Abstract
Epigenetics offers important opportunities in breeding to improve the potential yield in a wide variety of crops. Starting from a pure breeder seed lot of a rice (Oryza sativa ssp. indica) inbred population, repeated testing for improved cellular respiration rates and energy use efficiency (EUE) over three generations identified performant epilines with distinct epigenetic signatures and with improved seed yield in field trials. Epiline DNA methylomes were characterized by genome-wide bisulfite sequencing to discern cytosine methylation changes in relation to transcriptome and phenotype. Regional methylation changes were dispersed over the epiline genomes. A number of upstream-associated differentially methylated regions (DMRs) correlated with differentially expressed genes (DEGs) with a role in particular molecular functions like transmembrane transport and protein kinase activity. Targeted bisulfite sequencing confirmed epiline DMRs that anti-correlated with DEGs, identifying putative epialleles that were susceptible for cytosine methylation changes that might affect gene expression and contribute to the phenotype. Chromatin immunoprecipitation sequencing revealed the extensive enrichment of gene-associated histone H3 lysine-4 trimethylation (H3K4me3), which correlated with gene activation and reduced cytosine methylation. Our data indicate that seed formation is prone to epigenetic changes that might be used as a resource in crop improvement.
Highlights
When growing the future food crops, we have to meet the demands of a rising global population of above nine billion in 2050, requiring improved seed yield per hectare on existing agricultural land.Yield is affected by the chosen bred plant variety, climate, soil, and agricultural practices
The efficiency of energy use in plants is an important component of yield stability in the field under varying environmental conditions, and it is measured by low cellular respiration and steady NADPH content [3]
A pure breeder seed lot of an inbred line of a rice variety Oryza sativa L. ssp indica was subjected to a repeated testing and selection procedure (Figure S1), similar to that previously described in canola [3,4,5]
Summary
When growing the future food crops, we have to meet the demands of a rising global population of above nine billion in 2050, requiring improved seed yield per hectare on existing agricultural land. Yield is affected by the chosen bred plant variety, climate, soil, and agricultural practices. The growth optima for a wide range of parameters are broadened by introducing new (epi)genetic resources that determine crop physiological characteristics. Genetic and epigenetic mechanisms that regulate complex traits, such as yield, are not yet sufficiently understood [1,2]. The efficiency of energy use in plants is an important component of yield stability in the field under varying environmental conditions, and it is measured by low cellular respiration and steady NADPH content [3].
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