1
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Bhupenchandra I, Chongtham SK, Gangarani Devi A, Dutta P, Lamalakshmi E, Mohanty S, Choudhary AK, Das A, Sarika K, Kumar S, Yumnam S, Sagolsem D, Rupert Anand Y, Bhutia DD, Victoria M, Vinodh S, Tania C, Dhanachandra Sharma A, Deb L, Sahoo MR, Seth CS, Swapnil P, Meena M. Harnessing weedy rice as functional food and source of novel traits for crop improvement. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38436101 DOI: 10.1111/pce.14868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/12/2024] [Accepted: 02/15/2024] [Indexed: 03/05/2024]
Abstract
A relative of cultivated rice (Oryza sativa L.), weedy or red rice (Oryza spp.) is currently recognized as the dominant weed, leading to a drastic loss of yield of cultivated rice due to its highly competitive abilities like producing more tillers, panicles, and biomass with better nutrient uptake. Due to its high nutritional value, antioxidant properties (anthocyanin and proanthocyanin), and nutrient absorption ability, weedy rice is gaining immense research attentions to understand its genetic constitution to augment future breeding strategies and to develop nutrition-rich functional foods. Consequently, this review focuses on the unique gene source of weedy rice to enhance the cultivated rice for its crucial features like water use efficiency, abiotic and biotic stress tolerance, early flowering, and the red pericarp of the seed. It explores the debating issues on the origin and evolution of weedy rice, including its high diversity, signalling aspects, quantitative trait loci (QTL) mapping under stress conditions, the intricacy of the mechanism in the expression of the gene flow, and ecological challenges of nutrient removal by weedy rice. This review may create a foundation for future researchers to understand the gene flow between cultivated crops and weedy traits and support an improved approach for the applicability of several models in predicting multiomics variables.
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Affiliation(s)
- Ingudam Bhupenchandra
- ICAR-Farm Science Centre Tamenglong, ICAR Research Complex for NEH Region, Manipur Centre, Imphal, Manipur, India
| | - Sunil Kumar Chongtham
- Multi Technology Testing Centre and Vocational Training Centre, College of Horticulture, Central Agricultural University, Bermiok, Sikkim, India
| | - Ayam Gangarani Devi
- ICAR Research Complex for North Eastern Hill Region, Tripura Centre Lembucherra, Tripura, India
| | - Pranab Dutta
- School of Crop Protection, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya, India
| | - Elangbam Lamalakshmi
- ICAR Research Complex for North Eastern Hill Region, Sikkim Centre, Tadong, Sikkim, India
| | - Sansuta Mohanty
- Molecular Biology and Biotechnology Department, Faculty of Agricultural Sciences, Siksha O Anusandhan University, Bhubaneswar, Odisha, India
| | - Anil K Choudhary
- Division of Crop Production, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Anup Das
- ICAR Research Complex for North Eastern Hill Region, Lembucherra, Tripura, India
| | - Konsam Sarika
- ICAR Research Complex for North Eastern Hill Region, Manipur Centre, Imphal, Manipur, India
| | - Sumit Kumar
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
- Department of Plant Pathology, B.M. College of Agriculture, Khandwa, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior, Madhya Pradesh, India
| | - Sonika Yumnam
- All India Coordinated Research Project on Chickpea, Central Agricultural University, Imphal, Manipur, India
| | - Diana Sagolsem
- Multi Technology Testing Centre and Vocational Training Centre, College of Horticulture, Central Agricultural University, Bermiok, Sikkim, India
| | - Y Rupert Anand
- Multi Technology Testing Centre and Vocational Training Centre, College of Horticulture, Central Agricultural University, Bermiok, Sikkim, India
| | - Dawa Dolma Bhutia
- Multi Technology Testing Centre and Vocational Training Centre, College of Horticulture, Central Agricultural University, Bermiok, Sikkim, India
| | - M Victoria
- Multi Technology Testing Centre and Vocational Training Centre, College of Horticulture, Central Agricultural University, Bermiok, Sikkim, India
| | - S Vinodh
- Multi Technology Testing Centre and Vocational Training Centre, College of Horticulture, Central Agricultural University, Bermiok, Sikkim, India
| | - Chongtham Tania
- ICAR Research Complex for North Eastern Hill Region, Manipur Centre, Imphal, Manipur, India
| | | | - Lipa Deb
- School of Crop Protection, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya, India
| | - Manas Ranjan Sahoo
- ICAR Research Complex for North Eastern Hill Region, Manipur Centre, Imphal, Manipur, India
| | | | - Prashant Swapnil
- Department of Botany, School of Basic Science, Central University of Punjab, Bhatinda, Punjab, India
| | - Mukesh Meena
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
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2
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Li LF, Pusadee T, Wedger MJ, Li YL, Li MR, Lau YL, Yap SJ, Jamjod S, Rerkasem B, Hao Y, Song BK, Olsen KM. Porous borders at the wild-crop interface promote weed adaptation in Southeast Asia. Nat Commun 2024; 15:1182. [PMID: 38383554 PMCID: PMC10881511 DOI: 10.1038/s41467-024-45447-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 01/24/2024] [Indexed: 02/23/2024] Open
Abstract
High reproductive compatibility between crops and their wild relatives can provide benefits for crop breeding but also poses risks for agricultural weed evolution. Weedy rice is a feral relative of rice that infests paddies and causes severe crop losses worldwide. In regions of tropical Asia where the wild progenitor of rice occurs, weedy rice could be influenced by hybridization with the wild species. Genomic analysis of this phenomenon has been very limited. Here we use whole genome sequence analyses of 217 wild, weedy and cultivated rice samples to show that wild rice hybridization has contributed substantially to the evolution of Southeast Asian weedy rice, with some strains acquiring weed-adaptive traits through introgression from the wild progenitor. Our study highlights how adaptive introgression from wild species can contribute to agricultural weed evolution, and it provides a case study of parallel evolution of weediness in independently-evolved strains of a weedy crop relative.
