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Zgłobicki P, Hermanowicz P, Kłodawska K, Bażant A, Łabuz J, Grzyb J, Dutka M, Kowalska E, Jawor J, Leja K, Banaś AK. The photoreactivation of 6 - 4 photoproducts in chloroplast and nuclear DNA depends on the amount of the Arabidopsis UV repair defective 3 protein. BMC PLANT BIOLOGY 2024; 24:723. [PMID: 39080534 PMCID: PMC11287969 DOI: 10.1186/s12870-024-05439-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 07/19/2024] [Indexed: 08/03/2024]
Abstract
BACKGROUND 6 - 4 photoproducts are the second most common UV-induced DNA lesions after cyclobutane pyrimidine dimers. In plants, they are mainly repaired by photolyases in a process called photoreactivation. While pyrimidine dimers can be deleterious, leading to mutagenesis or even cell death, 6 - 4 photoproducts can activate specific signaling pathways. Therefore, their removal is particularly important, especially for plants exposed to high UV intensities due to their sessile nature. Although photoreactivation in nuclear DNA is well-known, its role in plant organelles remains unclear. In this paper we analyzed the activity and localization of GFP-tagged AtUVR3, the 6 - 4 photoproduct specific photolyase. RESULTS Using transgenic Arabidopsis with different expression levels of AtUVR3, we confirmed a positive trend between these levels and the rate of 6 - 4 photoproduct removal under blue light. Measurements of 6 - 4 photoproduct levels in chloroplast and nuclear DNA of wild type, photolyase mutants, and transgenic plants overexpressing AtUVR3 showed that the photoreactivation is the main repair pathway responsible for the removal of these lesions in both organelles. The GFP-tagged AtUVR3 was predominantly located in nuclei with a small fraction present in chloroplasts and mitochondria of transgenic Arabidopsis thaliana and Nicotiana tabacum lines. In chloroplasts, this photolyase co-localized with the nucleoid marked by plastid envelope DNA binding protein. CONCLUSIONS Photolyases are mainly localized in plant nuclei, with only a small fraction present in chloroplasts and mitochondria. Despite this unbalanced distribution, photoreactivation is the primary mechanism responsible for the removal of 6 - 4 photoproducts from nuclear and chloroplast DNA in adult leaves. The amount of the AtUVR3 photolyase is the limiting factor influencing the photoreactivation rate of 6 - 4 photoproducts. The efficient photoreactivation of 6 - 4 photoproducts in 35S: AtUVR3-GFP Arabidopsis and Nicotiana tabacum is a promising starting point to evaluate whether transgenic crops overproducing this photolyase are more tolerant to high UV irradiation and how they respond to other abiotic and biotic stresses under field conditions.
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Affiliation(s)
- Piotr Zgłobicki
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, 30-387, Poland
| | - Paweł Hermanowicz
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, Kraków, 30-387, Poland
| | - Kinga Kłodawska
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, 30-387, Poland
| | - Aneta Bażant
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, 30-387, Poland
| | - Justyna Łabuz
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, Kraków, 30-387, Poland
| | - Joanna Grzyb
- Department of Biophysics, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14a, Wrocław, 50-383, Poland
| | - Małgorzata Dutka
- Department of Molecular Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, 30-387, Poland
| | - Ewa Kowalska
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, 30-387, Poland
| | - Joanna Jawor
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, 30-387, Poland
| | - Katarzyna Leja
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, 30-387, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, prof. S. Łojasiewicza 11, Kraków, 30-348, Poland
| | - Agnieszka Katarzyna Banaś
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Kraków, 30-387, Poland.
