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Zhu S, Sun S, Zhao W, Yang X, Chen Z, Mao H, Sheng L. Comprehensive physiology and proteomics analysis revealed the resistance mechanism of rice (Oryza sativa L) to cadmium stress. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 278:116413. [PMID: 38728942 DOI: 10.1016/j.ecoenv.2024.116413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 04/25/2024] [Accepted: 04/27/2024] [Indexed: 05/12/2024]
Abstract
Cadmium contamination can lead to a decrease in crop yield and quality. However, Cd-tolerant rice can improve rice resistance genes, improve crop tolerance to heavy metals, and protect plants from oxidative damage. In this study, Japonica rice: Chunyou 987 and Indica rice: Chuanzhong you 3607 were used to reveal the molecular response mechanism of Cd-tolerant rice under cadmium concentration of 3 mg/kg through comparative experiments combined with physiology and proteomics. The results showed that compared with indica rice, japonica rice showed more robust resistance to Cd stress and effectively retained many Cd ions in roots. Moreover, it enhanced its enzymatic and non-enzymatic anti-oxidative stress mechanism, which increased the activities of catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) by 47.37%, 21.75%, and 55.42%, respectively. The contents of non-enzymatic antioxidant substances ascorbic acid (AsA), glutathione (GSH), cysteine (Cys), proline (PRO), anthocyanins (OPC), and flavonoids were increased by 25.32%, 42.67%, 21.43%, 50.81%, 33.23%, and 72.16%, respectively. Through proteomics analysis, it was found that in response to the damage caused by cadmium stress, Japonica rice makes Photosynthesis functional proteins (psbO and PetH), Photosynthesis antenna proteins (LHCA and ASCAB9), Carbon fixation functional proteins (PEPC and OsAld), Porphyrin metabolism functional proteins (OsRCCR1 and SE5), Glyoxylate and dicarboxylate The expression of metabolism functional proteins (CATC and GLO4.) and Glutathione metabolism functional proteins (APX8 and OsGSTU13) were significantly up-regulated, which stimulated the antioxidant stress mechanism and photosynthetic system, and constructed a robust energy supply system to ensure the normal metabolic activities of life. Strengthening the mechanisms of plant homeostasis. In summary, this study revealed the molecular mechanism of tolerance to Cd stress in japonica rice, and the results of this study will provide a possible way to improve Cd-resistant rice seedlings.
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Affiliation(s)
- Sixi Zhu
- College of Eco-environment Engineering, Guizhou Minzu University; The Karst Environmental Geological Hazard Prevention of Key Laboratory of State Ethnic Affairs Commission, Guiyang 550025, China.
| | - Suxia Sun
- College of Eco-environment Engineering, Guizhou Minzu University; The Karst Environmental Geological Hazard Prevention of Key Laboratory of State Ethnic Affairs Commission, Guiyang 550025, China
| | - Wei Zhao
- College of Eco-environment Engineering, Guizhou Minzu University; The Karst Environmental Geological Hazard Prevention of Key Laboratory of State Ethnic Affairs Commission, Guiyang 550025, China
| | - Xiuqin Yang
- College of Eco-environment Engineering, Guizhou Minzu University; The Karst Environmental Geological Hazard Prevention of Key Laboratory of State Ethnic Affairs Commission, Guiyang 550025, China
| | - Zhongbing Chen
- Department of Applied Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcka 129, Praha-Suchdol 16500, Czech Republic
| | - Huan Mao
- College of Eco-environment Engineering, Guizhou Minzu University; The Karst Environmental Geological Hazard Prevention of Key Laboratory of State Ethnic Affairs Commission, Guiyang 550025, China
| | - Luying Sheng
- College of Eco-environment Engineering, Guizhou Minzu University; The Karst Environmental Geological Hazard Prevention of Key Laboratory of State Ethnic Affairs Commission, Guiyang 550025, China
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Zhang T, Huang W, Zhang L, Li DZ, Qi J, Ma H. Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages. Nat Commun 2024; 15:3305. [PMID: 38632270 PMCID: PMC11024178 DOI: 10.1038/s41467-024-47428-9] [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: 07/13/2023] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
Poaceae members shared a whole-genome duplication called rho. However, little is known about the evolutionary pattern of the rho-derived duplicates among Poaceae lineages and implications in adaptive evolution. Here we present phylogenomic/phylotranscriptomic analyses of 363 grasses covering all 12 subfamilies and report nine previously unknown whole-genome duplications. Furthermore, duplications from a single whole-genome duplication were mapped to multiple nodes on the species phylogeny; a whole-genome duplication was likely shared by woody bamboos with possible gene flow from herbaceous bamboos; and recent paralogues of a tetraploid Oryza are implicated in tolerance of seawater submergence. Moreover, rho duplicates showing differential retention among subfamilies include those with functions in environmental adaptations or morphogenesis, including ACOT for aquatic environments (Oryzoideae), CK2β for cold responses (Pooideae), SPIRAL1 for rapid cell elongation (Bambusoideae), and PAI1 for drought/cold responses (Panicoideae). This study presents a Poaceae whole-genome duplication profile with evidence for multiple evolutionary mechanisms that contribute to gene retention and losses.
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Affiliation(s)
- Taikui Zhang
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA, 16802, USA
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Weichen Huang
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Lin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Ji Qi
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Hong Ma
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA, 16802, USA.
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Ahmad R, Ullah I, Ullah Z, Alam S, Rady A, Khan SS, Durrani IS. Genomic Exploration: Unraveling the Intricacies of Indica Rice Oryza sativa L. Germin-Like Protein Gene 12-3 ( OsGLP12-3) Promoter via Cloning, Sequencing, and In Silico Analysis. ACS OMEGA 2024; 9:15271-15281. [PMID: 38585130 PMCID: PMC10993326 DOI: 10.1021/acsomega.3c09670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/21/2024] [Accepted: 03/05/2024] [Indexed: 04/09/2024]
Abstract
Germin and Germin-like proteins (GLPs) are a class of plant proteins that are part of the Cupins superfamily, found in several plant organs including roots, seeds, leaves, and nectar glands. They play a crucial role in plant defense against pathogens and environmental stresses. Herein, this study focused on the promoter analysis of OsGLP12-3 in rice cultivar Swat-1 to elucidate its regulation and functions. The region (1863bp) of the OsGLP12-3 promoter from Swat-1 genomic DNA was amplified, purified, quantified, and cloned using Topo cloning technology, followed by sequencing. Further in silico comparative analysis was conducted between the OsGLP12-3 promoters from Nipponbare and Swat-1 using the Plant CARE database, identifying 24 cis-acting regulatory elements with diverse functions. These elements exhibited distinct distribution patterns in the 2 rice varieties. The OsGLP12-3 promoter revealed an abundance of regulatory elements associated with biotic and abiotic stress responses. Computational tools were employed to analyze the regulatory features of this region. In silico expression analysis of OsGLP12-3, considering various developmental stages, stress conditions, hormones, and expression timing, was performed using the TENOR tool. Pairwise alignment indicated 86% sequence similarity between Nipponbare and Swat-1. Phylogenetic analysis was conducted to explore the evolutionary relationship between the OsGLP12-3 and other plant GLPs. Additionally, 2 unique regulatory elements were modeled and docked, GARE and MBS to understand their hydrogen bonding interactions in gene regulation. The study highlights the importance of OsGLP12-3 in plant defense against biotic and abiotic stresses, supported by its expression patterns in response to various stressors and the presence of specific regulatory elements within its promoter region.
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Affiliation(s)
- Rashid Ahmad
- Institute
of Biotechnology and Genetic Engineering (IBGE), The University of Agriculture, Peshawar 25000, Khyber Pakhtunkhwa, Pakistan
| | - Irfan Ullah
- College
of Life Science and Technology, Beijing
University of Chemical Technology, Beijing 100029, China
| | - Zakir Ullah
- College
of Life Science and Technology, Beijing
University of Chemical Technology, Beijing 100029, China
| | - Shahab Alam
- Institute
of Biotechnology and Genetic Engineering (IBGE), The University of Agriculture, Peshawar 25000, Khyber Pakhtunkhwa, Pakistan
| | - Ahmed Rady
- Department
of Zoology, College of Science, King Saud
University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Shahin Shah Khan
- College
of Life Science and Technology, Beijing
University of Chemical Technology, Beijing 100029, China
| | - Irfan Safdar Durrani
- Institute
of Biotechnology and Genetic Engineering (IBGE), The University of Agriculture, Peshawar 25000, Khyber Pakhtunkhwa, Pakistan
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Mahendran A, Yadav MC, Tiwari S, Bairwa RK, Krishnan SG, Rana MK, Singh R, Mondal TK. Population structure and genetic differentiation analyses reveal high level of diversity and allelic richness in crop wild relatives of AA genome species of rice (Oryza sativa L.) in India. J Appl Genet 2023; 64:645-666. [PMID: 37743422 DOI: 10.1007/s13353-023-00787-3] [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: 06/27/2023] [Revised: 08/27/2023] [Accepted: 09/04/2023] [Indexed: 09/26/2023]
Abstract
Crop wild relatives (CWRs) are vital sources of variation for genetic improvement, but their populations are few in genebanks, eroded in natural habitats and inadequately characterized. With a view to explore genetic diversity in CWRs of AA genome rice (Oryza sativa L.) species in India, we analyzed 96 accessions of 10 Oryza species by using 17 quantitative traits and 45 microsatellite markers. The morpho-quantitative traits revealed a high extent of phenotypic variation in the germplasm. Diversity index (H') revealed a high level of within-species variability in O. nivara (H' = 1.09) and O. rufipogon (H' = 1.12). Principal component (PC) analysis explained 79.22% variance with five PCs. Among the traits related to phenology, morphology, and yield, days to heading showed strong positive association with days to 50% flowering (r = 0.99). However, filled grains per panicle revealed positive association with spikelet fertility (0.71) but negative with awn length (- 0.58) and panicle bearing tillers (- 0.39). Cluster analysis grouped all the accessions into three major clusters. Microsatellite analysis revealed 676 alleles with 15.02 alleles per locus. High polymorphism information content (PIC = 0.83) and Shannon's information index (I = 2.31) indicated a high level of genetic variation in the CWRs. Structure analysis revealed four subpopulations; first and second subpopulations comprised only of O. nivara accessions, while the third subpopulation included both O. nivara and O. rufipogon accessions. Population statistics revealed a moderate level of genetic differentiation (FST = 0.14), high gene diversity (HE = 0.87), and high gene flow (Nm = 1.53) among the subpopulations. We found a high level of molecular variance among the genotypes (70%) and low among populations (11%) and within genotypes (19%). The high level of molecular and morphological variability detected in the germplasm of CWRs could be utilized for the improvement of cultivated rice.
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Affiliation(s)
- Aswin Mahendran
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR) - National Bureau of Plant Genetic Resources, New Delhi, 110012, India
- The Graduate School, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Mahesh C Yadav
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR) - National Bureau of Plant Genetic Resources, New Delhi, 110012, India.
| | - Shailesh Tiwari
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR) - National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Rakesh Kumar Bairwa
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR) - National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - S Gopala Krishnan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Mukesh Kumar Rana
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR) - National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Rakesh Singh
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR) - National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Tapan Kumar Mondal
- ICAR-National Institute of Plant Biotechnology, New Delhi, 110012, India
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Thathapalli Prakash P, Chebotarov D, Zhang J, Kudrna DA, Torres RO, Natividad MA, Quintana MR, Song J, Maldonado CE, Hechanova SL, Jena K, Wing RA, Henry A. Oryza glumaepatula: A wild relative to improve drought tolerance in cultivated rice. PLANT PHYSIOLOGY 2023; 193:2381-2397. [PMID: 37665979 PMCID: PMC10663109 DOI: 10.1093/plphys/kiad485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 07/31/2023] [Accepted: 08/12/2023] [Indexed: 09/06/2023]
Abstract
Developing drought-resistant rice (Oryza sativa, L.) is essential for improving field productivity, especially in rain-fed areas affected by climate change. Wild relatives of rice are potential sources for drought-resistant traits. Therefore, we compared root growth and drought response among 22 wild Oryza species, from which Oryza glumaepatula was selected as a promising source for further exploration. A geographically diverse panel of 69 O. glumaepatula accessions was then screened for drought stress-related traits, and 6 of these accessions showed lower shoot dry weight (SDW) reduction, greater percentage of deep roots, and lower stomatal density (STO) under drought than the drought tolerant O. sativa variety, Sahbhagi dhan. Based on whole-genome resequencing of all 69 O. glumaepatula accessions and variant calling to a high-quality O. glumaepatula reference genome, we detected multiple genomic loci colocating for SDW, root dry weight at 30 to 45 cm depth, and STO in consecutive drought trials. Geo-referencing indicated that the potential drought donors originated in flood-prone locations, corroborating previous hypotheses about the coexistence of flood and drought tolerance within individual Oryza genomes. These findings present potential donor accessions, traits, and genomic loci from an AA genome wild relative of rice that, together with the recently developed reference genome, may be useful for further introgression of drought tolerance into the O. sativa backgrounds.
