There are some interesting findings and comments within this recent paper from the journal Foods. Below I have tried to distill out the most interesting points but the full article is available  to read at the following link: Foods| Breeding Bread-Making Wheat Varieties for Organic Farming Systems (mdpi.com)

Agronomic Protocols Used in Organic and Conventional Wheat Production 

Tillage

Long-term field experiments in both Northern Europe and North America suggest that, overall, the efficacy of mechanical weed control protocols used in organic farming is lower than the herbicide-based protocols used in conventional farming. Both the lower efficacy and crop damage associated with mechanical weed control protocols may have significant negative effects on wheat yields and quality in organic farming

Rotational Design 

A large proportion of organic wheat is produced in mixed farming systems which usually have a 2–3-year pure legume or mixed grass/legume sward in the rotation. Where wheat is produced on stockless organic farms, rotations usually include a 2–4-year legume or grass/legume ley phase for fertility building. In organic systems, wheat is often grown immediately after fertility building leys to achieve higher yields and/or to achieve the minimum bread-making quality standards (e.g., protein concentrations of 13% in the UK) set by processors for premium prices. Overall, organic rotations in Europe tend to be more diverse and may include field vegetables, potatoes and grain legumes; wheat is rarely grown following wheat or maize in the rotation (due to increasing the risk of pest and disease damage) and oilseed rape is less frequently used when compared with conventional arable rotations

 Fertilization Regimes

It is more difficult to estimate the mean total and available N inputs to organic wheat crops, since (i) residual N input from preceding legume leys is both highly variable and difficult to measure and (ii) both total and available N in animal manure can vary greatly depending on manure type, processing and storage methods

Crop Protection

In Northern Europe the severity of lodging and biotrophic diseases such as mildew and rust in manure-fertilized organic crops was (i) significantly lower than in mineral NPK-fertilized crops grown without fungicide/growth regulator treatment and (ii) below the threshold at which fungicide/growth regulator applications would become economically viable in conventional farming

The risk of Fusarium head blight and mycotoxin contamination of wheat grain is lower in organic compared with conventional production systems. They describe a range of agronomic factors linked to an increased risk of Fusarium infection and mycotoxin levels in conventional production. Interestingly, risk factors in conventional systems include (i) minimum tillage, (ii) short rotations, especially growing wheat after wheat or maize, (iii) high N fertilizer inputs, and (iv) the use of certain types of fungicide (e.g., strobilurins) and the growth regulator chlormequat, which is used to reduce stem length and the risk of lodging in wheat

Overall, the currently available evidence suggests that lodging, foliar diseases caused by biotrophic fungi such as powdery mildew and rusts, and plant residue/soil-borne diseases such as Fusarium head blight and take-all (which can cause major yield losses in intensive conventional systems) have no or a lower impact on grain and protein yields in organic compared with conventional wheat production

Wheat Breeding/Selection Objectives

Productivity

Meta-analyses of comparative cereal yield data found that grain yields in organic cereal production are significantly (15–30%) lower than those achieved in intensive, conventional production [48,52–55]. These estimates were confirmed by results from long-term, factorial field experiments with common wheat (T. aestivum) in Northern Europe and North America, which also demonstrated that differences in both crop protection protocols and fertilization regimes contribute to the yield gap

In organic production systems, weed competition and foliar disease caused by Septoria spp. were identified as the major yield-limiting crop protection challenges that may be addressed by crop breeding/selection [1,6,7,31,32]. In addition, bunt resistance has been identified as an important breeding target, especially for those organic farming systems which regularly save their own seed for planting in the next growing season [

Differences in N uptake efficiency/N harvest index between the two varieties are likely to at least partially explain these results, but the exact physiological mechanisms underlying these interactions have not been investigated. However, investigations into the physiological and genetic mechanisms responsible for these interactions may lead to the discovery of new breeding strategies for (i) grain and protein yield/yield stability in organic systems and (ii) resistance against Septoria, the main yield affecting disease in both organic and conventional production

More recently, a modelling-based study by Döring and Neuhoff [48] concluded that the inability to increase N availability in organic farming systems via biological nitrogen fixation from legume crops is the main barrier for closing the organic/conventional yield gap for wheat in Northern Europe. This view is supported by results from long-term field experiments which compared the performance of modern, short straw common wheat varieties in organic and conventional management systems [4,6,7,9]. These studies reported not only lower grain yields, but also lower protein concentrations and/or chlorophyll levels (traits that are known to be positively correlated with N availability/supply) in organically grown crops [4,6,7,9]. However, recent trials carried out in northern Britain reported that winter wheat varieties from organic wheat breeding programs in Switzerland produced similar yields and higher protein levels in organic production when compared with intensive conventional winter wheat production systems in the region

Correlation analyses of data from these trials showed (i) that both leaf chlorophyll and grain yield were negatively correlated with grain protein content and (ii) a weak positive correlation between stem length and protein content (Supplementary Table S1). These results were consistent with previous studies that reported (i) negative correlations between grain yield and protein content and (ii) positive correlations between stem length and protein content and/or bread-making quality of wheat grain

The most important yield-related breeding objectives suggested for organic farming focused wheat breeding/selection programs were (i) nutrient use efficiency (in particular N uptake efficiency from organic fertilizers), (ii) competitiveness against weeds, (iii) capacity to recover from mechanical weed control damage and (iv) Septoria and bunt resistance/tolerance

Protein Concentrations and Processing Quality Traits

There is a higher demand for wholegrain cereal products and in particular wheat grain that has high bread-making quality from wholegrain and stone-ground flour [63] and wheat varieties suitable for long fermentation (sour dough-type) breadmaking processes [64]. The higher demand is thought to result from greater awareness among organic consumers about the nutritional/health benefits linked to wholegrain products and sourdough bread consumption.

