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

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.

Knockout of OsPRP1, a gene encoding proline-rich protein, confers enhanced cold sensitivity in rice (Oryza sativa L.) at the seedling stage

Proline-rich proteins (PRPs) play multiple physiological and biochemical roles in plant growth and stress response. In this study, we reported that the knockout of OsPRP1 induced cold sensitivity in rice. Mutant plants were generated by CRISPR/Cas9 technology to investigate the role of OsPRP1 in cold stress and 26 mutant plants were obtained in T₀ generation with the mutation rate of 85% including 15% bi-allelic, 53.3% homozygous, and 16.7% heterozygous and 16 T-DNA-free lines in T₁ generation. The conserved amino acid sequence was changed and the expression level of OsPRP1 was reduced in mutant plants. The OsPRP1 mutant plants displayed more sensitivity to cold stress and showed low survival rate with decreased root biomass than wild-type (WT) and homozygous mutant line with large fragment deletion was more sensitive to low temperature. Mutant lines accumulated less antioxidant enzyme activity and lower levels of proline, chlorophyll, abscisic acid (ABA), and ascorbic acid (AsA) content relative to WT under low-temperature stress. The changes of antioxidant enzymes were examined in the leaves and roots with exogenous salicylic acid (SA) treatment which resulted in increased activity of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) under cold stress, while enzyme antioxidant activity was lower in untreated seedlings which showed that exogenous SA pretreatment could alleviate the low-temperature stress in rice. Furthermore, the expression of three genes encoding antioxidant enzyme activities (SOD4, POX1, and OsCAT3) was significantly down-regulated in the mutant lines as compared to WT. These results suggested that OsPRP1 enhances cold tolerance by modulating antioxidants and maintaining cross talk through signaling pathways. Therefore, OsPRP1 gene could be exploited for improving cold tolerance in rice and CRISPR/Cas9 technology is helpful to study the function of a gene by analyzing the phenotypes of knockout mutants generated.

Occurrence and tolerance mechanisms of seed cracking under low temperatures in soybean (Glycine max)

MAIN CONCLUSION

In soybean, occurrence of, or tolerance to, seed cracking under low temperatures may be related to the presence or absence, respectively, of proanthocyanidin accumulation in the seed coat dorsal region. Soybean seeds sometimes undergo cracking during low temperatures in summer. In this study, we focused on the occurrence and tolerance mechanisms of low-temperature-induced seed cracking in the sensitive yellow soybean cultivar Yukihomare and the tolerant yellow soybean breeding line Toiku 248. Yukihomare exhibited seed cracking when subjected to a 21-day low-temperature treatment from 10 days after flowering. In yellow soybeans, seed coat pigmentation is inhibited, leading to low proanthocyanidin levels in the seed coat. Proanthocyanidins accumulated on the dorsal side of the seed coat in Yukihomare under the 21-day low-temperature treatment. In addition, a straight seed coat split occurred on the dorsal side at the full-sized seed stage, resulting in seed cracking in this cultivar. Conversely, proanthocyanidin accumulation was suppressed throughout the seed coat in low-temperature-treated Toiku 248. We propose the following mechanism of seed cracking: proanthocyanidin accumulation and subsequent lignin deposition under low temperatures affects the physical properties of the seed coat, making it more prone to splitting. Further analyses uncovered differences in the physical properties of the seed coat between Yukihomare and Toiku 248. In particular, seed coat hardness decreased in Yukihomare, but not in Toiku 248, under the low-temperature treatment. Seed coat flexibility was higher in Toiku 248 than in Yukihomare under the low-temperature treatment, suggesting that the seed coat of low-temperature-treated Toiku 248 is more flexible than that of low-temperature-treated Yukihomare. These physical properties of the Toiku 248 seed coat observed under low-temperature conditions may contribute to its seed-cracking tolerance.

Accumulation of proanthocyanidins and/or lignin deposition in buff-pigmented soybean seed coats may lead to frequent defective cracking

MAIN CONCLUSION

Defective cracking frequently occurs in buff-pigmented soybean seed coats, where proanthocyanidins accumulate and lignin is deposited, suggesting that proanthocyanidins and/or lignin may change physical properties and lead to defective cracking. In the seed production of many yellow soybean (Glycine max) cultivars, very low percentages of self-pigmented seeds are commonly found. This phenomenon is derived from a recessive mutation of the I gene inhibiting seed coat pigmentation. In Japan, most of these self-pigmented seeds are buff-colored, and frequently show multiple defective cracks in the seed coat. However, it is not known why cracking occurs specifically in buff seed coats. In this study, quantitative analysis was performed between yellow and buff soybean seed coats. Compared with yellow soybeans, in which defective cracking rarely occurs, contents of proanthocyanidins (PAs) and lignin were significantly higher in buff seed coats. Histochemical data of PAs and lignin in the seed coats strongly supported this result. Measurements of the physical properties of seed coats using a texture analyzer showed that a hardness value was significantly decreased in the buff seed coats. These results suggest that PA accumulation and/or lignin deposition may affect the physical properties of buff seed coats and lead to the defective cracking. This work contributes to understanding of the mechanism of defective cracking, which decreases the seed quality of soybean and related legumes.

