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Yongbin Q, Summat P, Panyawut N, Sikaewtung K, Ditthab K, Tongmark K, Chakhonkaen S, Sangarwut N, Wasinanon T, Kaewmungkun K, Muangprom A. Identification of Rice Accessions Having Cold Tolerance at the Seedling Stage and Development of Novel Genotypic Assays for Predicting Cold Tolerance. Plants (Basel) 2023; 12:215. [PMID: 36616346 PMCID: PMC9823403 DOI: 10.3390/plants12010215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/08/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Rice is susceptible to cold stress at the seedling stage, which can delay growth and decrease yield. We evaluated 187 rice accessions for cold tolerance at the seedling stage and developed genotypic assays for three markers. All japonica (20/20) and 20/140 indica accessions were highly cold tolerant. Two SNP markers specific for COLD1 and LOC_Os10g34840 were practical to use by normal agarose gel. The SNP marker specific for COLD1 was highly specific for predicting cold tolerance. However, the sensitivity of this marker was low as several cold-tolerant indica accessions lacked the cold-tolerant allele. The LOC_Os10g34840 marker was slightly more sensitive than the COLD1 marker for predicting highly cold-tolerant accessions. An insertion/deletion variant in the NAC6 gene was identified as a novel cold tolerance marker. The NAC6 marker predicted more highly cold-tolerant accessions compared with the other two markers. The SNP marker specific for LOC_Os10g34840 and the NAC6 marker were present in several tested subgroups, suggesting their wide effects and distribution. The three markers combined predicted the most highly cold-tolerant accessions, indicating that the marker combination is superior for applications such as marker-assisted breeding. The cold-tolerant accessions and the genotypic marker assays will be useful for future rice breeding.
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Affiliation(s)
- Qi Yongbin
- Institute of Crop Science and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Patcharaporn Summat
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Centre, Khlong Luang, Pathum Thani 12120, Thailand
| | - Natjaree Panyawut
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
- Nadi District Agricultural Extension Office, Chamanan Road, Nadi Subdistrict, Nadi District, Prachinburi 25220, Thailand
| | - Kannika Sikaewtung
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Khanittha Ditthab
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Keasinee Tongmark
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Sriprapai Chakhonkaen
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Numphet Sangarwut
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Thiwawan Wasinanon
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Kanokwan Kaewmungkun
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Amorntip Muangprom
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
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Khlaimongkhon S, Chakhonkaen S, Tongmark K, Sangarwut N, Panyawut N, Wasinanon T, Sikaewtung K, Wanchana S, Mongkolsiriwatana C, Chunwonges J, Muangprom A. RNA Sequencing Reveals Rice Genes Involved in Male Reproductive Development under Temperature Alteration. Plants (Basel) 2021; 10:plants10040663. [PMID: 33808467 PMCID: PMC8066911 DOI: 10.3390/plants10040663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 11/25/2022]
Abstract
Rice (Oryza sativa L.) is one of the most important food crops, providing food for nearly half of the world population. Rice grain yields are affected by temperature changes. Temperature stresses, both low and high, affect male reproductive development, resulting in yield reduction. Thermosensitive genic male sterility (TGMS) rice is sterile at high temperature and fertile at low temperature conditions, facilitating hybrid production, and is a good model to study effects of temperatures on male development. Semithin sections of the anthers of a TGMS rice line under low (fertile) and high (sterile) temperature conditions showed differences starting from the dyad stage, suggesting that genes involved in male development play a role during postmeiotic microspore development. Using RNA sequencing (RNA-Seq), transcriptional profiling of TGMS rice panicles at the dyad stage revealed 232 genes showing differential expression (DEGs) in a sterile, compared to a fertile, condition. Using qRT-PCR to study expression of 20 selected DEGs using panicles of TGMS and wild type rice plants grown under low and high temperature conditions, revealed that six out of the 20 selected genes may be unique to TGMS, while the other 14 genes showed common responses to temperatures in both TGMS and wild-type rice plants. The results presented here would be useful for further investigation into molecular mechanisms controlling TGMS and rice responses to temperature alteration.
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Affiliation(s)
- Sudthana Khlaimongkhon
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Kamphaeng Saen 73140, Thailand; (S.K.); (J.C.)
- Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
| | - Sriprapai Chakhonkaen
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (S.C.); (K.T.); (N.S.); (N.P.); (T.W.); (K.S.); (S.W.)
| | - Keasinee Tongmark
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (S.C.); (K.T.); (N.S.); (N.P.); (T.W.); (K.S.); (S.W.)
| | - Numphet Sangarwut
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (S.C.); (K.T.); (N.S.); (N.P.); (T.W.); (K.S.); (S.W.)
| | - Natjaree Panyawut
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (S.C.); (K.T.); (N.S.); (N.P.); (T.W.); (K.S.); (S.W.)
| | - Thiwawan Wasinanon
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (S.C.); (K.T.); (N.S.); (N.P.); (T.W.); (K.S.); (S.W.)
| | - Kannika Sikaewtung
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (S.C.); (K.T.); (N.S.); (N.P.); (T.W.); (K.S.); (S.W.)
| | - Samart Wanchana
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (S.C.); (K.T.); (N.S.); (N.P.); (T.W.); (K.S.); (S.W.)
| | - Chareerat Mongkolsiriwatana
- Division of Genetics, Faculty of Liberal Arts and Science, Kasetsart University, Nakhon Pathom 73140, Thailand;
| | - Julapark Chunwonges
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Kamphaeng Saen 73140, Thailand; (S.K.); (J.C.)
- Department of Horticulture, Faculty of Agriculture, Kasetsart University, Nakhon Pathom 73140, Thailand
| | - Amorntip Muangprom
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Kamphaeng Saen 73140, Thailand; (S.K.); (J.C.)
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand; (S.C.); (K.T.); (N.S.); (N.P.); (T.W.); (K.S.); (S.W.)
- Correspondence: ; Tel.: +66-25646700 (ext. 3348)
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Tongmark K, Chakhonkaen S, Sangarwut N, Wasinanon T, Panyawut N, Ditthab K, Sikaewtung K, Janbuathong S, Taprab S, Deerusamee C, Muangprom A. Development of high yielding two-line hybrid rice in Thailand. ScienceAsia 2021. [DOI: 10.2306/scienceasia1513-1874.2021.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Chueasiri C, Chunthong K, Pitnjam K, Chakhonkaen S, Sangarwut N, Sangsawang K, Suksangpanomrung M, Michaelson LV, Napier JA, Muangprom A. Rice ORMDL controls sphingolipid homeostasis affecting fertility resulting from abnormal pollen development. PLoS One 2014; 9:e106386. [PMID: 25192280 PMCID: PMC4156325 DOI: 10.1371/journal.pone.0106386] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 08/07/2014] [Indexed: 12/27/2022] Open
Abstract
The orosomucoids (ORM) are ER-resisdent polypeptides encoded by ORM and ORMDL (ORM-like) genes. In humans, ORMDL3 was reported as genetic risk factor associated to asthma. In yeast, ORM proteins act as negative regulators of sphingolipid synthesis. Sphingolipids are important molecules regulating several processes including stress responses and apoptosis. However, the function of ORM/ORMDL genes in plants has not yet been reported. Previously, we found that temperature sensitive genetic male sterility (TGMS) rice lines controlled by tms2 contain a deletion of about 70 kb in chromosome 7. We identified four genes expressed in panicles, including an ORMDL ortholog, as candidates for tms2. In this report, we quantified expression of the only two candidate genes normally expressed in anthers of wild type plants grown in controlled growth rooms for fertile and sterile conditions. We found that only the ORMDL gene (LOC_Os07g26940) showed differential expression under these conditions. To better understand the function of rice ORMDL genes, we generated RNAi transgenic rice plants suppressing either LOC_Os07g26940, or all three ORMDL genes present in rice. We found that the RNAi transgenic plants with low expression of either LOC_Os07g26940 alone or all three ORMDL genes were sterile, having abnormal pollen morphology and staining. In addition, we found that both sphingolipid metabolism and expression of genes involved in sphingolipid synthesis were perturbed in the tms2 mutant, analogous to the role of ORMs in yeast. Our results indicated that plant ORMDL proteins influence sphingolipid homeostasis, and deletion of this gene affected fertility resulting from abnormal pollen development.
