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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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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 --- 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

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Rice feeds more than half of the world population. Its small genome size and ease in transformation have made rice the model crop in plant physiology and genetics. Molecular as well as Mendelian, forward as well as reverse genetics collaborate with each other to expand rice genetics. The wild relatives of rice belonging to the genus Oryza are distributed in Asia, Africa, Latin America and Oceania. They are good sources for the study of domestication and adaptation. Rice was the first crop to have its entire genome sequenced. With the help of the reference genome of Nipponbare and the advent of the next generation sequencer, the study of the rice genome has been accelerated. The mining of DNA polymorphism has permitted map-based cloning, QTL (quantitative trait loci) analysis, and the production of many kinds of experimental lines, such as recombinant inbred lines, backcross inbred lines, and chromosomal segment substitution lines. Inter- and intraspecific hybridization among Oryza species has opened the door to various levels of reproductive barriers ranging from prezygotic to postzygotic. This Special Issue contains eleven papers on genetic studies of rice and its relatives utilizing the rich genetic resources and/or rich genome information described above.

Research & information: general --- Biology, life sciences --- African rice --- climate change --- genomic resources --- genetic potential --- genome sequencing --- domestication --- transcriptome and chloroplast --- anther length --- cell elongation --- genetic architecture --- outcrossing --- perennial species --- rice --- reproductive barrier --- segregation distortion --- abortion --- wild rice --- O. meridionalis --- O. sativa --- gene duplication --- Oryza sativa --- hybrid weakness --- cell death --- reactive oxygen species --- leaf yellowing --- SPAD --- hypersensitive response --- semidawarf gene --- d60 --- sd1 --- yield component --- phenotyping --- growth --- Seed shattering --- O. barthii --- HS1 --- haplotype --- rice (Oryza sativa) --- evolutionary relationships --- chloroplast genome --- nuclear genome --- phylogeny --- rice (Oryza sativa L.) --- brown planthopper --- near-isogenic lines --- pyramided lines --- resistance --- virulence --- flowering time --- photoperiod sensitivity --- allelic variation --- fine-tuning --- Oryza --- speciation --- divergence --- life history --- phylogenetic relation --- Australian continent --- abiotic stress --- salinity --- whole genome re-sequencing --- African rice --- climate change --- genomic resources --- genetic potential --- genome sequencing --- domestication --- transcriptome and chloroplast --- anther length --- cell elongation --- genetic architecture --- outcrossing --- perennial species --- rice --- reproductive barrier --- segregation distortion --- abortion --- wild rice --- O. meridionalis --- O. sativa --- gene duplication --- Oryza sativa --- hybrid weakness --- cell death --- reactive oxygen species --- leaf yellowing --- SPAD --- hypersensitive response --- semidawarf gene --- d60 --- sd1 --- yield component --- phenotyping --- growth --- Seed shattering --- O. barthii --- HS1 --- haplotype --- rice (Oryza sativa) --- evolutionary relationships --- chloroplast genome --- nuclear genome --- phylogeny --- rice (Oryza sativa L.) --- brown planthopper --- near-isogenic lines --- pyramided lines --- resistance --- virulence --- flowering time --- photoperiod sensitivity --- allelic variation --- fine-tuning --- Oryza --- speciation --- divergence --- life history --- phylogenetic relation --- Australian continent --- abiotic stress --- salinity --- whole genome re-sequencing

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To meet the global food demand of an increasing population, food production has to be increased by 60% by 2050. The main production constraints, such as climate change, biotic stresses, abiotic stresses, soil nutrition deficiency problems, problematic soils, etc., have to be addressed on an urgent basis. More than 50% of human calories are from three major cereals: rice, wheat, and maize. The harnessing of genetic diversity by novel allele mining assisted by recent advances in biotechnological and bioinformatics tools will enhance the utilization of the hidden treasures in the gene bank. Technological advances in plant breeding will provide some solutions for the biofortification, stress resistance, yield potential, and quality improvement in staple crops. The elucidation of the genetic, physiological, and molecular basis of useful traits and the improvement of the improved donors containing multiple traits are key activities for variety development. High-throughput genotyping systems assisted by bioinformatics and data science provide efficient and easy tools for geneticists and breeders. Recently, new breeding techniques applied in some food crops have become game-changers in the global food crop market. With this background, we invited 18 eminent researchers working on food crops from across the world to contribute their high-quality original research manuscripts. The research studies covered modern food crop genetics and breeding.

