Seed Dormancy: Exploring Types, Mechanisms, QTL, and Seed Dispersal

This report provides a comprehensive overview of seed dormancy, a crucial survival mechanism for plants. It details the two main categories: seed coat-based and embryo-based dormancy, explaining the roles of factors such as water, light, temperature, and hormones like abscisic acid (ABA) and gibberellic acid (GA). The report further explores the significance of seed dormancy in both ecological and agricultural contexts, including its impact on pre-harvest sprouting and its genetic complexity. It also discusses the classification of dormancy into primary and secondary types, as well as the five classes of physiological dormancy. Furthermore, the report examines the structure and dispersal of seeds, including the role of the awn and the factors affecting seed dispersal. Finally, it delves into the concept of Quantitative Trait Loci (QTL) analysis, its application in identifying phenotypic characteristics, and its importance in plant breeding, including various mapping approaches. This report is a valuable resource for understanding the intricate processes governing seed dormancy and plant genetics.

Seed Dominancy
Seed dominancy is the state when seeds prohibited from germinating under
unfavourable conditions or environment. The conditions are responsible for complex
combination of water, light, mechanical restraint, temperature, gasses, hormone structure, and
seed coats 1.
Seed dormancy is divided into two categories: seed coat based and embryo based.
Seed coat dominancy is a state in which seed coat protects oxygen and water infusion into it.
The permeating nature cannot function properly in this condition and no chemical can
influence the seeds in this condition2. Germination inhibitor is responsible for seed coat based
dominance. The common germination inhibiting factors is abscisic acid (ABA) which
prevents any transfusion by interrupting the permeability of the seeds. Embryo-based
dominancy is dependent on the ABA and low GA sensitivity 3. Low ABA: GA ratio is
responsible for the embryo-based seed dormancy and the ratio of the acids is highly
significant.
1 Shu, K., Liu, X. D., Xie, Q., & He, Z. H. (2016). Two faces of one seed: hormonal regulation of dormancy and
germination. Molecular plant, 9(1), 34-45.
2 Debeaujon, I., Lepiniec, L., Pourcel, L., & Routaboul, J. M. (2018). Seed coat development and
dormancy. Annual Plant Reviews online, 25-49.
3 Yamaguchi, S., Kamiya, Y., & Nambara, E. (2018). Regulation of ABA and GA levels during seed
development and germination in Arabidopsis. Annual Plant Reviews online, 224-247.

Seed dormancy is one of the most significant survival mechanism and it is a
prolonged process for storage of seeds. In adverse condition or situations such as frost,
drought and excessive moisture, this process restricts germination. In situ process of
germination is prevented by the seed dormancy and this method is called vivipary4. Seed
dormancy has significance in both ecological and agricultural aspect. In cereal crops high
range of dormancy can be observed and this increases quality of seeds. Seed dormancy
prevents Pre Harvesting Sprouting (PHS), which means germination of seed in plant body
due to undesired circumstances such as excessive moisture in atmosphere and heavy
rain5.Pre-harvest sprouting is a seed germination on the plant after maturation, under moist
conditions, before harvesting. Seed dormancy as an adaptive trait is important for weedy
species to survive in advrse condition.Flowering plants are depended solely on seeds to
introduce next generation. As a result, protection of seeds is highly significant for flowering
plants. Dominance is the best way for plants to protect the seeds from adverse environmental
condition.
Seed dominance is one of the genetically complex trait, which is regulated by some
qualitative traits such as height of the plant, flowering time, seed colour etc. and hormone
activation, enzyme synthesis and other physiological or biological process.
4 Karssen, Cees M. "Hormonal regulation of seed development, dormancy, and germination studied by genetic
control." In Seed development and germination, pp. 333-350. Routledge, 2017.
5 Lin, Meng, Dadong Zhang, Shubing Liu, Guorong Zhang, Jianming Yu, Allan K. Fritz, and Guihua Bai.
"Genome-wide association analysis on pre-harvest sprouting resistance and grain color in US winter
wheat." BMC genomics 17, no. 1 (2016): 794.

