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[SANET-MG] marker assisted selection



25 July 2005
Prof. Joe Cummins
“Marker assisted selection: breeding using molecules as markers but not transgenes”
	
Currently crop biotechnology is based on the use of bacterial transgenes to impart herbicide tolerance or insect resistance on the crops. In this process an array of genes area added to the crops to make the primary bacterial transgenes work. This technology provides little hope of providing major advances in yield , stress tolerance or long term resistance to microbes or nematodes. Traditional breeding of crops and animals has been based on the use of markers that are usually inherited following Mendelian patterns. The main agricultural traits governing yield (or size), stress resistance or long term disease protection are the quantitative trait loci (QTL). One of the founders of the study of population genetics ,R.A. Fisher, described QTL as many independent loci that added together to provide traits such as size(1). QTL are seldom tightly linked on a chromosome and the loci are dispersed about many chromosomes in the genome. Selection of QTL traits has been inherently slow and meticulous but because the traits have fundamental importance the results have provided the main crop and animal enhancements. Fisher believed that QTL were made up very many loci each adding small increments to the selection for a trait such as size. How ever, QTL may be made up of a relatively small ,say twenty or so, loci that could be easily managed provided that the loci could be identified. Fisher’s idea of QTL is probably best served by the slow and meticulous selection strategies used in traditional genetics while QTL with relatively few loci can be readily selected using molecular markers. Currently, it appears that many QTL may have relatively few loci but some important QTL may be closer to the very large number of loci envisioned by Fisher, in which case the molecular markers are unlikely to be cost effective. In contrast to the added transgenes used in genetic modification there is a growing arsenal of molecular markers (polymorphisms) that aid in identifying QTL and selecting them for crop and animal enhancement. The process employing such markers is called marker assisted selection (MAS), that technology differs from genetic modification because the genes being selected for crop or animal improvement are not altered in any way. The molecular markers used in selection are probed using sequences from a gene bank but the genes in the crop or animal are not altered, only identified. The markers used to probe the progeny of a cross are not the QTL loci themselves but they are close to the QTL on the genetic map. Of course the markers can be used to determine the molecular identity of the QTL, but the molecular marker is used even when the QTL is identified because the marker is cheaper and quicker to use to identify a large number of progeny. Of course recombination may separate the marker from a QTL allele but the closer the marker is to the QTL the more remote is the chance of separation by recombination. The more polymorphic markers available for a breeding program the more effective will be that program. There are several types of molecular markers used in MAS these include restriction length polymorphism (RFLP),random amplification of polymorphic DNA (RAPD), amplified length polymorphism(AFLP) single sequence repeats (SSR) as the main marker strategies and single nucleotide polymorphisms SNPs(2) RFLP is the use of restriction enzymes to cut chromosomal DNA at short restriction sites, polymorphisms result from duplications or deletions between the sites or mutations at the restriction sites. RFLP provided the basis for most early work but requires a relatively large amount of DNA and is rather expensive in a large screening program (2). RAPD utilizes low stringency polymerase chain reaction (PCR) amplification with single primers of arbitrary sequence to generate strain-specific arrays of anonymous DNA fragments (3). The method requires tiny DNA samples and analyses a large number of polymorphic loci (2). AFLP requires digestion of cellular DNA with a restriction enzyme , ligating adapters to each restriction fragment and a subset of such fragments are amplified using primers with 16 adapter defined sequences with one arbitrary nucleotide (4). The method measures up to 100 polymorphic loci and requires a relatively small DNA sample for each test (4). SSR are based on DNA microsattelites that are widely dispersed through out the genome of eukaryotes. Microsattelites are selectively amplified to provide simple sequence repeat markers (5).SSR requires tiny DNA samples and has a low cost per analysis (2). SNPs are detected using PCR extension assays that efficiently pick up point mutations (6). The procedure requires little DNA per sample and costs little per sample once the method is established (2). One or two of methods described above are employed in a typical MAS breeding program. MAS has been employed in cereals. It was extensively deployed in maize breeding Corporations including Monsanto and Syngenta have invested heavily in the program. SNP