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This volume presents recent research achievements concerning the molecular genetic basis of agronomic traits in rice. Rice (Oryza sativa L.) is the most important food crop in the world, being a staple food for more than half of the world’s population. Recent improvements in living standards have increased the worldwide demand for high-yielding and high-quality rice cultivars. To achieve improved agricultural performance in rice, while overcoming the challenges presented by climate change, it is essential to understand the molecular basis of agronomically important traits. Recently developed techniques in molecular biology, especially in genomics and other related omics fields, can reveal the complex molecular mechanisms involved in the control of agronomic traits. As rice was the first crop genome to be sequenced, in 2004, molecular research tools for rice are well-established, and further molecular studies will enable the development of novel rice cultivars with superior agronomic performance.

Research & information: general --- Biology, life sciences --- Technology, engineering, agriculture --- chloroplast RNA splicing and ribosome maturation (CRM) domain --- intron splicing --- chloroplast development --- rice --- rice (Oryza sativa L.), grain size and weight --- Insertion/Deletion (InDel) markers --- multi-gene allele contributions --- genetic variation --- rice germplasm --- disease resistance --- microbe-associated molecular pattern (MAMP) --- Pyricularia oryzae (formerly Magnaporthe oryzae) --- Oryza sativa (rice) --- receptor-like cytoplasmic kinase (RLCK) --- reactive oxygen species (ROS) --- salinity --- osmotic stress --- combined stress --- GABA --- phenolic metabolism --- CIPKs genes --- shoot apical meristem --- transcriptomic analysis --- co-expression network --- tiller --- nitrogen rate --- rice (Oryza sativa L.) --- quantitative trait locus --- grain protein content --- single nucleotide polymorphism --- residual heterozygote --- rice (Oryza sativa) --- specific length amplified fragment sequencing --- Kjeldahl nitrogen determination --- near infrared reflectance spectroscopy --- heterosis --- yield components --- high-throughput sequence --- FW2.2-like gene --- tiller number --- grain yield --- CRISPR/Cas9 --- genome editing --- off-target effect --- heat stress --- transcriptome --- anther --- anthesis --- pyramiding --- bacterial blight --- marker-assisted selection --- foreground selection --- background selection --- japonica rice --- cold stress --- germinability --- high-density linkage map --- QTLs --- seed dormancy --- ABA --- seed germination --- chromosome segment substitution lines --- linkage mapping --- Oryza sativa L. --- chilling stress --- chlorophyll biosynthesis --- chloroplast biogenesis --- epidermal characteristics --- AAA-ATPase --- salicylic acid --- fatty acid --- Magnaporthe oryzae --- leaf senescence --- quantitative trait loci --- transcriptome analysis --- genetic --- epigenetic --- global methylation --- transgenic --- phenotype --- OsNAR2.1 --- dwarfism --- OsCYP96B4 --- metabolomics --- NMR --- qRT-PCR --- bHLH transcription factor --- lamina joint --- leaf angle --- long grain --- brassinosteroid signaling --- blast disease --- partial resistance --- pi21 --- haplotype --- high night temperature --- wet season --- dry season --- n/a

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In recent years, heavy metals have been widely used in agricultural, chemical, domestic, and technological applications, causing environmental and soil contaminations. Heavy metals enter the plant system through soil or via the atmosphere, and can accumulate, affecting physiological processes, plant growth, yield, and human health if heavy metals are stored in edible tissues. Understanding the regulation mechanisms of plant heavy metals accumulation and partitioning is important to improve the safety of the food chain. In this Special Issue book, a total of 19 articles were included; four reviews covering phytoremediation, manganese phytotoxicity in plants, the effect of cadmium on plant development, the genetic characteristics of Cd accumulation, and the research status of genes and QTLs in rice, respectively, as well as fifteen original research articles, mainly regarding the impact of cadmium on plants. Cadmium was therefore the predominant topic of this Special Issue, increasing the attention of the research community on the negative impacts determined by cadmium or cadmium associated with other heavy metals. The articles have highlighted a great genetic variability, suggesting different possibilities for accumulation, translocation and the reduction or control of heavy metal toxicity in plants.

Technology: general issues --- cotton (Gossypium hirsutum L.) --- transcriptome --- Cd stress --- GhHMAD5 --- overexpression --- VIGS (virus induced gene silence) --- cadmium --- glycinebetaine --- photosynthesis --- ultrastructure --- tobacco (Nicotiana tabacum L.) --- Cadmium --- hyperaccumulator --- Viola baoshanensis --- detoxification --- Cd --- PtoABCG36 --- tolerance --- poplar --- accumulation --- efflux --- phytoremediation --- heavy metals --- hyperaccumulation --- plant genotype improvement --- soil management --- cadmium accumulation --- absorption and transport --- QTL location --- mapping population --- rice (Oryza sativa L.) --- selenium --- cadmium stress --- auxin --- root architecture --- phosphate transporter --- Nicotiana tabacum --- oxidative stress --- cell cycle --- cell wall --- germination --- reproduction --- plant growth and development --- antioxidative system --- Brassicaceae family --- mitogen-activated protein kinases --- Ulva compressa --- antioxidant --- metal chelator --- in vivo chlorophyll a florescence --- physiology --- mitogen activated protein kinases --- metal accumulation --- DNA methylation --- ABCC transporters --- HMA2 --- wheat --- metal stress tolerance --- manganese toxicity --- Mn detoxification --- tolerance mechanism --- gene function --- subcellular compartment --- lead --- nicotianamine --- mugineic acid --- heavy metal --- toxic metal --- durum wheat --- Arabidopsis --- small heat shock protein --- OsMSR3 --- copper stress --- reactive oxygen species --- copper and zinc --- expression in bacteria --- metallothioneins --- marine alga --- Brassica campestris L. --- glutathione synthetase --- glutathione S-transferase --- alternative splicing --- Italian ryegrass root --- LmAUX1 --- hormesis --- growth --- chlorophyll a fluorescence --- n/a