There two types of seed dormancy such as primary and secondary dormancy, these
are included to traditionally accepted classification. Seeds are released from the plant in
dormant state in the condition of primary seed dormancy, for adverse external condition6.
There are two types of primary dormancies such as exogenous and endogenous dormancy.
Germination is affected by external influences and inhibit emergence of seed. This exogenous
incident takes place due to seed coat dormancy and tissues covering the embryo are also
affected in this condition. The endogenous dormancy can be influenced with internal
condition of embryo. ABA acid level during maturation of seeds in mother plant is
responsible for primary dominance7. Although primary dormancy in the mature seed may be
absent in the period of seed dormancy due to lack of ABA, no certain relationship has been
found between ABA content and the degree of dormancy On the contrary the secondary seed
dominancy is regulated by unfavourable condition of germination of seeds. ABA
biosynthesis genes can affect seed ABA content. Thus, increasing ABA content in seeds can
cause enhance seed dormancy or delay germination. Genes, which help in biosynthesis of
ABA can affect ABA content of seeds. Thus, increasing ABA content in seeds can cause
enhance seed dormancy or delay germination. Based on a study, breaking dormancy
techniques (e.g, post-ripening, stratification, dark and smoke) are connected with variations
in ABA content during water uptake. In early developing seeds accumulation of ABA is to
induce primary dormancy and qSD7-1 also underlying gene induces the nature of dormancy
by dormancy-inducing hormone ABA in early developing seed. On the other side, GA
6 Chahtane, Hicham, Woohyun Kim, and Luis Lopez-Molina. "Primary seed dormancy: a temporally
multilayered riddle waiting to be unlocked." Journal of Experimental Botany 68, no. 4 (2017): 857-869.
7 Song, Yuan, Jiaojun Zhu, and Qiaoling Yan. "Roles of abscisic acid and gibberellins in maintaining primary
and secondary dormancy of Korean pine seeds." Journal of Forestry Research (2019): 1-12.

promotes the expansion of the embryo and germination. In addition, seeds need to GA to
overcome the seed-covering layers to weaken. GA biosynthesis and response are activated
during seed imbibition at low temperature. The low GA content cause to more dormant seeds,
which can be protected by supplement of exogenous GA treatment. GA hormone is involved
in regulating many other physiological processes, such as flowering time. There is no
information about interaction between qSD1-2 and qSD8, or the influence of GA on the awn
elongation and the effect of qSD8.
There is another type of classification of seed dormancy with five classes:
physiological seed dormancy, morphological dormancy, morpho-physiological dormancy,
physical dormancy, combinational dormancy. Among the five-dormancy type physiological
dormancy is the most popular one. There are three type of physiological dormancy; PD deep,
PD non-deep, PD intermediate8. In PD deep dormancy the embryo controls germination but
without help of GA or Gibberelic Acid . In PD intermediate and deep GA promotes
germination and seed coat with the tissues surrounding embryo helps to control the
condition. In non-deep dormancy has several type of classifications and every type is
dependent on different physiological effect of different temperatures. Morphological
dormancy is effective in underdeveloped seeds and differentiated by cotyledons.
Morphophysiological dormancy requires dormancy breaking treatment depending upon
8 Lu, Juan J., Dun Y. Tan, Carol C. Baskin, and Jerry M. Baskin. "Effect of seed position on parental plant on
proportion of seeds produced with nondeep and intermediate physiological dormancy." Frontiers in plant
science 8 (2017): 147.

different temperatures9. PY or physical dormancy occurs in the seeds ,which require
prevention from the water permeability.
Seed and dispersal unit
The seeds re variable in different plants with their size, colour, quality, structure and
composition. Seed is an embryonic form of a plant protected in the outer covering. Seed
formation is one of the main process of reproduction in both gymnosperms and angiosperms.
It can be said that seed is a mature ovule consisting plant with storage of food and surrounded
by the seed coat10.
Fertilization of mature male and female gametes produces seed in the plants. In
flowering plants, there are three main tissues such as an embryo (2n), endosperm and testa or
seed coat. Movements or dispersal of the seeds from one maternal tissues to another
maternal tissue such as lemma, palea , seedlings is called dispersal of seed. The factors
affecting seed dispersal are air, water, gravity and animals. Another popular way of seed
dispersal is explosion of seed coat.
A diploid (2n) embryo specifies new or next generation of the plants. These plants
evolve out of a fertilized egg, which is produced by the fertilization egg cell (n) and sperm
(n). The precursor tissues for the leaves, stem, root are associated in embryo and one or two
cotyledons that are the seed leaves, residing to the embryonic axis. There are two types of
cotyledons such as monocotyledons and dicotyledons 11.
9 Zhou, Yuan M., Juan J. Lu, Dun Y. Tan, Carol C. Baskin, and Jerry M. Baskin. "Seed germination ecology of
the cold desert annual Isatis violascens (Brassicaceae): two levels of physiological dormancy and role of the
pericarp." PloS one 10, no. 10 (2015): e0140983.
10 Miller, Matthew D. "The Modifiable Conceptual Unit Problem demonstrated using pollen and seed
dispersal." Global ecology and conservation 6 (2016): 93-104.
11 Tereshchenko, Natalya, Olga Zmeeva, Boris Makarov, Aleksandra Kravets, Valeryi Svetlichny, Ivan Lapin,
Albina Zotikova, Lydmila Petrova, and Tatyana Yunusova. "The influence of silicon oxide nanoparticles on

