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Dwiningsih Y, Thomas J, Kumar A, Gupta C, Gill N, Ruiz C, Alkahtani J, Baisakh N, Pereira A. QTLs and Candidate Loci Associated with Drought Tolerance Traits of Kaybonnet x ZHE733 Recombinant Inbred Lines Rice Population. Int J Mol Sci 2023; 24:15167. [PMID: 37894848 PMCID: PMC10606886 DOI: 10.3390/ijms242015167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/02/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Rice is the most important staple crop for the sustenance of the world's population, and drought is a major factor limiting rice production. Quantitative trait locus (QTL) analysis of drought-resistance-related traits was conducted on a recombinant inbred line (RIL) population derived from the self-fed progeny of a cross between the drought-resistant tropical japonica U.S. adapted cultivar Kaybonnet and the drought-sensitive indica cultivar ZHE733. K/Z RIL population of 198 lines was screened in the field at Fayetteville (AR) for three consecutive years under controlled drought stress (DS) and well-watered (WW) treatment during the reproductive stage. The effects of DS were quantified by measuring morphological traits, grain yield components, and root architectural traits. A QTL analysis using a set of 4133 single nucleotide polymorphism (SNP) markers and the QTL IciMapping identified 41 QTLs and 184 candidate genes for drought-related traits within the DR-QTL regions. RT-qPCR in parental lines was used to confirm the putative candidate genes. The comparison between the drought-resistant parent (Kaybonnet) and the drought-sensitive parent (ZHE733) under DS conditions revealed that the gene expression of 15 candidate DR genes with known annotations and two candidate DR genes with unknown annotations within the DR-QTL regions was up-regulated in the drought-resistant parent (Kaybonnet). The outcomes of this research provide essential information that can be utilized in developing drought-resistant rice cultivars that have higher productivity when DS conditions are prevalent.
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Affiliation(s)
- Yheni Dwiningsih
- Department of Crop, Soil, and Environmental Sciences, Faculty of Agriculture Food and Life Sciences, University of Arkansas System Division of Agriculture, Fayetteville, AR 72701, USA; (Y.D.); (J.T.); (A.K.); (C.R.); (J.A.)
| | - Julie Thomas
- Department of Crop, Soil, and Environmental Sciences, Faculty of Agriculture Food and Life Sciences, University of Arkansas System Division of Agriculture, Fayetteville, AR 72701, USA; (Y.D.); (J.T.); (A.K.); (C.R.); (J.A.)
| | - Anuj Kumar
- Department of Crop, Soil, and Environmental Sciences, Faculty of Agriculture Food and Life Sciences, University of Arkansas System Division of Agriculture, Fayetteville, AR 72701, USA; (Y.D.); (J.T.); (A.K.); (C.R.); (J.A.)
| | - Chirag Gupta
- Waisman Center, University of Wisconsin-Madison, Madison, WI 53705, USA;
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Navdeep Gill
- Department of Biological Sciences, Nova Southeastern University, Fort Lauderdale, FL 33314, USA;
| | - Charles Ruiz
- Department of Crop, Soil, and Environmental Sciences, Faculty of Agriculture Food and Life Sciences, University of Arkansas System Division of Agriculture, Fayetteville, AR 72701, USA; (Y.D.); (J.T.); (A.K.); (C.R.); (J.A.)
| | - Jawaher Alkahtani
- Department of Crop, Soil, and Environmental Sciences, Faculty of Agriculture Food and Life Sciences, University of Arkansas System Division of Agriculture, Fayetteville, AR 72701, USA; (Y.D.); (J.T.); (A.K.); (C.R.); (J.A.)
| | - Niranjan Baisakh
- Department of School of Plant, Environmental and Soil Sciences, Louisiana State University, Baton Rouge, LA 70803, USA;
| | - Andy Pereira
- Department of Crop, Soil, and Environmental Sciences, Faculty of Agriculture Food and Life Sciences, University of Arkansas System Division of Agriculture, Fayetteville, AR 72701, USA; (Y.D.); (J.T.); (A.K.); (C.R.); (J.A.)
