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Wu ZY, Chapman MA, Liu J, Milne RI, Zhao Y, Luo YH, Zhu GF, Cadotte MW, Luan MB, Fan PZ, Monro AK, Li ZP, Corlett RT, Li DZ. Genomic variation, environmental adaptation, and feralization in ramie, an ancient fiber crop. PLANT COMMUNICATIONS 2024; 5:100942. [PMID: 38720463 PMCID: PMC11369781 DOI: 10.1016/j.xplc.2024.100942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 12/20/2023] [Accepted: 05/06/2024] [Indexed: 06/29/2024]
Abstract
Feralization is an important evolutionary process, but the mechanisms behind it remain poorly understood. Here, we use the ancient fiber crop ramie (Boehmeria nivea (L.) Gaudich.) as a model to investigate genomic changes associated with both domestication and feralization. We first produced a chromosome-scale de novo genome assembly of feral ramie and investigated structural variations between feral and domesticated ramie genomes. Next, we gathered 915 accessions from 23 countries, comprising cultivars, major landraces, feral populations, and the wild progenitor. Based on whole-genome resequencing of these accessions, we constructed the most comprehensive ramie genomic variation map to date. Phylogenetic, demographic, and admixture signal detection analyses indicated that feral ramie is of exoferal or exo-endo origin, i.e., descended from hybridization between domesticated ramie and the wild progenitor or ancient landraces. Feral ramie has higher genetic diversity than wild or domesticated ramie, and genomic regions affected by natural selection during feralization differ from those under selection during domestication. Ecological analyses showed that feral and domesticated ramie have similar ecological niches that differ substantially from the niche of the wild progenitor, and three environmental variables are associated with habitat-specific adaptation in feral ramie. These findings advance our understanding of feralization, providing a scientific basis for the excavation of new crop germplasm resources and offering novel insights into the evolution of feralization in nature.
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Affiliation(s)
- Zeng-Yuan Wu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Mark A Chapman
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Jie Liu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Richard I Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JH, UK
| | - Ying Zhao
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Ya-Huang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Guang-Fu Zhu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Marc W Cadotte
- Department of Biological Sciences, University of Toronto-Scarborough, Toronto, Ontario, Canada
| | - Ming-Bao Luan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan 410205, China.
| | - Peng-Zhen Fan
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Alex K Monro
- Royal Botanic Gardens Kew, Richmond, Surrey TW9 3AE, UK
| | - Zhi-Peng Li
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Richard T Corlett
- Royal Botanic Gardens Kew, Richmond, Surrey TW9 3AE, UK; Center for Integrative Conservation and Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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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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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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Westbrook AS, DiTommaso A. Hybridization in agricultural weeds: A review from ecological, evolutionary, and management perspectives. AMERICAN JOURNAL OF BOTANY 2023; 110:e16258. [PMID: 38031455 DOI: 10.1002/ajb2.16258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/22/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
Agricultural weeds frequently hybridize with each other or with related crop species. Some hybrid weeds exhibit heterosis (hybrid vigor), which may be stabilized through mechanisms like genome duplication or vegetative reproduction. Even when heterosis is not stabilized, hybridization events diversify weed gene pools and often enable adaptive introgression. Consequently, hybridization may promote weed evolution and exacerbate weed-crop competition. However, hybridization does not always increase weediness. Even when viable and fertile, hybrid weeds sometimes prove unsuccessful in crop fields. This review provides an overview of weed hybridization and its management implications. We describe intrinsic and extrinsic factors that influence hybrid fitness in agroecosystems. We also survey the rapidly growing literature on crop-weed hybridization and the link between hybridization and invasiveness. These topics are increasingly relevant in this era of genetic tools for crop improvement, intensive and simplified cropping systems, and globalized trade. The review concludes with suggested research priorities, including hybridization in the context of climate change, plant-insect interactions, and redesigned weed management programs. From a weed management perspective, hybridization is one of many reasons that researchers and land managers must diversify their weed control toolkits.
