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This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact

CRISPR/Cas9 --- genome edited plants --- biosafety --- agriculture --- policy and legislation

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Neurodegenerative diseases (NDs) are a heterogeneous group of disorders affecting the central nervous system. Despite significant differences in their causes, neuropathological abnormalities, and clinical outcomes, some similarities can be found among them, as for example: 1) frequent aggregation and deposition of misfolded proteins, 2) common molecular mechanisms leading to neurodegeneration, and 3) certain overlap in symptoms and clinical features. To date, there is no cure that could stop or delay the progression of these diseases. The advent of advanced gene therapy techniques such as gene silencing and gene editing opened a new avenue for the development of therapeutic strategies for NDs. The discovery of the RNA interference (RNAi) mechanism, in 1998, by Andrew Fire and Craig Mello allowed an important boost to the gene therapy field, providing a potential therapeutic strategy to treat inherited dominant genetic disorders. The use of small RNA sequences to control the expression of disease-causing genes rapidly implemented in the preclinical studies for different diseases. In the field of NDs, several successful studies using this technology proved its potential as a therapeutic option. However, issues like the type of delivery system (non-viral versus viral) or the potential toxicity of the small RNA molecules, made the translation of gene silencing therapeutics to human application very slow and difficult. Recently, a new hope in the gene therapy field emerged with the development of gene editing techniques like TALENs or CRISPR/Cas9 systems. The opportunity of editing or deleting gene sequences drove the scientific community euphoric, with an enormous increase in the number of published studies using this type of techniques. Recently, the first clinical trial using one of these systems was approved in China. For NDs, gene-editing technology also represents an important therapeutic option, and the first preclinical studies are now being published, showing the potential accomplishment for this technology.

Gene silencing --- Long non-coding RNAs --- RNA interference --- Neurodegenerative diseases --- CRISPR/Cas9 --- Neurodegeneration --- Gene editing --- Antisense oligonucleotides --- Neuroinflammation --- iPS cells

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Apomixis is the consequence of a concerted mechanism that harnesses the sexual machinery and coordinates developmental steps in the ovule to produce an asexual (clonal) seed. Altered sexual developments involve widely characterized functional and anatomical changes in meiosis, gametogenesis, and embryo and endosperm formation. The ovules of apomictic plants skip meiosis and form unreduced female gametophytes whose egg cells develop into a parthenogenetic embryo, and the central cells may or may not fuse to a sperm to develop the seed endosperm. Thus, functional apomixis involves at least three components, apomeiosis, parthenogenesis, and endosperm development, modified from sexual reproduction that must be coordinated at the molecular level to progress through the developmental steps and form a clonal seed. Despite recent progress uncovering specific genes related to apomixis-like phenotypes and the formation of clonal seeds, the molecular basis and regulatorynetwork of apomixis is still unknown. This is a central problem underlying the current limitations of apomixis breeding. This book collates twelve publications addressing different topics around the molecular basis of apomixis, illustrating recent discoveries and advances toward understanding the genetic regulation of the trait, discussing the possible origins of apomixis and the remaining challenges for its commercial deployment in plants.

apomixis --- evolution --- germline --- gene regulation --- sporogenesis --- plant reproduction --- ribosome --- RNA helicase --- sexual development --- stress response --- apomeiosis --- clonal seeds --- endosperm --- heterosis capture --- molecular breeding --- parthenogenesis --- differentially expressed genes --- hybridization --- microarrays --- polyploidy --- Ranunculus --- sexuality --- character segregation --- crop biotechnology --- heterosis --- meiosis --- recombination --- agamospermy --- basal angiosperms (ANA-grade) --- sporocyteless --- polycomb-group proteins --- reproductive systems --- apomixis evolution --- APOSTART --- Poa pratensis --- diplospory --- autonomous endosperm --- genetics --- Taraxacum --- dandelion --- weeping lovegrass --- drought stress --- RNA-seq --- plant breeding --- plant development --- Hieracium piloselloides --- CRISPR/Cas9 --- PHYTOENE DESATURASE (PDS) --- amplicon sequencing --- genome editing --- tissue culture --- haploid progeny --- dicotyledon --- PsASGR-BBML --- pseudogamy --- 5-azacytidine --- abscisic acid --- apospory --- expression profiling --- fluridone --- metabolic homeostasis --- oxidative stress --- sucrose non-fermenting-related protein kinase --- n/a

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This Special Issue on molecular genetics, genomics, and biotechnology in crop plant breeding seeks to encourage the use of the tools currently available. It features nine research papers that address quality traits, grain yield, and mutations by exploring cytoplasmic male sterility, the delicate control of flowering in rice, the removal of anti-nutritional factors, the use and development of new technologies for non-model species marker technology, site-directed mutagenesis and GMO regulation, genomics selection and genome-wide association studies, how to cope with abiotic stress, and an exploration of fruit trees adapted to harsh environments for breeding purposes. A further four papers review the genetics of pre-harvest spouting, readiness for climate-smart crop development, genomic selection in the breeding of cereal crops, and the large numbers of mutants in straw lignin biosynthesis and deposition.

