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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

Science: general issues --- Pharmacology --- liquid biopsy --- precision oncology --- ctDNA (circulating tumor DNA) --- Circulating molecular marker --- personalized medicine

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The papers included in this Special Issue address a variety of important aspects of Genetics, Genomics and Biotechnology of Plant Cytoplasmic Organelles, including new advances in the sequencing of both mitochondria and chloroplasts’ genomes using Next-Generation Sequencing technology in plant species and algae including important crop and tree species, in vitro culture protocol, and identification of a core module of genes involved in plastid development. In particular, the published studies focus on the description of adaptive evolution, elucidate mitochondrial mRNA processing, highlight the effect of domestication process on plastome variability and report the development of molecular markers. A meta-analysis of recently published genome-wide expression studies allowed the identification of novel nuclear genes, involved in the complex and still unrevealed mechanisms at the basis of communication between chloroplast and nucleus (retrograde signalling) during plastid development (biogenic control). Finally, an optimized regeneration protocol useful in plastid transformation of recalcitrant species, such as sugarcane, has been reported.

Research & information: general --- mitochondrial genome --- buckwheat --- plastid genome --- genetic diversity --- long reads --- targeted assembly --- genome assembly --- Fagus --- Fagaceae --- Fagales --- molecular marker --- mitochondrial marker --- taxon assignment --- CAPS marker --- SNP --- next-generation sequencing --- Solanum --- Italian landraces --- plastome --- molecular markers --- phylogenetic analysis --- plastid transformation --- sugarcane --- unfurled leaves --- streptomycin --- heteroplasmy --- mesophyll and bundle sheath cells --- plastids --- photomorphogenesis --- retrograde control --- biogenic signals --- lincomycin --- norflurazon --- pap7-1 mutant --- mitochondria --- RNA processing --- algal evolution --- circular RNA --- polycytidylation --- PacBio Iso-Seq --- Capparaceae --- chloroplast genome --- Cadaba --- Maerua --- phylogenetic relationships

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The papers included in this Special Issue address a variety of important aspects of Genetics, Genomics and Biotechnology of Plant Cytoplasmic Organelles, including new advances in the sequencing of both mitochondria and chloroplasts’ genomes using Next-Generation Sequencing technology in plant species and algae including important crop and tree species, in vitro culture protocol, and identification of a core module of genes involved in plastid development. In particular, the published studies focus on the description of adaptive evolution, elucidate mitochondrial mRNA processing, highlight the effect of domestication process on plastome variability and report the development of molecular markers. A meta-analysis of recently published genome-wide expression studies allowed the identification of novel nuclear genes, involved in the complex and still unrevealed mechanisms at the basis of communication between chloroplast and nucleus (retrograde signalling) during plastid development (biogenic control). Finally, an optimized regeneration protocol useful in plastid transformation of recalcitrant species, such as sugarcane, has been reported.

mitochondrial genome --- buckwheat --- plastid genome --- genetic diversity --- long reads --- targeted assembly --- genome assembly --- Fagus --- Fagaceae --- Fagales --- molecular marker --- mitochondrial marker --- taxon assignment --- CAPS marker --- SNP --- next-generation sequencing --- Solanum --- Italian landraces --- plastome --- molecular markers --- phylogenetic analysis --- plastid transformation --- sugarcane --- unfurled leaves --- streptomycin --- heteroplasmy --- mesophyll and bundle sheath cells --- plastids --- photomorphogenesis --- retrograde control --- biogenic signals --- lincomycin --- norflurazon --- pap7-1 mutant --- mitochondria --- RNA processing --- algal evolution --- circular RNA --- polycytidylation --- PacBio Iso-Seq --- Capparaceae --- chloroplast genome --- Cadaba --- Maerua --- phylogenetic relationships

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The exploitation of biodiversity is essential to select resilient genotypes for sustainable cropping systems as one of the main challenges for plant breeding. Mapping traits of agronomic interest in specific genomic regions appears as another pivotal effort for the future development of novel cultivars. For this purpose, there is evidence that MAGIC and other exotic populations will play a major role in the coming years in allowing for impressive gains in plant breeding for developing new generations of improved cultivars. This Special Issue focused on the application of advanced technologies devoted to crop improvement and exploit the available biodiversity in crops. In detail, next-generation sequencing (NGS) technologies supported the development of high-density genotyping arrays for different plants included in this issue.

