Isolation and Characterization of Mutants Defective in Seed Coat Mucilage Secretory Cell Development in Arabidopsis

In Arabidopsis, fertilization induces the epidermal cells of the outer ovule integument to differentiate into a specialized seed coat cell type producing extracellular pectinaceous mucilage and a volcano-shaped secondary cell wall. Differentiation involves a regulated series of cytological events including growth, cytoplasmic rearrangement, mucilage synthesis, and secondary cell wall production. We have tested the potential of Arabidopsis seed coat epidermal cells as a model system for the genetic analysis of these processes. A screen for mutants defective in seed mucilage identified five novel genes (MUCILAGE-MODIFIED [MUM]1–5). The seed coat development of these mutants, and that of three previously identified ones (TRANSPARENT TESTA GLABRA1, GLABRA2, and APETALA2) were characterized. Our results show that the genes identified define several events in seed coat differentiation. Although APETALA2 is needed for differentiation of both outer layers of the seed coat, TRANSPARENT TESTA GLABRA1, GLABRA2, and MUM4 are required for complete mucilage synthesis and cytoplasmic rearrangement. MUM3 and MUM5 may be involved in the regulation of mucilage composition, whereas MUM1 and MUM2 appear to play novel roles in post-synthesis cell wall modifications necessary for mucilage extrusion.     

A defective seed coat pattern (Net) is correlated with the post-transcriptional abundance of soluble proline-rich cell wall proteins

The pigmented seed coats of several soybean (Glycine max (L.) Merr.) plant introductions and isolines have unusual defects that result in cracking of the mature seed coat exposing the endosperm and cotyledons. It has previously been shown that the T (tawny) locus that controls the color of trichomes on stems and leaves also has an effect on both the structure and pigmentation of the seed coat. Distribution of pigmentation on the seed coat is controlled by alleles of the I (inhibitor) locus. It was also found that total seed coat proteins were difficult to extract from pigmented seed coats with i T genotypes because they have procyanidins that exhibit tannin properties. We report that the inclusion of poly-L-proline in the extraction buffer out-competes proteins for binding to procyanidins. Once this problem was solved, we examined expression of the proline-rich cell wall proteins PRP1 and PRP2 in pigmented genotypes with the dominant T allele. We found that both homozygous i T and i t genotypes have reduced soluble PRP1 levels. The epistatic interaction of the double recessive genotype at both loci is necessary to produce the pigmented, defective seed coat phenotype characteristic of seed coats with the double recessive i and t alleles. This implies a novel effect of an enzyme in the flavonoid pathway on seed coat structure in addition to its effect on flavonoids, anthocyanidins, and proanthocyanidins. No soluble PRP1 polypeptides were detectable in pigmented seed coats (i T genotypes) of isolines that also display a net-like pattern of seed coat cracking, known as the Net defect. PRP2 was also absent in one of the these lines. However, both PRP1 and PRP2 cytoplasmic mRNAs were found in the Net-defective seed coats. Together with in vitro translation studies, these results suggest that the absence of soluble PRP polypeptides in the defective Net lines is post-translational and could be due to a more rapid or premature insolubilization of PRP polypeptides within the cell wall matrix.     

Variation of proline rich cell wall proteins in soybean lines with anthocyanin mutations