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Affiliation(s)
- Anna S Westbrook
- Section of Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Antonio DiTommaso
- Section of Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
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5
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Hernández F, Palmieri L, Brunet J. Introgression and persistence of cultivar alleles in wild carrot (Daucus carota) populations in the United States. AMERICAN JOURNAL OF BOTANY 2023; 110:e16242. [PMID: 37681637 DOI: 10.1002/ajb2.16242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 09/06/2023] [Accepted: 09/06/2023] [Indexed: 09/09/2023]
Abstract
PREMISE Cultivated species and their wild relatives often hybridize in the wild, and the hybrids can survive and reproduce in some environments. However, it is unclear whether cultivar alleles are permanently incorporated into the wild genomes or whether they are purged by natural selection. This question is key to accurately assessing the risk of escape and spread of cultivar genes into wild populations. METHODS We used genomic data and population genomic methods to study hybridization and introgression between cultivated and wild carrot (Daucus carota) in the United States. We used single nucleotide polymorphisms (SNPs) obtained via genotyping by sequencing for 450 wild individuals from 29 wild georeferenced populations in seven states and 144 cultivars from the United States, Europe, and Asia. RESULTS Cultivated and wild carrot formed two genetically differentiated groups, and evidence of crop-wild admixture was detected in several but not all wild carrot populations in the United States. Two regions were identified where cultivar alleles were present in wild carrots: California and Nantucket Island (Massachusetts). Surprisingly, there was no evidence of introgression in some populations with a long-known history of sympatry with the crop, suggesting that post-hybridization barriers might prevent introgression in some areas. CONCLUSIONS Our results provide support for the introgression and long-term persistence of cultivar alleles in wild carrots populations. We thus anticipate that the release of genetically engineered (GE) cultivars would lead to the introduction and spread of GE alleles in wild carrot populations.
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Affiliation(s)
- Fernando Hernández
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés 800, 8000, Bahía Blanca, Argentina
- CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Camino La Carrindanga Km 7, 8000, Bahía Blanca, Argentina
- Department of Botany and Biodiversity Research Centre, University of British Columbia, 2212 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Luciano Palmieri
- Agricultural Research Service Research Participation Program, Oak Ridge Institute for Science and Education (ORISE), Madison, WI, USA
| | - Johanne Brunet
- Vegetable Crops Research Unit, USDA-ARS, Madison, WI, USA
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6
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Wang Z, Miao L, Chen Y, Peng H, Ni Z, Sun Q, Guo W. Deciphering the evolution and complexity of wheat germplasm from a genomic perspective. J Genet Genomics 2023; 50:846-860. [PMID: 37611848 DOI: 10.1016/j.jgg.2023.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/29/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023]
Abstract
Bread wheat provides an essential fraction of the daily calorific intake for humanity. Due to its huge and complex genome, progress in studying on the wheat genome is substantially trailed behind those of the other two major crops, rice and maize, for at least a decade. With rapid advances in genome assembling and reduced cost of high-throughput sequencing, emerging de novo genome assemblies of wheat and whole-genome sequencing data are leading to a paradigm shift in wheat research. Here, we review recent progress in dissecting the complex genome and germplasm evolution of wheat since the release of the first high-quality wheat genome. New insights have been gained in the evolution of wheat germplasm during domestication and modern breeding progress, genomic variations at multiple scales contributing to the diversity of wheat germplasm, and complex transcriptional and epigenetic regulations of functional genes in polyploid wheat. Genomics databases and bioinformatics tools meeting the urgent needs of wheat genomics research are also summarized. The ever-increasing omics data, along with advanced tools and well-structured databases, are expected to accelerate deciphering the germplasm and gene resources in wheat for future breeding advances.
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Affiliation(s)
- Zihao Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Lingfeng Miao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yongming Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
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Li X, Zhang S, Lowey D, Hissam C, Clevenger J, Perera S, Jia Y, Caicedo AL. A derived weedy rice × ancestral cultivar cross identifies evolutionarily relevant weediness QTLs. Mol Ecol 2023; 32:5971-5985. [PMID: 37861465 DOI: 10.1111/mec.17172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 09/02/2023] [Accepted: 10/06/2023] [Indexed: 10/21/2023]
Abstract
Weedy rice (Oryza spp.) is a weedy relative of the cultivated rice that competes with the crop and causes significant production loss. The BHA (blackhull awned) US weedy rice group has evolved from aus cultivated rice and differs from its ancestors in several important weediness traits, including flowering time, plant height and seed shattering. Prior attempts to determine the genetic basis of weediness traits in plants using linkage mapping approaches have not often considered weed origins. However, the timing of divergence between crossed parents can affect the detection of quantitative trait loci (QTL) relevant to the evolution of weediness. Here, we used a QTL-seq approach that combines bulked segregant analysis and high-throughput whole genome resequencing to map the three important weediness traits in an F2 population derived from a cross between BHA weedy rice with an ancestral aus cultivar. We compared these QTLs with those previously detected in a cross of BHA with a more distantly related crop, indica. We identified multiple QTLs that overlapped with regions under selection during the evolution of weedy BHA rice and some candidate genes possibly underlying the evolution weediness traits in BHA. We showed that QTLs detected with ancestor-descendant crosses are more likely to be involved in the evolution of weediness traits than those detected from crosses of more diverged taxa.
