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Saito N, Chen S, Kitajima K, Zhou Z, Koide Y, Encabo JR, Diaz MGQ, Choi IR, Koyanagi KO, Kishima Y. Phylogenetic analysis of endogenous viral elements in the rice genome reveals local chromosomal evolution in Oryza AA-genome species. Front Plant Sci 2023; 14:1261705. [PMID: 37965031 PMCID: PMC10641527 DOI: 10.3389/fpls.2023.1261705] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/29/2023] [Indexed: 11/16/2023]
Abstract
Introduction Rice genomes contain endogenous viral elements homologous to rice tungro bacilliform virus (RTBV) from the pararetrovirus family Caulimoviridae. These viral elements, known as endogenous RTBV-like sequences (eRTBVLs), comprise five subfamilies, eRTBVL-A, -B, -C, -D, and -X. Four subfamilies (A, B, C, and X) are present to a limited degree in the genomes of the Asian cultivated rice Oryza sativa (spp. japonica and indica) and the closely related wild species Oryza rufipogon. Methods The eRTBVL-D sequences are widely distributed within these and other Oryza AA-genome species. Fifteen eRTBVL-D segments identified in the japonica (Nipponbare) genome occur mostly at orthologous chromosomal positions in other AA-genome species. The eRTBVL-D sequences were inserted into the genomes just before speciation of the AA-genome species. Results and discussion Ten eRTBVL-D segments are located at six loci, which were used for our evolutionary analyses during the speciation of the AA-genome species. The degree of genetic differentiation varied among the eRTBVL-D segments. Of the six loci, three showed phylogenetic trees consistent with the standard speciation pattern (SSP) of the AA-genome species (Type A), and the other three represented phylogenies different from the SSP (Type B). The atypical phylogenetic trees for the Type B loci revealed chromosome region-specific evolution among the AA-genome species that is associated with phylogenetic incongruences: complex genome rearrangements between eRTBVL-D segments, an introgression between the distant species, and low genetic diversity of a shared eRTBVL-D segment. Using eRTBVL-D as an indicator, this study revealed the phylogenetic incongruence of local chromosomal regions with different topologies that developed during speciation.
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Affiliation(s)
- Nozomi Saito
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Sunlu Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Cyrus Tang Innovation Center for Seed Industry, Nanjing Agricultural University, Nanjing, China
| | - Katsuya Kitajima
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Zhitong Zhou
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yohei Koide
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Jaymee R. Encabo
- Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines, Los Baños, Laguna, Philippines
| | - Maria Genaleen Q. Diaz
- Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines, Los Baños, Laguna, Philippines
| | - Il-Ryong Choi
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Kanako O. Koyanagi
- Faculty of Information Science and Technology, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yuji Kishima
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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Lizardo RCM, Pinili MS, Diaz MGQ, Cumagun CJR. Screening for Resistance in Selected Tomato Varieties against the Root-Knot Nematode Meloidogyne incognita in the Philippines Using a Molecular Marker and Biochemical Analysis. Plants 2022; 11:plants11101354. [PMID: 35631779 PMCID: PMC9147681 DOI: 10.3390/plants11101354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/16/2022] [Accepted: 05/18/2022] [Indexed: 11/16/2022]
Abstract
Tomato is a high-value vegetable crop widely cultivated in the Philippines, and its production is threatened by various stresses including infection by the root-knot nematode M. incognita. In this study, we checked for resistance to M. incognita in selected tomato germplasm collections and commercially available varieties using a bioassay method, the molecular marker Mi23 and biochemical analysis. Among the eight varieties tested, none showed a resistant reaction against M. incognita. Use of the molecular marker Mi23 yielded 430 bp in all the tomato varieties screened. Phylogenetic analysis using the neighbor-joining method revealed the clustering of consensus sequence of the varieties tested with the susceptible variety S. lycopersicum cv. M82-1-8 and a wild relative, S. pimpinellifolium isolate LA2184. The biochemical analysis showed varying responses among the varieties when they were inoculated with M. incognita. Increased levels of total antioxidant activity were observed in Diamante Max F1, Ilocos Red and Tm 2016 11-1, while total phenolic content was found to be elevated in Athena, Avatar TY F1 and Rosanna. Increased levels of ascorbic acid were observed in Athena and Avatar TY F1 even at 45 dpi. Even though these varieties showed elevated levels of the abovementioned biochemical parameters related to a resistance reaction, all of them showed highly susceptible reactions. Hence, this study showed that these tomato varieties have no resistance against M. incognita and that there is a need to identify other sources of resistance against M. incongita and produce resistant tomato cultivars adapted to local conditions.