The I locus controls inhibition of anthocyanin accumulation in the epidermal cells of the soybean seed coat and affects abundance of PRP1, a proline-rich cell wall protein in the seed coat. Saline-soluble PRP1 is abundant in the developing seed coats of cultivar Richland (homozygous I, yellow), while it is significantly decreased in the pigmented isogenic mutant T157 (homozygous i, imperfect black). In this report, we examined soluble PRP1 in several cultivars containing alleles of the I locus which affect spatial distribution of pigmentation in the seed coat. We also characterized PRP1 in isolines with allelic variants of several other loci involved in seed coat pigmentation, including T and Im. The T gene is pleiotropic and affects both pubescence color and seed coat pigmentation and structure. Soluble PRP1 was abundant in the developing seed coats of lines with yellow seed (I or i ⁱ alleles) regardless of pubescence color, just as in Richland. Likewise, soluble PRP1 was decreased in pigmented seed coats (i ^k or i alleles) with grey (t) pubescence, as in T157. However, the total seed coat proteins were not extractable from pigmented seed coats with tawny pubescence (i, T genotypes) because they have proanthocyanidins that exhibit tannin properties. The dominant Im allele inhibits seed coat mottling (irregular patches of pigmentation) that occurs if plants are infected with soybean mosaic virus. PRP1 was 35 kDa in mottled (im) isolines and 34 kDa in non-mottled (Im) isolines. PRP2, which is expressed later in seed coat development and in the hypocotyl hooks of soybean seedlings, was also smaller in Im isolines. In summary, some of the anthocyanin mutations affect the quantity of soluble PRP1 polypeptides, while others correlate with structural changes in developmentally regulated proline-rich proteins.     

Quantitative proteomics of pomegranate varieties with contrasting seed hardness during seed development stages

In pomegranate (Punica granatum), seed hardness is an important trait directly affecting fruit marketability. However, seed formation in pomegranate has not been well studied. We investigated the genetic mechanism underlying pomegranate seed hardness by comparing protein expression profiles between soft- and hard-seeded varieties 60 and 120 days after flowering. We identified 1940 proteins, of which 399 were differentially expressed. Most of the differentially expressed proteins were involved in posttranslational modification and carbohydrate metabolism. Cell wall biosynthesis, which showed positive correlations with seed hardness, was selected as the candidate pathway. The mRNA levels of 14 proteins involved in cell wall biosynthesis were further analyzed by qPCR. Lignin biosynthesis-related differentially expressed proteins showed lower expression at protein and gene levels in a soft-seeded variety at the early stages. Moreover, cellulose biosynthesis-related differentially expressed proteins showed higher expression levels in the soft-seeded variety at 60 days after flowering. Thus, the soft-seeded variety showed lower lignin but higher cellulose biosynthesis at the early fruit developmental stage, suggesting that lignin and cellulose play opposing roles in cell wall formation in pomegranate seeds. Moreover, differentially expressed proteins involved in cell wall degradation showed higher expression levels in the soft-seeded variety at both developmental stages. These results suggested that differences in seed hardness between soft- and hard-seeded pomegranates might result from cell wall biosynthesis and also be affected by cell wall degradation. The present proteome-wide profiling of pomegranate genotypes with contrasting seed hardness adds to the current knowledge base of the molecular basis of seed hardness development.     

Maternal control of seed weight in rapeseed (Brassica napus L.): the causal link between the size of pod (mother,source) and seed (offspring,sink)

Seed size/weight is one of the key traits related to plant domestication and crop improvement. In rapeseed (Brassica napus L.) germplasm, seed weight shows extensive variation, but its regulatory mechanism is poorly understood. To identify the key mechanism of seed weight regulation, a systematic comparative study was performed. Genetic, morphological and cytological evidence showed that seed weight was controlled by maternal genotype, through the regulation of seed size mainly via cell number. The physiological evidence indicated that differences in the pod length might result in differences in pod wall photosynthetic area, carbohydrates and the final seed weight. We also identified two pleiotropic major quantitative trait loci that acted indirectly on seed weight via their effects on pod length. RNA‐seq results showed that genes related to pod development and hormones were significantly differentially expressed in the pod wall; genes related to development, cell division, nutrient reservoir and ribosomal proteins were all up‐regulated in the seeds of the large‐seed pool. Finally, we proposed a potential seed weight regulatory mechanism that is specific to rapeseed and novel in plants. The results demonstrate a causal link between the size of the pod (mother, source) and the seed (offspring, sink) in rapeseed, which provides novel insight into the maternal control of seed weight and will open a new research field in plants.     