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Mmbando GS, Teranishi M, Hidema J. Transgenic rice Oryza glaberrima with higher CPD photolyase activity alleviates UVB-caused growth inhibition. GM CROPS & FOOD 2021; 12:435-448. [PMID: 34935587 PMCID: PMC8820246 DOI: 10.1080/21645698.2021.1977068] [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] [Indexed: 10/28/2022]
Abstract
The ultraviolet B (UVB) sensitivity of rice cultivated in Asia and Africa varies greatly, with African rice cultivars (Oryza glaberrima Steud. and O. barthii A. Chev.) being more sensitive to UVB because of their low cyclobutane pyrimidine dimer (CPD) photolyase activity, which is a CPD repair enzyme, relative to Asian rice cultivars (O. sativa L.). Hence, the production of UVB-resistant African rice with augmented CPD photolyase activity is of great importance, although difficulty in transforming the African rice cultivars to this end has been reported. Here, we successfully produced overexpressing transgenic African rice with higher CPD photolyase activity by modifying media conditions for callus induction and regeneration using the parental line (PL), UVB-sensitive African rice TOG12380 (O. glaberrima). The overexpressing transgenic African rice carried a single copy of the CPD photolyase enzyme, with a 4.4-fold higher level of CPD photolyase transcripts and 2.6-fold higher activity than its PL counterpart. When the plants were grown for 21 days in a growth chamber under visible radiation or with supplementary various UVB radiation, the overexpressing transgenic plants have a significantly increased UVB resistance index compared to PL plants. These results strongly suggest that CPD photolyase remains an essential factor for tolerating UVB radiation stress in African rice. As a result, African rice cultivars with overexpressed CPD photolyase may survive better in tropical areas more prone to UVB radiation stress, including Africa. Collectively, our results provide strong evidence that CPD photolyase is a useful biotechnological tool for reducing UVB-induced growth inhibition in African rice crops of O. glaberrima.
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Affiliation(s)
| | - Mika Teranishi
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Jun Hidema
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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Li N, Teranishi M, Yamaguchi H, Matsushita T, Watahiki MK, Tsuge T, Li SS, Hidema J. UV-B-Induced CPD Photolyase Gene Expression is Regulated by UVR8-Dependent and -Independent Pathways in Arabidopsis. PLANT & CELL PHYSIOLOGY 2015; 56:2014-23. [PMID: 26272552 DOI: 10.1093/pcp/pcv121] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 08/09/2015] [Indexed: 05/21/2023]
Abstract
Plants have evolved various mechanisms that protect against the harmful effects of UV-B radiation (280-315 nm) on growth and development. Cyclobutane pyrimidine dimer (CPD) photolyase, the repair enzyme for UV-B-induced CPDs, is essential for protecting cells from UV-B radiation. Expression of the CPD photolyase gene (PHR) is controlled by light with various wavelengths including UV-B, but the mechanisms of this regulation remain poorly understood. In this study, we investigated the regulation of PHR expression by light with various wavelengths, in particular low-fluence UV-B radiation (280 nm, 0.2 µmol m(-2) s(-1)), in Arabidopsis thaliana seedlings grown under light-dark cycles for 7 d and then adapted to the dark for 3 d. Low-fluence UV-B radiation induced CPDs but not reactive oxygen species. AtPHR expression was effectively induced by UV-B, UV-A (375 nm) and blue light. Expression induced by UV-A and blue light was predominantly regulated by the cryptochrome-dependent pathway, whereas phytochromes A and B played a minor but noticeable role. Expression induced by UV-B was predominantly regulated by the UVR8-dependent pathway. AtPHR expression was also mediated by a UVR8-independent pathway, which is correlated with CPD accumulation induced by UV-B radiation. These results indicate that Arabidopsis has evolved diverse mechanisms to regulate CPD photolyase expression by multiple photoreceptor signaling pathways, including UVR8-dependent and -independent pathways, as protection against harmful effects of UV-B radiation.