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Affiliation(s)
- Parthiban Thathapalli Prakash
- Rice Breeding Innovations Department, International Rice Research Institute, UPLB Campus, Los Baños, Laguna 4031, Philippines
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Dmytro Chebotarov
- Rice Breeding Innovations Department, International Rice Research Institute, UPLB Campus, Los Baños, Laguna 4031, Philippines
| | - Jianwei Zhang
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - David A Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Rolando O Torres
- Rice Breeding Innovations Department, International Rice Research Institute, UPLB Campus, Los Baños, Laguna 4031, Philippines
| | - Mignon A Natividad
- Rice Breeding Innovations Department, International Rice Research Institute, UPLB Campus, Los Baños, Laguna 4031, Philippines
| | - Marinell R Quintana
- Rice Breeding Innovations Department, International Rice Research Institute, UPLB Campus, Los Baños, Laguna 4031, Philippines
| | - Jiaming Song
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Carlos E Maldonado
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Sherry Lou Hechanova
- Rice Breeding Innovations Department, International Rice Research Institute, UPLB Campus, Los Baños, Laguna 4031, Philippines
| | - Kshirod Jena
- Rice Breeding Innovations Department, International Rice Research Institute, UPLB Campus, Los Baños, Laguna 4031, Philippines
- School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
- Center for Desert Agriculture, King Abdullah University of Science & Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Amelia Henry
- Rice Breeding Innovations Department, International Rice Research Institute, UPLB Campus, Los Baños, Laguna 4031, Philippines
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6
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Zhang F, Kang H, Gao L. Complete Mitochondrial Genome Assembly of an Upland Wild Rice Species, Oryza granulata and Comparative Mitochondrial Genomic Analyses of the Genus Oryza. Life (Basel) 2023; 13:2114. [PMID: 38004254 PMCID: PMC10672236 DOI: 10.3390/life13112114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 10/15/2023] [Accepted: 10/18/2023] [Indexed: 11/26/2023] Open
Abstract
Wild upland rice species, including Oryza granulata, possess unique characteristics that distinguish them from other Oryza species. For instance, O. granulata characteristically has a GG genome and is accordingly classified as a basal lineage of the genus Oryza. Here, we deployed a versatile hybrid approach by integrating Illumina and PacBio sequencing data to generate a high-quality mitochondrial genome (mitogenome) assembly for O. granulata. The mitogenome of O. granulata was 509,311 base pairs (bp) with sixty-seven genes comprising two circular chromosomes, five ribosomal RNA (rRNA) coding genes, twenty-five transfer RNA (tRNA) coding genes, and thirty-seven genes coding for proteins. We identified a total of 378 simple sequence repeats (SSRs). The genome also contained 643 pairs of dispersed repeats comprising 340 palindromic and 303 forward. In the O. granulata mitogenome, the length of 57 homologous fragments in the chloroplast genome occupied 5.96% of the mitogenome length. Collinearity analysis of three Oryza mitogenomes revealed high structural variability and frequent rearrangements. Phylogenetic analysis showed that, compared to other related genera, O. granulata had the closest genetic relationship with mitogenomes reported for all members of Oryza, and occupies a position at the base of the Oryza phylogeny. Comparative analysis of complete mitochondrial genome assemblies for Oryza species revealed high levels of mitogenomic diversity, providing a foundation for future conservation and utilization of wild rice biodiversity.
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Affiliation(s)
- Fen Zhang
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China;
| | - Haiqi Kang
- Tropical Biodiversity and Genomics Research Center, Engineering Research Center for Selecting and Breeding New Tropical Crop Varieties, Ministry of Education, Hainan University, Haikou 570228, China;
| | - Lizhi Gao
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China;
- Tropical Biodiversity and Genomics Research Center, Engineering Research Center for Selecting and Breeding New Tropical Crop Varieties, Ministry of Education, Hainan University, Haikou 570228, China;
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7
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Tan M, Chen R, Chen X, Shahid MQ, Liu X, Wu J. In Vitro Induction of Interspecific Hybrid and Polyploidy Derived from Oryza officinalis Wall. PLANTS (BASEL, SWITZERLAND) 2023; 12:3001. [PMID: 37631212 PMCID: PMC10459038 DOI: 10.3390/plants12163001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023]
Abstract
Oryza officinalis Wall is a potential genetic resource for rice breeding; however, its distant genome limits its crossing ability with cultivated rice. The interspecific hybridization of O. officinalis and cultivated rice, establishment of its tissue culture, and induction of polyploidy are ways to improve O. officinalis's poor crossability. We developed an interspecific hybrid and studied its reproductive pollen development process in this work, and the results showed that abortive pollens (81.94%) and embryo sac abnormalities (91.04%) were the key causes of its high sterility. In order to induce callus formation in interspecific hybrid explants, two different culture media, namely Chu's N-6 medium (N6) and 1/2 Murashig and Skoog medium (1/2 MS), were employed. Additionally, two plant growth regulators (PGRs), namely 2,4-dichlorophenoxyacetic acid (2,4-D) and 6-benzylaminopurine (BA), along with L-proline (Pro) and acid hydrolyzed casein, were utilized in the experiment. The optimal N6 medium, supplemented with 2.0 mg·L-1 2,4-D, produced the highest induction rate (80.56 ± 5.44)%. For callus differentiation and proliferation, the MS medium supplemented with 2.0 mg·L-1 BA + 0.2 mg·L-1 NAA produced the highest differentiation rate (75.00 ± 4.97)% and seedling emergence ratio (28.97 ± 4.67)%. The optimal combination for seedling rooting was the 1/2 MS medium supplemented with 2.0 mg L-1 NAA and 0.2 mg L-1 BA, which produced an average of 13.95 roots per plant. For polyploidy induction in the interspecific hybrid, the concentration of colchicine treatment at 400 mg·L-1 for three days is an ideal protocol. We devised tissue culture and interspecific hybrid polyploidy induction to overcome O. officinalis' poor crossability and introduce its favorable features into cultivated rice.
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Affiliation(s)
- Meimei Tan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (M.T.); (R.C.); (X.C.); (M.Q.S.); (X.L.)
- Base Bank of Lingnan Rice Germplasm Resources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Ruoxin Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (M.T.); (R.C.); (X.C.); (M.Q.S.); (X.L.)
- Base Bank of Lingnan Rice Germplasm Resources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xingran Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (M.T.); (R.C.); (X.C.); (M.Q.S.); (X.L.)
- Base Bank of Lingnan Rice Germplasm Resources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (M.T.); (R.C.); (X.C.); (M.Q.S.); (X.L.)
- Base Bank of Lingnan Rice Germplasm Resources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (M.T.); (R.C.); (X.C.); (M.Q.S.); (X.L.)
- Base Bank of Lingnan Rice Germplasm Resources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Jinwen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; (M.T.); (R.C.); (X.C.); (M.Q.S.); (X.L.)
- Base Bank of Lingnan Rice Germplasm Resources, South China Agricultural University, Guangzhou 510642, China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China
- College of Agriculture, South China Agricultural University, Guangzhou 510642, China
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8
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Islam MR, Chowdhury R, Roy AS, Islam MN, Mita MM, Bashar S, Saha P, Rahat RA, Hasan M, Akter MA, Alam MZ, Latif MA. Native Trichoderma Induced the Defense-Related Enzymes and Genes in Rice against Xanthomonas oryzae pv. oryzae ( Xoo). PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091864. [PMID: 37176922 PMCID: PMC10180545 DOI: 10.3390/plants12091864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/16/2023] [Accepted: 02/27/2023] [Indexed: 05/15/2023]
Abstract
The application of Trichoderma is a form of biological control that has been effective in combating Xanthomonas oryzae pv. oryzae, the causative agent of the devastating disease known as bacterial blight of rice. In this present study, four strains of Trichoderma, viz., T. paraviridescens (BDISOF67), T. erinaceum (BDISOF91), T. asperellum (BDISOF08), and T. asperellum (BDISOF09), were collected from the rice rhizosphere and used to test their potentiality in reducing bacterial blight. The expression patterns of several core defense-related enzymes and genes related to SA and JA pathways were studied to explore the mechanism of induced resistance by those Trichoderma strains. The results primarily indicated that all Trichoderma were significantly efficient in reducing the lesion length of the leaf over rice check variety (IR24) through enhancing the expression of core defense-related enzymes, such as PAL, PPO, CAT, and POD activities by 4.27, 1.77, 3.53, and 1.57-fold, respectively, over control. Moreover, the results of qRT-PCR exhibited an upregulation of genes OsPR1, OsPR10, OsWRKY45, OsWRKY62, OsWRKY71, OsHI-LOX, and OsACS2 after 24 h of inoculation with all tested Trichoderma strains. However, in the case of RT-PCR, no major changes in OsPR1 and OsPR10 expression were observed in plants treated with different Trichoderma strains during different courses of time. Collectively, Trichoderma induced resistance in rice against X. oryzae pv. oryzae by triggering these core defense-related enzymes and genes associated with SA and JA pathways.
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Affiliation(s)
- Md Rashidul Islam
- Plant Bacteriology and Biotechnology Laboratory, Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Rabin Chowdhury
- Plant Bacteriology and Biotechnology Laboratory, Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Arpita Saha Roy
- Plant Bacteriology and Biotechnology Laboratory, Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Md Nazmul Islam
- Plant Bacteriology and Biotechnology Laboratory, Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Mamuna Mahjabin Mita
- Plant Bacteriology and Biotechnology Laboratory, Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Samrin Bashar
- Plant Bacteriology and Biotechnology Laboratory, Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Plabon Saha
- Plant Bacteriology and Biotechnology Laboratory, Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Ridwan Ahmed Rahat
- Faculty of Agriculture, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Mehedi Hasan
- Faculty of Agriculture, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Mst Arjina Akter
- Plant Bacteriology and Biotechnology Laboratory, Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Md Zahangir Alam
- Plant Bacteriology and Biotechnology Laboratory, Department of Plant Pathology, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Md Abdul Latif
- Plant Pathology Division, Bangladesh Rice Research Institute, Joydebpur, Gazipur 1701, Bangladesh
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9
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He N, Huang F, Lu L, Wang X, Li QQ, Yang D. SPR9 encodes a 60 S ribosomal protein that modulates panicle spreading and affects resistance to false smut in rice (Oryza sativa. L). BMC PLANT BIOLOGY 2023; 23:205. [PMID: 37081397 PMCID: PMC10116690 DOI: 10.1186/s12870-023-04172-4] [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: 11/09/2022] [Accepted: 03/15/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND The architecture of inflorescence in crops is a key agronomic feature determining grain yield and thus has been a major target trait of cereal domestication. RESULTS In this study, we show that a simple spreading panicle change in rice panicle shape, controlled by the Spreading Panicle 9 (SPR9) locus, also has a significant impact on the resistance to rice false smut (RFS). Meanwhile, we mapped a novel spr9 mutant gene between markers Indel5-18 and Indel5-22 encompassing a genomic region of 43-kb with six candidate genes. Through gene prediction and cDNA sequencing, we confirmed that LOC_Os05g38520 is the target gene in the spr9 mutant, which encodes 60 S ribosomal protein L36-2. Further analysis showed that the spr9 mutant is caused by a 1 bp deletion in the first exon that resulted in premature termination. Knockout experiments showed that the SPR9 gene is responsible for the spreading panicle phenotype of the spr9 mutant. Interestingly, the spr9 mutant was found to improve resistance to RFS without affecting major agronomic traits. Taken together, our results revealed that the spr9 allele has good application prospects in rice breeding for disease resistance and panicle improvement. CONCLUSIONS We report the map-based cloning and functional characterization of SPR9, which encodes a 60 S ribosomal protein that regulates spreading panicles and affects the resistance to false smut in rice.
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Affiliation(s)
- Niqing He
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fujian High Quality Rice Research and Development Center, Fuzhou, 350019, Fujian, China
| | - Fenghuang Huang
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fujian High Quality Rice Research and Development Center, Fuzhou, 350019, Fujian, China
| | - Libin Lu
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fujian High Quality Rice Research and Development Center, Fuzhou, 350019, Fujian, China
| | - Xun Wang
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fujian High Quality Rice Research and Development Center, Fuzhou, 350019, Fujian, China
| | - Qingshun Q Li
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fujian High Quality Rice Research and Development Center, Fuzhou, 350019, Fujian, China
- Biomedical Sciences, College of Dental Medicine, Western University of Health Sciences, Pomona, CA, 91766, USA
| | - Dewei Yang
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fujian High Quality Rice Research and Development Center, Fuzhou, 350019, Fujian, China.
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10
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Tong S, Ashikari M, Nagai K, Pedersen O. Can the Wild Perennial, Rhizomatous Rice Species Oryza longistaminata be a Candidate for De Novo Domestication? RICE (NEW YORK, N.Y.) 2023; 16:13. [PMID: 36928797 PMCID: PMC10020418 DOI: 10.1186/s12284-023-00630-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/05/2023] [Indexed: 06/18/2023]
Abstract
As climate change intensifies, the development of resilient rice that can tolerate abiotic stresses is urgently needed. In nature, many wild plants have evolved a variety of mechanisms to protect themselves from environmental stresses. Wild relatives of rice may have abundant and virtually untapped genetic diversity and are an essential source of germplasm for the improvement of abiotic stress tolerance in cultivated rice. Unfortunately, the barriers of traditional breeding approaches, such as backcrossing and transgenesis, make it challenging and complex to transfer the underlying resilience traits between plants. However, de novo domestication via genome editing is a quick approach to produce rice with high yields from orphans or wild relatives. African wild rice, Oryza longistaminata, which is part of the AA-genome Oryza species has two types of propagation strategies viz. vegetative propagation via rhizome and seed propagation. It also shows tolerance to multiple types of abiotic stress, and therefore O. longistaminata is considered a key candidate of wild rice for heat, drought, and salinity tolerance, and it is also resistant to lodging. Importantly, O. longistaminata is perennial and propagates also via rhizomes both of which are traits that are highly valuable for the sustainable production of rice. Therefore, O. longistaminata may be a good candidate for de novo domestication through genome editing to obtain rice that is more climate resilient than modern elite cultivars of O. sativa.
