Search Results (28)

The domesticated species currently available in the market have been developed through the breeding of wild relatives. Breeding strategies using wild relatives with high genetic diversity are attracting attention as an important approach for addressing climate change and ensuring sustainable food supply. However, studies examining gene expression variation in multiple wild and domesticated species are limited. Therefore, we aimed to investigate the changes in gene expression associated with domestication. We performed a meta-analysis of public gene expression data of domesticated species of rice, tomato, and soybean and their presumed ancestral species using 21 pairs for rice, 36 pairs for tomato, and 56 pairs for soybean. In wild relatives, the expression of genes involved in osmotic, drought, and wound stress tolerance was upregulated, with 18 genes included in the top 5% of DW scores. In domesticated species, upregulated expression was observed in genes related to auxin and those involved in the efflux of heavy metals and harmful substances, with 36 genes included in the top 5% of DW scores. These findings provide insights into how domestication influences changes in crop traits. Thus, our findings may contribute to rapid breeding and the development of new varieties capable of growing in harsh natural environments. Hence, a new cultivation method called “de novo domestication” has been proposed, which combines the genetic diversity of currently unused wild relatives and wild relatives with genome editing technologies that enable rapid breeding. Full article

The origin and evolution of genes are central themes in evolutionary biology and genomics, shedding light on how molecular innovations shape biological complexity and adaptation. This review explores the principal mechanisms underlying gene emergence in eukaryotes, including gene duplication, de novo gene birth, horizontal gene transfer, viral gene domestication, and exon shuffling. We examine the population dynamics that govern the fixation of new genes, their functional integration, and the selective forces acting upon them—from purifying selection to adaptive innovation. Examples such as NOTCH2NL and SRGAP2C, which originated through recent segmental duplications followed by neofunctionalization, illustrate how duplicate-derived de novo genes can play a key role in human brain development. In addition, we highlight the emerging relevance of nuclear architecture in determining the evolutionary fate of new genes, offering a spatial dimension to gene innovation. We also discuss methodological approaches for detecting new genes and inferring selection, and finally, we highlight the emerging role of the human pangenome in revealing hidden gene diversity and its implications for evolutionary and biomedical research. Understanding gene innovation not only enhances our grasp of evolutionary processes but also informs clinical studies on disease susceptibility and human uniqueness. Full article

Bacterial antibiotic resistance represents a major healthcare problem. In 2019, 4.95 million deaths were associated with antibiotic resistance, and it is estimated that, by 2050, up to 3.8% of the global gross domestic product could be lost due to this problem. Methicillin-resistant Staphylococcus aureus is one of the leading sources of hospital-acquired infections associated with increased mortality, length of hospital stay, and higher cost of treatment. Here, we describe the de novo synthesis of a library of 22 triazeneindole derivatives with high activity against a wide panel of multidrug-resistant MRSA clinical isolates. Leading compound BX-SI043 (ethyl 6-fluoro-3-[pyrrolidin-1-yl-azo]-1H-indole-2-carboxylate) showed high activity (minimal inhibitory concentration range, 0.125–0.5 mg/L) against 41 multidrug-resistant MRSA strains, as well as relatively low in vitro cytotoxicity (selectivity index, 76) and in vivo acute toxicity (maximum tolerated dose, 600 mg/kg), via intragastric administration in rats. These data suggest that BX-SI043 is a promising drug candidate for the development a novel MRSA treatment. Full article

Solanum bulbocastanum is a wild diploid tuber-bearing plant. We here demonstrate transgene-free genome editing of S. bulbocastanum protoplasts and regeneration of gene-edited plants. We use ribonucleoproteins, consisting of Cas9 and sgRNA, assembled in vitro, to target a gene belonging to the nitrate and peptide transporter family. Four different sgRNAs were designed and we observed efficiency in gene-editing in the protoplast pool between 8.5% and 12.4%. Twenty-one plants were re-generated from microcalli developed from individual protoplasts. In three of the plants we found that the target gene had been edited. Two of the edited plants had deletion mutations introduced into both alleles, whereas one only had a mutation in one of the alleles. Our work demonstrates that protocols for the transformation of Solanum tuberosum can be optimized to be applied to a wild Solanum species. Full article

