Societal Impact Statement Plant breeding for agroecological transition (AET) holds the potential to transform agriculture by fostering crop diversification and empowering farmers through collaborative, inter‐ and transdisciplinary research. By adopting a systemic, co‐learning approach, we can deepen our understanding of the complex interactions between plant diversity, management practices and socio‐ecological contexts. Achieving this transition requires responsible governance to co‐design cropping systems and ensure sustainable, safe and resilient agricultural systems with healthy nutrition. Embracing these integrative practices will not only advance plant breeding science for the transformation of sustainable food systems but also strengthen food security, safety and resilience in the face of pressing environmental and societal challenges. Summary This opinion paper advocates for a transformative approach to plant breeding to support the agroecological transition (AET), essential for addressing global challenges such as biodiversity loss and climate change. It emphasizes the need for inter‐ and transdisciplinary, collaborative and inclusive research to enhance plant and crop diversity while empowering farmers. Key strategies include co‐designing agroecological systems with stakeholders, leveraging crop inter‐ and intraspecies diversity and establishing responsible governance. The participatory approach encourages collaboration between farmers and researchers to co‐develop solutions that enhance crop inter‐ and intra‐species diversity within cropping systems. Through responsible governance, we aim to ensure inclusivity, participation and equitable access to knowledge at individual and institutional levels. In addition, researchers and institutions must collaborate with farmers to co‐design systems that prioritize context‐specific solutions, sustainability and diversity. Enhancing plant diversity for AET requires plant breeding tailored to diverse agroecological contexts and farming needs, supported by collaborative networks, participatory methods and appropriate experimental and modelling tools. We conclude with a call for inter‐ and transdisciplinary training to better prepare future researchers in plant breeding for AET.

Maize traditional populations (landraces) hold valuable genetic diversity for addressing climate change and low-input agriculture but remain underutilized due to lack of evaluations. High-throughput pool genotyping (HPG) has been previously used to characterize diversity but its potential for implementing genomic prediction (GP) and genomic offset (GO) for maize landraces has not been tested yet. We developed HPG-based GP models, combined or not with GO and within-population gene diversity (Hs), calibrated using 397 European landraces evaluated across environments and use cases. GP alone showed high predictive ability for yield (0.75), plant height (0.92) and male flowering time (0.94). Including Hs and GO in the GP model improved by 13% the predictive abilities for grain yield of new landraces in new environments. Our model provided phenotypic adaptive landscapes for each landrace in future climatic scenarios and predicted that agronomic performance stability increases with Hs. Combining GP with eco-genetic predictions made it possible to identify promising landraces to improve adaptation to future or new cultivation conditions. Teaser Identify promising landrace adapted to new and future environments by combining genomic selection and offset ### Competing Interest Statement All authors declare that they have no competing of interest. Dr. Alexandre Strigens is employed by the company DSP Delley Semences et Plantes SA, Switzerland. All authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Federal Ministry of Food and Agriculture, https://ror.org/04jw21793, GenRes 2019-2 Agence Nationale de la Recherche, https://ror.org/00rbzpz17, ANR-22-SUSC-0004 H2020, 771134

Since their inception, the French academic organizations dedicated to agricultural research have developed plant collections in genebanks, often within a public–private framework, to support the study of plant traits and the development of new improved varieties. In addition, since the 2000s, a centre for genomic resources has also been established in France. Over the last 20 years, this decentralized system, consisting of the academic genebanks and the centre for genomic resources, has been supported by a national coordination structure. The objectives were to align the network activities with the framework proposed by the Organisation for Economic Co-operation and Development (OECD) for Biological Resource Centres and to foster collaboration with other national stakeholders involved in the conservation and characterization of plant genetic resources (PGR). In 2015, the network was named BRC4Plants and become part of the French National Research Infrastructure RARe (www.agrobrc-rare.org), supported by the French Ministry of Research. This paper describes BRC4Plants, its users, services and cross-cutting activities. We also highlight its relations with its national and international stakeholders involved in the conservation and characterization of PGRs. BRC4Plants aims to be a key player in addressing societal and research challenges regarding agroecology, climate change mitigation and healthy food systems.

