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Sent: 28 November 2003 09:07
Subject: 51: Re: Successful use of MAS - cereal crops
From Kevin Williams, Australia.
The Moderator asked (in my previous message 37, November 25) about acreage planted to cultivars developed during MAS. Obviously the lead time is still very long, as markers are used in early generations. Markers have been used in Australia in some wheat and barley breeding programs for at least five years, and new varieties produced with MAS are just beginning to come to market. However, it is likely that in Australia all breeding programs with industry funding and probably also the private breeding companies are currently using MAS to some extent. So, although it may be too early to assess impact by acreage, I expect that a large percentage of future varieties will have at least some MAS conducted during their development.
Another aspect of MAS that I have found is often overlooked in the discussion of MAS is the impact that new genetic information has on breeders' decision-making. As we build up a detailed catalogue of gene locations from mapping studies in many species, linkages between genes, both beneficial and deleterious, become very apparent. In our studies we have revealed repulsion and coupling linkages that accord with breeders experiences. By having access to extensive new genetic information and using it in crossing decisions, the breeder can progress his/her germplasm much more rapidly towards the desired outcome. So even without a single MAS event, molecular genetics can have a large impact on a breeding program. If we endeavour to keep new genetic information in the public domain, programs in all countries can have equal access.
Finally, in response to a question from the Moderator about the use of MAS with backcross (BC) lines referred to in a sentence of my previous message (i.e. "Importantly, MAS can produce outcomes not easily achieved by traditional breeding, such as strategically selecting for resistance to exotic pests, pyramiding of race-specific resistance genes for potential durable resistance, and selection for multiple traits from single plants such as BCF1's rather than later segregating populations."), the critical detail is that these are F1 lines, i.e. single plants, which can be assayed with markers for multiple traits. In our local barley breeding program, this is currently the most important use of MAS. The selection can be made on BC1F1's, but has also been used on BC3F1's, prior to making doubled-haploids.
Dr Kevin Williams
Senior Research Scientist-Molecular Genetics
South Australian Research and Development Institute
PO Box 397
Adelaide SA 5001
Phone +61 8 8303 9369
Fax +61 8 8303 9393
williams.kevin (at) saugov.sa.gov.au
Sent: 28 November 2003 10:53
Subject: 52: Gene-based technologies for improving animal production and health in developing countries
I am Harinder Makkar from the Joint FAO/IAEA Division in Vienna, Austria.
An FAO/IAEA International Symposium on "Applications of Gene-Based Technologies for Improving Animal Production and Health in Developing Countries." was held from 6-10 October 2003 at the International Atomic Energy Agency (IAEA) in Vienna. I would like to share some of the points, relevant to this electronic conference, which emanated from the presentations and discussion sessions of the Symposium. The source of some of the below-mentioned points is an excellent presentation entitled "Combining gene-based methods and reproductive technologies to enhance genetic improvement of livestock in developing countries" by Julius Van der Werf and Karen Marshall presented at the Symposium. [The book of extended synopses from the symposium, containing a 2-page synopsis of the paper, is available at http://www.iaea.org/programmes/nafa/d3/mtc/synopses.pdf. Alternatively, the paper's synopsis is available on its own at http://centaur.vri.cz/news/prilohy/pril192.htm ...Moderator].
1. Marker assisted selection (MAS) is mainly useful for traits where phenotypic measurement is less valuable because of low heritability, sex-limited expression, unavailability before sexual maturity, and unavailability without sacrificing the animal, for example slaughter traits. Traits such as feed intake or disease resistance may also be expensive or difficult to measure, and information on genotype might be useful in selecting for these traits. Genotypic information has extra value in the case of early selection and where within-family variance can be exploited. Reproductive technologies usually lead to early selection and more emphasis on between-family selection. DNA marker technology and reproductive technologies are therefore highly synergistic and complementary.
2. In the low inputs system existing in developing countries, complete phenotypic and pedigree information is often not available, except in some intensive breeding units. Under these scenarios, it would be more difficult to realize the value of the marker information, and it would be harder and more expensive to determine linkage phase in the case of using linked markers.
3. Information is currently available for a number of 'direct markers', such as myostatin affecting double muscling in cattle, calipyge doing the same in sheep, and Booroola affecting fecundity. Many of these mutations have a major phenotypic effect. Even if the genetic marker was a direct marker, its effect on phenotype would have to be estimated for the population and the environment it is used in. The effects of individual genes are likely to be dependent upon the background.
4. Many studies on MAS have taken a single trait approach and for some traits genetic markers would have a large impact on response for individual traits. However, in a multi-trait breeding objective, more response for one trait often goes to the expense of another. For example, genetic markers for carcass traits allow an improved ability to select (i.e. earlier at higher accuracy for such traits) but selection emphasis on other traits would be reduced. Therefore, the overall effect of MAS on the breeding program will generally be smaller than predicted for MAS-favourable cases. An exception may be in dairy where most traits are sex-limited and therefore favoured by MAS.
5. Rather than exploiting existing QTL through within-breed selection, a more likely scenario for developing countries will be that valuable QTL will be introgressed from one population into another. In developing countries there is a huge variety across breeds, much of it being useful for exploitation in genetic improvement programs. This includes the variation coming from 'foreign' breeds in developing countries. Either indigenous breeds may contain valuable QTL, but could benefit from upgrading through crossing withsuperior exotic breeds, or valuable QTL could be introgressed from exogenous breeds. Examples are the Booroola gene in the Garole sheep breed in India having a moderate and desirable effect on number of lambs weaned, and a number of genes affecting resistance to endemic local diseases. There are many cases of QTL found in crosses of extreme breeds, and a number of those will be a candidate for introgression.
