RNA-Seq profiling of a defective seed coat mutation in Glycine max reveals differential expression of proline-rich and other cell wall protein transcripts

Physical Seed Dormancy in Legumes: Molecular Advances and Perspectives

Physical dormancy of seeds is a form of dormancy due to the presence of an impermeable seed coat layer, and it represents a feature for plants to adapt to environmental changes over an extended period of phylogenetic evolution. However, in agricultural practice, physical dormancy is problematic. because it prevents timely and uniform seed germination. Therefore, physical dormancy is an important agronomical trait to target in breeding and domestication, especially for many leguminous crops. Compared to the well-characterized physiological dormancy, research progress on physical dormancy at the molecular level has been limited until recent years, due to the lack of suitable research materials. This review focuses on the structure of seed coat, factors affecting physical dormancy, genes controlling physical dormancy, and plants suitable for studying physical dormancy at the molecular level. Our goal is to provide a plethora of information for further molecular research on physical dormancy.

Transcript profiling of hairy vetch (Vicia villosa Roth) identified interesting genes for seed dormancy

Hairy vetch, a diploid annual legume species, has a robust growth habit, high biomass yield, and winter hardy characteristics. Seed hardness is a major constraint for growing hairy vetch commercially. Hard seeded cultivars are valuable as forages, whereas soft seeded and shatter resistant cultivars have advantages for their use as a cover crop. Transcript analysis of hairy vetch was performed to understand the genetic mechanisms associated with important hairy vetch traits. RNA was extracted from leaves, flowers, immature pods, seed coats, and cotyledons of contrasting soft and hard seeded "AU Merit" plants. A range of 31.22-79.18 Gb RNA sequence data per tissue sample were generated with estimated coverage of 1040-2639×. RNA sequence assembly and mapping of the contigs against the Medicago truncatula (V4.0) genome identified 76,422 gene transcripts. A total of 24,254 transcripts were constitutively expressed in hairy vetch tissues. Key genes, such as KNOX4 (a class II KNOTTED-like homeobox KNOXII gene), qHs1 (endo-1,4-β-glucanase), GmHs1-1 (calcineurin-like metallophosphoesterase), chitinase, shatterproof 1 and 2 (SHP1, SHP2), shatter resistant 1-5 (SHAT1-5)(NAC transcription factor), PDH1 (prephenate dehydrogenase 1), and pectin methylesterases with a potential role in seed hardness and pod shattering, were further explored based on genes involved in seed hardness from other species to query the hairy vetch transcriptome data. Identification of interesting candidate genes in hairy vetch can facilitate the development of improved cultivars with desirable seed characteristics for use as a forage and as a cover crop.

Overexpression of an ethylene-forming ACC oxidase (ACO) gene precedes the Minute Hilum seed coat phenotype in Glycine max

BACKGROUND

To elucidate features of seed development, we investigated the transcriptome of a soybean isoline from the germplasm collection that contained an introgressed allele known as minute hilum (mi) which confers a smaller hilum region where the seed attaches to the pod and also results in seed coat cracking surrounding the hilum region.

RESULTS

RNAs were extracted from immature seed from an extended hilum region (i.e., the hilum and a small ring of tissue surrounding the hilum in which the cracks form) at three different developmental stages:10-25, 25-50 and 50-100 mg seed fresh weight in two independent replicates for each stage. The transcriptomes of these samples from both the Clark isoline containing the mi allele (PI 547628, UC413, ii R t mi G), and its recurrent Clark 63 parent isoline (PI 548532, UC7, ii R T Mi g), which was used for six generations of backcrossing, were compared for differential expression of 88,648 Glyma models of the soybean genome Wm82.a2. The RNA sequence data obtained from the 12 cDNA libraries were subjected to padj value < 0.05 and at least two-fold expression differences to select with confidence genes differentially expressed in the hilum-containing tissue of the seed coat between the two lines. Glyma.09G008400 annotated as encoding an ethylene forming enzyme, ACC oxidase (ACO), was found to be highly overexpressed in the mi hilum region at 165 RPKMs (reads per kilobase per million mapped reads) compared to the standard line at just 0.03 RPKMs. Evidence of changes in expression of genes downstream of the ethylene pathway included those involved in auxin and gibberellin hormone action and extensive differences in expression of cell wall protein genes. These changes are postulated to determine the restricted hilum size and cracking phenotypes.

