Legume seed system performance in sub-Saharan Africa: barriers, opportunities, and scaling options. A review.

As a fundamental pillar of food security in sub-Saharan Africa (SSA), ensuring seed security is critical to empowering farmers in cultivating food and livestock feed, thereby fostering income generation from agricultural outputs. Among the crops cultivated by smallholders, legumes have the potential to deliver multifaceted benefits. Legumes are nutrient-dense and enhance soil health through their nitrogen-fixing qualities. However, in many instances, the development, release, and supply of improved legume varieties are insufficient to meet the needs of smallholder farmers in SSA. Here, we systematically reviewed the literature to (i) identify and categorize existing legume seed systems, (ii) map legume varieties available to smallholders, (iii) identify barriers hindering the adoption of various legume varieties, and (iv) identify potential strategies and opportunities for strengthening legume seed systems in SSA. Our results demonstrate the coexistence of formal and informal seed systems within legume seed supply chains in SSA, each employing unique seed distribution channels. Smallholders, however, are shown to predominantly depend on the informal seed system to source most legume seeds except for commercially available varieties. We also identified a diverse range of legume varieties available to smallholders in the region, with farmers having varying trait preferences based on crop type and gender. Notably, high yield and abiotic stress tolerance were the most preferred traits. The adoption of these varieties, however, is influenced by various factors, including lack of timely access to seeds in adequate quantities from the formal seed system, high seed costs, and limited information on new varieties. The reviewed literature highlighted that utilizing improved legume varieties had a positive effect on smallholders, leading to improved welfare, food security, dietary diversity, and income. We conclude that the effective scaling of legume systems in SSA is contingent upon the presence of supportive policy frameworks and well-established technical support structures. Graphical Abstract: Packets of legume seeds within a legume germplasm and breeding program at the University of Zambia (Photo by Caitlin Breen, 2022). Supplementary Information: The online version contains supplementary material available at 10.1007/s13593-024-00956-6.

Linkage mapping and genomic prediction of grain quality traits in tropical maize (Zea mays L.).

The suboptimal productivity of maize systems in sub-Saharan Africa (SSA) is a pressing issue, with far-reaching implications for food security, nutrition, and livelihood sustainability within the affected smallholder farming communities. Dissecting the genetic basis of grain protein, starch and oil content can increase our understanding of the governing genetic systems, improve the efficacy of future breeding schemes and optimize the end-use quality of tropical maize. Here, four bi-parental maize populations were evaluated in field trials in Kenya and genotyped with mid-density single nucleotide polymorphism (SNP) markers. Genotypic (G), environmental (E) and G×E variations were found to be significant for all grain quality traits. Broad sense heritabilities exhibited substantial variation (0.18-0.68). Linkage mapping identified multiple quantitative trait loci (QTLs) for the studied grain quality traits: 13, 7, 33, 8 and 2 QTLs for oil content, protein content, starch content, grain texture and kernel weight, respectively. The co-localization of QTLs identified in our research suggests the presence of shared genetic factors or pleiotropic effects, implying that specific genomic regions influence the expression of multiple grain quality traits simultaneously. Genomic prediction accuracies were moderate to high for the studied traits. Our findings highlight the polygenic nature of grain quality traits and demonstrate the potential of genomic selection to enhance genetic gains in maize breeding. Furthermore, the identified genomic regions and single nucleotide polymorphism markers can serve as the groundwork for investigating candidate genes that regulate grain quality traits in tropical maize. This, in turn, can facilitate the implementation of marker-assisted selection (MAS) in breeding programs focused on improving grain nutrient levels.

Unlocking allelic variation in circadian clock genes to develop environmentally robust and productive crops.