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Affiliation(s)
- Nan Li
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577 Japan
| | - Mika Teranishi
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577 Japan
| | - Hiroko Yamaguchi
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577 Japan
| | - Tomonao Matsushita
- Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581 Japan PRESTO, JST, Saitama, 332-0012 Japan
| | - Masaaki K Watahiki
- Division of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, 060-0810 Japan
| | - Tomohiko Tsuge
- Institute for Chemical Research, Kyoto University, Uji, 611-0011 Japan
| | - Shao-Shan Li
- Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Jun Hidema
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577 Japan
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5
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Takano N, Takahashi Y, Yamamoto M, Teranishi M, Yamaguchi H, Sakamoto AN, Hase Y, Fujisawa H, Wu J, Matsumoto T, Toki S, Hidema J. Isolation of a novel UVB-tolerant rice mutant obtained by exposure to carbon-ion beams. JOURNAL OF RADIATION RESEARCH 2013; 54:637-48. [PMID: 23381954 PMCID: PMC3709678 DOI: 10.1093/jrr/rrt007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 01/04/2013] [Accepted: 01/09/2013] [Indexed: 05/25/2023]
Abstract
UVB radiation suppresses photosynthesis and protein biosynthesis in plants, which in turn decreases growth and productivity. Here, an ultraviolet-B (UVB)-tolerant rice mutant, utr319 (UV Tolerant Rice 319), was isolated from a mutagenized population derived from 2500 M1 seeds (of the UVB-resistant cultivar 'Sasanishiki') that were exposed to carbon ions. The utr319 mutant was more tolerant to UVB than the wild type. Neither the levels of UVB-induced cyclobutane pyrimidine dimers (CPDs) or (6-4) pyrimidine-pyrimidone photodimers [(6-4) photoproducts], nor the repair of CPDs or (6-4) photoproducts, was altered in the utr319 mutant. Thus, the utr319 mutant may be impaired in the production of a previously unidentified factor that confers UVB tolerance. To identify the mutated region in the utr319 mutant, microarray-based comparative genomic hybridization analysis was performed. Two adjacent genes on chromosome 7, Os07g0264900 and Os07g0265100, were predicted to represent the mutant allele. Sequence analysis of the chromosome region in utr319 revealed a deletion of 45 419 bp. RNAi analysis indicated that Os07g0265100 is most likely the mutated gene. Database analysis indicated that the Os07g0265100 gene, UTR319, encodes a putative protein with unknown characteristics or function. In addition, the homologs of UTR319 are conserved only among land plants. Therefore, utr319 is a novel UVB-tolerant rice mutant and UTR319 may be crucial for the determination of UVB sensitivity in rice, although the function of UTR319 has not yet been determined.
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Affiliation(s)
- Nao Takano
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Yuko Takahashi
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Mitsuru Yamamoto
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Mika Teranishi
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Hiroko Yamaguchi
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Ayako N. Sakamoto
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, Takasaki, 370-1292, Japan
| | - Yoshihiro Hase
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, Takasaki, 370-1292, Japan
| | - Hiroko Fujisawa
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
| | - Jianzhong Wu
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
| | - Takashi Matsumoto
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
| | - Seiichi Toki
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
| | - Jun Hidema
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
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Abstract
Most agronomic traits are governed by quantitative trait loci (QTLs) and exhibit continuous distribution in a segregating population. The hereditary characteristics of these traits are more complicated than those of monogenic traits. Detection and isolation of these QTLs can greatly improve crop production throughout the world. In recent times, significant progress has been made toward understanding the molecular basis underlying quantitative traits. Herein, we describe a QTL-mapping protocol for detecting and cloning a major QTL regulating rice shoot K(+) concentration under salt stress conditions. This QTL-mapping approach combined with the marker-assisted selection technique can be applied for the elucidation of complex traits in rice and other cereal crops.
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7
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Teranishi M, Taguchi T, Ono T, Hidema J. Augmentation of CPD photolyase activity in japonica and indica rice increases their UVB resistance but still leaves the difference in their sensitivities. Photochem Photobiol Sci 2012; 11:812-20. [PMID: 22362193 DOI: 10.1039/c2pp05392f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rice cultivars vary widely in their sensitivity to ultraviolet B (UVB, 280-320 nm). Specifically, many indica rice cultivars from tropical regions, where UVB radiation is higher, are hypersensitive to UVB. Photoreactivation mediated by the photolyase enzyme is the major pathway for repairing UVB-induced cyclobutane pyrimidine dimers (CPDs) in plants. Still, these UVB-sensitive cultivars are less able to repair CPDs through photoreactivation than UVB-resistant cultivars. Here, we produced CPD photolyase-overexpressing transgenic rice plants with higher CPD photolyase activity using UVB-sensitive rice Norin 1 (japonica) and UVB-hypersensitive rice Surjamkhi (indica) as parental line (PL) plants. The results show that these transgenic rice plants were much more resistant to UVB-induced growth inhibition than were PL cultivars. The present findings strongly indicate that UVB-resistance, caused by an increase in CPD photolyase activity, can be achieved in various rice cultivars. However, there was a difference in the level of reduction of UVB-induced growth inhibition among rice cultivars; the level of reduction of growth inhibition in transgenic rice plants generated from the indica strain was lower than that of transgenic rice plants generated from japonica strains. These results indicate that the growth of the UVB-hypersensitive indica strain was strongly inhibited by other factors in addition to CPD levels.
