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SYMPOSIUM ON GENOMICS AND PLANT BREEDING: THE EXPERIENCE OF THE INITIATIVE FOR FUTURE AGRICULTURAL AND FOOD SYSTEMS

Marker-Assisted Selection in Public Breeding Programs

The Wheat Experience

Dep. of Agronomy & Range Science, Univ. of California, One Shields Ave., Davis, CA 95616

^* Corresponding author (jdubcovsky{at}ucdavis.edu)

Abbreviations: BAC, bacterial artificial chromosome • MAS, marker-assisted selection • SNP, single nucleotide polymorphism

	INTRODUCTION

TOP INTRODUCTION Wheat Breeding in the... MASwheat: A Public MAS... Conclusions REFERENCES

 
IT HAS BEEN SUGGESTED that the recent progress in the area of plant molecular biology and plant genomics have the potential to initiate a new Green Revolution. However, these discoveries need to be implemented in new cultivars to realize that potential. The controversy about transgenic crops has delayed the incorporation of alien genes into plants and significantly increased the cost to develop and release transgenic crops. These costs are usually beyond the resources of public breeding programs and, therefore, are not currently used in most cultivated plants.

Fortunately, biotechnology has provided additional tools that do not require the use of transgenic crops to revolutionize plant breeding. Progress in molecular genetics has resulted in the development of DNA tags, which can be used in marker-assisted selection (MAS) strategies for cultivar development (Paterson et al., 1991). These molecular markers can be used as chromosome landmarks to facilitate the selection of chromosome segments including useful agronomic traits during the breeding process. These markers are particularly useful for incorporating genes that are highly affected by the environment, genes for resistance to diseases that cannot be easily screened for, and to accumulate multiple genes for resistance to specific pathogens and pests within the same cultivar, a process called gene pyramiding. An additional advantage of the incorporation of MAS into breeding programs is that very different types of traits, e.g. a disease resistance gene or a gene to increase grain protein content, can be manipulated using the same technology. Dekkers and Hospital (2002) have recently reviewed some of the potential limitations of MAS strategies, and concluded that the use of MAS will be determined by the economic benefit relative to conventional selection.

The alleles that are incorporated by MAS are generally present within the gene pool of a particular crop and are transferred by meiotic chromosome recombination. One of the positive aspects of this approach is that these genes reside at their natural chromosomal locations, thereby minimizing the possibility of gene silencing. Another important aspect of cultivars developed by MAS is that they are not transgenic and therefore, do not face the public resistance against transgenic crops.

The MAS strategy is a way to capitalize on available markers and to incorporate valuable traits into elite lines that are suitable for cultivar release. In addition, release of these MAS-improved cultivars is an efficient way of demonstrating the power of these technologies to the public. However, limited funding for implementation efforts had delayed the incorporation of these powerful technologies into most public breeding programs.

	Wheat Breeding in the USA: A Public Effort

TOP INTRODUCTION Wheat Breeding in the... MASwheat: A Public MAS... Conclusions REFERENCES

 
Wheat (Triticum aestivum L.) is a self-pollinating species and therefore, growers can save seed from one harvest for the next year. This has reduced the profitability of wheat breeding for the private sector and has resulted in the continuous existence of a large, vibrant public sector involved in cultivar development. For example, the total number of cereal crop breeders in the USA in the last census was 893, with 80% being in the private sector and 20% being in the public sector (Frey, 1996). In wheat, approximately 60% of the breeders were in the public sector. By comparison, only 7% of the corn breeders were in the public sector. Public investments in wheat breeding during the past century have resulted in the development of the majority of cultivars grown by U.S. farmers. State agricultural colleges and experimental stations, USDA, or CIMMYT developed approximately 60% of the cultivars released in the USA during the 20th century. In addition, a high percentage of the area of wheat production in the USA is attributed to publicly developed cultivars (KS 62%, ND 64%, WA 88%, NE 90%) (NASS, 2001).

Fuglie et al. (1996) found a typical range of 40 to 60% return on public research investment, with public wheat breeding consistently at the top of this range. In addition, nine out of the 10 interspecific translocations involving the introgression of novel genes into cultivated germplasm that significantly affected U.S. wheat production were developed in public plant breeding programs (Mercado et al., 1996). These data provide convincing support of the broad impact of public wheat breeding efforts both in cultivar development and in germplasm enhancement.

Public wheat-breeding programs are typically supported by wheat grower associations. However, low wheat prices in the past years have resulted in a reduction of resources available to the U.S. wheat growers and a shrinking of resources for research and development in new technologies. This situation was aggravated by a limited investment of federal funding agencies during the 1990s in implementation grants for public wheat breeding programs. This limited investment in practical applications is difficult to understand in light of the large investment made by the same funding agencies in wheat molecular genetics and wheat genomics.

