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This book is open access under a CC BY 4.0 license This open access book brings together the latest genome base prediction models currently being used by statisticians, breeders and data scientists. It provides an accessible way to understand the theory behind each statistical learning tool, the required pre-processing, the basics of model building, how to train statistical learning methods, the basic R scripts needed to implement each statistical learning tool, and the output of each tool. To do so, for each tool the book provides background theory, some elements of the R statistical software for its implementation, the conceptual underpinnings, and at least two illustrative examples with data from real-world genomic selection experiments. Lastly, worked-out examples help readers check their own comprehension. The book will greatly appeal to readers in plant (and animal) breeding, geneticists and statisticians, as it provides in a very accessible way the necessary theory, the appropriate R code, and illustrative examples for a complete understanding of each statistical learning tool. In addition, it weighs the advantages and disadvantages of each tool.

Agricultural science --- Life sciences: general issues --- Botany & plant sciences --- Animal reproduction --- Probability & statistics --- open access --- Statistical learning --- Bayesian regression --- Deep learning --- Non linear regression --- Plant breeding --- Crop management --- multi-trait multi-environments models

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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