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Affiliation(s)
- Mika Teranishi
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan.
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8
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Zhou L, Zeng Y, Zheng W, Tang B, Yang S, Zhang H, Li J, Li Z. Fine mapping a QTL qCTB7 for cold tolerance at the booting stage on rice chromosome 7 using a near-isogenic line. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:895-905. [PMID: 20512559 DOI: 10.1007/s00122-010-1358-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 05/12/2010] [Indexed: 05/03/2023]
Abstract
Low temperature at the booting stage is a serious abiotic stress in rice, and cold tolerance is a complex trait controlled by many quantitative trait loci (QTL). A QTL for cold tolerance at the booting stage in cold-tolerant near-isogenic rice line ZL1929-4 was analyzed. A total of 647 simple sequence repeat (SSR) markers distributed across 12 chromosomes were used to survey for polymorphisms between ZL1929-4 and the cold-sensitive japonica cultivar Towada, and nine were polymorphic. Single marker analysis revealed that markers on chromosome 7 were associated with cold tolerance. By interval mapping using an F(2) population from ZL1929-4 x Towada, a QTL for cold tolerance was detected on the long arm of chromosome 7. The QTL explained 9 and 21% of the phenotypic variances in the F(2) and F(3) generations, respectively. Recombinant plants were screened for two flanking markers, RM182 and RM1132, in an F(2) population with 2,810 plants. Two-step substitution mapping suggested that the QTL was located in a 92-kb interval between markers RI02905 and RM21862. This interval was present in BAC clone AP003804. We designated the QTL as qCTB7 (quantitative trait locus for cold tolerance at the booting stage on chromosome 7), and identified 12 putative candidate genes.
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Affiliation(s)
- Lei Zhou
- Key Laboratory of Crop Genomics and Genetic Improvement, Ministry of Agriculture, and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
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9
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Xu C, Sullivan JH. Reviewing the technical designs for experiments with ultraviolet-B radiation and impact on photosynthesis, DNA and secondary metabolism. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2010; 52:377-387. [PMID: 20377699 DOI: 10.1111/j.1744-7909.2010.00939.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The ultraviolet-B (UV-B) portion of sunlight has received much attention in the last three decades, because radiation from this spectral region increases due to the stratospheric ozone depletion, which results from increases of chlorofluorocarbons in the atmosphere. Plant responses to UV-B exposure vary greatly and the interpretation of and comparison between studies is hindered, mainly by the contrasting experimental conditions used and interactive factors such as low light levels and possible artifacts due to the artificial experimental conditions. It seems likely that increases in solar UV-B radiation of the magnitude anticipated under current stratospheric ozone projections will not significantly inhibit photosynthesis and cause DNA damage in plants. This is in part due to the well-evolved protection mechanisms present in most plant species. One of the significant plant responses to UV-B is changes in foliar secondary chemistry, which could be translated into significant effects at higher trophic levels through plant-herbivore interactions and decomposition. Enhanced UV-B radiation due to stratospheric ozone depletion could also cause morphological changes that would affect competitive interactions, especially if contrasting UV-B sensitivity exists among the competitors.
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Affiliation(s)
- Chenping Xu
- Department of Plant Biology & Pathology, Rutgers University, New Brunswick, NJ 08901, USA.
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Yamamoto T, Yonemaru J, Yano M. Towards the understanding of complex traits in rice: substantially or superficially? DNA Res 2009; 16:141-54. [PMID: 19359285 PMCID: PMC2695773 DOI: 10.1093/dnares/dsp006] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Completion of the genome analysis followed by extensive comprehensive studies on a variety of genes and gene families of rice (Oryza sativa) resulted in rapid accumulation of information concerning the presence of many complex traits that are governed by a number of genes of distinct functions in this most important crop cultivated worldwide. The genetic and molecular biological dissection of many important rice phenotypes has contributed to our understanding of the complex nature of the genetic control with respect to these phenotypes. However, in spite of the considerable advances made in the field, details of genetic control remain largely unsolved, thereby hampering our exploitation of this useful information in the breeding of new rice cultivars. To further strengthen the field application of the genome science data of rice obtained so far, we need to develop more powerful genomics-assisted methods for rice breeding based on information derived from various quantitative trait loci (QTL) and related analyses. In this review, we describe recent progresses and outcomes in rice QTL analyses, problems associated with the application of the technology to rice breeding and their implications for the genetic study of other crops along with future perspectives of the relevant fields.