MAIN CONCLUSION: Molecular mechanisms of biological rhythms provide opportunities to harness functional allelic diversity in core (and trait- or stress-responsive) oscillator networks to develop more climate-resilient and productive germplasm. The circadian clock senses light and temperature in day-night cycles to drive biological rhythms. The clock integrates endogenous signals and exogenous stimuli to coordinate diverse physiological processes. Advances in high-throughput non-invasive assays, use of forward- and inverse-genetic approaches, and powerful algorithms are allowing quantitation of variation and detection of genes associated with circadian dynamics. Circadian rhythms and phytohormone pathways in response to endogenous and exogenous cues have been well documented the model plant Arabidopsis. Novel allelic variation associated with circadian rhythms facilitates adaptation and range expansion, and may provide additional opportunity to tailor climate-resilient crops. The circadian phase and period can determine adaptation to environments, while the robustness in the circadian amplitude can enhance resilience to environmental changes. Circadian rhythms in plants are tightly controlled by multiple and interlocked transcriptional-translational feedback loops involving morning (CCA1, LHY), mid-day (PRR9, PRR7, PRR5), and evening (TOC1, ELF3, ELF4, LUX) genes that maintain the plant circadian clock ticking. Significant progress has been made to unravel the functions of circadian rhythms and clock genes that regulate traits, via interaction with phytohormones and trait-responsive genes, in diverse crops. Altered circadian rhythms and clock genes may contribute to hybrid vigor as shown in Arabidopsis, maize, and rice. Modifying circadian rhythms via transgenesis or genome-editing may provide additional opportunities to develop crops with better buffering capacity to environmental stresses. Models that involve clock gene‒phytohormone‒trait interactions can provide novel insights to orchestrate circadian rhythms and modulate clock genes to facilitate breeding of all season crops.

Haploid rhapsody: the molecular and cellular orchestra of in vivo haploid induction in plants.

In planta haploid induction (HI), which reduces the chromosome number in the progeny after fertilization, has garnered increasing attention for its significant potential in crop breeding and genetic research. Despite the identification of several natural and synthetic HI systems in different plant species, the molecular and cellular mechanisms underlying these HI systems remain largely unknown. This review synthesizes the current understanding of HI systems in plants (with a focus on genes and molecular mechanisms involved), including the molecular and cellular interactions which orchestrate the HI process. As most HI systems can function across taxonomic boundaries, we particularly discuss the evidence for conserved mechanisms underlying the process. These include mechanisms involved in preserving chromosomal integrity, centromere function, gamete communication and/or fusion, and maintenance of karyogamy. While significant discoveries and advances on haploid inducer systems have arisen over the past decades, we underscore gaps in understanding and deliberate on directions for further research for a more comprehensive understanding of in vivo HI processes in plants.

Unravelling the Transcriptional Response of Agaricus bisporus under Lecanicillium fungicola Infection.

Mushrooms are a nutritionally rich and sustainably-produced food with a growing global market. Agaricus bisporus accounts for 11% of the total world mushroom production and it is the dominant species cultivated in Europe. It faces threats from pathogens that cause important production losses, including the mycoparasite Lecanicillium fungicola, the causative agent of dry bubble disease. Through quantitative real-time polymerase chain reaction (qRT-PCR), we determine the impact of L. fungicola infection on the transcription patterns of A. bisporus genes involved in key cellular processes. Notably, genes related to cell division, fruiting body development, and apoptosis exhibit dynamic transcriptional changes in response to infection. Furthermore, A. bisporus infected with L. fungicola were found to accumulate increased levels of reactive oxygen species (ROS). Interestingly, the transcription levels of genes involved in the production and scavenging mechanisms of ROS were also increased, suggesting the involvement of changes to ROS homeostasis in response to L. fungicola infection. These findings identify potential links between enhanced cell proliferation, impaired fruiting body development, and ROS-mediated defence strategies during the A. bisporus (host)-L. fungicola (pathogen) interaction, and offer avenues for innovative disease control strategies and improved understanding of fungal pathogenesis.

Discovery of genomic regions associated with grain yield and agronomic traits in Bi-parental populations of maize (Zea mays. L) Under optimum and low nitrogen conditions.

Low soil nitrogen levels, compounded by the high costs associated with nitrogen supplementation through fertilizers, significantly contribute to food insecurity, malnutrition, and rural poverty in maize-dependent smallholder communities of sub-Saharan Africa (SSA). The discovery of genomic regions associated with low nitrogen tolerance in maize can enhance selection efficiency and facilitate the development of improved varieties. To elucidate the genetic architecture of grain yield (GY) and its associated traits (anthesis-silking interval (ASI), anthesis date (AD), plant height (PH), ear position (EPO), and ear height (EH)) under different soil nitrogen regimes, four F3 maize populations were evaluated in Kenya and Zimbabwe. GY and all the traits evaluated showed significant genotypic variance and moderate heritability under both optimum and low nitrogen stress conditions. A total of 91 quantitative trait loci (QTL) related to GY (11) and other secondary traits (AD (26), PH (19), EH (24), EPO (7) and ASI (4)) were detected. Under low soil nitrogen conditions, PH and ASI had the highest number of QTLs. Furthermore, some common QTLs were identified between secondary traits under both nitrogen regimes. These QTLs are of significant value for further validation and possible rapid introgression into maize populations using marker-assisted selection. Identification of many QTL with minor effects indicates genomic selection (GS) is more appropriate for their improvement. Genomic prediction within each population revealed low to moderately high accuracy under optimum and low soil N stress management. However, the accuracies were higher for GY, PH and EH under optimum compared to low soil N stress. Our findings indicate that genetic gain can be improved in maize breeding for low N stress tolerance by using GS.

