TY - CHAP
T1 - Incorporation of Trait-Specific Genetic Information into Genomic Prediction Models
AU - Shi, Shaolei
AU - Zhang, Zhe
AU - Li, Bingjie
AU - Zhang, Shengli
AU - Fang, Lingzhao
PY - 2022/4/22
Y1 - 2022/4/22
N2 - Due to the rapid development of high-throughput sequencing technology, we can easily obtain not only the genetic variants at the whole-genome sequence level (e.g., from 1000 Genomes project and 1000 Bull Genomes project), but also a wide range of functional annotations (e.g., enhancers and promoters from ENCODE, FAANG, and FarmGTEx projects) across a wide range of tissues, cell types, developmental stages, and environmental conditions. This huge amount of information leads to a revolution in studying genetics and genomics of complex traits in humans, livestock, and plant species. In this chapter, we focused on and reviewed the genomic prediction methods that incorporate external biological information into genomic prediction, such as sequence ontology, linkage disequilibrium (LD) of SNPs, quantitative trait loci (QTL), and multi-layer omics data (e.g., transcriptome, epigenome, and microbiome).
AB - Due to the rapid development of high-throughput sequencing technology, we can easily obtain not only the genetic variants at the whole-genome sequence level (e.g., from 1000 Genomes project and 1000 Bull Genomes project), but also a wide range of functional annotations (e.g., enhancers and promoters from ENCODE, FAANG, and FarmGTEx projects) across a wide range of tissues, cell types, developmental stages, and environmental conditions. This huge amount of information leads to a revolution in studying genetics and genomics of complex traits in humans, livestock, and plant species. In this chapter, we focused on and reviewed the genomic prediction methods that incorporate external biological information into genomic prediction, such as sequence ontology, linkage disequilibrium (LD) of SNPs, quantitative trait loci (QTL), and multi-layer omics data (e.g., transcriptome, epigenome, and microbiome).
KW - Humans
KW - Linkage Disequilibrium
KW - Cattle
KW - Genome-Wide Association Study
KW - Polymorphism, Single Nucleotide
KW - Male
KW - QTL
KW - Models, Genetic
KW - Omics data
KW - Genomics - methods
KW - Phenotype
KW - Animals
KW - Genomic prediction
KW - Quantitative Trait Loci
KW - Functional annotation
UR - http://www.scopus.com/inward/record.url?scp=85129126013&partnerID=8YFLogxK
U2 - 10.1007/978-1-0716-2205-6_11
DO - 10.1007/978-1-0716-2205-6_11
M3 - Chapter
C2 - 35451781
VL - 2467
T3 - Methods in Molecular Biology
SP - 329
EP - 340
BT - Complex Trait Prediction
ER -