CONCLUSIONS

We present transcriptome and phenotypic evidence that substantially higher expression of an ethylene-forming ACO gene likely shifts hormone balance and sets in motion downstream changes resulting in a smaller hilum phenotype and the cracks observed in the minute hilum (mi) isoline as compared to its recurrent parent.

Mapping Quantitative Trait Loci for Soybean Seedling Shoot and Root Architecture Traits in an Inter-Specific Genetic Population

Wild soybean species (Glycine soja Siebold & Zucc.) comprise a unique resource to widen the genetic base of cultivated soybean [Glycine max (L.) Merr.] for various agronomic traits. An inter-specific mapping population derived from a cross of cultivar Williams 82 and PI 483460B, a wild soybean accession, was utilized for genetic characterization of root architecture traits. The objectives of this study were to identify and characterize quantitative trait loci (QTL) for seedling shoot and root architecture traits, as well as to determine additive/epistatic interaction effects of identified QTLs. A total of 16,469 single nucleotide polymorphisms (SNPs) developed for the Illumina beadchip genotyping platform were used to construct a high resolution genetic linkage map. Among the 11 putative QTLs identified, two significant QTLs on chromosome 7 were determined to be associated with total root length (RL) and root surface area (RSA) with favorable alleles from the wild soybean parent. These seedling root traits, RL (BARC_020495_04641 ~ BARC_023101_03769) and RSA (SNP02285 ~ SNP18129_Magellan), could be potential targets for introgression into cultivated soybean background to improve both tap and lateral roots. The RL QTL region harbors four candidate genes with higher expression in root tissues: Phosphofructokinase (Glyma.07g126400), Snf7 protein (Glyma.07g127300), unknown functional gene (Glyma.07g127900), and Leucine Rich-Repeat protein (Glyma.07g127100). The novel alleles inherited from the wild soybean accession could be used as molecular markers to improve root system architecture and productivity in elite soybean lines.

Comparative proteomic and transcriptomic analyses provide new insight into the formation of seed size in castor bean

BACKGROUND

Little is known about the molecular basis of seed size formation in endospermic seed of dicotyledons. The seed of castor bean (Ricinus communis L.) is considered as a model system in seed biology studies because of its persistent endosperms throughout seed development.

RESULTS

We compared the size of endosperm and endospermic cells between ZB107 and ZB306 and found that the larger seed size of ZB107 resulted from a higher cell count in the endosperm, which occupy a significant amount of the total seed volume. In addition, fresh weight, dry weight, and protein content of seeds were remarkably higher in ZB107 than in ZB306. Comparative proteomic and transcriptomic analyses were performed between large-seed ZB107 and small-seed ZB306, using isobaric tags for relative and absolute quantification (iTRAQ) and RNA-seq technologies, respectively. A total of 1416 protein species were identified, of which 173 were determined as differentially abundant protein species (DAPs). Additionally, there were 9545 differentially expressed genes (DEGs) between ZB306 and ZB107. Functional analyses revealed that these DAPs and DEGs were mainly involved in cell division and the metabolism of carbohydrates and proteins.

CONCLUSIONS

These findings suggest that both cell number and storage-component accumulation are critical for the formation of seed size, providing new insight into the potential mechanisms behind seed size formation in endospermic seeds.

Big data from small tissues: extraction of high-quality RNA for RNA-sequencing from different oilseed Brassica seed tissues during seed development

BACKGROUND

Obtaining high-quality RNA for gene expression analyses from different seed tissues is challenging due to the presence of various contaminants, such as polyphenols, polysaccharides and lipids which interfere with RNA extraction methods. At present, the available protocols for extracting RNA from seeds require high amounts of tissue and are mainly focused on extracting RNA from whole seeds. However, extracting RNA at the tissue level enables more detailed studies regarding tissue specific transcriptomes during seed development.

