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Yuhazu M, Mikuriya S, Mori A, Dwiyanti MS, Senda M, Kanazawa A. Pigmentation of soybean seed coats via a mutation that abolishes production of multiple-phased siRNAs of chalcone synthase genes. Genes Genet Syst 2024; 99:n/a. [PMID: 38382925 DOI: 10.1266/ggs.23-00260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024] Open
Abstract
Lack of pigmentation in seed coats of soybean is caused by natural RNA silencing of chalcone synthase (CHS) genes. This phenomenon is an evolutionary consequence of structural changes in DNA that resulted in the production of double-stranded RNAs (dsRNAs) that trigger RNA degradation. Here we determined that a mutant with pigmented seed coats derived from a cultivar that lacked the pigmentation had a deletion between DNA regions ICHS1 and a cytochrome P450 gene; the deletion included GmIRCHS, a candidate gene that triggers CHS RNA silencing via production of CHS dsRNAs. We also characterized CHS short interfering RNAs (siRNAs) produced in the wild-type seed coats that had CHS RNA silencing. Phased 21-nt CHS siRNAs were detected in all 21 phases and were widely distributed in exon 2 of CHS7, which indicates commonality in the pattern of RNA degradation in natural CHS RNA silencing between distantly related species. These results with the similarities in the rearrangements found in spontaneous mutants suggest that the structural organization that generates dsRNAs that trigger phased siRNA production is vulnerable to further structural changes, which eventually abolish the induction of RNA silencing.
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Affiliation(s)
| | - Shun Mikuriya
- Research Faculty of Agriculture, Hokkaido University
| | - Ayumi Mori
- Research Faculty of Agriculture, Hokkaido University
| | | | - Mineo Senda
- Faculty of Agriculture and Life Science, Hirosaki University
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Yang Y, Zhao T, Wang F, Liu L, Liu B, Zhang K, Qin J, Yang C, Qiao Y. Identification of candidate genes for soybean seed coat-related traits using QTL mapping and GWAS. FRONTIERS IN PLANT SCIENCE 2023; 14:1190503. [PMID: 37384360 PMCID: PMC10293793 DOI: 10.3389/fpls.2023.1190503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 04/17/2023] [Indexed: 06/30/2023]
Abstract
Seed coat color is a typical morphological trait that can be used to reveal the evolution of soybean. The study of seed coat color-related traits in soybeans is of great significance for both evolutionary theory and breeding practices. In this study, 180 F10 recombinant inbred lines (RILs) derived from the cross between the yellow-seed coat cultivar Jidou12 (ZDD23040, JD12) and the wild black-seed coat accession Y9 (ZYD02739) were used as materials. Three methods, single-marker analysis (SMA), interval mapping (IM), and inclusive composite interval mapping (ICIM), were used to identify quantitative trait loci (QTLs) controlling seed coat color and seed hilum color. Simultaneously, two genome-wide association study (GWAS) models, the generalized linear model (GLM) and mixed linear model (MLM), were used to jointly identify seed coat color and seed hilum color QTLs in 250 natural populations. By integrating the results from QTL mapping and GWAS analysis, we identified two stable QTLs (qSCC02 and qSCC08) associated with seed coat color and one stable QTL (qSHC08) related to seed hilum color. By combining the results of linkage analysis and association analysis, two stable QTLs (qSCC02, qSCC08) for seed coat color and one stable QTL (qSHC08) for seed hilum color were identified. Upon further investigation using Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, we validated the previous findings that two candidate genes (CHS3C and CHS4A) reside within the qSCC08 region and identified a new QTL, qSCC02. There were a total of 28 candidate genes in the interval, among which Glyma.02G024600, Glyma.02G024700, and Glyma.02G024800 were mapped to the glutathione metabolic pathway, which is related to the transport or accumulation of anthocyanin. We considered the three genes as potential candidate genes for soybean seed coat-related traits. The QTLs and candidate genes detected in this study provide a foundation for further understanding the genetic mechanisms underlying soybean seed coat color and seed hilum color and are of significant value in marker-assisted breeding.
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Affiliation(s)
- Yue Yang
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Tiantian Zhao
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Fengmin Wang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
- Hebei Key Laboratory of Molecular and Cellular Biology, Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Hebei Collaboration Innovation Center for Cell Signaling, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Luping Liu
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Bingqiang Liu
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Kai Zhang
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Jun Qin
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Chunyan Yang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Yake Qiao
- College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
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Yamaguchi N, Sato Y, Taguchi-Shiobara F, Yamashita K, Kawasaki M, Ishimoto M, Senda M. A novel QTL associated with tolerance to cold-induced seed cracking in the soybean cultivar Toyomizuki. BREEDING SCIENCE 2023; 73:204-211. [PMID: 37404349 PMCID: PMC10316309 DOI: 10.1270/jsbbs.22066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/25/2022] [Indexed: 07/06/2023]
Abstract
Low temperatures after flowering cause seed cracking (SC) in soybean. Previously, we reported that proanthocyanidin accumulation on the dorsal side of the seed coat, controlled by the I locus, may lead to cracked seeds; and that homozygous IcIc alleles at the I locus confer SC tolerance in the line Toiku 248. To discover new genes related to SC tolerance, we evaluated the physical and genetic mechanisms of SC tolerance in the cultivar Toyomizuki (genotype II). Histological and texture analyses of the seed coat revealed that the ability to maintain hardness and flexibility under low temperature, regardless of proanthocyanidin accumulation in the dorsal seed coat, contributes to SC tolerance in Toyomizuki. This indicated that the SC tolerance mechanism differed between Toyomizuki and Toiku 248. A quantitative trait loci (QTL) analysis of recombinant inbred lines revealed a new, stable QTL related to SC tolerance. The relationship between this new QTL, designated as qCS8-2, and SC tolerance was confirmed in residual heterozygous lines. The distance between qCS8-2 and the previously identified QTL qCS8-1, which is likely the Ic allele, was estimated to be 2-3 Mb, so it will be possible to pyramid these regions to develop new cultivars with increased SC tolerance.
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Affiliation(s)
- Naoya Yamaguchi
- Hokkaido Research Organization Tokachi Agricultural Experiment Station, Shinsei, Memuro-cho, Kasai-gun, Hokkaido 082-0081, Japan
| | - Yumi Sato
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Fumio Taguchi-Shiobara
- Institute of Crop Science, The National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518, Japan
| | - Kazuki Yamashita
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Michio Kawasaki
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Masao Ishimoto
- Institute of Crop Science, The National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518, Japan
| | - Mineo Senda
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo, Hirosaki, Aomori 036-8561, Japan
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Novel Seed Size: A Novel Seed-Developing Gene in Glycine max. Int J Mol Sci 2023; 24:ijms24044189. [PMID: 36835599 PMCID: PMC9967547 DOI: 10.3390/ijms24044189] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023] Open
Abstract
Soybean-seed development is controlled in multiple ways, as in many known regulating genes. Here, we identify a novel gene, Novel Seed Size (NSS), involved in seed development, by analyzing a T-DNA mutant (S006). The S006 mutant is a random mutant of the GmFTL4pro:GUS transgenic line, with phenotypes with small and brown seed coats. An analysis of the metabolomics and transcriptome combined with RT-qPCR in the S006 seeds revealed that the brown coat may result from the increased expression of chalcone synthase 7/8 genes, while the down-regulated expression of NSS leads to small seed size. The seed phenotypes and a microscopic observation of the seed-coat integument cells in a CRISPR/Cas9-edited mutant nss1 confirmed that the NSS gene conferred small phenotypes of the S006 seeds. As mentioned in an annotation on the Phytozome website, NSS encodes a potential DNA helicase RuvA subunit, and no such genes were previously reported to be involved in seed development. Therefore, we identify a novel gene in a new pathway controlling seed development in soybeans.
