Signatures of local adaptation and maladaptation to future climate in wild Zizania latifolia

Global climate change poses challenges to agricultural production and food security. Assessing the adaptive capacity of crop wild relatives to future climate is important for protecting key germplasm resources and breeding new crops. We performed population genomics, genotype-environment association analyses, and genomic offset assessment of Chinese wild rice, Zizania latifolia, a crop wild relative and potential new grain crop, based on 168 individuals from 42 populations. We found two genetic lineages in Z. latifolia, corresponding to the south and north of its range, that diverged during the Late Pleistocene. We also identified lineage-specific positively selected genes associated with flower development and flowering, seed shattering, pathogen defense response and cold tolerance. We further found that populations from southeastern China are the most maladapted to future climate and should be prioritized for conservation. Our findings provide important clues for leveraging existing genetic diversity to identify important germplasm resources and create climate-resilient crops.

Unveiling the Genomic Symphony: Identification Cultivar-Specific Genes and Enhanced Insights on Sweet Sorghum Genomes Through Comprehensive superTranscriptomic Analysis

Sorghum (Sorghum bicolor (L.) Moench) is a multipurpose crop grown for food, fodder, and bioenergy production. Its cultivated varieties, along with their wild counterparts, contribute to the core genetic pool. Despite the availability of several re-sequenced sorghum genomes, a variable portion of sorghum genomes is not reported during reference genome assembly and annotation. The present analysis used 223 publicly available RNA-seq datasets from seven sweet sorghum cultivars to construct superTranscriptome. This approach yielded 45,864 Representative Transcript Assemblies (RTAs) that showcased intriguing Presence/Absence Variation (PAV) across 15 published sorghum genomes. We found 301 superTranscripts were exclusive to sweet sorghum, including 58 de novo genes encoded core and linker histones, zinc finger domains, glucosyl transferases, cellulose synthase, etc. The superTranscriptome added 2,802 new protein-coding genes to the Sweet Sorghum Reference Genome (SSRG), of which 559 code for different transcription factors (TFs). Our analysis revealed that MULE-like transposases were abundant in the sweet sorghum genome and could play a hidden role in the evolution of sweet sorghum. We observed large deletions in the D locus and terminal deletions in four other NAC encoding loci in the SSRG compared to its wild progenitor (353) suggesting non-functional NAC genes contributed to trait development in sweet sorghum. Moreover, superTranscript-based methods for Differential Exon Usage (DEU) and Differential Gene Expression (DGE) analyses were more accurate than those based on the SSRG. This study demonstrates that the superTranscriptome can enhance our understanding of fundamental sorghum mechanisms, improve genome annotations, and potentially even replace the reference genome.

Pleiotropy, a feature or a bug? Toward co-ordinating plant growth, development, and environmental responses through engineering plant hormone signaling

The advent of gene editing technologies such as CRISPR has simplified co-ordinating trait development. However, identifying candidate genes remains a challenge due to complex gene networks and pathways. These networks exhibit pleiotropy, complicating the determination of specific gene and pathway functions. In this review, we explore how systems biology and single-cell sequencing technologies can aid in identifying candidate genes for co-ordinating specifics of plant growth and development within specific temporal and tissue contexts. Exploring sequence-function space of these candidate genes and pathway modules with synthetic biology allows us to test hypotheses and define genotype-phenotype relationships through reductionist approaches. Collectively, these techniques hold the potential to advance breeding and genetic engineering strategies while also addressing genetic diversity issues critical for adaptation and trait development.

Lessons from Ethiopian coffee landscapes for global conservation in a post-wild world

The reality for conservation of biodiversity across our planet is that all ecosystems are modified by humans in some way or another. Thus, biodiversity conservation needs to be implemented in multifunctional landscapes. In this paper we use a fascinating coffee-dominated landscape in southwest Ethiopia as our lens to derive general lessons for biodiversity conservation in a post-wild world. Considering a hierarchy of scales from genes to multi-species interactions and social-ecological system contexts, we focus on (i) threats to the genetic diversity of crop wild relatives, (ii) the mechanisms behind trade-offs between biodiversity and agricultural yields, (iii) underexplored species interactions suppressing pest and disease levels, (iv) how the interactions of climate change and land-use change sometimes provide opportunities for restoration, and finally, (v) how to work closely with stakeholders to identify scenarios for sustainable development. The story on how the ecology and evolution of coffee within its indigenous distribution shape biodiversity conservation from genes to social-ecological systems can inspire us to view other landscapes with fresh eyes. The ubiquitous presence of human-nature interactions demands proactive, creative solutions to foster biodiversity conservation not only in remote protected areas but across entire landscapes inhabited by people.

Introgression from local cultivars is a driver of agricultural adaptation in Argentinian weedy rice

Weedy rice, a pervasive and troublesome weed found across the globe, has often evolved through fertilization of rice cultivars with little importance of crop-weed gene flow. In Argentina, weedy rice has been reported as an important constraint since the early 1970s, and, in the last few years, strains with herbicide-resistance are suspected to evolve. Despite their importance, the origin and genetic composition of Argentinian weedy rice as well its adaptation to agricultural environments has not been explored so far. To study this, we conducted genotyping-by-sequencing on samples of Argentinian weedy and cultivated rice and compared them with published data from weedy, cultivated and wild rice accessions distributed worldwide. In addition, we conducted a phenotypic characterization for weedy-related traits, a herbicide resistance screening and genotyped accessions for known mutations in the acetolactate synthase (ALS) gene, which confers herbicide resistance. Our results revealed large phenotypic variability in Argentinian weedy rice. Most strains were resistant to ALS-inhibiting herbicides with a high frequency of the ALS mutation (A122T) present in Argentinian rice cultivars. Argentinian cultivars belonged to the three major genetic groups of rice: japonica, indica and aus while weeds were mostly aus or aus-indica admixed, resembling weedy rice strains from the Southern Cone region. Phylogenetic analysis supports a single origin for aus-like South American weeds, likely as seed contaminants from the United States, and then admixture with local indica cultivars. Our findings demonstrate that crop to weed introgression can facilitate rapid adaptation to agriculture environments.

Crop-to-wild gene flow in wild coffee species: the case of Coffea canephora in the Democratic Republic of the Congo

BACKGROUND AND AIMS

Plant breeders are increasingly turning to crop wild relatives (CWRs) to ensure food security in a rapidly changing environment. However, CWR populations are confronted with various human-induced threats, including hybridization with their nearby cultivated crops. This might be a particular problem for wild coffee species, which often occur near coffee cultivation areas. Here, we briefly review the evidence for wild Coffea arabica (cultivated as Arabica coffee) and Coffea canephora (cultivated as Robusta coffee) and then focused on C. canephora in the Yangambi region in the Democratic Republic of the Congo. There, we examined the geographical distribution of cultivated C. canephora and the incidence of hybridization between cultivated and wild individuals within the rainforest.

METHODS

We collected 71 C. canephora individuals from home gardens and 12 C. canephora individuals from the tropical rainforest in the Yangambi region and genotyped them using genotyping-by-sequencing (GBS). We compared the fingerprints with existing GBS data from 388 C. canephora individuals from natural tropical rainforests and the INERA Coffee Collection, a Robusta coffee field gene bank and the most probable source of cultivated genotypes in the area. We then established robust diagnostic fingerprints that genetically differentiate cultivated from wild coffee, identified cultivated-wild hybrids and mapped their geographical position in the rainforest.

KEY RESULTS

We identified cultivated genotypes and cultivated-wild hybrids in zones with clear anthropogenic activity, and where cultivated C. canephora in home gardens may serve as a source for crop-to-wild gene flow. We found relatively few hybrids and backcrosses in the rainforests.

CONCLUSIONS

The cultivation of C. canephora in close proximity to its wild gene pool has led to cultivated genotypes and cultivated-wild hybrids appearing within the natural habitats of C. canephora. Yet, given the high genetic similarity between the cultivated and wild gene pool, together with the relatively low incidence of hybridization, our results indicate that the overall impact in terms of risk of introgression remains limited so far.

