The role of molecular markers and marker assisted selection in breeding for organic agriculture

Breeders stressed advantages of the use of molecular markers to improve varieties for the organic sector (Table 1, Strengths). Allowing the application of molecular markers in breeding programmes to improve varieties for OA, would allow a breeder to combine breeding for OA with conventional breeding programmes for low-input agriculture.

The participants from the OA could also see some advantages of MAS as a non-GMO strategy to improve the efficiency of breeding programmes for urgently needed, better adapted varieties (Table 2, Strengths). MAS may help to overcome some hurdles, such as selection with pyramiding of (monogenic) resistance sources for potato late blight which is very difficult to achieve without molecular markers (Tan 2008). Phytophthora infestans is a real threat for OA and resistant varieties would improve the position of potatoes in organic farming (Lammerts van Bueren et al. 2008; Vos 2009). Although horizontal resistance with a polygenetic base is seen as more advantageous in OA, it is also recognized that such is not in all cases available or optimal (Finckh 2009). However, this strategy of stacking genes has to prove itself as a durable resistance strategy and apprehensions were expressed that a fail of this strategy would result in a loss of several resistance genes at a time and an even more rapid turn-over of varieties (Table 2, weakness). Whether this strategy will be applicable in the late blight case is still under discussion as the effectiveness of gene stacking for blight resistance in potato remains uncertain due to the evolutionary potential for rapid adaptability of P. infestans to host plants (Haas et al. 2009).

There was not much discussion about the use of molecular markers for specific monogenetic traits. However, there was more concern about the efficacy of molecular markers for quantitative traits. To create conditions to optimise yield stability and good quality, OA is stressing more emphasis on achieving varieties adapted to low-input growing conditions. The low-input management of OA results in a larger influence of varying environmental conditions (in time and geographically) on crop performance. To cope with varying environmental conditions, adaptive and robust varieties are required (Lammerts van Bueren et al. 2002, Wolfe et al. 2008). Specific for organic, low-input farming methods is the need for an adapted plant architecture above and below ground resulting in e.g. improved weed competitiveness and nutrient efficiency (e.g. Mason and Spaner 2006; Østergård et al. 2007). Traits such as nutrient efficiency are quantitative traits largely influenced by environment and management. Especially for such complex traits, the representatives of OA feared that marker research is too complicated and expensive (Table 2, Weaknesses). Further, there was the concern that markers developed under and for conventional conditions might not be effective, when applied in an organic context (Table 2, Weaknesses), e.g. with respect to markers for baking quality. First of all the baking procedures in the organic sector differ to a large extent from conventional baking that relies mainly on industrial baking procedures. Many organic bakeries do not work with frozen dough as the industrialized bakers do, so organic baking procedures require dough with less strong glutenin types. Thus the required phenotype in organic bread wheat production is different from conventional wheat production and therefore markers for conventional conditions may not always be relevant for organic conditions. Secondly, QTL may interact with environmental conditions. For instance, not only the protein level but also the protein composition can change under low-input growing conditions compared to high-input conditions (Wieser and Seilmeie 1998; Triboï et al. 2003; Tuvesson et al. 2009). In that case the same QTLs and/or the same power of the QTLs can not be automatically applied. Nevertheless, the organic sector would be interested in markers for baking quality under low-input growing conditions of wheat to replace the laborious and costly baking tests during the breeding process.

As selection is a key tool in breeding, this topic was dealt with from both the breeders and organic sector’s perspective and was controversially discussed. As organic farmers have to rely on a diversity of measures that support and complement each other under varying conditions and as they have less means to promptly interfere and compensate during crop growth, there is more need for overall improved performance of a variety combining many desired characteristics to support yield stability. This requires a more holistic, integrated systems approach in designing the most appropriate set of measures, including crop improvement. In the OA sector, a primary reaction is often to consider genomics as a result of reductionist science and therefore not much of value for organic agriculture (Table 2, Weaknesses). Accordingly, the organic sector tends to put more emphasis on the weaknesses and threats (loss of diversity, high costs, narrow focus etc.) and is less inclined to appreciate the potential strengths and opportunities of molecular markers. Lack of knowledge of marker assisted selection procedures leads to fear that crops will be selected in the lab and no longer evaluated in the field.

Also breeders recognize the ‘molecularisation’ in modern breeding. Koornneef and Stam (2001) describe how in plant breeding the paradigm has changed from selection of phenotypes toward indirect or direct selection of genes. Koebner and Summers (2003) however argue with respect to wheat breeding that the breeding paradigm will be touched but not overturned by genomics driven MAS, as wheat breeding will continue to be primarily driven by field selection. The representatives of the organic sector are not merely concerned about an over-emphasis on increasing knowledge on the underlying molecular genetics, but also stress that the organic sector is urging for more knowledge on higher integration levels applying an agro-ecological approach at crop and farm system level. Nevertheless, to our opinion analytical tools such as markers can be of additional value in an approach that departs from a holistic view when the results of such an analysis are carefully converted to the level of farming and processing practices.