Detection of Gene Expression in an Individual Cell Type within a Cell Mixture Using Microarray Analysis

Background

A central issue in the design of microarray-based analysis of global gene expression is the choice between using cells of single type and a mixture of cells. This study quantified the proportion of lipopolysaccharide (LPS) induced differentially expressed monocyte genes that could be measured in peripheral blood mononuclear cells (PBMC), and determined the extent to which gene expression in the non-monocyte cell fraction diluted or obscured fold changes that could be detected in the cell mixture.

Methodology/Principal Findings

Human PBMC were stimulated with LPS, and monocytes were then isolated by positive (Mono+) or negative (Mono−) selection. The non-monocyte cell fraction (MonoD) remaining after positive selection of monocytes was used to determine the effect of non-monocyte cells on overall expression. RNA from LPS-stimulated PBMC, Mono+, Mono− and MonoD samples was co-hybridised with unstimulated RNA for each cell type on oligonucleotide microarrays. There was a positive correlation in gene expression between PBMC and both Mono+ (0.77) and Mono− (0.61–0.67) samples. Analysis of individual genes that were differentially expressed in Mono+ and Mono− samples showed that the ability to detect expression of some genes was similar when analysing PBMC, but for others, differential expression was either not detected or changed in the opposite direction. As a result of the dilutional or obscuring effect of gene expression in non-monocyte cells, overall about half of the statistically significant LPS-induced changes in gene expression in monocytes were not detected in PBMC. However, 97% of genes with a four fold or greater change in expression in monocytes after LPS stimulation, and almost all (96–100%) of the top 100 most differentially expressed monocyte genes were detected in PBMC.

Conclusions/Significance

The effect of non-responding cells in a mixture dilutes or obscures the detection of subtle changes in gene expression in an individual cell type. However, for studies in which only the most highly differentially expressed genes are of interest, separating and analysing individual cell types may be unnecessary.     

Relationships between Respiration Rate and Adenylate and Carbohydrate Pools of the Soybean Fruit

Relationships between respiration rate and adenylate and carbohydrate pools of the soybean (Glycine max L. Merrill) fruit during rapid seed growth were evaluated. Plants at mid pod-fill were subjected to different concentrations of CO(2) to alter the amount of photosynthate produced and, thus, available to the fruit. Respiration rate of the intact fruits was measured, along with glucose, sucrose, and starch concentrations, adenylate energy charge (AEC), and total adenylate pool (SigmaAdN) in the pod wall, seed coat, and cotyledons. The concentration of sucrose remained relatively constant in the pod wall (1.0 milligram per 100 milligrams dry weight), seed coat (6.5 milligrams per 100 milligrams dry weight), and cotyledons (4.5 milligrams per 100 milligrams dry weight) at moderate and high respiration rates. Furthermore, AEC remained relatively constant in the pod wall (0.55), seed coat (0.24), and cotyledons (0.44) during changes in respiration rate. This suggests that the amount of assimilate transported to the fruit, and its flux through the sucrose pools of the fruit parts, were important in the regulation of the respiration rate of the fruit. The average SigmaAdN in the seed coat (1300 picomoles per milligram dry weight) was significantly greater than in the cotyledons (750 picomoles per milligram dry weight) and pod wall (300 picomoles per milligram dry weight). In addition, the SigmaAdN in the seed coat and cotyledons increased with increasing respiration rate of the fruit. The high SigmaAdN in the seed coat and its increase with increases in respiration rate of the fruit suggest that an energy-requiring process is involved in the movement of sucrose through the seed coat.     

赤霉素诱导甘蔗节间伸长的cDNA-AFLP差异显示

以‘新台糖22号’甘蔗为材料,在其伸长初期以200mg/L的赤霉素进行叶面喷施处理,对照喷清水,分别提取对照和处理(0、6、12、24h)的总RNA进行等量混合,获得2种不同处理的样品池,采用cDNA-AFLP技术对赤霉素诱导下甘蔗节间伸长的差异表达进行分析。结果显示:(1)通过169对引物组合的选择性扩增,共得到了约11 000条大小在50～700bp的cDNA片段,获得186条差异条带。(2)经反向Northern杂交,于结果显示阳性的TDFs中选取56个片段进行克隆和序列分析,获得56条大小在80～500bp的差异条带。(3)经BLAST分析,按功能可将获得的56条TDFs分为7类,分别为能量与代谢相关基因、未知功能蛋白、未知基因、植物抗性相关基因、细胞壁生物合成与修饰相关基因、信号传导相关基因和转录因子相关基因。该研究获得了一些与甘蔗节间伸长相关的差异基因片段,为进一步研究甘蔗节间伸长的分子机理奠定了基础。     