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Affiliation(s)
- Roden Carlo M. Lizardo
- Institute of Weed Science, Entomology and Plant Pathology, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Los Baños 4031, Laguna, Philippines;
| | - Marita S. Pinili
- National Crop Protection Center, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Los Baños 4031, Laguna, Philippines;
| | - Maria Genaleen Q. Diaz
- Institute of Biological Sciences, College of Arts and Science, University of the Philippines Los Baños, College, Los Baños 4031, Laguna, Philippines;
| | - Christian Joseph R. Cumagun
- Institute of Weed Science, Entomology and Plant Pathology, College of Agriculture and Food Science, University of the Philippines Los Baños, College, Los Baños 4031, Laguna, Philippines;
- Molecular Phytopathology and Mycotoxin Research, University of Göttingen, Grisebachstrasse, 637077 Göttingen, Germany
- Correspondence:
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Dimaano NGB, Ali J, Mahender A, Sta. Cruz PC, Baltazar AM, Diaz MGQ, Pang YL, Acero BL, Li Z. Identification of quantitative trait loci governing early germination and seedling vigor traits related to weed competitive ability in rice. Euphytica 2020; 216:159. [PMID: 33029032 PMCID: PMC7510932 DOI: 10.1007/s10681-020-02694-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 09/04/2020] [Indexed: 05/10/2023]
Abstract
Weed competitive ability (WCA) is vital for the improvement of grain yield under direct-seeded and aerobic rice ecosystems where weeds are a major limiting factor. Early seed germination (ESG) and early seedling vigor (ESV) are the crucial traits for WCA. This study attempted to map the quantitative trait loci (QTLs) and hotspot regions governing ESG and ESV traits. A total of 167 BC1F5 selective introgression lines developed from an early backcross population involving Weed Tolerant Rice 1 (WTR-1) as the recipient parent and Y-134 as the donor parent were phenotyped for ESG and ESV traits. Analysis of variance revealed significant differences in ESG-related traits except for root length and in ESV-related traits except for plant height at 7 days after sowing. A total of 677-high quality single nucleotide polymorphism (SNP) markers were used to analyze the marker-trait association from a 6 K SNP genotyping array. Forty-three QTLs were identified on all chromosomes, except on chromosomes 4 and 8. Thirty QTLs were contributed by a desirable allele from Y-134, whereas 13 QTLs were from WTR-1. Twenty-eight of the identified genetic loci associated with ESG and ESV traits were novel. Two QTL hotspot regions were mapped on chromosomes 11 and 12. The genomic regions of QTL hotspots were fine-tuned and a total of 13 putative candidate genes were discovered on chromosomes 11 and 12 collectively. The mapped QTLs will be useful in advancing the marker aided-selection schemes and breeding programs for the development of rice cultivars with WCA traits.
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Affiliation(s)
| | - Jauhar Ali
- Rice Breeding Platform, International Rice Research Institute (IRRI), 4031 Los Baños, Laguna Philippines
| | - Anumalla Mahender
- Rice Breeding Platform, International Rice Research Institute (IRRI), 4031 Los Baños, Laguna Philippines
| | - Pompe C. Sta. Cruz
- University of the Philippines Los Baños, 4031 Los Baños, Laguna Philippines
| | - Aurora M. Baltazar
- University of the Philippines Los Baños, 4031 Los Baños, Laguna Philippines
| | | | - Yun Long Pang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Taian, 271018 People’s Republic of China
| | - Bart L. Acero
- Rice Breeding Platform, International Rice Research Institute (IRRI), 4031 Los Baños, Laguna Philippines
| | - Zhikang Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081 People’s Republic of China
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Dimaano NGB, Ali J, Cruz PCS, Baltazar AM, Diaz MGQ, Acero BL, Li Z. Performance of Newly Developed Weed-Competitive Rice Cultivars under Lowland and Upland Weedy Conditions. Weed Sci 2017; 65:798-817. [PMID: 33583962 PMCID: PMC7797629 DOI: 10.1017/wsc.2017.57] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 08/31/2019] [Indexed: 05/13/2023]
Abstract
Four early-generation backcross populations (BC1F2) derived from one common recipient parental background, Weed Tolerant Rice 1 ('WTR1'), and four different donor parents ('Y134', 'Zhong 143', 'Khazar', and 'Cheng Hui-448') were tested to identify suitable donor and recipient parents for weed competitiveness and to standardize evaluation of the weed-competitive ability in rice. 'GSR IR2-6' (G-6) derived from a backcross of WTR1/Y134//WTR1 was selected as the best population and was advanced for phenotypic experiments in the 2014 dry season. The introgression lines (ILs) derived from the G-6 population were evaluated for seed germination and seedling vigor in greenhouse conditions and for weed-competitive ability under field conditions (upland weed-free, upland weedy, and lowland weedy). Parents and checks were included for comparison. Selection pressure for weed competitiveness was relatively stronger in upland conditions than in lowland conditions. After three rounds of selection and based on their relative grain yield performances across conditions, a total of 21 most-promising introgression fixed lines showing superior traits and weed-competitive ability were identified. G-6-L2-WL-3, G-6-RF6-WL-3, G-6-L15-WU-1,G-6-Y16-WL-2, and G-6-L6-WU-3 were the top ILs in lowland weedy conditions, whereas G-6-Y7-WL-3, G-6-Y6-WU-3, G-6-Y3-WL-3, and G-6-Y8-WU-1 were the highest yielding in upland weedy conditions. The use of weed-competitive rice cultivars in African and Asian countries will be a highly effective strategy to reduce production costs and provide alternative solutions to the unavailability of herbicides. Competitive rice varieties will also significantly improve grain yields in aerobic rice systems and can become an important strategy for successful upland rice production. Nomenclature: Rice, Oryza sativa L.
