conservation.
6.b.
Recurrent selection activities reports
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Each institution dealing with recurrent selection breeding method should report annual
activities to the central coordinator, responsible for preparing a global report on the use
of the rice gene pools and populations. The information will be sent to all participants
whose names are in the coordinator’s file.
References
CIRAD-CA, 1993. Recommendations. International Upland Rice Breeders Workshop,
September 6-10, Montpellier, France.
International Rice Research Institute (IRRI), 1988. Standard Evaluation System for
Rice. 3rd Edition, Los Baños, Philippines. 54p.
Taillebois, J. and E. P. Guimaraes, 1989. CNA-IRAT 5 upland rice population. IRRN
14:3.
West Africa Rice Development Association (WARDA). WARDA’s Varietal
Nomenclature System (monograph) 4p.