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Tabara M, Yamanashi R, Kuriyama K, Koiwa H, Fukuhara T. The dicing activity of DCL3 and DCL4 is negatively affected by flavonoids. PLANT MOLECULAR BIOLOGY 2023; 111:107-116. [PMID: 36219366 DOI: 10.1007/s11103-022-01314-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
The dicing activities of DCL3 and DCL4 are inhibited by accumulated metabolites in soybean leaves. Epicatechin and 7,4'-dihydroxyflavone inhibited Arabidopsis DCL3 and DCL4 in vitro. Flavonoids are major secondary metabolites in plants, and soybean (Glycine max L.) is a representative plant that accumulates flavonoids, including isoflavonoids, to high levels. Naturally-occurring RNA interference (RNAi) against the chalcone synthase (CHS) gene represses flavonoid (anthocyanin) biosynthesis in an organ-specific manner, resulting in a colorless (yellow) seed coat in many soybean cultivars. To better understand seed coat-specific naturally-occurring RNAi in soybean, we characterized soybean Dicer-like (DCL) 3 and 4, which play critical roles in RNAi. Using a previously established dicing assay, two dicing activities producing 24- and 21-nt siRNAs, corresponding to DCL3 and DCL4, respectively, were detected in soybean. Dicing activity was detected in colorless seed coats where RNAi against CHS genes was found, but no dicing activity was detected in leaves where CHS expression was prevalent. Biochemical analysis revealed that soybean leaves contained two types of inhibitors effective for Arabidopsis Dicers (AtDCL3 and AtDCL4), one of which was a heat-labile high molecular weight compound of 50 to 100 kD while another was a low molecular weight substance. We found that some flavonoids, such as epicatechin and 7,4'-dihydroxyflavone, inhibited both AtDCL3 and AtDCL4, but AtDCL4 was more sensitive to these flavonoids than AtDCL3. These results suggest that flavonoids inhibit the dicing activity of DCL4 and thereby attenuate RNAi in soybean leaves.
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Affiliation(s)
- Midori Tabara
- Ritsumeikan-Global Innovation Research Organization, Ritsumeikan University, 1-1-1, Noji-Higashi, Kusatsu, Shiga, 525-8577, Japan.
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan.
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan.
| | - Riho Yamanashi
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Kazunori Kuriyama
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
| | - Hisashi Koiwa
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
- Vegetable and Fruit Improvement Center and Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Toshiyuki Fukuhara
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
- Department of Applied Biological Sciences, Tokyo University of Agriculture and Technology, 3-5-8 Saiwaicho, Fuchu, Tokyo, 183-8509, Japan
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Ohta Y, Atsumi G, Yoshida C, Takahashi S, Shimizu M, Nishihara M, Nakatsuka T. Post-transcriptional gene silencing of the chalcone synthase gene CHS causes corolla lobe-specific whiting of Japanese gentian. PLANTA 2021; 255:29. [PMID: 34964920 DOI: 10.1007/s00425-021-03815-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
Post-transcriptional gene silencing of the chalcone synthase gene CHS specifically suppresses anthocyanin biosynthesis in corolla lobes and is responsible for the formation of a stripe type bicolor in Japanese gentian. The flower of Japanese gentian is a bell-shaped corolla composed of lobes and plicae, which is painted uniformly blue. However, the gentian cultivar 'Hakuju' shows bicolor phenotype (blue-white stripe corolla), in which anthocyanin accumulation is suppressed only in corolla lobes. Expression analysis indicated that steady-state levels of chalcone synthase (CHS) transcripts were remarkably reduced in corolla lobes compared with plicae during petal pigmentation initiation. However, no significant difference in expression levels of other flavonoid biosynthetic structural and regulatory genes was detected in its lobes and plicae. On feeding naringenin in white lobes, anthocyanin accumulation was recovered. Northern blotting probed with CHS confirmed the abundant accumulation of small RNAs in corolla lobes. Likewise, small RNA-seq analysis indicated that short reads from its lobes were predominantly mapped onto the 2nd exon region of the CHS gene, whereas those from the plicae were scarcely mapped. Subsequent infection with the gentian ovary ringspot virus (GORV), which had an RNA-silencing activity, showed the recovery of partial pigmentation in lobes. Hence, these results strongly suggested that suppressing anthocyanin accumulation in the lobes of bicolored 'Hakuju' was attributed to the specific degradation of CHS mRNA in corolla lobes, which was through post-transcriptional gene silencing (PTGS). Herein, we revealed the molecular mechanism of strip bicolor formation in Japanese gentian, and showed that PTGS of CHS was also responsible for flower color pattern in a floricultural plant other than petunia and dahlia.
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Affiliation(s)
- Yuka Ohta
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan
| | - Go Atsumi
- Iwate Biotechnology Research Center, Kitakami, 024-0003, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Sapporo, 062-8517, Japan
| | - Chiharu Yoshida
- Iwate Biotechnology Research Center, Kitakami, 024-0003, Japan
| | | | - Motoki Shimizu
- Iwate Biotechnology Research Center, Kitakami, 024-0003, Japan
| | | | - Takashi Nakatsuka
- Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan.
- College of Agriculture, Academic Institute, Shizuoka University, Shizuoka, 422-8529, Japan.
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Ohno S, Makishima R, Doi M. Post-transcriptional gene silencing of CYP76AD controls betalain biosynthesis in bracts of bougainvillea. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6949-6962. [PMID: 34279632 DOI: 10.1093/jxb/erab340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/17/2021] [Indexed: 06/13/2023]
Abstract
Betalain is one of four major plant pigments and shares some features with anthocyanin; however, no plant has been found to biosynthesize both pigments. Previous studies have reported that anthocyanin biosynthesis in some plants is regulated by post-transcriptional gene-silencing (PTGS), but the importance of PTGS in betalain biosynthesis remains unclear. In this study, we report the occurrence of PTGS in betalain biosynthesis in bougainvillea (Bougainvillea peruviana) 'Thimma', which produces bracts of three different color on the same plant, namely pink, white, and pink-white. This resembles the unstable anthocyanin pigmentation phenotype that is associated with PTGS, and hence we anticipated the presence of PTGS in the betalain biosynthetic pathway. To test this, we analysed pigments, gene expression, small RNAs, and transient overexpression. Our results demonstrated that PTGS of BpCYP76AD1, a gene encoding one of the betalain biosynthesis enzymes, is responsible for the loss of betalain biosynthesis in 'Thimma'. Neither the genetic background nor DNA methylation in the BpCYP76AD1 sequence could explain the induction of PTGS, implying that another locus controls the unstable pigmentation. Our results indicate that naturally occurring PTGS contributes to the diversification of color patterns not only in anthocyanin biosynthesis but also in betalain biosynthesis.
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Affiliation(s)
- Sho Ohno
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Rikako Makishima
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Motoaki Doi
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, Japan
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Yamaguchi N, Suzuki C, Yamashita Y, Senda M. A pubescence color gene enhances tolerance to cold-induced seed cracking in yellow soybean. BREEDING SCIENCE 2021; 71:467-473. [PMID: 34912173 PMCID: PMC8661493 DOI: 10.1270/jsbbs.21035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/14/2021] [Indexed: 06/14/2023]
Abstract
In yellow soybean, severe cold weather causes seed cracking on the dorsal side. Yellow soybeans carry the I or ii allele of the I locus and have a yellow (I) or pigmented (ii ) hilum. We previously isolated an additional allele, designated as Ic, of the I locus, and reported that yellow soybeans with the IcIc genotype may be tolerant to cold-induced seed cracking. The Ic allele by itself, however, does not confer high tolerance. The association of a pubescence color gene (T) with suppression of low-temperature-induced seed coat deterioration has been previously reported. In the present study, we tested whether T is effective for the suppression of cold-induced seed cracking using two pairs of near-isogenic lines for the T locus in the iiii or IcIc background. In both backgrounds, the cracked seed rate of the near-isogenic line with the TT genotype was significantly lower than that with the tt genotype, which indicates that T has an inhibitory effect on cold-induced seed cracking. Furthermore, we also showed that gene pyramiding of Ic and T can improve tolerance to cold-induced seed cracking. Our findings should aid the development of highly SC-tolerant cultivars in soybean breeding programs.
