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Since the 1980s, agriculture and plant breeding have changed with the development of molecular marker technology. In recent decades, different types of molecular markers have been used for different purposes: mapping, marker-assisted selection, characterization of genetic resources, etc. These have produced effective genotyping, but the results have been costly and time-consuming due to the small number of markers that could be tested simultaneously. Recent advances in molecular marker technologies such as the development of high-throughput genotyping platforms, genotyping by sequencing, and the release of the genome sequences of major crop plants have opened new possibilities for advancing crop improvement. This Special Issue collects 16 research studies, including the application of molecular markers in 11 crop species, from the generation of linkage maps and diversity studies to the application of marker-assisted selection and genomic prediction.

Research & information: general --- Biology, life sciences --- durum wheat --- landraces --- marker-trait association --- root system architecture --- sugarcane --- parental line --- population structure --- plant breeding --- genetic diversity --- simple sequence repeats (SSR) --- Persea americana --- SMRT sequencing --- simple sequence repeat --- genetic relationship --- flavonoid biosynthesis --- fruit coloration --- marker-assisted selection --- microsatellites --- Rubus --- gene prioritization --- linkage disequilibrium --- tropical maize --- brown rice recovery --- milled rice recovery --- head rice recovery --- milling yield traits --- QTL mapping --- rice (Oryza sativa L.) --- tetraploid potato --- SNP markers --- SLAF-seq technology --- high-density genetic linkage map --- genome wide association study --- GWAS water use --- agronomic traits --- MTAs --- candidate genes --- TKW --- sedimentation volume --- SDS --- YR --- drought stress --- association mapping --- QTL hotspot --- seminal root --- gene pyramiding --- aroma --- QTL --- chromosome --- selection --- introgression line --- maize (Zea mays L.) --- Striga resistance/tolerance --- F2:3 biparental mapping --- Marker-assisted selection --- persimmon --- sex determination --- fruit astringency --- molecular markers --- genomics --- genomic selection --- genomic prediction --- whole genome regression --- grain quality --- near infra-red spectroscopy --- cereal crop --- sorghum --- multi-trait --- Triticum aestivum --- mapping population --- leaf rust --- stem rust --- pathogen races --- disease resistance --- apricot --- MAS --- breeding --- MATH --- PPV resistance --- agarose --- ParPMC --- ParPMC2-del --- high resolution melting --- ISBP markers --- drought --- MQTL --- wheat variability --- crop breeding --- genetic maps --- GWAS --- marker assisted selection --- DNA sequencing --- durum wheat --- landraces --- marker-trait association --- root system architecture --- sugarcane --- parental line --- population structure --- plant breeding --- genetic diversity --- simple sequence repeats (SSR) --- Persea americana --- SMRT sequencing --- simple sequence repeat --- genetic relationship --- flavonoid biosynthesis --- fruit coloration --- marker-assisted selection --- microsatellites --- Rubus --- gene prioritization --- linkage disequilibrium --- tropical maize --- brown rice recovery --- milled rice recovery --- head rice recovery --- milling yield traits --- QTL mapping --- rice (Oryza sativa L.) --- tetraploid potato --- SNP markers --- SLAF-seq technology --- high-density genetic linkage map --- genome wide association study --- GWAS water use --- agronomic traits --- MTAs --- candidate genes --- TKW --- sedimentation volume --- SDS --- YR --- drought stress --- association mapping --- QTL hotspot --- seminal root --- gene pyramiding --- aroma --- QTL --- chromosome --- selection --- introgression line --- maize (Zea mays L.) --- Striga resistance/tolerance --- F2:3 biparental mapping --- Marker-assisted selection --- persimmon --- sex determination --- fruit astringency --- molecular markers --- genomics --- genomic selection --- genomic prediction --- whole genome regression --- grain quality --- near infra-red spectroscopy --- cereal crop --- sorghum --- multi-trait --- Triticum aestivum --- mapping population --- leaf rust --- stem rust --- pathogen races --- disease resistance --- apricot --- MAS --- breeding --- MATH --- PPV resistance --- agarose --- ParPMC --- ParPMC2-del --- high resolution melting --- ISBP markers --- drought --- MQTL --- wheat variability --- crop breeding --- genetic maps --- GWAS --- marker assisted selection --- DNA sequencing

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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