Increasing protein content and other processing quality-related traits has therefore been one of the most important objectives in organic farming focused breeding/selection programs for bread-wheat in Europe

Nutritional Quality Traits 

Systematic literature reviews/meta-analyses, long-term factorial field experiments, retail surveys and dietary intervention studies reported that organically produced wheat products contain (i) higher levels of nutritionally desirable minerals, phenolics and/or antioxidant activity and/or (ii) lower concentrations of nutritionally undesirable/toxic pesticides, Cd and/or Fusarium mycotoxins. The mounting evidence for higher nutritional quality of organic foods and potential positive health impacts from organic food consumption is therefore likely to (a) reinforce existing consumer perceptions that organic cereal products have a higher nutritional value and (b) increase demand for organic and especially organic–wholegrain cereal products

Experiments with common winter wheat in the UK reported higher levels of phenolics and mineral micronutrients when manure and a longer straw variety (Aszita) developed for the organic sector were used compared with mineral N as the fertilizer and the modern short straw variety Solstice, respectively. Breeding for nutritional quality traits is likely to be linked to selection for baking and bread-making quality from wholegrain flour, because (i) refining removes most of the nutritionally desirable mineral micronutrients, phenolics, vitamins and antioxidants from wheat grains/flour and (ii) the relative demand for wholegrain products is thought to be greater among organic consumers

 Breeding/Selection Methods, Strategies and Approaches

 Traditional Breeding Programs

Experiments in the UK demonstrated that the longer-straw, winter wheat variety Aszita (a Sativa variety developed via an organic farming focused breeding program) had similar grain yields, but (i) significantly lower foliar disease levels of Septoria and rust and (ii) higher leaf phenolic concentrations, protein contents and bread-making quality when grown in organic agronomic background conditions when compared to the modern short straw Solstice (which was developed via a conventional farming focused breeding program)

Based on the success of these pioneering organic breeding programs, it is now widely accepted that selection of varieties for the organic farming sector should be carried out in agronomic backgrounds that reflect crop rotation, mechanical weed control practices and fertilization regimes used in commercial organic farming practices.

Farmer Participatory Breeding Approaches

PPB approaches have been widely adopted in organic farming focused breeding programs, not only because they can reduce the cost, but also because they increase the efficiency of the final selection for farm or region-specific quality-related traits, functional traits and/or trait combinations for diverse production environments

Adaptation of wheat varieties to local or regional pedo-climatic and also agronomic background conditions is widely considered to be particularly important for the organic farming sector [32,57,67]. This is mainly because most agrochemical interventions, which generate a “level playing field” across environments in conventional farming (with respect to both soil fertility and weed, disease and pest pressure), are prohibited in organic farming  In addition, adaptation is necessary because agronomic protocols used in organic farming are more diverse, which in turn is due to the need to adjust rotations, fertilization and crop protection regimes to (i) local pedo-climatic conditions, (ii) pest, disease and weed pressures, and (iii) farm-specific input availability (e.g., type of manure or organic waste based composts)

when the performance of six contrasting common spring wheat varieties was compared on three UK organic farms with contrasting pedo-climatic background conditions, a range of complex interactions were identified and the ranking of varieties differed considerably for both yield and quality parameters (Tables 6–8). In addition, when the performance of the variety Paragon grown with different organic fertilizer input types (chicken manure pellets, cattle farmyard manure and green waste compost) and fertilizer input levels on the same three farms were analyzed, a range of complex A × E interactions were detected

The need for farmer participation throughout the breeding program (from the selection of parents for crosses to local/regional selection/adaptation) is also increasingly recognized and advocated

Evolutionary Plant Breeding

Evolutionary plant breeding (EPB) has been advocated as an approach to develop locally adapted wheat cultivars, usually described as “heterogeneous populations”, for organic farming systems [99]. EPB is based on a cycle of sowing mixtures of varieties or crosses of different varieties with a high level of genetic diversity and then resowing seeds year after year and relying on natural selection for the development locally adapted evolving populations (EP). EP are now available for commercial wheat production in some European countries and the philosophy, methods, relative performance of wheat populations and challenges of EPB have been reviewed extensively

A recent assessment of EP performance in the US reported that “EPs performance was dependent on their pedigree and were statistically similar and even out-performed some of their respective parents in regards to grain yield, grain protein concentration, and disease resistance” and that both “bi-parental and composite-cross populations demonstrated significantly greater stability over the parents across precipitation zones, confirming the capacity of genetically diverse EP populations to adapt to different environments” 

Breeding for Nutritional Quality Traits 

organic breeding programs tend to select for longer-straw phenotypes to improve competitiveness against weeds and protein content/bread-making quality (parameters which are thought to be positively correlated with straw length) and there is increasing evidence that longer straw varieties of both common and spelt wheat also produce grain with higher mineral micronutrient concentrations

There is also some evidence that selection for longer-straw varieties may co-select for improved capacity for mineral micronutrient acquisition and/or translocation into the grain. Specifically, a recent study into the evolution of mycorrhizal competence and grain traits in wheat and other cereals reported that (i) the introduction of semi-dwarfing genes to shorten stem length has reduced the capacity of major cereal species to develop and gain the full benefits (which include micronutrient uptake) from mycorrhizal associations [113] and (ii) both straw length and the mineral content of wheat grain has gradually decreased over time since the start of the introduction of semi-dwarfing genes in the early 1970s