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

The plant cell wall performs a number of essential functions including providing shape to many different cell types and serving as a defense against potential pathogens. The net pattern mutation creates breaks in the seed coat of soybean (Glycine max) because of ruptured cell walls. Using RNA-Seq, we examined the seed coat transcriptome from three stages of immature seed development in two pairs of isolines with normal or defective seed coat phenotypes due to the net pattern. The genome-wide comparative study of the transcript profiles of these isolines revealed 364 differentially expressed genes in common between the two varieties that were further divided into different broad functional categories. Genes related to cell wall processes accounted for 19% of the differentially expressed genes in the middle developmental stage of 100-200 mg seed weight. Within this class, the cell wall proline-rich and glycine-rich protein genes were highly differentially expressed in both genetic backgrounds. Other genes that showed significant expression changes in each of the isoline pairs at the 100-200 mg seed weight stage were xylem serine proteinase, fasciclin-related genes, auxin and stress response related genes, TRANSPARENT TESTA 1 (TT1) and other transcription factors. The mutant appears to shift the timing of either the increase or decrease in the levels of some of the transcripts. The analysis of these data sets reveals the physiological changes that the seed coat undergoes during the formation of the breaks in the cell wall.

[Progress in genes related to seed-coat color in soybean]

Seed-coat color has changed from black to yellow during natural and artificial selection of cultivated soybean from wild soybean, and it is also an important morphological marker. Therefore, discovering genes related to the soybean seed-coat color will play a very important role in breeding and evolutionary study. Different seed-coat colors caused by deposition of various anthocyanin pigments. Although pigmentation has been well dissected at molecular level in several plant species, the genes controlling natural variation of seed-coat color in soybean remain to be unknown. Genes related to seed-coat color in soybean were discussed in this paper, including 5 genetic loci (I, T, W1, R and O). Locus I is located in a region that riches in chalcone synthase (CHS) genes on chromosome 8. Gene CHS is a multi-gene family with highly conserved sequences in soybean. Locus T located on chromosome 6 has been cloned and verified, which encodes a flavon-oid-3'-hydroxylase. Mutant of F3'H can not interact with the heme-binding domain due to lack of conservative domain GGEK caused by a nucleotide deletion in the coding region of F3'H. Locus R is located between A668-1 and K387-1 on chromosome 9 (linkage group K). This locus may encode a R2R3 MYB transcription factor or a UDP flavonoid 3-O glyco-syltransferase. Locus O is located between Satt207 and Satt493 on chromosome 8 (linkage group A2) and its molecular characteristics has not been characterized. Locus W1 may be a homology of F3'5'H gene.

OsPRP3, a flower specific proline-rich protein of rice, determines extracellular matrix structure of floral organs and its overexpression confers cold-tolerance

Proline-rich protein (PRP), a cell wall protein of plant, has been studied in many plant species. Yet, none of the PRPs has been functionally elucidated. Here we report a novel flower-specific PRP designated OsPRP3 from rice. Expression analysis showed that the OsPRP3 transcript was mainly present in rice flower and accumulated abundantly during the late stage of the flower development. To study the function of OsPRP3, we constructed and transformed a binary vector containing a full clone of OsPRP3 in sense orientation and also an RNAi vector to achieve overexpression and knockout of the gene, respectively. Our overexpression plants showed a significant increase in cold tolerance than the WT plants which is conferred by the accumulation of OsPRP3 protein during cold treatment. Further the microscopic analysis revealed that OsPRP3 enhances the cell wall integrity in the cold tolerant plant and confers cold-tolerance in rice. Microscopic analysis of the RNAi mutant flower revealed that blocking OsPRP3 function caused significant defects in floral organogenesis. Taken together, the results suggested that OsPRP3 is a cell wall protein, playing a crucial role in determining extracellular matrix structure of floral organs.

QTL analysis of seed-flooding tolerance in soybean (Glycine max [L.] Merr.)

