Report from 1996 ITMI Workshop in Sydney Australia
From Pat McGuire, November 1996
REPORT FROM SYDNEY
The 1996 ITMI Workshop was held August 30 and 31 in Sydney Australia, hosted
by PETER SHARP at the Plant Breeding Institute, University of Sydney,
assisted by RUDI APPELS, PETER LANGRIDGE, and ROBERT HENRY. Approximately 75
persons were in attendence representing at least 10 countries. Twenty
posters were presented and the program featured 15 speakers in addition to
the reports on mapping progress in the seven homoeologous chromosome groups.
Brief summaries of the speaker's topics are provided below.
PROCEEDINGS TO FOLLOW
The proceedings of this meeting (speaker and poster abstracts) will be
combined with those of the last workshop (Norwich UK, 1995) and published
along with up-to-date reports on the status of mapping in the seven
homoeologous groups and some diploid genomes. The document is planned to be
available by the time of the Plant and Animal Genome Conference in San
Diego, CA USA, January 12-16, 1997.
NEXT YEAR'S MEETING TO BE IN FRANCE
An invitation from INRA, France was accepted and the 1997 ITMI Workshop
will be held in Clermont-Ferrand, France in late June or early July.
Details will be announced to the GrainGenes email group and elsewhere as
plans are developed.
Contact the ITMI Management Office at itmi@ucdavis.edu for further
information.
SPEAKER SUMMARIES, ITMI 1996 WORKSHOP
PHILIPPE LEROY, INRA Plant Breeding Station, Clermont-Ferrand FRANCE,
demonstrated the role of the ITMI mapping population (created by CIMMYT and
the Cornell University lab of Mark Sorrells from a cross between bread wheat
cultivar Opata 85 and a synthetic hexaploid produced from the durum cultivar
Altar 84 and an accession of Aegilops tauschii) as a reference mapping
population for bread wheat. As a result of collaborative mapping by ITMI
coordinators and others, Leroy reported that there are over a thousand
markers and 21 genes mapped to date in the population. With its high level
of polymorphism, the population is being increasingly widely used for
investigating the genetics of quantitative trait loci.
PETER LANGRIDGE, Center for Cereal Biotechnology, Waite Agricultural
Research Institute, University of Adelaide, Glen Osmond SA AUSTRALIA,
reported on the Australian National Barley Genome Project, begun in 1994 for
barley improvement utilizing molecular markers. Three doubled haploid
mapping populations are being used, chosen for their potential to map cereal
cyst nematode resistance, boron tolerance, manganese efficiency, and loci
relevant to malting quality. He reported that they have developed a
consensus map based on these three crosses with 600 markers including 14
enzyme loci, loci controlling enzyme activity, and malting quality QTLs. The
Project can claim two good instances of molecular markers being directly
used in breeding projects: an RFLP marker for cereal cyst nematode
resistance and a PCR marker for the Yd2 gene conferring resistance to barley
yellow dwarf disease. In addition, the Project seeks to develop a molecular
database for barley varieties that either are commercially grown in
Australia or have provided or may provide useful germplasm to Australian
breeding programs. They have used 77 markers generating 1443 polymorphic
bands to characterize the 96 varieties in their database. A direct
application of this information to breeding programs is its use in selecting
parents for crosses.
ANDY KLEINHOFS, Crop & Soil Sciences, Washington State University, Pullman
WA USA, reported that for the North American Barley Genome Mapping Project,
the mapping stage is essentially over. There will always a need for more
markers and mapping does continue, but current major activities are
consolidation and integration of the map information from the three
different mapping populations and practical application of the maps. To
facilitate the latter activity, there is a need for large insert libraries
for barley and better international cooperation. The situation with rice
serves both as a model with BAC libraries available and a strong
international network of collaboration and as an arena for locating and
cloning sequences relevant to barley targets. There is no evidence to date
for rearrangements in any of the barley maps and the most up-to-date
versions can be found on GrainGenes.
HENRY NGUYEN, Plant & Soil Science, Texas Tech University, Lubbock TX USA,
reported on progress in mapping genes controlling abiotic stress resistances
in cereals. A major obstacle has been resolving complex traits such as
drought resistance into component discrete characters amenable to replicable
field and lab analyses and thus genetic analyses. Examples of progress
include the five genes relevant to salt tolerance mapped in the lab of Jan
Dvorak, University of California, Davis, genes controlling drought-induced
ABA production and the Vrn and Fr genes mapped at the John Innes Center,
Norwich UK, and the barley dehydrin gene mapped by the lab of Pat Hayes,
Oregon State University, Corvallis.