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Affiliation(s)
- Xiang Li
- Plant Biology Graduate Program and Department of Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Shulin Zhang
- College of Biology and Food Engineering, Innovation and Practice Base for Postdoctors, Anyang Institute of Technology, Anyang, China
| | - Daniel Lowey
- Plant Biology Graduate Program and Department of Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Carter Hissam
- Plant Biology Graduate Program and Department of Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Josh Clevenger
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
| | - Sherin Perera
- Plant Biology Graduate Program and Department of Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Yulin Jia
- United States Department of Agriculture-Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, USA
| | - Ana L Caicedo
- Plant Biology Graduate Program and Department of Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
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Vercellino RB, Hernández F, Presotto A. The role of intraspecific crop-weed hybridization in the evolution of weediness and invasiveness: Cultivated and weedy radish (Raphanus sativus) as a case study. AMERICAN JOURNAL OF BOTANY 2023; 110:e16217. [PMID: 37659092 DOI: 10.1002/ajb2.16217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/26/2023] [Accepted: 05/30/2023] [Indexed: 09/04/2023]
Abstract
PREMISE The phenotype of hybrids between a crop and its wild or weed counterpart is usually intermediate and maladapted compared to that of their parents; however, hybridization has sometimes been associated with increased fitness, potentially leading to enhanced weediness and invasiveness. Since the ecological context and maternal genetic effects may affect hybrid fitness, they could influence the evolutionary outcomes of hybridization. Here, we evaluated the performance of first-generation crop-weed hybrids of Raphanus sativus and their parents in two contrasting ecological conditions. METHODS Using experimental hybridization and outdoor common garden experiments, we assessed differences in time to flowering, survival to maturity, plant biomass, and reproductive components between bidirectional crop-weed hybrids and their parents in agrestal (wheat cultivation, fertilization, weeding) and ruderal (human-disturbed, uncultivated area) conditions over 2 years. RESULTS Crop, weeds, and bidirectional hybrids overlapped at least partially during the flowering period, indicating a high probability of gene flow. Hybrids survived to maturity at rates at least as successful as their parents and had higher plant biomass and fecundity, which resulted in higher fitness compared to their parents in both environments, without any differences associated with the direction of the hybridization. CONCLUSIONS Intraspecific crop-weed hybridization, regardless of the cross direction, has the potential to promote weediness in weedy R. sativus in agrestal and ruderal environments, increasing the chances for introgression of crop alleles into weed populations. This is the first report of intraspecific crop-weed hybridization in R. sativus.