Genomic evidence of genuine wild versus admixed olive populations evolving in the same natural environments in western Mediterranean Basin

Crop-to-wild gene flow is a mechanism process widely documented, both in plants and animals. This can have positive or negative impacts on the evolution of admixed populations in natural environments, yet the phenomenon is still misunderstood in long-lived woody species, contrary to short-lived crops. Wild olive Olea europaea L. occurs in the same eco-geographical range as domesticated olive, i.e. the Mediterranean Basin (MB). Moreover, it is an allogamous and anemophilous species whose seeds are disseminated by birds, i.e. factors that drive gene flow between crops and their wild relatives. Here we investigated the genetic structure of western MB wild olive populations in natural environments assuming a homogenous gene pool with limited impact of cultivated alleles, as previously suggested. We used a target sequencing method based on annotated genes from the Farga reference genome to analyze 27 western MB olive tree populations sampled in natural environments in France, Spain and Morocco. We also target sequenced cultivated olive tree accessions from the Worldwide Olive Germplasm Bank of Marrakech and Porquerolles and from an eastern MB wild olive tree population. We combined PCA, sNMF, pairwise FST and TreeMix and clearly identified genuine wild olive trees throughout their natural distribution range along a north-south gradient including, for the first time, in southern France. However, contrary to our assumption, we highlighted more admixed than genuine wild olive trees. Our results raise questions regarding the admixed population evolution pattern in this environment, which might be facilitated by crop-to-wild gene flow.

Resurrecting urban sunflowers: Phenotypic and molecular changes between antecedent and modern populations separated by 36 years

Resurrection experiments provide a unique opportunity to evaluate phenotypic and molecular evolution in response to environmental challenges. To understand the evolution of urban populations of Helianthus annuus, we compared plants from 36-year-old antecedent seed collections to modern seed collections from the same area using molecular and quantitative genetic approaches. We found 200 differentially expressed transcripts between antecedent and modern groups, and transcript expression was generally higher in modern samples as compared to antecedent samples. Admixture analysis indicated gene flow from domesticated to modern populations over time. After a greenhouse refresher generation, one antecedent-modern population pair was grown under two water availability (well-watered and drought) and temperature (ambient and elevated by 2.8°C) conditions reflecting historical and contemporary climates. Overall, 78% (7 out of 9) of traits differed between the antecedent and modern populations, with modern individuals displaying some trait changes that are coherent with climate changes expectations and some trait changes in the direction of crop varieties. Phenotypic selection analysis showed that modern trait values were often favoured by selection, especially in environmental treatments resembling modern conditions. Trait heritability in the antecedent population was five times as high as in the modern population, on average. In addition, phenotypic plasticity for some traits, such as flowering phenology, was present in the antecedent population but absent in the modern population. The combination of phenotypic and molecular information suggests that evolution has been influenced by crop-wild introgression, adaptive processes and drift. We discuss these results in the context of continued evolution in response to anthropogenic factors.

Origins and evolution of biological novelty

Understanding the origins and impacts of novel traits has been a perennial interest in many realms of ecology and evolutionary biology. Here, we build on previous evolutionary and philosophical treatments of this subject to encompass novelties across biological scales and eco-evolutionary perspectives. By defining novelties as new features at one biological scale that have emergent effects at other biological scales, we incorporate many forms of novelty that have previously been treated in isolation (such as novelty from genetic mutations, new developmental pathways, new morphological features, and new species). Our perspective is based on the fundamental idea that the emergence of a novelty, at any biological scale, depends on its environmental and genetic context. Through this lens, we outline a broad array of generative mechanisms underlying novelty and highlight how genomic tools are transforming our understanding of the origins of novelty. Lastly, we present several case studies to illustrate how novelties across biological scales and systems can be understood based on common mechanisms of change and their environmental and genetic contexts. Specifically, we highlight how gene duplication contributes to the evolution of new complex structures in visual systems; how genetic exchange in symbiosis alters functions of both host and symbiont, resulting in a novel organism; and how hybridisation between species can generate new species with new niches.

Limited genetic changes observed during in situ and ex situ conservation in Nordic populations of red clover (Trifolium pratense)

Introduction

In situ and ex situ conservation are the two main approaches for preserving genetic diversity. The advantages and disadvantages of the two approaches have been discussed but their genetic effects have not been fully evaluated.

Methods

In this study we investigate the effects of the two conservation approaches on genetic diversity in red clover. Seed samples collected from wild populations in Sweden and Norway in 1980, their subsequent generations created during seed regeneration at the gene bank and samples recollected from the same location as the original samples, were analyzed with microsatellite markers, alongside reference samples from cultivars.

Results

Overall, there was a differentiation between cultivars and the wild material and between wild material from Sweden and Norway. In general, the original collections clustered together with the later generations of the same accession in the gene bank, and with the recollected samples from the same location, and the level of diversity remained the same among samples of the same accession. Limited gene flow from cultivated varieties to the wild populations was detected; however, some wild individuals are likely to be escapees or affected by gene flow.

Discussion

In conclusion, there were examples of genetic changes within individual accessions both in situ and ex situ, as is also to be expected in any living population. However, we observed only limited genetic changes in both in situ and ex situ conservation over the generations included in this study and with the relatively large populations used in the ex situ conservation in the gene bank at NordGen.

Demographic and reproductive impacts of hybridization unrelated to hybrid viability in a native plant

PREMISE

Introduced species can influence native congeners through production of hybrids and introgression, but impacts not involving viable hybrids, such as reduced conspecific offspring and increased asexual seed production, are rarely examined. Here we tested for these demographic and reproductive consequences of hybridization between introduced, domesticated apple (Malus domestica) and native crabapple (M. coronaria) in southern Canada.

METHODS

We applied four pollination treatments (open, M. coronaria, M. domestica, open + M. coronaria) to focal M. coronaria trees across multiple years and assessed the number and reproductive origins of resulting seeds (hybrid or conspecific endosperm and, for each, sexual or asexual embryo) using flow cytometry.

RESULTS

In open-pollinated fruit, 27% of seeds had hybrid endosperm; 52% of embryos were asexual. The number of conspecific embryos (sexual or asexual) per fruit did not decline significantly with increasing hybridization, indicating no seed discounting, but hand pollinations using only domestic apple or crabapple pollen reduced the number of conspecific embryos significantly. Hybridization was not associated with a change in percentage asexual embryos, overall, but there was an increase in asexual embryos in tetraploid seeds, the maternal and most common offspring ploidy.

CONCLUSIONS

We conclude that hybridization can influence native Malus in ways beyond the production of viable hybrids, with significant implications for population dynamics and genetic structure.

Diamonds in the not-so-rough: Wild relative diversity hidden in crop genomes

Crop production is becoming an increasing challenge as the global population grows and the climate changes. Modern cultivated crop species are selected for productivity under optimal growth environments and have often lost genetic variants that could allow them to adapt to diverse, and now rapidly changing, environments. These genetic variants are often present in their closest wild relatives, but so are less desirable traits. How to preserve and effectively utilize the rich genetic resources that crop wild relatives offer while avoiding detrimental variants and maladaptive genetic contributions is a central challenge for ongoing crop improvement. This Essay explores this challenge and potential paths that could lead to a solution.

The Role of Home Gardens in Promoting Biodiversity and Food Security

Plant genetic resources provide the basis for sustainable agricultural production, adaptation to climate change, and economic development. Many present crop plants are endangered due to extreme environmental conditions induced by climate change or due to the use of a limited selection of plant materials. Changing environmental conditions are a challenge for plant production and food security, emphasizing the urgent need for access to a wider range of plant genetic resources than what are utilized today, for breeding novel crop varieties capable of resilience and adaptation to climate change and other environmental challenges. Besides large-scale agricultural production, it is important to recognize that home gardens have been an integral component of family farming and local food systems for centuries. It is remarkable how home gardens have allowed the adaptation and domestication of plants to extreme or specific ecological conditions, thus contributing to the diversification of cultivated plants. Home gardens can help in reducing hunger and malnutrition and improve food security. In addition, they provide opportunities to broaden the base of cultivated plant materials by harboring underutilized crop plants and crop wild relative species. Crop wild relatives contain a wide range of genetic diversity not available in cultivated crops. Although the importance of home gardens in conserving plant genetic resources is well recognized, there is a risk that local genetic diversity will be lost if traditional plant materials are replaced by high-yielding modern cultivars. This paper provides an overview of home gardens and their present role and future potential in conserving and utilizing plant genetic resources and enhancing food and nutritional security under global challenges.