In soybean (Glycine max [L.] Merr.), varieties with seed-flooding tolerance at the geminating stage are desirable for breeding in countries with much rainfall at sowing time. Our study revealed great intervarietal variation in seed-flooding tolerance as evaluated by germination rate (GR) and normal seedling rate (NS). Pigmented seed coat and small seed weight tended to give a positive effect on seed-flooding tolerance. Subsequently, QTL analysis of GR and NS were performed and a total of four QTLs were detected. Among them, Sft1 on the linkage group H (LG_H) exhibited a large effect on GR after a 24-h treatment; however, Sft2 near the I locus on LG_A2 involved in seed coat pigmentation exhibited the largest effect on seed-flooding tolerance. Sft1, Sft3 and Sft4 were independent of seed coat color and seed weight. Based on the results, we discussed the physiological effects of genetic factors responsible for seed-flooding tolerance in soybean.

Genomic amplification of the Gret1 retroelement in white-fruited accessions of wild vitis and interspecific hybrids

Retrotransposons are retrovirus-related mobile sequences that have the potential to replicate via RNA intermediates and increase the genome size by insertion into new sites. The retroelement, Gret1, has been identified as playing a key role in generating fruit color variation in cultivated grape (Vitis vinifera L.) due to its insertion into the promoter of VvMybA1. Fruit color variation is an important distinguishing feature of cultivated grapes and virtually no fruit color variation is observed in wild grape species. The presence and relative copy number of Gret1 was assessed using quantitative PCR on 22 different Vitis species, only four of which (plus interspecific hybrids) are known to contain white accessions. Gret1 copy number was observed to vary by species as well as by color within species and was significantly higher in white-fruited accessions across all taxa tested. Additionally, genomic regions surrounding Gret1 insertion were sequenced in white V. vinifera, hybrid, V. labrusca, V. aestivalis, and V. riparia accessions.

Analysis of flavonoids in pubescence of soybean near-isogenic lines for pubescence color loci

T and Td loci control pubescence color of soybean with epistatic effects (TT TdTd, tawny; TT tdtd, light tawny or near-gray; tt TdTd or tt tdtd, gray). The objective of this study was to investigate the nature of flavonoids in the pubescence of near-isogenic lines (NILs) for these loci. Flavonoids were extracted with methanol from pubescence of cultivar Clark with tawny pubescence (TT TdTd) and its NILs; from Clark-t with gray pubescence (tt TdTd) and Clark-td with near-gray pubescence (TT tdtd); and from a pair of NILs, To7B with tawny (TT TdTd) and To7G with gray pubescence (tt TdTd). Primary flavonoids were flavone aglycones. Luteolin and apigenin were predominant in NILs with tawny and gray pubescence, respectively. Small amount of 7-O-glucosides of the 2 flavones were also detected. Alleles at T locus were associated with 3'-hydroxylation in the B-ring of the flavones. The primary flavonoids in Clark-td were luteolin similar to Clark, but its amount was halved. High performance liquid chromatography peaks probably corresponding to isoflavonoids were found only in Clark-td in 2003. However, the peaks were not observed in 2005. The above results suggest that Td may encode a structural or a regulatory gene controlling flavone biosynthesis. Pigments remained visible in pubescence after methanol extraction, suggesting that a major part of the pigments was polymerized. Surface rinsing experiments revealed that flavone aglycones exist outside the surface of cells.

Molecular linkage mapping and phylogeny of the chalcone synthase multigene family in soybean

Chalcone synthase (CHS), the key enzyme in the flavonoid biosynthesis pathway, is encoded by a multigene family, CHS1-CHS8 and dCHS1 in soybean. A tandem repeat of CHS1, CHS3 and CHS4, and dCHS1 that is believed to be located in the vicinity comprises the I locus that suppresses coloration of the seed coat. This study was conducted to determine the location of all CHS members by using PCR-based DNA markers. Primers were constructed based on varietal differences in either the nucleotide sequence of the 5'-upstream region or the first intron of two cultivars, Misuzudaizu, with a yellow seed coat (II), and Moshidou Gong 503, with a brown seed coat (ii). One hundred and fifty recombinant inbred lines that originated from a cross between these two cultivars were used for linkage mapping together with 360 markers. Linkage mapping confirmed that CHS1, CHS3, CHS4, dCHS1, and the I locus are located at the same position in molecular linkage group (MLG) A2. CHS5 was mapped at a distance of 0.3 cM from the gene cluster. CHS2 and CHS6 were located in the middle region of MLGs A1 and K, respectively, while CHS7 and CHS8 were found at the distal end of MLGs D1a and B1, respectively. Phylogenetic analysis indicated that CHS1, CHS3, CHS4, and CHS5 are closely related, suggesting that gene duplication may have occurred repeatedly to form the I locus. In addition, CHS7 and CHS8 located at the distal end and CHS2, CHS6, and CHS members around the I locus located around the middle of the MLG are also related. Ancient tetraploidization and repeated duplication may be responsible for the evolution of the complex genetic loci of the CHS multigene family in soybean.