Maize landraces (Zea mays subsp. mays) have evolved under the joint action of environmental factors and of the farmers who cultivated them. In this study, we aim to quantify the selection gradients exerted by farmers by proposing them a selection test consisting in choosing the ears they would select if they were to grow maize landraces the following year. The study focused on the Pyrenees region of France, where landraces were cultivated until the arrival of hybrids in the 1960s and conserved ex-situ ever since. We interviewed former Pyrenean farmers or their children who were cultivating landraces 60 years ago. The survey documented seed management practices and know-how. Our selection test showed that their selection was based solely on ears: old farmers selected healthy and productive ears by using ear length and volume as the first two selection criteria. Both were highly correlated with the kernel weight per ear. Heritabilities of ear traits at an individual plant level were estimated in one trial for four landraces and were found variable between traits and landraces (average 0.36 ranging between 0 and 0.76). We calculated the expected genetic change after one generation of mass selection, following farmer selection criteria. For ear length, genetic change was expected to reach about 3.4% (from 1 to 7.5% over the 17 selection tests). We investigated seed selection practices both east and west of the Pyrenees and compared them qualitatively with those of native American farmers.

Correction to: Genetic Resources https://doi.org/10.46265/genresj.ASZO2413; published online 04 March 2025 Incorrect affiliation In the published article, there was an error in the affiliations of Nilda Paulo-de-la-Réberdiere. Instead of “[h,g]”, it should have been “[g,h]”. Incorrect author names In the published article, two author names were incorrectly written: - Cristophe Jenny (correct: Christophe Jenny) - Françoise Nuissier (correct: Franciane Nuissier) Error in Table 1 In the published article, there was an error in Table 1: - [Perennial plants in Guyana (PPG)]: Instead of “Guyana”, it should have been “French Guiana”. - [Coffea spp., Theobroma spp., Hevea spp., Dalbergia spp.]: Instead of Dalbergia, it should have been Aniba rosodora. The authors apologize for these errors and state that they do not affect the scientific conclusions of the article in any way.The PDF and HTML versions of the original article have been updated and are available at https://doi.org/10.46265/genresj.ASZO2413

The ECPGR European Evaluation Network (EVA) for Maize involves genebanks, research institutions, and private breeding companies from nine countries focusing on the valorization of maize genetic resources across Europe. This study describes a diverse collection of 626 local landraces and traditional varieties of maize (Zea mays L.) from nine European genebanks, including criteria for selection of the collection and its genetic and phenotypic diversity. High-throughput pool genotyping grouped the landraces into nine genetic groups with a threshold of 0.6 admixture, while 277 accessions were designated admixed and likely to have resulted from previous breeding activities. The grouping correlated well with the geographic origins of the collection, also reflecting the various pathways of introduction of maize to Europe. Phenotypic evaluations of 588 accessions for flowering time and plant architecture in multilocation trials over three years confirmed the great diversity within the collection, although phenotypic clusters only partially correlated with the genetic grouping. The EVA approach promotes conservation of genetic resources and opens an opportunity to increase genetic variability for developing improved varieties and populations for farmers, with better adaptation to specific environments and greater tolerance to various stresses. As such, the EVA maize collection provides valuable sources of diversity for facing climate change due to the varieties' local adaptation.

Landraces, that is, traditional varieties, have a large diversity that is underexploited in modern breeding. A novel DNA pooling strategy was implemented to identify promising landraces and genomic regions to enlarge the genetic diversity of modern varieties. As proof of concept, DNA pools from 156 American and European maize landraces representing 2340 individuals were genotyped with an SNP array to assess their genome-wide diversity. They were compared to elite cultivars produced across the 20th century, represented by 327 inbred lines. Detection of selective footprints between landraces of different geographic origin identified genes involved in environmental adaptation (flowering times, growth) and tolerance to abiotic and biotic stress (drought, cold, salinity). Promising landraces were identified by developing two novel indicators that estimate their contribution to the genome of inbred lines: (i) a modified Roger's distance standardized by gene diversity and (ii) the assignation of lines to landraces using supervised analysis. It showed that most landraces do not have closely related lines and that only 10 landraces, including famous landraces as Reid's Yellow Dent, Lancaster Surecrop and Lacaune, cumulated half of the total contribution to inbred lines. Comparison of ancestral lines directly derived from landraces with lines from more advanced breeding cycles showed a decrease in the number of landraces with a large contribution. New inbred lines derived from landraces with limited contributions enriched more the haplotype diversity of reference inbred lines than those with a high contribution. Our approach opens an avenue for the identification of promising landraces for pre-breeding.