Genomic conservation of crop wild relatives: A case study of citrus

Conservation of crop wild relatives is critical for plant breeding and food security. The lack of clarity on the genetic factors that lead to endangered status or extinction create difficulties when attempting to develop concrete recommendations for conserving a citrus wild relative: the wild relatives of crops. Here, we evaluate the conservation of wild kumquat (Fortunella hindsii) using genomic, geographical, environmental, and phenotypic data, and forward simulations. Genome resequencing data from 73 accessions from the Fortunella genus were combined to investigate population structure, demography, inbreeding, introgression, and genetic load. Population structure was correlated with reproductive type (i.e., sexual and apomictic) and with a significant differentiation within the sexually reproducing population. The effective population size for one of the sexually reproducing subpopulations has recently declined to ~1,000, resulting in high levels of inbreeding. In particular, we found that 58% of the ecological niche overlapped between wild and cultivated populations and that there was extensive introgression into wild samples from cultivated populations. Interestingly, the introgression pattern and accumulation of genetic load may be influenced by the type of reproduction. In wild apomictic samples, the introgressed regions were primarily heterozygous, and genome-wide deleterious variants were hidden in the heterozygous state. In contrast, wild sexually reproducing samples carried a higher recessive deleterious burden. Furthermore, we also found that sexually reproducing samples were self-incompatible, which prevented the reduction of genetic diversity by selfing. Our population genomic analyses provide specific recommendations for distinct reproductive types and monitoring during conservation. This study highlights the genomic landscape of a wild relative of citrus and provides recommendations for the conservation of crop wild relatives.

Crop-Weed Introgression Plays Critical Roles in Genetic Differentiation and Diversity of Weedy Rice: A Case Study of Human-Influenced Weed Evolution

As an important driving force, introgression plays an essential role in shaping the evolution of plant species. However, knowledge concerning how introgression affects plant evolution in agroecosystems with strong human influences is still limited. To generate such knowledge, we used InDel (insertion/deletion) molecular fingerprints to determine the level of introgression from japonica rice cultivars into the indica type of weedy rice. We also analyzed the impact of crop-to-weed introgression on the genetic differentiation and diversity of weedy rice, using InDel (insertion/deletion) and SSR (simple sequence repeat) molecular fingerprints. Results based on the STRUCTURE analysis indicated an evident admixture of some weedy rice samples with indica and japonica components, suggesting different levels of introgression from japonica rice cultivars to the indica type of weedy rice. The principal coordinate analyses indicated indica-japonica genetic differentiation among weedy rice samples, which was positively correlated with the introgression of japonica-specific alleles from the rice cultivars. In addition, increased crop-to-weed introgression formed a parabola pattern of dynamic genetic diversity in weedy rice. Our findings based on this case study provide evidence that human activities, such as the frequent change in crop varieties, can strongly influence weed evolution by altering genetic differentiation and genetic diversity through crop-weed introgression in agroecosystems.

Rate of crop-weed hybridization in Sorghum bicolor × Sorghum halepense is influenced by genetic background, pollen load, and the environment

The potential for gene flow between cultivated species and their weedy relatives poses agronomic and environmental concerns, particularly when there are opportunities for the transfer of adaptive or agronomic traits such as herbicide resistance into the weedy forms. Grain sorghum (Sorghum bicolor) is an important crop capable of interspecific hybridization with its weedy relative johnsongrass (Sorghum halepense). Previous findings have shown that triploid progenies resulting from S. bicolor × S. halepense crosses typically collapse with only a few developing into mature seeds, whereas tetraploids often fully develop. The objective of this experiment was to determine the impact of S. bicolor genotype and pollen competition on the frequency of hybridization between S. bicolor and S. halepense. A total of 12 different cytoplasmic male sterile S. bicolor genotypes were compared with their respective male fertile lines across 2 years, to assess the frequency of hybridization and seed set when S. halepense served as the pollinator parent. Results indicate significant differences in the frequency of interspecific hybridization among the S. bicolor genotypes, and pollen fertility in S. bicolor reduced the rate of this interspecific hybridization by up to two orders of magnitude. Further, hybridization rates greatly varied across the two study environments. Results are helpful for developing appropriate gene flow mitigation strategies and indicate that gene flow could be reduced by the selection of appropriate seed parents for sorghum hybrids.

Studying Wild Plant Pathosystems to Understand Crop Plant Pathosystems: Status, Gaps, Challenges, and Perspectives

Phytopathology is a highly complex scientific discipline. Initially, its focus was on the study of plant-pathogen interactions in agricultural and forestry production systems. Host-pathogen interactions in natural plant communities were generally overlooked until the 1970s when plant pathologists and evolutionary biologists started to take an interest in these interactions, and their dynamics in natural plant populations, communities, and ecosystems. This article introduces the general principles of plant pathosystems, provides a basic critical overview of current knowledge of host-pathogen interactions in natural plant pathosystems, and shows how this knowledge is important for future developments in plant pathology especially as it applies in cropping systems, ecology, and evolutionary biology. Plant pathosystems can be further divided according to the structure and origin of control, as autonomous (wild plant pathosystems, WPPs) or deterministic (crop plant pathosystems, CPPs). WPPs are characterized by the disease triangle and closed-loop (feedback) controls, and CPPs are characterized by the disease tetrahedron and open-loop (non-feedback) controls. Basic general, ecological, genetic, and population structural and functional differences between WPPs and CPPs are described. It is evident that we lack a focus on long-term observations and research of diseases and their dynamics in natural plant populations, metapopulations, communities, ecosystems, and biomes, as well as their direct or indirect relationships to CPPs. Differences and connections between WPPs and CPPs, and why, and how, these are important for agriculture varies. WPP and CPP may be linked by strong biological interactions, especially where the pathogen is in common. This is demonstrated through a case study of lettuce (Lactuca spp., L. serriola and L. sativa) and lettuce downy mildew (Bremia lactucae). In other cases where there is no such direct biological linkage, the study of WPPs can provide a deeper understanding of how ecology and genetics interacts to drive disease through time. These studies provide insights into ways in which farming practices may be changed to limit disease development. Research on interactions between pathosystems, the "cross-talk" of WPPs and CPPs, is still very limited and, as shown in interactions between wild and cultivated Lactuca spp.-B. lactucae associations, can be highly complex. The implications and applications of this knowledge in plant breeding, crop management, and disease control measures are considered. This review concludes with a discussion of theoretical, general and specific aspects, challenges and limits of future WPP research, and application of their results in agriculture.

Multiplexed ISSR Genotyping by Sequencing (MIG-Seq)

Multiplexed inter-simple sequence repeat (ISSR) genotyping by sequencing (MIG-seq) is a simple, rapid, and inexpensive method for detecting single-nucleotide polymorphisms (SNPs) using next-generation sequencing (NGS). The advantages of MIG-seq include easy application to various species without prior genetic information. In addition, this method opens the door to genome-wide nucleotide sequence analyses of low-quality and trace-level deoxyribonucleic acid (DNA) samples, which have previously been difficult to analyze. Another advantage is that the procedure is simple, time-saving, and inexpensive. Recently, MIG-seq has been applied to wild and cultivated plants and has produced novel results. Using invisible DNA information, questions related to gene flow through pollination and seed dispersal, the genetic structure and diversity of populations, clonality, and the hybridization of wild and cultivated plants are being rapidly answered. In this chapter, I present the results of plant research based on MIG-seq and describe the procedure for this method as a user of MIG-seq.