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Affiliation(s)
- Naoya Yamaguchi
- Hokkaido Research Organization Tokachi Agricultural Experiment Station, 2, Minami 9 sen, Shinsei, Memuro-cho, Kasai-gun, Hokkaido 082-0081, Japan
| | - Chika Suzuki
- Hokkaido Research Organization Tokachi Agricultural Experiment Station, 2, Minami 9 sen, Shinsei, Memuro-cho, Kasai-gun, Hokkaido 082-0081, Japan
| | - Yoko Yamashita
- Hokkaido Research Organization Central Agricultural Experiment Station, Higashi 6 Kita 15, Naganuma, Hokkaido 069-1395, Japan
| | - Mineo Senda
- Faculty of Agriculture and Life Sciences, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
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Zhu J, Zhao H, Kong F, Liu B, Liu M, Dong Z. Cotranscriptional and Posttranscriptional Features of the Transcriptome in Soybean Shoot Apex and Leaf. FRONTIERS IN PLANT SCIENCE 2021; 12:649634. [PMID: 33897737 PMCID: PMC8063115 DOI: 10.3389/fpls.2021.649634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/02/2021] [Indexed: 05/13/2023]
Abstract
Transcription is the first step of central dogma, in which the genetic information stored in DNA is copied into RNA. In addition to mature RNA sequencing (RNA-seq), high-throughput nascent RNA assays have been established and applied to provide detailed transcriptional information. Here, we present the profiling of nascent RNA from trifoliate leaves and shoot apices of soybean. In combination with nascent RNA (chromatin-bound RNA, CB RNA) and RNA-seq, we found that introns were largely spliced cotranscriptionally. Although alternative splicing (AS) was mainly determined at nascent RNA biogenesis, differential AS between the leaf and shoot apex at the mature RNA level did not correlate well with cotranscriptional differential AS. Overall, RNA abundance was moderately correlated between nascent RNA and mature RNA within each tissue, but the fold changes between the leaf and shoot apex were highly correlated. Thousands of novel transcripts (mainly non-coding RNA) were detected by CB RNA-seq, including the overlap of natural antisense RNA with two important genes controlling soybean reproductive development, FT2a and Dt1. Taken together, we demonstrated the adoption of CB RNA-seq in soybean, which may shed light on gene expression regulation of important agronomic traits in leguminous crops.
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Affiliation(s)
- Jiafu Zhu
- Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
| | - Han Zhao
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Fanjiang Kong
- Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
| | - Baohui Liu
- Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
| | - Min Liu
- Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
- *Correspondence: Min Liu,
| | - Zhicheng Dong
- Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
- Zhicheng Dong,
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Saruta M, Ashina H, Matsumoto T, Okubo H, Hiraoka M, Kasai A, Ohnishi S, Funatsuki H, Kawasaki M, Sano T, Senda M. A major gene for tolerance to cold-induced seed coat discoloration relieves viral seed mottling in soybean. BREEDING SCIENCE 2020; 70:449-455. [PMID: 32968347 PMCID: PMC7495198 DOI: 10.1270/jsbbs.19162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/06/2020] [Indexed: 06/11/2023]
Abstract
In yellow soybeans, inhibition of seed coat pigmentation by RNA silencing of CHS genes is suppressed by low temperature and a viral suppressor, resulting in 'cold-induced seed coat discoloration' and 'seed mottling', respectively. Differences exist in the degree of cold-induced seed coat discoloration among Japanese yellow soybean cultivars; for example, Toyomusume is sensitive, Toyohomare has some tolerance, and Toyoharuka is highly tolerant. In this study, we compared the degree of seed mottling severity due to soybean mosaic virus (SMV) among these three soybean cultivars. Obvious differences were found, with the order of severity as follows: Toyohomare > Toyomusume > Toyoharuka. RNA gel blot analysis indicated that CHS transcript abundance in the seed coat, which was increased by SMV infection, was responsible for the severity of seed mottling. Quantitative reverse transcription PCR analysis revealed why mottling was most severe in SMV-infected Toyohomare: the SMV titer in its seed coat was higher than in the other two infected cultivars. We further suggest that a major gene (Ic) for tolerance to cold-induced seed coat discoloration can relieve the severity of seed mottling in SMV-infected Toyoharuka.
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Affiliation(s)
- Masayasu Saruta
- National Agricultural Research Organization Western Region Agricultural Research Center, 1-3-1 Senyu, Zentsuji, Kagawa 765-8508, Japan
| | - Hirotaka Ashina
- Faculty of Agriculture and Life Sciences, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Takuro Matsumoto
- Faculty of Agriculture and Life Sciences, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Harumitsu Okubo
- Faculty of Agriculture and Life Sciences, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Miho Hiraoka
- Faculty of Agriculture and Life Sciences, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Atsushi Kasai
- Faculty of Agriculture and Life Sciences, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Shizen Ohnishi
- Hokkaido Research Organization Tokachi Agricultural Experiment Station, 2, Minami 9 sen, Shinsei, Memuro-cho, Kasai-gun, Hokkaido 082-0081, Japan
| | - Hideyuki Funatsuki
- National Agricultural Research Organization Hokkaido Region Agricultural Research Center, Hitsujigaoka, Sapporo, Hokkaido 062-8555, Japan
| | - Michio Kawasaki
- Faculty of Agriculture and Life Sciences, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Teruo Sano
- Faculty of Agriculture and Life Sciences, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Mineo Senda
- Faculty of Agriculture and Life Sciences, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
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11
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Yamaguchi N, Hagihara S, Hirai D. Field assessment of a major QTL associated with tolerance to cold-induced seed coat discoloration in soybean. BREEDING SCIENCE 2019; 69:521-528. [PMID: 31598087 PMCID: PMC6776143 DOI: 10.1270/jsbbs.19024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/23/2019] [Indexed: 05/21/2023]
Abstract
In Hokkaido, the northernmost region of Japan, soybean [Glycine max (L.) Merr.] crops are damaged by cold weather. Chilling temperatures negatively affect seed appearance by causing seed coat discoloration around the hilum region, which is called cold-induced discoloration (CD). An assay for CD tolerance using a phytotron was developed, and two quantitative trait loci (QTLs) associated with CD tolerance were identified. The major QTL was located in the proximal region of the I locus, and structural variation of this locus can serve as a useful DNA marker, called the Ic marker. To use this marker in breeding programs, the effects need to be assessed under field conditions because the Ic marker has been developed solely under phytotron conditions. The aim of this study was thus to assess the effect of the Ic marker under a cool field environment. We confirmed that the Ic allele was highly effective using 27 cultivars and breeding lines including a near-isogenic line grown in the field where severe cold-weather damage occurred. This allele had no negative influence on the agronomic traits in the near-isogenic line. Our results suggest that marker-assisted selection for the Ic allele is effective for improving CD tolerance in breeding programs.
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Affiliation(s)
- Naoya Yamaguchi
- Hokkaido Research Organization Tokachi Agricultural Experiment Station,
2, Minami 9 sen, Shinsei, Memuro-cho, Kasai-gun, Hokkaido 082-0081,
Japan
- Corresponding author (e-mail: )
| | - Seiji Hagihara
- Hokkaido Research Organization Kitami Agricultural Experiment Station,
Yayoi 52, Kunneppu-cho, Tokoro-gun, Hokkaido 099-1496,
Japan
| | - Dai Hirai
- Hokkaido Research Organization Central Agricultural Experiment Station,
Higashi 6 sen Kita 15 Gou, Naganuma-cho, Yubari-gun, Hokkaido 069-1395,
Japan
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12
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Cho YB, Jones SI, Vodkin LO. Nonallelic homologous recombination events responsible for copy number variation within an RNA silencing locus. PLANT DIRECT 2019; 3:e00162. [PMID: 31468028 PMCID: PMC6710647 DOI: 10.1002/pld3.162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/02/2019] [Accepted: 08/05/2019] [Indexed: 05/18/2023]
Abstract
The structure of chalcone synthase (CHS) gene repeats in different alleles of the I (inhibitor) locus in soybean spawns endogenous RNA interference (RNAi) that leads to phenotypic change in seed coat color of this major agronomic crop. Here, we examined CHS gene copy number by digital PCR and single nucleotide polymorphisms (SNPs) through whole genome resequencing of 15 cultivars that varied in alleles of the I locus (I, ii , ik , and i) that control the pattern distribution of pigments in the seed coats. Lines homozygous for the ii allele had the highest copy number followed by the I and ik cultivars which were more related to each other than to the lines with ii alleles. Some of the recessive i alleles were spontaneous mutations, and each revealed a loss of copy number by digital PCR relative to the parent varieties. Amplicon sequencing and whole genome resequencing determined that the breakpoints of several ii to i mutations resulted from nonallelic homologous recombination (NAHR) events between CHS genes located in segmental duplications leading to large 138-kilobase deletions that erase the structure generating the CHS siRNAs along with eight other non-CHS genes. Functional hybrid CHS genes (designated CHS5:1) were formed in the process and represent rare examples of NAHR in higher plants that have been captured by examining spontaneous mutational events in isogenic mutant lines.
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Affiliation(s)
- Young B. Cho
- Department of Crop SciencesUniversity of IllinoisUrbanaIllinois
- Present address:
Carl R. Woese Institute for Genomic BiologyUniversity of IllinoisUrbanaIllinois
| | - Sarah I. Jones
- Department of Crop SciencesUniversity of IllinoisUrbanaIllinois
| | - Lila O. Vodkin
- Department of Crop SciencesUniversity of IllinoisUrbanaIllinois
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13
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Senda M, Kawasaki M, Hiraoka M, Yamashita K, Maeda H, Yamaguchi N. Occurrence and tolerance mechanisms of seed cracking under low temperatures in soybean (Glycine max). PLANTA 2018; 248:369-379. [PMID: 29737417 DOI: 10.1007/s00425-018-2912-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 04/29/2018] [Indexed: 05/22/2023]
Abstract
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.