Research & information: general --- natural variation --- maize --- nucleotide diversity --- domestication selection --- ZmPGP1 gene --- Ipomoea batatas --- genetic diversity --- SSR markers --- qualitative traits --- pure lines --- F1 hybrids --- microsatellite markers --- marker-assisted breeding --- crop improvement --- varieties --- Fragaria --- Rubus --- microsatellites --- transferability --- polymorphism --- introns --- exons --- flavonoid biosynthesis pathway --- transcription factor genes --- chitinase --- multiple population --- linkage mapping --- JLAM --- QTL --- validation --- genomic prediction --- maize lethal necrosis --- herbaceous peony --- molecular marker --- next-generation sequencing --- pedigree --- Vicia faba L., genetic diversity --- in situ conservation --- Olea europaea L. --- olive --- cpSSR --- nuSSR --- population structure --- Mediterranean Region --- GWAS --- drought --- barley --- spikelet development --- candidate gene --- linkage map --- RAD --- Solanum melongena --- n/a

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The way plants grow and develop organs significantly impacts the overall performance and yield of crop plants. The basic knowledge now available in plant development has the potential to help breeders in generating plants with defined architectural features to improve productivity. Plant translational research effort has steadily increased over the last decade due to the huge increase in the availability of crop genomic resources and Arabidopsis-based sequence annotation systems. However, a consistent gap between fundamental and applied science has yet to be filled. One critical point often brought up is the unreadiness of developmental biologists on one side to foresee agricultural applications for their discoveries, and of the breeders to exploit gene function studies to apply to candidate gene approaches when advantageous on the other. In this book, both developmental biologists and breeders make a special effort to reconcile research on the basic principles of plant development and organogenesis with its applications to crop production and genetic improvement. Fundamental and applied science contributions intertwine and chase each other, giving the reader different but complementary perspectives from only apparently distant corners of the same world.

HD-Zip transcription factors --- Plant in vitro cultures --- plant breeding --- recalcitrant species --- CLV --- wounding --- semi-dwarf --- photoreceptors --- Arabidopsis thaliana --- root development --- morphogenesis --- embryogenesis --- cytokinin --- auxin conjugation --- molecular marker --- Development --- boundaries --- translational research --- proline biosynthesis --- Brassicaceae --- meristem formation --- phytohormones --- stem cells --- meristem --- cytoskeleton --- hydrogen peroxide --- ligule --- genetic improvement --- tree phase change --- Rht18 --- hairy roots --- WUS --- GRETCHEN HAGEN 3 (GH3) IAA-amido synthase group II --- photoperiod --- linkage map --- SAM --- ground tissue --- signaling --- differentiation --- protoxylem --- ambient temperature --- gibberellins --- molecular regulation --- proximodistal patterning --- wheat-rye hybrids --- RolD --- somatic cell selection --- flowering time --- plant development and organogenesis --- grass --- root --- wheat --- crop productivity --- genetic transformation --- regulatory networks --- light environment --- rol genes --- root plasticity --- morphogenic --- stem apical meristem --- auxin --- shoot meristem --- Arabidopsis --- organogenesis --- transformation --- Vasculature --- Organogenesis --- radial patterning --- plant development --- reduced height --- root apical meristem --- Asteraceae --- vernalization --- KNOX transcription factors --- locule --- plant cell and tissue culture --- Agrobacterium rhizogenes --- genes of reproductive isolation --- cell wall --- lateral root cap --- CLE --- auxin minimum --- age