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Affiliation(s)
- Román B Vercellino
- Departamento de Agronomía, CERZOS, Universidad Nacional del Sur (UNS)-CONICET, San Andrés 800, Bahía Blanca, 8000, Argentina
| | - Fernando Hernández
- Departamento de Agronomía, CERZOS, Universidad Nacional del Sur (UNS)-CONICET, San Andrés 800, Bahía Blanca, 8000, Argentina
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alejandro Presotto
- Departamento de Agronomía, CERZOS, Universidad Nacional del Sur (UNS)-CONICET, San Andrés 800, Bahía Blanca, 8000, Argentina
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Ilnitskaya ET, Makarkina MV, Gorbunov IV, Stepanov IV, Kozina TD, Kozhevnikov EA, Kotlyar VK. Genetic structure of the population of wild-growing vines of the Utrish Nature Reserve. Vavilovskii Zhurnal Genet Selektsii 2023; 27:316-322. [PMID: 37469454 PMCID: PMC10352994 DOI: 10.18699/vjgb-23-38] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/11/2022] [Accepted: 10/31/2022] [Indexed: 07/21/2023] Open
Abstract
Grapes are one of the most common agricultural crops in the world. Currently, the analysis of genotypes directly at the DNA level is considered to be the most accurate method for studying the plant gene pool. The study of wild vines and ancient varieties in various regions of viticulture is an important direction of research in this field. The purpose of this work was to study the population of wild grapes growing on the territory of the Utrish Nature Reserve on the Black Sea coast of Krasnodar Region. The territory of the reserve is of interest as it is a site of ancient settlements, and the environmental conditions are suitable for the growth of wild grapes. During the survey of the territory, 24 samples of wild grapes were found, which were described according to the main morphological characteristics and analyzed by the molecular genetic method. The found vines were genotyped using 15 DNA markers, including nine commonly used for DNA fingerprinting (VVS2, VVMD5, VVMD7, VVMD25, VVMD27, VVMD28, VVMD32, VrZAG62, VrZAG79) and VVIb23, which allows determining hermaphrodite and dioecious vines. Statistical processing of microsatellite loci polymorphism data was carried out using the GenAlEx 6.5 program. The genetic relationships of the studied vines were evaluated using the PAST 2.17c program. The samples were found to be morphologically and genetically polymorphic. The number of alleles identified in the sample varied from 5 to 18 and averaged 8 alleles per locus. Statistical processing of DNA analysis data made it possible to identify two genetically different populations among the wild discovered vines. An assessment of genetic similarity of the found vines with some local varieties of geographically close viticulture regions, rootstocks and representatives of Vitis sylvestris from other territories was made. One of the populations found in the Utrish Nature Reserve is close to a number of V. sylvestris genotypes, the DNA profiles of which are presented in the Vitis International Variety Catalogue.
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Affiliation(s)
- E T Ilnitskaya
- North Caucasian Federal Scientific Center of Horticulture, Viticulture, Wine-making, Krasnodar, Russia
| | - M V Makarkina
- North Caucasian Federal Scientific Center of Horticulture, Viticulture, Wine-making, Krasnodar, Russia
| | - I V Gorbunov
- Anapa Zonal Experimental Station of Viticulture and Wine-making - Branch of North Caucasian Federal Scientific Center of Horticulture, Viticulture, Wine-making, Anapa, Russia
| | - I V Stepanov
- North Caucasian Federal Scientific Center of Horticulture, Viticulture, Wine-making, Krasnodar, Russia
| | - T D Kozina
- North Caucasian Federal Scientific Center of Horticulture, Viticulture, Wine-making, Krasnodar, Russia
| | - E A Kozhevnikov
- North Caucasian Federal Scientific Center of Horticulture, Viticulture, Wine-making, Krasnodar, Russia
| | - V K Kotlyar
- North Caucasian Federal Scientific Center of Horticulture, Viticulture, Wine-making, Krasnodar, Russia
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10
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Dwivedi SL, Chapman MA, Abberton MT, Akpojotor UL, Ortiz R. Exploiting genetic and genomic resources to enhance productivity and abiotic stress adaptation of underutilized pulses. Front Genet 2023; 14:1193780. [PMID: 37396035 PMCID: PMC10311922 DOI: 10.3389/fgene.2023.1193780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/07/2023] [Indexed: 07/04/2023] Open
Abstract
Underutilized pulses and their wild relatives are typically stress tolerant and their seeds are packed with protein, fibers, minerals, vitamins, and phytochemicals. The consumption of such nutritionally dense legumes together with cereal-based food may promote global food and nutritional security. However, such species are deficient in a few or several desirable domestication traits thereby reducing their agronomic value, requiring further genetic enhancement for developing productive, nutritionally dense, and climate resilient cultivars. This review article considers 13 underutilized pulses and focuses on their germplasm holdings, diversity, crop-wild-crop gene flow, genome sequencing, syntenic relationships, the potential for breeding and transgenic manipulation, and the genetics of agronomic and stress tolerance traits. Recent progress has shown the potential for crop improvement and food security, for example, the genetic basis of stem determinacy and fragrance in moth bean and rice bean, multiple abiotic stress tolerant traits in horse gram and tepary bean, bruchid resistance in lima bean, low neurotoxin in grass pea, and photoperiod induced flowering and anthocyanin accumulation in adzuki bean have been investigated. Advances in introgression breeding to develop elite genetic stocks of grass pea with low β-ODAP (neurotoxin compound), resistance to Mungbean yellow mosaic India virus in black gram using rice bean, and abiotic stress adaptation in common bean, using genes from tepary bean have been carried out. This highlights their potential in wider breeding programs to introduce such traits in locally adapted cultivars. The potential of de-domestication or feralization in the evolution of new variants in these crops are also highlighted.
