A Single-Nucleotide Polymorphism in an Endo-1,4-β-Glucanase Gene Controls Seed Coat Permeability in Soybean

Jang, Seong-Jin; Sato, Minoru; Sato, Kei; Jitsuyama, Yutaka; Fujino, Kazuo; Mori, Haruhide; Takahashi, Ryōsuke; Benitez, Eduardo R.; Liu, Baohui; Yamada, Tetsuya; Abe, Jun

doi:10.1371/journal.pone.0128527

Cited by 48 publications

(70 citation statements)

References 49 publications

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“…Recently, a quantitative trait locus encoding calcineurin-like protein, GmHs1-1, was isolated by map-based cloning and reported to contribute to hardseededness in soybean with unknown mechanism (20). At the same time, an endo-1,4-β-glucanase gene, qHS1, was cloned by fine mapping and reported to be responsible for the formation of minute cracks by changing cell wall structure (19). Interestingly, these two genes are adjacent to each other in the physical map.…”

Section: Discussionmentioning

confidence: 99%

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A class II KNOX gene, KNOX4 , controls seed physical dormancy

Chai

Zhou

Molina

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Physical dormancy of seed is an adaptive trait that widely exists in higher plants. This kind of dormancy is caused by a waterimpermeable layer that blocks water and oxygen from the surrounding environment and keeps embryos in a viable status for a long time. Most of the work on hardseededness has focused on morphological structure and phenolic content of seed coat. The molecular mechanism underlying physical dormancy remains largely elusive. By screening a large number of Tnt1 retrotransposontagged Medicago truncatula lines, we identified nondormant seed mutants from this model legume species. Unlike wild-type hard seeds exhibiting physical dormancy, the mature mutant seeds imbibed water quickly and germinated easily, without the need for scarification. Microscopic observations of cross sections showed that the mutant phenotype was caused by a dysfunctional palisade cuticle layer in the seed coat. Chemical analysis found differences in lipid monomer composition between the wild-type and mutant seed coats. Genetic and molecular analyses revealed that a class II KNOTTED-like homeobox (KNOXII) gene, KNOX4, was responsible for the loss of physical dormancy in the seeds of the mutants. Microarray and chromatin immunoprecipitation analyses identified CYP86A, a gene associated with cutin biosynthesis, as one of the downstream target genes of KNOX4. This study elucidated a novel molecular mechanism of physical dormancy and revealed a new role of class II KNOX genes. Furthermore, KNOX4-like genes exist widely in seed plants but are lacking in nonseed species, indicating that KNOX4 may have diverged from the other KNOXII genes during the evolution of seed plants.S eed dormancy is a complex adaptive trait of higher plants that allows embryos to survive extended periods of unfavorable environmental conditions (1). Over the course of evolution, plant seeds have evolved diverse dormancy forms in response to various climates to maintain viability (2). Physical dormancy, also termed hardseededness, is an exogenous dormancy caused by a water-impermeable hard seed coat. Physical dormancy plays a key role in protecting seeds against microbial attacks and predators and maintaining seed banks in soils (3-5). This type of dormancy has been found in at least 17 plant families and is very common in legume species (2, 6, 7). Seed exhibiting physical dormancy is characterized by specific morphological features, including a water-impermeable palisade cell layer covered by intact cuticles in the hard seed coat. This structure blocks water and oxygen from its surrounding environment and preserves seeds in a viable status for a long time, sometimes for more than hundreds of years (8). Another common type of seed dormancy is physiological dormancy, which is caused by endogenous factors (e.g., abscisic acid) in embryos. Most molecular studies on seed dormancy have focused on physiological dormancy, using model species Arabidopsis thaliana (9, 10).However, A. thaliana seed is water-permeable, and thus not a suitable model to study physical dor...