PICKLE RELATED 2 is a Neofunctionalized Gene Duplicate Under Positive Selection With Antagonistic Effects to the Ancestral PICKLE Gene on the Seed Transcriptome.

The evolution and diversification of proteins capable of remodeling domains has been critical for transcriptional reprogramming during cell fate determination in multicellular eukaryotes. Chromatin remodeling proteins of the CHD3 family have been shown to have important and antagonistic impacts on seed development in the model plant, Arabidopsis thaliana, yet the basis of this functional divergence remains unknown. In this study, we demonstrate that genes encoding the CHD3 proteins PICKLE (PKL) and PICKLE-RELATED 2 (PKR2) originated from a duplication event during the diversification of crown Brassicaceae, and that these homologs have undergone distinct evolutionary trajectories since this duplication, with PKR2 fast evolving under positive selection, while PKL is subject to purifying selection. We find that the rapid evolution of PKR2 under positive selection reduces the encoded protein's intrinsic disorder, possibly suggesting a tertiary structure configuration which differs from that of PKL. Our whole genome transcriptome analysis in seeds of pkr2 and pkl mutants reveals that they act antagonistically on the expression of specific sets of genes, providing a basis for their differing roles in seed development. Our results provide insights into how gene duplication and neofunctionalization can lead to differing and antagonistic selective pressures on transcriptomes during plant reproduction, as well as on the evolutionary diversification of the CHD3 family within seed plants.

Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs.

Alternative splicing (AS) is a gene regulatory mechanism modulating gene expression in multiple ways. AS is prevalent in all eukaryotes including plants. AS generates two or more mRNAs from the precursor mRNA (pre-mRNA) to regulate transcriptome complexity and proteome diversity. Advances in next-generation sequencing, omics technology, bioinformatics tools, and computational methods provide new opportunities to quantify and visualize AS-based quantitative trait variation associated with plant growth, development, reproduction, and stress tolerance. Domestication, polyploidization, and environmental perturbation may evolve novel splicing variants associated with agronomically beneficial traits. To date, pre-mRNAs from many genes are spliced into multiple transcripts that cause phenotypic variation for complex traits, both in model plant Arabidopsis and field crops. Cataloguing and exploiting such variation may provide new paths to enhance climate resilience, resource-use efficiency, productivity, and nutritional quality of staple food crops. This review provides insights into AS variation alongside a gene expression analysis to select for novel phenotypic diversity for use in breeding programs. AS contributes to heterosis, enhances plant symbiosis (mycorrhiza and rhizobium), and provides a mechanistic link between the core clock genes and diverse environmental clues.

Regulation of Carotenoid Biosynthesis and Degradation in Lettuce (Lactuca sativa L.) from Seedlings to Harvest.

Lettuce (Lactuca sativa L.) is one of the commercially important leafy vegetables worldwide. However, lettuce cultivars vary widely in their carotenoid concentrations at the time of harvest. While the carotenoid content of lettuce can depend on transcript levels of key biosynthetic enzymes, genes that can act as biomarkers for carotenoid accumulation at early stages of plant growth have not been identified. Transcriptomic and metabolomic analysis was performed on the inner and outer leaves of the six cultivars at different developmental stages to identify gene-to-metabolite networks affecting the accumulation of two key carotenoids, ß-carotene and lutein. Statistical analysis, including principal component analysis, was used to better understand variations in carotenoid concentration between leaf age and cultivars. Our results demonstrate that key enzymes of carotenoid biosynthesis pathway can alter lutein and ß-carotene biosynthesis across commercial cultivars. To ensure high carotenoids content in leaves, the metabolites sink from ß-carotene and lutein to zeaxanthin, and subsequently, abscisic acid needs to be regulated. Based on 2-3-fold carotenoids increase at 40 days after sowing (DAS) as compared to the seedling stage, and 1.5-2-fold decline at commercial stage (60 DAS) compared to the 40 DAS stage, we conclude that the value of lettuce for human nutrition would be improved by use of less mature plants, as the widely-used commercial stage is already at plant senescence stage where carotenoids and other essential metabolites are undergoing degradation.