RESULTS

Seeds from heart stage embryo to mature developmental stages of Brassica napus and B. oleracea were sampled for isolation of the embryo, endosperm and seed coat tissues. Ovules and ovary wall tissue were also collected from pre-fertilized buds. Subsequent to testing several RNA extraction methods, modifications applied to E.Z.N.A. Plant RNA and Picopure RNA Isolation kit extraction methods resulted in RNA with high yield and quality. Furthermore, the use of polyvinylpolypyrrolidone for seed coats and endosperm at green stages resulted in high-quality RNA. As a result of the introduced modifications to established RNA extraction methods, the RNA from all the above-mentioned tissues presented clear 28S and 18S bands and high RIN values, ranging from 7.0 to 10.0. The protocols reported in this study are not only suitable for different and challenging seed tissue types, but also enable the extraction of high-quality RNA using only 2 to 3 mg of starting tissue.

CONCLUSIONS

Here, we present efficient, reproducible and reliable high-quality RNA extraction methods for diverse oilseed Brassica spp reproductive tissue types including pre-fertilization and developing seed tissues for diploid and polyploid species. The high-quality RNA obtained is suitable for RNA-Sequencing and subsequent gene expression analysis.

A QTL associated with high seed coat cracking rate of a leading Japanese soybean variety

Seed coat cracking in soybeans [Glycine max (L). Merr.] leads to commercial and agronomic losses. The Japanese elite soybean cultivar 'Fukuyutaka' is often used as a parent for breeding, but its high rate of seed coat cracking is an obstacle to its further use in breeding programs. To establish a DNA marker-assisted selection system for seed coat cracking, genetic factors related to high rates of seed coat cracking were surveyed, and a quantitative trait locus (QTL) with a stable effect on seed coat cracking in both years of a two-year replication experiment was detected on chromosome 20. Comparison of a set of near-isogenic lines (NILs) around this locus verified that the presence of the 'Fukuyutaka' allele significantly increased seed coat cracking in the kernel. The locus is located in a genomic region spanning 3.2 Mb. Marker-assisted selection for the locus will improve the selection efficiency of 'Fukuyutaka'-derived breeding populations.

Comparative morphology and transcriptome analysis reveals distinct functions of the primary and secondary laticifer cells in the rubber tree

Laticifers are highly specialized cells that synthesize and store natural rubber. Rubber trees (Hevea brasiliensis Muell. Arg.) contain both primary and secondary laticifers. Morphological and functional differences between the two types of laticifers are largely unknown, but such information is important for breeding and cultivation practices. Morphological comparison using paraffin sections revealed only distribution differences: the primary laticifers were distributed randomly, while the secondary laticifers were distributed in concentric rings. Using isolated laticifer networks, the primary laticifers were shown to develop via intrusive "budding" and formed necklace-like morphology, while the secondary laticifers developed straight and smooth cell walls. Comparative transcriptome analysis indicated that genes involved in cell wall modification, such as pectin esterase, lignin metabolic enzymes, and expansins, were highly up-regulated in the primary laticifers and correspond to its necklace-like morphology. Genes involved in defense against biotic stresses and rubber biosynthesis were highly up-regulated in the primary laticifers, whereas genes involved in abiotic stresses and dormancy were up-regulated in the secondary laticifers, suggesting that the primary laticifers are more adequately prepared to defend against biotic stresses, while the secondary laticifers are more adequately prepared to defend against abiotic stresses. Therefore, the two types of laticifers are morphologically and functionally distinct.

A Combined Comparative Transcriptomic, Metabolomic, and Anatomical Analyses of Two Key Domestication Traits: Pod Dehiscence and Seed Dormancy in Pea (Pisum sp.)

