Science in Society Archive

Marker Assisted Selective Breeding

Prof. Joe Cummins gives the current state of play in how molecular genetic analysis can aid in selective breeding without genetic modification

Quantitative traits not determined by single genes

Genetically modified (GM) crops are based on inserting synthetic foreign genes mainly from bacteria, to impart herbicide tolerance or insect resistance into the genomes of crop plants. This technology has so far provided little if any increase 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 genetic markers that are inherited. The main agricultural traits governing yield (or size), stress resistance or long-term disease protection are quantitative trait loci (QTL, ‘loci’ is another word for genes). One of the founders of the study of population genetics, Ronald A. Fisher, described QTL as many independent loci that added together to determine traits such as size [1]. QTL are seldom tightly linked on a chromosome and the loci are dispersed over many chromosomes in the genome.  Selection of QTL traits has been inherently slow and meticulous, but has resulted in major improvements to crops and livestock.

While Fisher believed that QTL were made up of very many genes each adding small increments to a trait, recent findings indicate that some QTL may be made up of a relatively small number, say twenty or so, genetic markers that could be easily selectedprovided they could be identified. Currently, it appears that many QTL may have relatively few loci but some important QTL may be closer to the very large number of genes envisioned by Fisher, in which case, identifying and selecting such traits by the molecular markers are unlikely to be cost-effective.

Molecular markers can be used to aid selective breeding

There is a growing arsenal of molecular markers (polymorphisms) that aid in identifying QTL and selecting them for crop and animal enhancement. The process ofusing such markers is called marker-assisted selection (MAS), which 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 and identified. The markers used to probe the progeny of a cross are not the QTL genes 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. Recombination may separate the marker from a QTL, 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 programme, the more effective it will be.

There are several types of molecular markers used in MAS; these include restriction fragment length polymorphism (RFLP), random amplification of polymorphic DNA (RAPD), amplified restriction fragment length polymorphism (AFLP), single sequence repeats (SSR) and single nucleotide polymorphisms SNPs [2]. RFLP involves the use of restriction enzymes to cut chromosomal DNA at specific 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, then using PCR and selective nucleotides in the primers to amplify specific fragments [4]. The method measures up to 100 polymorphic loci and requires a relatively small DNA sample for each test [4]. SSR analysis is based on DNA micro-satellites (short-repeat) sequences that are widely dispersed throughout the genome of eukaryotes, which are selectively amplified to detect variations in simple sequence repeat [5]. SSR analysis 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 methods are used in a typical MAS breeding programme.

MAS has been employed in breeding cereals, and extensively so in maize breeding. Corporations including Monsanto and Syngenta have invested heavily in the programme. 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, and there was a strong response [8]. The pome fruits, apple and pear, have extensive MAS programmes, 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 assessment of genetic markers will greatly enhance the conservation of genetic diversity in wild crop relatives [11], and the information from wild crop relatives could be directly employed in MAS of the crop plant.

Does MAS actually work?

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 that could be selected, but only with patience [12]. Hill’s report suggested that Fisher’s view of QTLs prevailed and that the use of MAS might not be cost-effective. It may be that MAS is effective in traits such as disease resistance and certain agronomic performance but that important traits such as oil production in maize or body size in chickens are most effectively bred 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 help the farmer breed 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 scientists working with indigenous farmers would recognize markers linked to valuable agronomic traits and pass on that knowledge to the indigenous plant breeders to assist them in making selections that are beneficial.

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 has been claimed by advocates. MAS should not affect organic certification because transgenes are not introduced into the crop. Molecular genetics is used only in analyzing the crosses. Nevertheless, MAS has far more to offer in crop and animal improvement than genetic modification.

Article first published 08/09/05


  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? Food and Agriculture Organization, 2003
  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.
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  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? Food and Agriculture Organization, 2003
  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? Food and Agriculture Organization, 2003
  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? Food and Agriculture Organization, 2003
  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? Food and Agriculture Organization, 2003
  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 selection.  Science 2005, 307,683-4.

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