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Affiliation(s)
- Lin-Feng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63105, USA
| | - Tonapha Pusadee
- Department of Plant and Soil Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Marshall J Wedger
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63105, USA
| | - Ya-Ling Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Ming-Rui Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yee-Ling Lau
- Department of Parasitology, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | | | - Sansanee Jamjod
- Department of Plant and Soil Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Benjavan Rerkasem
- Plant Genetic Resources and Nutrition Laboratory, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Yan Hao
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Beng-Kah Song
- School of Sciences, Monash University Malaysia, 47500, Bandar Sunway, Selangor, Malaysia.
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63105, USA.
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3
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Osakina A, Jia Y. Genetic Diversity of Weedy Rice and Its Potential Application as a Novel Source of Disease Resistance. PLANTS (BASEL, SWITZERLAND) 2023; 12:2850. [PMID: 37571004 PMCID: PMC10421194 DOI: 10.3390/plants12152850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/13/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023]
Abstract
Weeds that infest crops are a primary factor limiting agricultural productivity worldwide. Weedy rice, also called red rice, has experienced independent evolutionary events through gene flow from wild rice relatives and de-domestication from cultivated rice. Each evolutionary event supplied/equipped weedy rice with competitive abilities that allowed it to thrive with cultivated rice and severely reduce yields in rice fields. Understanding how competitiveness evolves is important not only for noxious agricultural weed management but also for the transfer of weedy rice traits to cultivated rice. Molecular studies of weedy rice using simple sequence repeat (SSR), restriction fragment length polymorphism (RFLP), and whole-genome sequence have shown great genetic variations in weedy rice populations globally. These variations are evident both at the whole-genome and at the single-allele level, including Sh4 (shattering), Hd1 (heading and flowering), and Rc (pericarp pigmentation). The goal of this review is to describe the genetic diversity of current weedy rice germplasm and the significance of weedy rice germplasm as a novel source of disease resistance. Understanding these variations, especially at an allelic level, is also crucial as individual loci that control important traits can be of great target to rice breeders.
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Affiliation(s)
- Aron Osakina
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA;
- USDA ARS Dale Bumpers National Rice Research Center, Stuttgart, AR 72160, USA
| | - Yulin Jia
- USDA ARS Dale Bumpers National Rice Research Center, Stuttgart, AR 72160, USA
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4
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Imaizumi T, Kawahara Y, Auge G. Hybrid-derived weedy rice maintains adaptive combinations of alleles associated with seed dormancy. Mol Ecol 2022; 31:6556-6569. [PMID: 36178060 DOI: 10.1111/mec.16709] [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: 03/17/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 01/13/2023]
Abstract
Plant hybridization is a pathway for the evolution of adaptive traits. However, hybridization between adapted and nonadapted populations may affect the persistence of combinations of adaptive alleles evolved through natural selection. Seed dormancy is an adaptive trait for weedy rice because it regulates the timing of seed germination and the persistence of the soil seed bank. Hybridization between weedy and cultivated rice has been confirmed with an adaptive introgression of deep seed dormancy alleles from cultivated rice. Here, we explored the influence of hybridization on the conservation of adaptive allele combinations by evaluating natural variation and genetic structure in seed dormancy-associated genomic regions. Based on sequence variation in the genomic regions associated with seed dormancy, hybrid-derived weedy rice strains maintained most of the adaptive combinations for this trait observed in the parental weedy rice, despite equal representation of the parental weedy and cultivated rice in the whole genome sequence. Moreover, hybrid-derived weedy rice strains were more dormant than their parental weedy rice strains, and this trait was strongly influenced by the environment. This study suggests that hybridization between weedy rice (adaptive allelic combinations for seed dormancy) and cultivated rice (nonadaptive combinations) generates weedy rice strains expressing deep seed dormancy caused by genome stabilization through the removal of alleles derived from cultivated rice, in addition to the adaptive introgression of deep seed dormancy alleles derived from cultivated rice. Thus, hybridization between adapted and nonadapted populations appears to be reinforcing the trajectory towards the evolution of adaptive traits.
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Affiliation(s)
- Toshiyuki Imaizumi
- Institute for Plant Protection, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | | | - Gabriela Auge
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET) - Instituto de Biociencias, Biotecnología y Biología Traslacional, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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5
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Genomic revolution of US weedy rice in response to 21st century agricultural technologies. Commun Biol 2022; 5:885. [PMID: 36076028 PMCID: PMC9458635 DOI: 10.1038/s42003-022-03803-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 08/04/2022] [Indexed: 11/08/2022] Open
Abstract
Weedy rice is a close relative of cultivated rice that devastates rice productivity worldwide. In the southern United States, two distinct strains have been historically predominant, but the 21st century introduction of hybrid rice and herbicide resistant rice technologies has dramatically altered the weedy rice selective landscape. Here, we use whole-genome sequences of 48 contemporary weedy rice accessions to investigate the genomic consequences of crop-weed hybridization and selection for herbicide resistance. We find that population dynamics have shifted such that most contemporary weeds are now crop-weed hybrid derivatives, and that their genomes have subsequently evolved to be more like their weedy ancestors. Haplotype analysis reveals extensive adaptive introgression of cultivated alleles at the resistance gene ALS, but also uncovers evidence for convergent molecular evolution in accessions with no signs of hybrid origin. The results of this study suggest a new era of weedy rice evolution in the United States.
