Root and foot diseases severely impede grain legume cultivation worldwide. Breeding lines with resistance against individual pathogens exist, but these resistances are often overcome by the interaction of multiple pathogens in field situations. Novel tools allow to decipher plant–microbiome interactions in unprecedented detail and provide insights into resistance mechanisms that consider both simultaneous attacks of various pathogens and the interplay with beneficial microbes. Although it has become clear that plant‐associated microbes play a key role in plant health, a systematic picture of how and to what extent plants can shape their own detrimental or beneficial microbiome remains to be drawn. There is increasing evidence for the existence of genetic variation in the regulation of plant–microbe interactions that can be exploited by plant breeders. We propose to consider the entire plant holobiont in resistance breeding strategies in order to unravel hidden parts of complex defence mechanisms. This review summarizes (a) the current knowledge of resistance against soil‐borne pathogens in grain legumes, (b) evidence for genetic variation for rhizosphere‐related traits, (c) the role of root exudation in microbe‐mediated disease resistance and elaborates (d) how these traits can be incorporated in resistance breeding programmes.

In this paper, we describe the development of a set of guiding principles for the evaluation of breeding techniques by the organic sector over time. The worldwide standards of organic agriculture (OA) do not allow genetic engineering (GE) or any products derived from genetic engineering. The standards in OA are an expression of the underlying principles of health, ecology, fairness and care. The derived norms are process and not product oriented. As breeding is considered part of the process in agriculture, GE is not a neutral tool for the organic sector. The incompatibility between OA and GE is analyzed, including the “novel breeding techniques”. Instead, alternative breeding approaches are pursued based on the norms and values of organic agriculture not only on the technical level but also on the social and organizational level by including other value chain players and consumers. The status and future perspectives of the alternative directions for organic breeding are described and discussed.

The new European Organic Regulation 2018/848 has announced the phasing out of derogations for the use of untreated non-organic seed by 2036. However, the use of organic seed by organic farmers is currently limited. This paper aims to identify the factors affecting the use of organic seed. It is based on data collected from 749 organic farmers in 20 European countries, by conducting an online survey and using a network sampling. Results of the descriptive statistics and linear mixed models indicate that: (1) the situation of organic seed use is not consistent across geographical regions and crop sectors; (2) the use of organic seed is higher on farms selling directly to consumers than on those selling to supermarkets; (3) larger and more recently converted farms use less organic seed than established organic farms. In the second part of the paper, we analyse farmers’ attitudes towards organic seed use. The structural equation model (SEM) suggests that the highest contribution to explaining intention to use organic seed comes from social norms, i.e., farmers’ perception of societal expectations, particularly from the consumer and the organic certifier. Such expectations, if communicated in the public and political discourse, could stimulate the use of organic seed.

Resistance against cotton bollworm is one of the main arguments for the use of genetically modified (GM) Bt cotton around the globe. The use of GM is prohibited in organic systems and thus the remunerative value of organic cotton cultivation depends on effective bollworm control. In this study, we investigated the extent of bollworm and sucking pest damage in 68 different hybrid and varietal lines of Gossypium hirsutum and varietal lines of G. arboreum at two different locations with contrasting soil fertility and water dynamics. The damage potential of bollworms was assessed from open capsules at two time points. Sucking pests were assessed at three time points using a scoring method. G. arboreum varietal lines and G. hirsutum hybrids were on average significantly more tolerant than G. hirsutum varietal lines to bollworm under fertile and irrigated situations. For sucking pests, the G. arboreum varietal lines were clearly more tolerant than G. hirsutum hybrids and varietal lines. Since, recently, pink bollworm (Pectinophora gossypiella) became resistant against Bt cotton and pressure of sucking pests severely increased, screening of genetic resources and systems-based cotton breeding for bollworm and sucking pest tolerance will improve sustainability of organic and conventional cotton production.

Key message: GWAS identifies candidate gene controlling resistance to anthracnose disease in white lupin. White lupin (Lupinus albus L.) is a promising grain legume to meet the growing demand for plant-based protein. Its cultivation, however, is severely threatened by anthracnose disease caused by the fungal pathogen Colletotrichum lupini. To dissect the genetic architecture for anthracnose resistance, genotyping by sequencing was performed on white lupin accessions collected from the center of domestication and traditional cultivation regions. GBS resulted in 4611 high-quality single-nucleotide polymorphisms (SNPs) for 181 accessions, which were combined with resistance data observed under controlled conditions to perform a genome-wide association study (GWAS). Obtained disease phenotypes were shown to highly correlate with overall three-year disease assessments under Swiss field conditions (r > 0.8). GWAS results identified two significant SNPs associated with anthracnose resistance on gene Lalb_Chr05_g0216161 encoding a RING zinc-finger E3 ubiquitin ligase which is potentially involved in plant immunity. Population analysis showed a remarkably fast linkage disequilibrium decay, weak population structure and grouping of commercial varieties with landraces, corresponding to the slow domestication history and scarcity of modern breeding efforts in white lupin. Together with 15 highly resistant accessions identified in the resistance assay, our findings show promise for further crop improvement. This study provides the basis for marker-assisted selection, genomic prediction and studies aimed at understanding anthracnose resistance mechanisms in white lupin and contributes to improving breeding programs worldwide.

Cotton is essentially a smallholder crop across tropical countries. Being a major cash crop, it plays a decisive role in the livelihoods of cotton-producing farmers. Both conventional and organic production systems offer alternative yet interesting propositions to cotton farmers. This study was conducted in Nimar valley, a prominent cotton-producing region of central India, with the aim of categorically evaluating the contribution of management and fixed factors to productivity on conventional and organic cotton farms. A study framework was developed considering the fixed factors, which cannot be altered within reasonable limits of time, capacity and resources, e.g., landholding or years of age and/or practice; and management factors, which can be altered/influenced within a reasonable time by training, practice and implementation. Using this framework, a structured survey of conventional and organic farms operating under comparable circumstances was conducted. Landholding and soil types were significant contributors/predictors of yield on organic farms. In contrast, landholding was not the main factor related to yields on conventional farms, which produced the highest yields when led by farmers with more than five years of formal education and living in a joint family. Nitrogen application, the source of irrigation (related to timely and adequate supply), crop rotation and variables related to adequate plant population (seed source, germination rate and plant thinning) were the main management factors limiting cotton yields among conventional and organic farms. Both organic and conventional farms in the Nimar valley exhibited a similar pattern of variation in cotton yields and technical efficiency. This study highlights the enormous scope for improving cotton productivity in the region by improving technical efficiency, strengthening extension services and making appropriate policy interventions.