Genetic Diversity, Conservation, and Utilization of Plant Genetic Resources

Plant genetic resources (PGRs) are the total hereditary material, which includes all the alleles of various genes, present in a crop species and its wild relatives. They are a major resource that humans depend on to increase farming resilience and profit. Hence, the demand for genetic resources will increase as the world population increases. There is a need to conserve and maintain the genetic diversity of these valuable resources for sustainable food security. Due to environmental changes and genetic erosion, some valuable genetic resources have already become extinct. The landraces, wild relatives, wild species, genetic stock, advanced breeding material, and modern varieties are some of the important plant genetic resources. These diverse resources have contributed to maintaining sustainable biodiversity. New crop varieties with desirable traits have been developed using these resources. Novel genes/alleles linked to the trait of interest are transferred into the commercially cultivated varieties using biotechnological tools. Diversity should be maintained as a genetic resource for the sustainable development of new crop varieties. Additionally, advances in biotechnological tools, such as next-generation sequencing, molecular markers, in vitro culture technology, cryopreservation, and gene banks, help in the precise characterization and conservation of rare and endangered species. Genomic tools help in the identification of quantitative trait loci (QTLs) and novel genes in plants that can be transferred through marker-assisted selection and marker-assisted backcrossing breeding approaches. This article focuses on the recent development in maintaining the diversity of genetic resources, their conservation, and their sustainable utilization to secure global food security.

Plant pan-genomics and its applications

Plant genomes are so highly diverse that a substantial proportion of genomic sequences are not shared among individuals. The variable DNA sequences, along with the conserved core sequences, compose the more sophisticated pan-genome that represents the collection of all non-redundant DNA in a species. With rapid progress in genome sequencing technologies, pan-genome research in plants is now accelerating. Here we review recent advances in plant pan-genomics, including major driving forces of structural variations that constitute the variable sequences, methodological innovations for representing the pan-genome, and major successes in constructing plant pan-genomes. We also summarize recent efforts toward decoding the remaining dark matter in telomere-to-telomere or gapless plant genomes. These new genome resources, which have remarkable advantages over numerous previously assembled less-than-perfect genomes, are expected to become new references for genetic studies and plant breeding.

Reducing Seed Shattering in Weedy Rice by Editing SH4 and qSH1 Genes: Implications in Environmental Biosafety and Weed Control through Transgene Mitigation

Mitigating the function of acquired transgenes in crop wild/weedy relatives can provide an ideal strategy to reduce the possible undesired environmental impacts of pollen-mediated transgene flow from genetically engineered (GE) crops. To explore a transgene mitigation system in rice, we edited the seed-shattering genes, SH4 and qSH1, using a weedy rice line ("C9") that originally had strong seed shattering. We also analyzed seed size-related traits, the total genomic transcriptomic data, and RT-qPCR expression of the SH4 or qSH1 gene-edited and SH4/qSH1 gene-edited weedy rice lines. Substantially reduced seed shattering was observed in all gene-edited weedy rice lines. The single gene-edited weedy rice lines, either the SH4 or qSH1 gene, did not show a consistent reduction in their seed size-related traits. In addition, reduced seed shattering was closely linked with the weakness and absence of abscission layers and reduced abscisic acid (ABA). Additionally, the genes closely associated with ABA biosynthesis and signaling transduction, as well as cell-wall hydrolysis, were downregulated in all gene-edited weedy rice lines. These findings facilitate our deep insights into the underlying mechanisms of reduced seed shattering in plants in the rice genus Oryza. In addition, such a mitigating technology also has practical applications for reducing the potential adverse environmental impacts caused by transgene flow and for managing the infestation of weedy rice by acquiring the mitigator from GE rice cultivars through natural gene flow.

Transgene Was Silenced in Hybrids between Transgenic Herbicide-Resistant Crops and Their Wild Relatives Utilizing Alien Chromosomes

The commercialization of transgenic herbicide-resistant (HR) crops may cause gene flow risk. If a transgene in progenies of transgenic crops and wild relatives is silencing, these progenies should be killed by the target herbicide, thus, the gene flow risk could be decreased. We obtained the progenies of backcross generations between wild Brassca juncea (AABB, 2n = 36) and glufosinate-resistant transgenic Brassica napus (AACC, 2n = 38, PAT gene located on the C-chromosome). They carried the HR gene but did not express it normally, i.e., gene silencing occurred. Meanwhile, six to nine methylation sites were found on the promoter of PAT in transgene-silencing progenies, while no methylation sites occurred on that in transgene-expressing progenies. In addition, transgene expressing and silencing backcross progenies showed similar fitness with wild Brassica juncea. In conclusion, we elaborate on the occurrence of transgene-silencing event in backcross progenies between transgenic crop utilizing alien chromosomes and their wild relatives, and the DNA methylation of the transgene promoter was an important factor leading to gene silencing. The insertion site of the transgene could be considered a strategy to reduce the ecological risk of transgenic crops, and applied to cultivate lower gene flow HR crops in the future.

Fitness and Rhizobacteria of F2, F3 Hybrids of Herbicide-Tolerant Transgenic Soybean and Wild Soybean

The introduction of herbicide-tolerant (HT) transgenic soybeans (Glycine max (L.) Merr.) into farming systems raises great concern that transgenes may flow to endemic wild soybeans (Glycine soja Sieb. et Zucc.) via pollen, which may increase the ecological risks by increasing the fitness of hybrids under certain conditions and threaten the genetic diversity of wild soybean populations. In order to demonstrate the potential risk of gene flow from the HT soybean to the wild soybean, the fitness of F2 and F3 hybrids obtained from two wild soybean populations (HLJHRB-1, JSCZ) collected from China and the HT soybean was measured under farmland and wasteland soil conditions, as well as with or without weed competition. Compared with their wild progenitors, the F2 and F3 hybrids of HLJHRB-1 displayed a higher emergence rate, higher aboveground dry biomass, more pods and filled-seed plants, as well as better composite fitness under four planting conditions. The F2 and F3 hybrids of JSCZ also displayed a higher emergence rate, higher aboveground dry biomass, more pods, and more filled seeds per plant under mixed planting, whereas these characteristics were lower under pure planting conditions in wasteland and farmland soil. Therefore, the composite fitness of JSCZ hybrids was higher or lower depending on the planting conditions. Furthermore, the soil microbial communities of the F3 of HLJHRB-1, JSCZ, and the wild soybean were investigated with 16S rDNA sequencing, which showed that low alpha diversity of rhizobacteria was relative to high fitness, and Rhizobium played an important role in promoting F3 plant growth.

Genetic diversity, asexual reproduction and conservation of the edible fruit tree Spondias purpurea L. (Anacardiaceae) in the Costa Rican tropical dry forest

The term circa situm has been used to describe different conservation strategies within agricultural landscapes. Circa situm conserves planted or remnant species in farmlands, where natural vegetation has been modified through anthropogenic intervention. It has been proposed that trees planted or retained under circa situm conditions may contribute to maintaining genetic diversity, however information on the role of this strategy in preserving genetic diversity is scarce. The aim of this study was to determine the levels of genetic diversity and structure, and mating patterns in planted and unmanaged stands of the tropical fruit tree Spondias purpurea L. in north western Costa Rica. In three localities, we used seven polymorphic microsatellite loci and genotyped 201 adults and 648 seeds from planted and wild stands. We found no differences in genetic diversity among planted and wild stands. Genetic structure analysis revealed that gene flow occurs among planted and wild stands within localities. Clones were present and their diversity and evenness were both high and similar between planted and wild stands. The number of pollen donors per progeny array was low (Nep = 1.01) which resulted in high levels of correlated paternity (rp = 0.9). Asexual seeds were found in 4.6% of the progeny arrays, which had multilocus genotypes that were identical to the maternal trees. Our results show that although planted stands under circa situm conditions can maintain similar levels of genetic diversity than wild stands, the low number of sires and asexual seed formation could threaten the long term persistence of populations.