Research & information: general --- Biology, life sciences --- Technology, engineering, agriculture --- dry direct-seeded rice --- early vigor --- QTL --- candidate gene --- phenotyping --- EMS --- MutMap --- mutagenesis --- CLE7 --- tropical maize --- fasciation --- mapping --- radish --- microspore culture --- regeneration rate --- outcrossing --- two-way pseudo-testcross model --- Oryza sativa L. --- PPDK --- flo4-5 --- floury endosperm --- rice --- allelopathy --- yield --- HYV --- Tongil --- indica --- japonica --- SNP --- molecular breeding --- wheat quality --- wheat milling --- wheat hardness --- puroindolines --- water absorption capacity --- crop genetics --- Solanum tuberosum --- abiotic stress --- phenylpropanoids --- essential amino acid --- transcriptome --- small RNA --- comparative genomics --- nutrition --- days to heading --- Hd1 --- Ghd7 --- Hd16 --- chromosome segment substitution lines (CSSLs) --- quantitative trait locus (QTL) --- marker-assisted selection (MAS) --- cold tolerance (CT) --- gene editing --- genetically modified --- genetically modified organism (GMO) --- crop breeding --- ribonucleoprotein complex (RNP) --- genetic screening --- landraces --- genetic diversity --- population structure --- West Africa --- maize improvement --- DArTseq markers --- co-expression network --- drought-tolerant-yield --- reproductive-stage drought --- qDTYs --- transcriptomics --- watermelon --- pentatricopeptide-repeat (PPR) gene family --- comprehensive analysis --- expression profiling --- flesh color --- canola --- Brassica napus --- genetics --- gene technology --- genomics --- disease resistance --- CSSLs --- drought stress --- ‘KDML105’ rice --- low-temperature germinability --- interspecific cross --- interaction --- peanut --- core collection --- genome-wide association study --- linkage disequilibrium --- dry direct-seeded rice --- early vigor --- QTL --- candidate gene --- phenotyping --- EMS --- MutMap --- mutagenesis --- CLE7 --- tropical maize --- fasciation --- mapping --- radish --- microspore culture --- regeneration rate --- outcrossing --- two-way pseudo-testcross model --- Oryza sativa L. --- PPDK --- flo4-5 --- floury endosperm --- rice --- allelopathy --- yield --- HYV --- Tongil --- indica --- japonica --- SNP --- molecular breeding --- wheat quality --- wheat milling --- wheat hardness --- puroindolines --- water absorption capacity --- crop genetics --- Solanum tuberosum --- abiotic stress --- phenylpropanoids --- essential amino acid --- transcriptome --- small RNA --- comparative genomics --- nutrition --- days to heading --- Hd1 --- Ghd7 --- Hd16 --- chromosome segment substitution lines (CSSLs) --- quantitative trait locus (QTL) --- marker-assisted selection (MAS) --- cold tolerance (CT) --- gene editing --- genetically modified --- genetically modified organism (GMO) --- crop breeding --- ribonucleoprotein complex (RNP) --- genetic screening --- landraces --- genetic diversity --- population structure --- West Africa --- maize improvement --- DArTseq markers --- co-expression network --- drought-tolerant-yield --- reproductive-stage drought --- qDTYs --- transcriptomics --- watermelon --- pentatricopeptide-repeat (PPR) gene family --- comprehensive analysis --- expression profiling --- flesh color --- canola --- Brassica napus --- genetics --- gene technology --- genomics --- disease resistance --- CSSLs --- drought stress --- ‘KDML105’ rice --- low-temperature germinability --- interspecific cross --- interaction --- peanut --- core collection --- genome-wide association study --- linkage disequilibrium

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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 --- 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