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6
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Whole-Genome Sequencing and RNA-Seq Reveal Differences in Genetic Mechanism for Flowering Response between Weedy Rice and Cultivated Rice. Int J Mol Sci 2022; 23:ijms23031608. [PMID: 35163531 PMCID: PMC8836195 DOI: 10.3390/ijms23031608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/16/2022] [Accepted: 01/26/2022] [Indexed: 02/01/2023] Open
Abstract
Flowering is a key agronomic trait that influences adaptation and productivity. Previous studies have indicated the genetic complexity associated with the flowering response in a photoinsensitive weedy rice accession PSRR-1 despite the presence of a photosensitive allele of a key flowering gene Hd1. In this study, we used whole-genome and RNA sequencing data from both cultivated and weedy rice to add further insights. The de novo assembly of unaligned sequences predicted 225 genes, in which 45 were specific to PSRR-1, including two genes associated with flowering. Comparison of the variants in PSRR-1 with the 3K rice genome (RG) dataset identified unique variants within the heading date QTLs. Analyses of the RNA-Seq result under both short-day (SD) and long-day (LD) conditions revealed that many differentially expressed genes (DEGs) colocalized with the flowering QTLs, and some DEGs such as Hd1, OsMADS56, Hd3a, and RFT1 had unique variants in PSRR-1. Ehd1, Hd1, OsMADS15, and OsMADS56 showed different alternate splicing (AS) events between genotypes and day length conditions. OsMADS56 was expressed in PSRR-1 but not in Cypress under both LD and SD conditions. Based on variations in both sequence and expression, the unique flowering response in PSRR-1 may be due to the high-impact variants of flowering genes, and OsMADS56 is proposed as a key regulator for its day-neutral flowering response.
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7
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Brhane H, Haileselassie T, Tesfaye K, Hammenhag C, Ortiz R, Abreha KB, Geleta M. Novel Expressed Sequence Tag-Derived and Other Genomic Simple Sequence Repeat Markers Revealed Genetic Diversity in Ethiopian Finger Millet Landrace Populations and Cultivars. FRONTIERS IN PLANT SCIENCE 2021; 12:735610. [PMID: 34630485 PMCID: PMC8495221 DOI: 10.3389/fpls.2021.735610] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/26/2021] [Indexed: 06/02/2023]
Abstract
Finger millet (Eleusine coracana (L.) Geartn.) is a self-pollinating amphidiploid crop cultivated with minimal input for food and feed, as well as a source of income for small-scale farmers. To efficiently assess its genetic diversity for conservation and use in breeding programs, polymorphic DNA markers that represent its complex tetraploid genome have to be developed and used. In this study, 13 new expressed sequence tag-derived simple sequence repeat (EST-SSR) markers were developed based on publicly available finger millet ESTs. Using 10 polymorphic SSR markers (3 genomic and 7 novel EST-derived), the genetic diversity of 55 landrace accessions and 5 cultivars of finger millet representing its major growing areas in Ethiopia was assessed. In total, 26 alleles were detected across the 10 loci, and the average observed number of alleles per locus was 5.6. The polymorphic information content (PIC) of the loci ranged from 0.045 (Elco-48) to 0.71 (UGEP-66). The level of genetic diversity did not differ much between the accessions with the mean gene diversity estimates ranging only from 0.44 (accession 216054) to 0.68 (accession 237443). Similarly, a narrow range of variation was recorded at the level of regional states ranging from 0.54 (Oromia) to 0.59 (Amhara and Tigray). Interestingly, the average gene diversity of the landrace accessions (0.57) was similar to that of the cultivars (0.58). The analysis of molecular variance (AMOVA) revealed significant genetic variation both within and among accessions. The variation among the accessions accounted for 18.8% of the total variation (F ST = 0.19; P < 0.001). Similarly, significant genetic variation was obtained among the geographic regions, accounting for 6.9% of the total variation (P < 0.001). The results of the cluster, principal coordinate, and population structure analyses suggest a poor correlation between the genetic makeups of finger millet landrace populations and their geographic regions of origin, which in turn suggests strong gene flow between populations within and across geographic regions. This study contributed novel EST-SSR markers for their various applications, and those that were monomorphic should be tested in more diverse finger millet genetic resources.
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Affiliation(s)
- Haftom Brhane
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Biotechnology Institute, Ministry of Science and Technology, Addis Ababa, Ethiopia
| | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Kibrom B. Abreha
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
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8
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Key Roles of De-Domestication and Novel Mutation in Origin and Diversification of Global Weedy Rice. BIOLOGY 2021; 10:biology10090828. [PMID: 34571705 PMCID: PMC8472751 DOI: 10.3390/biology10090828] [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: 07/30/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary Weedy rice is a noxious weed infesting rice fields worldwide and causing tremendous losses of rice yield and quality. The control of this conspecific weed is difficult owing to abundant genetic diversity associated with its complex origins and evolution. Applying different molecular methods, we demonstrate the multiple origins of weedy rice with the major pathway from its cultivar progenitors. The origin and diversification of weedy rice are also closely associated with differentiation of indica-japonica rice varieties. In addition, novel mutations are identified, which may promote continued evolution and genetic diversity of weedy rice. Knowledge generated from this study provides deep insights into the origin and evolution of conspecific weeds, in addition to the design of effective measures to control these weeds. Abstract Agricultural weeds pose great challenges to sustainable crop production, owing to their complex origins and abundant genetic diversity. Weedy rice (WD) infests rice fields worldwide causing tremendous losses of rice yield/quality. To explore WD origins and evolution, we analyzed DNA sequence polymorphisms of the seed shattering genes (sh4 and qsh1) in weedy, wild, and cultivated rice from a worldwide distribution. We also used microsatellite and insertion/deletion molecular fingerprinting to determine their genetic relationship and structure. Results indicate multiple origins of WD with most samples having evolved from their cultivated progenitors and a few samples from wild rice. WD that evolved from de-domestication showed distinct genetic structures associated with indica and japonica rice differentiation. In addition, the weed-unique haplotypes that were only identified in the WD samples suggest their novel mutations. Findings in this study demonstrate the key role of de-domestication in WD origins, in which indica and japonica cultivars stimulated further evolution and divergence of WD in various agroecosystems. Furthermore, novel mutations promote continued evolution and genetic diversity of WD adapting to different environments. Knowledge generated from this study provides deep insights into the origin and evolution of conspecific weeds, in addition to the design of effective measures to control these weeds.
