Abstract
BackgroundHeterosis, the superior performance of hybrids relative to parents, has clear agricultural value, but its genetic control is unknown. Our objective was to test the hypotheses that hybrids expressing heterosis for biomass yield would show more gene expression levels that were different from midparental values and outside the range of parental values than hybrids that do not exhibit heterosis.ResultsWe tested these hypotheses in three Medicago sativa (alfalfa) genotypes and their three hybrids, two of which expressed heterosis for biomass yield and a third that did not, using Affymetrix M. truncatula GeneChip arrays. Alfalfa hybridized to approximately 47% of the M. truncatula probe sets. Probe set signal intensities were analyzed using MicroArray Suite v.5.0 (MAS) and robust multi-array average (RMA) algorithms. Based on MAS analysis, the two heterotic hybrids performed similarly, with about 27% of genes showing differential expression among the parents and their hybrid compared to 12.5% for the non-heterotic hybrid. At a false discovery rate of 0.15, 4.7% of differentially expressed genes in hybrids (~300 genes) showed nonadditive expression compared to only 0.5% (16 genes) in the non-heterotic hybrid. Of the nonadditively expressed genes, approximately 50% showed expression levels that fell outside the parental range in heterotic hybrids, but only one of 16 showed a similar profile in the non-heterotic hybrid. Genes whose expression differed in the parents were three times more likely to show nonadditive expression than genes whose parental transcript levels were equal.ConclusionThe higher proportions of probe sets with expression level that differed from the parental midparent value and that were more extreme than either parental value in the heterotic hybrids compared to a non-heterotic hybrid were also found using RMA. We conclude that nonadditive expression of transcript levels may contribute to heterosis for biomass yield in alfalfa.
Highlights
Heterosis, the superior performance of hybrids relative to parents, has clear agricultural value, but its genetic control is unknown
The entries we used in this experiment were grown in the growth chamber, but the biomass production we measured in this experiment showed the same relative patterns of heterosis as observed previously in field experiments [18]
The 10% of M. sativa genes that were not present in any individual may represent genes that were not expressed in leaves at this developmental stage and under these environmental conditions, or that were expressed at a level too low to be detected
Summary
The superior performance of hybrids relative to parents, has clear agricultural value, but its genetic control is unknown. Our objective was to test the hypotheses that hybrids expressing heterosis for biomass yield would show more gene expression levels that were different from midparental values and outside the range of parental values than hybrids that do not exhibit heterosis. One is the dominance hypothesis, which suggests heterosis results from the complementation of favorable alleles of different loci in F1 hybrids. The second is the over-dominance hypothesis, which states that a heterozygous locus in an F1 hybrid will perform better than either homozygous locus in parents; heterozygosity per se causes heterosis. All three hypotheses postulate that physical allelic variation between parents results in allelic interactions at given loci in F1 hybrids, which in turn causes heterosis. Not always explicitly stated, all three mechanisms concurrently may play a role in heterosis
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