The worldwide agricultural system confronts a significant challenge represented by the increasing demand for food in the face of a growing global population. This challenge is exacerbated by a reduction in cultivable land and the adverse effects of climate change on crop yield quantity and quality. Breeders actively embrace cutting-edge omics technologies to pursue resilient genotypes in response to these pressing issues. In this global context, new breeding techniques (NBTs) are emerging as the future of agriculture, offering a solution to introduce resilient crops that can ensure food security, particularly against challenging climate events. Indeed, the search for domestication genes as well as the genetic modification of these loci in wild species using genome editing tools are crucial steps in carrying out de novo domestication of wild plants without compromising their genetic background. Current knowledge allows us to take different paths from those taken by early Neolithic farmers, where crop domestication has opposed natural selection. In this process traits and alleles negatively correlated with high resource environment performance are probably eradicated through artificial selection, while others may have been lost randomly due to domestication and genetic bottlenecks. Thus, domestication led to highly productive plants with little genetic diversity, owing to the loss of valuable alleles that had evolved to tolerate biotic and abiotic stresses. Recent technological advances have increased the feasibility of de novo domestication of wild plants as a promising approach for crafting optimal crops while ensuring food security and using a more sustainable, low-input agriculture. Here, we explore what crucial domestication genes are, coupled with the advancement of technologies enabling the precise manipulation of target sequences, pointing out de novo domestication as a promising application for future crop development. Full article

Crop breeding is an important global strategy to meet sustainable food demand. CRISPR/Cas is a most promising gene-editing technology for rapid and precise generation of novel germplasm and promoting the development of a series of new breeding techniques, which will certainly lead to the transformation of agricultural innovation. In this review, we summarize recent advances of CRISPR/Cas technology in gene function analyses and the generation of new germplasms with increased yield, improved product quality, and enhanced resistance to biotic and abiotic stress. We highlight their applications and breakthroughs in agriculture, including crop de novo domestication, decoupling the gene pleiotropy tradeoff, crop hybrid seed conventional production, hybrid rice asexual reproduction, and double haploid breeding; the continuous development and application of these technologies will undoubtedly usher in a new era for crop breeding. Moreover, the challenges and development of CRISPR/Cas technology in crops are also discussed. Full article

De novo domestication is a novel trend in plant genetics, where traits of wild or semi-wild species are changed by the use of modern precision breeding techniques so that they conform to modern cultivation. Out of more than 300,000 wild plant species, only a few were fully domesticated by humans in prehistory. Moreover, out of these few domesticated species, less than 10 species dominate world agricultural production by more than 80% today. Much of this limited diversity of crop exploitation by modern humans was defined early in prehistory at the emergence of sedentary agro-pastoral cultures that limited the number of crops evolving a favorable domestication syndrome. However, modern plant genetics have revealed the roadmaps of genetic changes that led to these domestication traits. Based on such observations, plant scientists are now taking steps towards using modern breeding technologies to explore the potential of de novo domestication of plant species that were neglected in the past. We suggest here that in this process of de novo domestication, the study of Late Paleolithic/Late Archaic and Early Neolithic/Early Formative exploration of wild plants and identification of neglected species can help identify the barriers towards domestication. Modern breeding technologies may then assist us to break these barriers in order to perform de novo domestication to increase the crop species diversity of modern agriculture. Full article

For higher sustainability in biomass production the use of new perennial species can lead to sustainable progress in the energy production and manufacturing industry. During the last decades, two different species of Silphium were discussed for biomass production. However, some questions regarding their cultivation and different uses are still to be answered. In this study, two accessions of Silphium perfoliatum L. and Silphium integrifolium Michx. were investigated during the year of establishment, and the first generative year for the phenotypic characteristics and suitability for cultivation, under Central European field conditions. Intra- and interspecific comparisons were made with special attention to their growth kinetics. While cup plant (S. perfoliatum) is well known as a potential biomass crop in Europe, silflower (S. integrifolium) is still unknown. In intraspecific comparison, S. integrifolium shows a more uniform development than S perfoliatum. In parallel, the development of S. perfoliatum accessions is temporally shifted, so that the S. perfoliatum accessions differ in the length of their phases of generative growth and onset of senescence in comparison to S. integrifolium. To make these results applicable, an improvement proposal was made to the existing BBCH scale for S. perfoliatum. In addition, an adaptation was conducted on S. integrifolium. Full article