Unlocking the hidden variation from wild repository for accelerating genetic gain in legumes

The fluctuating climates, rising human population, and deteriorating arable lands necessitate sustainable crops to fulfil global food requirements. In the countryside, legumes with intriguing but enigmatic nitrogen-fixing abilities and thriving in harsh climatic conditions promise future food security. However, breaking the yield plateau and achieving higher genetic gain are the unsolved problems of legume improvement. Present study gives emphasis on 15 important legume crops, i.e., chickpea, pigeonpea, soybean, groundnut, lentil, common bean, faba bean, cowpea, lupin, pea, green gram, back gram, horse gram, moth bean, rice bean, and some forage legumes. We have given an overview of the world and India's area, production, and productivity trends for all legume crops from 1961 to 2020. Our review article investigates the importance of gene pools and wild relatives in broadening the genetic base of legumes through pre-breeding and alien gene introgression. We have also discussed the importance of integrating genomics, phenomics, speed breeding, genetic engineering and genome editing tools in legume improvement programmes. Overall, legume breeding may undergo a paradigm shift once genomics and conventional breeding are integrated in the near future.

Genomic revolution of US weedy rice in response to 21st century agricultural technologies

Weedy rice is a close relative of cultivated rice that devastates rice productivity worldwide. In the southern United States, two distinct strains have been historically predominant, but the 21^st century introduction of hybrid rice and herbicide resistant rice technologies has dramatically altered the weedy rice selective landscape. Here, we use whole-genome sequences of 48 contemporary weedy rice accessions to investigate the genomic consequences of crop-weed hybridization and selection for herbicide resistance. We find that population dynamics have shifted such that most contemporary weeds are now crop-weed hybrid derivatives, and that their genomes have subsequently evolved to be more like their weedy ancestors. Haplotype analysis reveals extensive adaptive introgression of cultivated alleles at the resistance gene ALS, but also uncovers evidence for convergent molecular evolution in accessions with no signs of hybrid origin. The results of this study suggest a new era of weedy rice evolution in the United States.

Gene flow between wild trees and cultivated varieties shapes the genetic structure of sweet chestnut (Castanea sativa Mill.) populations

Gene flow between cultivated and wild gene pools is common in the contact zone between agricultural lands and natural habitats and can be used to study the development of adaptations and selection of novel varieties. This is likely the case in the northern Adriatic region, where centuries-old cultivated orchards of sweet chestnut (Castanea sativa Mill.) are planted within the natural distribution area of the species. Thus, we investigated the population structure of several orchards of sweet chestnuts. Furthermore, the genetic background of three toponymous clonal varieties was explored. Six genomic simple sequence repeat (gSSR) and nine EST-derived SSR (EST-SSR) loci were utilized in this research, and both grafted and non-grafted individuals were included in this study. Five closely related clones were identified, which represent a singular, polyclonal marron variety, found in all three cultivation areas. Furthermore, many hybrids, a result of breeding between cultivated and wild chestnuts, have been found. Analyzed semi-wild orchards defined by a diverse genetic structure, represent a hotspot for further selection and could result in creation of locally adapted, high-yielding varieties.

Consequences of introgression and gene flow on the genetic structure and diversity of Lima bean (Phaseolus lunatus L.) in its Mesoamerican diversity area

We evaluated the role of gene flow and wild-crop introgression on the structure and genetic diversity of Lima bean (Phaseolus lunatus) in the Yucatan Peninsula, an important Mesoamerican diversity area for this crop, using a genotyping-by-sequencing approach (15,168 SNP markers) and two scales. At the local scale, STRUCTURE and NGSEP analyses showed predominantly crop-to-wild introgression, but also evidence of a bidirectional gene flow in the two wild-weedy-crop complexes studied (Itzinté and Dzitnup). The ABBA-BABA tests showed a higher introgression in Itzinté (the older complex) than in Dzitnup (the younger one); at the allelic level, the wild-crop introgression in Itzinté was similar in both directions, in Dzitnup it was higher from crop-to-wild; and at the chromosomal level, introgression in Itzinté was from wild-to-crop, whereas in Dzitnup it occured in the opposite direction. Also, we found H _E values slightly higher in the domesticated accessions than in the wild ones, in both complexes (Itzinté: wild = 0.31, domesticated = 0.34; Dzinup: wild = 0.27, domesticated = 0.36), but %P and π estimators were higher in the wild accessions than in the domesticated ones. At a regional scale, STRUCTURE and MIGRATE showed a low gene flow, predominantly from crop-to-wild; and STRUCTURE, Neighbor-Joining and PCoA analyses indicated the existence of two wild groups and one domesticated group, with a marked genetic structure based in the existence of domesticated MI and wild MII gene pools. Also, at the regional scale, we found a higher genetic diversity in the wild accessions than in the domesticated ones, in all estimators used (e.g., H _E = 0.27 and H _E = 0.17, respectively). Our results indicate that gene flow and introgression are playing an important role at the local scale, but its consequences on the structure and genetic diversity of the Lima bean are not clearly reflected at the regional scale, where diversity patterns between wild and domesticated populations could be reflecting historical events.

Assessment of genetically modified oilseed rape MON 94100 for food and feed uses, under regulation (EC) No 1829/2003 (application EFSA-GMO-NL-2020-169)

Oilseed rape MON 94100 was developed to confer tolerance to dicamba herbicide. The molecular characterisation data and bioinformatic analyses do not identify issues requiring food/feed safety assessment. None of the identified differences in the agronomic/phenotypic and compositional characteristics tested between oilseed rape MON 94100 and its conventional counterpart needs further assessment, except for the levels of carbohydrates, calcium and ADF in seeds, which do not raise nutritional and safety concerns. The GMO Panel does not identify safety concerns regarding the toxicity and allergenicity of the dicamba mono-oxygenase (DMO) protein as expressed in oilseed rape MON 94100. The GMO Panel finds no evidence that the genetic modification impacts the overall safety of oilseed rape MON 94100. In the context of this application, the consumption of food and feed from oilseed rape MON 94100 does not represent a nutritional concern in humans and animals. The GMO Panel concludes that oilseed rape MON 94100 is as safe as the conventional counterpart and non-GM oilseed rape reference varieties tested, and no post-market monitoring of food/feed is considered necessary. In the case of accidental release of viable oilseed rape MON 94100 seeds into the environment, this would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of oilseed rape MON 94100. The GMO Panel concludes that oilseed rape MON 94100 is as safe as its conventional counterpart and the tested non-GM oilseed rape reference varieties with respect to potential effects on human and animal health and the environment.

Pollen-mediated flow of herbicide resistance genes in Beckmannia syzigachne

BACKGROUND

Beckmannia syzigachne (Steud.) Fernald has evolved herbicide resistance due to the long-term sole use of herbicides and has become a dominant weed in wheat fields in the middle and lower reaches of the Yangtze River in China. In addition to the selection pressure imposed by herbicides, pollen-mediated gene flow (PMGF) has been reported to cause the spread of herbicide resistance between populations within a certain range in some farmland weeds. It is not clear whether the same is true for the self-pollinated grass weed B. syzigachne.

RESULTS

In this study, we confirmed and quantified the level of PMGF in B. syzigachne through concentric circle planting and herbicide resistance tests. Results show that when the B. syzigachne pollen donor was close to the recipient (0.5 m), the average gene flow was 0.66%. Gene flow was detected as far as 10 m (the farthest distance studied) and decreased exponentially with increasing distance, which could be described by a double exponential decay model. Temperature also affected gene flow, whilst the average level of gene flow in all directions of wind was similar and wind speed caused insignificant difference in gene flow.

CONCLUSION

The results of this study confirmed that PMGF can occur between B. syzigachne populations in adjacent fields. Although the level of resistance spreading by pollen was low, especially across long distance, the results were relevant for smallholding farms, which is the dominant form of agricultural operation in China. It is therefore important to take proactive measures and integrate chemical and ecological weed control methods to prevent the spread of resistant B. syzigachne via both seeds and pollens. © 2022 Society of Chemical Industry.