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9
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Wu D, Lao S, Fan L. De-Domestication: An Extension of Crop Evolution. TRENDS IN PLANT SCIENCE 2021; 26:560-574. [PMID: 33648850 DOI: 10.1016/j.tplants.2021.02.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/24/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
De-domestication or feralization is an interesting phenomenon in crops and livestock. Previously, evidence for crop de-domestication was based mainly on studies using phenotypic and genotypic data from limited molecular markers or gene segments. Recent genomic studies in rice, barley, and wheat provide comprehensive landscapes of de-domestication on a whole-genome scale. Here, we summarize crop de-domestication processes, ecological roles of de-domesticates, mechanisms underlying crop de-domestication syndromes, and conditions potentially favoring de-domestication events. We further explain how recent de-domestication studies have expanded our understanding of the complexity of crop evolution, and highlight the genetic novelties of de-domesticates beneficial for modern crop breeding.
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Affiliation(s)
- Dongya Wu
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Sangting Lao
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Longjiang Fan
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China; Hainan Institute of Zhejiang University, Yonyou Industrial Park, Sanya 572025, China.
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10
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Kim M, Xi H, Park J. Genome-wide comparative analyses of GATA transcription factors among 19 Arabidopsis ecotype genomes: Intraspecific characteristics of GATA transcription factors. PLoS One 2021; 16:e0252181. [PMID: 34038437 PMCID: PMC8153473 DOI: 10.1371/journal.pone.0252181] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 05/11/2021] [Indexed: 12/30/2022] Open
Abstract
GATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif (CX2CX17-20CX2C) followed by a basic region. Due to the low cost of genome sequencing, multiple strains of specific species have been sequenced: e.g., number of plant genomes in the Plant Genome Database (http://www.plantgenome.info/) is 2,174 originated from 713 plant species. Thus, we investigated GATA TFs of 19 Arabidopsis thaliana genome-widely to understand intraspecific features of Arabidopsis GATA TFs with the pipeline of GATA database (http://gata.genefamily.info/). Numbers of GATA genes and GATA TFs of each A. thaliana genome range from 29 to 30 and from 39 to 42, respectively. Four cases of different pattern of alternative splicing forms of GATA genes among 19 A. thaliana genomes are identified. 22 of 2,195 amino acids (1.002%) from the alignment of GATA domain amino acid sequences display variations across 19 ecotype genomes. In addition, maximally four different amino acid sequences per each GATA domain identified in this study indicate that these position-specific amino acid variations may invoke intraspecific functional variations. Among 15 functionally characterized GATA genes, only five GATA genes display variations of amino acids across ecotypes of A. thaliana, implying variations of their biological roles across natural isolates of A. thaliana. PCA results from 28 characteristics of GATA genes display the four groups, same to those defined by the number of GATA genes. Topologies of bootstrapped phylogenetic trees of Arabidopsis chloroplasts and common GATA genes are mostly incongruent. Moreover, no relationship between geographical distribution and their phylogenetic relationships was found. Our results present that intraspecific variations of GATA TFs in A. thaliana are conserved and evolutionarily neutral along with 19 ecotypes, which is congruent to the fact that GATA TFs are one of the main regulators for controlling essential mechanisms, such as seed germination and hypocotyl elongation.
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Affiliation(s)
- Mangi Kim
- InfoBoss Inc., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
| | - Hong Xi
- InfoBoss Inc., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
| | - Jongsun Park
- InfoBoss Inc., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
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11
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Graf L, Shin Y, Yang JH, Choi JW, Hwang IK, Nelson W, Bhattacharya D, Viard F, Yoon HS. A genome-wide investigation of the effect of farming and human-mediated introduction on the ubiquitous seaweed Undaria pinnatifida. Nat Ecol Evol 2021; 5:360-368. [PMID: 33495590 PMCID: PMC7929912 DOI: 10.1038/s41559-020-01378-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/03/2020] [Indexed: 02/06/2023]
Abstract
Human activity is an important driver of ecological and evolutionary change on our planet. In particular, domestication and biological introductions have important and long-lasting effects on species' genomic architecture and diversity. However, genome-wide analysis of independent domestication and introduction events within a single species has not previously been performed. The Pacific kelp Undaria pinnatifida provides such an opportunity because it has been cultivated in its native range in Northeast Asia but also introduced to four other continents in the past 50 years. Here we present the results of a genome-wide analysis of natural, cultivated and introduced populations of U. pinnatifida to elucidate human-driven evolutionary change. We demonstrate that these three categories of origin can be distinguished at the genome level, reflecting the combined influence of neutral (demography and migration) and non-neutral (selection) processes.
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Affiliation(s)
- Louis Graf
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Younhee Shin
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Ji Hyun Yang
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Ji Won Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea
| | - Il Ki Hwang
- Aquaculture Management Division, National Institute of Fisheries Science, Busan, South Korea
| | - Wendy Nelson
- National Institute of Water & Atmospheric Research, Wellington, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Frédérique Viard
- Sorbonne Université, CNRS, AD2M, Station Biologique de Roscoff, Roscoff, France
- ISEM, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, Korea.
