1
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Wu CC, Wei FJ, Chiou WY, Tsai YC, Wu HP, Gotarkar D, Wei ZH, Lai MH, Hsing YIC. Studies of rice Hd1 haplotypes worldwide reveal adaptation of flowering time to different environments. PLoS One 2020; 15:e0239028. [PMID: 32941524 PMCID: PMC7498076 DOI: 10.1371/journal.pone.0239028] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/29/2020] [Indexed: 11/30/2022] Open
Abstract
Rice domestication/adaptation is a good model for studies of the development and spread of this important crop. Mutations that caused morphological and physiological change, followed by human selection/expansion, finally led to the improvement of phenotypes suitable for different kinds of environments. We used the sequence information for Heading date 1 (Hd1) gene to reveal the association between sequence changes and flowering phenotypes of rice in different regions. Seven loss-of-function hd1 haplotypes had been reported. By data-mining the genome sequencing information in the public domain, we discovered 3 other types. These loss-of-function allele haplotypes are present in subtropical and tropical regions, which indicates human selection. Some of these haplotypes are present locally. However, types 7 and 13 are present in more than one-third of the world's rice accessions, including landraces and modern varieties. In the present study, phylogenetic, allele network and selection pressure analyses revealed that these two haplotypes might have occurred early in Southeastern Asia and then were introgressed in many local landraces in nearby regions. We also demonstrate that these haplotypes are present in weedy rice populations, which again indicates that these alleles were present in rice cultivation for long time. In comparing the wild rice sequence information, these loss-of-function haplotypes occurred in agro but were not from wild rice.
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Affiliation(s)
- Cheng-Chieh Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Institute of Plant Science, National Taiwan University, Taipei, Taiwan
| | - Fu-Jin Wei
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Wan-Yi Chiou
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yuan-Ching Tsai
- Department of Agronomy, National Chia-yi University, Chiayi, Taiwan
| | - Hshin-Ping Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Dhananjay Gotarkar
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Zhi-Han Wei
- Department of Agronomy, National Chia-yi University, Chiayi, Taiwan
| | - Ming-Hsin Lai
- Crop Science Division, Taiwan Agriculture Research Institute, Taichung, Taiwan
| | - Yue-Ie Caroline Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Department of Agronomy, National Taiwan University, Taipei, Taiwan
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2
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Xie H, Han Y, Li X, Dai W, Song X, Olsen KM, Qiang S. Climate‐dependent variation in cold tolerance of weedy rice and rice mediated by
OsICE1
promoter methylation. Mol Ecol 2019; 29:121-137. [DOI: 10.1111/mec.15305] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 10/23/2019] [Accepted: 10/28/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Hongjie Xie
- Weed Research Laboratory Nanjing Agricultural University Nanjing China
| | - Yihao Han
- Weed Research Laboratory Nanjing Agricultural University Nanjing China
| | - Xinyue Li
- Weed Research Laboratory Nanjing Agricultural University Nanjing China
| | - Weimin Dai
- Weed Research Laboratory Nanjing Agricultural University Nanjing China
| | - Xiaoling Song
- Weed Research Laboratory Nanjing Agricultural University Nanjing China
| | - Kenneth M. Olsen
- Department of Biology Washington University in St. Louis St. Louis MO USA
| | - Sheng Qiang
- Weed Research Laboratory Nanjing Agricultural University Nanjing China
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3
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Yan Y, Chao J, Wang Y, Mo S, Kong M, Shi Z, Song X, Qiang S, Dai W.