Evolutionary dynamics and adaptive benefits of deleterious mutations in crop gene pools.

Mutations with deleterious consequences in nature may be conditionally deleterious in crop plants. That is, while some genetic variants may reduce fitness under wild conditions and be subject to purifying selection, they can be under positive selection in domesticates. Such deleterious alleles can be plant breeding targets, particularly for complex traits. The difficulty of distinguishing favorable from unfavorable variants reduces the power of selection, while favorable trait variation and heterosis may be attributable to deleterious alleles. Here, we review the roles of deleterious mutations in crop breeding and discuss how they can be used as a new avenue for crop improvement with emerging genomic tools, including HapMaps and pangenome analysis, aiding the identification, removal, or exploitation of deleterious mutations.

Breed and ruminal fraction effects on bacterial and archaeal community composition in sheep.

While the breed of cattle can impact on the composition and structure of microbial communities in the rumen, breed-specific effects on rumen microbial communities have rarely been examined in sheep. In addition, rumen microbial composition can differ between ruminal fractions, and be associated with ruminant feed efficiency and methane emissions. In this study, 16S rRNA amplicon sequencing was used to investigate the effects of breed and ruminal fraction on bacterial and archaeal communities in sheep. Solid, liquid and epithelial rumen samples were obtained from a total of 36 lambs, across 4 different sheep breeds (Cheviot (n = 10), Connemara (n = 6), Lanark (n = 10) and Perth (n = 10)), undergoing detailed measurements of feed efficiency, who were offered a nut based cereal diet ad-libitum supplemented with grass silage. Our results demonstrate that the feed conversion ratio (FCR) was lowest for the Cheviot (most efficient), and highest for the Connemara breed (least efficient). In the solid fraction, bacterial community richness was lowest in the Cheviot breed, while Sharpea azabuensis was most abundant in the Perth breed. Lanark, Cheviot and Perth breeds exhibited a significantly higher abundance of epithelial associated Succiniclasticum compared to the Connemara breed. When comparing ruminal fractions, Campylobacter, Family XIII, Mogibacterium, and Lachnospiraceae UCG-008 were most abundant in the epithelial fraction. Our findings indicate that breed can impact the abundance of specific bacterial taxa in sheep while having little effect on the overall composition of the microbial community. This finding has implications for genetic selection breeding programs aimed at improving feed conversion efficiency of sheep. Furthermore, the variations in the distribution of bacterial species identified between ruminal fractions, notably between solid and epithelial fractions, reveals a rumen fraction bias, which has implications for sheep rumen sampling techniques.

Maternal control of triploid seed development by the TRANSPARENT TESTA 8 (TT8) transcription factor in Arabidopsis thaliana.

The balance between parental genome dosage is critical to offspring development in both animals and plants. In some angiosperm species, despite the imbalance between maternally and paternally inherited chromosome sets, crosses between parental lines of different ploidy may result in viable offspring. However, many plant species, like Arabidopsis thaliana, present a post-zygotic reproductive barrier, known as triploid block which results in the inability of crosses between individuals of different ploidy to generate viable seeds but also, in defective development of the seed. Several paternal regulators have been proposed as active players in establishing the triploid block. Maternal regulators known to be involved in this process are some flavonoid biosynthetic (FB) genes, expressed in the innermost layer of the seed coat. Here we explore the role of selected flavonoid pathway genes in triploid block, including TRANSPARENT TESTA 4 (TT4), TRANSPARENT TESTA 7 (TT7), SEEDSTICK (STK), TRANSPARENT TESTA 16 (TT16), TT8 and TRANSPARENT TESTA 13 (TT13). This approach allowed us to detect that TT8, a bHLH transcription factor, member of this FB pathway is required for the paternal genome dosage, as loss of function tt8, leads to complete rescue of the triploid block to seed development.

Climate change and land-use change impacts on future availability of forage grass species for Ethiopian dairy systems.