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Affiliation(s)
- Mineo Senda
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori, 036-8561, Japan.
| | - Michio Kawasaki
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori, 036-8561, Japan
| | - Miho Hiraoka
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori, 036-8561, Japan
| | - Kazuki Yamashita
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori, 036-8561, Japan
| | - Hayato Maeda
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori, 036-8561, Japan
| | - Naoya Yamaguchi
- Hokkaido Research Organization, Tokachi Agricultural Experiment Station, Shinsei, Memuro-cho, Kasai-gun, Hokkaido, 082-0081, Japan
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14
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Ohno S, Hori W, Hosokawa M, Tatsuzawa F, Doi M. Post-transcriptional silencing of chalcone synthase is involved in phenotypic lability in petals and leaves of bicolor dahlia (Dahlia variabilis) 'Yuino'. PLANTA 2018; 247:413-428. [PMID: 29063185 DOI: 10.1007/s00425-017-2796-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 10/14/2017] [Indexed: 06/07/2023]
Abstract
Post-transcriptional gene silencing (PTGS) of a chalcone synthase ( DvCHS2 ) occurred in the white part of bicolor petals and flavonoid-poor leaves; however, it did not in red petals and flavonoid-rich leaves. Petal color lability is a prominent feature of bicolor dahlia cultivars, and causes plants to produce not only original bicolor petals with colored bases and pure white tips, but also frequently single-colored petals without white tips. In this study, we analysed the molecular mechanisms that are associated with petal color lability using the red-white bicolor cultivar 'Yuino'. Red single-colored petals lose their white tips as a result of recover of flavonoid biosynthesis. Among flavonoid biosynthetic genes including four chalcone synthase (CHS)-like genes (DvCHS1, DvCHS2, DvCHS3, and DvCHS4), DvCHS1 and DvCHS2 had significantly lower expression levels in the white part of bicolor petals than in red petals, while DvCHS3, DvCHS4, and other flavonoid biosynthetic genes had almost the same expression levels. Small RNAs from the white part of a bicolor petal were mapped onto DvCHS1 and DvCHS2, while small RNAs from a red single-colored petal were not mapped onto any of the four CHS genes. A relationship between petal color and leaf flavonoid accumulation has previously been demonstrated, whereby red petal-producing plants accumulate flavonoids in their leaves, while bicolor petal-producing plants tend not to. The expression level of DvCHS2 was down-regulated in flavonoid-poor leaves and small RNAs from flavonoid-poor leaves were mapped onto DvCHS2, suggesting that the down-regulation of DvCHS2 in flavonoid-poor leaves occurs post-transcriptionally. Genomic analysis also suggested that DvCHS2 is the key gene involved in bicolor formation. Together, these results suggest that post-transcriptional gene silencing of DvCHS2 plays a key role in phenotypic lability in this bicolor dahlia.
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Affiliation(s)
- Sho Ohno
- Laboratory of Vegetable and Ornamental Horticulture, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan.
| | - Wakako Hori
- Laboratory of Vegetable and Ornamental Horticulture, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Munetaka Hosokawa
- Laboratory of Vegetable and Ornamental Horticulture, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Fumi Tatsuzawa
- Faculty of Agriculture, Iwate University, Morioka, 020-8550, Japan
| | - Motoaki Doi
- Laboratory of Vegetable and Ornamental Horticulture, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
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15
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Genome-Wide Identification and Comparative Analysis of the 3-Hydroxy-3-methylglutaryl Coenzyme A Reductase (HMGR) Gene Family in Gossypium. Molecules 2018; 23:molecules23020193. [PMID: 29364830 PMCID: PMC6017885 DOI: 10.3390/molecules23020193] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/19/2018] [Accepted: 01/21/2018] [Indexed: 11/25/2022] Open
Abstract
Terpenes are the largest and most diverse class of secondary metabolites in plants and play a very important role in plant adaptation to environment. 3-Hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) is a rate-limiting enzyme in the process of terpene biosynthesis in the cytosol. Previous study found the HMGR genes underwent gene expansion in Gossypium raimondii, but the characteristics and evolution of the HMGR gene family in Gossypium genus are unclear. In this study, genome-wide identification and comparative study of HMGR gene family were carried out in three Gossypium species with genome sequences, i.e., G. raimondii, Gossypium arboreum, and Gossypium hirsutum. In total, nine, nine and 18 HMGR genes were identified in G. raimondii, G. arboreum, and G. hirsutum, respectively. The results indicated that the HMGR genes underwent gene expansion and a unique gene cluster containing four HMGR genes was found in all the three Gossypium species. The phylogenetic analysis suggested that the expansion of HMGR genes had occurred in their common ancestor. There was a pseudogene that had a 10-bp deletion resulting in a frameshift mutation and could not be translated into functional proteins in G. arboreum and the A-subgenome of G. hirsutum. The expression profiles of the two pseudogenes showed that they had tissue-specific expression. Additionally, the expression pattern of the pseudogene in the A-subgenome of G. hirsutum was similar to its paralogous gene in the D-subgenome of G. hirsutum. Our results provide useful information for understanding cytosolic terpene biosynthesis in Gossypium species.
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16
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Senda M, Yamaguchi N, Hiraoka M, Kawada S, Iiyoshi R, Yamashita K, Sonoki T, Maeda H, Kawasaki M. Accumulation of proanthocyanidins and/or lignin deposition in buff-pigmented soybean seed coats may lead to frequent defective cracking. PLANTA 2017; 245:659-670. [PMID: 27995313 DOI: 10.1007/s00425-016-2638-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Accepted: 12/08/2016] [Indexed: 06/06/2023]
Abstract
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.
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Affiliation(s)
- Mineo Senda
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori, 036-8561, Japan.
| | - Naoya Yamaguchi
- Hokkaido Research Organization Tokachi Agricultural Experiment Station, 2, Minami 9 sen, Shinsei, Memuro-cho, Kasai-gun, Hokkaido, 082-0081, Japan
| | - Miho Hiraoka
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori, 036-8561, Japan
| | - So Kawada
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori, 036-8561, Japan
| | - Ryota Iiyoshi
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori, 036-8561, Japan
| | - Kazuki Yamashita
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori, 036-8561, Japan
| | - Tomonori Sonoki
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori, 036-8561, Japan
| | - Hayato Maeda
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori, 036-8561, Japan
| | - Michio Kawasaki
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori, 036-8561, Japan
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17
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Qu C, Zhao H, Fu F, Zhang K, Yuan J, Liu L, Wang R, Xu X, Lu K, Li JN. Molecular Mapping and QTL for Expression Profiles of Flavonoid Genes in Brassica napus. FRONTIERS IN PLANT SCIENCE 2016; 7:1691. [PMID: 27881992 PMCID: PMC5102069 DOI: 10.3389/fpls.2016.01691] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 10/26/2016] [Indexed: 05/18/2023]
Abstract
Flavonoids are secondary metabolites that are extensively distributed in the plant kingdom and contribute to seed coat color formation in rapeseed. To decipher the genetic networks underlying flavonoid biosynthesis in rapeseed, we constructed a high-density genetic linkage map with 1089 polymorphic loci (including 464 SSR loci, 97 RAPD loci, 451 SRAP loci, and 75 IBP loci) using recombinant inbred lines (RILs). The map consists of 19 linkage groups and covers 2775 cM of the B. napus genome with an average distance of 2.54 cM between adjacent markers. We then performed expression quantitative trait locus (eQTL) analysis to detect transcript-level variation of 18 flavonoid biosynthesis pathway genes in the seeds of the 94 RILs. In total, 72 eQTLs were detected and found to be distributed among 15 different linkage groups that account for 4.11% to 52.70% of the phenotypic variance atrributed to each eQTL. Using a genetical genomics approach, four eQTL hotspots together harboring 28 eQTLs associated with 18 genes were found on chromosomes A03, A09, and C08 and had high levels of synteny with genome sequences of A. thaliana and Brassica species. Associated with the trans-eQTL hotspots on chromosomes A03, A09, and C08 were 5, 17, and 1 genes encoding transcription factors, suggesting that these genes have essential roles in the flavonoid biosynthesis pathway. Importantly, bZIP25, which is expressed specifically in seeds, MYC1, which controls flavonoid biosynthesis, and the R2R3-type gene MYB51, which is involved in the synthesis of secondary metabolites, were associated with the eQTL hotspots, and these genes might thus be involved in different flavonoid biosynthesis pathways in rapeseed. Hence, further studies of the functions of these genes will provide insight into the regulatory mechanism underlying flavonoid biosynthesis, and lay the foundation for elaborating the molecular mechanism of seed coat color formation in B. napus.