appear to be the dominant marker for selection. Wheat has seen less progress in MAS than maize but there is good success in the area of quantitative disease resistance. Rice has also seen extensive activity in MAS centering on pyramiding disease resistance genes. SNPs appear to be identified for all the major cereals (7). MAS is being used to improve forage crops through QTL for nitrogen use efficiency. There was a strong response to marker selection on nitrogen use efficiency (8). The pome fruits, apple and pear, have extensive MAS , mainly based on RFLP,RAPD,SSR and AFLP. The traits being selected include fruit production, storage and disease resistance (9). A global strategy using MAS for livestock genetic improvement in the developing world was proposed . QTL mapping would be used in genetic improvement and to bring together desirable traits from around the world (10). It has been proposed that conservation of allelic richness in wild crop relatives is greatly enhanced by assessment of genetic markers (11). The information from wild crop relatives could be directly employed in MAS of the crop plant. A recent review by William Hill of Edinburgh University focused on the QTLs for oil production in maize and for body size in chickens. In neither case could individual QTL with substantive quality be detected. Instead , Identified QTLs created small additive increments which could be selected , but with patience (12). Hill’s report suggested that the Fisher view of QTLs prevailed and that the use of MAS might not be cost effective in such selections. It may be that MAS may be effective in areas such as disease resistance and some agronomic traits but that important traits such as oil production in maize or body size in chickens are dealt with most effectively using traditional selection methods. Farmers in developing countries and even some farmers in the developed world face the growing control of seed production by a few multinational corporations. One solution has been to educate farmers in the art of plant breeding to provide varieties tuned to the local environment and free of the greedy demands of seed corporations. It is highly unlikely that indigenous farmers will take to MAS and molecular genomics. However, those who advise indigenous farmers would gain valuable insights in recognizing markers linked to valuable agronomic traits and pass on those insights to the indigenous plant breeders to assist them in making selections with immediate benefits. In the long run it seems likely that MAS will play an important role in plant breeding, even though it may not be as large as is being claimed by promoters. MAS should not effect organic certification because transgenes are not introduced into the crop. Molecular genetics is only used in analyzing the crosses. It may be best to tentatively accept MAS and to point out that the technique is far more effective in crop and animal improvement than is the use of transgenes.
References
1. Fisher,R The Genetics of Natural Selection, Oxford University Press,Oxford 1930 2. Korzun,V. Molecular markers and their application in cereal breeding Marker Assisted selection: A fast track to increase genetic gain in plant and animal breeding? 2003 http://www.fao.org/biotech/Conf10.htm 3. Wang,G,Whittam,T,Berg,C. and Berg,D. RAPD (arbitrary primer)PCR is more sensitive than multilocus enzyme electrophoresis for distinquishing related bacterial strains Nucleic Acid Research 1993,21,5930-3 4. Lin,J,Kuo,J. and Ma,J. A PCR based DNA fingerprinting technique:AFLP for molecular typing of bacteria Nucleic Acid Research 1996, 24,3649-50 5. Hayden,M. and Sharp,J. Targeted development of informative microsatellite (SSR) markers Nucleic Acid Research 2001,29, E44-4 6. Torjek O, Berger D, Meyer RC, Mussig C, Schmid KJ, Rosleff Sorensen T, Weisshaar B, Mitchell-Olds T. and Altmann T. Establishment of a high-efficiency SNP-based framework marker set for Arabidopsis. Plant J. 2003,36(1):122-4 7. Koebner,R. MAS in cereals: Green for maize, amber for rice , still red for wheat and barley Marker Assisted selection: A fast track to increase genetic gain in plant and animal breeding? 2003 http://www.fao.org/biotech/Conf10.htm 8. Dolstra,O,Denneboom,C,deVos,A. and vanLoo,E. Marker assisted selection in improvement of quantitative traits for forage crops Marker Assisted selection: A fast track to increase genetic gain in plant and animal breeding? 2003 http://www.fao.org/biotech/Conf10.htm 9. Tartarini,S. Marker-assisted selection in pome fruit breeding Marker Assisted selection: A fast track to increase genetic gain in plant and animal breeding? 2003 http://www.fao.org/biotech/Conf10.htm 10. Gibson,J. Strategies for utilizing molecular marker data for livestock genetic improvement in the developing world Marker Assisted selection: A fast track to increase genetic gain in plant and animal breeding? 2003 http://www.fao.org/biotech/Conf10.htm 11. Schoen,D. and Brown,A. Conservation of allelic richness in wild crop relatives is aided by assessment of genetic markers Proc. Natnl. Acad. Sci. USA 1993,90,10623,27
12.	Hill,W. A century of corn selelction Science , 2005,307,683-4
	
	

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