The narrow genomic diversity of modern cultivars is a major bottleneck for enhancing the crop’s salinity stress tolerance. The close relatives of modern cultivated plants, crop wild relatives (CWRs), can be a promising and sustainable resource to broaden the diversity of crops. Advances in transcriptomic technologies have revealed the untapped genetic diversity of CWRs that represents a practical gene pool for improving the plant’s adaptability to salt stress. Thus, the present study emphasizes the transcriptomics of CWRs for salinity stress tolerance. In this review, the impacts of salt stress on the plant’s physiological processes and development are overviewed, and the transcription factors (TFs) regulation of salinity stress tolerance is investigated. In addition to the molecular regulation, a brief discussion on the phytomorphological adaptation of plants under saline environments is provided. The study further highlights the availability and use of transcriptomic resources of CWR and their contribution to pangenome construction. Moreover, the utilization of CWRs’ genetic resources in the molecular breeding of crops for salinity stress tolerance is explored. Several studies have shown that cytoplasmic components such as calcium and kinases, and ion transporter genes such as Salt Overly Sensitive 1 (SOS1) and High-affinity Potassium Transporters (HKTs) are involved in the signaling of salt stress, and in mediating the distribution of excess Na⁺ ions within the plant cells. Recent comparative analyses of transcriptomic profiling through RNA sequencing (RNA-Seq) between the crops and their wild relatives have unraveled several TFs, stress-responsive genes, and regulatory proteins for generating salinity stress tolerance. This review specifies that the use of CWRs transcriptomics in combination with modern breeding experimental approaches such as genomic editing, de novo domestication, and speed breeding can accelerate the CWRs utilization in the breeding programs for enhancing the crop’s adaptability to saline conditions. The transcriptomic approaches optimize the crop genomes with the accumulation of favorable alleles that will be indispensable for designing salt-resilient crops. Full article

Kiwifruit (Actinidia) has been recently domesticated as a horticultural crop with remarkably economic and nutritional value. In this study, by combining sequence datasets from Oxford Nanopore long-reads and Illumina short-reads, we de novo assembled two mitogenomes of Actinidia latifolia and A. valvata, respectively. The results indicated that the A. latifolia mitogenome has a single, circular, 825,163 bp molecule while the A. valvata mitogenome possesses two distinct circular molecules, 781,709 and 301,558 bp, respectively. We characterized the genome structure, repeated sequences, DNA transfers, and dN/dS selections. The phylogenetic analyses showed that A. valvata and A. arguta, or A. latifolia and A. eriantha, were clustered together, respectively. This study provides valuable sequence resources for evolutionary study and molecular breeding in kiwifruit. Full article

The domestication syndrome is defined as a collection of domestication-related traits that have undergone permanent genetic changes during the domestication of cereals. Australian wild rice populations have not been exposed to gene flow from domesticated rice populations. A high level of natural variation of the sequences at domestication loci (e.g., seed shattering, awn development, and grain size) was found in Australian AA genome wild rice from the primary gene pool of rice. This natural variation is much higher than that found in Asian cultivated rice and wild Asian rice populations. The Australian Oryza meridionalis populations exhibit a high level of homozygous polymorphisms relative to domesticated rice, inferring the fixation of distinct wild and domesticated alleles. Alleles of the seed shattering genes (SH4/SHA1 and OsSh1/SH1) present in the shattering-prone O. meridionalis populations are likely to be functional, while the dysfunctional alleles of these seed shattering genes are found in domesticated rice. This confirms that unlike Asian wild rice populations, Australian wild rice populations have remained genetically isolated from domesticated rice, retaining pre-domestication alleles in their wild populations that uniquely allow the impact of domestication on the rice genome to be characterized. This study also provides key information about the domestication loci in Australian wild rice populations that will be valuable in the utilization of these genetic resources in crop improvement and de novo domestication. Full article