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12
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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: 7] [Impact Index Per Article: 1.8] [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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13
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Hoyos V, Plaza G, Li X, Caicedo AL. Something old, something new: Evolution of Colombian weedy rice ( Oryza spp.) through de novo de-domestication, exotic gene flow, and hybridization. Evol Appl 2020; 13:1968-1983. [PMID: 32908598 PMCID: PMC7463356 DOI: 10.1111/eva.12955] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/21/2020] [Accepted: 02/26/2020] [Indexed: 12/17/2022] Open
Abstract
Weedy rice (Oryza spp.) is a worldwide weed of domesticated rice (O. sativa), considered particularly problematic due to its strong competition with the crop, which leads to reduction in yields and harvest quality. Several studies have established multiple independent origins for weedy rice populations in the United States and various parts of Asia; however, the origins of weedy rice in South America have not been examined in a global context. We evaluated the genetic variation of weedy rice populations in Colombia, as well as the contributions of local wild Oryza species, local cultivated varieties, and exotic Oryza groups to the weed, using polymorphism generated by genotyping by sequencing (GBS). We found no evidence for genomic contributions from local wild Oryza species (O. glumaepatula, O. grandiglumis, O. latifolia, and O. alta) to Colombian weedy rice. Instead, Colombian weedy rice has evolved from local indica cultivars and has also likely been inadvertently imported as an exotic pest from the United States. Additionally, weeds comprising de novo admixture between these distinct weedy populations now represent a large proportion of genomic backgrounds in Colombian weedy rice. Our results underscore the impressive ability of weedy rice to evolve through multiple evolutionary pathways, including in situ de-domestication, range expansion, and hybridization.
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Affiliation(s)
- Verónica Hoyos
- Departamento de AgronomíaUniversidad Nacional de ColombiaBogotáColombia
| | - Guido Plaza
- Departamento de AgronomíaUniversidad Nacional de ColombiaBogotáColombia
| | - Xiang Li
- Plant Biology Graduate ProgramUniversity of MassachusettsAmherstMAUSA
| | - Ana L. Caicedo
- Biology DepartmentUniversity of MassachusettsAmherstMAUSA
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14
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Islam MS, Coronejo S, Subudhi PK. Whole-genome sequencing reveals uniqueness of black-hulled and straw-hulled weedy rice genomes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2461-2475. [PMID: 32488303 DOI: 10.1007/s00122-020-03611-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 05/13/2020] [Indexed: 05/22/2023]
Abstract
Both SH and BHA weedy rice genotypes evolved independently and have distinct genomic composition. Different genetic mechanisms may be responsible for their competitiveness and adaptation to diverse environmental conditions. Two major types of weedy rice are recognized in the USA based on morphology: straw-hull (SH) and black-hull awned (BHA) weedy rice. We performed whole-genome resequencing of a SH weedy rice 'PSRR-1', a BHA weedy rice 'BHA1115', and a japonica cultivar 'Cypress' to delineate genome-wide differences and their relevance to genetics and evolution of weedy attributes. The high-quality reads were uniformly distributed with 82-88% genome coverage. The number of genotype-specific SNPs and InDels was highest in Cypress, followed by BHA1115 and PSRR-1. However, more genes were affected in BHA1115 compared with other two genotypes which is evident from the number of high-impact SNPs and InDels. Haplotype analysis of selected genes involved in domestication, adaptation, and agronomic performance not only differentiated SH from BHA weedy rice and supported evolution of weedy rice through de-domestication, but also validated the function of several genes such as qAn-1, qAn-2, Bh4, Rc, SD1, OsLG1, and OsC1. Several candidate genes were identified for previously reported seed dormancy and seed shattering QTLs. The SH and BHA weedy rice have distinct genomic composition, and the BHA weedy rice likely diverged earlier than SH weedy rice. The accumulation of plant development, reproduction, and defense-related genes in weedy rice possibly helped them to compete, survive, and spread under a wide range of environmental conditions by employing novel and diverse mechanisms. The genomic resources will be useful for both weed management and rice improvement by exploring the molecular basis of key agronomic, adaptive, and domestication attributes.
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Affiliation(s)
- Md Shofiqul Islam
- 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
| | - Sapphire Coronejo
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Prasanta Kumar Subudhi
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA.
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15
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Grimm A, Sahi VP, Amann M, Vidotto F, Fogliatto S, Devos KM, Ferrero A, Nick P. Italian weedy rice-A case of de-domestication? Ecol Evol 2020; 10:8449-8464. [PMID: 32788993 PMCID: PMC7417233 DOI: 10.1002/ece3.6551] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 06/10/2020] [Indexed: 01/22/2023] Open
Abstract
Weedy rice is a representative of the extensive group of feral weeds that derive from crops, but has returned to the lifestyle of a wild species. These weeds develop either from a hybridization of crops with wild relatives (exoferality), or by mutation of crops to weedy forms (endoferality). Due to the close relation of weed and crop, the methods for weed-targeted containment are limited to date. A deeper understanding of the development of such weeds might help to design more efficient and sustainable approaches for weed management. Weedy rice poses a serious threat to rice yields worldwide. It is widely accepted that weedy rice has originated independently in different regions all over the world. However, details of its evolution have remained elusive. In the current study, we investigated the history of weedy rice in northern Italy, the most important rice-growing area in Europe. Our approach was to analyze genes related to weedy traits (SD1, sh4, Rc) in weedy rice accessions compared to cultivars, and to integrate these results with phenotypic and physiological data, as well as historical information about rice farming in Italy. We arrive at a working model for the timeline of evolution of weedy rice in Italy indicating that both exoferality and endoferality acted as forces driving the development of the diverse weedy rice populations found in the region today. Models of weed evolution can help to predict the direction which weed development might take and to develop new, sustainable methods to control feral weeds.