6. In developing countries, use of genotype information is therefore likely going to be more useful in marker-assisted introgression (MAI) compared with selection within breeds. Also in the case of MAI, reproductive technologies will be beneficial because they can help increase the number of animals with the desired genotype.
7. MAS is best utilized when embedded in a breeding program that already relies on extensive recording of phenotypes and pedigree. Phenotypic information will therefore not become redundant in MAS selection programs. Rather, phenotypic information may be less used in the actual selection, but recording of phenotype will be continuously needed for the purpose of monitoring the QTL effect (retrospectively) and genetic change over time. Therefore, breeding programs in developing countries are unlikely going to benefit much from MAS within populations.
8. Most breeding programs, in both developed and developing countries, struggle to obtain rates of genetic response that are anywhere near to what might be expected based on theoretical considerations. The discrepancy between the actual rate of genetic response and what might be expected based on theoretical considerations is often due to the lack of control of selection decisions and the lack of clear breeding objectives. Implementation of advanced genetic and reproductive technologies may therefore not be first priority in such programs.
9. The ongoing FAO survey of the State of the World for livestock genetic resources has already revealed several consistent demands for technology applications in the developing world. Demands for breed characterisation, for cryopreservation of livestock germplasm, and for application of embryo transfer technologies were highlighted. There was little expressed demand for advanced genetic technologies and the gap between developed and developing world in such technologies was clear. Where demand for advanced biotechnologies was expressed, there was little evidence of an underlying strategic plan. These results identify needs for capacity development and technology access in advanced biotechnologies and strategic planning. [As part of its country-driven strategy for the management of farm animal genetic resources, FAO has invited 188 countries to participate in the First Report on the State of the World's Animal Genetic Resources, to be completed before 2006. At the FAO/IAEA symposium mentioned above, a paper by R. Cardellino, I. Hoffmann and K.A. Tempelman was presented entitled "First report on the state of the world's animal genetic resources: Views on biotechnologies as expressed in country reports". The synopsis is available at http://www.iaea.org/programmes/nafa/d3/mtc/synopses.pdf or contact ricardo.cardellino (at) fao.org for more information...Moderator].
Harinder P.S. Makkar MSc, PhD (Nott.), Habil. (Hohenheim)
Animal Production and Health Section
International Atomic Energy Agency
P.O. Box 100, Wagramerstr. 5
E-mail: H.Makkar (at) iaea.org
Internet: http://www.iaea.org/programmes/nafa/d3/index.html http://www.fao.org/
FAO/IAEA Symposium on Biotechnology: http://www.iaea.org/programmes/nafa/d3/index-symp2003.html
Sent: 28 November 2003 11:15
Subject: 53: Re: Marker assisted backcrossing
From Prof. H. Dulieu, France.
Thank you to Dr Kuldeep Singh (Message 44, November 26) for his response to my message (42, November 26).
In my message, I did not support the idea that MAS during BCs requires a larger number of backcross (BC) generations. I agree with him concerning the strategy to select around 50% of the BC individuals on a visual basis over a large sample size and, in a second step, to perform analysis of markers, allowing us to keep only individuals which have recovered most markers of the recurrent parent and the markers from the donor, linked to the trait itself. In these conditions, it is obvious that MAS-BC selection will be efficient in very few generations, if the numbers of individuals to be analysed are estimated on a likelihood basis, namely the numbers of chromosomes, allowing us to know the expected frequencies of individuals homozygous for the markers located on the chromosomes which are not implicated by the transmission of the character. It will, of course, be necessary to search further for recombinants (see the remarks of the Moderator, message 42) and, finally, to establish the new variety by selfing and selecting for homozygosity at the loci (chromosome) linked to the selected character. I agree that it is a matter of numbers of individuals more than generations. Then, the protocol will save several generations (years!) if well designed and based upon the molecular map.
Prof. H. Dulieu,
Plant genetics and Biology,
University of Burgundy,
hdulieu (at) u_bourgogne.fr
Sent: 28 November 2003 14:22
Subject: 54: Gene pyramiding - crops
This is from R. Sridhar, India.
This refers to message 37 (November 25) of Kevin Williams regarding use of MAS in gene pyramiding (selection of plants for traits which could not be done by conventional phenotyping, as in the case of assessing resistance to different disease resistance genes) and further description of this by Kevin Williams in message 51 (November 29).
In fact, our experience (detailed in message 35, November 24) was to combine three bacterial leaf blight resistance genes in two popular rice cultivars to enhance the durability of their resistance to this disease. We were fortunate to have a pyramided line carrying all these three genes as the donor parent. We did MAS (employing markers for these three different resistance genes) right from BC1F1 through BC4F1 at each generation and finally selfed the BC4F1 plants. Again, MAS was performed in BC4F2 to select plants possessing all the three genes. Subsequently, the generation was advanced to BC4F5 and this provides opportunity for evaluation for disease reaction and further selection of other agronomic traits. We selected a fairly large number of population and this helped to identify plants which are even marginally superior to the recurrent parent with similar grain qualities. (The donor parent itself yields slightly higher than the recurrent parent). Some others prefer to use a background selection with microsatellite markers for selecting plants almost identical in all respects to the recurrent parent. Obviously, this would eliminate the probability of selecting genotypes which are marginally superior to the recurrent parent.
Dr. R. Sridhar
Flat 5, Rajparis Kings Castle
(Old No. 19), New No. 11, First Main Road
I-Block, Anna Nagar East, Chennai 600 102
Tamil Nadu, India
rangsridhar (at) yahoo.com