WA
352
gene indicates booming outcrossing progenies (three‐line hybrid rice × weedy rice) in weedy rice populations. Ecosphere 2019. [DOI: 10.1002/ecs2.2646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Yu‐jiang Yan
- Weed Research Laboratory Nanjing Agricultural University Nanjing 210095 Jiangsu Province China
| | - Jing Chao
- Weed Research Laboratory Nanjing Agricultural University Nanjing 210095 Jiangsu Province China
| | - Yuan Wang
- Weed Research Laboratory Nanjing Agricultural University Nanjing 210095 Jiangsu Province China
| | - Shu‐da Mo
- Weed Research Laboratory Nanjing Agricultural University Nanjing 210095 Jiangsu Province China
| | - Meng‐yao Kong
- Weed Research Laboratory Nanjing Agricultural University Nanjing 210095 Jiangsu Province China
| | - Zhi‐hua Shi
- Weed Research Laboratory Nanjing Agricultural University Nanjing 210095 Jiangsu Province China
| | - Xiao‐ling Song
- Weed Research Laboratory Nanjing Agricultural University Nanjing 210095 Jiangsu Province China
| | - Sheng Qiang
- Weed Research Laboratory Nanjing Agricultural University Nanjing 210095 Jiangsu Province China
| | - Wei‐min Dai
- Weed Research Laboratory Nanjing Agricultural University Nanjing 210095 Jiangsu Province China
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4
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Chai C, Shankar R, Jain M, Subudhi PK. Genome-wide discovery of DNA polymorphisms by whole genome sequencing differentiates weedy and cultivated rice. Sci Rep 2018; 8:14218. [PMID: 30242197 PMCID: PMC6155081 DOI: 10.1038/s41598-018-32513-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 09/10/2018] [Indexed: 12/13/2022] Open
Abstract
Analyzing the genome level DNA polymorphisms between weedy and cultivated rice is crucial to elucidate the molecular basis of weedy and agronomic traits, which in turn can enhance our ability to control weedy rice and its utilization for rice improvement. Here, we presented the genome-wide genetic variations between a weedy rice accession PSRR-1 and two cultivated rice accessions, Bengal and Nona Bokra, belonging to japonica and indica subspecies, respectively. The total number of SNPs and InDels in PSRR/Bengal was similar to that of Nona Bokra/Bengal, but was three times greater than that of PSRR/Nona Bokra. There were 11546 large-effect SNPs/InDels affecting 5673 genes, which most likely differentiated weedy rice from cultivated rice. These large effect DNA polymorphisms were mostly resulted in stop codon gain and least by start codon loss. Analysis of the molecular functions and biological processes of weedy rice specific SNPs/InDels indicated that most of these genes were involved in protein modification/phosphorylation, protein kinase activity, and protein/nucleotide binding. By integrating previous QTL mapping results with the DNA polymorphisms data, the candidate genes for seed dormancy and seed shattering were narrowed down. The genomic resource generated in this study will facilitate discovery of functional variants for weedy and agronomic traits.
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Affiliation(s)
- Chenglin Chai
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Rama Shankar
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Prasanta K Subudhi
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA.
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5
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Zhang J, Kang Y, Valverde BE, Dai W, Song X, Qiang S. Feral rice from introgression of weedy rice genes into transgenic herbicide-resistant hybrid-rice progeny. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3855-3865. [PMID: 29873749 DOI: 10.1093/jxb/ery210] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 06/04/2018] [Indexed: 06/08/2023]
Abstract
Pollen-mediated transgenic flow of herbicide resistance occurs bidirectionally between transgenic cultivated rice and weedy rice. The potential risk of weedy traits introgressing into hybrid rice has been underestimated and is poorly understood. In this study, two glufosinate-resistant transgenic rice varieties, hybrid rice (F1), and their succeeding generations (F2-F4) were planted for 3 years in field plots free of weedy rice adjacent to experimental weedy-rice fields. Weedy-rice-like (feral) plants that were both glufosinate-resistant and had red-pericarp seed were initially found only among the F3 generations of the two glufosinate-resistant transgenic hybrid cultivars. The composite fitness (an index based on eight productivity and weediness traits) of the feral progeny was significantly higher than that of the glufosinate-resistant transgenic hybrid (the original female parent of the feral progeny) under monoculture common garden conditions. The hybrid rice progeny segregated into individuals of variable height and extended flowering. The hybrid rice F2 generations had higher outcrossing rates by pollen reception (0.96-1.65%) than their progenitors (0.07-0.98%). The results show that herbicide-resistant weedy rice can rapidly arise by pollen-mediated gene flow from weedy to transgenic hybrid rice, and their segregating pollen-receptive progeny pose a greater agro-ecological risk than transgenic varieties. The safety assessment and management regulations for transgenic hybrid rice should take into account the risk of bidirectional gene flow.
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Affiliation(s)
- Jingxu Zhang
- Weed Research Laboratory of Nanjing Agricultural University, Xuanwu District, Nanjing, China
| | - Ye Kang
- Weed Research Laboratory of Nanjing Agricultural University, Xuanwu District, Nanjing, China
| | - Bernal E Valverde
- Weed Research Laboratory of Nanjing Agricultural University, Xuanwu District, Nanjing, China
- Investigación y Desarrollo en Agricultura Tropical, S.A., Tambor, Alajuela, Costa Rica
| | - Weimin Dai
- Weed Research Laboratory of Nanjing Agricultural University, Xuanwu District, Nanjing, China
| | - Xiaoling Song
- Weed Research Laboratory of Nanjing Agricultural University, Xuanwu District, Nanjing, China
| | - Sheng Qiang
- Weed Research Laboratory of Nanjing Agricultural University, Xuanwu District, Nanjing, China
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6
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Qiu J, Zhou Y, Mao L, Ye C, Wang W, Zhang J, Yu Y, Fu F, Wang Y, Qian F, Qi T, Wu S, Sultana MH, Cao YN, Wang Y, Timko MP, Ge S, Fan L, Lu Y. Genomic variation associated with local adaptation of weedy rice during de-domestication. Nat Commun 2017; 8:15323. [PMID: 28537247 PMCID: PMC5477509 DOI: 10.1038/ncomms15323] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 03/17/2017] [Indexed: 11/09/2022] Open
Abstract
De-domestication is a unique evolutionary process by which domesticated crops are converted into ‘wild predecessor like' forms. Weedy rice (Oryza sativa f. spontanea) is an excellent model to dissect the molecular processes underlying de-domestication. Here, we analyse the genomes of 155 weedy and 76 locally cultivated rice accessions from four representative regions in China that were sequenced to an average 18.2 × coverage. Phylogenetic and demographic analyses indicate that Chinese weedy rice was de-domesticated independently from cultivated rice and experienced a strong genetic bottleneck. Although evolving from multiple origins, critical genes underlying convergent evolution of different weedy types can be found. Allele frequency analyses suggest that standing variations and new mutations contribute differently to japonica and indica weedy rice. We identify a Mb-scale genomic region present in weedy rice but not cultivated rice genomes that shows evidence of balancing selection, thereby suggesting that there might be more complexity inherent to the process of de-domestication. De-domestication is the process by which cultivated plants adopt characteristics similar to that of their wild predecessors. Here Qiu et al. re-sequence de-domesticated weedy rice and matched cultivated varieties and identify genetic variants indicative of convergent evolution across multiple de-domestication events.
