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. 2009 Nov 24;106(47):20109-14.
doi: 10.1073/pnas.0908755106. Epub 2009 Nov 6.

Energy use efficiency is characterized by an epigenetic component that can be directed through artificial selection to increase yield

Miriam Hauben  1 , Boris Haesendonckx, Evi Standaert, Katrien Van Der Kelen, Abdelkrim Azmi, Hervé Akpo, Frank Van Breusegem, Yves Guisez, Marc Bots, Bart Lambert, Benjamin Laga, Marc De Block
Affiliations

Energy use efficiency is characterized by an epigenetic component that can be directed through artificial selection to increase yield

Miriam Hauben et al. Proc Natl Acad Sci U S A. .

Abstract

Quantitative traits, such as size and weight in animals and seed yield in plants, are distributed normally, even within a population of genetically identical individuals. For example, in plants, various factors, such as local soil quality, microclimate, and sowing depth, affect growth differences among individual plants of isogenic populations. Besides these physical factors, also epigenetic components contribute to differences in growth and yield. The network that regulates crop yield is still not well understood. Although this network is expected to have epigenetic elements, it is completely unclear whether it would be possible to shape the epigenome to increase crop yield. Here we show that energy use efficiency is an important factor in determining seed yield in canola (Brassica napus) and that it can be selected artificially through an epigenetic feature. From an isogenic canola population of which the individual plants and their self-fertilized progenies were recursively selected for respiration intensity, populations with distinct physiological and agronomical characteristics could be generated. These populations were found to be genetically identical, but epigenetically different. Furthermore, both the DNA methylation patterns as well as the agronomical and physiological characteristics of the selected lines were heritable. Hybrids derived from parent lines selected for high energy use efficiencies had a 5% yield increase on top of heterosis. Our results demonstrate that artificial selection allows the increase of the yield potential by selecting populations with particular epigenomic states.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
Artificial selection for respiration and EUE in canola. The selection was initiated from an isogenic doubled haploid line. Approximately five selected plants with the lowest and highest respiration were self-fertilized, and the progenies were tested for respiration and EUE. The next rounds of selections were done in one direction for low or high respiration with the two lines with the lowest and highest respiration, respectively. Three to five rounds of selection were sufficient to generate lines with distinct respiration and EUE.
Fig. 2.
Fig. 2.
Respiration of six selected populations versus the original starting population. The values were percent-normalized versus the average of the starting line “Simon.” Each node represents an individual plant. Each population contains approximately 200 plants. The bar in the boxes represents the median of the population and the other bars, the standard deviation with indication of the mean.
Fig. 3.
Fig. 3.
Characterization of the histone modifications and quantification of the global methylation of the genomic DNA by the cytosine extension assay. (A) Histones prepared from leaf 3 of the control line “Simon” and selected sublines. Below the immunoblots, the corresponding SYPRO Ruby-stained gel is shown to demonstrate the equal loading. (B) Cytosine extension assay using genomic DNA prepared from leaf 3 of “Simon” (control) and selected sublines. Leaves were harvested from the same population as used for studying the histone modifications. (C) Cytosine extension assay with genomic DNA prepared from cotyledons and the fourth leaf of a nonselected (control) and a selected hybrid. The cytosine extension assays were done on 10 individual plants. The error bars indicate the standard error.
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