Cloning of the pleiotropic T locus in soybean and two recessive alleles that differentially affect structure and expression of the encoded flavonoid 3' hydroxylase

Three loci (I, R, and T) control pigmentation of the seed coats in Glycine max and are genetically distinct from those controlling flower color. The T locus also controls color of the trichome hairs. We report the identification and isolation of a flavonoid 3' hydroxylase gene from G. max (GmF3'H) and the linkage of this gene to the T locus. This GmF3'H gene was highly expressed in early stages of seed coat development and was expressed at very low levels or not at all in other tissues. Evidence that the GmF3'H gene is linked to the T locus came from the occurrence of multiple RFLPs in lines with varying alleles of the T locus, as well as in a population of plants segregating at that locus. GmF3'H genomic and cDNA sequence analysis of color mutant lines with varying t alleles revealed a frameshift mutation in one of the alleles. In another line derived from a mutable genetic stock, the abundance of the mRNAs for GmF3'H was dramatically reduced. Isolation of the GmF3'H gene and its identification as the T locus will enable investigation of the pleiotropic effects of the T locus on cell wall integrity and its involvement in the regulation of the multiple branches of the flavonoid pathway in soybean.

Characterization and expression of four proline-rich cell wall protein genes in Arabidopsis encoding two distinct subsets of multiple domain proteins

We have characterized the molecular organization and expression of four proline-rich protein genes from Arabidopsis (AtPRPs). These genes predict two classes of cell wall proteins based on DNA sequence identity, repetitive motifs, and domain organization. AtPRP1 and AtPRP3 encode proteins containing an N-terminal PRP-like domain followed by a C-terminal domain that is biased toward P, T, Y, and K. AtPRP2 and AtPRP4 represent a second, novel group of PRP genes that encode two-domain proteins containing a non-repetitive N-terminal domain followed by a PRP-like region rich in P, V, K, and C. Northern hybridization analysis indicated that AtPRP1 and AtPRP3 are exclusively expressed in roots, while transcripts encoding AtPRP2 and AtPRP4 were most abundant in aerial organs of the plant. Histochemical analyses of promoter/beta-glucuronidase fusions localized AtPRP3 expression to regions of the root containing root hairs. AtPRP2 and AtPRP4 expression was detected in expanding leaves, stems, flowers, and siliques. In addition, AtPRP4 expression was detected in stipules and during the early stages of lateral root formation. These studies support a model for involvement of PRPs in specifying cell-type-specific wall structures, and provide the basis for a genetic approach to dissect the function of PRPs during growth and development.

Assessment of the protein quality of nine northern adapted yellow and brown seed coated soybean cultivars by amino acid analysis

Accurate and detailed amino acid determinations were carried out on nine northern adapted soybean cultivars to ascertain whether their amino acid profiles could be used as potentially useful indices for assessing their protein quality. The cultivars were Maple Amber, Maple Donovan, Maple Glen, Maple Isle, Maple Presto, Maple Ridge, and three brown seed coat near-isogenic lines, Maple Presto Brown, Maple Ridge Brown, and Maple Arrow Brown. Their total protein and amino acid composition were compared with those of an established cultivar, Maple Arrow. Mean protein values for the new cultivars ranged from 30.1 to 33.1% compared to Maple Arrow, which was 33.2%. The total nitrogen content was also variable among these cultivars, ranging from 5.0 to 5.4%. All nine Maple series soybean cultivars were higher in their essential amino acid (EAA) content, that is, EAA(9) = 45.2-46.5%, than the FAO/WHO reference protein pattern value of EAA(9) = 33.9%, for a 2-5-year-old child. Each of the nine new soybean cultivars was limited only in methionine and to a lesser extent in valine and isoleucine and had a protein digestibility corrected amino acid score of 91% for all cultivars, compared to the value of egg protein (97%). These results suggest that the most accurate evaluation of protein quality in soybeans, and possibly other legumes and cereals, is by the protein digestibility-corrected amino acid score.