Combined phenomic and genomic approaches are required to evaluate the margin of progress of breeding strategies. Here, we analyze 65 years of genetic progress in maize yield, which was similar (101 kg ha −1 year −1 ) across most frequent environmental scenarios in the European growing area. Yield gains were linked to physiologically simple traits (plant phenology and architecture) which indirectly affected reproductive development and light interception in all studied environments, marked by significant genomic signatures of selection. Conversely, studied physiological processes involved in stress adaptation remained phenotypically unchanged (e.g. stomatal conductance and growth sensitivity to drought) and showed no signatures of selection. By selecting for yield, breeders indirectly selected traits with stable effects on yield, but not physiological traits whose effects on yield can be positive or negative depending on environmental conditions. Because yield stability under climate change is desirable, novel breeding strategies may be needed for exploiting alleles governing physiological adaptive traits.

From the 17th century until the arrival of hybrids in 1960s, maize landraces were cultivated in the South-West of France (SWF), a traditional region for maize cultivation. A set of landraces were collected in this area between the 1950s and 1980s and were then conserved ex situ in a germplam collection. Previous studies using molecular markers on approx. twenty landraces from this region suggested that they belonged to a Pyrenees-Galicia Flint genetic group and originated from hybridizations between Caribbean and Northern Flint germplasms introduced to Europe. In this study, we assessed the structure and genetic diversity of 194 SWF maize landraces to better elucidate their origin, using a 50K SNP array and a bulk DNA approach. We identified two weakly differentiated genetic groups, one in the Western part and the other in the Eastern part of the studied region. We highlighted the existence of a longitudinal gradient along the SWF area that was probably maintained through the interplay between genetic drifts and restricted gene flows. The contact zone between the two groups observed near the Garonne valley may be the result of these evolutionnary forces. We found in landraces from the East part of the region significant cases of admixture between landraces from the Northern Flint group and landraces from either the Caribbean, Andean or Italian groups. We then assumed that SWF landraces had a multiple origin with a predonderance of Northern Flint germplasm for the two SWF groups, notably for the East part.

Genebanks harbor original landraces carrying many original favorable alleles for mitigating biotic and abiotic stresses. Their genetic diversity remains, however, poorly characterized due to their large within genetic diversity. We developed a high-throughput, cheap and labor saving DNA bulk approach based on single-nucleotide polymorphism (SNP) Illumina Infinium HD array to genotype landraces. Samples were gathered for each landrace by mixing equal weights from young leaves, from which DNA was extracted. We then estimated allelic frequencies in each DNA bulk based on fluorescent intensity ratio (FIR) between two alleles at each SNP using a two step-approach. We first tested either whether the DNA bulk was monomorphic or polymorphic according to the two FIR distributions of individuals homozygous for allele A or B, respectively. If the DNA bulk was polymorphic, we estimated its allelic frequency by using a predictive equation calibrated on FIR from DNA bulks with known allelic frequencies. Our approach: (i) gives accurate allelic frequency estimations that are highly reproducible across laboratories, (ii) protects against false detection of allele fixation within landraces. We estimated allelic frequencies of 23,412 SNPs in 156 landraces representing American and European maize diversity. Modified Roger’s genetic Distance between 156 landraces estimated from 23,412 SNPs and 17 simple sequence repeats using the same DNA bulks were highly correlated, suggesting that the ascertainment bias is low. Our approach is affordable, easy to implement and does not require specific bioinformatics support and laboratory equipment, and therefore should be highly relevant for large-scale characterization of genebanks for a wide range of species.

The quality of yield prediction is linked to that of leaf area. We first analysed the consequences of flowering time and environmental conditions on the area of individual leaves in 127 genotypes presenting contrasting flowering times in fields of Europe, Mexico, and Kenya. Flowering time was the strongest determinant of leaf area. Combined with a detailed field experiment, this experiment showed a large effect of flowering time on the final leaf number and on the distribution of leaf growth rate and growth duration along leaf ranks, in terms of both length and width. Equations with a limited number of genetic parameters predicted the beginning, end, and maximum growth rate (length and width) for each leaf rank. The genotype-specific environmental effects were analysed with datasets in phenotyping platforms that assessed the effects (i) of the amount of intercepted light on leaf width, and (ii) of temperature, evaporative demand, and soil water potential on leaf elongation rate. The resulting model was successfully tested for 31 hybrids in 15 European and Mexican fields. It potentially allows prediction of the vertical distribution of leaf area of a large number of genotypes in contrasting field conditions, based on phenomics and on sensor networks.