Seed coat development, anatomy and scanning electron microscopy of Harpagophytum procumbens (Devil's Claw), Pedaliaceae

Seed coat development of Harpagophytum procumbens (Devil's Claw) and the possible role of the mature seed coat in seed dormancy were studied by light microscopy (LM), transmission electron microscopy (TEM) and environmental scanning electron microscopy (ESEM). Very young ovules of H. procumbens have a single thick integument consisting of densely packed thin-walled parenchyma cells that are uniform in shape and size. During later developmental stages the parenchyma cells differentiate into 4 different zones. Zone 1 is the multi-layered inner epidermis of the single integument that eventually develops into a tough impenetrable covering that tightly encloses the embryo. The inner epidermis is delineated on the inside by a few layers of collapsed remnant endosperm cell wall layers and on the outside by remnant cell wall layers of zone 2, also called the middle layer. Together with the inner epidermis these remnant cell wall layers from collapsed cells may contribute towards seed coat impermeability. Zone 2 underneath the inner epidermis consists of large thin-walled parenchyma cells. Zone 3 is the sub-epidermal layers underneath the outer epidermis referred to as a hypodermis and zone 4 is the single outer seed coat epidermal layer. Both zones 3 and 4 develop unusual secondary wall thickenings. The primary cell walls of the outer epidermis and hypodermis disintegrated during the final stages of seed maturation, leaving only a scaffold of these secondary cell wall thickenings. In the mature seed coat the outer fibrillar seed coat consists of the outer epidermis and hypodermis and separates easily to reveal the dense, smooth inner epidermis of the seed coat. Outer epidermal and hypodermal wall thickenings develop over primary pit fields and arise from the deposition of secondary cell wall material in the form of alternative electron dense and electron lucent layers. ESEM studies showed that the outer epidermal and hypodermal seed coat layers are exceptionally hygroscopic. At 100% relative humidity within the ESEM chamber, drops of water readily condense on the seed surface and react in various ways with the seed coat components, resulting in the swelling and expansion of the wall thickenings. The flexible fibrous outer seed coat epidermis and hypodermis may enhance soil seed contact and retention of water, while the inner seed coat epidermis maintains structural and perhaps chemical seed dormancy due to the possible presence of inhibitors.     

A subtilisin-like serine protease essential for mucilage release from Arabidopsis seed coats

During Arabidopsis seed development large quantities of mucilage, composed of pectins, are deposited into the apoplast underneath the outer wall of the seed coat. Upon imbibition of mature seeds, the stored mucilage expands through hydration and breaks the outer cell wall that encapsulates the whole seed. Mutant seeds carrying loss-of-function alleles of AtSBT1.7 that encodes one of 56 Arabidopsis thaliana subtilisin-like serine proteases (subtilases) do not release mucilage upon hydration. Microscopic analysis of the mutant seed coat revealed no visible structural differences compared with wild-type seeds. Weakening of the outer primary wall using cation chelators triggered mucilage release from the seed coats of mutants. However, in contrast to mature wild-type seeds, the mutant's outer cell walls did not rupture at the radial walls of the seed coat epidermal cells, but instead opened at the chalazal end of the seed, and were released in one piece. In atsbt1.7, the total rhamnose and galacturonic acid contents, representing the backbone of mucilage, remained unchanged compared with wild-type seeds. Thus, extrusion and solubility, but not the initial deposition of mucilage, are affected in atsbt1.7 mutants. AtSBT1.7 is localized in the developing seed coat, indicating a role in testa development or maturation. The altered mode of rupture of the outer seed coat wall and mucilage release indicate that AtSBT1.7 triggers the accumulation, and/or activation, of cell wall modifying enzymes necessary either for the loosening of the outer primary cell wall, or to facilitate swelling of the mucilage, as indicated by elevated pectin methylesterase activity in developing atsbt1.7 mutant seeds.     