Structure of seed contains embryo, endosperm, hull. The embryo has four parts
radicle, plumule, epiblast and scutellum. Plumule ,which is another important part of embryo,
is the tip of the epicotyl The embryo portion is at the bottom of structure of a seed. The end
sperm of the seed consists of subaleurone layer and scratchy endosperm and the upper part of
subaleurone layer is aleurone layer. Tegmen and pericarp are upper layers of the endosperm.
Seed has two parts embryo and endosperms. Caryopsis is included with seed, tegmen and
pericarp. Pericarp is referred to fruit coat and testa is the seed coat of fruits. Testa is
developed from the integument or the inner cell layer of ovule and one layer of nucleus. Hull
is a beak like structure at the apex of the seed. The extension of apex of the lemma is called
awn, and it is a modified lead blade. It prevents the seeds from several predators such as birds
and mammals. Scutellum is a storage organ during the seed development and seed
germination process. It helps to transfer endosperm nutrients though the seeds. Seed
dormancy is associated with the awn in rice and the other segregated plants. The dispersal
unit may be named based on the species as caryopsis, that is a seed covered by pericarp, or
fruit coat, or spikelet. There is no such importance of awn in studies of rice cultivation and its
practices. For example, long and sharp awns can hamper manual harvesting in agricultural
practice during artificial selection of rice. Awn lacks of chlorenchyma as a result it is not
effective in the rice cultivation. On the contrary, there are some studies which reported that
removal of awn has adverse effect on the plant. Some of the studies said that awn of seed and
seed dispersal unit burial has important correlation. Seed dormancy and awn are two traits
that have adaptive significant for wild species. However, it can be said that long awns are not
favorable during harvest and storage; hence, this trait was artificially selected during
domestication. The studies emphasized on the effect of awn on seed survival in soil and how
awn can help to increase the probability of seed survival. Some correlations have been
morphometric parameters of monocotyledons and dicotyledons in soil and climatic conditions of western
Siberia, as well as on microbiological soil properties." BioNanoScience 7, no. 4 (2017): 703-711.

reported between mean seed stratification requirements and mean bud chilling requirements
among families.
Fig. Morphological and structure of rice seed.
Source: http://jeaheerice.cafe24.com/e_03_01.html
QTL
QTL stands for quantitative trait locus and helps in identification of a particular
phenotypic characteristic. QTL varies in different level of polygenic effects such as product
of multiple genes, surrounding environments. Architecture of plant body is dependent on the
phenotypic trait of an organisms12. QTL helps in detection of continuous trait (height of a
plant) and some opposed characters (smooth vs. wrinkled seeds). Multiple phenotypic
12 Luo, Meijie, Yanxin Zhao, Ruyang Zhang, Jinfeng Xing, Minxiao Duan, Jingna Li, Naishun Wang et al.
"Mapping of a major QTL for salt tolerance of mature field-grown maize plants based on SNP markers." BMC
plant biology 17, no. 1 (2017): 140.

