INTRODUCTION
The seed (grain) of rice (Oryza sativa ) is a complex but delicate
biological system, containing three genetically distinct tissues, the
diploid embryo, the triploid endosperm, and the diploid maternal tissues
(An et al., 2020). Rice is a main contributor of dietary calories and
nutrients for nearly half of the global population (Wu, Müller,
Gruissem, & Bhullar, 2020). Rice grain yield has to be sustainably
improved both in quantity and quality, to solve formidable challenges
including the ever-increasing population, climate change, and the quest
for high-quality rice that has accompanied the rise in living standards
(Sreenivasulu et al., 2015). A detailed understanding of the molecular
and physiological mechanisms underpinning seed development may enable
the design of effective strategies to boost rice quality and yield.
Milled rice is the main form of rice for consumption produced by milling
during which the outer maternal layers, the embryo, the aleurone, and
part of the starchy endosperm are removed. End use quality of rice seed
is dominated by the physico-chemical properties of endosperm that are
predominately packed with starch granules and protein bodies (Xi et al.,
2014). Grain chalkiness affects grain quality due to perturbation of
carbohydrate metabolism (Nakata et al., 2017) or protein synthesis
(Ishimaru et al. 2019; Wada et al., 2019). Up to now, the majority of
research on rice quality has been centered on the starchy endosperm,
revealing that it is a rather sophisticated trait controlled by multiple
genes and by environmental conditions (Fitzgerald, McCouch, & Hall,
2009; Ishimaru et al., 2019; Lin et al., 2017).
The composition, structure, and size of endosperm are affected by its
interactions with other tissues, in particular the embryo, during the
whole process of seed development. Endosperm provides nutrients to drive
embryo growth, and physically restrains its size and development. The
embryo is the germline component of the seed, and affects the allocation
of sugars and other nutrients like amino acids and minerals to the
endosperm. Concomitant development of embryo and endosperm under the
constraint of maternal tissues (seed coat or pericarp) requires
coordination of the two compartments (Doll et al., 2020; Lafon-Placette
& Köhler, 2014). Growing evidence in rice as well as Arabidopsis
(Arabidopsis thaliana ) and maize (Zea mays ) supports
bidirectional communication between embryo and endosperm, as reviewed by
Lafon-Placette and Köhler (2014); An et al. (2020) and Ingram (2020).
Therefore, both embryo and endosperm and their interaction affect grain
filling and quality.
Transcriptome analyses of seed development have already identified most
genes expressed in the different compartments (Olsen, 2020). These
comprehensive studies provided insights into the molecular networks and
pathway interactions that function during the development of individual
seed compartments for Arabidopsis (Belmonte et al., 2013), maize (Chen
et al., 2014; Yi et al., 2019), wheat (Triticum aestivum ; Xiang
et al., 2019), and barley (Hordeum vulgare ; Bian et al., 2019).
In rice, Ishimaru et al. (2019)
isolated the aleurone, dorsal, central and lateral tissues of developing
endosperm by laser-capture microdissection (LCM), and profiled the gene
expression by a 44 K microarray, revealing that high molecular weight
heat shock proteins have a role in mediating redox, nitrogen and amino
acid metabolism in the chalky tissue under heat stress. Wu et al. (2020)
profiled gene expression activity in the nucellar epidermis, ovular
vascular trace, endosperm and the aleurone at three distinct grain
development stages, offering insights into the molecular aspects of
grain development. Ram et al. (2020) employed an rapid LCM approach to
individually collect pericarp, aleurone, embryo and endosperm at 10 DAF
(days after anthesis). Subsequent RNA-Seq analysis identified 7760
differentially expressed genes, by which the authors built some key
tissue-specific pathways responsible for nutrient partitioning.
However, these studies do not enable an integrated understanding of the
cellular processes governing the formation of rice grain, because of the
scarcity of information on embryo-endosperm communication and its
influence on rice yield and quality, which is partly attributed to the
complexity of seed structures (Doll et al., 2020).
Notched-belly grain is a misshapen type of rice grain, having a
notched-line on its ventral side and thus being inferior in appearance
and milling quality (Tong et al., 2018). Previously, we identified a
notched-belly mutant (NB) of a japonica rice Wuyujing 3 using a chemical
mutagen (Lin et al., 2014). It has high occurrence of white-belly
grains, and the notched line is visible at 5 DAF, which separates the
endosperm into two sub-compartments, the translucent upper part and the
chalky bottom. Using this mutant, we developed a novel comparison system
that can evaluate the embryo effect on endosperm composition, with a
conclusion that embryo demonstrated a negative effect on the contents of
proteins, amino acids, and minerals in the chalky endosperm (Lin et al.,
2016). Complementary proteome and transcriptome profiling of the NB
mutant suggested the transporters for metabolites and the signal
messengers of hormones as potential signals for embryo-endosperm
communications, confirming the value of the NB mutant for examining the
role of embryo in grain filling and quality formation (Lin et al.,
2017).
In this study, we used the NB mutant to characterize the genome-wide
gene expression profile of embryo and endosperm samples
between 0-60 DAF.
In combination with physiological
and histological investigations, we aimed to: (i) unravel the
commonalities and specificities between embryo and endosperm in
developmental processes as well as molecular and metabolic signatures;
(ii) manifest the effect of embryo on endosperm development; and (iii)
frame a holistic and dynamic picture of seed development by integrating
the information of embryo-endosperm crosstalk.
Comprehensive
comparison of mRNAs datasets revealed a dragging effect of embryo on the
developmental transition of the endosperm, which might be mediated by
hormonal (GA and IAA) and T6P-SnRK1 signaling pathways. A new staging
system is subsequently proposed by integrating the information about
embryo-endosperm bidirectional communications. The findings obtained
should offer insights into the biological processes and signatures of
grain formation, hence providing a valuable resource for the
manipulation of molecular and physiological processes responsible for
cereal grain yield and quality.