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Affiliation(s)
- Niña Gracel B. Dimaano
- First, third, fourth, and fifth authors: Graduate Student, Professor 6, Adjunct Professor, and Professor 3, University of the Philippines-Los Banos, Los Banos, Laguna 4031, Philippines; second and sixth authors: Senior Scientist and Researcher, International Rice Research Institute, Los Banos, Laguna 4031, Philippines; seventh author: Chief Scientist, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jauhar Ali
- First, third, fourth, and fifth authors: Graduate Student, Professor 6, Adjunct Professor, and Professor 3, University of the Philippines-Los Banos, Los Banos, Laguna 4031, Philippines; second and sixth authors: Senior Scientist and Researcher, International Rice Research Institute, Los Banos, Laguna 4031, Philippines; seventh author: Chief Scientist, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Pompe C. Sta. Cruz
- First, third, fourth, and fifth authors: Graduate Student, Professor 6, Adjunct Professor, and Professor 3, University of the Philippines-Los Banos, Los Banos, Laguna 4031, Philippines; second and sixth authors: Senior Scientist and Researcher, International Rice Research Institute, Los Banos, Laguna 4031, Philippines; seventh author: Chief Scientist, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Aurora M. Baltazar
- First, third, fourth, and fifth authors: Graduate Student, Professor 6, Adjunct Professor, and Professor 3, University of the Philippines-Los Banos, Los Banos, Laguna 4031, Philippines; second and sixth authors: Senior Scientist and Researcher, International Rice Research Institute, Los Banos, Laguna 4031, Philippines; seventh author: Chief Scientist, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Maria Genaleen Q. Diaz
- First, third, fourth, and fifth authors: Graduate Student, Professor 6, Adjunct Professor, and Professor 3, University of the Philippines-Los Banos, Los Banos, Laguna 4031, Philippines; second and sixth authors: Senior Scientist and Researcher, International Rice Research Institute, Los Banos, Laguna 4031, Philippines; seventh author: Chief Scientist, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bart L. Acero
- First, third, fourth, and fifth authors: Graduate Student, Professor 6, Adjunct Professor, and Professor 3, University of the Philippines-Los Banos, Los Banos, Laguna 4031, Philippines; second and sixth authors: Senior Scientist and Researcher, International Rice Research Institute, Los Banos, Laguna 4031, Philippines; seventh author: Chief Scientist, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhikang Li
- First, third, fourth, and fifth authors: Graduate Student, Professor 6, Adjunct Professor, and Professor 3, University of the Philippines-Los Banos, Los Banos, Laguna 4031, Philippines; second and sixth authors: Senior Scientist and Researcher, International Rice Research Institute, Los Banos, Laguna 4031, Philippines; seventh author: Chief Scientist, Chinese Academy of Agricultural Sciences, Beijing, China
- Corresponding author’s E-mail:
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Lang JM, Hamilton JP, Diaz MGQ, Van Sluys MA, Burgos MRG, Vera Cruz CM, Buell CR, Tisserat NA, Leach JE. Genomics-Based Diagnostic Marker Development for Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola. Plant Dis 2010; 94:311-319. [PMID: 30754246 DOI: 10.1094/pdis-94-3-0311] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A computational genomics pipeline was used to compare sequenced genomes of Xanthomonas spp. and to rapidly identify unique regions for development of highly specific diagnostic markers. A suite of diagnostic primers was selected to monitor diverse loci and to distinguish the rice bacterial blight and bacterial leaf streak pathogens, Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola, respectively. A subset of these primers was combined into a multiplex polymerase chain reaction set that accurately distinguished the two rice pathogens in a survey of a geographically diverse collection of X. oryzae pv. oryzae, X. oryzae pv. oryzicola, other xanthomonads, and several genera of plant-pathogenic and plant- or seed-associated bacteria. This computational approach for identification of unique loci through whole-genome comparisons is a powerful tool that can be applied to other plant pathogens to expedite development of diagnostic primers.
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Affiliation(s)
- Jillian M Lang
- Department of Bioagricultural Sciences and Pest Management, Colorado State University (CSU), Fort Collins 80523-1177
| | - John P Hamilton
- Department of Plant Biology, Michigan State University, East Lansing 48824-1312
| | - Maria Genaleen Q Diaz
- Department of Bioagricultural Sciences and Pest Management, CSU and University of the Philippines, Los Baños, Los Baños, Philippines
| | - Marie Anne Van Sluys
- Department of Bioagricultural Sciences and Pest Management, CSU and Departamento de Botânica, IB-USP, São Paulo 05508-090, Brazil
| | - Ma Ruby G Burgos
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Casiana M Vera Cruz
- Plant Breeding, Genetics and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - C Robin Buell
- Department of Plant Biology, Michigan State University
| | - Ned A Tisserat
- Department of Bioagricultural Sciences and Pest Management, CSU
| | - Jan E Leach
- Department of Bioagricultural Sciences and Pest Management, CSU
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