Abstract
Small RNAs (sRNAs) regulate gene expression, play important roles in epigenetic pathways, and are hypothesized to contribute to hybrid vigor in plants. Prior investigations have provided valuable insights into associations between sRNAs and heterosis, often using a single hybrid genotype or tissue, but our understanding of the role of sRNAs and their potential value to plant breeding are limited by an incomplete picture of sRNA variation between diverse genotypes and development stages. Here, we provide a deep exploration of sRNA variation and inheritance among a panel of 108 maize (Zea mays) samples spanning five tissues from eight inbred parents and 12 hybrid genotypes, covering a spectrum of heterotic groups, genetic variation, and levels of heterosis for various traits. We document substantial developmental and genotypic influences on sRNA expression, with varying patterns for 21-nucleotide (nt), 22-nt, and 24-nt sRNAs. We provide a detailed view of the distribution of sRNAs in the maize genome, revealing a complex makeup that also shows developmental plasticity, particularly for 22-nt sRNAs. sRNAs exhibited substantially more variation between inbreds as compared with observed variation for gene expression. In hybrids, we identify locus-specific examples of nonadditive inheritance, mostly characterized as partial or complete dominance, but rarely outside the parental range. However, the global abundance of 21-nt, 22-nt, and 24-nt sRNAs varies very little between inbreds and hybrids, suggesting that hybridization affects sRNA expression principally at specific loci rather than on a global scale. This study provides a valuable resource for understanding the potential role of sRNAs in hybrid vigor.
Highlights
Molecular variation is widely studied to understand the basis of plant traits
Small RNAs were sequenced for five tissues (15 DAP endosperm, V7/8 leaf, Vegetative 1 (V1) seedling root, V1 seedling shoot, and V7/V8 internode) of a panel of maize inbreds and hybrids (Supplemental Table 1)
When small RNAs (sRNAs) map to multiple genomic locations the ‘count’ attributed to each location was scaled proportional to the number of locations to which it mapped
Summary
Molecular variation is widely studied to understand the basis of plant traits This can include variation in DNA sequence, DNA methylation or chromatin modifications, changes in abundance of messenger RNA (mRNA) or small RNAs (sRNAs), as well as changes in the proteome or metabolome. These types of variation differ substantially in their heritability across generations and stability in different cells or tissues of the same organism. Changes in DNA sequence are highly stable among the cells of an organism while the abundance of mRNAs or metabolites can vary during development or in response to environmental conditions This stability is a key factor when considering experimental designs for detecting molecular variation and for attempting to link molecular variation to plant traits. We monitored variation in sRNA abundance in different tissues and genotypes of maize to understand the patterns of sRNA variation and inheritance
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