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Affiliation(s)
- Shuai Tong
- Department of Biology, University of Copenhagen, Universitetsparken 4, 3Rd Floor, 2100, Copenhagen, Denmark
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center of Nagoya University, Furo-Cho, Chikusa, Nagoya, Aichi, 464-8602, Japan
| | - Keisuke Nagai
- Bioscience and Biotechnology Center of Nagoya University, Furo-Cho, Chikusa, Nagoya, Aichi, 464-8602, Japan.
| | - Ole Pedersen
- Department of Biology, University of Copenhagen, Universitetsparken 4, 3Rd Floor, 2100, Copenhagen, Denmark.
- School of Agriculture and Environment, The University of Western Australia, 35 Stirling Highway, Crawley, WA, 6009, Australia.
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11
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Mmbando GS. Challenges and prospects in using biotechnological interventions in O. glaberrima, an African cultivated rice. GM CROPS & FOOD 2022; 13:372-387. [DOI: 10.1080/21645698.2022.2149212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Gideon Sadikiel Mmbando
- Department of Biology, College of Natural and Mathematical Sciences, University of Dodoma (Udom), Dodoma, Tanzania
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12
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Transcriptional Comparison of Genes Associated with Photosynthesis, Photorespiration, and Photo-Assimilate Allocation and Metabolic Profiling of Rice Species. Int J Mol Sci 2022; 23:ijms23168901. [PMID: 36012167 PMCID: PMC9408291 DOI: 10.3390/ijms23168901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/29/2022] [Accepted: 07/30/2022] [Indexed: 11/17/2022] Open
Abstract
The ever-increasing human population alongside environmental deterioration has presented a pressing demand for increased food production per unit area. As a consequence, considerable research effort is currently being expended in assessing approaches to enhance crop yields. One such approach is to harness the allelic variation lost in domestication. This is of particular importance since crop wild relatives often exhibit better tolerance to abiotic stresses. Here, we wanted to address the question as to why wild rice species have decreased grain production despite being characterized by enhanced rates of photosynthesis. In order to do so, we selected ten rice species on the basis of the presence of genome information, life span, the prominence of distribution, and habitat type and evaluated the expression of genes in photosynthesis, photorespiration, sucrose and starch synthesis, sucrose transport, and primary and secondary cell walls. We additionally measured the levels of a range of primary metabolites via gas chromatography–mass spectrometry. The results revealed that the wild rice species exhibited not only higher photosynthesis but also superior CO2 recovery by photorespiration; showed greater production of photosynthates such as soluble sugars and starch and quick transportation to the sink organs with a possibility of transporting forms such as RFOs, revealing the preferential consumption of soluble sugars to develop both primary and secondary cell walls; and, finally, displayed high glutamine/glutamic acid ratios, indicating that they likely exhibited high N-use efficiency. The findings from the current study thus identify directions for future rice improvement through breeding.
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13
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Than Kutay Soe, Kunieda M, Sunohara H, Inukai Y, Reyes VP, Nishiuchi S, Doi K. A Novel Combination of Genes Causing Temperature-Sensitive Hybrid Weakness in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:908000. [PMID: 35837460 PMCID: PMC9274174 DOI: 10.3389/fpls.2022.908000] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 05/26/2022] [Indexed: 09/29/2023]
Abstract
Reproductive isolation is an obstacle for plant breeding when a distant cross is demanded. It can be divided into two main types based on different growth stages: prezygotic isolation and postzygotic isolation. The hybrid weakness, which is a type of postzygotic isolation, can become a problem in crop breeding. In order to overcome reproductive isolation, it is necessary to elucidate its mechanism. In this study, genetic analysis for low temperature-dependent hybrid weakness was conducted in a rice F2 population derived from Taichung 65 (T65, Japonica) and Lijiangxintuanheigu (LTH, Japonica). The weak and severe weak plants in F2 showed shorter culm length, late heading, reduced panicle number, decreased grain numbers per panicle, and impaired root development in the field. Our result also showed that hybrid weakness was affected by temperature. It was observed that 24°C enhanced hybrid weakness, whereas 34°C showed recovery from hybrid weakness. In terms of the morphology of embryos, no difference was observed. Therefore, hybrid weakness affects postembryonic development and is independent of embryogenesis. The genotypes of 126 F2 plants were determined through genotyping-by-sequencing and a linkage map consisting of 862 single nucleotide polymorphism markers was obtained. Two major quantitative trait loci (QTLs) were detected on chromosomes 1 [hybrid weakness j 1 (hwj1)] and 11 [hybrid weakness j 2 (hwj2)]. Further genotyping indicated that the hybrid weakness was due to an incompatible interaction between the T65 allele of hwj1 and the LTH allele of hwj2. A large F2 populations consisting of 5,722 plants were used for fine mapping of hwj1 and hwj2. The two loci, hwj1 and hwj2, were mapped in regions of 65-kb on chromosome 1 and 145-kb on chromosome 11, respectively. For hwj1, the 65-kb region contained 11 predicted genes, while in the hwj2 region, 22 predicted genes were identified, two of which are disease resistance-related genes. The identified genes along these regions serve as preliminary information on the molecular networks associated with hybrid weakness in rice.
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Affiliation(s)
- Than Kutay Soe
- Laboratory of Information Sciences in Agricultural Lands, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Department of Botany, University of Yangon, Yangon, Myanmar
| | - Mai Kunieda
- Laboratory of Information Sciences in Agricultural Lands, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Hidehiko Sunohara
- Laboratory of Information Sciences in Agricultural Lands, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
- Environmental Control Center Co., Ltd., Hachioji, Japan
| | - Yoshiaki Inukai
- International Center for Research and Education in Agriculture, Nagoya University, Nagoya, Japan
| | - Vincent Pamugas Reyes
- Laboratory of Information Sciences in Agricultural Lands, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Shunsaku Nishiuchi
- Laboratory of Information Sciences in Agricultural Lands, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kazuyuki Doi
- Laboratory of Information Sciences in Agricultural Lands, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
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14
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Eizenga GC, Kim H, Jung JKH, Greenberg AJ, Edwards JD, Naredo MEB, Banaticla-Hilario MCN, Harrington SE, Shi Y, Kimball JA, Harper LA, McNally KL, McCouch SR. Phenotypic Variation and the Impact of Admixture in the Oryza rufipogon Species Complex ( ORSC). FRONTIERS IN PLANT SCIENCE 2022; 13:787703. [PMID: 35769295 PMCID: PMC9235872 DOI: 10.3389/fpls.2022.787703] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 04/13/2022] [Indexed: 06/15/2023]
Abstract
Crop wild relatives represent valuable reservoirs of variation for breeding, but their populations are threatened in natural habitats, are sparsely represented in genebanks, and most are poorly characterized. The focus of this study is the Oryza rufipogon species complex (ORSC), wild progenitor of Asian rice (Oryza sativa L.). The ORSC comprises perennial, annual and intermediate forms which were historically designated as O. rufipogon, O. nivara, and O. sativa f. spontanea (or Oryza spp., an annual form of mixed O. rufipogon/O. nivara and O. sativa ancestry), respectively, based on non-standardized morphological, geographical, and/or ecologically-based species definitions and boundaries. Here, a collection of 240 diverse ORSC accessions, characterized by genotyping-by-sequencing (113,739 SNPs), was phenotyped for 44 traits associated with plant, panicle, and seed morphology in the screenhouse at the International Rice Research Institute, Philippines. These traits included heritable phenotypes often recorded as characterization data by genebanks. Over 100 of these ORSC accessions were also phenotyped in the greenhouse for 18 traits in Stuttgart, Arkansas, and 16 traits in Ithaca, New York, United States. We implemented a Bayesian Gaussian mixture model to infer accession groups from a subset of these phenotypic data and ascertained three phenotype-based group assignments. We used concordance between the genotypic subpopulations and these phenotype-based groups to identify a suite of phenotypic traits that could reliably differentiate the ORSC populations, whether measured in tropical or temperate regions. The traits provide insight into plant morphology, life history (perenniality versus annuality) and mating habit (self- versus cross-pollinated), and are largely consistent with genebank species designations. One phenotypic group contains predominantly O. rufipogon accessions characterized as perennial and largely out-crossing and one contains predominantly O. nivara accessions characterized as annual and largely inbreeding. From these groups, 42 "core" O. rufipogon and 25 "core" O. nivara accessions were identified for domestication studies. The third group, comprising 20% of our collection, has the most accessions identified as Oryza spp. (51.2%) and levels of O. sativa admixture accounting for more than 50% of the genome. This third group is potentially useful as a "pre-breeding" pool for breeders attempting to incorporate novel variation into elite breeding lines.
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Affiliation(s)
- Georgia C. Eizenga
- Dale Bumpers National Rice Research Center, USDA-ARS, Stuttgart, AR, United States
| | - HyunJung Kim
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Janelle K. H. Jung
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | | | - Jeremy D. Edwards
- Dale Bumpers National Rice Research Center, USDA-ARS, Stuttgart, AR, United States
| | | | | | - Sandra E. Harrington
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Yuxin Shi
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Jennifer A. Kimball
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Lisa A. Harper
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | | | - Susan R. McCouch
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
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15
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Wang C, Han B. Twenty years of rice genomics research: From sequencing and functional genomics to quantitative genomics. MOLECULAR PLANT 2022; 15:593-619. [PMID: 35331914 DOI: 10.1016/j.molp.2022.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/04/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Since the completion of the rice genome sequencing project in 2005, we have entered the era of rice genomics, which is still in its ascendancy. Rice genomics studies can be classified into three stages: structural genomics, functional genomics, and quantitative genomics. Structural genomics refers primarily to genome sequencing for the construction of a complete map of rice genome sequence. This is fundamental for rice genetics and molecular biology research. Functional genomics aims to decode the functions of rice genes. Quantitative genomics is large-scale sequence- and statistics-based research to define the quantitative traits and genetic features of rice populations. Rice genomics has been a transformative influence on rice biological research and contributes significantly to rice breeding, making rice a good model plant for studying crop sciences.
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Affiliation(s)
- Changsheng Wang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China.
| | - Bin Han
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China.
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16
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Beerelli K, Balakrishnan D, Addanki KR, Surapaneni M, Rao Yadavalli V, Neelamraju S. Mapping of QTLs for Yield Traits Using F 2:3:4 Populations Derived From Two Alien Introgression Lines Reveals qTGW8.1 as a Consistent QTL for Grain Weight From Oryza nivara. FRONTIERS IN PLANT SCIENCE 2022; 13:790221. [PMID: 35356124 PMCID: PMC8959756 DOI: 10.3389/fpls.2022.790221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
Wild introgressions play a crucial role in crop improvement by transferring important novel alleles and broadening allelic diversity of cultivated germplasm. In this study, two stable backcross alien introgression lines 166s and 14s derived from Swarn/Oryza nivara IRGC81848 were used as parents to generate populations to map quantitative trait loci (QTLs) for yield-related traits. Field evaluation of yield-related traits in F2, F3, and F4 population was carried out in normal irrigated conditions during the wet season of 2015 and dry seasons of 2016 and 2018, respectively. Plant height, tiller number, productive tiller number, total dry matter, and harvest index showed a highly significant association to single plant yield in F2, F3, and F4. In all, 21, 30, and 17 QTLs were identified in F2, F2:3, and F2:4, respectively, for yield-related traits. QTLs qPH6.1 with 12.54% phenotypic variance (PV) in F2, qPH1.1 with 13.01% PV, qTN6.1 with 10.08% PV in F2:3, and qTGW6.1 with 15.19% PV in F2:4 were identified as major effect QTLs. QTLs qSPY4.1 and qSPY6.1 were detected for grain yield in F2 and F2:3 with PV 8.5 and 6.7%, respectively. The trait enhancing alleles of QTLs qSPY4.1, qSPY6.1, qPH1.1, qTGW6.1, qTGW8.1, qGN4.1, and qTDM5.1 were from O. nivara. QTLs of the yield contributing traits were found clustered in the same chromosomal region. qTGW8.1 was identified in a 2.6 Mb region between RM3480 and RM3452 in all three generations with PV 6.1 to 9.8%. This stable and consistent qTGW8.1 allele from O. nivara can be fine mapped for identification of causal genes. From this population, lines C212, C2124, C2128, and C2143 were identified with significantly higher SPY and C2103, C2116, and C2117 had consistently higher thousand-grain weight values than both the parents and Swarna across the generations and are useful in gene discovery for target traits and further crop improvement.
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Affiliation(s)
- Kavitha Beerelli
- National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, India
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
| | - Divya Balakrishnan
- National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Krishnam Raju Addanki
- National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, India
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, India
| | - Malathi Surapaneni
- National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | | | - Sarla Neelamraju
- National Professor Project, ICAR-Indian Institute of Rice Research, Hyderabad, India
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17
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Lang X, Xu A, Wang Y, Song Z. Seasonal variation of aerosol fungal community structure in reed constructed wetlands. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:19420-19431. [PMID: 34718950 DOI: 10.1007/s11356-021-17138-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/17/2021] [Indexed: 06/13/2023]
Abstract
In recent years, the impact of biological aerosols produced by sewage treatment plants on air quality and human health has become a hot spot of concern. Airborne fungi were characterized via KC-1000 large-flow air sampler and Anderson-type six-stage sampler, at free surface flowing reed constructed wetland located in Qingdao City, Shandong Province. The high-throughput sequencing technology and fungal culture-dependent method were selected to analyze the composition and dynamic changes of the fungal community attached to the atmospheric particulate matter in the free surface flow constructed wetland. The results showed that the aerosol concentration of fungi in the constructed wetlands varied from 587 to approximately 3382 CFU m-3, with a peak at the range of 1.10 to 2.10 μm particle size, and the particles (< 4.70 μm) that easily entered the lungs accounted for 57.03 ~ 96.03%. Significant seasonal differences in fungal richness and community diversity were found. The particle size distribution of fungi in atmospheric particles was not obvious. Fungal genera in the atmospheric particulate matter were mainly driven by humidity. However, other factors, i.e., temperature, NO2, SO2, and PM10 contents, also contributed.