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Affiliation(s)
- Toshio Yamamoto
- QTL Genomics Research Center, National Institute of Agrobiological Science, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan
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11
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[Analysis of features of 15 successful positional cloning of QTL in rice]. YI CHUAN = HEREDITAS 2008; 30:1121-6. [PMID: 18779168 DOI: 10.3724/sp.j.1005.2008.01121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
As the most efficient strategy in gene clone, positional cloning has been used widely in QTL cloning in rice. The objective of this paper is to make summary features of QTL positional cloning based on 15 successful positional cloning attempts. (1) most of the populations used in the analysis were derived from interspecific or intersubspecies; (2) the target QTL had been identified with very large phenotypic effects; (3) the candidate genomic region was usually narrowed down to 40 kb; (4) the primary mapping result was exact; and the fine mapping population was more than 6,000, while the number of recessive population was more than 1,500. Otherwise, the nodus of QTL positional cloning and the corresponding solving methods were discussed.
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Le Cunff L, Garsmeur O, Raboin LM, Pauquet J, Telismart H, Selvi A, Grivet L, Philippe R, Begum D, Deu M, Costet L, Wing R, Glaszmann JC, D'Hont A. Diploid/polyploid syntenic shuttle mapping and haplotype-specific chromosome walking toward a rust resistance gene (Bru1) in highly polyploid sugarcane (2n approximately 12x approximately 115). Genetics 2008; 180:649-60. [PMID: 18757946 PMCID: PMC2535714 DOI: 10.1534/genetics.108.091355] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2008] [Accepted: 07/10/2008] [Indexed: 11/18/2022] Open
Abstract
The genome of modern sugarcane cultivars is highly polyploid (approximately 12x), aneuploid, of interspecific origin, and contains 10 Gb of DNA. Its size and complexity represent a major challenge for the isolation of agronomically important genes. Here we report on the first attempt to isolate a gene from sugarcane by map-based cloning, targeting a durable major rust resistance gene (Bru1). We describe the genomic strategies that we have developed to overcome constraints associated with high polyploidy in the successive steps of map-based cloning approaches, including diploid/polyploid syntenic shuttle mapping with two model diploid species (sorghum and rice) and haplotype-specific chromosome walking. Their applications allowed us (i) to develop a high-resolution map including markers at 0.28 and 0.14 cM on both sides and 13 markers cosegregating with Bru1 and (ii) to develop a physical map of the target haplotype that still includes two gaps at this stage due to the discovery of an insertion specific to this haplotype. These approaches will pave the way for the development of future map-based cloning approaches for sugarcane and other complex polyploid species.
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Doi K, Yasui H, Yoshimura A. Genetic variation in rice. CURRENT OPINION IN PLANT BIOLOGY 2008; 11:144-148. [PMID: 18316240 DOI: 10.1016/j.pbi.2008.01.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2007] [Revised: 01/30/2008] [Accepted: 01/30/2008] [Indexed: 05/26/2023]
Abstract
Completion of the genomic sequencing of rice has enhanced the discovery of new genes. Wild rice relatives are good sources for extending the genetic variation of cultivated rice. Reproductive barriers are commonly found in distant crosses of rice and are attracting attention. The combination of genetic analyses and molecular tools has greatly facilitated the molecular cloning of rice genes based on the classical approach and enabled the tracking of dissemination of the alleles for domestication. Basic information for population genetics study in rice is still being collected and is expected to provide an alternative approach for finding new genes. The wide genetic variation available in wild rice relatives and the combination of various genetic approaches will allow the analysis and understanding of genetic variation at the nucleotide sequence level, as well as the discovery of novel alleles by sequence-based approaches.
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Affiliation(s)
- Kazuyuki Doi
- Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, Hakozaki 6-10-1, Fukuoka 812-8581, Japan.