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Affiliation(s)
- Cunmin Qu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
| | - Huiyan Zhao
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
| | - Fuyou Fu
- Department of Botany and Plant Pathology, Purdue UniversityWest Lafayette, IN, USA
| | - Kai Zhang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
| | - Jianglian Yuan
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
| | - Liezhao Liu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
| | - Rui Wang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
| | - Xinfu Xu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
| | - Kun Lu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
- *Correspondence: Kun Lu
| | - Jia-Na Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
- Jia-na Li
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18
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Qu C, Zhao H, Fu F, Wang Z, Zhang K, Zhou Y, Wang X, Wang R, Xu X, Tang Z, Lu K, Li JN. Genome-Wide Survey of Flavonoid Biosynthesis Genes and Gene Expression Analysis between Black- and Yellow-Seeded Brassica napus. FRONTIERS IN PLANT SCIENCE 2016; 7:1755. [PMID: 27999578 PMCID: PMC5139615 DOI: 10.3389/fpls.2016.01755] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 11/07/2016] [Indexed: 05/20/2023]
Abstract
Flavonoids, the compounds that impart color to fruits, flowers, and seeds, are the most widespread secondary metabolites in plants. However, a systematic analysis of these loci has not been performed in Brassicaceae. In this study, we isolated 649 nucleotide sequences related to flavonoid biosynthesis, i.e., the Transparent Testa (TT) genes, and their associated amino acid sequences in 17 Brassicaceae species, grouped into Arabidopsis or Brassicaceae subgroups. Moreover, 36 copies of 21 genes of the flavonoid biosynthesis pathway were identified in Arabidopsis thaliana, 53 were identified in Brassica rapa, 50 in Brassica oleracea, and 95 in B. napus, followed the genomic distribution, collinearity analysis and genes triplication of them among Brassicaceae species. The results showed that the extensive gene loss, whole genome triplication, and diploidization that occurred after divergence from the common ancestor. Using qRT-PCR methods, we analyzed the expression of 18 flavonoid biosynthesis genes in 6 yellow- and black-seeded B. napus inbred lines with different genetic background, found that 12 of which were preferentially expressed during seed development, whereas the remaining genes were expressed in all B. napus tissues examined. Moreover, 14 of these genes showed significant differences in expression level during seed development, and all but four of these (i.e., BnTT5, BnTT7, BnTT10, and BnTTG1) had similar expression patterns among the yellow- and black-seeded B. napus. Results showed that the structural genes (BnTT3, BnTT18, and BnBAN), regulatory genes (BnTTG2 and BnTT16) and three encoding transfer proteins (BnTT12, BnTT19, and BnAHA10) might play an crucial roles in the formation of different seed coat colors in B. napus. These data will be helpful for illustrating the molecular mechanisms of flavonoid biosynthesis in Brassicaceae species.
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Affiliation(s)
- Cunmin Qu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
- Food and Bioproduct Science, University of SaskatchewanSaskatoon, SK, Canada
| | - Huiyan Zhao
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
| | - Fuyou Fu
- Department of Botany and Plant Pathology, Purdue UniversityWest Lafayette, IN, USA
| | - Zhen Wang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
| | - Kai Zhang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
| | - Yan Zhou
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
| | - Xin Wang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
| | - Rui Wang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
| | - Xinfu Xu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
| | - Zhanglin Tang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
| | - Kun Lu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
- *Correspondence: Kun Lu
| | - Jia-Na Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest UniversityChongqing, China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest UniversityChongqing, China
- Jia-Na Li
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19
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Kim YH, Park HM, Hwang TY, Lee SK, Choi MS, Jho S, Hwang S, Kim HM, Lee D, Kim BC, Hong CP, Cho YS, Kim H, Jeong KH, Seo MJ, Yun HT, Kim SL, Kwon YU, Kim WH, Chun HK, Lim SJ, Shin YA, Choi IY, Kim YS, Yoon HS, Lee SH, Lee S. Variation block-based genomics method for crop plants. BMC Genomics 2014; 15:477. [PMID: 24929792 PMCID: PMC4229737 DOI: 10.1186/1471-2164-15-477] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 06/03/2014] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND In contrast with wild species, cultivated crop genomes consist of reshuffled recombination blocks, which occurred by crossing and selection processes. Accordingly, recombination block-based genomics analysis can be an effective approach for the screening of target loci for agricultural traits. RESULTS We propose the variation block method, which is a three-step process for recombination block detection and comparison. The first step is to detect variations by comparing the short-read DNA sequences of the cultivar to the reference genome of the target crop. Next, sequence blocks with variation patterns are examined and defined. The boundaries between the variation-containing sequence blocks are regarded as recombination sites. All the assumed recombination sites in the cultivar set are used to split the genomes, and the resulting sequence regions are termed variation blocks. Finally, the genomes are compared using the variation blocks. The variation block method identified recurring recombination blocks accurately and successfully represented block-level diversities in the publicly available genomes of 31 soybean and 23 rice accessions. The practicality of this approach was demonstrated by the identification of a putative locus determining soybean hilum color. CONCLUSIONS We suggest that the variation block method is an efficient genomics method for the recombination block-level comparison of crop genomes. We expect that this method will facilitate the development of crop genomics by bringing genomics technologies to the field of crop breeding.
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Affiliation(s)
- Yul Ho Kim
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Hyang Mi Park
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Tae-Young Hwang
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Seuk Ki Lee
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Man Soo Choi
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Sungwoong Jho
- Personal Genomics Institute, Genome Research Foundation, Suwon 443-270, Republic of Korea
| | - Seungwoo Hwang
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 306-809, Republic of Korea
| | - Hak-Min Kim
- Personal Genomics Institute, Genome Research Foundation, Suwon 443-270, Republic of Korea
| | - Dongwoo Lee
- Personal Genomics Institute, Genome Research Foundation, Suwon 443-270, Republic of Korea
| | - Byoung-Chul Kim
- Personal Genomics Institute, Genome Research Foundation, Suwon 443-270, Republic of Korea
| | - Chang Pyo Hong
- Theragen Bio Institute, TheragenEtex, Suwon 443-270, Republic of Korea
| | - Yun Sung Cho
- Personal Genomics Institute, Genome Research Foundation, Suwon 443-270, Republic of Korea
| | - Hyunmin Kim
- Theragen Bio Institute, TheragenEtex, Suwon 443-270, Republic of Korea
| | - Kwang Ho Jeong
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Min Jung Seo
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Hong Tai Yun
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Sun Lim Kim
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Young-Up Kwon
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Wook Han Kim
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Hye Kyung Chun
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Sang Jong Lim
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Young-Ah Shin
- Personal Genomics Institute, Genome Research Foundation, Suwon 443-270, Republic of Korea
| | - Ik-Young Choi
- National Instrumentation Center for Environmental Management, College of Agriculture and Life Science, Seoul National University, Seoul 151-921, Republic of Korea
| | - Young Sun Kim
- Department of Biology, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Ho-Sung Yoon
- Department of Biology, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Suk-Ha Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
| | - Sunghoon Lee
- Personal Genomics Institute, Genome Research Foundation, Suwon 443-270, Republic of Korea
- Theragen Bio Institute, TheragenEtex, Suwon 443-270, Republic of Korea
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20
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Takagi K, Nishizawa K, Hirose A, Kurauchi T, Senda M, Masuta C, Ishimoto M. Seed coat pigmentation in transgenic soybean expressing the silencing suppressor 2b gene of Cucumber mosaic virus. PLANT CELL REPORTS 2013; 32:1903-12. [PMID: 24022064 DOI: 10.1007/s00299-013-1502-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 08/21/2013] [Accepted: 08/26/2013] [Indexed: 06/02/2023]
Abstract
KEY MESSAGE Soybean expressing the Cucumber mosaic virus 2b gene manifests seed coat pigmentation due to suppression of endogenous RNA silencing but no other morphological abnormality. This gene may help prevent transgene silencing. RNA silencing is an important mechanism for gene regulation and antiviral defense in plants. It is also responsible for transgene silencing, however, and thus hinders the establishment of transgenic plants. The 2b protein of Cucumber mosaic virus (CMV) functions as a suppressor of RNA silencing and therefore might prove beneficial for stabilization of transgene expression. We have now generated transgenic soybean that harbors the 2b gene of a CMV-soybean strain under the control of a constitutive promoter to investigate the effects of 2b expression. No growth abnormality was apparent in 2b transgenic plants, although the seed coat was pigmented in several of the transgenic lines. Genes for chalcone synthase (CHS), a key enzyme of the flavonoid pathway, are posttranscriptionally silenced by the inhibitor (I) locus in nonpigmented (yellow) soybean seeds. The levels of CHS mRNA and CHS small interfering RNA in strongly pigmented 2b transgenic seed coats were higher and lower, respectively, than those in the seed coat of a control transgenic line. The expression level of 2b also correlated with the extent of seed coat pigmentation. On the other hand, introduction of the 2b gene together with the DsRed2 gene into somatic embryos prevented the time-dependent decrease in transient DsRed2 expression. Our results indicate that the 2b gene alone is able to suppress RNA silencing of endogenous CHS genes regulated by the I locus, and that 2b is of potential utility for stabilization of transgene expression in soybean without detrimental effects other than seed coat pigmentation.