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Affiliation(s)
| | - Mark A. Chapman
- Biological Sciences, University of Southampton, Southampton, United Kingdom
| | | | | | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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11
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Vercellino RB, Hernández F, Pandolfo C, Ureta S, Presotto A. Agricultural weeds: the contribution of domesticated species to the origin and evolution of feral weeds. PEST MANAGEMENT SCIENCE 2023; 79:922-934. [PMID: 36507604 DOI: 10.1002/ps.7321] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/04/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Agricultural weeds descended from domesticated ancestors, directly from crops (endoferality) and/or from crop-wild hybridization (exoferality), may have evolutionary advantages by rapidly acquiring traits pre-adapted to agricultural habitats. Understanding the role of crops on the origin and evolution of agricultural weeds is essential to develop more effective weed management programs, minimize crop losses due to weeds, and accurately assess the risks of cultivated genes escaping. In this review, we first describe relevant traits of weediness: shattering, seed dormancy, branching, early flowering and rapid growth, and their role in the feralization process. Furthermore, we discuss how the design of "super-crops" can affect weed evolution. We then searched for literature documenting cases of agricultural weeds descended from well-domesticated crops, and describe six case studies of feral weeds evolved from major crops: maize, radish, rapeseed, rice, sorghum, and sunflower. Further studies on the origin and evolution of feral weeds can improve our understanding of the physiological and genetic mechanisms underpinning the adaptation to agricultural habitats and may help to develop more effective weed-control practices and breeding better crops. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Román B Vercellino
- Departamento de Agronomía, CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | - Fernando Hernández
- Departamento de Agronomía, CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | - Claudio Pandolfo
- Departamento de Agronomía, CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | - Soledad Ureta
- Departamento de Agronomía, CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | - Alejandro Presotto
- Departamento de Agronomía, CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
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12
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Li B, Gschwend AR, Hovick SM, Gutek A, McHale L, Harrison SK, Regnier EE. Evolution of weedy giant ragweed ( Ambrosia trifida): Multiple origins and gene expression variability facilitates weediness. Ecol Evol 2022; 12:e9590. [PMID: 36514541 PMCID: PMC9731915 DOI: 10.1002/ece3.9590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022] Open
Abstract
Agricultural weeds may originate from wild populations, but the origination patterns and genetics underlying this transition remain largely unknown. Analysis of weedy-wild paired populations from independent locations may provide evidence to identify key genetic variation contributing to this adaptive shift. We performed genetic variation and expression analyses on transcriptome data from 67 giant ragweed samples collected from different locations in Ohio, Iowa, and Minnesota and found geographically separated weedy populations likely originated independently from their adjacent wild populations, but subsequent spreading of weedy populations also occurred locally. By using eight closely related weedy-wild paired populations, we identified thousands of unique transcripts in weedy populations that reflect shared or specific functions corresponding, respectively, to both convergently evolved and population-specific weediness processes. In addition, differential expression of specific groups of genes was detected between weedy and wild giant ragweed populations using gene expression diversity and gene co-expression network analyses. Our study suggests an integrated route of weedy giant ragweed origination, consisting of independent origination combined with the subsequent spreading of certain weedy populations, and provides several lines of evidence to support the hypothesis that gene expression variability plays a key role in the evolution of weedy species.