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Padmashree R, Barbadikar KM, Honnappa, Magar ND, Balakrishnan D, Lokesha R, Gireesh C, Siddaiah AM, Madhav MS, Ramesha YM, Bharamappanavara M, Phule AS, Senguttuvel P, Diwan JR, Subrahmanyam D, Sundaram RM. Genome-wide association studies in rice germplasm reveal significant genomic regions for root and yield-related traits under aerobic and irrigated conditions. FRONTIERS IN PLANT SCIENCE 2023; 14:1143853. [PMID: 37538056 PMCID: PMC10395336 DOI: 10.3389/fpls.2023.1143853] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/19/2023] [Indexed: 08/05/2023]
Abstract
The development of nutrient-use efficient rice lines is a priority amidst the changing climate and depleting resources viz., water, land, and labor for achieving sustainability in rice cultivation. Along with the traditional transplanted irrigated system of cultivation, the dry direct-seeded aerobic system is gaining ground nationwide. The root-related traits play a crucial role in nutrient acquisition, adaptation and need to be concentrated along with the yield-attributing traits. We phenotyped an association panel of 118 rice lines for seedling vigour index (SVI) traits at 14 and 21 days after sowing (DAS), root-related traits at panicle initiation (PI) stage in polythene bags under controlled aerobic condition, yield and yield-related traits under the irrigated condition at ICAR-IIRR, Hyderabad, Telangana; irrigated and aerobic conditions at ARS, Dhadesugur, Raichur, Karnataka. The panel was genotyped using simple sequence repeats (SSR) markers and genome-wide association studies were conducted for identifying marker-trait associations (MTAs). Significant correlations were recorded for root length, root dry weight with SVI, root volume at the PI stage, number of productive tillers per plant, spikelet fertility, the total number of grains per panicle with grain yield per plant under irrigated conditions, and the total number of grains per panicle with grain yield per plant under aerobic condition. The panel was divided into three sub-groups (K = 3) and correlated with the principal component analysis. The maximum number of MTAs were found on chromosomes 2, 3, and 12 with considerable phenotypic variability. Consistent MTAs were recorded for SVI traits at 14 and 21 DAS (RM25310, RM80, RM22961, RM1385), yield traits under irrigated conditions (RM2584, RM5179, RM410, RM20698, RM14753) across years at ICAR-IIRR, grain yield per plant (RM22961, RM1146) under the aerobic condition, grain yield per plant at irrigated ICAR-IIRR and SVI (RM5501), root traits at PI stage (RM2584, RM80, RM410, RM1146, RM18472). Functionally relevant genes near the MTAs through in-silico expression analysis in root and panicle tissues viz., HBF2 bZIP transcription factor, WD40 repeat-like domain, OsPILS6a auxin efflux carrier, WRKY108, OsSCP42, OsMADS80, nodulin-like domain-containing protein, amino acid transporter using various rice expression databases were identified. The identified MTAs and rice lines having high SVI traits (Langphou, TI-128, Mouli, TI-124, JBB-631-1), high yield under aerobic (Phouren, NPK-43, JBB-684, Ratnamudi, TI-112), irrigated conditions (KR-209, KR-262, Phouren, Keibi-Phou, TI-17), robust root traits like root length (MoirangPhou-Angouba, Wangoo-Phou, JBB-661, Dissi, NPK-45), root volume (Ratnachudi, KJ-221, Mow, Heimang-Phou, PUP-229) can be further employed in breeding programs for the targeted environments aimed at improving seedling vigour, yield-related traits under irrigated condition, aerobic condition as adaptability to water-saving technology.
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Affiliation(s)
- Revadi Padmashree
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
- University of Agricultural Sciences (UAS), Raichur, India
| | - Kalyani M. Barbadikar
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Honnappa
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
- University of Agricultural Sciences (UAS), Raichur, India
| | - Nakul D. Magar
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
- Chaudhary Charan Singh University, Meerut, India
| | - Divya Balakrishnan
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - R. Lokesha
- University of Agricultural Sciences (UAS), Raichur, India
| | - C. Gireesh
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Anantha M. Siddaiah
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Maganti Sheshu Madhav
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Y. M Ramesha
- Agricultural Research Station (ARS) Dhadesugur, University of Agricultural Sciences (UAS), Raichur, India
| | | | - Amol S. Phule
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - P. Senguttuvel
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - J. R. Diwan
- University of Agricultural Sciences (UAS), Raichur, India
| | - D. Subrahmanyam
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Raman Menakshi Sundaram
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
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Yang Y, Zhang Y, Li J, Xu P, Wu Z, Deng X, Pu Q, Lv Y, Elgamal WHAS, Maniruzzaman S, Deng W, Zhou J, Tao D. Three QTL from Oryza meridionalis Could Improve Panicle Architecture in Asian Cultivated Rice. RICE (NEW YORK, N.Y.) 2023; 16:22. [PMID: 37129647 PMCID: PMC10154444 DOI: 10.1186/s12284-023-00640-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 04/20/2023] [Indexed: 05/03/2023]
Abstract
Rice panicle architecture is directly associated with grain yield and is also the key target in high-yield rice breeding program. In this study, three BC6F2 segregation populations derived from the crosses between two accessions of Oryza meridionalis and a O. sativa spp. japonica cultivar Dianjingyou 1, were employed to map QTL for panicle architecture. Three QTL, EP4.2, DEP7 and DEP8 were identified and validated using substitution mapping strategy on chromosome 4, 9 and 8, respectively. The three QTL showed pleiotropic phenotype on panicle length (PL), grain number per panicle (GNPP), number of primary branches (NPB), number of secondary branches (NSB), and grain width. DEP7 and DEP8 showed yield-enhancing potential by increasing GNPP, NPB and NSB, while EP4.2 exhibited wide grain, short stalk and panicle which can improve plant and panicle architecture, too. Moreover, epistatic interaction for PL was detected between EP4.2 and DEP7, and epistatic analysis between DEP7 and DEP8 for GNPP and NPB also revealed significant two QTL interactions. The result would help us understand the molecular basis of panicle architecture and lay the foundation for using these three QTL in rice breeding.