attribute can be regulated by a single gene. QTL can identify the pre-specific or candidate
gene of a particular trait and defined a specific sequence in DNA as a marker assisted
technique. Quantitative Trait Loci (QTL) mapping is based on finding the relation between
genetic marker and known phenotype. One of the type called During the progress of a
recombination inbreed line population, traditional bi-parental of QTL mapping is limited by
the recombination actions arranged over a few generations. As a result. It can be said that
most of the biological seed dormancy mechanisms would have a clearly stated concepts in
this particular aspect.
Researchers prefer the mapping technique as population of any particular organisms
can be localized by the technique. QTL is used in statistical analysis of any particular gene to
find variation of the quantitative traits with the reference of selected population. Plant
breeding is mostly shows quantitative traits and the variance of those selective traits 13.
Genetic variation of quantitative attributes are related to collective effects of QTL, epistasis
and interaction between QTLs with surrounding environments. In QTL mapping linkage,
analysis and associative mapping are responsible methods for QTL mapping. The pattern of
unique gene expression in several genes and that of the GO profiles, together with the
absence of strong epistatic relations, strongly indicate that natural differences for seed
dormancy in different plants. The effectiveness of different QTL is regulated by distinct
genetic and molecular pathways Exploitation of molecular markers or probes is used for plant
breeding and finding the associated sub sets of the complex traits in plant body 14. Recently
13 Young, Nevin D. "QTL mapping and quantitative disease resistance in plants." Annual review of
phytopathology 34, no. 1 (1996): 479-501.
14 Iquira, Elmer, Sonah Humira, and Belzile François. "Association mapping of QTLs for sclerotinia stem rot
resistance in a collection of soybean plant introductions using a genotyping by sequencing (GBS)
approach." BMC plant biology 15, no. 1 (2015): 5.

various researches related to QTL mapping have promoted proportion of phenotypic effect or
variance as a result assessments regarding Marker Assisted Selection has been found. One of
the most Most common technique to identify a QTL is map-based cloning by narrowing
down the QTL to a short.
The importance of QTL can be seen in intensification of the biological knowledge
regarding heritage and genomic architecture. The QTL helps in analysing the specific species
or across the species of any particular organisms. The QTL identify markers act as the
secondary tool for breeding of organisms. There are several approaches of QTL mapping
such as single marker approach , single interval mapping, composite interval mapping ,
multiple interval mapping15. The single maker approach has several limitations as QTL
detection decreases with increase of distance between marker and QTL. Method cannot
specifies the relation between markers and associated one or two QTLs. The effects of QTL
are possibly ignored as the methods are perplexed with recombination frequencies. Simple
Interval Mapping evaluates the association between the attribute values and the genotype of
a hypothetical QTL (at the specific QTL) multiple analysis facts between pair of subsequent
marker loci (the appropriate interval). This method has been the most broadly attitude as it
can be easily retrieved through statistical combinations such as MAPMAKER/QTL16.
Composite Interval Mapping for the single QTL in a definite time of interval with numerous
regression analysis based on marker oriented QTL. The MIM indicates location of QTLs
15 Bennewitz, Stefan, and Alain Tissier. "QTL mapping of the shape of type VI glandular trichomes in
tomato." Frontiers in plant science 9 (2018): 1421.
16 Kadambari, Gopalakrishnamurty, Lakshminarayana R. Vemireddy, Akkareddy Srividhya, Ranjithkumar
Nagireddy, Siddhartha Swarup Jena, Mahendranath Gandikota, Santosh Patil et al. "QTL-Seq-based genetic
analysis identifies a major genomic region governing dwarfness in rice (Oryza sativa L.)." Plant cell reports 37,
no. 4 (2018): 677-687.

with the position between markers or probes. The method shows appropriate grants or the
allowance for absent genotype data and that helps to allow relations among QTLs. It can be
said that major problem in multiple QTL method is model selection and the main concerned
factor is formation of suitable criteria or base line for comparing models or replicas.
Qualitative traits are regulated by the polygenes and the genomes containing gene associated
attributes with definite quantitative traits.
Flowering initiation is called heading in rice plants. Heading date 3a (Hd3a ) and
Rice Flowering Locus T1 (RFLT) are encoded florigen for the rice plants17. Ehd1 or Early
heading date 1 is a highly valued gene in plants for flowering time for a short day condition.
Ehd1 gene is responsible for the B type response regulator. Moreover, different rice plants
have varieties of diverged alleles such as Ehd1 and Hd3a/RFT1 which are unclear in
interaction18. RFT1 is expressed under short time period and long day period condition. The
non-functional RFT1 allele but the homozygous ehd1 and hd3a /rft1are failed to influence the
floral transition under long and short daytime. There is another florigen receptor called 14-3-
3 proteins which cannot relate to the mutated E105K with the non-functional state of RFT1
gene due to long or short day time19.
17 Mulki, Muhammad Aman, Xiaojing Bi, and Maria von Korff. "FLOWERING LOCUS T3 controls spikelet
initiation but not floral development." Plant physiology 178, no. 3 (2018): 1170-1186.
18 Pasriga, Richa, Jinmi Yoon, Lae-Hyeon Cho, and Gynheung An. "Overexpression of RICE FLOWERING
LOCUS T 1 (RFT1) Induces Extremely Early Flowering in Rice." Molecules and cells 42, no. 5 (2019): 406.
19 Camoni, Lorenzo, Sabina Visconti, Patrizia Aducci, and Mauro Marra. "14-3-3 proteins in plant hormone
signaling: Doing several things at once." Frontiers in plant science 9 (2018): 297.