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Affiliation(s)
- Xiulu Lang
- School of Geography, Nanjing Normal University, Nanjing, 210023, China
- Key Laboratory of Virtual Geographic Environment (Nanjing Normal University), Ministry of Education, Nanjing, 210023, China
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, 210023, China
| | - Ailing Xu
- School of Environment and Municipal Engineering, Qingdao University of Technology, Qingdao, 266033, China
| | - Yanhua Wang
- School of Geography, Nanjing Normal University, Nanjing, 210023, China.
- Key Laboratory of Virtual Geographic Environment (Nanjing Normal University), Ministry of Education, Nanjing, 210023, China.
- Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, 210023, China.
| | - Zhiwen Song
- School of Environment and Municipal Engineering, Qingdao University of Technology, Qingdao, 266033, China.
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18
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Heredia MC, Kant J, Prodhan MA, Dixit S, Wissuwa M. Breeding rice for a changing climate by improving adaptations to water saving technologies. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:17-33. [PMID: 34218290 DOI: 10.1007/s00122-021-03899-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 06/25/2021] [Indexed: 06/13/2023]
Abstract
Climate change is expected to increasingly affect rice production through rising temperatures and decreasing water availability. Unlike other crops, rice is a main contributor to greenhouse gas emissions due to methane emissions from flooded paddy fields. Climate change can therefore be addressed in two ways in rice: through making the crop more climate resilient and through changes in management practices that reduce methane emissions and thereby slow global warming. In this review, we focus on two water saving technologies that reduce the periods lowland rice will be grown under fully flooded conditions, thereby improving water use efficiency and reducing methane emissions. Rice breeding over the past decades has mostly focused on developing high-yielding varieties adapted to continuously flooded conditions where seedlings were raised in a nursery and transplanted into a puddled flooded soil. Shifting cultivation to direct-seeded rice or to introducing non-flooded periods as in alternate wetting and drying gives rise to new challenges which need to be addressed in rice breeding. New adaptive traits such as rapid uniform germination even under anaerobic conditions, seedling vigor, weed competitiveness, root plasticity, and moderate drought tolerance need to be bred into the current elite germplasm and to what extent this is being addressed through trait discovery, marker-assisted selection and population improvement are reviewed.
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Affiliation(s)
| | | | - M Asaduzzaman Prodhan
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
| | - Shalabh Dixit
- International Rice Research Institute (IRRI), Los Baños, The Philippines
| | - Matthias Wissuwa
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan.
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19
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Development and validation of diagnostic SNP markers for quality control genotyping in a collection of four rice (Oryza) species. Sci Rep 2021; 11:18617. [PMID: 34545105 PMCID: PMC8452751 DOI: 10.1038/s41598-021-97689-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/30/2021] [Indexed: 02/08/2023] Open
Abstract
Morphological identification of closely related rice species, particularly those in the Oryza AA genome group, presents major challenges and often results in cases of misidentification. Recent work by this group identified diagnostic single nucleotide polymorphic (SNP) markers specific for several rice species and subspecies based on DArTseq next-generation sequencing technology ("DArTseq"). These SNPs can be used for quality control (QC) analysis in rice breeding and germplasm maintenance programs. Here, we present the DArTseq-based diagnostic SNPs converted into Kompetitive allele-specific PCR (KASPar or KASP) assays and validation data for a subset of them; these can be used for low-cost routine genotyping quality control (QC) analysis. Of the 224 species/subspecies' diagnostic SNPs tested, 158 of them produced working KASP assays, a conversion success rate of 70%. Two validation experiments were run with 87 of the 158 SNP markers to ensure that the assays amplified, were polymorphic, and distinguished the five species/subspecies tested. Based on these validation test results, we recommend a panel of 36 SNP markers that clearly delineate O. barthii, O. glaberrima, O. longistaminata, O. sativa spp. indica and japonica. The KASP assays provide a flexible, rapid turnaround and cost-effective tool to facilitate germplasm curation and management of these four Oryza AA genome species across multiple genebanks.
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20
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KHARSHIING GAYLE, CHRUNGOO NIKHILK. Wx alleles in rice: relationship with apparent amylose content of starch and a possible role in rice domestication. J Genet 2021. [DOI: 10.1007/s12041-021-01311-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Villacastin AJ, Adams KS, Boonjue R, Rushton PJ, Han M, Shen JQ. Dynamic differential evolution schemes of WRKY transcription factors in domesticated and wild rice. Sci Rep 2021; 11:14887. [PMID: 34290268 PMCID: PMC8295372 DOI: 10.1038/s41598-021-94109-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/05/2021] [Indexed: 01/30/2023] Open
Abstract
WRKY transcription factors play key roles in stress responses, growth, and development. We previously reported on the evolution of WRKYs from unicellular green algae to land plants. To address recent evolution events, we studied three domesticated and eight wild species in the genus Oryza, an ideal model due to its long history of domestication, economic importance, and central role as a model system. We have identified prevalence of Group III WRKYs despite differences in breeding of cultivated and wild species. Same groups of WRKY genes tend to cluster together, suggesting recent, multiple duplication events. Duplications followed by divergence may result in neofunctionalizations of co-expressed WRKY genes that finely tune the regulation of target genes in a same metabolic or response pathway. WRKY genes have undergone recent rearrangements to form novel genes. Group Ib WRKYs, unique to AA genome type Oryza species, are derived from Group III genes dated back to 6.76 million years ago. Gene tree reconciliation analysis with the species tree revealed details of duplication and loss events in the 11 genomes. Selection analysis on single copy orthologs reveals the highly conserved nature of the WRKY domain and clusters of fast evolving sites under strong positive selection pressure. Also, the numbers of single copy orthologs under positive or negative selection almost evenly split. Our results provide valuable insights into the preservation and diversification of an important gene family under strong selective pressure for biotechnological improvements of the world's most valued food crop.
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Affiliation(s)
- Anne J Villacastin
- School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Keeley S Adams
- School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Rin Boonjue
- School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Paul J Rushton
- School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Mira Han
- School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA
| | - Jeffery Q Shen
- School of Life Sciences, University of Nevada Las Vegas, 4505 Maryland Parkway, Las Vegas, NV, 89154, USA.
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Shenton M, Kobayashi M, Terashima S, Ohyanagi H, Copetti D, Hernández-Hernández T, Zhang J, Ohmido N, Fujita M, Toyoda A, Ikawa H, Fujiyama A, Furuumi H, Miyabayashi T, Kubo T, Kudrna D, Wing R, Yano K, Nonomura KI, Sato Y, Kurata N. Evolution and Diversity of the Wild Rice Oryza officinalis Complex, across Continents, Genome Types, and Ploidy Levels. Genome Biol Evol 2021; 12:413-428. [PMID: 32125373 PMCID: PMC7531200 DOI: 10.1093/gbe/evaa037] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2020] [Indexed: 12/15/2022] Open
Abstract
The Oryza officinalis complex is the largest species group in
Oryza, with more than nine species from four continents, and is a
tertiary gene pool that can be exploited in breeding programs for the improvement of
cultivated rice. Most diploid and tetraploid members of this group have a C genome. Using
a new reference C genome for the diploid species O. officinalis, and
draft genomes for two other C genome diploid species Oryza eichingeri and
Oryza rhizomatis, we examine the influence of transposable elements on
genome structure and provide a detailed phylogeny and evolutionary history of the
Oryza C genomes. The O. officinalis genome is 1.6
times larger than the A genome of cultivated Oryza sativa, mostly due to
proliferation of Gypsy type long-terminal repeat transposable elements,
but overall syntenic relationships are maintained with other Oryza
genomes (A, B, and F). Draft genome assemblies of the two other C genome diploid species,
Oryza eichingeri and Oryza rhizomatis, and short-read
resequencing of a series of other C genome species and accessions reveal that after the
divergence of the C genome progenitor, there was still a substantial degree of variation
within the C genome species through proliferation and loss of both DNA and long-terminal
repeat transposable elements. We provide a detailed phylogeny and evolutionary history of
the Oryza C genomes and a genomic resource for the exploitation of the
Oryza tertiary gene pool.
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Affiliation(s)
| | | | | | - Hajime Ohyanagi
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Dario Copetti
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona.,T.T. Chang Genetic Resources Center, International Rice Research Institute, Los Baños, Philippines
| | | | - Jianwei Zhang
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona
| | - Nobuko Ohmido
- Division of the Living Environment, Kobe University, Japan
| | | | | | | | | | | | | | - Takahiko Kubo
- National Institute of Genetics, Mishima, Japan.,Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - David Kudrna
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona
| | - Rod Wing
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona.,T.T. Chang Genetic Resources Center, International Rice Research Institute, Los Baños, Philippines.,Biological and Environment Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Kentaro Yano
- School of Agriculture, Meiji University, Tokyo, Japan
| | | | - Yutaka Sato
- National Institute of Genetics, Mishima, Japan
| | - Nori Kurata
- National Institute of Genetics, Mishima, Japan
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23
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Exploring the Loci Responsible for Awn Development in Rice through Comparative Analysis of All AA Genome Species. PLANTS 2021; 10:plants10040725. [PMID: 33917982 PMCID: PMC8068336 DOI: 10.3390/plants10040725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/31/2021] [Accepted: 04/06/2021] [Indexed: 11/17/2022]
Abstract
Wild rice species have long awns at their seed tips, but this trait has been lost through rice domestication. Awn loss mitigates harvest and seed storage; further, awnlessness increases the grain number and, subsequently, improves grain yield in Asian cultivated rice, highlighting the contribution of the loss of awn to modern rice agriculture. Therefore, identifying the genes regulating awn development would facilitate the elucidation of a part of the domestication process in rice and increase our understanding of the complex mechanism in awn morphogenesis. To identify the novel loci regulating awn development and understand the conservation of genes in other wild rice relatives belonging to the AA genome group, we analyzed the chromosome segment substitution lines (CSSL). In this study, we compared a number of CSSL sets derived by crossing wild rice species in the AA genome group with the cultivated species Oryza sativa ssp. japonica. Two loci on chromosomes 7 and 11 were newly discovered to be responsible for awn development. We also found wild relatives that were used as donor parents of the CSSLs carrying the functional alleles responsible for awn elongation, REGULATOR OF AWN ELONGATION 1 (RAE1) and RAE2. To understand the conserveness of RAE1 and RAE2 in wild rice relatives, we analyzed RAE1 and RAE2 sequences of 175 accessions among diverse AA genome species retrieved from the sequence read archive (SRA) database. Comparative sequence analysis demonstrated that most wild rice AA genome species maintained functional RAE1 and RAE2, whereas most Asian rice cultivars have lost either or both functions. In addition, some different loss-of-function alleles of RAE1 and RAE2 were found in Asian cultivated species. These findings suggest that different combinations of dysfunctional alleles of RAE1 and RAE2 were selected after the speciation of O. sativa, and that two-step loss of function in RAE1 and RAE2 contributed to awnlessness in Asian cultivated rice.
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24
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Peng X, Xie J, Li W, Xie H, Cai Y, Ding X. Comparison of wild rice (Oryza longistaminata) tissues identifies rhizome-specific bacterial and archaeal endophytic microbiomes communities and network structures. PLoS One 2021; 16:e0246687. [PMID: 33556120 PMCID: PMC7870070 DOI: 10.1371/journal.pone.0246687] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/23/2021] [Indexed: 11/18/2022] Open
Abstract
Compared with root-associated habitats, little is known about the role of microbiota inside other rice organs, especially the rhizome of perennial wild rice, and this information may be of importance for agriculture. Oryza longistaminata is perennial wild rice with various agronomically valuable traits, including large biomass on poor soils, high nitrogen use efficiency, and resistance to insect pests and disease. Here, we compared the endophytic bacterial and archaeal communities and network structures of the rhizome to other compartments of O. longistaminata using 16S rRNA gene sequencing. Diverse microbiota and significant variation in community structure were identified among different compartments of O. longistaminata. The rhizome microbial community showed low taxonomic and phylogenetic diversity as well as the lowest network complexity among four compartments. Rhizomes exhibited less phylogenetic clustering than roots and leaves, but similar phylogenetic clustering with stems. Streptococcus, Bacillus, and Methylobacteriaceae were the major genera in the rhizome. ASVs belonging to the Enhydrobacter, YS2, and Roseburia are specifically present in the rhizome. The relative abundance of Methylobacteriaceae in the rhizome and stem was significantly higher than that in leaf and root. Noteworthy type II methanotrophs were observed across all compartments, including the dominant Methylobacteriaceae, which potentially benefits the host by facilitating CH4-dependent N2 fixation under nitrogen nutrient-poor conditions. Our data offers a robust knowledge of host and microbiome interactions across various compartments and lends guidelines to the investigation of adaptation mechanisms of O. longistaminata in nutrient-poor environments for biofertilizer development in agriculture.