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14
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Iwamatsu Y, Aoki C, Takahashi M, Teranishi M, Ding Y, Sun C, Kumagai T, Hidema J. UVB sensitivity and cyclobutane pyrimidine dimer (CPD) photolyase genotypes in cultivated and wild rice species. Photochem Photobiol Sci 2008; 7:311-20. [PMID: 18389148 DOI: 10.1039/b719034d] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We investigated the UVB-sensitivity in 12 rice strains belonging to two cultivated species (O. sativa and O. glaberrima) and three wild species (O. barthii, O. meridionalis and O. rufipogon) of rice possessing the AA genome, while focusing on the CPD photolyase activity and the genotypes of CPD photolyase. Although the UVB sensitivity, CPD photolyase activity, and CPD photolyase genotype varied widely among these rice species, the sensitivity to UVB radiation depended on the activity of the CPD photolyase, regardless of grass shape, habitat, or species. The rice strains examined here clearly divided into three groups based on the CPD photolyase activity, and the activity of the strains greatly depended on amino acid residues at positions 126 and 296, with the exception of the W1299 strain (O. meridionalis). The amino acid residues 126 and 296 of CPD photolyase in Sasanishiki strain (O. sativa), which showed higher enzymatic activity and more resistance to UVB, were glutamine (Gln) and Gln, respectively. An amino acid change at position 126 from Gln to arginine ("Nori"-type) in the photolyase led to a reduction of enzymatic activity. Additionally, an amino acid change at position 296 from Gln to histidine led to a further reduction in activity. The activity of the W1299 strain, which possesses a "Nori"-type CPD photolyase, was the highest among the strains examined here, and was similar to that of the Sasanishiki. The CPD photolyase of the W1299 contains ten amino acid substitutions, compared to Sasanishiki. The alterations in amino acid residues in the W1299 CPD photolyase compensated for the reduction in activity caused by the amino acid substitutions at positions 126. Knowledge of the activity of different CPD photolyase genotypes will be useful in developing improved rice cultivars.
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Affiliation(s)
- Yutaka Iwamatsu
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
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15
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Detection and Molecular Cloning of Genes Underlying Quantitative Phenotypic Variations in Rice. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/978-3-540-74250-0_22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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Dinka SJ, Campbell MA, Demers T, Raizada MN. Predicting the size of the progeny mapping population required to positionally clone a gene. Genetics 2007; 176:2035-54. [PMID: 17565938 PMCID: PMC1950612 DOI: 10.1534/genetics.107.074377] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A key frustration during positional gene cloning (map-based cloning) is that the size of the progeny mapping population is difficult to predict, because the meiotic recombination frequency varies along chromosomes. We describe a detailed methodology to improve this prediction using rice (Oryza sativa L.) as a model system. We derived and/or validated, then fine-tuned, equations that estimate the mapping population size by comparing these theoretical estimates to 41 successful positional cloning attempts. We then used each validated equation to test whether neighborhood meiotic recombination frequencies extracted from a reference RFLP map can help researchers predict the mapping population size. We developed a meiotic recombination frequency map (MRFM) for approximately 1400 marker intervals in rice and anchored each published allele onto an interval on this map. We show that neighborhood recombination frequencies (R-map, >280-kb segments) extracted from the MRFM, in conjunction with the validated formulas, better predicted the mapping population size than the genome-wide average recombination frequency (R-avg), with improved results whether the recombination frequency was calculated as genes/cM or kb/cM. Our results offer a detailed road map for better predicting mapping population size in diverse eukaryotes, but useful predictions will require robust recombination frequency maps based on sampling more progeny.
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Affiliation(s)
- Stephen J Dinka
- Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, Ontario, Canada
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Hidema J, Taguchi T, Ono T, Teranishi M, Yamamoto K, Kumagai T. Increase in CPD photolyase activity functions effectively to prevent growth inhibition caused by UVB radiation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 50:70-9. [PMID: 17397507 DOI: 10.1111/j.1365-313x.2007.03041.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Rice cultivars vary widely in their sensitivity to ultraviolet B (UVB) and this has been correlated with cyclobutane pyrimidine dimer (CPD) photolyase mutations that alter the structure/function of this photorepair enzyme. Here, we tested whether CPD photolyase function determines the UVB sensitivity of rice (Oryza sativa) by generating transgenic rice plants bearing the CPD photolyase gene of the UV-resistant rice cultivar Sasanishiki in the sense orientation (S-B and S-C lines) or the antisense orientation (AS-D line). The S-B and S-C plants had 5.1- and 45.7-fold higher CPD photolyase activities than the wild-type, respectively, were significantly more resistant to UVB-induced growth damage, and maintained significantly lower CPD levels in their leaves during growth under elevated UVB radiation. Conversely, the AS-D plant had little photolyase activity, was severely damaged by elevated UVB radiation, and maintained higher CPD levels in its leaves during growth under UVB radiation. Notably, the S-C plant was not more resistant to UVB-induced growth inhibition than the S-B plant, even though it had much higher CPD photolyase activity. These results strongly indicate that UVB-induced CPDs are one of principal causes of UVB-induced growth inhibition in rice plants grown under supplementary UVB radiation, and that increasing CPD photolyase activity can significantly alleviate UVB-caused growth inhibition in rice. However, further protection from UVB-induced damage may require the genetic enhancement of other systems as well.