Distinct early life stage gene expression effects of hybridization among European and North American farmed and wild Atlantic salmon populations

Due to multi-generation domestication selection, farmed and wild Atlantic salmon diverge genetically, which raises concerns about potential genetic interactions among escaped farmed and wild populations and disruption of local adaptation through introgression. When farmed strains of distant geographic origin are used, it is unknown whether the genetic consequences posed by escaped farmed fish will be greater than if more locally derived strains are used. Quantifying gene transcript expression differences among divergent farmed, wild and F₁ hybrids under controlled conditions is one of the ways to explore the consequences of hybridization. We compared the transcriptomes of fry at the end of yolk sac absorption of a European (EO) farmed ("StofnFiskur", Norwegian strain), a North American (NA) farmed (Saint John River, NB strain), a Newfoundland (NF) wild population with EO ancestry, and related F₁ hybrids using 44K microarrays. Our findings indicate that the wild population showed greater transcriptome differences from the EO farmed strain than that of the NA farmed strain. We also found the largest differences in global gene expression between the two farmed strains. We detected the fewest differentially expressed transcripts between F₁ hybrids and domesticated/wild maternal strains. We also found that the differentially expressed genes between cross types over-represented GO terms associated with metabolism, development, growth, immune response, and redox homeostasis processes. These findings suggest that the interbreeding of escaped EO/NA farmed and NF wild population would alter gene transcription, and the consequences of hybridization would be greater from escaped EO farmed than NA farmed salmon, resulting in potential effects on the wild populations.

Agrobiological features of eggplant cultivation in protected ground

The interest and spread of eggplant culture are defined worldwide due to the nutritional and dietary properties of the fruits. Nowadays, there is a rising trend towards increasing the areas under eggplant in plastic ground greenhouses. Nevertheless, the issues of the production of high-quality eggplants are essential. The studies were performed from 2018 to 2021 on the territory of the V.I. Edelstein Educational and Scientific Production Center for Horticulture and Vegetable Growing at the Russian State Agrarian University – Moscow Timiryazev Agricultural Academy. Two methods of plant formation (two and three stems), rationing of flowers in the inflorescences of eggplant plants (without rationing, rationing for a flower, rationing for 2 flowers), and eggplant hybrids were studied. As a result of the study, the agrobiological features of growing eggplant plants in plastic ground greenhouses were defined. The highest vendibility of the fruits of the studied hybrids was observed during the formation of plants in three stems, with rationing and preservation of the first flower in the inflorescence - 87.6%, rationing for two flowers – 82.8%, and without rationing of flowers – 77.2%.

Modeling the evolution of herbicide resistance in weed species with a complex life cycle

A growing number of weed species have evolved resistance to herbicides in recent years, which causes an immense financial burden to farmers. An increasingly popular method of weed control is the adoption of crops that are resistant to specific herbicides, which allows farmers to apply the herbicide during the growing season without harming the crop. If such crops are planted in the presence of closely related weed species, it is possible that resistance genes could transfer from the crop species to feral populations of the wild species via gene flow and become stably introgressed under ongoing selective pressure by the herbicide. We use a density-dependent matrix model to evaluate the effect of planting such crops on the evolution of herbicide resistance under a range of management scenarios. Our model expands on previous simulation studies by considering weed species with a more complex life cycle (perennial, rhizomatous weed species), studying the effect of environmental variation in herbicide effectiveness, and evaluating the role of common simplifying genetic assumptions on resistance evolution. Our model predictions are qualitatively similar to previous modeling studies using species with a simpler life cycle, which is, crop rotation in combination with rotation of herbicide site of action effectively controls weed populations and slows the evolution of herbicide resistance. We find that ignoring the effect of environmental variation can lead to an over- or under-prediction of the speed of resistance evolution. The effect of environmental variation in herbicide effectiveness depends on the resistance allele frequency in the weed population at the beginning of the simulation. Finally, we find that degree of dominance and ploidy level have a much larger effect on the predicted speed of resistance evolution compared to the rate of gene flow.

Key Roles of De-Domestication and Novel Mutation in Origin and Diversification of Global Weedy Rice

Simple Summary

Weedy rice is a noxious weed infesting rice fields worldwide and causing tremendous losses of rice yield and quality. The control of this conspecific weed is difficult owing to abundant genetic diversity associated with its complex origins and evolution. Applying different molecular methods, we demonstrate the multiple origins of weedy rice with the major pathway from its cultivar progenitors. The origin and diversification of weedy rice are also closely associated with differentiation of indica-japonica rice varieties. In addition, novel mutations are identified, which may promote continued evolution and genetic diversity of weedy rice. Knowledge generated from this study provides deep insights into the origin and evolution of conspecific weeds, in addition to the design of effective measures to control these weeds.

Abstract

Agricultural weeds pose great challenges to sustainable crop production, owing to their complex origins and abundant genetic diversity. Weedy rice (WD) infests rice fields worldwide causing tremendous losses of rice yield/quality. To explore WD origins and evolution, we analyzed DNA sequence polymorphisms of the seed shattering genes (sh4 and qsh1) in weedy, wild, and cultivated rice from a worldwide distribution. We also used microsatellite and insertion/deletion molecular fingerprinting to determine their genetic relationship and structure. Results indicate multiple origins of WD with most samples having evolved from their cultivated progenitors and a few samples from wild rice. WD that evolved from de-domestication showed distinct genetic structures associated with indica and japonica rice differentiation. In addition, the weed-unique haplotypes that were only identified in the WD samples suggest their novel mutations. Findings in this study demonstrate the key role of de-domestication in WD origins, in which indica and japonica cultivars stimulated further evolution and divergence of WD in various agroecosystems. Furthermore, novel mutations promote continued evolution and genetic diversity of WD adapting to different environments. Knowledge generated from this study provides deep insights into the origin and evolution of conspecific weeds, in addition to the design of effective measures to control these weeds.

Increased Longevity and Dormancy of Soil-Buried Seeds from Advanced Crop–Wild Rice Hybrids Overexpressing the EPSPS Transgene

Simple Summary

Estimating the survival and reproductive ability caused by a transgene moved from a genetically engineered (GE) crop to its wild relative populations through gene flow plays an important role in assessing the potential environmental risks of the GE crop. Such estimation has essentially focused on the survival and reproduction-related characteristics above the ground, but with little attention to the GE seeds shattered in the soil seed banks. We demonstrated that the herbicide-resistant transgene overexpressing the rice endogenous EPSP enzyme increased the survival and longevity of the GE crop–wild (Oryza rufipogon) hybrid seeds in soil seed banks. In addition, enhanced survival and longevity of the GE hybrid seeds are likely associated with increases in seed dormancy and a growth hormone (auxin) via overexpressing the EPSPS transgene. Therefore, the EPSPS transgene can persist in the soil seed banks and spread in the environment, causing unwanted environmental impacts.

Abstract

Estimating the fitness effect conferred by a transgene introgressed into populations of wild relative species from a genetically engineered (GE) crop plays an important role in assessing the potential environmental risks caused by transgene flow. Such estimation has essentially focused on the survival and fecundity-related characteristics measured above the ground, but with little attention to the fate of GE seeds shattered in the soil seed banks after maturation. To explore the survival and longevity of GE seeds in soil, we examined the germination behaviors of crop–wild hybrid seeds (F₄–F₆) from the lineages of a GE herbicide-tolerant rice (Oryzasativa) line that contains an endogenous EPSPS transgene hybridized with two wild O. rufipogon populations after the seeds were buried in soil. The results showed significantly increased germination of the GE crop–wild hybrid seeds after soil burial, compared with that of the non-GE hybrid seeds. Additionally, the proportion of dormant seeds and the content of the growth hormone auxin (indole-3-acetic acid, IAA) in the GE crop–wild hybrid seeds significantly increased. Evidently, the EPSPS transgene enhances the survival and longevity of GE crop–wild rice seeds in the soil seed banks. The enhanced survival and longevity of the GE hybrid seeds is likely associated with the increases in seed dormancy and auxin (IAA) by overexpressing the rice endogenous EPSPS transgene. Thus, the fate of GE seeds in the soil seed banks should be earnestly considered when assessing the environmental risks caused by transgene flow.