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Grants
- 31991221 National Natural Science Foundation of China
- 31991221 National Natural Science Foundation of China
- 31991221 National Natural Science Foundation of China
- 31991221 National Natural Science Foundation of China
- 31991221 National Natural Science Foundation of China
- 31991221 National Natural Science Foundation of China
- 202101AS070036, 202101AT070193, 202001AS070003, 202003AD150007, 530000210000000013809 Yunnan Provincial Science and Technology Department, China
- 202101AS070036, 202101AT070193, 202001AS070003, 202003AD150007, 530000210000000013809 Yunnan Provincial Science and Technology Department, China
- 202101AS070036, 202101AT070193, 202001AS070003, 202003AD150007, 530000210000000013809 Yunnan Provincial Science and Technology Department, China
- 202101AS070036, 202101AT070193, 202001AS070003, 202003AD150007, 530000210000000013809 Yunnan Provincial Science and Technology Department, China
- 202101AS070036, 202101AT070193, 202001AS070003, 202003AD150007, 530000210000000013809 Yunnan Provincial Science and Technology Department, China
- 202101AS070036, 202101AT070193, 202001AS070003, 202003AD150007, 530000210000000013809 Yunnan Provincial Science and Technology Department, China
- 202101AS070036, 202101AT070193, 202001AS070003, 202003AD150007, 530000210000000013809 Yunnan Provincial Science and Technology Department, China
- 202101AS070036, 202101AT070193, 202001AS070003, 202003AD150007, 530000210000000013809 Yunnan Provincial Science and Technology Department, China
- 202101AS070036, 202101AT070193, 202001AS070003, 202003AD150007, 530000210000000013809 Yunnan Provincial Science and Technology Department, China
- 202101AS070036, 202101AT070193, 202001AS070003, 202003AD150007, 530000210000000013809 Yunnan Provincial Science and Technology Department, China
- YNWR-QNBJ-2018-359 Yunnan Provincial Government
- YNWR-QNBJ-2018-359 Yunnan Provincial Government
- YNWR-QNBJ-2018-359 Yunnan Provincial Government
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Affiliation(s)
- Ying Yang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650200, China
| | - Yu Zhang
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650200, China
| | - Jing Li
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650200, China
| | - Peng Xu
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650200, China
- Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, 650233, China
| | - Zhijuan Wu
- School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Xianneng Deng
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650200, China
| | - Qiuhong Pu
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650200, China
| | - Yonggang Lv
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650200, China
| | - Walid Hassan Ali Soliman Elgamal
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650200, China
- Rice Research Department, Field Crops Research Institute, Agricultural Research Center, Sakha, 33717, Egypt
| | - Sheikh Maniruzzaman
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650200, China
- Plant Breeding Division, Bangladesh Rice Research Institute, Gazipur, 1701, Bangladesh
| | - Wei Deng
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650200, China
| | - Jiawu Zhou
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650200, China.
| | - Dayun Tao
- Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650200, China.
