The "MiniGB" is a core collection of 280 accessions of O. sativa
established by scientists from Cirad and from IRRI on the basis of
the species enzymatic diversity. The collection was assembled to
represent the geographic, ecotypic and enzymatic diversity of O.
sativa, drawing on the enzymatic and phytopathological studies
performed on this material by Glaszmann (1987), Bonman et al
(1990) and Glaszmann et al (1995).
References concerning the MiniGB:
» Bonman JM, Mackill AO, Glaszmann J-C (1990) Resistance to
Gerlachia oryzae in rice. Plant Disease 74:306-309
» Glaszmann J-C (1987) Isozymic classification of Asian rice
varieties. Theor Appl Genet, 74:21-30
» Glaszmann J-C, de los Reyes BG, Khush GS (1988)
Electrophoretic variation of isozymes in plumules of rice: a key
to identification of 76 alleles at 24 loci. IRRI Research Paper
Series, 134, 13p.
» Glaszmann J-C, Mew T, Hibino H, Kim CK, Mew TI, Vera Cruz
CH, Notteghem J-L, Bonman JM (1995) Molecular variation as a
diverse source of disease resistance in cultivated rice. In: Rice
Genetics III, IRRI, Los Banos, Phillipines, p460-46
» Glaszmann J-C, Grivet L, Courtois B, Noyer JL, Luce C,
Jacquot M, Albar M, Ghesquière A, Second G (2003) Asian rices. In:
Genetic Diversity of Cultivated Tropical Crops, Hamon P, Seguin M,
Perrier X, Glaszmann JC (eds), CIRAD, Montpellier, France, p77-98.
The rice synthetic map available under CMap is actually just a
list of genetic markers with their physical position on the
pseudomolecules (TIGR v4.0). For each marker, the data source is
given in the "remark" field.
Gramene data or Blast results
based on sequence information were used when available. Otherwise,
as in the case of AFLPs, the nearest marker with a known sequence
on the relevant genetic map was used as a proxy.
QTLs for tolerance/resistance to abiotic stress
The QTLs listed in this DB come from a compilation of the
published literature on rice. We extracted from the QTL papers the
data we thought were relevant for the purpose of meta-analysis.
This statistical approach allows combining QTL results from
independent studies in a single result (Goffinet and Gerber, 2000;
Veyrieras et al, 2007). In the present version, QTL for drought
resistance, salinity tolerance, duration and those detected on the
IR64 x Azucena population, all traits confounded, are
compiled. In comparison with the QTL module of Gramene,
additional parameters characterizing each individual QTLs were
recorded, notably parameters concerning the experimental
conditions important to qualify abiotic stresses (e.g. well
watered versus stressed conditions; aerobic versus anaerobic
The data result from our interpretation of published papers in the
framework of a meta-analysis and may sometimes appear to be
different from the original paper. For reasons of homogeneity
across studies, we had to modify some elements.
The most common modification concerned trait names. An
associated to a trait definition largely inspired from Gramene but
adapted by us to an abiotic stress context was developed and is
available elsewhere in Tropgene.
Because of missing information on genetic distances and
discrepancies between genetic maps, we chose to define a QTL
position by the physical position of its flanking markers on the
pseudo molecules (see synthetic map above) rather than by their
genetic position on a composite genetic map.
For original data or additional details on the experiments, users
should go back to the initial publications that constitute the
References concerning the QTLs:
» Goffinet B, Gerber S (2000) Quantitative trait loci: a
meta-analysis. Genetics 155:463-4733
» Veyrieras JB, Goffinet B, Charcosset A (2007) Meta QTL: a
package of new computational methods for the meta-analysis of QTL
mapping experiments. BMC Bioinformatics 8:49