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Genetic Bases of Complex Traits: From Quantitative Trait Loci to Prediction

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Genomic Prediction of Complex Traits

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2467))

Abstract

Conceived as a general introduction to the book, this chapter is a reminder of the core concepts of genetic mapping and molecular marker-based prediction. It provides an overview of the principles and the evolution of methods for mapping the variation of complex traits, and methods for QTL-based prediction of human disease risk and animal and plant breeding value. The principles of linkage-based and linkage disequilibrium–based QTL mapping methods are described in the context of the simplest, single-marker, methods. Methodological evolutions are analysed in relation with their ability to account for the complexity of the genotype–phenotype relations. Main characteristics of the genetic architecture of complex traits, drawn from QTL mapping works using large populations of unrelated individuals, are presented. Methods combining marker–QTL association data into polygenic risk score that captures part of an individual’s susceptibility to complex diseases are reviewed. Principles of best linear mixed model-based prediction of breeding value in animal- and plant-breeding programs using phenotypic and pedigree data, are summarized and methods for moving from BLUP to marker–QTL BLUP are presented. Factors influencing the additional genetic progress achieved by using molecular data and rules for their optimization are discussed.

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Abbreviations

AUC:

Area under the receiver-operating characteristic (ROC) curves

BLUE:

Best linear unbiased estimate

BLUP:

Best linear unbiased prediction

BV:

Breeding value

CIM:

Composite interval mapping

EM:

Expectation maximization

G × E:

Genotype by environment

GWAS :

Genome-wide association study

IBD:

Identity by descent

IM:

Interval mapping

Lasso:

Least absolute shrinkage and selection operator

LD:

Linkage disequilibrium

LE:

Linkage equilibrium

LR:

Linear regression

MAF :

Minor allele frequency

MAS :

Marker assisted selection

MIM:

Multiple interval mapping

ML:

Maximum Likelihood

MLM:

Mixed linear model

QTL:

Quantitative trait loci

RR:

Ridge regression

SM:

Single marker

SNP:

Single nucleotide polymorphism

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Authors and Affiliations

  1. CIRAD, UMR AGAP Institut, Montpellier, France

    Nourollah Ahmadi

  2. AGAP Institut, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France

    Nourollah Ahmadi

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    Nourollah Ahmadi

  2. UMR AGAP Institut, CIRAD, Montpellier, France

    Jérôme Bartholomé

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Ahmadi, N. (2022). Genetic Bases of Complex Traits: From Quantitative Trait Loci to Prediction. In: Ahmadi, N., Bartholomé, J. (eds) Genomic Prediction of Complex Traits. Methods in Molecular Biology, vol 2467. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2205-6_1

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