Forage grasses are central feed resources for livestock globally. In Ethiopian dairy systems, they serve as feed sources during both wet and dry seasons, yet escalating climate change could threaten forage supply. Here, we investigate projected climate change impacts on three forage grasses currently recommended for Ethiopian dairy systems. We determine areas of geographical suitability for each species using three climate projections generated by General Circulation Models (GCMs) and calculate their ability to meet predicted dry matter demand under four scenarios for livestock intensification and land availability. By 2050, Buffel grass (Cenchrus ciliaris) is likely to be negatively affected by climate change in regions such as Tigray, while Rhodes grass (Chloris gayana) and Napier grass (Cenchrus purpureus) may have improved suitability under future climates. Our findings suggest that feed demands could theoretically be met by production of these forage grasses under current and future climates. However, if land availability is reduced and herd composition shifts towards higher-productivity exotic breeds, forage resources will not meet cattle demand even with improved agronomic management.

Clinical Performance of Direct RT-PCR Testing of Raw Saliva for Detection of SARS-CoV-2 in Symptomatic and Asymptomatic Individuals.

RT-PCR tests based on RNA extraction from nasopharyngeal swabs (NPS) are promoted as the "gold standard" for SARS-CoV-2 detection. However, the use of saliva samples offers noninvasive self-collection more suitable for high-throughput testing. This study evaluated performance of the TaqPath COVID-19 Fast PCR Combo kit 2.0 assay for detection of SARS-CoV-2 in raw saliva relative to a lab-developed direct RT-PCR test (SalivaDirect-based PCR, SDB-PCR) and an RT-PCR test based on RNA extraction from NPS. Saliva and NPS samples were collected from symptomatic and asymptomatic individuals (N = 615). Saliva samples were tested for SARS-CoV-2 using the TaqPath COVID-19 Fast PCR Combo kit 2.0 and the SDB-PCR, while NPS samples were tested by RT-PCR in RNA extracts according to the Irish national testing system. TaqPath COVID-19 Fast PCR Combo kit 2.0 detected SARS-CoV-2 in 52 saliva samples, of which 51 were also positive with the SDB-PCR. Compared to the NPS "gold standard" biospecimen method, 49 samples displayed concordant results, while three samples (35

Genome-wide association studies of grain yield and quality traits under optimum and low-nitrogen stress in tropical maize (Zea mays L.).

KEY MESSAGE: Genome-wide association study (GWAS) demonstrated that multiple genomic regions influence grain quality traits under nitrogen-starved soils. Using genomic prediction, genetic gains can be improved through selection for grain quality traits. Soils in sub-Saharan Africa are nitrogen deficient due to low fertilizer use and inadequate soil fertility management practices. This has resulted in a significant yield gap for the major staple crop maize, which is undermining nutritional security and livelihood sustainability across the region. Dissecting the genetic basis of grain protein, starch and oil content under nitrogen-starved soils can increase our understanding of the governing genetic systems and improve the efficacy of future breeding schemes. An association mapping panel of 410 inbred lines and four bi-parental populations were evaluated in field trials in Kenya and South Africa under optimum and low nitrogen conditions and genotyped with 259,798 SNP markers. Genetic correlations demonstrated that these populations may be utilized to select higher performing lines under low nitrogen stress. Furthermore, genotypic, environmental and GxE variations in nitrogen-starved soils were found to be significant for oil content. Broad sense heritabilities ranged from moderate (0.18) to high (0.86). Under low nitrogen stress, GWAS identified 42 SNPs linked to grain quality traits. These significant SNPs were associated with 51 putative candidate genes. Linkage mapping identified multiple QTLs for the grain quality traits. Under low nitrogen conditions, average prediction accuracies across the studied genotypes were higher for oil content (0.78) and lower for grain yield (0.08). Our findings indicate that grain quality traits are polygenic and that using genomic selection in maize breeding can improve genetic gain. Furthermore, the identified genomic regions and SNP markers can be utilized for selection to improve maize grain quality traits.

Parent-of-Origin Effects on Seed Size Modify Heterosis Responses in Arabidopsis thaliana.