During the last 10 yr, public researchers constructed detailed wheat genetic maps including more than 3000 molecular markers and physical maps including more than 16000 loci (http://wheat.pw.usda.gov/NSF/; verified 2 July 2004). In addition to mapping, U.S. federal agencies have funded the sequencing of more than 105000 wheat ESTs, the construction of wheat Bacterial Artificial Chromosome (BAC) libraries (Cenci et al., 2003; Lijavetzky et al., 1999), the assembly of BACs into physical maps (http://wheat.pw.usda.gov/PhysicalMapping/; verified 2 July 2004), and the sequencing of large segments of wheat DNA (SanMiguel et al., 2002). These powerful genomic resources have started to yield the first successful positional cloning efforts in wheat (Faris et al., 2003; Feuillet et al., 2003; Huang et al., 2003; Yahiaoui et al., 2004; Yan et al., 2003; Yan et al., 2004). Cloning of agronomically important genes has made possible to develop "perfect markers," based directly on the allelic variation responsible for the differences in the trait. Examples of perfect markers in wheat include the glutenin genes for gluten strength (Anderson et al., 1989), the waxy genes for starch properties (Briney et al., 1998), the puroindoline genes for hardness (Beecher et al., 2002), the vernalization genes for vernalization requirement (Yan et al., 2003; Yan et al., 2004), the Rht genes for semi-dwarf habit (Peng et al., 1999), and the Lr10 and Lr21 genes for leaf rust resistance (Feuillet et al., 2003; Huang et al., 2003). Wheat researchers have also developed closely linked molecular markers to yet unidentified genes with positive effects on quality characteristics and resistance to fungi, viruses, and insects (reviewed by Dubcovsky et al., 2000; Anderson, 2000).

The most efficient way to develop a positive synergistic effect between the large research investments in wheat genomics and the growers' investment in public wheat breeding is to fund implementation research projects. The MAS programs are good examples of implementation projects that have the potential to facilitate the transfer of valuable genes identified in basic research programs into public wheat varieties.

	MASwheat: A Public MAS Program

TOP INTRODUCTION Wheat Breeding in the... MASwheat: A Public MAS... Conclusions REFERENCES

 
The wheat public research sector has a long tradition of collaborative projects that were initiated at the beginning of the 1990s by the International Triticeae Mapping Initiative. Large multi-laboratory projects continued later in the USA under the funding of the NSF-Plant Genome Initiative (http://wheat.pw.usda.gov/NSF/; verified 2 July 2004). Many of the collaborators of these projects were wheat breeders, facilitating the integration of basic and applied wheat researchers. This integrated research community and the availability of the results from previous research efforts in marker development were instrumental in developing a successful proposal for MAS in wheat.

Wheat researchers and breeders from 12 public programs across the USA organized a national wheat MAS consortium (MASwheat) that was funded by the USDA Initiative for the Future of Agriculture and Food Systems (2001–2004). The MASwheat project structure is similar to the Australian National Wheat Molecular Marker Program (NWMMP) implemented in 1996. The main objective of both projects is to empower the breeders by implementing MAS capacities within each of the existing public breeding programs. This strategy has been successful in closing the funding gap between the development of genomic tools and the public investment in cultivar development, and in transferring the value of genomic research to the wheat growers' fields.

The MASwheat project is committed to transfer new developments in wheat genomics and biotechnology to U.S. wheat production through marker-assisted selection. Available molecular markers are being used to transfer 22 resistance genes to fungi, viruses, and insects; and 21 gene variants related to bread, pasta, and noodle quality into 75 different recurrent parents (34 whites, 33 reds and 8 durums). Eighty MAS projects have been already completed and additional 350 backcrossing programs are currently being advanced in average two generations a year by MAS.

All the information and protocols used in the MASwheat project are publicly available through the project WEB site (http://maswheat.ucdavis.edu; verified 2 July 2004). The collaborative nature of the project and the public access to the information was lauded in a recent article in Nature focused on the current difficulties of public breeding programs (Knight, 2003). The numerous presentations in growers' meetings, field days and symposiums by the members of the MASwheat consortium are also improving the public understanding of the potential benefits of biotechnology.

	Conclusions

TOP INTRODUCTION Wheat Breeding in the... MASwheat: A Public MAS... Conclusions REFERENCES

 
Marker technologies are continuously evolving. The development of 96-well DNA extraction protocols and high-throughput genotyping equipment resulted in substantial reduction of MAS costs. A new generation of molecular markers based on the detection of single nucleotide polymorphisms (SNP) promises high-throughput assays at relatively low costs, along with the potential for high levels of multiplexing. Implementation of this multiplexing technology in plant improvement strategies can provide cost-effective tools for selection of multiple traits in breeding populations.

The challenge for the public plant breeders and for the federal funding agencies will be to generate the integrated proposals and necessary funding to continue the actual MAS programs and to incorporate new marker technologies.

One important aspect of the new genomic revolution is that most of the information is publicly available. Therefore, competitiveness will not be determined by access to the information but by the speed in which these technologies are incorporated into the breeding programs. This represents both a challenge and a fantastic opportunity for the public breeding programs that have the expertise to utilize successfully MAS technologies.

	ACKNOWLEDGMENTS

 
The authors acknowledge financial support from USDA- IFAFS competitive grant 2001-04462. The first author thanks J. Anderson, B.S. Gill, S. Kianian, N. Lapitan, J. Sherman, and M.A. Soria for a critical review of this article.

Received for publication July 23, 2003.

	REFERENCES

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