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The development of new plant varieties is a long and tedious process involving the generation of large seedling populations for the selection of the best individuals. While the ability of breeders to generate large populations is almost unlimited, the selection of these seedlings is the main factor limiting the generation of new cultivars. Molecular studies for the development of marker-assisted selection (MAS) strategies are particularly useful when the evaluation of the character is expensive, time-consuming, or with long juvenile periods. The papers published in the Special Issue “Plant Genetics and Molecular Breeding” report highly novel results and testable new models for the integrative analysis of genetic (phenotyping and transmission of agronomic characters), physiology (flowering, ripening, organ development), genomic (DNA regions responsible for the different agronomic characters), transcriptomic (gene expression analysis of the characters), proteomic (proteins and enzymes involved in the expression of the characters), metabolomic (secondary metabolites), and epigenetic (DNA methylation and histone modifications) approaches for the development of new MAS strategies. These molecular approaches together with an increasingly accurate phenotyping will facilitate the breeding of new climate-resilient varieties resistant to abiotic and biotic stress, with suitable productivity and quality, to extend the adaptation and viability of the current varieties.

n/a --- GA2ox7 --- cabbage --- OsGPAT3 --- oleic acid --- OsCDPK1 --- nutrient use efficiency --- stem borer --- yellow-green-leaf mutant --- branching --- epigenetics --- NPK fertilizers --- particle bombardment --- stress tolerance --- overexpression --- glycine --- heat-stress --- bulk segregant RNA-seq --- Prunus --- protein-protein interaction --- AdRAP2.3 --- plant architecture --- waterlogging stress --- genes --- Cucumis sativus L. --- Flower color --- resistance --- Tobacco --- gynomonoecy --- drought stress --- Brassica oleracea --- starch biosynthesis --- Overexpression --- WUS --- agronomic traits --- Ghd7 --- the modified MutMap method --- cry2A gene --- light-induced --- gene expression --- breeding --- Heterodera schachtii --- ABA --- Green tissue-specific expression --- subcellular localization --- squamosa promoter binding protein-like --- transcriptome --- FAD2 --- As3+ stress --- metallothionein --- flowering --- bisulfite sequencing --- tomato --- quantitative trait loci --- Promoter --- marker–trait association --- DEGs --- cytoplasmic male sterile --- Rosa rugosa --- MADS transcription factor --- yield --- P. suffruticosa --- CYC2 --- common wild rice --- Actinidia deliciosa --- gene-by-gene interaction --- Aechmea fasciata --- hybrid rice --- soybean --- R2R3-MYB --- bread wheat --- BRANCHED1 (BRC1) --- linoleic acid --- differentially expressed genes --- complex traits --- transgenic chrysanthemum --- D-genome --- Brassica --- candidate gene --- SmJMT --- gene expression pattern --- RNA-Seq --- candidate genes --- leaf shape --- Brassica napus --- recombination-suppressed region --- anthocyanin --- WRKY transcription factor --- Idesia polycarpa var --- single nucleotide polymorphism --- bud abortion --- QTL --- reproductive organ --- transient overexpression --- Elongated Internode (EI) --- sugarcane --- abiotic stress --- Oryza sativa L. --- RrGT2 gene --- Hd1 --- cZR3 --- cytoplasmic male sterility (CMS) --- seed development --- tapetum --- near-isogenic line (NIL) --- phytohormones --- TCP transcription factor --- pollen accumulation --- Anthocyanin --- WRKY --- quantitative trait loci (QTLs) --- salt stress --- floral scent --- sucrose --- Ogura-CMS --- root traits --- endosperm development --- Zea mays L. --- sesame --- Bryum argenteum --- AP2/ERF genes --- transcriptional regulation --- WB1 --- haplotype block --- broccoli --- agronomic efficiency --- durum wheat --- gene pyramiding --- Oryza sativa --- genetics --- flowering time --- Cicer arietinum --- Hs1pro-1 --- endosperm appearance --- phenolic acids --- anther wall --- bromeliad --- genomics --- transgenic --- DgWRKY2 --- Clone --- yield trait --- flower symmetry --- partial factor productivity --- rice --- molecular breeding --- genotyping-by-sequencing --- Chimonanthus praecox --- nectary --- Salvia miltiorrhiza --- pollen development --- regulation --- ZmES22 --- genome-wide association study --- VIGS --- iTRAQ --- genome-wide association study (GWAS) --- ethylene-responsive factor --- starch --- molecular markers --- rice quality --- Chrysanthemum morifolium --- marker-trait association