The transition to agricultural cultivation of neo-crops may fail to account for wild genetic diversity patterns: insights from the Cape Floristic Region

Aim

The global increase in the cultivation of native wild plants has raised concerns regarding potential risks associated with translocating genetic lineages beyond their natural range. This study aimed to investigate whether agricultural cultivation of neo-crops (a) accounts for the levels of genetic diversity present in wild populations, and whether (b) cultivated populations are genetically divergent from wild populations and thus pose a potential threat to wild genetic diversity.

Location

The Cape Floristic Region (CFR), located along the southern Cape of South Africa.

Methods

High Resolution Melt analysis (HRM) coupled with Sanger sequencing was used to screen three non-coding chloroplast DNA loci in Cyclopia Vent. (Fabaceae), a CFR endemic neo-crop cultivated for the production of a herbal infusion referred to as Honeybush tea. Wild and cultivated populations for three of three widely cultivated Honeybush species (C. intermedia, C. longifolia, and C. subternata) were screened. Genetic diversity and differentiation were measured and compared between wild and cultivated groups.

Results

Across all asseccions, a total of 17 haplotypes were detected, four of which were shared between wild and cultivated populations, while the remaining 13 were only detected in wild populations. Genetic diversity and differentiation was significantly higher in wild populations than in cultivated populations.

Conclusions

If no guidelines exist to facilitate the introduction of native wild plant taxa to a cultivated setting, wild genetic diversity patterns are likely to be compromised by cultivated populations. In the case presented here, cultivation represents a genetic bottleneck, failing to account for rare haplotypes, and may have disrupted species boundaries by initiating interspecific hybridization. More empirical work is required to evaluate the extent to which neo-crop cultivation poses a risk to wild genetic resources in the CFR and globally.

Assessment of genetically modified oilseed rape 73496 for food and feed uses, under Regulation (EC) No 1829/2003 (application EFSA-GMO-NL-2012-109)

Oilseed rape 73496 was developed to confer tolerance to the herbicidal active substance glyphosate through the expression of the glyphosate acetyltransferase protein GAT4621. The molecular characterisation data and bioinformatic analyses identify no issues requiring food/feed safety assessment. None of the identified differences between oilseed rape 73496 and its conventional counterpart in the agronomic/phenotypic endpoints tested needs further assessment. Differences identified in seed composition of oilseed rape 73496 as compared to its conventional counterpart raise no safety and nutritional concerns in the context of the scope of this application. No safety concerns are identified regarding toxicity and allergenicity of the GAT4621 protein as expressed in oilseed rape 73496. No evidence is found that the genetic modification would change the overall allergenicity of oilseed rape 73496. Based on the outcome of the comparative and nutritional assessments, the consumption of oilseed rape 73496 does not represent any nutritional concern, in the context of the scope of this application. The implementation of a post-market monitoring plan is recommended to confirm the predicted consumption data and to verify that the conditions of use are those considered during the pre-market risk assessment. In the case of accidental release of viable oilseed rape 73496 seeds into the environment, oilseed rape 73496 would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of oilseed rape 73496. The GMO Panel concludes that oilseed rape 73496, as described in this application, is as safe as its conventional counterpart and the non-genetically modified oilseed rape reference varieties tested with respect to potential effects on human and animal health and the environment.

Recent and Historical Gene Flow in Cultivars, Landraces, and a Wild Taxon of Cucurbita pepo in Mexico

Gene flow among crops and their wild relatives is an active study area in evolutionary biology and horticulture, because genetic exchange between them may impact their evolutionary trajectories and increase the genetic variation of the cultivated lineages. Mexico is a center of diversity for the genus Cucurbita that includes pumpkins, squash and gourds. Gene flow between domesticated and wild species has been reported as common in Cucurbita; but gene flow among populations of C. pepo ssp. pepo from Mexico and its wild relative has not been studied. We used 2,061 SNPs, derived from tunable genotyping by sequencing (tGBS) to estimate gene flow among 14 Mexican traditional landraces of C. pepo ssp. pepo, also including individuals from five improved cultivars of C. pepo ssp. pepo and C. pepo ssp. ovifera var. ovifera, and individuals of their wild relative C. pepo ssp. fraterna. We found moderate to high levels of genetic diversity, and low to moderate genetic differentiation. In the test of introgression between lineages, we found that all possible arrangements for ancestral and derived sites between the lineages showed similar frequencies; thus, incomplete lineage sorting, but also gene flow, might be taking place in C. pepo. Overall, our results suggest that gene flow between these subspecies and cultigens, incomplete lineage sorting and the retention of ancestral characters shaped the evolutionary trajectory of C. pepo in its area of origin and diversification. In addition, we found evidence of the use of Mexican landraces as genetic material for the improvement of commercial cultivars. The landraces of Mexico are an important source of genetic diversity for C. pepo, which has been preserved both by management practices of small farmers and by the natural gene flow that exists between the different crop fields of the region.

Gene Flow in Phaseolus Beans and Its Role as a Plausible Driver of Ecological Fitness and Expansion of Cultigens

The genus Phaseolus, native to the Americas, is composed of more than eighty wild species, five of which were domesticated in pre-Columbian times. Since the beginning of domestication events in this genus, ample opportunities for gene flow with wild relatives have existed. The present work reviews the extent of gene flow in the genus Phaseolus in primary and secondary areas of domestication with the aim of illustrating how this evolutionary force may have conditioned ecological fitness and the widespread adoption of cultigens. We focus on the biological bases of gene flow in the genus Phaseolus from a spatial and time perspective, the dynamics of wild-weedy-crop complexes in the common bean and the Lima bean, the two most important domesticated species of the genus, and the usefulness of genomic tools to detect inter and intraspecific introgression events. In this review we discuss the reproductive strategies of several Phaseolus species, the factors that may favor outcrossing rates and evidence suggesting that interspecific gene flow may increase ecological fitness of wild populations. We also show that wild-weedy-crop complexes generate genetic diversity over which farmers are able to select and expand their cultigens outside primary areas of domestication. Ultimately, we argue that more studies are needed on the reproductive biology of the genus Phaseolus since for most species breeding systems are largely unknown. We also argue that there is an urgent need to preserve wild-weedy-crop complexes and characterize the genetic diversity generated by them, in particular the genome-wide effects of introgressions and their value for breeding programs. Recent technological advances in genomics, coupled with agronomic characterizations, may make a large contribution.

Changes in Reproductive Traits in Physalis philadelphica; An Unexpected Shift Toward Self-Incompatibility in a Domesticated Annual Fruit Crop

Domestication is an evolutionary process with an impact on plant reproduction. Many domesticated plants are self-compatible (i.e., they lack mechanisms to reject their own pollen), but few domesticated plants are fully or partially self-incompatible. We used the husk tomato, Physalis philadelphica, as a study model to investigate changes in the reproductive strategy of an annual partially self-incompatible plant during the process of domestication. Wild and cultivated populations of this species coexist in close proximity. These different populations present a high level of morphological and genetic variation associated with different degrees of domestication. We hypothesized that artificial selection favors self-compatibility in cultivated plants through changes in their reproductive strategy and some reproductive parameters associated with domestication. To test this hypothesis, we characterized the floral morphology and some reproductive parameters of weedy plants (wild plants), landraces (semi-domesticated plant), and commercial plants (domesticated plants). We conducted an artificial crossing experiment, germinated the seeds, and recorded seedling growth. Commercial plants had the largest flowers and the highest number of ovules. Yet, they did not differ in other reproductive parameters (e.g., herkogamy, size of pollen grains, stigmatic area, and pollen:ovule ratio) from landraces and weedy plants. Physalis philadelphica produced fruits by autonomous autogamy in the artificial crossing experiment. These fruits were the smallest and lightest fruits at all degrees of domestication; however, fruit set of autonomous autogamy was higher in weedy plants. In addition, fruit production was higher when weedy plants donated pollen to commercial plants. Although seeds produced by autonomous autogamy of weedy plants had a low germination percentage, their cotyledons and the embryonic foliage leaves appeared earlier than in landraces and commercial plants. In conclusion, the domestication syndrome in this plant was manifested as increments in flower size and ovule production. Contrary to expectations, there was higher fruit production by autonomous autogamy in weedy plants than in cultivated plants. It seems that artificial selection in P. philadelphica favors self-incompatibility in cultivated plants. Nonetheless, spontaneous self-pollination seems to be advantageous in weedy populations because they produced viable seeds from which cotyledons and the embryonic foliage leaves emerged earlier than in cultivated plants.