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Affiliation(s)
- Annabelle Grimm
- Molecular Cell BiologyBotanical InstituteKarlsruhe Institute of TechnologyKarlsruheGermany
| | - Vaidurya P. Sahi
- Molecular Cell BiologyBotanical InstituteKarlsruhe Institute of TechnologyKarlsruheGermany
| | - Manuel Amann
- Molecular Cell BiologyBotanical InstituteKarlsruhe Institute of TechnologyKarlsruheGermany
| | - Francesco Vidotto
- Dipartimento di Scienze AgrarieForestali e AlimentariUniversita degli Studi di TorinoTorinoItaly
| | - Silvia Fogliatto
- Dipartimento di Scienze AgrarieForestali e AlimentariUniversita degli Studi di TorinoTorinoItaly
| | - Katrien M. Devos
- Institute of Plant Breeding, Genetics and Genomics (Department of Crop and Soil Sciences), and Department of Plant BiologyThe University of GeorgiaAthensGAUSA
| | - Aldo Ferrero
- Dipartimento di Scienze AgrarieForestali e AlimentariUniversita degli Studi di TorinoTorinoItaly
| | - Peter Nick
- Molecular Cell BiologyBotanical InstituteKarlsruhe Institute of TechnologyKarlsruheGermany
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16
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Han B, Ma X, Cui D, Wang Y, Geng L, Cao G, Zhang H, Koh H, Han L. Analysis of evolutionary relationships provides new clues to the origins of weedy rice. Ecol Evol 2020; 10:891-900. [PMID: 32015852 PMCID: PMC6988545 DOI: 10.1002/ece3.5948] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 11/18/2022] Open
Abstract
Weedy rice (WR) (Oryza sativa f. spontanea) is considered to be a pest in modern rice production systems because it competes for resources, has poor yield characteristics, and subsequently has a negative effect on rice grain yield. The evolutionary relationships among WR, landrace rice (LR), improved rice (IR) cultivars, and wild rice are largely unknown. In this study, we conducted a population genetic analysis based on neutral markers and gene haplotypes in 524 rice accessions and a comparative transcriptomic analysis using 15 representative samples. The results showed that WR populations have the highest level of genetic diversity (H e = 0.8386) and can be divided into two groups (japonica-type and indica-type). The japonica-type WR accessions from Heilongjiang province (HLJ), Jilin province (JL), Liaoning province (LN), and NX provinces clustered with the landraces grown in these same provinces. The indica-types from Jiangsu province (JS) also clustered with the indica-type landraces from JS province. Comparative transcriptome analysis of WR' IR and LR from HLJ, JL, and LN provinces showed that the WR still clustered with the LR, and that the IR lines comprise a single population. Thirty-two differentially expressed genes were shared by the IR and LR groups as well as between the IR and WR groups. Using Gene ontology (GO) analysis, we identified 19 shared GO terms in the IR and LR groups as well as between the IR and WR groups. Our results suggest that WR populations in China have diverse origins, and comparative transcriptome analysis of different types of rice from HLJ, JL, and LN provinces suggests that IR populations have become a end point in the evolution of WR, which provides a new perspective for the study of WR origins and lays a solid foundation for rice breeding.
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Affiliation(s)
- Bing Han
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Xiaoding Ma
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Di Cui
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yanjie Wang
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Leiyue Geng
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Guilan Cao
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Hui Zhang
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Hee‐Jong Koh
- Department of Plant Science, Plant Genomics and Breeding Institute of Agriculture and Life ScienceSeoul National UniversitySeoulKorea
| | - Longzhi Han
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
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17
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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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18
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De Leon TB, Karn E, Al‐Khatib K, Espino L, Blank T, Andaya CB, Andaya VC, Brim‐DeForest W. Genetic variation and possible origins of weedy rice found in California. Ecol Evol 2019; 9:5835-5848. [PMID: 31161002 PMCID: PMC6540678 DOI: 10.1002/ece3.5167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 03/04/2019] [Accepted: 03/18/2019] [Indexed: 12/12/2022] Open
Abstract
Control of weeds in cultivated crops is a pivotal component in successful crop production allowing higher yield and higher quality. In rice-growing regions worldwide, weedy rice (Oryza sativa f. spontanea Rosh.) is a weed related to cultivated rice which infests rice fields. With populations across the globe evolving a suite of phenotypic traits characteristic of weeds and of cultivated rice, varying hypotheses exist on the origin of weedy rice. Here, we investigated the genetic diversity and possible origin of weedy rice in California using 98 simple sequence repeat (SSR) markers and an Rc gene-specific marker. By employing phylogenetic clustering analysis, we show that four to five genetically distinct biotypes of weedy rice exist in California. Analysis of population structure and genetic distance among individuals reveals diverse evolutionary origins of California weedy rice biotypes, with ancestry derived from indica, aus, and japonica cultivated rice as well as possible contributions from weedy rice from the southern United States and wild rice. Because this diverse parentage primarily consists of weedy, wild, and cultivated rice not found in California, most existing weedy rice biotypes likely originated outside California.
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Affiliation(s)
- Teresa B. De Leon
- Department of Plant SciencesUniversity of California, DavisDavisCalifornia
- Rice Experiment StationCalifornia Cooperative Rice Research Foundation, Inc.BiggsCalifornia
| | - Elizabeth Karn
- Cooperative Extension Sutter‐Yuba CountiesUniversity of California Division of Agricultural and Natural Resources (UC ANR)Yuba CityCalifornia
| | - Kassim Al‐Khatib
- Department of Plant SciencesUniversity of California, DavisDavisCalifornia
| | - Luis Espino
- Cooperative Extension Colusa CountyUniversity of California Division of Agricultural and Natural Resources (UC ANR)ColusaCalifornia
| | - Timothy Blank
- California Crop Improvement AssociationUniversity of California, DavisDavisCalifornia
| | - Cynthia B. Andaya
- Rice Experiment StationCalifornia Cooperative Rice Research Foundation, Inc.BiggsCalifornia
| | - Virgilio C. Andaya
- Rice Experiment StationCalifornia Cooperative Rice Research Foundation, Inc.BiggsCalifornia
| | - Whitney Brim‐DeForest
- Cooperative Extension Sutter‐Yuba CountiesUniversity of California Division of Agricultural and Natural Resources (UC ANR)Yuba CityCalifornia
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19
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Guo L, Qiu J, Li LF, Lu B, Olsen K, Fan L. Genomic Clues for Crop-Weed Interactions and Evolution. TRENDS IN PLANT SCIENCE 2018; 23:1102-1115. [PMID: 30293809 DOI: 10.1016/j.tplants.2018.09.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/10/2018] [Accepted: 09/11/2018] [Indexed: 05/11/2023]
Abstract
Agronomically critical weeds that have evolved alongside crop species are characterized by rapid adaptation and invasiveness, which can result in an enormous reduction in annual crop yield worldwide. We discuss here recent genome-based research studies on agricultural weeds and crop-weed interactions that reveal several major evolutionary innovations such as de-domestication, interactions mediated by allelochemical secondary metabolites, and parasitic genetic elements that play crucial roles in enhancing weed invasiveness in agricultural settings. We believe that these key studies will guide future research into the evolution of crop-weed interactions, and further the development of practical applications in agricultural weed control and crop breeding.
