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Plant Physiol. 2019 Oct 1. pii: pp.00817.2019. doi: 10.1104/pp.19.00817. [Epub ahead of print]

Variation and inheritance of small RNAs in maize inbreds and F1 hybrids.

Author information

1
The University of Minnesota CITY: St Paul STATE: MN POSTAL_CODE: 55108 United States Of America [US].
2
Univ. of Delaware CITY: Newark United States Of America [US].
3
University of Minnesota CITY: St. Paul STATE: MN POSTAL_CODE: 55108 United States Of America [US].
4
Michigan State University CITY: East Lansing United States Of America [US].
5
U.S. Department of Energy Joint Genome Institute CITY: Walnut Creek United States Of America [US].
6
US Department of Energy Joint Genome Institute CITY: Walnut Creek United States Of America [US].
7
University of Wisconsin, Madison CITY: Madison STATE: Wisconsin POSTAL_CODE: 53706 United States Of America [US].
8
Michigan State University CITY: East Lansing STATE: Michigan POSTAL_CODE: 48824 United States Of America [US].
9
University of Wisconsin 1575 Linden Drive CITY: Madison STATE: Wisconsin POSTAL_CODE: 53575 United States Of America [US].
10
Donald Danforth Plant Science Center CITY: St. Louis STATE: Missouri POSTAL_CODE: 63132 United States Of America [US].
11
University of Minnesota CITY: Saint Paul STATE: Minnesota POSTAL_CODE: 55108 United States Of America [US].
12
University of Minnesota CITY: St. Paul STATE: Minnesota POSTAL_CODE: 55108 United States Of America [US] springer@umn.edu.

Abstract

Small RNAs (sRNAs) regulate gene expression, play important roles in epigenetic pathways, and are hypothesised 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-nt, 22-nt and 24-nt sRNAs. We provide a detailed view of the distribution of sRNAs in the maize genome, revealing a complex make-up that also shows developmental plasticity, particularly for 22-nt sRNAs. sRNAs exhibited substantially more variation between inbreds as compared to observed variation for gene expression. In hybrids, we identify locus-specific examples of non-additive inheritance, mostly characterised 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 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.

PMID:
31575624
DOI:
10.1104/pp.19.00817
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