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Affiliation(s)
- Chutharat Chueasiri
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Klong Luang, Pathumthani, Thailand
| | - Ketsuwan Chunthong
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Klong Luang, Pathumthani, Thailand
| | - Keasinee Pitnjam
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Klong Luang, Pathumthani, Thailand
| | - Sriprapai Chakhonkaen
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Klong Luang, Pathumthani, Thailand
| | - Numphet Sangarwut
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Klong Luang, Pathumthani, Thailand
| | - Kanidta Sangsawang
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Klong Luang, Pathumthani, Thailand
| | - Malinee Suksangpanomrung
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Klong Luang, Pathumthani, Thailand
| | - Louise V. Michaelson
- Biological Chemistry Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Johnathan A. Napier
- Biological Chemistry Department, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Amorntip Muangprom
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Klong Luang, Pathumthani, Thailand
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Chakhonkaen S, Pitnjam K, Saisuk W, Ukoskit K, Muangprom A. Genetic structure of Thai rice and rice accessions obtained from the International Rice Research Institute. Rice (N Y) 2012; 5:19. [PMID: 27234241 PMCID: PMC5520827 DOI: 10.1186/1939-8433-5-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 06/13/2012] [Indexed: 05/22/2023]
Abstract
BACKGROUND Although the genetic structure of rice germplasm has been characterized worldwide, few studies investigated germplasm from Thailand, the world's largest exporter of rice. Thailand and the International Rice Research Institute (IRRI) have diverse collections of rice germplasm, which could be used to develop breeding lines with desirable traits. This study aimed to investigate the level of genetic diversity and structures of Thai and selected IRRI germplasm. Understanding the genetic structure and relationships among these germplasm will be useful for parent selection used in rice breeding programs. RESULTS From the 98 InDel markers tested for single copy and polymorphism, 19 markers were used to evaluate 43 Thai and 57 IRRI germplasm, including improved cultivars, breeding lines, landraces, and 5 other Oryza species. The Thai accessions were selected from all rice ecologies such as irrigated, deep water, upland, and rainfed lowland ecosystems. The IRRI accessions were groups of germplasm having agronomic desirable traits, including temperature-sensitive genetic male sterility (TGMS), new plant type, early flowering, and biotic and abiotic stress resistances. Most of the InDel markers were genes with diverse functions. These markers produced the total of 127 alleles for all loci, with a mean of 6.68 alleles per locus, and a mean Polymorphic Information Content (PIC) of 0.440. Genetic diversity of Thai rice were 0.3665, 0.4479 and 0.3972 for improved cultivars, breeding lines, and landraces, respectively, while genetic diversity of IRRI improved and breeding lines were 0.3272 and 0.2970, respectively. Cluster, structure, and differentiation analyses showed six distinct groups: japonica, TGMS, deep-water, IRRI germplasm, Thai landraces and breeding lines, and other Oryza species. CONCLUSIONS Thai and IRRI germplasm were significantly different. Thus, they can be used to broaden the genetic base and trait improvements. Cluster, structure, and differentiation analyses showed concordant results having six distinct groups, in agreement with their development, and ecologies.
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Affiliation(s)
- Sriprapai Chakhonkaen
- Laboratory of Plant Molecular Genetics, National Center for Genetic Engineering and Biotechnology, Pathum thani, 12120 Thailand
| | - Keasinee Pitnjam
- Laboratory of Plant Molecular Genetics, National Center for Genetic Engineering and Biotechnology, Pathum thani, 12120 Thailand
| | - Wachira Saisuk
- Department of Biotechnology, Faculty of Science and Technology, Thammasart University, Rangsit, Pathum thani, 12120 Thailand
| | - Kittipat Ukoskit
- Department of Biotechnology, Faculty of Science and Technology, Thammasart University, Rangsit, Pathum thani, 12120 Thailand
| | - Amorntip Muangprom
- Laboratory of Plant Molecular Genetics, National Center for Genetic Engineering and Biotechnology, Pathum thani, 12120 Thailand
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Pitnjam K, Chakhonkaen S, Toojinda T, Muangprom A. Identification of a deletion in tms2 and development of gene-based markers for selection. Planta 2008; 228:813-22. [PMID: 18642025 DOI: 10.1007/s00425-008-0784-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2008] [Accepted: 07/03/2008] [Indexed: 05/05/2023]
Abstract
Rice is one of the most important food crops. The temperature-sensitive genic male sterility (TGMS) system provides a great potential for improving food production by hybrids. The use of TGMS system is simple, inexpensive, effective, and eliminates the limitations of the conventional three-line system. A rice gene, tms2, generated by irradiation of a japonica variety has been reported to control TGMS in several rice lines. Previous studies reported genetic markers linked to this gene, and the gene was transferred to an aromatic Thai cultivar. Using information obtained from published databases, we located positions of the reported genetic markers flanking the gene in rice genomic sequences, and developed gene-based markers located inside the flanking markers for polymorphism detection. We found that inbred indica tms2 mutant plants contain about 1 Mb of japonica DNA, in which at least 70 kb was deleted. Using RT-PCR for expression analysis, four genes out of seven genes annotated as expressed proteins located inside the deletion showed expression in panicles. These genes could be responsible for TGMS phenotypes of tms2. In addition, we developed gene-based markers flanking and inside the deletion for selecting the tms2 gene in breeding populations. By genotyping 102 diverse rice lines including 38 Thai rice lines, 5 species of wild rice, and 59 exotic rice lines including TGMS lines and cultivars with desirable traits, a gene-based marker located inside the deletion and one flanking marker were shown to be highly specific for the tms2 mutant.
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Affiliation(s)
- Keasinee Pitnjam
- Laboratory of Plant Molecular Genetics, Central Research Unit, National Center for Genetic Engineering and Biotechnology, Phathum Thanee, Thailand
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