Beside the special concerns for MAS in organic farming, there are more general concerns on the use of markers for selection for quantitative traits, as there is still a large gap between phenotyping and genotyping of crops (e.g. Xu and Crouch 2008; Backes and Østergard 2008; Table 1, weakness). Although the efficiency of MAS largely depends on exact initial phenotyping, an even more effective way to bridge the gap and to deal with the interaction between genotype, environment and management (cultivation practices) is the opportunity given by integrating genetics, agronomy and crop physiology (Yin and Struik 2008; Struik and Yin 2009). Their approach, including QTL-based ecophysiological modeling, could also provide the tools to breed for complex trait, such as nutrient-use efficiency, in a more efficient way and making use of markers. Integrating more disciplines in breeding research is also what Moose and Mumm (2008) suggest in their commentary on the recent molecular advances to meet the challenge of identifying the best gene combinations for optimal crop improvement.

All the participating breeders acknowledged that there will always be a certain gap between genotype and phenotype as molecular markers will never give full information especially where there is more interaction of environment such as is the case under the varying low-input farming conditions. The breeders clearly stressed that in breeding programmes phenotypic selection will always be needed, and that research on developing easy phenotypic selection methods is still required. MAS will increase breeders’ flexibility because it enables them to work with smaller populations and MAS can also lead to a more efficient use of field trial capacity (Heselmans 2009) (Table 1, Strengths). In conclusion, there is no need that molecular marker have to stand their ground as an exclusive selection tool, as they rather should be considered as a complement to phenotypic selection (Table 2, Weaknesses).

The emphasis of OA is on ‘prevention management’ based on ecological principles. This includes applying organic fertilisers to build up soil fertility, using a wide crop rotation, mechanical weed management, etc. Exploiting biodiversity is one of the central measures to create resilience within the farm ecosystem (Østergård et al. 2009b).

One of the strengths of MAS identified is the ability to improve the introgression of ‘exotic’ and wild alleles and thereby to increase the genetic diversity in the pool of available varieties. As biodiversity and thus also genetic diversity is one of the key tools of OA in building up resilience in the agro-ecosystems, technologies with this potential are of interest. As discussed above on the issue of backcrossing, marker-assisted introgression makes access to new genetic resources more feasible by screening genetic resources with molecular markers and by making selection of newly introduced quality or resistance alleles from wild relatives more efficient. The reason is that the targeted gene can more easily be followed in the successive generations of backcrossing and distinguished from undesired linkage drag (Hospital 2001).

However, although the participants from OA were positive about the above described strength, they also expressed the concern that too much focus on genetic markers may decrease diversity during the breeding process for economic reasons (Tables 1 and 2, Threats). This concern was also expressed in the policy paper of the Soil Association (Soil Association 2001). The breeders with molecular experience recognized this concern, but were more confident about the positive gains. The future practice will tell whether there is more chance to lose or to gain diversity by applying MAS in breeding.

Some of the issues put forward by OA concerned the assignment of instrumental values and were related to the potential positive or negative consequences of the use of molecular markers. Other arguments concerned the assignment of intrinsic values and were related to the methodology and protocols for the development of the molecular markers. This last aspect leads to one of the threats identified by the breeders that not all molecular marker technologies will be allowed in breeding programmes for OA (Table 1, Threats). This is related to one of the very important reservations of the organic sector against the use of molecular markers due to the fact that harmful chemicals and enzymes produced from genetically modified organisms are used in the process of marker development (Table 2, Weaknesses). At the same time a threat was identified that the development of protocols with non-genetically modified enzymes is slow and not of high priority (Table 2, Threats). One of the opportunities is that the general development within molecular techniques is moving towards replacing harmful chemicals by alternatives that cause less damage to the lab-workers and the environment (Table 1, Opportunities) (e.g. Yoza et al. 2002, Zipper et al. 2004).

For the enzymes required for the process, of which the heat-stable DNA polymerase for the PCR reaction is the most important, the common trend goes toward enzymes produced by recombinant micro-organisms; this is because of their higher efficiency and standardization of production. Nevertheless, most suppliers of Taq-polymerase offer the native (non-recombinant) enzyme at only slightly higher prices. A minor disadvantage might be that advanced features engineered in the recombinant Taq-polymerase, like the activation by heat exposure in order to avoid premature enzyme activity, are not available for the native enzymes (Kellogg et al. 1994, Lebedev et al. 2008).