Soybean (Glycine max) is an important oil crop, but the regulatory mechanisms underlying seed oil accumulation remain unclear. We identified a member of the GmWRI1s transcription factor family, GmWRI1c, that is involved in regulating soybean oil content and nodulation. Overexpression of GmWRI1c in soybean hairy roots increased the expression of genes involved in glycolysis and de novo lipogenesis, the proportion of palmitic acid (16:0), and the number of root nodules. The effect of GmWRI1c in increasing the number of root nodules via regulating the proportion of palmitic acid was confirmed in a recombinant inbred line (RIL) population. GmWRI1c shows abundant sequence diversity and has likely undergone artificial selection during domestication. An association analysis revealed a correlation between seed oil content and five linked natural variations (Hap1/Hap2) in the GmWRI1c promoter region. Natural variations in the GmWRI1c promoter were strongly associated with the GmWRI1c transcript level, with higher GmWRI1c transcript levels in lines carrying GmWRI1c^Hap1 than in those carrying GmWRI1c^Hap2. The effects of GmWRI1c alleles on seed oil content were confirmed in natural and RIL populations. We identified a favourable GmWRI1c allele that can be used to breed new varieties with increased seed oil content and nodulation. Full article

Maize will continue to expand and diversify as an industrial resource and a feed and fuel crop in the near future. The United Nations estimate that in 2050 the global population will reach 9.7 billion people. In this context, food security is increasingly being discussed. Additionally, another threat to food security is global warming. It is predicted that both the quantity and the quality of crops will be seriously affected by climate change in the near future. Scientists and breeders need to speed up the process of creating new maize cultivars that are resistant to climate stress without diminishing yield or quality. The present paper provides a brief overview of some of the most important genomics tools that can be used to develop high-performance and well-adapted hybrids of maize and also emphasizes the contribution of bioinformatics to an advanced maize breeding. Genomics tools are essential for a precise, fast, and efficient breeding of crops especially in the context of climate challenges. Maize breeders are able now to develop new cultivars with better traits more easily as a result of the new genomic approaches, either by aiding the selection process or by increasing the available diversity through precision breeding procedures. Furthermore, the use of genomic tools may in the future represent a way to accelerate the processes of de novo domestication of the species. Full article

Dirofilaria immitis is a zoonotic parasitic nematode that infects domestic and wild canids, among its vertebrate hosts. The genetic analysis of D. immitis nowadays transcends the need for genetic taxonomy of nematodes, such as the study of resistance to macrocyclic lactone. We expanded the use of long-read nanopore-based sequencing technology on nematodes by performing genomic de novo assembly of a D. immitis specimen retrieved from a canine cardiopulmonary dirofilariasis case using the ONT MinION platform, followed by the study of macrocyclic lactone resistance. The assembled genome of D. immitis consists of 110 contigs with an N50 of 3687191. The genome size is 87899012 and contains a total of 9741 proteins; 6 ribosomal RNAs, with three belonging to the small subunit (18S) and three to the large subunit (28S); and 73 tRNAs. Subsequent analysis of six loci previously characterized as being associated to macrocyclic lactone resistance selection pressure showed that four have a genotype associated with either some loss of efficacy or the resistance phenotype. Considering the zoonotic potential of D. immitis, the identification of a resistant parasite alerts for the overuse of macrocyclic lactone in the region, which poses a potential risk to both veterinary and human public health. Full article

Legumes are one of the most economically important and biodiverse families in plants recognised as the basis to develop functional foods. Among these, the Vigna genus stands out as a good representative because of its relatively recent African origin as well as its outstanding potential. Africa is a great biodiversity centre in which a great number of species are spread, but only three of them, Vigna unguiculata, Vigna subterranea and Vigna vexillata, were successfully domesticated. This review aims at analysing and valorising these species by considering the perspective of human activity and what effects it exerts. For each species, we revised the origin history and gave a focus on where, when and how many times domestication occurred. We provided a brief summary of bioactive compounds naturally occurring in these species that are fundamental for human wellbeing. The great number of wild lineages is a key point to improve landraces since the domestication process caused a loss of gene diversity. Their genomes hide a precious gene pool yet mostly unexplored, and genes lost during human activity can be recovered from the wild lineages and reintroduced in cultivated forms through modern technologies. Finally, we describe how all this information is game-changing to the design of future crops by domesticating de novo. Full article