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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