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Affiliation(s)
- Xiaojue Peng
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
- Jiangxi Provincial People’s Hospital, Nanchang University, Nanchang, Jiangxi, China
| | - Jian Xie
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Wenzhuo Li
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Hongwei Xie
- Jiangxi Super-Rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Yaohui Cai
- Jiangxi Super-Rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Xia Ding
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
- Jiangxi Provincial People’s Hospital, Nanchang University, Nanchang, Jiangxi, China
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25
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Zhang W, Sun Y, Liu J, Xu C, Zou X, Chen X, Liu Y, Wu P, Yang X, Zhou S. DNA barcoding of Oryza: conventional, specific, and super barcodes. PLANT MOLECULAR BIOLOGY 2021; 105:215-228. [PMID: 32880855 PMCID: PMC7858216 DOI: 10.1007/s11103-020-01054-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 08/13/2020] [Indexed: 06/11/2023]
Abstract
We applied the phylogenomics to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity. Rice (genus Oryza) is one of the most important crops in the world, supporting half of the world's population. Breeding of high-yielding and quality cultivars relies on genetic resources from both cultivated and wild species, which are collected and maintained in seed banks. Unfortunately, numerous seeds are mislabeled due to taxonomic issues or misidentifications. Here, we applied the phylogenomics of 58 complete chloroplast genomes and two hypervariable nuclear genes to determine species identity in rice seeds. Twenty-one Oryza species were identified. Conspecific relationships were determined between O. glaberrima and O. barthii, O. glumipatula and O. longistaminata, O. grandiglumis and O. alta, O. meyeriana and O. granulata, O. minuta and O. malampuzhaensis, O. nivara and O. sativa subsp. indica, and O. sativa subsp. japonica and O. rufipogon. D and L genome types were not found and the H genome type was extinct. Importantly, we evaluated the performance of four conventional plant DNA barcodes (matK, rbcL, psbA-trnH, and ITS), six rice-specific chloroplast DNA barcodes (psaJ-rpl33, trnC-rpoB, rps16-trnQ, rpl22-rps19, trnK-matK, and ndhC-trnV), two rice-specific nuclear DNA barcodes (NP78 and R22), and a chloroplast genome super DNA barcode. The latter was the most reliable marker. The six rice-specific chloroplast barcodes revealed that 17% of the 53 seed accessions from rice seed banks or field collections were mislabeled. These results are expected to clarify the concept of rice species, aid in the identification and use of rice germplasms, and support rice biodiversity.
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Affiliation(s)
- Wen Zhang
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuzhe Sun
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jia Liu
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Science, Sichuan Agricultural University, Yaan, 625014, Sichuan, China
| | - Chao Xu
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xinhui Zou
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xun Chen
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Landscape Architecture, Northeast Forestry University, Haerbin, 150040, China
| | - Yanlei Liu
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ping Wu
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xueying Yang
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, China, Beijing, 100038, China.
| | - Shiliang Zhou
- State Key Laboratory of Systematic & Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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26
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Haq SU, Kumari D, Dhingra P, Kothari SL, Kachhwaha S. Variant biochemical responses: intrinsic and adaptive system for ecologically different rice varieties. JOURNAL OF CROP SCIENCE AND BIOTECHNOLOGY 2020; 24:279-292. [PMID: 33024519 PMCID: PMC7530552 DOI: 10.1007/s12892-020-00076-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 09/17/2020] [Indexed: 01/17/2023]
Abstract
India has a diverse range of agro-ecological conditions which support the cultivation of different rice varieties differing in the adaptation which is so important for sustainable development of rice crop. Specific ecotypes of rice adapted to diverse conditions have divergence in their morphology, physiology, biochemistry, molecular function, agronomy, and stress response. In the present study, 12 different rice varieties viz., PB-1, PB-1509, Pusa-RH-10, CSR-30, HKR-47, PR-126, Govind, Sharbati, ADT-37, ADT-39, ADT-45, White Ponni, were selected for the study of intrinsic biochemical behaviour and these varieties belong to different Agro-ecological zones and basmati or non-basmati rice varieties. Amongst intrinsic biochemicals activity, the differential response of radical scavenging, superoxide dismutase (SOD), catalase (CAT) and guaiacol peroxidase (POX) activities, were observed in the selected rice varieties at 14 days old seedling stage, developed under controlled growth conditions. Comparatively, North India region rice varieties displayed an enhanced intrinsic biochemical response than south India region rice varieties. Similarly, basmati rice varieties showed increased biochemical response compared to non-basmati rice varieties. Thus, the differential biochemical responses (radical scavenging, SOD, CAT, and POX activities) observed creates a significant difference between rice varieties and provides valuable information about rice ecotype-biochemical interaction for sustainable adaptive value under different ecological conditions.
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Affiliation(s)
- Shamshad Ul Haq
- Department of Botany, University of Rajasthan, Jaipur, Rajasthan 302004 India
| | - Deepa Kumari
- Department of Botany, University of Rajasthan, Jaipur, Rajasthan 302004 India
| | - Prerna Dhingra
- Department of Botany, University of Rajasthan, Jaipur, Rajasthan 302004 India
| | - S. L. Kothari
- Institute of Biotechnology, Amity University Rajasthan, Jaipur, 302006 India
| | - Sumita Kachhwaha
- Department of Botany, University of Rajasthan, Jaipur, Rajasthan 302004 India
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Li J, Zhou J, Zhang Y, Yang Y, Pu Q, Tao D. New Insights Into the Nature of Interspecific Hybrid Sterility in Rice. FRONTIERS IN PLANT SCIENCE 2020; 11:555572. [PMID: 33072142 PMCID: PMC7538986 DOI: 10.3389/fpls.2020.555572] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 09/01/2020] [Indexed: 06/01/2023]
Abstract
Interspecific and intraspecific hybrid sterility is a typical and common phenomenon of postzygotic reproductive barrier in rice. This is an indicator of speciation involved in the formation of new species or subspecies, and it significantly hampers the utilization of favorable genes from distant parents for rice improvement. The Oryza genus includes eight species with the same AA genome and is a model plant for studying the nature of hybrid sterility and its relationship with speciation. Hybrid sterility in rice is mostly controlled by nuclear genes, with more than 50 sterility loci genetically identified to date, of which 10 hybrid sterility loci or pairs were cloned and characterized at the molecular level. Comparing the mapping results for all sterility loci reported indicated that some of these loci from different species should be allelic to each other. Further research revealed that interactions between the multiple alleles at the hybrid sterility locus caused various genetic effect. One hypothesis for this important phenomenon is that the hybrid sterility loci are orthologous loci, which existed in ancient ancestors of rice. When one or more ancestors drifted to different continents, genetic divergence occurred because of adaptation, selection, and isolation among them such that various alleles from orthologous loci emerged over evolutionary time; hence, interspecific hybrid sterility would be mainly controlled by a few orthologous loci with different alleles. This hypothesis was tested and supported by the molecular characterization of hybrid sterility loci from S1, S5, Sa, qHMS7, and S27. From this, we may further deduce that both allelic and non-allelic interactions among different loci are the major genetic basis for the interspecific hybrid sterility between O. sativa and its AA genome relatives, and the same is true for intraspecific hybrid sterility in O. sativa. Therefore, it is necessary to raise the near-isogenic lines with various alleles/haplotypes and pyramided different alleles/haplotypes from sterile loci in the same genetic background aiming to study allelic and non-allelic interaction among different hybrid sterility loci in the AA genome species. Furthermore, the pyramiding lines ought to be used as bridge parents to overcome hybrid sterility for rice breeding purposes.
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Chatterjee J, Thakur V, Nepomuceno R, Coe RA, Dionora J, Elmido-Mabilangan A, Llave AD, Reyes AMD, Monroy AN, Canicosa I, Bandyopadhyay A, Jena KK, Brar DS, Quick WP. Natural Diversity in Stomatal Features of Cultivated and Wild Oryza Species. RICE (NEW YORK, N.Y.) 2020; 13:58. [PMID: 32816163 PMCID: PMC7441136 DOI: 10.1186/s12284-020-00417-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 08/06/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Stomata in rice control a number of physiological processes by regulating gas and water exchange between the atmosphere and plant tissues. The impact of the structural diversity of these micropores on its conductance level is an important area to explore before introducing stomatal traits into any breeding program in order to increase photosynthesis and crop yield. Therefore, an intensive measurement of structural components of stomatal complex (SC) of twenty three Oryza species spanning the primary, secondary and tertiary gene pools of rice has been conducted. RESULTS Extensive diversity was found in stomatal number and size in different Oryza species and Oryza complexes. Interestingly, the dynamics of stomatal traits in Oryza family varies differently within different Oryza genetic complexes. Example, the Sativa complex exhibits the greatest diversity in stomatal number, while the Officinalis complex is more diverse for its stomatal size. Combining the structural information with the Oryza phylogeny revealed that speciation has tended towards increasing stomatal density rather than stomatal size in rice family. Thus, the most recent species (i.e. the domesticated rice) eventually has developed smaller yet numerous stomata. Along with this, speciation has also resulted in a steady increase in stomatal conductance (anatomical, gmax) in different Oryza species. These two results unambiguously prove that increasing stomatal number (which results in stomatal size reduction) has increased the stomatal conductance in rice. Correlations of structural traits with the anatomical conductance, leaf carbon isotope discrimination (∆13C) and major leaf morphological and anatomical traits provide strong supports to untangle the ever mysterious dependencies of these traits in rice. The result displayed an expected negative correlation in the number and size of stomata; and positive correlations among the stomatal length, width and area with guard cell length, width on both abaxial and adaxial leaf surfaces. In addition, gmax is found to be positively correlated with stomatal number and guard cell length. The ∆13C values of rice species showed a positive correlation with stomatal number, which suggest an increased water loss with increased stomatal number. Interestingly, in contrast, the ∆13C consistently shows a negative relationship with stomatal and guard cell size, which suggests that the water loss is less when the stomata are larger. Therefore, we hypothesize that increasing stomatal size, instead of numbers, is a better approach for breeding programs in order to minimize the water loss through stomata in rice. CONCLUSION Current paper generates useful data on stomatal profile of wild rice that is hitherto unknown for the rice science community. It has been proved here that the speciation has resulted in an increased stomatal number accompanied by size reduction during Oryza's evolutionary course; this has resulted in an increased gmax but reduced water use efficiency. Although may not be the sole driver of water use efficiency in rice, our data suggests that stomata are a potential target for modifying the currently low water use efficiency in domesticated rice. It is proposed that Oryza barthii can be used in traditional breeding programs in enhancing the stomatal size of elite rice cultivars.
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Affiliation(s)
- Jolly Chatterjee
- C4 Rice Center, International Rice Research Institute (IRRI), Los Baños, DAPO BOX 7777, Metro Manila, Philippines
| | - Vivek Thakur
- C4 Rice Center, International Rice Research Institute (IRRI), Los Baños, DAPO BOX 7777, Metro Manila, Philippines
- Department of Systems & Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Robert Nepomuceno
- C4 Rice Center, International Rice Research Institute (IRRI), Los Baños, DAPO BOX 7777, Metro Manila, Philippines
- National Institute of Molecular Biology and Biotechnology - University of the Philippines Los Banos, Los Banos, Laguna, Philippines
| | - Robert A Coe
- C4 Rice Center, International Rice Research Institute (IRRI), Los Baños, DAPO BOX 7777, Metro Manila, Philippines
- CSIRO Agriculture Flagship, High Resolution Plant Phenomics, GPO Box 1500, Canberra, ACT, 2601, Australia
| | - Jacqueline Dionora
- C4 Rice Center, International Rice Research Institute (IRRI), Los Baños, DAPO BOX 7777, Metro Manila, Philippines
| | - Abigail Elmido-Mabilangan
- C4 Rice Center, International Rice Research Institute (IRRI), Los Baños, DAPO BOX 7777, Metro Manila, Philippines
| | - Abraham Darius Llave
- C4 Rice Center, International Rice Research Institute (IRRI), Los Baños, DAPO BOX 7777, Metro Manila, Philippines
| | - Anna Mae Delos Reyes
- C4 Rice Center, International Rice Research Institute (IRRI), Los Baños, DAPO BOX 7777, Metro Manila, Philippines
| | - Apollo Neil Monroy
- C4 Rice Center, International Rice Research Institute (IRRI), Los Baños, DAPO BOX 7777, Metro Manila, Philippines
| | - Irma Canicosa
- C4 Rice Center, International Rice Research Institute (IRRI), Los Baños, DAPO BOX 7777, Metro Manila, Philippines
| | - Anindya Bandyopadhyay
- C4 Rice Center, International Rice Research Institute (IRRI), Los Baños, DAPO BOX 7777, Metro Manila, Philippines
| | - Kshirod K Jena
- Plant Breeding Division, International Rice Research Institute (IRRI), Los Baños, DAPO BOX 7777, Metro Manila, Philippines
| | - Darshan S Brar
- Plant Breeding Division, International Rice Research Institute (IRRI), Los Baños, DAPO BOX 7777, Metro Manila, Philippines
- Present Address: School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - William Paul Quick
- C4 Rice Center, International Rice Research Institute (IRRI), Los Baños, DAPO BOX 7777, Metro Manila, Philippines.
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK.
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A chromosome-level genome assembly of the wild rice Oryza rufipogon facilitates tracing the origins of Asian cultivated rice. SCIENCE CHINA-LIFE SCIENCES 2020; 64:282-293. [PMID: 32737856 DOI: 10.1007/s11427-020-1738-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 05/19/2020] [Indexed: 01/15/2023]
Abstract
Oryza rufipogon Griff. is a wild progenitor of the Asian cultivated rice Oryza sativa. To better understand the genomic diversity of the wild rice, high-quality reference genomes of O. rufipogon populations are needed, which also facilitate utilization of the wild genetic resources in rice breeding. In this study, we generated a chromosome-level genome assembly of O. rufipogon using a combination of short-read sequencing, single-molecule sequencing, BioNano and Hi-C platforms. The genome sequence (399.8 Mb) was assembled into 46 scaffolds on the 12 chromosomes, with contig N50 and scaffold N50 of 13.2 Mb and 20.3 Mb, respectively. The genome contains 36,520 protein-coding genes, and 49.37% of the genome consists of repetitive elements. The genome has strong synteny with those of the O. sativa subspecies indica and japonica, but containing some large structural variations. Evolutionary analysis unveiled the polyphyletic origins of O. sativa, in which the japonica and indica genome formations involved different divergent O. rufipogon (including O. nivara) lineages, accompanied by introgression of genomic regions between japonica and indica. This high-quality reference genome provides insight on the genome evolution of the wild rice and the origins of the O. sativa subspecies, and valuable information for basic research and rice breeding.
