357
ISSN 1021-4437, Russian Journal of Plant Physiology, 2018, Vol. 65, No. 3, pp. 357–363. © Pleiades Publishing, Ltd., 2018.
DNA Methylation Differences in Soybean Hybrids
and Their Parental Lines
1
C. B. Zhang
a, 2
, C. J. Lin
a, 2
, Z. R. Xu
b
, Z. H. Chen
b
, B. Peng
a
, P. N. Wang
a
, X. Y. Ding
a
, and L. M. Zhao
a,
*
a
Soybean Research Institute, National Engineering Research Center for Soybean, Jilin Academy of Agricultural Sciences,
Changchun, China
b
College of Life Sciences, Northeast Forest University, Harbin, China
*e-mail: lmzhao@cjaas.com
Received April 18, 2017
Abstract⎯To understand the methylation level and genetic delivery from parental line to their hybrid in soy-
bean (Glycine max (L.) Merr.), four groups of parental lines and their hybrids were analyzed using methylation
sensitive amplification polymorphism (MSAP). Comparisons of the different methylation distributions
revealed. (1) The methylation level of the whole hybrid was lower than that of the corresponding parent lines,
and the internal cytosine-methylation pattern was dominant. (2) In this study, comparing the total methyla-
tion levels in hybrids and the midparent values we assume that the larger differences in DNA methylation
between parental lines lead to stronger heterosis. (3) Four demethylated and one hyper-methylated fragments
were sequenced and located in the reference genome by blast analysis. These methylation changes could cause
expression levels changes of a protein kinase, zinc finger protein and a mitochondrial transcript, which would
affect a variety of metabolic pathways in soybean, providing an explanation for the observed heterosis.
Keywords: Glycine max, soybean, DNA methylation, heterosis, hybrid, parental lines
DOI: 10.1134/S1021443718030160
INTRODUCTION
It is generally believed that there is a relationship
between methylation and heterosis: as the level of meth-
ylation gradually increase, gene expression decrease,
which could lead to inbreeding depression. Altered
methylation patterns were observed in maize intraspe-
cific hybrids [1] and rice interspecific hybrids [2]; how-
ever, only a slight variation in DNA methylation was
observed in Arabidopsis intraspecific hybrids [3]. Het-
erotic F1 hybrids with hybrid vigour exhibit unusual
patterns of gene expression or epigenetic DNA modi-
fication compared with their inbred parents [4, 5].
DNA methylation levels of rice hybrid KRH2 and its
parent lines at three developmental stages were ana-
lyzed using MSAP technology. Compared with their
parents, methylation was higher in the hybrid during
the initial growth stage [6]. These pilot studies pro-
vided an opportunity to understand the molecular
mechanisms of heterosis in plants from the view of
epigenetics. Some studies have explored the epig-
enomic and transcriptomic variation simultaneously
among hybrids and their parental lines and surveyed
the methylome variations in the Arabidopsis hybrids
using high-throughput bisulfite sequencing [7]. In
that study, in both reciprocal hybrids, cytosine meth-
ylation in all sequence contexts increased across the
entire genomes, especially in transposable elements,
and parental differences in DNA methylation made a
major contribution to the increased methylation in the
hybrid. This study also suggested that DNA methyla-
tion changes in hybrids correlates with the altered
expression of a subset of genes. Furthermore, reduc-
tion of DNA methylation in hybrids compromised the
growth vigor, which provided direct evidence for the
potential role of DNA methylation in heterosis in
plants. There was a significant difference in the DNA
methylation status between two parental lines of Larix
kaempferi intraspecific hybrids [8]. The genomic DNA
methylation level in heterotic hybrids (26.47%) was
significantly lower than the midparent value (MPV;
33.80%), indicating that significant and extensive
demethylation had occurred. However, non-heterotic
hybrids displayed a DNA methylation level (33.59%)
that was close to the MPV, and they contained similar
numbers of methylation and demethylation events.
Soybean has been cultivated for 5000 years as one
of the most important oil crops in the world. Although
yield records for soybean have grown in recent years,
yield increase for soybean have not kept pace with
1
The article is published in the original.
2
These authors contributed equally to this work.
Abbreviations: AFLP—amplified fragment length polymorphism;
MPV—midparent value; MSAP—methylation sensitive amplifi-
cation polymorphism.
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