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  • Review Article
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Multifactorial genetics

The use of molecular genetics in the improvement of agricultural populations

Nature Reviews Genetics volume 3, pages 22–32 (2002)Cite this article

Key Points

  • Genetic improvement of domesticated plant and animal species, by selection on economically important quantitative traits, such as yield, product quality and so on, has been carried out very successfully for several decades. Until recently, this has been accomplished by selection on phenotype, with little knowledge of the genetic nature of the selected traits. Such selection is, therefore, limited by the accuracy and availability of phenotypic information.

  • More recently, tools have become available to elucidate the genetics that underlies complex quantitative traits through the identification of chromosomal regions that harbour quantitative trait loci (QTL) and, in rare cases, their functional mutations. This has opened the door for the use of molecular genetics to enhance breeding programmes.

  • Two types of marker can be used: (rare) functional genetic variants that directly affect the trait of interest; and (more abundant) linked anonymous markers that are co-inherited with a QTL.

  • The broad term that describes the use of markers to enhance breeding strategies is marker-assisted selection (MAS). Selection programmes in which MAS has been used include genotype building, which aims to establish lines that combine favourable genes from different lines, and recurrent selection programmes, which aim to enhance the genetic performance of a breeding population for a quantitative trait.

  • Molecular information removes, although only partly, some of the limitations of selection on phenotype, by allowing selection at the genotype (DNA) level, which results in more accurate and/or faster and/or cheaper selection.

  • The potential limitations of MAS include inaccuracy and overestimation of QTL effects, gene–gene and gene–environment interactions, and incomplete knowledge of the genes involved in a trait. In general, selection on molecular information must be combined with selection on phenotype, so that the full genetic complement that underlies the trait of interest can be exploited.

  • Ultimately, the use of MAS will be determined by the economic benefit relative to conventional selection. Further work on the economic evaluation of selection strategies that exploit molecular genetic methods is urgently required.

  • Further applications of MAS might require the redesign of breeding strategies and their integration with other emerging technologies, such as reproductive technologies in animals, higher-resolution genetic maps and high-throughput genotyping technologies.

Abstract

Substantial advances have been made in the genetic improvement of agriculturally important animal and plant populations through artificial selection on quantitative traits. Most of this selection has been on the basis of observable phenotype, without knowledge of the genetic architecture of the selected characteristics. However, continuing molecular genetic analysis of traits in animal and plant populations is leading to a better understanding of quantitative trait genetics. The genes and genetic markers that are being discovered can be used to enhance the genetic improvement of breeding stock through marker-assisted selection.

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Figure 1: Examples of genetic improvements in livestock and crops.
Figure 2: Gene pyramiding.
Figure 3: Marker-assisted pre-selection for progeny testing.
Figure 4: Introgression of the avian naked neck gene.

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Acknowledgements

The authors thank A. Charcosset, D. Mather, J.-M. Ribaut, J. Dudley, L. Moreau and R. Pong-Wong for providing valuable input into aspects of this paper.

Author information

Authors and Affiliations

  1. Department of Animal Science, Iowa State University, 225 Kildee Hall, Ames, 50011, Iowa, USA

    Jack C. M. Dekkers

  2. Station de Génétique Végétale, INRA/UPS/INAPG, Ferme du Moulon, 91190, Gif sur Yvette, France

    Frédéric Hospital

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Correspondence to Jack C. M. Dekkers.

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DATABASES

ArkDB 

naked neck 

LocusLink 

Apoe

Glossary

CROSSBRED OR HYBRID

Progeny that result from the cross of two parental lines or breeds.

QUANTITATIVE TRAIT LOCI (QTL).

Genetic loci or chromosomal regions that contribute to variability in complex quantitative traits (such as plant height or body weight), as identified by statistical analysis. Quantitative traits are typically affected by several genes, and the environment.

HERITABILITY

The fraction of the phenotypic variance that is due to additive genetic variance.

GENETIC VARIANCE

Variation in a trait in a population that is caused by genetic differences.

GENETIC CORRELATION

The correlation between traits that is caused by genetic as opposed to environmental factors. A genetic correlation between two traits results if the same gene affects both traits (pleiotropy) or if genes that affect the two traits are in linkage disequilibrium.

BREEDING VALUE

A measure of the value of an individual for breeding purposes, as assessed by the mean performance of its progeny.

HETEROSIS OR HYBRID VIGOUR

When a hybrid or crossbred individual has a higher performance than the average of its two parents (the animal breeding definition), or than the best parent (the plant breeding definition). This is the result of non-additive actions of genes ((over-)dominance and/or epistasis).

LINKAGE DISEQUILIBRIUM (LD)

The condition in which the frequency of a particular haplotype for two loci is significantly different from that expected under random mating. The expected frequency is the product of observed allelic frequencies at each locus.

LINKAGE PHASE

The arrangement of alleles at two loci on homologous chromosomes. For example, in a diploid individual with genotype Mm at a marker locus and genotype Qq at a quantitative trait locus, possible linkage phases are MQ/mq and Mq/mQ, for which '/' separates the two homologous chromosomes.

MOLECULAR SCORE

A score that quantifies the value of an individual for selection purposes derived on the basis of molecular genetic data.

PROGENY TESTING

Evaluation of the breeding value of an individual based on the mean performance of its progeny.

DOUBLE-HAPLOID LINE (DH line)

A population of fully homozygous individuals that is obtained by artificially 'doubling' the gametes produced by an F1 hybrid.

BACKCROSS

Crossing a crossbred population back to one of its parents.

SELECTION INDEX THEORY

Theory of selection that combines several traits or sources of information, such that the accuracy of the index as a predictor of the selection goal (for example, the breeding value) is maximized.

RECOMBINANT INBRED LINE

A population of fully homozygous individuals that is obtained by repeated selfing from an F1 hybrid, and that comprises ∼50% of each parental genome in different combinations.

NEAR-ISOGENIC LINE

Lines that are genetically identical, except for one locus or chromosome segment.

HAPLOTYPE

The combination of alleles at several loci on a single chromosome. For example, for a marker with alleles M and m that is linked to a quantitative trait locus with alleles Q and q, possible haplotypes are MQ, Mq, mQ and mq.

EFFECTIVE POPULATION SIZE

The size of a random mating population that would lead to the same rate of inbreeding as the breeding population that is under selection. Quantifies the amount of random change in allele and haplotype frequencies that can occur in the population, which can give rise to linkage disequilibrium.

EXOTIC GENETIC RESOURCE

Wild, unadapted or non-commercial population that can be used as a source of new genetic material for improved populations.

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Dekkers, J., Hospital, F. The use of molecular genetics in the improvement of agricultural populations. Nat Rev Genet 3, 22–32 (2002). https://doi.org/10.1038/nrg701

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