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21
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Senda M, Nishimura S, Kasai A, Yumoto S, Takada Y, Tanaka Y, Ohnishi S, Kuroda T. Comparative analysis of the inverted repeat of a chalcone synthase pseudogene between yellow soybean and seed coat pigmented mutants. BREEDING SCIENCE 2013; 63:384-92. [PMID: 24399910 PMCID: PMC3859349 DOI: 10.1270/jsbbs.63.384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 08/17/2013] [Indexed: 05/13/2023]
Abstract
In soybean, the I gene inhibits pigmentation over the entire seed coat, resulting in yellow seeds. It is thought that this suppression of seed coat pigmentation is due to naturally occurring RNA silencing of chalcone synthase genes (CHS silencing). Fully pigmented seeds can be found among harvested yellow seeds at a very low percentage. These seed coat pigmented (scp) mutants are generated from yellow soybeans by spontaneous recessive mutation of the I gene. A candidate for the I gene, GmIRCHS, contains a perfect inverted repeat (IR) of a CHS pseudogene (pseudoCHS3) and transcripts of GmIRCHS form a double-stranded CHS RNA that potentially triggers CHS silencing. One CHS gene, ICHS1, is located 680 bp downstream of GmIRCHS. Here, the GmIRCHS-ICHS1 cluster was compared in scp mutants of various origins. In these mutants, sequence divergence in the cluster resulted in complete or partial loss of GmIRCHS in at least the pseudoCHS3 region. This result is consistent with the notion that the IR of pseudoCHS3 is sufficient to induce CHS silencing, and further supports that GmIRCHS is the I gene.
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Affiliation(s)
- Mineo Senda
- Faculty of Agriculture and Life Sciences, Hirosaki University,
3 Bunkyo-cho, Hirosaki, Aomori 036-8561,
Japan
- Corresponding author (e-mail: )
| | - Satsuki Nishimura
- Faculty of Agriculture and Life Sciences, Hirosaki University,
3 Bunkyo-cho, Hirosaki, Aomori 036-8561,
Japan
| | - Atsushi Kasai
- Faculty of Agriculture and Life Sciences, Hirosaki University,
3 Bunkyo-cho, Hirosaki, Aomori 036-8561,
Japan
| | - Setsuzo Yumoto
- Research Support Center, National Agricultural Research Center for Tohoku Region,
Yotsuya, Daisen, Akita 014-0102,
Japan
| | - Yoshitake Takada
- National Agricultural Research Organization (NARO) Western Region Agricultural Research Center,
1-3-1 Senyu, Zentsuji, Kagawa 765-8508,
Japan
| | - Yoshinori Tanaka
- Hokkaido Research Organization Tokachi Agricultural Experiment Station,
S9-2 Shinsei, Memuro, Kasai, Hokkaido 082-0081,
Japan
| | - Shizen Ohnishi
- Hokkaido Research Organization Kitami Agricultural Experiment Station,
52 Yayoi, Kunneppu, Tokoro, Hokkaido 099-1406,
Japan
| | - Tomohisa Kuroda
- Niigata Agricultural Research Institute,
857 Nagakura-machi, Nagaoka, Niigata 940-0826,
Japan
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22
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Qu C, Fu F, Lu K, Zhang K, Wang R, Xu X, Wang M, Lu J, Wan H, Zhanglin T, Li J. Differential accumulation of phenolic compounds and expression of related genes in black- and yellow-seeded Brassica napus. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:2885-98. [PMID: 23698630 PMCID: PMC3697950 DOI: 10.1093/jxb/ert148] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Developing yellow-seeded Brassica napus (rapeseed) with improved qualities is a major breeding goal. The intermediate and final metabolites of the phenylpropanoid and flavonoid pathways affect not only oil quality but also seed coat colour of B. napus. Here, the accumulation of phenolic compounds was analysed in the seed coats of black-seeded (ZY821) and yellow-seeded (GH06) B. napus. Using toluidine blue O staining and liquid chromatography-mass spectrometry, histochemical and biochemical differences were identified in the accumulation of phenolic compounds between ZY821 and GH06. Two and 13 unique flavonol derivatives were detected in ZY821 and GH06, respectively. Quantitative real-time PCR analysis revealed significant differences between ZY821 and GH06 in the expression of common phenylpropanoid biosynthetic genes (BnPAL and BnC4H), common flavonoid biosynthetic genes (BnTT4 and BnTT6), anthocyanin- and proanthocyandin-specific genes (BnTT3 and BnTT18), proanthocyandin-specific genes (BnTT12, BnTT10, and BnUGT2) and three transcription factor genes (BnTTG1, BnTTG2, and BnTT8) that function in the flavonoid biosynthetic pathway. These data provide insight into pigment accumulation in B. napus, and serve as a useful resource for researchers analysing the formation of seed coat colour and the underlying regulatory mechanisms in B. napus.
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Affiliation(s)
- Cunmin Qu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, 216 Tiansheng Road, Beibei, Chongqing 400716, People’s Republic of China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, People’s Republic of China
- *These authors contributed equally to this work
| | - Fuyou Fu
- Agriculture and Agri-Food Canada, Saskatoon Research Centre, 107 Science Place, S7N 02X, Saskatoon Saskatchewan, Canada
- *These authors contributed equally to this work
| | - Kun Lu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, 216 Tiansheng Road, Beibei, Chongqing 400716, People’s Republic of China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, People’s Republic of China
- *These authors contributed equally to this work
| | - Kai Zhang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, 216 Tiansheng Road, Beibei, Chongqing 400716, People’s Republic of China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, People’s Republic of China
| | - Rui Wang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, 216 Tiansheng Road, Beibei, Chongqing 400716, People’s Republic of China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, People’s Republic of China
| | - Xinfu Xu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, 216 Tiansheng Road, Beibei, Chongqing 400716, People’s Republic of China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, People’s Republic of China
| | - Min Wang
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, 216 Tiansheng Road, Beibei, Chongqing 400716, People’s Republic of China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, People’s Republic of China
| | - Junxing Lu
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, 216 Tiansheng Road, Beibei, Chongqing 400716, People’s Republic of China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, People’s Republic of China
| | - Huafang Wan
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, 216 Tiansheng Road, Beibei, Chongqing 400716, People’s Republic of China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, People’s Republic of China
| | - Tang Zhanglin
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, 216 Tiansheng Road, Beibei, Chongqing 400716, People’s Republic of China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, People’s Republic of China
| | - Jiana Li
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, 216 Tiansheng Road, Beibei, Chongqing 400716, People’s Republic of China
- Engineering Research Center of South Upland Agriculture of Ministry of Education, Southwest University, Beibei, Chongqing 400716, People’s Republic of China
- To whom correspondence should be addressed. E-mail:
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23
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Kasai M, Matsumura H, Yoshida K, Terauchi R, Taneda A, Kanazawa A. Deep sequencing uncovers commonality in small RNA profiles between transgene-induced and naturally occurring RNA silencing of chalcone synthase-A gene in petunia. BMC Genomics 2013; 14:63. [PMID: 23360437 PMCID: PMC3608071 DOI: 10.1186/1471-2164-14-63] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 01/22/2013] [Indexed: 11/12/2022] Open
Abstract
Background Introduction of a transgene that transcribes RNA homologous to an endogenous gene in the plant genome can induce silencing of both genes, a phenomenon termed cosuppression. Cosuppression was first discovered in transgenic petunia plants transformed with the CHS-A gene encoding chalcone synthase, in which nonpigmented sectors in flowers or completely white flowers are produced. Some of the flower-color patterns observed in transgenic petunias having CHS-A cosuppression resemble those in existing nontransgenic varieties. Although the mechanism by which white sectors are generated in nontransgenic petunia is known to be due to RNA silencing of the CHS-A gene as in cosuppression, whether the same trigger(s) and/or pattern of RNA degradation are involved in these phenomena has not been known. Here, we addressed this question using deep-sequencing and bioinformatic analyses of small RNAs. Results We analyzed short interfering RNAs (siRNAs) produced in nonpigmented sectors of petal tissues in transgenic petunia plants that have CHS-A cosuppression and a nontransgenic petunia variety Red Star, that has naturally occurring CHS-A RNA silencing. In both silencing systems, 21-nt and 22-nt siRNAs were the most and the second-most abundant size classes, respectively. CHS-A siRNA production was confined to exon 2, indicating that RNA degradation through the RNA silencing pathway occurred in this exon. Common siRNAs were detected in cosuppression and naturally occurring RNA silencing, and their ranks based on the number of siRNAs in these plants were correlated with each other. Noticeably, highly abundant siRNAs were common in these systems. Phased siRNAs were detected in multiple phases at multiple sites, and some of the ends of the regions that produced phased siRNAs were conserved. Conclusions The features of siRNA production found to be common to cosuppression and naturally occurring silencing of the CHS-A gene indicate mechanistic similarities between these silencing systems especially in the biosynthetic processes of siRNAs including cleavage of CHS-A transcripts and subsequent production of secondary siRNAs in exon 2. The data also suggest that these events occurred at multiple sites, which can be a feature of these silencing phenomena.