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Affiliation(s)
- Longbiao Guo
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China; These authors contributed equally to this work
| | - Jie Qiu
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA; These authors contributed equally to this work
| | - Lin-Feng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Baorong Lu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Kenneth Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Longjiang Fan
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
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20
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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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21
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22
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Strategies for identification of mutations induced by carbon-ion beam irradiation in Arabidopsis thaliana by whole genome re-sequencing. Mutat Res 2017; 807:21-30. [PMID: 29268080 DOI: 10.1016/j.mrfmmm.2017.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 11/08/2017] [Accepted: 12/06/2017] [Indexed: 12/27/2022]
Abstract
Heavy-ion beam irradiation is a powerful physical mutagen that has been used to create numerous mutant materials in plants. These materials are an essential resource for functional genomics research in the post-genome era. The advent of Next-Generation Sequencing (NGS) technology has promoted the study of functional genomics and molecular breeding. A wealth of information can be gathered from whole genome re-sequencing; however, understanding the molecular mutation profile at genome wide, as well as identifying causal genes for a given phenotype are big challenging issues for researchers. The huge outputs created by NGS make it difficult to capture key information. It is worthy to explore an effective and efficient data-sieving strategy for mutation scanning at whole genome scale. Re-sequencing data from one laboratory wild type (Columbia) and eleven M3Arabidopsis thaliana lines derived from carbon-ion beam irradiation were used in present study. Both the number and different combinations of samples used for analysis affected the sieving results. The result indicated that using six samples was sufficient to filter out the shared mutation (background interference) sites as well as to identify the true mutation sites in the whole genome. The final number of candidate mutation sites could be further narrowed down by combining traditional rough map-based cloning. Our results demonstrated the feasibility of a parallel sequencing analysis as an efficient tool for the identification of mutations induced by carbon-ion beam irradiation. For the first time, we presented different analysis strategies for handling massive parallel sequencing data sets to detect the mutations induced by carbon-ion beam irradiation in Arabidopsis thaliana with low false-positive rate, as well as to identify the causative nucleotide changes responsible for a mutant phenotype.
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23
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Comparative Mapping of Seed Dormancy Loci Between Tropical and Temperate Ecotypes of Weedy Rice ( Oryza sativa L.). G3-GENES GENOMES GENETICS 2017; 7:2605-2614. [PMID: 28592557 PMCID: PMC5555466 DOI: 10.1534/g3.117.040451] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Genotypic variation at multiple loci for seed dormancy (SD) contributes to plant adaptation to diverse ecosystems. Weedy rice (Oryza sativa) was used as a model to address the similarity of SD genes between distinct ecotypes. A total of 12 quantitative trait loci (QTL) for SD were identified in one primary and two advanced backcross (BC) populations derived from a temperate ecotype of weedy rice (34.3°N Lat.). Nine (75%) of the 12 loci were mapped to the same positions as those identified from a tropical ecotype of weedy rice (7.1°N Lat.). The high similarity suggested that the majority of SD genes were conserved during the ecotype differentiation. These common loci are largely those collocated/linked with the awn, hull color, pericarp color, or plant height loci. Phenotypic correlations observed in the populations support the notion that indirect selections for the wild-type morphological characteristics, together with direct selections for germination time, were major factors influencing allelic distributions of SD genes across ecotypes. Indirect selections for crop-mimic traits (e.g., plant height and flowering time) could also alter allelic frequencies for some SD genes in agroecosystems. In addition, 3 of the 12 loci were collocated with segregation distortion loci, indicating that some gametophyte development genes could also influence the genetic equilibria of SD loci in hybrid populations. The SD genes with a major effect on germination across ecotypes could be used as silencing targets to develop transgene mitigation (TM) strategies to reduce the risk of gene flow from genetically modified crops into weed/wild relatives.