Parent-of-origin effects arise when a phenotype depends on whether it is inherited maternally or paternally. Parent-of-origin effects can exert a strong influence on F1 seed size in flowering plants, an important agronomic and life-history trait that can contribute to biomass heterosis. Here we investigate the natural variation in the relative contributions of the maternal and paternal genomes to F1 seed size across 71 reciprocal pairs of F1 hybrid diploids and the parental effect on F1 seed size heterosis. We demonstrate that the paternally derived genome influences F1 seed size more significantly than previously appreciated. We further demonstrate (by disruption of parental genome dosage balance in F1 triploid seeds) that hybridity acts as an enhancer of genome dosage effects on F1 seed size, beyond that observed from hybridity or genome dosage effects on their own. Our findings indicate that interactions between genetic hybridity and parental genome dosage can enhance heterosis effects in plants, opening new avenues for boosting heterosis breeding in crop plants.

Plastid ribosome protein L5 is essential for post-globular embryo development in Arabidopsis thaliana.

Plastid ribosomal proteins (PRPs) can play essential roles in plastid ribosome functioning that affect plant function and development. However, the roles of many PRPs remain unknown, including elucidation of which PRPs are essential or display redundancy. Here, we report that the nuclear-encoded PLASTID RIBOSOMAL PROTEIN L5 (PRPL5) is essential for early embryo development in A. thaliana, as homozygous loss-of-function mutations in the PRPL5 gene impairs chloroplast development and leads to embryo failure to develop past the globular stage. We confirmed the prpl5 embryo-lethal phenotype by generating a mutant CRISPR/Cas9 line and by genetic complementation. As PRPL5 underwent transfer to the nuclear genome early in the evolution of Embryophyta, PRPL5 can be expected to have acquired a chloroplast transit peptide. We identify and validate the presence of an N-terminal chloroplast transit peptide, but unexpectedly also confirm the presence of a conserved and functional Nuclear Localization Signal on the protein C-terminal end. This study highlights the fundamental role of the plastid translation machinery during the early stages of embryo development in plants and raises the possibility of additional roles of plastid ribosomal proteins in the nucleus.

Combining Ability and Heterosis for Endosperm Carotenoids and Agronomic Traits in Tropical Maize Lines.

Provitamin A enrichment of staple crops through biofortification breeding is a powerful approach to mitigate the public health problem of vitamin A deficiency in developing countries. Twenty-four genetically diverse yellow and orange endosperm maize inbred lines with differing levels of provitamin A content were used for the analysis of their combining ability. Each inbred line was developed from crosses and backcrosses between temperate and tropical germplasm. The inbred lines were grouped into different sets according to their provitamin A levels and were then intercrossed in a factorial mating scheme to generate 80 different single-cross hybrids. The hybrids were evaluated in field trials across a range of agroecological zones in Nigeria. The effect of hybrids was significant on all the measured provitamin A and non-provitamin A carotenoids and agronomic traits. While the effect of genotype-by-environment (GxE) interaction was significant for almost all traits, it was a non-crossover-type interaction for carotenoid content. Partitioning of the variances associated with the carotenoid and agronomic traits into their respective components revealed the presence of significant positive and negative estimates of general combining ability (GCA) and specific combining ability (SCA) effects for both carotenoid content and agronomic traits. The preponderance of GCA effects indicates the importance of additive gene effects in the inheritance of carotenoid content. We found F1 hybrids displaying high parent heterosis for both provitamin A content and agronomic performance. Our study demonstrates that provitamin A biofortification can be effectively implemented in maize breeding programs without adverse effects on important agronomic traits, including grain yield.

Kinship networks of seed exchange shape spatial patterns of plant virus diversity.

By structuring farmers' informal networks of seed exchange, kinship systems play a key role in the dynamics of crop genetic diversity in smallholder farming systems. However, because many crop diseases are propagated through infected germplasm, local seed systems can also facilitate the dissemination of seedborne pathogens. Here, we investigate how the interplay of kinship systems and local networks of germplasm exchange influences the metapopulation dynamics of viruses responsible for the cassava mosaic disease (CMD), a major threat to food security in Africa. Combining anthropological, genetic and plant epidemiological data, we analyzed the genetic structure of local populations of the African cassava mosaic virus (ACMV), one of the main causal agents of CMD. Results reveal contrasted patterns of viral diversity in patrilineal and matrilineal communities, consistent with local modes of seed exchange. Our results demonstrate that plant virus ecosystems have also a cultural component and that social factors that shape regional seed exchange networks influence the genetic structure of plant virus populations.