An issue that is of concern of both breeders and the organic sector is related to the costs of marker application in MAS, both for investments and running costs (Table 1 and 2). Apart from other features, such as the resolving power, determined by the level of polymorphism detected, co-dominance and reproducibility (Xu and Crouch 2008) the costs are certainly an important factor in the breeder’s choice of a specific type of marker. Costs, first of all depends on the possibilities for automation in a marker method. The use of agarose gels for visualization, for instance, require lower investment costs, but offer nearly no possibility of automation, while in the case of a detection on a sequencer, both the potential for automation and the investment costs are high. For the actual costs, it is important to separate development and application costs as in many cases the breeder will either rely on existing markers or include the marker development into publicly financed research projects (Backes and Østergard 2008).

The possible strategies for marker applications range from a complete ‘in-house’ solution to a complete outsourcing of all marker activities to a service provider. The most expensive solution would be to develop a marker ‘from scratch’ by establishing the linkage between marker and trait. Only large companies have the necessary scientific and budgetary capacity to meet this challenge. This fact results in concerns of small and medium-sized breeding companies that depend on the public availability of markers and fear not to be able to keep with those global players (Table 2, Weaknesses). Further, if a breeder applying MAS gets an advantage by being the first on the market with an improved trait for a certain crop, the competitors might like also to invest in molecular marker techniques. If these new techniques form a mere addendum to the established breeding process, this would certainly enhance the costs of plant breeding and, thereby, also increase the price of the seeds (Table 1, Threats). If, in contrast, the breeder is able to replace part of the phenotypic trials by MAS, it might be cost-neutral. However, new technologies that increase productivity have always an impact on the adapting company relative to its competitors. In addition, the development of better DNA extraction technologies and DNA analysis tools leading to decreasing cost per data point will make molecular marker strategies possible for budget restricted breeding programmes too (Weyen 2009).

An increasing number of service providers for MAS give also smaller breeding companies the freedom to choose to adopt or not to adopt MAS on a case by case basis without making larger investments in this technology themselves.

Breeding for organic farming still is a niche-market of low interest for global players, which makes their competitiveness a less critical factor. The application of molecular markers in breeding companies challenges the ability of the breeder to re-consider an accustomed (and likely successful) breeding system and to acquire new skills to deal with this instrument (Table 1, weakness). The most important challenge might be to decide where and when it pays to replace or complement phenotypic selection for a specific trait by MAS.

Another concern that is shared by both the organic sector and breeders is that the emerging science of molecular genetics tend to generate more attention in breeding education, as most of the breeding research at the universities in which the students participate deals with molecular techniques (Tables 1 and 2, Threats). The private breeding sector requires a curriculum dealing with molecular techniques as well as with ‘traditional’, phenotype-based field selection in actual populations (Gepts and Hancock 2005). This may help to develop skills how molecular genetics can be incorporated into traditional breeding programmes (Ransom et al. 2006).

The rejection of genetic engineering by the organic sector and promoting traditional, phenotype based selection does not imply that there is no innovation in breeding for organic agriculture. On the contrary, organic agriculture challenges the breeding sector to broaden the scope of approaches by including (additional) morphological and physiological traits (Burger et al. 2008, Löschenberger et al. 2008, Osman et al. 2008, Pswarayi et al. 2008, Voorrips et al. 2008). Breeders as well as the organic sector stressed that acceptance of the use of molecular technology in OA requires good communication (Tables 1 and 2, Weaknesses). Although it may be difficult for farmers and consumers to understand and accept MAS in OA, as it is too much associated with genetic engineering (Table 2, Threats), there are interesting examples of needs for varietal improvement with a role for MAS. Emphasizing these examples may help in getting acceptance for the use of molecular technology in OA.

The workshop revealed that there is a lack of knowledge in organic sector on the pros and cons of molecular markers and marker assisted selection and that there is not much active interaction and communication between the organic sector and molecular scientists.

Many scientists tend to believe that a broad public understanding of each and any detail in science and technology is an indispensible prerequisite for public acceptance of new technologies and the applications thereof. This belief has resulted in communication strategies that flood the public with large amounts of information about new technologies and the benefits of potential applications (Office of Science and Technology 2000). We seriously doubt whether it is useful to explain MAS to the general public as our own experience is that organic consumers (laypersons) even question the need for (traditional) breeding as such assuming that old varieties are the best to apply and have difficulties to understand technical aspects. In our opinion it would make more sense to discuss the use of molecular markers with (organic) farmers as the first line users. However, it would be worthwhile to put more emphasis on educating the public that plant breeding is a natural component of agriculture in general and also for organic agriculture.