Harnessing Crop Wild Diversity for Climate Change Adaptation

Warming and drought are reducing global crop production with a potential to substantially worsen global malnutrition. As with the green revolution in the last century, plant genetics may offer concrete opportunities to increase yield and crop adaptability. However, the rate at which the threat is happening requires powering new strategies in order to meet the global food demand. In this review, we highlight major recent 'big data' developments from both empirical and theoretical genomics that may speed up the identification, conservation, and breeding of exotic and elite crop varieties with the potential to feed humans. We first emphasize the major bottlenecks to capture and utilize novel sources of variation in abiotic stress (i.e., heat and drought) tolerance. We argue that adaptation of crop wild relatives to dry environments could be informative on how plant phenotypes may react to a drier climate because natural selection has already tested more options than humans ever will. Because isolated pockets of cryptic diversity may still persist in remote semi-arid regions, we encourage new habitat-based population-guided collections for genebanks. We continue discussing how to systematically study abiotic stress tolerance in these crop collections of wild and landraces using geo-referencing and extensive environmental data. By uncovering the genes that underlie the tolerance adaptive trait, natural variation has the potential to be introgressed into elite cultivars. However, unlocking adaptive genetic variation hidden in related wild species and early landraces remains a major challenge for complex traits that, as abiotic stress tolerance, are polygenic (i.e., regulated by many low-effect genes). Therefore, we finish prospecting modern analytical approaches that will serve to overcome this issue. Concretely, genomic prediction, machine learning, and multi-trait gene editing, all offer innovative alternatives to speed up more accurate pre- and breeding efforts toward the increase in crop adaptability and yield, while matching future global food demands in the face of increased heat and drought. In order for these 'big data' approaches to succeed, we advocate for a trans-disciplinary approach with open-source data and long-term funding. The recent developments and perspectives discussed throughout this review ultimately aim to contribute to increased crop adaptability and yield in the face of heat waves and drought events.

Bootstrap simulations for evaluating the model estimation of the extent of cross-pollination in maize at the field-scale level

With the recent advent of genetic engineering, numerous genetically modified (GM) crops have been developed, and field planting has been initiated. In open-environment cultivation, the cross-pollination (CP) of GM crops with wild relatives, conventional crops, and organic crops can occur. This exchange of genetic material results in the gene flow phenomenon. Consequently, studies of gene flow among GM crops have primarily focused on the extent of CP between the pollen source plot and the adjacent recipient field. In the present study, Black Pearl Waxy Corn (a variety of purple glutinous maize) was used to simulate a GM-maize pollen source. The pollen recipient was Tainan No. 23 Corn (a variety of white glutinous maize). The CP rate (%) was calculated according to the xenia effect on kernel color. We assessed the suitability of common empirical models of pollen-mediated gene flow (PMGF) for GM maize, and the field border (FB) effect of the model was considered for small-scale farming systems in Asia. Field-scale data were used to construct an optimal model for maize PMGF in the maize-producing areas of Chiayi County, southern Taiwan (R.O.C). Moreover, each model was verified through simulation and by using the 95% percentile bootstrap confidence interval length. According to the results, a model incorporating both the distance from the source and the FB can have optimal fitting and predictive abilities.

Proximity to crop relatives determines some patterns of natural selection in a wild sunflower

Abiotic and biotic heterogeneity result in divergent patterns of natural selection in nature, with important consequences for fundamental evolutionary processes including local adaptation, speciation, and diversification. However, increasing amounts of the global terrestrial surface are homogenized by agriculture (which covers nearly 50% of terrestrial vegetated land surface) and other anthropogenic activities. Agricultural intensification leads to highly simplified biotic communities for many taxa, which may alter natural selection through biotic selective agents. In particular, the presence of crops may alter selection on traits of closely related wild relatives via shared mutualists and antagonists such as pollinators and herbivores. We asked how the presence of crop sunflowers (Helianthus annuus) alters natural selection on reproductive traits of wild sunflowers (Helianthus annuus texanus). Across two years and multiple sites, we planted replicated paired populations of wild H. a. texanus bordering sunflower crop fields versus approximately 2.5 km away. We measured fitness, floral traits, and interactions of the plants with insect pollinators and seed predators. We found limited evidence that proximity to crop sunflowers altered selection on individual traits, as total or direct selection differed by proximity for only three of eleven traits: ray length (a marginally significant effect), Isophrictis (Gelechiidae, moth) attack, and Neolasioptera (Cecidomyiidae, midge) attack. Direct (but not total) selection was significantly more heterogenous far from crop sunflowers relative to near crop sunflowers. Both mutualist pollinators and antagonist seed predators mediated differences in selection in some population-pairs near versus far from crop sunflowers. Here, we demonstrate that agriculture can influence the evolution of wild species via altered selection arising from shared biotic interactions, complementing previously demonstrated evolutionary effects via hybridization.

Investigating the status of transgenic crops in Iran in terms of cultivation, consumption, laws and rights in comparison with the world

Recently, there has been a development in transgenic technologies in many countries to meet nutritional needs of increasing worlds҆ population. However, there are some concerns about possible risks in the field of growing genetically modified (GM) food, such as threats of biodiversity and food allergies making their use a challenge. Therefore, the present study was conducted to investigate the economic effects and political scopes of GM foods in production sector and policies made by different countries in the world and Iran. Moreover, essential (practical and legal) solutions and guidelines were provided for production and consumption of GM foods, which are useful for governmental entities, Iranian politicians, and consumers' rights. The latest situation of transgenic crops in the countries with which Iran has the highest exchange of agricultural products (including Turkey, Pakistan, and the European Union (EU)) was also studied. Although, Iran has been one of leading Asian countries not only in the field of transfer of technical knowledge of genetic engineering, but also in development of the specialized knowledge of biosafety, and despite production of several transgenic plant lines by Iranian researchers, unfortunately no GM crop has obtained release and cultivation license except for GM rice that its growing process was banned after change of government. According to findings of this study, in Iran, growing and production process of GM crops does not follow the global trend owing to scientific and legal infrastructures.

Opportunities to improve China's biodiversity protection laws

Since 1989, China has established a system of powerful laws and regulations aimed to preserve its rich natural flora and fauna. However, this legislative framework still has shortcomings, in terms of sentencing standards across related crimes and the extent of scientific basis for sentences. Here, we review Chinese biodiversity protection laws and some example cases with the goal of suggesting ways to increase law compliance and thus better protect biodiversity. In particular, our suggestions involve regular updates of threat assessments based on scientific evidence including herbaceous plants, fungi and algae; considering ecological differences among the species groups and ensuing ecological damage and financial profit gained; and a differentiation of punishment between organized and individual crimes, with a preference for custodial sentences for the former and monetary fines for the latter, to comply better with international standards and to minimize the incentive to engage in such conduct.

Ongoing ecological and evolutionary consequences by the presence of transgenes in a wild cotton population

After 25 years of genetically modified cotton cultivation in Mexico, gene flow between transgenic individuals and their wild relatives represents an opportunity for analysing the impacts of the presence of novel genes in ecological and evolutionary processes in natural conditions. We show comprehensive empirical evidence on the physiological, metabolic, and ecological effects of transgene introgression in wild cotton, Gossypium hirsutum. We report that the expression of both the cry and cp4-epsps genes in wild cotton under natural conditions altered extrafloral nectar inducibility and thus, its association with different ant species: the dominance of the defensive species Camponotus planatus in Bt plants, the presence of cp4-epsps without defence role of Monomorium ebeninum ants, and of the invasive species Paratrechina longicornis in wild plants without transgenes. Moreover, we found an increase in herbivore damage to cp4-epsps plants. Our results reveal the influence of transgene expression on native ecological interactions. These findings can be useful in the design of risk assessment methodologies for genetically modified organisms and the in situ conservation of G. hirsutum metapopulations.