MIKE WANOUS, Biological Sciences, University of Missouri, Columbia MO USA,
reported on the progress in mapping of the rye genome in the lab of Perry
Gustafson, USDA, ARS and Agronomy, University of Missouri, Columbia. Linkage
groups for all seven chromosomes have now been determined, incorporating 65
RFLP markers and 8 C-band markers, 6 of the 8 were terminal C-bands. The
probes contributing to the map have come from rye libraries at Missouri,
Hannover FRG, and Madrid Spain and from wheat, Aegilops tauschii, barley,
oat, and sorghum libraries. The main mapping population is derived from a
cross between the dwarf rye 'UC 90' with a standard karyotype and 'E-line',
missing about 80% of the telomeric C-bands. While almost 650 probes have
been screened on the population, only 38% of which have shown polymorphism.
A further complication is that of this 38%, about two-thirds show
segregation distortion. This a relatively high level, which may be
associated with the extreme outcrossing nature of rye. Also notable is the
high number of markers which are inherited as presence/absence loci.
Finally, there is a large amount of recombination occurring between the most
distal molecular markers and the terminal C-bands, consistent with the
pattern of nonrandom localization of recombination found in other Triticeae
taxa.
BIKRAM GILL, Plant Pathology, Kansas State University, Manhattan KS USA,
reported that the most recent focus of his lab's mapping effort with the
D-genome diploid species Aegilops tauschii has been to analyze marker
segregation for 200 loci spanning the entire genome. Sixty-three loci
deviated from the expected 1:2:1 ratio. Major segregation distortion loci
were detected on chromosome arms 1DL, 3DL, 4DS, 5DL, and 7DS. In all cases,
the distortion was caused by an absence of homozygotes for alleles from the
same parent except for the 7DS case which was an absence of homozygotes for
the other parent's alleles. To further investigate this phenomon, they have
created a reciprocal backcross population of almost 200 individuals based on
male and female meiosis. Initial analysis has shown that the deviant loci on
5DL show normal segregation through female gametes, but that the alleles
from the nondeficient parent are preferentially transmitted though the male
gametes. Future work will address the alleles associated with the other
segregation distortion loci and the effect of segregation distortion loci on
genetic map length.
EVANS LAGUDAH, Division of Plant Industry, CSIRO, Canberra ACT AUSTRALIA,
presented the story of the mapping and innovative cloning effort for the
Cre3 gene on chromosome 2D in Aegilops tauschii, conferring resistance to
cereal cyst nematode. This elegant display of map-based cloning resulted in
the determination that the resistance gene family at the Cre3 locus is
related to members of the cytoplasmic NBS-leucine rich repeat class of plant
disease resistance genes.
JAMES ANDERSON, USDA, ARS, Washington State University, Pullman WA USA,
reported the mapping of tan spot resistance genes carried out in his former
lab at North Dakota State University, Fargo ND. Two genetically distinct
symptoms are elicited in wheat by the tan spot organism: tan necrosis and
extensive chlorosis. The population used to map the tan necrosis resistance
character consisted of 58 lines from the cross of a resistant synthetic
hexaploid, W-7976, with the susceptible cultivar 'Kulm'. A single nuclear
gene was identified, located by aneuploid analysis to chromosome 5BL and
given the proposed designation tsn1. The mapping population used to map the
chlorosis resistance character is the same one used extensively for RFLP
mapping of wheat by ITMI coordinators and others, with an additional 21
recombinant inbred lines for a total of 135. A major QTL was identified on
chromosome 1AS (given the proposed designation QTsc.ndsu-1A), a minor QTL on
4A, and an epistatic interaction between the 1AS locus and a locus near the
centromere of chromosome 2DL.
JORGE DUBCOVSKY, INTA, Castelar, Buenos Aires ARGENTINA, reported the
mapping of vernalization genes in the diploid species Triticum monococcum
employing two segregating populations from crosses between winter and spring
lines of T. monococcum. The first population segregated for a single gene,
dominant for spring habit, mapped to chromosome 5AmL, closely linked to a
marker that is closely linked to Vrn1 in T. aestivum 5AL and to the
orthologous gene Sh2 in barley 5HL, suggesting that the T. monococcum gene
is orthologous to Vrn1. The second population segregates for a different
single gene that differs from other Vrn genes by its dominant winter habit.
The proposed designation for this gene is Vrn7 and it appears to be
epistatic to vrn1. Vrn7 was mapped to the distal segment of chromosome 5AmL
translocated from 4AmL.