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Affiliation(s)
- Jun Hidema
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
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Hidema J, Kumagai T. Sensitivity of rice to ultraviolet-B radiation. ANNALS OF BOTANY 2006; 97:933-42. [PMID: 16520342 PMCID: PMC2803405 DOI: 10.1093/aob/mcl044] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2005] [Revised: 11/15/2005] [Accepted: 12/22/2005] [Indexed: 05/07/2023]
Abstract
BACKGROUND Depletion of the stratospheric ozone layer leads to an increase in ultraviolet-B (UVB: 280-320 nm) radiation reaching the earth's surface, and the enhanced solar UVB radiation predicted by atmospheric models will result in reduction of growth and yield of crops in the future. Over the last two decades, extensive studies of the physiological, biochemical and morphological effects of UVB in plants, as well as the mechanisms of UVB resistance, have been carried out. SCOPE In this review, we describe recent research into the mechanisms of UVB resistance in higher plants, with an emphasis on rice (Oryza sativa), one of the world's most important staple food crops. Recent studies have brought to light the following remarkable findings. UV-absorbing compounds accumulating in the epidermal cell layers have traditionally been considered to function as UV filters, and to play an important role in countering the damaging effects of UVB radiation. Although these compounds are effective in reducing cyclobutane pyrimidine dimer (CPD) induction in plants exposed to a challenge exposure to UVB, certain levels of CPD are maintained constitutively in light conditions containing UVB, regardless of the quantity or presence of visible light. These findings imply that the systems for repairing DNA damage and scavenging reactive oxygen species (ROS) are essential for plants to grow in light conditions containing UVB. CONCLUSION CPD photolyase activity is a crucial factor determining the differences in UVB sensitivity between rice cultivars. The substitution of one or two bases in the CPD photolyase gene can alter the activity of the enzyme, and the associated resistance of the plant to UVB radiation. These findings open up the possibility, in the near future, of increasing the resistance of rice to UVB radiation, by selective breeding or bioengineering of the genes encoding CPD photolyase.
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Affiliation(s)
- Jun Hidema
- Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan.
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Kunz BA, Cahill DM, Mohr PG, Osmond MJ, Vonarx EJ. Plant responses to UV radiation and links to pathogen resistance. INTERNATIONAL REVIEW OF CYTOLOGY 2006; 255:1-40. [PMID: 17178464 DOI: 10.1016/s0074-7696(06)55001-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Increased incident ultraviolet (UV) radiation due to ozone depletion has heightened interest in plant responses to UV because solar UV wavelengths can reduce plant genome stability, growth, and productivity. These detrimental effects result from damage to cell components including nucleic acids, proteins, and membrane lipids. As obligate phototrophs, plants must counter the onslaught of cellular damage due to prolonged exposure to sunlight. They do so by attenuating the UV dose received through accumulation of UV-absorbing secondary metabolites, neutralizing reactive oxygen species produced by UV, monomerizing UV-induced pyrimidine dimers by photoreactivation, extracting UV photoproducts from DNA via nucleotide excision repair, and perhaps transiently tolerating the presence of DNA lesions via replicative bypass of the damage. The signaling mechanisms controlling these responses suggest that UV exposure also may be beneficial to plants by increasing cellular immunity to pathogens. Indeed, pathogen resistance can be enhanced by UV treatment, and recent experiments suggest DNA damage and its processing may have a role.
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Affiliation(s)
- Bernard A Kunz
- School of Life and Environmental Sciences, Deakin University, Geelong, Victoria 3217, Australia
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