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Affiliation(s)
- Bo Li
- Department of Horticulture and Crop SciencesThe Ohio State UniversityColumbusOhioUSA
| | - Andrea R. Gschwend
- Department of Horticulture and Crop SciencesThe Ohio State UniversityColumbusOhioUSA
| | - Stephen M. Hovick
- Department of Evolution, Ecology and Organismal BiologyThe Ohio State UniversityColumbusOhioUSA
| | - Amanda Gutek
- Department of Horticulture and Crop SciencesThe Ohio State UniversityColumbusOhioUSA
| | - Leah McHale
- Department of Horticulture and Crop SciencesThe Ohio State UniversityColumbusOhioUSA
| | - S. Kent Harrison
- Department of Horticulture and Crop SciencesThe Ohio State UniversityColumbusOhioUSA
| | - Emilie E. Regnier
- Department of Horticulture and Crop SciencesThe Ohio State UniversityColumbusOhioUSA
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13
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Ma J, Wei H, Yu X, Lv Y, Zhang Y, Qian Q, Shang L, Guo L. Compared analysis with a high-quality genome of weedy rice reveals the evolutionary game of de-domestication. FRONTIERS IN PLANT SCIENCE 2022; 13:1065449. [PMID: 36466225 PMCID: PMC9716140 DOI: 10.3389/fpls.2022.1065449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
The weedy rice (Oryza sativa f. spontanea) harbors large numbers of excellent traits and genetic diversities, which serves as a valuable germplasm resource and has been considered as a typical material for research about de-domestication. However, there are relatively few reference genomes on weedy rice that severely limit exploiting these genetic resources and revealing more details about de-domestication events. In this study, a high-quality genome (~376.4 Mb) of weedy rice A02 was assembled based on Nanopore ultra-long platform with a coverage depth of about 79.3× and 35,423 genes were predicted. Compared to Nipponbare genome, 5,574 structural variations (SVs) were found in A02. Based on super pan-genome graph, population SVs of 238 weedy rice and cultivated rice accessions were identified using public resequencing data. Furthermore, the de-domestication sites of weedy rice and domestication sites of wild rice were analyzed and compared based on SVs and single-nucleotide polymorphisms (SNPs). Interestingly, an average of 2,198 genes about de-domestication could only be found by F ST analysis based on SVs (SV-F ST) while not by F ST analysis based on SNPs (SNP-F ST) in divergent region. Additionally, there was a low overlap between domestication and de-domestication intervals, which demonstrated that two different mechanisms existed in these events. Our finding could facilitate pinpointing of the evolutionary events that had shaped the genomic architecture of wild, cultivated, and weedy rice, and provide a good foundation for cloning of the superior alleles for breeding.
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Affiliation(s)
- Jie Ma
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Hua Wei
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Xiaoman Yu
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Yang Lv
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Yu Zhang
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Qian Qian
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Lianguang Shang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Longbiao Guo
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
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14
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McSteen P, Kellogg EA. Molecular, cellular, and developmental foundations of grass diversity. Science 2022; 377:599-602. [PMID: 35926032 DOI: 10.1126/science.abo5035] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Humans have cultivated grasses for food, feed, beverages, and construction materials for millennia. Grasses also dominate the landscape in vast parts of the world, where they have adapted morphologically and physiologically, diversifying to form ~12,000 species. Sequences of hundreds of grass genomes show that they are essentially collinear; nonetheless, not all species have the same complement of genes. Here, we focus on the molecular, cellular, and developmental bases of grain yield and dispersal-traits that are essential for domestication. Distinct genes, networks, and pathways were selected in different crop species, reflecting underlying genomic diversity. With increasing genomic resources becoming available in nondomesticated species, we anticipate advances in coming years that illuminate the ecological and economic success of the grasses.