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30
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Li W, Zhang Q, Zhu T, Tong Y, Li K, Shi C, Zhang Y, Liu Y, Jiang J, Liu Y, Xia E, Huang H, Zhang L, Zhang D, Shi C, Jiang W, Zhao Y, Mao S, Jiao J, Xu P, Yang L, Gao L. Draft genomes of two outcrossing wild rice, Oryza rufipogon and O. longistaminata, reveal genomic features associated with mating-system evolution. PLANT DIRECT 2020; 4:e00232. [PMID: 32537559 PMCID: PMC7287411 DOI: 10.1002/pld3.232] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 05/07/2020] [Accepted: 05/15/2020] [Indexed: 05/04/2023]
Abstract
Oryza rufipogon and O. longistaminata are important wild relatives of cultivated rice, harboring a promising source of novel genes for rice breeding programs. Here, we present de novo assembled draft genomes and annotation of O. rufipogon and O. longistaminata. Our analysis reveals a considerable number of lineage-specific gene families associated with the self-incompatibility (SI) and formation of reproductive separation. We show how lineage-specific expansion or contraction of gene families with functional enrichment of the recognition of pollen, thus enlightening their reproductive diversification. We documented a large number of lineage-specific gene families enriched in salt stress, antifungal response, and disease resistance. Our comparative analysis further shows a genome-wide expansion of genes encoding NBS-LRR proteins in these two outcrossing wild species in contrast to six other selfing rice species. Conserved noncoding sequences (CNSs) in the two wild rice genomes rapidly evolve relative to selfing rice species, resulting in the reduction of genomic variation owing to shifts of mating systems. We find that numerous genes related to these rapidly evolving CNSs are enriched in reproductive structure development, flower development, and postembryonic development, which may associate with SI in O. rufipogon and O. longistaminata.
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Affiliation(s)
- Wei Li
- Institution of Genomics and BioinformaticsSouth China Agricultural UniversityGuangzhouChina
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Qun‐Jie Zhang
- Institution of Genomics and BioinformaticsSouth China Agricultural UniversityGuangzhouChina
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Ting Zhu
- Institution of Genomics and BioinformaticsSouth China Agricultural UniversityGuangzhouChina
- College of Life ScienceLiaoning Normal UniversityDalianChina
| | - Yan Tong
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Kui Li
- Institution of Genomics and BioinformaticsSouth China Agricultural UniversityGuangzhouChina
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Cong Shi
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Yun Zhang
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Yun‐Long Liu
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Jian‐Jun Jiang
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Yuan Liu
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - En‐Hua Xia
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Hui Huang
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Li‐Ping Zhang
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Dan Zhang
- Institution of Genomics and BioinformaticsSouth China Agricultural UniversityGuangzhouChina
| | - Chao Shi
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Wen‐Kai Jiang
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - You‐Jie Zhao
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Shu‐Yan Mao
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Jun‐ying Jiao
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Ping‐Zhen Xu
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Li‐Li Yang
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Li‐Zhi Gao
- Institution of Genomics and BioinformaticsSouth China Agricultural UniversityGuangzhouChina
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
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Nan H, Li W, Lin YL, Gao LZ. Genome-Wide Analysis of WRKY Genes and Their Response to Salt Stress in the Wild Progenitor of Asian Cultivated Rice, Oryza rufipogon. Front Genet 2020. [DOI: 10.3389/fgene.2020.00359] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Solis CA, Yong MT, Vinarao R, Jena K, Holford P, Shabala L, Zhou M, Shabala S, Chen ZH. Back to the Wild: On a Quest for Donors Toward Salinity Tolerant Rice. FRONTIERS IN PLANT SCIENCE 2020; 11:323. [PMID: 32265970 PMCID: PMC7098918 DOI: 10.3389/fpls.2020.00323] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 03/05/2020] [Indexed: 05/20/2023]
Abstract
Salinity stress affects global food producing areas by limiting both crop growth and yield. Attempts to develop salinity-tolerant rice varieties have had limited success due to the complexity of the salinity tolerance trait, high variation in the stress response and a lack of available donors for candidate genes for cultivated rice. As a result, finding suitable donors of genes and traits for salinity tolerance has become a major bottleneck in breeding for salinity tolerant crops. Twenty-two wild Oryza relatives have been recognized as important genetic resources for quantitatively inherited traits such as resistance and/or tolerance to abiotic and biotic stresses. In this review, we discuss the challenges and opportunities of such an approach by critically analyzing evolutionary, ecological, genetic, and physiological aspects of Oryza species. We argue that the strategy of rice breeding for better Na+ exclusion employed for the last few decades has reached a plateau and cannot deliver any further improvement in salinity tolerance in this species. This calls for a paradigm shift in rice breeding and more efforts toward targeting mechanisms of the tissue tolerance and a better utilization of the potential of wild rice where such traits are already present. We summarize the differences in salinity stress adaptation amongst cultivated and wild Oryza relatives and identify several key traits that should be targeted in future breeding programs. This includes: (1) efficient sequestration of Na+ in mesophyll cell vacuoles, with a strong emphasis on control of tonoplast leak channels; (2) more efficient control of xylem ion loading; (3) efficient cytosolic K+ retention in both root and leaf mesophyll cells; and (4) incorporating Na+ sequestration in trichrome. We conclude that while amongst all wild relatives, O. rufipogon is arguably a best source of germplasm at the moment, genes and traits from the wild relatives, O. coarctata, O. latifolia, and O. alta, should be targeted in future genetic programs to develop salt tolerant cultivated rice.
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Affiliation(s)
- Celymar A. Solis
- School of Science, Western Sydney University, Penrith, NSW, Australia
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Miing T. Yong
- School of Science, Western Sydney University, Penrith, NSW, Australia
| | - Ricky Vinarao
- International Rice Research Institute, Metro Manila, Philippines
| | - Kshirod Jena
- International Rice Research Institute, Metro Manila, Philippines
| | - Paul Holford
- School of Science, Western Sydney University, Penrith, NSW, Australia
| | - Lana Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
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Lacchini E, Kiegle E, Castellani M, Adam H, Jouannic S, Gregis V, Kater MM. CRISPR-mediated accelerated domestication of African rice landraces. PLoS One 2020; 15:e0229782. [PMID: 32126126 PMCID: PMC7053755 DOI: 10.1371/journal.pone.0229782] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 02/13/2020] [Indexed: 11/18/2022] Open
Abstract
African Oryza glaberrima and Oryza sativa landraces are considered valuable resources for breeding traits due to their adaptation to local environmental and soil conditions. They often possess superior resistance to endemic pests and tolerance to drought and nutrient deficiencies when compared to the "imported" high production Asian rice varieties. In contrast, "domestication traits" such as seed shattering, lodging, and seed yield are not well established in these African landraces. Therefore, the use of these African varieties for high production agriculture is limited by unpredictable yield and grain quality. We are addressing this shortcoming by developing protocols for genetically transforming African landraces to allow the use of CRISPR-Cas mediated breeding approaches. Here we use as proof of concept the cultivated African landrace Kabre to target selected known "domestication loci" and improve the agronomic potential of Kabre rice. Stable genetic transformation with CRISPR-Cas9-based vectors generated single and simultaneous multiple gene knockouts. Plants with reduced stature to diminish lodging were generated by disrupting the HTD1 gene. Furthermore, three loci shown to control seed size and/or yield (GS3, GW2 and GN1A) were targeted using a multiplex CRISPR-Cas9 construct. This resulted in mutants with significantly improved seed yield. Our study provides an example of how new breeding technologies can accelerate the development of highly productive African landrace rice varieties, an important advancement considering that Africa is a hotspot for worldwide population growth and therefore prone to food shortage.
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Affiliation(s)
- Elia Lacchini
- Department of Biosciences, University of Milan, Milan, Italy
| | - Edward Kiegle
- Department of Biosciences, University of Milan, Milan, Italy
| | | | - Hélène Adam
- University of Montpellier, DIADE, IRD, Montpellier, France
| | | | - Veronica Gregis
- Department of Biosciences, University of Milan, Milan, Italy
| | - Martin M. Kater
- Department of Biosciences, University of Milan, Milan, Italy
- * E-mail:
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Evaluation of rice wild relatives as a source of traits for adaptation to iron toxicity and enhanced grain quality. PLoS One 2020; 15:e0223086. [PMID: 31899771 PMCID: PMC6941827 DOI: 10.1371/journal.pone.0223086] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 12/09/2019] [Indexed: 11/19/2022] Open
Abstract
Rice wild relatives (RWR) constitute an extended gene pool that can be tapped for the breeding of novel rice varieties adapted to abiotic stresses such as iron (Fe) toxicity. Therefore, we screened 75 Oryza genotypes including 16 domesticated O. sativa genotypes, one O. glaberrima, and 58 RWR representing 21 species, for tolerance to Fe toxicity. Plants were grown in a semi-artificial greenhouse setup, in which they were exposed either to control conditions, an Fe shock during the vegetative growth stage (acute treatment), or to a continuous moderately high Fe level (chronic treatment). In both stress treatments, foliar Fe concentrations were characteristic of Fe toxicity, and plants developed foliar stress symptoms, which were more pronounced in the chronic Fe stress especially toward the end of the growing season. Among the genotypes that produced seeds, only the chronic stress treatment significantly reduced yields due to increases in spikelet sterility. Moreover, a moderate but non-significant increase in grain Fe concentrations, and a significant increase in grain Zn concentrations were seen in chronic stress. Both domesticated rice and RWR exhibited substantial genotypic variation in their responses to Fe toxicity. Although no RWR strikingly outperformed domesticated rice in Fe toxic conditions, some genotypes scored highly in individual traits. Two O. meridionalis accessions were best in avoiding foliar symptom formation in acute Fe stress, while an O. rufipogon accession produced the highest grain yields in both chronic and acute Fe stress. In conclusion, this study provides the basis for using interspecific crosses for adapting rice to Fe toxicity.
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Matsubara K. How Hybrid Breakdown Can Be Handled in Rice Crossbreeding? FRONTIERS IN PLANT SCIENCE 2020; 11:575412. [PMID: 33193514 PMCID: PMC7641626 DOI: 10.3389/fpls.2020.575412] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 09/30/2020] [Indexed: 05/16/2023]
Abstract
In crosses between genetically divergent parents, traits such as weakness and sterility often segregate in later generations. This hybrid breakdown functions as a reproductive barrier and reduces selection efficiency in crossbreeding. Here, I provide an overview of hybrid breakdown in rice crosses and discuss ways to avoid and mitigate the effects of hybrid breakdown on rice crossbreeding, including genomics-assisted breeding.
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Wairich A, de Oliveira BHN, Arend EB, Duarte GL, Ponte LR, Sperotto RA, Ricachenevsky FK, Fett JP. The Combined Strategy for iron uptake is not exclusive to domesticated rice (Oryza sativa). Sci Rep 2019; 9:16144. [PMID: 31695138 PMCID: PMC6834603 DOI: 10.1038/s41598-019-52502-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/14/2019] [Indexed: 01/12/2023] Open
Abstract
Iron (Fe) is an essential micronutrient that is frequently inaccessible to plants. Rice (Oryza sativa L.) plants employ the Combined Strategy for Fe uptake, which is composed by all features of Strategy II, common to all Poaceae species, and some features of Strategy I, common to non-Poaceae species. To understand the evolution of Fe uptake mechanisms, we analyzed the root transcriptomic response to Fe deficiency in O. sativa and its wild progenitor O. rufipogon. We identified 622 and 2,017 differentially expressed genes in O. sativa and O. rufipogon, respectively. Among the genes up-regulated in both species, we found Fe transporters associated with Strategy I, such as IRT1, IRT2 and NRAMP1; and genes associated with Strategy II, such as YSL15 and IRO2. In order to evaluate the conservation of these Strategies among other Poaceae, we identified the orthologs of these genes in nine species from the Oryza genus, maize and sorghum, and evaluated their expression profile in response to low Fe condition. Our results indicate that the Combined Strategy is not specific to O. sativa as previously proposed, but also present in species of the Oryza genus closely related to domesticated rice, and originated around the same time the AA genome lineage within Oryza diversified. Therefore, adaptation to Fe2+ acquisition via IRT1 in flooded soils precedes O. sativa domestication.
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Affiliation(s)
- Andriele Wairich
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Ben Hur Neves de Oliveira
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Ezequiel Barth Arend
- Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Guilherme Leitão Duarte
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Lucas Roani Ponte
- Departamento de Biologia, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, Brazil
| | - Raul Antonio Sperotto
- Programa de Pós-Graduação em Biotecnologia, Universidade do Vale do Taquari - Univates, Lajeado, Brazil
| | - Felipe Klein Ricachenevsky
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
- Departamento de Biologia, Centro de Ciências Naturais e Exatas, Universidade Federal de Santa Maria, Santa Maria, Brazil.
| | - Janette Palma Fett
- Programa de Pós-Graduação em Biologia Celular e Molecular, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
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Fujino K, Hirayama Y, Obara M, Ikegaya T. Introgression of the chromosomal region with the Pi-cd locus from Oryza meridionalis into O. sativa L. during rice domestication. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1981-1990. [PMID: 30911779 DOI: 10.1007/s00122-019-03332-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 03/19/2019] [Indexed: 05/04/2023]
Abstract
The genotype of the Pi-cd locus found in blast-resistant rice variety Kitakurin, which is a cultivated rice from Japan belonging to Oryza sativa japonica, is identical to that of its wild relative O. meridionalis. Crop domestication from wild relatives to cultivated species has encompassed significant phenotypic changes. However, little is known about the genetic changes involved in domestication. Here, we surveyed the origin of the Pi-cd locus across Oryza species with AA genomes by comparison with the genome sequences of Hoshinoyume (HS), which does not carry the Pi-cd blast resistance gene, and Kitakurin (KK), which carries the Pi-cd blast resistance gene. We found that variety-specific transposons were enriched at the Pi-cd locus. The genotype of the Pi-cd locus characterized by transposons in HS and KK was specific to each Oryza species with the AA genome. The Kitaake (KT) genotype at the Pi-cd locus found in KK was identical only to that of O. meridionalis and distributed only in subgroups of japonica in the World Rice Collection and tropical japonica in the Japanese Rice Collection, whereas it was not present in O. rufipogon accessions. The distinct distributions of genotypes of the Pi-cd locus clearly demonstrated that the Pi-cd locus was introgressed from O. meridionalis into O. sativa, specific to tropical japonica.