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Section: Discussionmentioning

confidence: 99%

“…At the molecular level, seed hardness has been identified as a quantitative trait in soybean (17,18). With quantitative trait locus marker analysis, two single nucleotide polymorphism alleles were found to be associated with a seed coat permeability trait in various soybean cultivars (19,20). The mechanisms that change seed coat properties remain unknown.…”

mentioning

confidence: 99%

A class II KNOX gene, KNOX4 , controls seed physical dormancy

Chai

Zhou

Molina

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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“…Although its cellular functions are unknown, a large percentage of soybean landraces carry a SNP that causes an amino acid substitution and show low polymorphism in the c. 160 kb genomic region surrounding GmHs1-1, indicating a possible signature of artificial selection during soybean domestication. Water permeability is controlled by several additional QTLs (Liu et al, 2007;Orazaly et al, 2015); of those, the causal gene of the qHS1 locus is shown to encode an endo-1,4-b-glucanase that controls the amount of b-1,4-glucans in the outer layer of palisade cells of the seed coat on the dorsal side of seeds, a point of water entrance (Jang et al, 2015). Some of the seed permeability QTLs underlie seed coat cracking (Nakamura et al, 2003).…”

Section: Seed Hardnessmentioning

confidence: 99%

Soybean domestication: the origin, genetic architecture and molecular bases

2017

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SummaryDomestication provides an important model for the study of evolution, and information learned from domestication research aids in the continued improvement of crop species. Recent progress in de novo assembly and whole-genome resequencing of wild and cultivated soybean genomes, in addition to new archeological discoveries, sheds light on the origin of this important crop and provides a clearer view on the modes of artificial selection that drove soybean domestication and diversification. This novel genomic information enables the search for polymorphisms that underlie variation in agronomic traits and highlights genes that exhibit a signature of selection, leading to the identification of a number of candidate genes that may have played important roles in soybean domestication, diversification and improvement. These discoveries provide a novel point of comparison on the evolutionary bases of important agronomic traits among different crop species.

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“…At molecular level, a single nucleotide polymorphism (SNP) has been reported to convert the impermeable wild type seeds to permeable one. A base substitution (T→G; Isoleucine→Serine) in Endo-1,4-β-Glucanase gene led to accumulation of β-1,4glucan derivatives such as xyloglucan which resulted in impermeability of seed coat in soybean (Jang et al 2015). Sun et al (2015) also indicated involvement of similar mechanism in seed coat permeability in soybean.…”

Section: Viability Versus Seed Coat Permeabilitymentioning

confidence: 99%

Genetic studies on seed coat permeability and viability in RILs derived from an inter-specific cross of soybean [Glycine max (L.) Merrill]

Kumar¹,

Chandra²,

Talukdar³

et al. 2019

IJGPB

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Soybean seeds loss viability very rapidly during ambient storage in the tropical and sub-tropical environments. In this study, interrelationship between seed coat permeability and viability over periods of ambient storage was assessed using a set of 217 recombinant inbred lines (RIL) developed from an inter-specific cross between wild type (Glycine soja) accession DC2008-1 and cultivated (G. max) variety DS9712. G. soja seeds were tiny, black, impermeable and highly viable while G. max seeds were large, yellow, permeable and poorly viable during ambient storage. Seed coat permeability and viability of the fresh, one-year and two-year-stored seeds (stored in room temperature, av. 25±2°C and 65±5% RH) were tested as per standard protocols in completely randomized design with two replications. Significant variation was found among genotypes for the seed viability, permeability, periods of storage and their interactions. Permeability of the seed coat increased with the period of storage. In the fresh, one-year and two-yearstored seeds, the seed coat permeability was 62.87, 75.17 and 90.52%, respectively. Viability of the seeds was negatively correlated with period of storage and seed size. In the fresh, one-year and two-year-stored seeds, average viability was 90.7, 75.6 and 54.1%, respectively. Scanning electron microscopy (SEM) indicated presence of intact hilum, strong hourglass cells and non-cracked seed coat in the highly viable seeds. A set of 24 RILs were found that maintained higher viability (>80%) with varying degree of permeability after two years of storage. Among the highly viable RILs, more were black seeded. RIL Nos. 7-12-3, 7-24- 1, 13-2-2, 13-31-4 found to maintain both viability and permeability in higher order during storage and would pave the way for development of soybean genotypes with high viability and permeability.

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A Single-Nucleotide Polymorphism in an Endo-1,4-β-Glucanase Gene Controls Seed Coat Permeability in Soybean

Cited by 48 publications

References 49 publications

A class II KNOX gene, KNOX4 , controls seed physical dormancy

A class II KNOX gene, KNOX4 , controls seed physical dormancy

Soybean domestication: the origin, genetic architecture and molecular bases

Genetic studies on seed coat permeability and viability in RILs derived from an inter-specific cross of soybean [Glycine max (L.) Merrill]

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