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24
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Liu W, Ghouri F, Yu H, Li X, Yu S, Shahid MQ, Liu X. Genome wide re-sequencing of newly developed Rice Lines from common wild rice (Oryza rufipogon Griff.) for the identification of NBS-LRR genes. PLoS One 2017; 12:e0180662. [PMID: 28700714 PMCID: PMC5507442 DOI: 10.1371/journal.pone.0180662] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 06/19/2017] [Indexed: 12/12/2022] Open
Abstract
Common wild rice (Oryza rufipogon Griff.) is an important germplasm for rice breeding, which contains many resistance genes. Re-sequencing provides an unprecedented opportunity to explore the abundant useful genes at whole genome level. Here, we identified the nucleotide-binding site leucine-rich repeat (NBS-LRR) encoding genes by re-sequencing of two wild rice lines (i.e. Huaye 1 and Huaye 2) that were developed from common wild rice. We obtained 128 to 147 million reads with approximately 32.5-fold coverage depth, and uniquely covered more than 89.6% (> = 1 fold) of reference genomes. Two wild rice lines showed high SNP (single-nucleotide polymorphisms) variation rate in 12 chromosomes against the reference genomes of Nipponbare (japonica cultivar) and 93-11 (indica cultivar). InDels (insertion/deletion polymorphisms) count-length distribution exhibited normal distribution in the two lines, and most of the InDels were ranged from -5 to 5 bp. With reference to the Nipponbare genome sequence, we detected a total of 1,209,308 SNPs, 161,117 InDels and 4,192 SVs (structural variations) in Huaye 1, and 1,387,959 SNPs, 180,226 InDels and 5,305 SVs in Huaye 2. A total of 44.9% and 46.9% genes exhibited sequence variations in two wild rice lines compared to the Nipponbare and 93-11 reference genomes, respectively. Analysis of NBS-LRR mutant candidate genes showed that they were mainly distributed on chromosome 11, and NBS domain was more conserved than LRR domain in both wild rice lines. NBS genes depicted higher levels of genetic diversity in Huaye 1 than that found in Huaye 2. Furthermore, protein-protein interaction analysis showed that NBS genes mostly interacted with the cytochrome C protein (Os05g0420600, Os01g0885000 and BGIOSGA038922), while some NBS genes interacted with heat shock protein, DNA-binding activity, Phosphoinositide 3-kinase and a coiled coil region. We explored abundant NBS-LRR encoding genes in two common wild rice lines through genome wide re-sequencing, which proved to be a useful tool to exploit elite NBS-LRR genes in wild rice. The data here provide a foundation for future work aimed at dissecting the genetic basis of disease resistance in rice, and the two wild rice lines will be useful germplasm for the molecular improvement of cultivated rice.
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Affiliation(s)
- Wen Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- Department of Tropical Crops, Guangdong Agriculture Industry Business Polytechnic College, Guangzhou, China
| | - Fozia Ghouri
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
| | - Hang Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
| | - Xiang Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
| | - Shuhong Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- * E-mail: (MQS); (XDL)
| | - Xiangdong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
- * E-mail: (MQS); (XDL)
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25
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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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26
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Huang Z, Young ND, Reagon M, Hyma KE, Olsen KM, Jia Y, Caicedo AL. All roads lead to weediness: Patterns of genomic divergence reveal extensive recurrent weedy rice origins from South Asian
Oryza. Mol Ecol 2017; 26:3151-3167. [DOI: 10.1111/mec.14120] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 01/21/2017] [Accepted: 03/10/2017] [Indexed: 01/28/2023]
Affiliation(s)
- Zhongyun Huang
- Department of Biology University of Massachusetts Amherst MA USA
| | - Nelson D. Young
- Department of Biology University of Massachusetts Amherst MA USA
| | - Michael Reagon
- Department of Biology Ohio State University Lima Lima OH USA
| | - Katie E. Hyma
- Department of Biology University of Massachusetts Amherst MA USA
| | | | - Yulin Jia
- Dale Bumpers National Rice Research Center USDA‐ARS Stuttgart AR USA
| | - Ana L. Caicedo
- Department of Biology University of Massachusetts Amherst MA USA
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27
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Li LF, Li YL, Jia Y, Caicedo AL, Olsen KM. Signatures of adaptation in the weedy rice genome. Nat Genet 2017; 49:811-814. [PMID: 28369039 DOI: 10.1038/ng.3825] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 03/02/2017] [Indexed: 12/19/2022]
Abstract
Crop domestication provided the calories that fueled the rise of civilization. For many crop species, domestication was accompanied by the evolution of weedy crop relatives, which aggressively outcompete crops and reduce harvests. Understanding the genetic mechanisms that underlie the evolution of weedy crop relatives is critical for agricultural weed management and food security. Here we use whole-genome sequences to examine the origin and adaptation of the two major strains of weedy rice found in the United States. We find that de-domestication from cultivated ancestors has had a major role in their evolution, with relatively few genetic changes required for the emergence of weediness traits. Weed strains likely evolved both early and late in the history of rice cultivation and represent an under-recognized component of the domestication process. Genomic regions identified here that show evidence of selection can be considered candidates for future genetic and functional analyses for rice improvement.
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Affiliation(s)
- Lin-Feng Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Ya-Ling Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Yulin Jia
- US Department of Agriculture-Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, USA
| | - Ana L Caicedo
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
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28
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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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29
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He Q, Kim K, Park Y. Population genomics identifies the origin and signatures of selection of Korean weedy rice. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:357-366. [PMID: 27589078 PMCID: PMC5316921 DOI: 10.1111/pbi.12630] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 07/25/2016] [Accepted: 08/21/2016] [Indexed: 05/25/2023]
Abstract
Weedy rice is the same biological species as cultivated rice (Oryza sativa); it is also a noxious weed infesting rice fields worldwide. Its formation and population-selective or -adaptive signatures are poorly understood. In this study, we investigated the phylogenetics, population structure and signatures of selection of Korean weedy rice by determining the whole genomes of 30 weedy rice, 30 landrace rice and ten wild rice samples. The phylogenetic tree and results of ancestry inference study clearly showed that the genetic distance of Korean weedy rice was far from the wild rice and near with cultivated rice. Furthermore, 537 genes showed evidence of recent positive or divergent selection, consistent with some adaptive traits. This study indicates that Korean weedy rice originated from hybridization of modern indica/indica or japonica/japonica rather than wild rice. Moreover, weedy rice is not only a notorious weed in rice fields, but also contains many untapped valuable traits or haplotypes that may be a useful genetic resource for improving cultivated rice.
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Affiliation(s)
- Qiang He
- Department of Plant ResourcesCollege of Industrial ScienceKongju National UniversityYesan32439Korea
| | - Kyu‐Won Kim
- Department of Plant ResourcesCollege of Industrial ScienceKongju National UniversityYesan32439Korea
| | - Yong‐Jin Park
- Department of Plant ResourcesCollege of Industrial ScienceKongju National UniversityYesan32439Korea
- Center for crop genetic resource and breeding (CCGRB)Kongju National UniversityCheonan31080Republic of Korea
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