JAN DVORAK, Agronomy & Range Science, University of California, Davis CA USA
reported on an analysis of bread wheat baking quality parameters using
RFLPs. Recombinant substitution lines of chromosomes 1A, 1B, and 1D of
Cheyenne, a wheat cultivar with good baking quality, in the genetic
background of Chinese Spring, with poor baking quality, were used to assess
the relationship of RFLPs and baking quality parameters (such as grain
protein content, flour protein content, mixing time, and loaf volume) and
associated indirect tests of baking quality (such as the Pelshenke test and
the SDS-sedimentation test). MapMaker QTL was used to identify chromosome
regions in which Chinese Spring and Cheyenne differed. A number of regions
were identified for each quality parameter. Some of them coincide with the
high molecular weight glutenin locus Glu1 on the long arm of these
chromosomes as expected and with the low molecular weight glutenin locus
Glu3 on the short arm of these chromosomes. Most surprising was finding
regions in each of the three chromosomes having strong effects on these
parameters in which there are no known seed storage protein loci, e.g., the
end of chromosome 1AL and the middle of 1BL.
STUART SEAH, Plant Sciences, The University of Western Australia, Nedlands
WA AUSTRALIA, reported on the PCR-based isolation of disease resistance gene
sequences from wheat and barley. PCR primers based on conserved nucleotide
regions from the RPS2 gene (confering resistance to a bacterial pathogen)
and the Cre3 gene (potentially conferring resistance to cereal cyst
nematode) were used to amplify other related gene sequences from wheat and
barley. As a result, five independent clones resembling resistance genes
were obtained. These clones have been mapped to wheat and barley chromosomes
and the determination of their relationships to known resistance genes on
those chromosomes is being carried out.
PERRY CREGAN, USDA, ARS, Agriculture Research Center, Beltsville MD USA,
gave an account of his laboratory's experience with a collaborative approach
to the development of microsatellite markers for soybean as a background for
considering approaches to developing microsatellite markers for wheat. Their
success rate from an initial set of clones through sequencing to primer
choice was similar to that achieved for human markers. While initial reports
for wheat have lower success rates, this should not rule out pursuit of
their development. He emphasized that the effort in wheat will require a
substantial investment of time and resources and will be enhanced by a focus
on trinucleotide microsatellites, optimization of primer selection, and high
throughput of primer testing and characterization.
MIKE GALE, John Innes Center, Norwich Research Park, Colney, Norwich UK,
discussed the experience with microsatellite markers for wheat at his
laboratory. Initially there was a large privately funded program that
produced 70 single sequence repeats and now there's a publicly funded one as
well. In retrospect, they would use PstI-generated and enriched libraries
now instead of the EcoRI library that they did use. They explored the use of
several different gel systems and now recommend using only sequencing gels,
not agarose or acrylamide. They found that sequences in the 400 to 600 bp
range were too small and now focus on sequences 800 bp or larger. The first
paper on this work is in press now in Theoretical and Applied Genetics and
the lab will distribute markers in sets of microtiter plates usable with
mixed primer pairs with the restrictions that they be used in laboratories
for research and not commercial purposes, not passed on, and not sequenced.
GREG PENNER, Winnipeg Agricultural Research Station, Agriculture & Agri-Food
Canada, Winnipeg MT CANADA, discussed the successful use of AFLP markers in
wheat in his laboratory. They were using a technique modified from SCRI.
They expect good transportability between maps since SCRI reported good
conservation of map order generated by AFLP markers across three crosses.
They have not yet attempted to convert AFLP markers to specific markers.
MOSHE FELDMAN, Weizmann Institute of Science, Rehovot ISRAEL, reported on
isolation of chromosome-specific DNA sequences in wheat beginning with
production of single arm genomic DNA libraries. In the example given,
chromosome arm 5BL was microdissected and its DNA was amplified by
degenerate oligonucleotide-primed PCR. Of the resulting inserts, about 55%
were low-copy, noncoding sequences. About half of these were 5BL specific.
These 5BL-specific sequences were further characterized by their presence in
genomes of diploid species that are either considered progenitor species of
bread wheat or are closely related to genome donor species of bread wheat.
Group I sequences were found only in a single diploid genome, either A, B,
or D. There showed high polymorphism and are suitable for phylogenetic
studies among diploid taxa or between diploids and polyploids. Group II
sequences were found in diploid species of all three genomes and other
studied diploids in Triticeae and are relatively conserved, implying an
origin ancient in the development of the tribe. Their location was clustered
in 5BL near the telomeres and near the Ph1 locus. He discussed the
intriguing possibility that these Group II sequences are involved with the
physical basis for the diploid-like meiotic behavior of polyploid wheat
since these sequences occur only in one pair of chromosomes in polyploids,
supposedly having been eliminated from homoeologous chromosomes. Studies
with newly synthesized amphiploids show that this elimination is rapid,
occurring soon after the formation of the polyploid.
------------------------------------------------
Patrick McGuire
ITMI/Genetic Resources Conservation Program
University of California
Davis, CA 95616 USA
(916) 754-8503 FAX (916) 754-8505
itmi@ucdavis.edu