The origin of the agriculture was one of the turning points in human history, and a central part of this was the evolution of new plant forms, domesticated crops. Seed dispersal and germination are two key traits which have been selected to facilitate cultivation and harvesting of crops. The objective of this study was to analyze anatomical structure of seed coat and pod, identify metabolic compounds associated with water-impermeable seed coat and differentially expressed genes involved in pea seed dormancy and pod dehiscence. Comparative anatomical, metabolomics, and transcriptomic analyses were carried out on wild dormant, dehiscent Pisum elatius (JI64, VIR320) and cultivated, indehiscent Pisum sativum non-dormant (JI92, Cameor) and recombinant inbred lines (RILs). Considerable differences were found in texture of testa surface, length of macrosclereids, and seed coat thickness. Histochemical and biochemical analyses indicated genotype related variation in composition and heterogeneity of seed coat cell walls within macrosclereids. Liquid chromatography-electrospray ionization/mass spectrometry and Laser desorption/ionization-mass spectrometry of separated seed coats revealed significantly higher contents of proanthocyanidins (dimer and trimer of gallocatechin), quercetin, and myricetin rhamnosides and hydroxylated fatty acids in dormant compared to non-dormant genotypes. Bulk Segregant Analysis coupled to high throughput RNA sequencing resulted in identification of 770 and 148 differentially expressed genes between dormant and non-dormant seeds or dehiscent and indehiscent pods, respectively. The expression of 14 selected dormancy-related genes was studied by qRT-PCR. Of these, expression pattern of four genes: porin (MACE-S082), peroxisomal membrane PEX14-like protein (MACE-S108), 4-coumarate CoA ligase (MACE-S131), and UDP-glucosyl transferase (MACE-S139) was in agreement in all four genotypes with Massive analysis of cDNA Ends (MACE) data. In case of pod dehiscence, the analysis of two candidate genes (SHATTERING and SHATTERPROOF) and three out of 20 MACE identified genes (MACE-P004, MACE-P013, MACE-P015) showed down-expression in dorsal and ventral pod suture of indehiscent genotypes. Moreover, MACE-P015, the homolog of peptidoglycan-binding domain or proline-rich extensin-like protein mapped correctly to predicted Dpo1 locus on PsLGIII. This integrated analysis of the seed coat in wild and cultivated pea provides new insight as well as raises new questions associated with domestication and seed dormancy and pod dehiscence.

Transcriptome Analysis of a New Peanut Seed Coat Mutant for the Physiological Regulatory Mechanism Involved in Seed Coat Cracking and Pigmentation

Seed-coat cracking and undesirable color of seed coat highly affects external appearance and commercial value of peanuts (Arachis hypogaea L.). With an objective to find genetic solution to the above problems, a peanut mutant with cracking and brown colored seed coat (testa) was identified from an EMS treated mutant population and designated as "peanut seed coat crack and brown color mutant line (pscb)." The seed coat weight of the mutant was almost twice of the wild type, and the germination time was significantly shorter than wild type. Further, the mutant had lower level of lignin, anthocyanin, proanthocyanidin content, and highly increased level of melanin content as compared to wild type. Using RNA-Seq, we examined the seed coat transcriptome in three stages of seed development in the wild type and the pscb mutant. The RNA-Seq analysis revealed presence of highly differentially expressed phenylpropanoid and flavonoid pathway genes in all the three seed development stages, especially at 40 days after flowering (DAF40). Also, the expression of polyphenol oxidases and peroxidase were found to be activated significantly especially in the late seed developmental stage. The genome-wide comparative study of the expression profiles revealed 62 differentially expressed genes common across all the three stages. By analyzing the expression patterns and the sequences of the common differentially expressed genes of the three stages, three candidate genes namely c36498_g1 (CCoAOMT1), c40902_g2 (kinesin), and c33560_g1 (MYB3) were identified responsible for seed-coat cracking and brown color phenotype. Therefore, this study not only provided candidate genes but also provided greater insights and molecular genetic control of peanut seed-coat cracking and color variation. The information generated in this study will facilitate further identification of causal gene and diagnostic markers for breeding improved peanut varieties with smooth and desirable seed coat color.