Relation of seed dormancy, QTL and flowering time with Cultivated, wild
and weedy rice
Genetic background of alleles from the weedy rice from cultivated rice line is influenced
by the Mendelian factors. Weedy rice (Oriza sativa) is responsible for the higher rice
growing areas. Wild and weedy rice cannot be found in the similar areas. The weedy rice is
related to cultivated Asian rice. Rice researchers have studied the inheritance of dormancy to
determine the trait in common cultivars to enforce resistance to preharvest sprouting. Most
geneticists focused on hull-imposed dormancy in cultivated rice. Some of the research
determined that the seed dormancy is one of the quantitative traits controlled by multiple
genes with cumulative and it is effected by environmental conditions during seed
development. De domestication or degeneration of the rice evolves the weedy and wild rice.
If genomes can be compared , size of genome of weedy rice is similar to the cultivated rice.
International Rice Genome Sequencing Project in 2005 identified total genome sequence of
rice is 389 Mb and total protein is 37.544 in the weedy rice (Oriza sativa). Some of rice
cultivars and weedy rice have advanced plant height in comparison to fresh rice producers.
This scenario was changed by the green revolution. The germination tests revealed that Aus
and indica rice had stronger seed dormancy than japonica rice and the result shows that the
germination tendency is varied from one plant to another. Short stature plant height is
associated with the green evolution. Some QTL factors such as qSD1-2 and qSD8 have been
isolated from the seed dormancy20. qSD8 had small additive-dominance effect and qSD8 had
13 % of the phenotypic variance. Based on our multiple linear regression model (Equation
20 Huang, Fanghao, Wei Zhang, Zheng Chen, Jianzhong Tang, Wei Song, and Shiqiang Zhu. "RBFNN-based
adaptive sliding mode control design for nonlinear bilateral teleoperation system under time-varying
delays." IEEE Access 7 (2019): 11905-11912.

2.4), we detected additive effect for chromosome 1 and dominance effect for both of two loci
and there is no any interaction between these two loci. The factors, which are enhancing seed
dormancy, present from the weedy rice line SS18-2 into the genetic scenario of the EM93-1
rice line cultivers. The qSD1-2 was cloned as the GA synthase enzyme gene OsGA20-ox2 to
control the hormone production in the developing and germinating seeds21. The EM93-1 rice
line is recurrent by the back cross and marker assisted selectors.
Flowering time:
The flowering time of a plant is referred to as the stage of its flowering. Flowering
requires the presence of light at most of the times. This acts as the predetermine if seed
dormancy. Most of the plant species require light to start their flowering stage. Light is
divided into small packets of energy called photons. These photons are accepted by the
phytochrome receptors of plants and start their response towards light. According to Endo et
al. (2016) flowering depends on the presence of photoreceptors. Photoperiodism also exists in
case of many plant species22. The plants fixed their flowers at an optimum time period for
seed development, pollination, and dispersal. In addition, flowering time controls the shift
from vegetative to reproductive development to complete the life cycle of plant and to help in
reproduction of plants. It can be said that the factor of flowering time is responsible for
various types of plants depending upon their periodic nature of flowering such as long day
21 Korkmaz, Ugur. "Genetic Component Effects of Two Loci on Seed Dormancy, Awn, Low-Temperature
Germination, Plant Height, and Flowering Time in Rice (Oryza sativa L.)." (2018).
22 Endo, Motomu, Takashi Araki, and Akira Nagatani. "Tissue-specific regulation of flowering by
photoreceptors." Cellular and molecular life sciences 73, no. 4 (2016): 829-839.