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Affiliation(s)
- Kenji Fujino
- Hokkaido Agricultural Research Center, National Agricultural Research Organization, Sapporo, 062-8555, Japan.
| | - Yuji Hirayama
- Rice Breeding Group, Kamikawa Agricultural Experiment Station, Local Independent Administrative Agency Hokkaido Research Organization, Pippu, 078-0397, Japan
| | - Mari Obara
- Hokkaido Agricultural Research Center, National Agricultural Research Organization, Sapporo, 062-8555, Japan
| | - Tomohito Ikegaya
- Hokkaido Agricultural Research Center, National Agricultural Research Organization, Sapporo, 062-8555, Japan
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Liu H, Liu H, Zhou L, Lin Z. Genetic Architecture of domestication- and improvement-related traits using a population derived from Sorghum virgatum and Sorghum bicolor. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 283:135-146. [PMID: 31128683 DOI: 10.1016/j.plantsci.2019.02.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 02/16/2019] [Accepted: 02/22/2019] [Indexed: 06/09/2023]
Abstract
The genetic basis of domestication and improvement remains largely unknown in sorghum as a typical multiple-origins species. In this study, the F2 and F3 populations derived from a cross between Sorghum virgatum and domesticated sorghum were used to study the genetic architecture of domestication- and improvement-related traits. We found that human selection had greatly reshaped sorghum through the Quantitative Trait Loci (QTLs) with large genetic effects in the traits of harvest, plant architecture and grain taste including the reduction of shattering, few branches, short plant stature and the removal of polyphenols from seed. The expansion of seed width was selected to improve the yield through accumulating small-effect QTLs. Two major QTLs of plant height (QTI-ph1 and dw1) were narrowed down into 24.5-kilobase (kb) and 13.9-kb, respectively. DNA diversity analysis and association mapping of dw1 gene suggested the functional variant (A1361 T) might originate from the same event not long time ago. Our results supported that parallel phenotypic changes across different species during domestication and improvement might share the same genetic basis, QTL × QTL interactions might not play an important role in the reshaping of traits during sorghum domestication and improvement, and offered new views on transgressive segregation and segregation distortion. Our study greatly deepens our understandings of the genetic basis of sorghum domestication and improvement.
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Affiliation(s)
- Huanhuan Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, Department of Plant Genomics and Bioinformatics, China Agricultural University, Beijing 100193, China
| | - Hangqin Liu
- National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, Department of Plant Genomics and Bioinformatics, China Agricultural University, Beijing 100193, China
| | - Leina Zhou
- National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, Department of Plant Genomics and Bioinformatics, China Agricultural University, Beijing 100193, China
| | - Zhongwei Lin
- National Maize Improvement Center, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, Joint International Research Laboratory of Crop Molecular Breeding, Department of Plant Genomics and Bioinformatics, China Agricultural University, Beijing 100193, China.
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The potentiality of rice microsatellite markers in assessment of cross-species transferability and genetic diversity of rice and its wild relatives. 3 Biotech 2019; 9:217. [PMID: 31114741 DOI: 10.1007/s13205-019-1757-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 05/11/2019] [Indexed: 10/26/2022] Open
Abstract
The main aim of this study is to assess the potentiality of SSR markers for the identification of the cross-species transferability frequency in a large set of the diverse genome types of wild relative rice along with cultivated rice. Here, we used 18 different rice genotypes representing nine different genome types with 70 SSR markers to investigate the potentiality of cross-species transferability rate. The overall cross-species transferability of SSR markers across the 18 rice genotypes ranged from 38.9% (RM280 and RM447) to 100% (RM490, RM318, RM279, RM18877 and RM20033, RM19303) with an average of 76.58%. Also, cross-species transferability across chromosome ranged from 54.4% (chromosome 4) to 86.5% (chromosome 2) with an average of 74.35%. The polymorphism information content of the markers varied from 0.198 (RM263) to 0.868 (RM510) with a mean of 0.549 ± 0.153, showing high discriminatory power. The highest rate of cross-transferability was observed in O. rufipogon (97%), The highest rate of cross-species transferability was in O. rufipogon (97.00%), followed by O. glaberrima (94.20%), O. nivara (92.80%), Swarna (92.80%), O. longistaminata (91.40%), O. eichingeri (90%), O. barthii (88.50%), O. alta (82.80%), O. australiensis (77.10%), O. grandiglumis (74.20%), O. officinalis (74.20%), Zizania latifolia (70.00%), O. latifolia (68.50%), O. brachyantha (62.80%), Leersia perrieri (57.10%) and O. ridleyi (41.40%) with least in O. coarctata (28.50%). A total of 341 alleles from 70 loci were detected with the number of alleles per locus ranged from 2 to 12. Based on dendrogram analysis, the AA genome groups was separated as distinct group from the rest of the genome types. Similarly, principal coordinate analysis and structure analysis clearly separated the AA genome type from the rest of the genome types. Through the analysis of molecular variance, more variance (51%) was observed among the individual, whereas less (14%) was observed among the population. Thus, our findings may offer a valuable resource for studying the genetic diversity and relationship to facilitate the understanding of the complex mechanism of the origin and evolutionary processes of different Oryza species and wild relative rice.
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Ndjiondjop MN, Alachiotis N, Pavlidis P, Goungoulou A, Kpeki SB, Zhao D, Semagn K. Comparisons of molecular diversity indices, selective sweeps and population structure of African rice with its wild progenitor and Asian rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1145-1158. [PMID: 30578434 PMCID: PMC6449321 DOI: 10.1007/s00122-018-3268-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/11/2018] [Indexed: 05/20/2023]
Abstract
The extent of molecular diversity parameters across three rice species was compared using large germplasm collection genotyped with genomewide SNPs and SNPs that fell within selective sweep regions. Previous studies conducted on limited number of accessions have reported very low genetic variation in African rice (Oryza glaberrima Steud.) as compared to its wild progenitor (O. barthii A. Chev.) and to Asian rice (O. sativa L.). Here, we characterized a large collection of African rice and compared its molecular diversity indices and population structure with the two other species using genomewide single nucleotide polymorphisms (SNPs) and SNPs that mapped within selective sweeps. A total of 3245 samples representing African rice (2358), Asian rice (772) and O. barthii (115) were genotyped with 26,073 physically mapped SNPs. Using all SNPs, the level of marker polymorphism, average genetic distance and nucleotide diversity in African rice accounted for 59.1%, 63.2% and 37.1% of that of O. barthii, respectively. SNP polymorphism and overall nucleotide diversity of the African rice accounted for 20.1-32.1 and 16.3-37.3% of that of the Asian rice, respectively. We identified 780 SNPs that fell within 37 candidate selective sweeps in African rice, which were distributed across all 12 rice chromosomes. Nucleotide diversity of the African rice estimated from the 780 SNPs was 8.3 × 10-4, which is not only 20-fold smaller than the value estimated from all genomewide SNPs (π = 1.6 × 10-2), but also accounted for just 4.1%, 0.9% and 2.1% of that of O. barthii, lowland Asian rice and upland Asian rice, respectively. The genotype data generated for a large collection of rice accessions conserved at the AfricaRice genebank will be highly useful for the global rice community and promote germplasm use.
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Affiliation(s)
- Marie Noelle Ndjiondjop
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire.
| | - Nikolaos Alachiotis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
| | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
| | - Alphonse Goungoulou
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire
| | - Sèdjro Bienvenu Kpeki
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire
| | - Dule Zhao
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire
| | - Kassa Semagn
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire.
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Mastinu A, Bonini SA, Rungratanawanich W, Aria F, Marziano M, Maccarinelli G, Abate G, Premoli M, Memo M, Uberti D. Gamma-oryzanol Prevents LPS-induced Brain Inflammation and Cognitive Impairment in Adult Mice. Nutrients 2019; 11:nu11040728. [PMID: 30934852 PMCID: PMC6520753 DOI: 10.3390/nu11040728] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/19/2019] [Accepted: 03/26/2019] [Indexed: 12/20/2022] Open
Abstract
Background: Rice (Oryza sativa L.) is the main food source for more than half of humankind. Rice is rich in phytochemicals and antioxidants with several biological activities; among these compounds, the presence of γ-oryzanol is noteworthy. The present study aims to explore the effects of γ-oryzanol on cognitive performance in a mouse model of neuroinflammation and cognitive alterations. Methods: Mice received 100 mg/kg γ-oryzanol (ORY) or vehicle once daily for 21 consecutive days and were then exposed to an inflammatory stimulus elicited by lipopolysaccharide (LPS). A novel object recognition test and mRNA expression of antioxidant and neuroinflammatory markers in the hippocampus were evaluated. Results: ORY treatment was able to improve cognitive performance during the neuroinflammatory response. Furthermore, phase II antioxidant enzymes such as heme oxygenase-1 (HO-1) and NADPH-dehydrogenase-quinone-1 (NQO1) were upregulated in the hippocampi of ORY and ORY+LPS mice. Lastly, γ-oryzanol showed a strong anti-inflammatory action by downregulating inflammatory genes after LPS treatment. Conclusion: These results suggest that chronic consumption of γ-oryzanol can revert the LPS-induced cognitive and memory impairments by promoting hippocampal antioxidant and anti-inflammatory molecular responses.
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Affiliation(s)
- Andrea Mastinu
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy.
| | - Sara Anna Bonini
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy.
| | - Wiramon Rungratanawanich
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy.
| | - Francesca Aria
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy.
| | - Mariagrazia Marziano
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy.
| | - Giuseppina Maccarinelli
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy.
| | - Giulia Abate
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy.
| | - Marika Premoli
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy.
| | - Maurizio Memo
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy.
| | - Daniela Uberti
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy.
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42
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Rapid evolution of protein diversity by de novo origination in Oryza. Nat Ecol Evol 2019; 3:679-690. [PMID: 30858588 DOI: 10.1038/s41559-019-0822-5] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 01/23/2019] [Indexed: 12/22/2022]
Abstract
New protein-coding genes that arise de novo from non-coding DNA sequences contribute to protein diversity. However, de novo gene origination is challenging to study as it requires high-quality reference genomes for closely related species, evidence for ancestral non-coding sequences, and transcription and translation of the new genes. High-quality genomes of 13 closely related Oryza species provide unprecedented opportunities to understand de novo origination events. Here, we identify a large number of young de novo genes with discernible recent ancestral non-coding sequences and evidence of translation. Using pipelines examining the synteny relationship between genomes and reciprocal-best whole-genome alignments, we detected at least 175 de novo open reading frames in the focal species O. sativa subspecies japonica, which were all detected in RNA sequencing-based transcriptomes. Mass spectrometry-based targeted proteomics and ribosomal profiling show translational evidence for 57% of the de novo genes. In recent divergence of Oryza, an average of 51.5 de novo genes per million years were generated and retained. We observed evolutionary patterns in which excess indels and early transcription were favoured in origination with a stepwise formation of gene structure. These data reveal that de novo genes contribute to the rapid evolution of protein diversity under positive selection.
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Evolutionary Analysis of GH3 Genes in Six Oryza Species/Subspecies and Their Expression under Salinity Stress in Oryza sativa ssp. japonica. PLANTS 2019; 8:plants8020030. [PMID: 30682815 PMCID: PMC6409606 DOI: 10.3390/plants8020030] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 01/09/2023]
Abstract
Glycoside Hydrolase 3 (GH3), a member of the Auxin-responsive gene family, is involved in plant growth, the plant developmental process, and various stress responses. The GH3 gene family has been well-studied in Arabidopsis thaliana and Zea mays. However, the evolution of the GH3 gene family in Oryza species remains unknown and the function of the GH3 gene family in Oryza sativa is not well-documented. Here, a systematic analysis was performed in six Oryza species/subspecies, including four wild rice species and two cultivated rice subspecies. A total of 13, 13, 13, 13, 12, and 12 members were identified in O. sativa ssp. japonica, O. sativa ssp. indica, Oryza rufipogon, Oryza nivara, Oryza punctata, and Oryza glumaepatula, respectively. Gene duplication events, structural features, conserved motifs, a phylogenetic analysis, chromosome locations, and Ka/Ks ratios of this important family were found to be strictly conservative across these six Oryza species/subspecies, suggesting that the expansion of the GH3 gene family in Oryza species might be attributed to duplication events, and this expansion could occur in the common ancestor of Oryza species, even in common ancestor of rice tribe (Oryzeae) (23.07~31.01 Mya). The RNA-seq results of different tissues displayed that OsGH3 genes had significantly different expression profiles. Remarkably, the qRT-PCR result after NaCl treatment indicated that the majority of OsGH3 genes play important roles in salinity stress, especially OsGH3-2 and OsGH3-8. This study provides important insights into the evolution of the GH3 gene family in Oryza species and will assist with further investigation of OsGH3 genes’ functions under salinity stress.