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Pang Z, Zhao Y, Xu P, Yu D. Microbial Diversity of Upland Rice Roots and Their Influence on Rice Growth and Drought Tolerance. Microorganisms 2020; 8:microorganisms8091329. [PMID: 32878310 PMCID: PMC7564600 DOI: 10.3390/microorganisms8091329] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 08/27/2020] [Accepted: 08/30/2020] [Indexed: 01/25/2023] Open
Abstract
Among abiotic stresses, drought is one of the most important factors limiting plant growth. To increase their drought tolerance and survival, most plants interact directly with a variety of microbes. Upland rice (Oryza sativa L.) is a rice ecotype that differs from irrigated ecotype rice; it is adapted to both drought-stress and aerobic conditions. However, its root microbial resources have not been explored. We isolated bacteria and fungi from roots of upland rice in Xishuangbanna, China. Four hundred sixty-two endophytic and rhizospheric isolates (337 bacteria and 125 fungi) were distributed. They were distributed among 43 genera on the basis of 16S rRNA and internal transcribed spacer (ITS) gene sequence analysis. Notably, these root microbes differed from irrigated rice root microbes in irrigated environments; for example, members of the Firmicutes phylum were enriched (by 28.54%) in the roots of the upland plants. The plant growth-promoting (PGP) potential of 217 isolates was investigated in vitro. The PGP ability of 17 endophytic and 10 rhizospheric isolates from upland rice roots was evaluated under well-irrigated and drought-stress conditions, and 9 fungal strains increased rice seedling shoot length, shoot and root fresh weight (FW), antioxidant capability, and proline (Pro) and soluble sugar contents. Our work suggests that fungi from upland rice roots can increase plant growth under irrigated and drought-stress conditions and can serve as effective microbial resources for sustainable agricultural production in arid regions.
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Affiliation(s)
- Zhiqiang Pang
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (Z.P.); (Y.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Zhao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (Z.P.); (Y.Z.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
| | - Peng Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (Z.P.); (Y.Z.)
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Menglun, Mengla, Yunnan 666303, China
- Correspondence: (P.X.); (D.Y.)
| | - Diqiu Yu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650223, China; (Z.P.); (Y.Z.)
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650091, China
- Correspondence: (P.X.); (D.Y.)
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Uddin MN, Fukuta Y. A Region on Chromosome 7 Related to Differentiation of Rice ( Oryza sativa L.) Between Lowland and Upland Ecotypes. FRONTIERS IN PLANT SCIENCE 2020; 11:1135. [PMID: 32849696 PMCID: PMC7398126 DOI: 10.3389/fpls.2020.01135] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/13/2020] [Indexed: 05/03/2023]
Abstract
Due to global population expansion and climate change impacts, the development of a stable yielding variety that adapts well to unfavorable conditions for rice cultivation, can contribute to sustainable and stable production in rice (Oryza sativa L.). Understanding genetic differentiations to ecotypes for rice cultivations, such as upland, rainfed lowland, and irrigated lowland, is very important to develop the breeding materials for adapting to each environmental condition. The upland landrace variety basically has low tiller/panicle numbers and a large panicle, and the plant architecture is different from that of the lowland variety. The tiller and panicle numbers have been considered as one of the most difficult traits for genetic changes artificially in rice breeding. A low tiller recessive gene ltn2 originated from a New Plant Type variety, IR 65600-87-2-23, harboring segments from an upland variety, Ketan Lumbu (Tropical Japonica Group), was found on chromosome 7, and the other QTLs for culm length, culm weight, panicle length, panicle weight, seed fertility, harvest index, and soil surface rooting were also detected in the same chromosome region. These low tiller genes and the other QTLs were estimated to play an important role in developing the architecture for upland rice. Some QTLs for root growth angle, DRO3 and qSFR7, were also found in the same chromosome region from upland varieties categorized into the Tropical Japonica Group, and the QTLs may also be relevant to upland adaptation together with other traits. Previous studies using high throughput re-sequencing (whole genome variation data) of a large batch of rice accessions could identify the ecotype differentiated genomic regions (EDRs) and Ecotype differentiated genes (EDGs) such as Os07g0449700, a type response regulator, which is critical in upland adaptation in the same region of chromosome 7. Two selective loci, E3735 and E4208, for upland and lowland differentiation, and their corresponding genes Os07g0260000 and Os07g0546500 were also detected on chromosome 7 by drought-responding EST-SSRs. These findings indicate that the region on chromosome 7 is highly possible to related to the plant shoot and root architecture in the upland rice variety that has an important role and differentiates between upland and lowland ecotypes.
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Affiliation(s)
- Md. Nashir Uddin
- Department of Biochemistry and Microbiology, School of Health and Life Sciences, North South University, Dhaka, Bangladesh
| | - Yoshimichi Fukuta
- Tropical Agricultural Research Front, Japan International Research Center for Agricultural Science (JIRCAS), Ishigaki, Japan
- *Correspondence: Yoshimichi Fukuta,
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