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Affiliation(s)
- Paula McSteen
- Division of Biological Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, University of Missouri, 1201 Rollins Street, Columbia, MO 65211, USA
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15
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Han Z, Li F, Qiao W, Nong B, Cheng Y, Zhang L, Huang J, Wang Y, Lou D, Ge J, Xing M, Fan W, Nie Y, Guo W, Wang S, Liu Z, Li D, Zheng X, Yang Q. Identification of candidate genes and clarification of the maintenance of the green pericarp of weedy rice grains. FRONTIERS IN PLANT SCIENCE 2022; 13:930062. [PMID: 35937328 PMCID: PMC9354532 DOI: 10.3389/fpls.2022.930062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
The weedy rice (Oryza sativa f. spontanea) pericarp has diverse colors (e.g., purple, red, light-red, and white). However, research on pericarp colors has focused on red and purple, but not green. Unlike many other common weedy rice resources, LM8 has a green pericarp at maturity. In this study, the coloration of the LM8 pericarp was evaluated at the cellular and genetic levels. First, an examination of their ultrastructure indicated that LM8 chloroplasts were normal regarding plastid development and they contained many plastoglobules from the early immature stage to maturity. Analyses of transcriptome profiles and differentially expressed genes revealed that most chlorophyll (Chl) degradation-related genes in LM8 were expressed at lower levels than Chl a/b cycle-related genes in mature pericarps, suggesting that the green LM8 pericarp was associated with inhibited Chl degradation in intact chloroplasts. Second, the F2 generation derived from a cross between LM8 (green pericarp) and SLG (white pericarp) had a pericarp color segregation ratio of 9:3:4 (green:brown:white). The bulked segregant analysis of the F2 populations resulted in the identification of 12 known genes in the chromosome 3 and 4 hotspot regions as candidate genes related to Chl metabolism in the rice pericarp. The RNA-seq and sqRT-PCR assays indicated that the expression of the Chl a/b cycle-related structural gene DVR (encoding divinyl reductase) was sharply up-regulated. Moreover, genes encoding magnesium-chelatase subunit D and the light-harvesting Chl a/b-binding protein were transcriptionally active in the fully ripened dry pericarp. Regarding the ethylene signal transduction pathway, the CTR (encoding an ethylene-responsive protein kinase) and ERF (encoding an ethylene-responsive factor) genes expression profiles were determined. The findings of this study highlight the regulatory roles of Chl biosynthesis- and degradation-related genes influencing Chl accumulation during the maturation of the LM8 pericarp.
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Affiliation(s)
- Zhenyun Han
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fei Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weihua Qiao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China
| | - Baoxuan Nong
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yunlian Cheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lifang Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jingfen Huang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanyan Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Danjing Lou
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinyue Ge
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Meng Xing
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weiya Fan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yamin Nie
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenlong Guo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shizhuang Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ziran Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Danting Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Xiaoming Zheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China
- International Rice Research Institute, Metro Manila, Philippines
| | - Qingwen Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China
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16
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Zhang Y, Liu Y, Sun L, Baskin CC, Baskin JM, Cao M, Yang J. Seed dormancy in space and time: global distribution, paleoclimatic and present climatic drivers, and evolutionary adaptations. THE NEW PHYTOLOGIST 2022; 234:1770-1781. [PMID: 35292965 DOI: 10.1111/nph.18099] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
Seed dormancy is an important life history state that increases survival and fitness of seed plants, and thus it has attracted much attention. However, global biogeography, effects of paleoenvironment, evolutionary roles of dormancy transitions, and differences in adaptations of seed dormancy between life-forms are poorly understood. We compiled global distribution records for seed dormancy of 12 743 species and their phylogeny to explore the biogeographic patterns, environmental drivers, and evolutionary transitions between seed dormancy and nondormancy. Biogeographic patterns reveal a low proportion of dormancy in tropical rainforest regions and arctic regions and a high proportion of dormancy in remaining tropical, subtropical, and temperate regions for all species and woody species. Herbaceous plants show a greater proportion of dormancy in most global regions except arctic regions. Seasonal environments have a consistent positive influence on the dormancy pattern for both life-forms, but precipitation and temperature were important driving factors for woody and herbaceous plants, respectively. Seed dormancy was the dominating state during the evolutionary history of seed plants, and dormancy transitions had a significant relationship with paleotemperatures. Dormancy and nondormancy transitions in response to fluctuating environments during long-term evolutionary history may have played important roles in the diversification of seed plants. Our results add to the current knowledge about seed dormancy from macro-adaptive perspectives and the potential adaptive mechanisms of seed plants.