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Affiliation(s)
- Megumi Kasai
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
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24
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Song J, Guo Y, Yu LJ, Qiu LJ. [Progress in genes related to seed-coat color in soybean]. YI CHUAN = HEREDITAS 2012; 34:687-94. [PMID: 22698739 DOI: 10.3724/sp.j.1005.2012.00687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
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.
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Affiliation(s)
- Jian Song
- College of Biological Science and Technology, Harbin Normal University, Harbin 150025, China.
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25
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Kasai M, Koseki M, Goto K, Masuta C, Ishii S, Hellens RP, Taneda A, Kanazawa A. Coincident sequence-specific RNA degradation of linked transgenes in the plant genome. PLANT MOLECULAR BIOLOGY 2012; 78:259-73. [PMID: 22146813 DOI: 10.1007/s11103-011-9863-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Accepted: 11/18/2011] [Indexed: 05/23/2023]
Abstract
The expression of transgenes in plant genomes can be inhibited by either transcriptional gene silencing or posttranscriptional gene silencing (PTGS). Overexpression of the chalcone synthase-A (CHS-A) transgene triggers PTGS of CHS-A and thus results in loss of flower pigmentation in petunia. We previously demonstrated that epigenetic inactivation of CHS-A transgene transcription leads to a reversion of the PTGS phenotype. Although neomycin phosphotransferase II (nptII), a marker gene co-introduced into the genome with the CHS-A transgene, is not normally silenced in petunia, even when CHS-A is silenced, here we found that nptII was silenced in a petunia line in which CHS-A PTGS was induced, but not in the revertant plants that had no PTGS of CHS-A. Transcriptional activity, accumulation of short interfering RNAs, and restoration of mRNA level after infection with viruses that had suppressor proteins of gene silencing indicated that the mechanism for nptII silencing was posttranscriptional. Read-through transcripts of the CHS-A gene toward the nptII gene were detected. Deep-sequencing analysis revealed a striking difference between the predominant size class of small RNAs produced from the read-through transcripts (22 nt) and that from the CHS-A RNAs (21 nt). These results implicate the involvement of read-through transcription and distinct phases of RNA degradation in the coincident PTGS of linked transgenes and provide new insights into the destabilization of transgene expression.
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Affiliation(s)
- Megumi Kasai
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
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26
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Tsubokura Y, Hajika M, Kanamori H, Xia Z, Watanabe S, Kaga A, Katayose Y, Ishimoto M, Harada K. The β-conglycinin deficiency in wild soybean is associated with the tail-to-tail inverted repeat of the α-subunit genes. PLANT MOLECULAR BIOLOGY 2012; 78:301-9. [PMID: 22193750 DOI: 10.1007/s11103-011-9865-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 11/23/2011] [Indexed: 05/11/2023]
Abstract
β-conglycinin, a major seed protein in soybean, is composed of α, α', and β subunits sharing a high homology among them. Despite its many health benefits, β-conglycinin has a lower amino acid score and lower functional gelling properties compared to glycinin, another major soybean seed protein. In addition, the α, α', and β subunits also contain major allergens. A wild soybean (Glycine soja Sieb et Zucc.) line, 'QT2', lacks all of the β-conglycinin subunits, and the deficiency is controlled by a single dominant gene, Scg-1 (Suppressor of β-conglycinin). This gene was characterized using a soybean cultivar 'Fukuyutaka', 'QY7-25', (its near-isogenic line carrying the Scg-1 gene), and the F₂ population derived from them. The physical map of the Scg-1 region covered by lambda phage genomic clones revealed that the two α-subunit genes, a β-subunit gene, and a pseudo α-subunit gene were closely organized. The two α-subunit genes were arranged in a tail-to-tail orientation, and the genes were separated by 197 bp in Scg-1 compared to 3.3 kb in the normal allele (scg-1). In addition, small RNA was detected in immature seeds of the mutants by northern blot analysis using an RNA probe of the α subunit. These results strongly suggest that β-conglycinin deficiency in QT2 is controlled by post-transcriptional gene silencing through the inverted repeat of the α subunits.
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Affiliation(s)
- Yasutaka Tsubokura
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
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27
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Senda M, Kurauchi T, Kasai A, Ohnishi S. Suppressive mechanism of seed coat pigmentation in yellow soybean. BREEDING SCIENCE 2012; 61:523-30. [PMID: 23136491 PMCID: PMC3406792 DOI: 10.1270/jsbbs.61.523] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 08/08/2011] [Indexed: 05/14/2023]
Abstract
In soybean seeds, numerous variations in colors and pigmentation patterns exist, most of which are observed in the seed coat. Patterns of seed coat pigmentation are determined by four alleles (I, i(i), i(k) and i) of the classically defined I locus, which controls the spatial distribution of anthocyanins and proanthocyanidins in the seed coat. Most commercial soybean cultivars produce yellow seeds with yellow cotyledons and nonpigmented seed coats, which are important traits of high-quality seeds. Plants carrying the I or i(i) allele show complete inhibition of pigmentation in the seed coat or pigmentation only in the hilum, respectively, resulting in a yellow seed phenotype. Classical genetic analyses of the I locus were performed in the 1920s and 1930s but, until recently, the molecular mechanism by which the I locus regulated seed coat pigmentation remained unclear. In this review, we provide an overview of the molecular suppressive mechanism of seed coat pigmentation in yellow soybean, with the main focus on the effect of the I allele. In addition, we discuss seed coat pigmentation phenomena in yellow soybean and their relationship to inhibition of I allele action.