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Affiliation(s)
- Jie Qiu
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yongjun Zhou
- China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Lingfeng Mao
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chuyu Ye
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Weidi Wang
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jianping Zhang
- China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Yongyi Yu
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Fei Fu
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yunfei Wang
- Zhejiang Sheng Ting Biotechnology Co., Ltd., Taizhou 318020, China
| | - Feijian Qian
- Zhejiang Sheng Ting Biotechnology Co., Ltd., Taizhou 318020, China
| | - Ting Qi
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Sanling Wu
- Analysis Center of Agrobiology and Environmental Sciences, Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University, Hangzhou 310058, China
| | - Most Humaira Sultana
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ya-Nan Cao
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, Zhejiang University, Hangzhou 310058, China
| | - Yu Wang
- Department of Biology, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Longjiang Fan
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yongliang Lu
- China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
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7
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Genetic variation architecture of mitochondrial genome reveals the differentiation in Korean landrace and weedy rice. Sci Rep 2017; 7:43327. [PMID: 28256554 PMCID: PMC5335689 DOI: 10.1038/srep43327] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 01/24/2017] [Indexed: 01/09/2023] Open
Abstract
Mitochondrial genome variations have been detected despite the overall conservation of this gene content, which has been valuable for plant population genetics and evolutionary studies. Here, we describe mitochondrial variation architecture and our performance of a phylogenetic dissection of Korean landrace and weedy rice. A total of 4,717 variations across the mitochondrial genome were identified adjunct with 10 wild rice. Genetic diversity assessment revealed that wild rice has higher nucleotide diversity than landrace and/or weedy, and landrace rice has higher diversity than weedy rice. Genetic distance was suggestive of a high level of breeding between landrace and weedy rice, and the landrace showing a closer association with wild rice than weedy rice. Population structure and principal component analyses showed no obvious difference in the genetic backgrounds of landrace and weedy rice in mitochondrial genome level. Phylogenetic, population split, and haplotype network evaluations were suggestive of independent origins of the indica and japonica varieties. The origin of weedy rice is supposed to be more likely from cultivated rice rather than from wild rice in mitochondrial genome level.
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8
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Lu B, Yang X, Ellstrand NC. Fitness correlates of crop transgene flow into weedy populations: a case study of weedy rice in China and other examples. Evol Appl 2016; 9:857-70. [PMID: 27468304 PMCID: PMC4947148 DOI: 10.1111/eva.12377] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 03/02/2016] [Indexed: 02/04/2023] Open
Abstract
Whether transgene flow from crops to cross‐compatible weedy relatives will result in negative environmental consequences has been the topic of discussion for decades. An important component of environmental risk assessment depends on whether an introgressed transgene is associated with a fitness change in weedy populations. Several crop‐weed pairs have received experimental attention. Perhaps, the most worrisome example is transgene flow from genetically engineered cultivated rice, a staple for billions globally, to its conspecific weed, weedy rice. China's cultivated/weedy rice system is one of the best experimentally studied systems under field conditions for assessing how the presence of transgenes alters the weed's fitness and the likely impacts of that fitness change. Here, we present the cultivated/weedy rice system as a case study on the consequences of introgressed transgenes in unmanaged populations. The experimental work on this system reveals considerable variation in fitness outcomes ‐ increased, decreased, and none ‐ based on the transgenic trait, its introgressed genomic background, and the environment. A review of similar research from a sample of other crop‐wild pairs suggests such variation is the rule. We conclude such variation in fitness correlates supports the case‐by‐case method of biosafety regulation is sound.
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Affiliation(s)
- Bao‐Rong Lu
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering Department of Ecology and Evolutionary Biology Fudan University Shanghai China
| | - Xiao Yang
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering Department of Ecology and Evolutionary Biology Fudan University Shanghai China
| | - Norman C. Ellstrand
- Department of Botany and Plant Sciences Center for Conservation Biology University of California Riverside CA USA
- Center for Invasive Species Research University of California Riverside CA USA
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