Wx --- transgenic cereals --- GWAS --- anther --- cytoplasmic male sterility --- mutants --- oleic acid --- QTL --- plant breeding --- QTL/genes --- lignin --- maintainer --- Japanese plum --- pre-harvest sprouting --- mutations --- RNA-seq --- fertility restoration --- Rf1 gene --- association mapping --- estimated breeding value --- non-open hull 1(noh1) --- protein --- gene mapping --- electrospray ionisation --- climate change --- genome editing --- fatty acid composition --- phloem metabolites --- ISSR --- gold hull and internode --- genotyping by sequencing --- gibberellin --- cultivar --- GmDof4 --- bioinformatics --- CRISPR/Cas9 site directed mutagenesis --- quality groups --- linkage map --- ddRAD sequencing --- breeding scheme --- mutation breeding --- PPR genes --- genetic structure --- genetic resources --- Pentatricopeptide Repeats --- crops --- amylose content --- genetic value --- seed dormancy --- diversity --- mapping populations --- cytoplasmic male sterile --- genomic prediction --- SNP --- TGW6 --- mass spectrometry --- abscisic acid --- wheat --- lodicule --- genome-wide association scan --- genomic selection --- RNA editing --- CRISPR/Cas9 --- nitrogen --- faba bean --- next generation sequencing --- zt-1 --- grass family --- differentially expressed genes --- rice --- brown midrib --- sunflower --- pedigree --- genotyping-by-sequencing --- “omics” data --- quantitative genetics --- orange lemma --- F1 hybrids --- SSR --- drought --- candidate genes --- Brassica napus --- GmDof11 --- new plant breeding techniques --- mutational breeding --- genetic modification --- cell wall --- monolignol pathway

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Viruses are microscopic agents that exist worldwide and are present in humans, animals, plants, and other living organisms in which they can cause devastating diseases. However, the advances of biotechnology and next-generation sequencing technologies have accelerated novel virus discovery, identification, sequencing, and manipulation, showing that they present unique characteristics that place them as valuable tools for a wide variety of biotechnological applications. Many applications of viruses have been used for agricultural purposes, namely concerning plant breeding and plant protection. Nevertheless, it is interesting to mention that plants have also many advantages to be used in vaccine production, such as the low cost and low risks they entail, showing once more the versatility of the use of viruses in biotechnology. Although it will obviously never be ignored that viruses are responsible for devastating diseases, it is clear that the more they are studied, the more possibilities they offer to us. They are now on the front line of the most revolutionizing techniques in several fields, providing advances that would not be possible without their existence. In this book there are presented studies that demonstrate the work developed using viruses in biotechnology. These studies were brought by experts that focus on the development and applications of many viruses in several fields, such as agriculture, the pharmaceutical industry, and medicine.

Bacteriophage --- Salmonella --- biocontrol --- comparative genomics --- phage diversity --- grapevine --- apple latent spherical virus vector --- virus-induced flowering --- reduced generation time --- breeding of grapevine --- virus elimination --- Newcastle disease virus --- reverse genetics --- vaccines --- infectious diseases --- cancer --- porcine epidemic diarrhea virus --- VLP --- chemokines --- pig --- vaccine --- SARS-CoV-2 --- COVID-19 --- phages --- CRISPR --- viruses --- prevention --- diagnosis --- treatment --- adeno-associated virus (AAV) vector --- jaagsiekte sheep retrovirus (JSRV) --- LTR --- enhancer --- transduction --- viral vaccines --- cancers --- COVID-19 vaccines --- self-replicating RNA vectors --- DNA-based vaccines --- RNA-based vaccines --- plant virus --- viroid --- viral vector --- virus-induced gene silencing (VIGS) --- CRISPR/Cas9 --- genome editing --- carotenoid biosynthesis --- circular RNA --- infectious bursal disease virus --- immunization --- recombinant Lactococcus lactis --- variant strain --- baculovirus --- insect cells --- bacmid --- Tn7 --- genome stability --- protein expression --- chikungunya virus --- VLPs --- bioreactor --- CRISPR/Cas systems --- viral vectors --- gene editing --- plant genome engineering --- viral resistance --- adeno-associated virus --- AAV --- cancer gene therapy --- prophage --- hydrothermal vent --- Hypnocyclicus thermotrophus --- lytic cassette --- Escherichia coli --- heterologous expression --- codon optimization --- codon harmonization --- expression vectors --- aspect ratio --- VNPs --- TMV --- PVX --- CPMV --- geminivirus --- theranostics --- CRISPR-cas9 --- clodronate --- macrophage --- gene therapy --- gene expression --- nanotechnology