ABSTRACT Maize landraces preserved in genebanks have a large genetic diversity that is still poorly characterized and underexploited in modern breeding programs. Here, we genotyped DNA pools from 156 American and European landraces with a 50K SNP Illumina array to study the effect of both human selection and environmental adaptation on the genome-wide diversity of maize landraces. Genomic diversity of landraces varied strongly in different parts of the genome and with geographic origin. We detected selective footprints between landraces of different geographic origin in genes involved in the starch pathway ( Su1, Waxy1 ), flowering time ( Zcn8, Vgt3, ZmCCT9 ) and tolerance to abiotic and biotic stress ( ZmASR, NAC and dkg genes). Landrace diversity was compared to that of (i) 327 inbred lines representing American and European diversity (“CK lines) and (ii) 103 new lines derived directly from landraces (“DH-SSD lines”). We observed limited diversity loss or selective sweep between landraces and CK lines, except in peri-centromeric regions. However, analysis of modified Roger’s distance between landraces and the CK lines showed that most landraces were not closely related to CK lines. Assignment of CK lines to landraces using supervised analysis showed that only a few landraces, such as Reid’s Yellow Dent, Lancaster Surecrop and Lacaune, strongly contributed to modern European and American breeding pools. Haplotype diversity of CK lines was more enriched by DH-SSD lines that derived from the landraces with no related lines and the lowest contribution to CK lines. Our approach opens an avenue for the identification of promising landraces for pre-breeding. SIGNIFICANCE STATEMENTS Maize landraces are a valuable source of genetic diversity for addressing the challenges of climate change and the requirements of low input agriculture as they have been long selected to be well adapted to local agro-climatic conditions and human uses. However, they are underutilized in modern breeding programs because they are poorly characterized, genetically heterogeneous and exhibit poor agronomic performance compared to elite hybrid material. In this study, we developed a high-throughput approach to identify landraces that could potentially enlarge the genetic diversity of modern breeding pools. We genotyped DNA pools from landraces using 50K array technology, which is widely used by breeders to characterize the genetic diversity of inbred lines. To identify landraces that could enrich the modern maize germplasm, we estimated their contribution to inbred lines using supervised analysis and a new measurement of genetic distance.

Genotyping by sequencing is suitable for analysis of global diversity in maize. We showed the distinctiveness of flint maize inbred lines of interest to enrich the diversity of breeding programs.

The plant-beneficial bacterium Pseudomonas fluorescens F113 harbours an acdS gene, which enables deamination of 1-aminocyclopropane-1-carboxylate. The impact of abiotic and biotic factors on the expression of this gene was assessed, as well as the plant-beneficial properties of F113 under different soil moistures.

Breeding maize for drought tolerance is becoming a major challenge in a context of climate changes and restricted irrigation. Gene banks contain underused genetic resources and adaptation traits for drought tolerance may be present in some populations originating from dry regions. We screened, under contrasted water regimes in dry-Mediterranean climate, populations originating from dry cropping zones in Southern Europe, and other populations from temperate regions with a good combining ability for yield and good agronomic features under drought scenarios in a previous study. We evaluated 78 populations for leaf growth, anthesis-silking interval, number of ears per plant, number of kernels per plot, and grain yield in the presence and absence of water stress, in field conditions, over 2 years. Maximum grain yield and the sensitivity of grain yield to water deficit were highly variable. Positive correlations between sensitivity and performance in well-watered conditions were found for yield and number of kernels. Landraces originating from dry regions were generally less sensitive to water stress and had a limited grain yield potential, with variability observed even among accessions from the same survey area. However, some of them had a relatively high yield under stress conditions. During screening for traits associated with the maintenance of grain yield under conditions of water limitation, we identified sources of drought tolerance in breeding populations and landraces from temperate areas as well as in landraces collected in dry regions, indicating large reservoir of native traits in collections for breeding for drought-prone environments.