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Affiliation(s)
- Mineo Senda
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
- Corresponding author (e-mail: )
| | - Tasuku Kurauchi
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Atsushi Kasai
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Shizen Ohnishi
- Hokkaido Research Organization Central Agricultural Experiment Station, Higashi 6 Kita 15, Naganuma, Yubari, Hokkaido 069-1395, Japan
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28
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Gillman JD, Tetlow A, Lee JD, Shannon JG, Bilyeu K. Loss-of-function mutations affecting a specific Glycine max R2R3 MYB transcription factor result in brown hilum and brown seed coats. BMC PLANT BIOLOGY 2011; 11:155. [PMID: 22070454 PMCID: PMC3229458 DOI: 10.1186/1471-2229-11-155] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 11/09/2011] [Indexed: 05/17/2023]
Abstract
BACKGROUND Although modern soybean cultivars feature yellow seed coats, with the only color variation found at the hila, the ancestral condition is black seed coats. Both seed coat and hila coloration are due to the presence of phenylpropanoid pathway derivatives, principally anthocyanins. The genetics of soybean seed coat and hilum coloration were first investigated during the resurgence of genetics during the 1920s, following the rediscovery of Mendel's work. Despite the inclusion of this phenotypic marker into the extensive genetic maps developed for soybean over the last twenty years, the genetic basis behind the phenomenon of brown seed coats (the R locus) has remained undetermined until now. RESULTS In order to identify the gene responsible for the r gene effect (brown hilum or seed coat color), we utilized bulk segregant analysis and identified recombinant lines derived from a population segregating for two phenotypically distinct alleles of the R locus. Fine mapping was accelerated through use of a novel, bioinformatically determined set of Simple Sequence Repeat (SSR) markers which allowed us to delimit the genomic region containing the r gene to less than 200 kbp, despite the use of a mapping population of only 100 F6 lines. Candidate gene analysis identified a loss of function mutation affecting a seed coat-specific expressed R2R3 MYB transcription factor gene (Glyma09g36990) as a strong candidate for the brown hilum phenotype. We observed a near perfect correlation between the mRNA expression levels of the functional R gene candidate and an UDP-glucose:flavonoid 3-O-glucosyltransferase (UF3GT) gene, which is responsible for the final step in anthocyanin biosynthesis. In contrast, when a null allele of Glyma09g36990 is expressed no upregulation of the UF3GT gene was found. CONCLUSIONS We discovered an allelic series of four loss of function mutations affecting our R locus gene candidate. The presence of any one of these mutations was perfectly correlated with the brown seed coat/hilum phenotype in a broadly distributed survey of soybean cultivars, barring the presence of the epistatic dominant I allele or gray pubescence, both of which can mask the effect of the r allele, resulting in yellow or buff hila. These findings strongly suggest that loss of function for one particular seed coat-expressed R2R3 MYB gene is responsible for the brown seed coat/hilum phenotype in soybean.
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Affiliation(s)
- Jason D Gillman
- USDA-ARS, Plant Genetics Research Unit, 110 Waters Hall, Columbia, MO 65211, USA
| | - Ashley Tetlow
- University of Missouri, Division of Plant Sciences, 110 Waters Hall, Columbia, MO 65211, USA
| | - Jeong-Deong Lee
- Division of Plant Biosciences, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - J Grover Shannon
- University of Missouri, Division of Plant Sciences, University of Missouri-Delta Research Center, Portageville, MO 63873, USA
| | - Kristin Bilyeu
- USDA-ARS, Plant Genetics Research Unit, 110 Waters Hall, Columbia, MO 65211, USA
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29
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Kurauchi T, Kasai A, Tougou M, Senda M. Endogenous RNA interference of chalcone synthase genes in soybean: formation of double-stranded RNA of GmIRCHS transcripts and structure of the 5' and 3' ends of short interfering RNAs. JOURNAL OF PLANT PHYSIOLOGY 2011; 168:1264-70. [PMID: 21295373 DOI: 10.1016/j.jplph.2011.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2010] [Revised: 01/06/2011] [Accepted: 01/06/2011] [Indexed: 05/15/2023]
Abstract
In yellow soybean, seed coat pigmentation is inhibited via endogenous RNA interference (RNAi) of the chalcone synthase (CHS) genes. Genetic studies have shown that a single dominant gene, named the I gene, inhibits pigmentation over the entire seed coat in soybean. We previously isolated a candidate for the I gene from the yellow soybean genome with the I/I genotype, and designated it GmIRCHS. A structural feature of GmIRCHS is a perfect inverted repeat of the pseudoCHS gene lacking 5'-coding region. This suggests that the double-stranded RNA (dsRNA) structure of the pseudoCHS gene may be formed in the GmIRCHS transcript. RNAi is triggered by the dsRNA for a target gene, so the GmIRCHS transcript is likely to be a trigger for RNAi of CHS genes. In this study, we identified a 1087-bp dsRNA, including pseudoCHS region ranging from most of exon 2 to 3'-UTR, in the GmIRCHS transcript. Interestingly, this dsRNA was detected not only in the seed coat but also in the cotyledon and leaf tissues. Previously, CHS RNAi has been shown to be restricted to the seed coat, and we reported that endogenous short interfering RNAs of CHS genes (CHS siRNAs) are detected only in the seed coat and not in the cotyledon and leaf tissues. Taken together with these previous reports, our result suggests that seed-coat specificity of CHS RNAi may be determined in the amplification step of CHS siRNAs rather than dsRNA formation in the GmIRCHS transcript. Our studies further revealed that CHS siRNAs are modified at the 3' ends and bear 5' monophosphorylated ends, suggesting that CHS siRNA duplexes are generated by Dicer-like enzyme from CHS dsRNA and subsequently modified at the 3' ends for stabilizing CHS siRNAs.
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Affiliation(s)
- Tasuku Kurauchi
- Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki, Aomori 036-8561, Japan
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Ohnishi S, Funatsuki H, Kasai A, Kurauchi T, Yamaguchi N, Takeuchi T, Yamazaki H, Kurosaki H, Shirai S, Miyoshi T, Horita H, Senda M. Variation of GmIRCHS (Glycine max inverted-repeat CHS pseudogene) is related to tolerance of low temperature-induced seed coat discoloration in yellow soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:633-42. [PMID: 20981401 DOI: 10.1007/s00122-010-1475-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 10/11/2010] [Indexed: 05/08/2023]
Abstract
In yellow soybean, seed coat pigmentation is inhibited by post-transcriptional gene silencing (PTGS) of chalcone synthase (CHS) genes. A CHS cluster named GmIRCHS (Glycine max inverted-repeat CHS pseudogene) is suggested to cause PTGS in yellow-hilum cultivars. Cold-induced seed coat discoloration (CD), a commercially serious deterioration of seed appearance, is caused by an inhibition of this PTGS upon exposure to low temperatures. In the highly CD-tolerant cultivar Toyoharuka, the GmIRCHS structure differs from that of other cultivars. The aim of this study was to determine whether the variation of GmIRCHS structure among cultivars is related to variations in CD tolerance. Using two sets of recombinant inbred lines between Toyoharuka and CD-susceptible cultivars, we compared the GmIRCHS genotype and CD tolerance phenotype during low temperature treatment. The GmIRCHS genotype was related to the phenotype of CD tolerance. A QTL analysis around GmIRCHS showed that GmIRCHS itself or a region located very close to it was responsible for CD tolerance. The variation in GmIRCHS can serve as a useful DNA marker for marker-assisted selection for breeding CD tolerance. In addition, QTL analysis of the whole genome revealed a minor QTL that also affected CD tolerance.
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Affiliation(s)
- Shizen Ohnishi
- Hokkaido Research Organization Tokachi Agricultural Experiment Station, Shinsei, Memuro, Kasai-gun, Hokkaido, Japan.
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Kasai A, Ohnishi S, Yamazaki H, Funatsuki H, Kurauchi T, Matsumoto T, Yumoto S, Senda M. Molecular mechanism of seed coat discoloration induced by low temperature in yellow soybean. PLANT & CELL PHYSIOLOGY 2009; 50:1090-8. [PMID: 19395413 DOI: 10.1093/pcp/pcp061] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Seed coat pigmentation is inhibited in yellow soybean. The I gene inhibits pigmentation over the entire seed coat. In yellow soybean, seed coat discoloration occurs when plants are exposed to low temperatures after the onset of flowering, a phenomenon named 'cold-induced discoloration (CD)'. Inhibition of seed coat pigmentation results from post-transcriptional gene silencing (PTGS) of the chalcone synthase (CHS) genes. PTGS is a sequence-specific RNA degradation mechanism in plants and occurs via short interfering RNAs (siRNAs). Similar post-transcriptional suppression is called RNAi (RNA interference) in animals. Recently, we identified a candidate of the I gene designated GmIRCHS. In this study, to elucidate the molecular mechanism of CD, CHS mRNA and siRNA levels in the seed coat were compared between CD-sensitive and CD-tolerant cultivars (Toyomusume and Toyoharuka, respectively). In Toyomusume, the CHS siRNA level was reduced markedly by low temperature treatment, and subsequently the CHS mRNA level increased rapidly after treatment. In contrast, low temperature treatment did not result in severe reduction of the CHS siRNA level in Toyoharuka, and the CHS mRNA level did not increase after the treatment. These results suggest that the rapid increase in CHS mRNA level after low temperature treatment may lead to enhanced pigmentation in some of the seed coat cells and finally in seed coat discoloration. Interestingly, we found a Toyoharuka-specific difference in the GmIRCHS region, which may be involved in CD tolerance.
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Affiliation(s)
- Atsushi Kasai
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan
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