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Zhong H, Kong W, Gong Z, Fang X, Deng X, Liu C, Li Y. Evolutionary Analyses Reveal Diverged Patterns of SQUAMOSA Promoter Binding Protein-Like ( SPL) Gene Family in Oryza Genus. FRONTIERS IN PLANT SCIENCE 2019; 10:565. [PMID: 31139200 PMCID: PMC6517846 DOI: 10.3389/fpls.2019.00565] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/15/2019] [Indexed: 05/07/2023]
Abstract
The SPL (SQUAMOSA promoter binding protein-like) gene family is one of the plant-specific transcription factor families and controls a considerable number of biological functions, including floral development, phytohormone signaling, and toxin resistance. However, the evolutionary patterns and driving forces of SPL genes in the Oryza genus are still not well-characterized. In this study, we investigated a total of 105 SPL genes from six AA genome Oryza representative species (O. barthii, O. glumipatula, O. nivara, O. rufipogon, O. glaberrima, and O. sativa). Phylogenetic and motif analyses indicated that SPL proteins could be divided into two distinct lineages (I and II), and further studies showed lineage II consisted of three clades (IIA, IIB, and IIC). We found that clade I had comparable structural features with clade IIA, whereas genes in clade IIC displayed intrinsic differences, such as lower exon numbers and the presence of miR156 regulation elements. Nineteen orthologous groups of OsSPLs in Oryza were also identified, and most exons within those genes maintained constant length, whereas length of intron changed relatively. All groups were constrained by stronger purifying selection and diversified continually including alterative gene number, intron length, and miR156 regulation. Subsequently, cis-acting element analyses revealed the potential role of SPLs in wild rice, which might participate in light-responsive, phytohormone response, and plant growth and development. Our results shed light on that different evolutionary rates and duplication events might result in divergent evolutionary patterns in each lineage of SPL genes, providing a guide in exploring diverse function in the rice gene family among six closely related Oryza species.
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45
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Nadir S, Khan S, Zhu Q, Henry D, Wei L, Lee DS, Chen L. An overview on reproductive isolation in Oryza sativa complex. AOB PLANTS 2018; 10:ply060. [PMID: 30538811 PMCID: PMC6280023 DOI: 10.1093/aobpla/ply060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 11/21/2018] [Indexed: 05/27/2023]
Abstract
Reproductive isolation is generally regarded as the essence of the speciation process. Studying closely related species is convenient for understanding the genetic basis of reproductive isolation. Therefore, the present review is restricted to the species and subspecies of the Oryza sativa complex, which includes the two domestic rice cultivars and six wild species. Although closely related, these rice species are separated from each other by a range reproductive barriers. This review presents a comprehensive understanding of the forces that shaped the formation of reproductive barriers among and between the species of the O. sativa complex. We suggest the possibility that domestication and artificial breeding in these rice species can lead to the early stages of speciation. Understanding the evolutionary and molecular mechanisms underlying reproductive isolation in rice will increase our knowledge in speciation and would also offer practical significance for the implementation of crop improvement strategies.
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Affiliation(s)
- Sadia Nadir
- Rice Research Institute, Yunnan Agriculture University, Kunming, Yunnan, China
- Department of Chemistry, University of Science and Technology, Bannu, Khyber Pakhtunkhwa, Pakistan
- Centre for Mountain Ecosystem Studies, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Sehroon Khan
- Centre for Mountain Ecosystem Studies, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Qian Zhu
- Rice Research Institute, Yunnan Agriculture University, Kunming, Yunnan, China
| | - Doku Henry
- Rice Research Institute, Yunnan Agriculture University, Kunming, Yunnan, China
- Biotechnology Lab Complex, CSIR-Crops Research Institute, Ghana
| | - Li Wei
- Rice Research Institute, Yunnan Agriculture University, Kunming, Yunnan, China
| | - Dong Sun Lee
- Rice Research Institute, Yunnan Agriculture University, Kunming, Yunnan, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
| | - LiJuan Chen
- Rice Research Institute, Yunnan Agriculture University, Kunming, Yunnan, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
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Sandamal S, Tennakoon A, Meng Q, Marambe B, Ratnasekera D, Melo A, Ge S. Population genetics and evolutionary history of the wild rice species Oryza rufipogon and O. nivara in Sri Lanka. Ecol Evol 2018; 8:12056-12065. [PMID: 30598799 PMCID: PMC6303766 DOI: 10.1002/ece3.4665] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 10/02/2018] [Indexed: 11/07/2022] Open
Abstract
Genetic diversity and population genetic structure of the wild rice species Oryza rufipogon and O. nivara in Sri Lanka were studied using 33 microsatellite markers. A total of 315 individuals of 11 natural populations collected from the wet, intermediate, and dry zones of the country were used in the study. We found a moderate to high level of genetic diversity at the population level, with the polymorphic loci (P) ranging from 60.6% to 100% (average 81.8%) and the expected heterozygosity (H E) varying from 0.294 to 0.481 (average 0.369). A significant genetic differentiation between species and strong genetic structure within species were also observed. Based on species distribution modeling, we detected the dynamics of the preferred habitats for the two species in Sri Lanka and demonstrated that both O. rufipogon and O. nivara populations have expanded substantially since the last internal glacial. In addition, we showed that the geographical distribution of the two species corresponded to the climate zones and identified a few of key environmental variables that contribute to the distribution of the two species, implying the potential mechanism for ecological adaptation of these two species in Sri Lanka. These studies provided important insights into the population genetics and evolution of these wild species in Sri Lanka and are of great significance to the in situ conservation and utilization of these wild resources in genetic improvement of rice.
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Affiliation(s)
- Salinda Sandamal
- Department of Agricultural Biology, Faculty of AgricultureUniversity of RuhunaMataraSri Lanka
| | - Asanka Tennakoon
- Department of Agricultural Biology, Faculty of AgricultureUniversity of RuhunaMataraSri Lanka
| | - Qing‐Lin Meng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of BotanyChinese Academy of SciencesBeijingChina
| | - Buddhi Marambe
- Department of Crop Science, Faculty of AgricultureUniversity of PeradeniyaPeradeniyaSri Lanka
| | - Disna Ratnasekera
- Department of Agricultural Biology, Faculty of AgricultureUniversity of RuhunaMataraSri Lanka
| | - Arthur Melo
- Department of Agriculture, Nutrition and Food SystemsUniversity of New HampshireDurhamNew Hampshire
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of BotanyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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Potential of Oryza officinalis to augment the cold tolerance genetic mechanisms of Oryza sativa by network complementation. Sci Rep 2018; 8:16346. [PMID: 30397229 PMCID: PMC6218501 DOI: 10.1038/s41598-018-34608-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 10/15/2018] [Indexed: 12/22/2022] Open
Abstract
Oryza officinalis is an accessible alien donor for genetic improvement of rice. Comparison across a representative panel of Oryza species showed that the wild O. officinalis and cultivated O. sativa ssp. japonica have similar cold tolerance potentials. The possibility that either distinct or similar genetic mechanisms are involved in the low temperature responses of each species was addressed by comparing their transcriptional networks. General similarities were supported by shared transcriptomic signatures indicative of equivalent metabolic, hormonal, and defense status. However, O. officinalis has maintained an elaborate cold-responsive brassinosteroid-regulated BES1-network that appeared to have been fragmented in O. sativa. BES1-network is potentially important for integrating growth-related responses with physiological adjustments and defenses through the protection of photosynthetic machinery and maintenance of stomatal aperture, oxidative defenses, and osmotic adjustment. Equivalent physiological processes are functional in O. sativa but their genetic mechanisms are under the direct control of ABA-dependent, DREB-dependent and/or oxidative-mediated networks uncoupled to BES1. While O. officinalis and O. sativa represent long periods of speciation and domestication, their comparable cold tolerance potentials involve equivalent physiological processes but distinct genetic networks. BES1-network represents a novel attribute of O. officinalis with potential applications in diversifying or complementing other mechanisms in the cultivated germplasm.
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48
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Hechanova SL, Prusty MR, Kim SR, Ballesfin L, Ramos J, Prahalada GD, Jena KK. Monosomic alien addition lines (MAALs) of Oryza rhizomatis in Oryza sativa: production, cytology, alien trait introgression, molecular analysis and breeding application. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2197-2211. [PMID: 30032316 DOI: 10.1007/s00122-018-3147-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 07/14/2018] [Indexed: 05/23/2023]
Abstract
Key message Development of MAALs and disomic introgression lines derived from the cross between O. sativa and O. rhizomatis to exploit and utilize the valuable traits for rice improvement. The CC genome wild species, Oryza rhizomatis, possesses valuable traits for rice improvement. Unlike other CC genome wild rice, O. rhizomatis is less studied and none of the research has focused on the utilization of this resource in rice breeding. The transfer of novel genes governing the valuable traits from O. rhizomatis is difficult due to high genome incompatibility with O. sativa. Here we report the development of backcross progenies and complete sets of monosomic alien addition lines (MAALs) for the first time from O. rhizomatis in O. sativa line IR31917-45-3-2. Autotetraploid IR31917-45-3-2 (4x = AAAA) was used to generate allotriploid F1, and the F1 plant was backcrossed to IR31917-45-3-2 (2x). Forty-seven BC1F1 and 73 BC2F1 plants were produced with chromosome numbers ranging from 24 to 33 (2x + 9) and 24 to 27 (2x + 3), respectively. A complete set of MAALs were identified by morphological, cytological and marker-based analysis. A total of 116 CC genome-specific InDel markers across the 12 chromosome of rice were used to detect O. rhizomatis chromosome segments in F1, BC1F1, BC2F2, MAALs and disomic introgression lines (DILs). Expressions of major phenotypic traits inherited from O. rhizomatis were observed in MAAL-derived DILs. Small chromosomal segments of O. rhizomatis for chromosomes 1, 2, 4, 5, 6, 7, 10 and 12 were detected in DILs, and some of the introgression lines showed insect resistance against brown planthopper and green leafhopper. These newly developed MAALs and DILs will be useful for gene mining and more precise faster transfer of favorable genes to improve rice cultivars.
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Affiliation(s)
- Sherry Lou Hechanova
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Manas R Prusty
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Sung-Ryul Kim
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - LaRue Ballesfin
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Joie Ramos
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - G D Prahalada
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Kshirod K Jena
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
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Ballesfin MLE, Vinarao RB, Sapin J, Kim SR, Jena KK. Development of an intergeneric hybrid between Oryza sativa L. and Leersia perrieri (A. Camus) Launert. BREEDING SCIENCE 2018; 68:474-480. [PMID: 30369822 PMCID: PMC6198897 DOI: 10.1270/jsbbs.18045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 06/15/2018] [Indexed: 06/08/2023]
Abstract
An intergeneric hybrid was successfully developed between Oryza sativa L. (IRRI 154) and Leersia perrieri (A. Camus) Launert using embryo rescue technique in this study. A low crossability value (0.07%) implied that there was high incompatibility between the two species of the hybrid. The F1 hybrid showed intermediate phenotypic characteristics between the parents but the plant height was very short. The erect plant type resembled the female parent IRRI 154 but the leaves were similar to L. perrieri. Cytological analysis revealed highly non-homology between chromosomes of the two species as the F1 plants showed 24 univalents without any chromosome pairing. The F1 hybrid plant was further confirmed by PCR analysis using the newly designed 11 indel markers showing polymorphism between O. sativa and L. perrieri. This intergeneric hybrid will open up opportunities to transfer novel valuable traits from L. perrieri into cultivated rice.
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Affiliation(s)
- Ma. LaRue E. Ballesfin
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute,
DAPO Box 7777, Metro Manila,
Philippines
| | - Ricky B. Vinarao
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute,
DAPO Box 7777, Metro Manila,
Philippines
| | - Janice Sapin
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute,
DAPO Box 7777, Metro Manila,
Philippines
| | - Sung-Ryul Kim
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute,
DAPO Box 7777, Metro Manila,
Philippines
| | - Kshirod K. Jena
- Novel Gene Resources Laboratory, Strategic Innovation Platform, International Rice Research Institute,
DAPO Box 7777, Metro Manila,
Philippines
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50
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De novo genome assembly of Oryza granulata reveals rapid genome expansion and adaptive evolution. Commun Biol 2018; 1:84. [PMID: 30271965 PMCID: PMC6123737 DOI: 10.1038/s42003-018-0089-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 06/08/2018] [Indexed: 12/18/2022] Open
Abstract
The wild relatives of rice have adapted to different ecological environments and constitute a useful reservoir of agronomic traits for genetic improvement. Here we present the ~777 Mb de novo assembled genome sequence of Oryza granulata. Recent bursts of long-terminal repeat retrotransposons, especially RIRE2, led to a rapid twofold increase in genome size after O. granulata speciation. Universal centromeric tandem repeats are absent within its centromeres, while gypsy-type LTRs constitute the main centromere-specific repetitive elements. A total of 40,116 protein-coding genes were predicted in O. granulata, which is close to that of Oryza sativa. Both the copy number and function of genes involved in photosynthesis and energy production have undergone positive selection during the evolution of O. granulata, which might have facilitated its adaptation to the low light habitats. Together, our findings reveal the rapid genome expansion, distinctive centromere organization, and adaptive evolution of O. granulata. Zhigang Wu, Dongming Fang, Rui Yang, et al. present the genome assembly of a wild rice species Oryza granulata, revealing critical insights about the rapid genome expansion and evolution observed in the Oryza genus. They find that recent bursts of LTR retrotransposons have led to the rapid increase in O. granulate genome size following speciation.
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