Internal recycling of respiratory CO2 in pods of chickpea (Cicer arietinum L.): the role of pod wall, seed coat, and embryo

It has previously been proposed that respiratory CO2 released from the embryo in grain legume pods is refixed by a layer of cells on the inner pod wall. In chickpea this refixation process is thought to be of significance to the seed carbon budget, particularly under drought. In this study it is reported that the excised embryo, seed coat, and pod wall in chickpea are all photosynthetically competent, but the pod wall alone is capable of net O2 evolution over and above respiration. The predominant role of the pod wall in refixation is supported by measurements of fixation of isotopically labelled CO2, which show that more than 80% of CO2 is fixed by this tissue when provided to the pod interior. Chlorophyll concentrations are of the same order for embryo, seed coat, and pod wall tissues in younger pods on both an area and a fresh weight basis, but decline differentially with development from 12-30 d after podding. Imaging of chlorophyll distribution in the pod wall suggests that less than 15% of chloroplasts are located in the inner layer of cells thought to refix CO2 in legumes; this would be sufficient to refix less than 40% of respired CO2. It is concluded that while all tissues of the pod are capable of refixing respiratory carbon, the entire pod wall is responsible for the majority of this process, rather than a specialized layer of cells on the inner epidermis. The role of this fixed carbon in the pod for reallocation to the seed is discussed     

Structure and expression analysis of rice paleo duplications

Having a well-known history of genome duplication, rice is a good model for studying structural and functional evolution of paleo duplications. Improved sequence alignment criteria were used to characterize 10 major chromosome-to-chromosome duplication relationships associated with 1440 paralogous pairs, covering 47.8% of the rice genome, with 12.6% of genes that are conserved within sister blocks. Using a micro-array experiment, a genome-wide expression map has been produced, in which 2382 genes show significant differences of expression in root, leaf and grain. By integrating both structural (1440 paralogous pairs) and functional information (2382 differentially expressed genes), we identified 115 paralogous gene pairs for which at least one copy is differentially expressed in one of the three tissues. A vast majority of the 115 paralogous gene pairs have been neofunctionalized or subfunctionalized as 88%, 89% and 96% of duplicates, respectively, expressed in grain, leaf and root show distinct expression patterns. On the basis of a Gene Ontology analysis, we have identified and characterized the gene families that have been structurally and functionally preferentially retained in the duplication showing that the vast majority (>85%) of duplicated have been either lost or have been subfunctionalized or neofunctionalized during 50–70 million years of evolution.     

In silico identification and characterization of putative differentially expressed genes involved in common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L.) seed development

Two genotypes of common bean (Phaseolus vulgaris L.) were studied to determine the structural cause of seed abortion in this species. In the non-abortive control (wild-type, cultivar BAT93), the histological analysis revealed a classical pattern of seed development and showed coordinated differentiation of the embryo proper, suspensor, endosperm tissue and seed coat. In contrast, the ethyl methanesulfonate (EMS) mutant (cultivar BAT93) showed disruption in the normal seed development leading to embryo abortion. Aborted embryos from these degenerate seeds showed abnormalities in suspensor and cotyledons at the globular, heart, torpedo and cotyledon stages. Exploring the feasibility of incorporating the available online bioinformatics databases, we identified 22 genes revealing high homology with genes involved in Arabidopsis thaliana embryo development and expressed in common bean immature seeds. The expression patterns of these genes were confirmed by RT–PCR. All genes were highly expressed in seed tissues. To study the expression profiles of isolated genes during Phaseolus embryogenesis, six selected genes were examined by quantitative RT–PCR analysis on the developing embryos of wild-type and EMS mutant plants. All selected genes were expressed differentially at different stages of embryo development. These results could help to improve understanding of the mechanism of common bean embryogenesis.