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The use of general and specific combining abilities in a context of gene expression relevant to plant breeding

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Abstract

Many common traits are believed to be a composite reflection of multiple genetic and environmental factors. Recent advances suggest that subtle variations in the regulation of gene expression may contribute to quantitative traits. The nature of sequence variation affecting the regulation of gene expression either in cis (that is, affecting the expression of only one of the two alleles in a heterozygous diploid) or in trans (that is, affecting the expression of both alleles in a heterozygous diploid) is a key and usually unknown feature for the breeders. If the change in expression acts entirely in cis, then the structural gene can be treated as a candidate gene and a potential target for marker-assisted selection. Therefore, gene surveys for cis-regulatory variation are a first step in identifying potential targets for marker-assisted breeding. Here, we discuss in detail the “genome-wide analysis of allele-specific expression differences” (GASED) approach. The GASED approach was developed to screen for cis-regulatory variation on a genome-wide scale. In GASED, mRNA abundance is treated as if it were a quantitative phenotypic response variable, whose genetic between-F1 hybrid variance is partitioned into additive and non-additive components. In plant breeding, this partitioning of the genetic variance is well known in the context of estimation of general and specific combining abilities for diallel crossing schemes. We demonstrate the GASED method using Arabidopsis thaliana data. The method can be used to screen for cis-regulatory variation in any crop species for which diallel crossing schemes are appropriate and genomic tools are available.

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Abbreviations

ASE:

Allele-specific expression

eQTL:

Expression quantitative trait loci

FDR:

False discovery rate

FNR:

False non-discovery rate

GASED:

Genome-wide analysis of ASE differences

GCA:

General combining ability

LD:

Linkage disequilibrium

MAS:

Marker-assisted selection

SCA:

Specific combining ability

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Acknowledgments

This work was partly supported by grants from the Ministerie van de Vlaamse Gemeenschap-Landbouwkundig Onderzoek (IWT/020176), the European Commission within its FP5 Programme (QLK3-CT-2002-02035), and the Interuniversity Poles of Attraction Programme-Belgian Science Policy (P5/13).

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Authors and Affiliations

  1. Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium

    Marnik Vuylsteke

  2. Department of Molecular Genetics, Ghent University, Ghent, Belgium

    Marnik Vuylsteke

  3. Biometris – Applied Statistics, Department of Plant Sciences, Wageningen University, P.O Box 100, 6700 AC, Wageningen, The Netherlands

    Fred van Eeuwijk

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  1. Marnik Vuylsteke
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  2. Fred van Eeuwijk
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Correspondence to Marnik Vuylsteke.

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Vuylsteke, M., van Eeuwijk, F. The use of general and specific combining abilities in a context of gene expression relevant to plant breeding. Euphytica 161, 115–122 (2008). https://doi.org/10.1007/s10681-007-9452-0

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