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Affiliation(s)
- Yazhou Zhang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - Yuan Liu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lu Sun
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - Carol C Baskin
- Department of Biology, University of Kentucky, Lexington, KY, 40506, USA
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546, USA
| | - Jerry M Baskin
- Department of Biology, University of Kentucky, Lexington, KY, 40506, USA
| | - Min Cao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
| | - Jie Yang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, 666303, China
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17
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Wu D, Qiu J, Sun J, Song BK, Olsen KM, Fan L. Weedy rice, a hidden gold mine in the paddy field. MOLECULAR PLANT 2022; 15:566-568. [PMID: 35032686 DOI: 10.1016/j.molp.2022.01.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Dongya Wu
- Zhejiang University City College, Hangzhou 310015, China; College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jian Sun
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
| | - Beng-Kah Song
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor 46150, Malaysia
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Longjiang Fan
- Zhejiang University City College, Hangzhou 310015, China; College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
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18
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Hernández F, Vercellino RB, Pandolfo C, Mandel JR, Presotto A. Rapid evolution of seed dormancy during sunflower de-domestication. J Hered 2022; 113:288-297. [PMID: 35192723 DOI: 10.1093/jhered/esac009] [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: 08/27/2021] [Accepted: 02/21/2022] [Indexed: 11/14/2022] Open
Abstract
Hybridization between crops and their wild relatives may promote the evolution of de-domesticated (feral) weeds. Wild sunflower (Helianthus annuus L.) is typically found in ruderal environments, but crop-wild hybridization may facilitate the evolution of weedy populations. Using one crop-specific mitochondrial marker (CMS-PET1) and 14 nuclear SSR markers, we studied the origin and genetic diversity of a recently discovered weedy population of sunflower (named BRW). Then, using a resurrection approach, we tested for rapid evolution of weedy traits (seed dormancy, herbicide resistance, and competitive ability) by sampling weedy and wild populations 10 years apart (2007 and 2017). All the weedy plants present the CMS-PET1 cytotype, confirming their feral origin. At the nuclear markers, BRW showed higher genetic diversity than the cultivated lines and low differentiation with one wild population, suggesting that wild hybridization increased their genetic diversity. We found support for rapid evolution towards higher seed dormancy, but not for higher competitive ability or herbicide resistance. Our results highlight the importance of seed dormancy during the earliest stages of adaptation and show that crop-wild hybrids can evolve quickly in agricultural environments.
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Affiliation(s)
- Fernando Hernández
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés, Bahía Blanca, Argentina.,CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Camino La Carrindanga, Bahía Blanca, Argentina
| | - Roman B Vercellino
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés, Bahía Blanca, Argentina.,CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Camino La Carrindanga, Bahía Blanca, Argentina
| | - Claudio Pandolfo
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés, Bahía Blanca, Argentina.,CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Camino La Carrindanga, Bahía Blanca, Argentina
| | - Jennifer R Mandel
- Department of Biological Sciences, Center for Biodiversity Research, University of Memphis, Memphis, TN
| | - Alejandro Presotto
- Departamento de Agronomía, Universidad Nacional del Sur (UNS), San Andrés, Bahía Blanca, Argentina.,CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Camino La Carrindanga, Bahía Blanca, Argentina
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19
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Toulotte JM, Pantazopoulou CK, Sanclemente MA, Voesenek LACJ, Sasidharan R. Water stress resilient cereal crops: Lessons from wild relatives. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:412-430. [PMID: 35029029 PMCID: PMC9255596 DOI: 10.1111/jipb.13222] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/10/2022] [Indexed: 05/20/2023]
Abstract
Cereal crops are significant contributors to global diets. As climate change disrupts weather patterns and wreaks havoc on crops, the need for generating stress-resilient, high-yielding varieties is more urgent than ever. One extremely promising avenue in this regard is to exploit the tremendous genetic diversity expressed by the wild ancestors of current day crop species. These crop wild relatives thrive in a range of environments and accordingly often harbor an array of traits that allow them to do so. The identification and introgression of these traits into our staple cereal crops can lessen yield losses in stressful environments. In the last decades, a surge in extreme drought and flooding events have severely impacted cereal crop production. Climate models predict a persistence of this trend, thus reinforcing the need for research on water stress resilience. Here we review: (i) how water stress (drought and flooding) impacts crop performance; and (ii) how identification of tolerance traits and mechanisms from wild relatives of the main cereal crops, that is, rice, maize, wheat, and barley, can lead to improved survival and sustained yields in these crops under water stress conditions.
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Affiliation(s)
- Justine M. Toulotte
- Department of Biology, Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrecht3584 CHThe Netherlands
| | - Chrysoula K. Pantazopoulou
- Department of Biology, Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrecht3584 CHThe Netherlands
| | - Maria Angelica Sanclemente
- Department of Biology, Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrecht3584 CHThe Netherlands
| | - Laurentius A. C. J. Voesenek
- Department of Biology, Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrecht3584 CHThe Netherlands
| | - Rashmi Sasidharan
- Department of Biology, Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrecht3584 CHThe Netherlands
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20
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Iyer A, Guerrier L, Leveque S, Bestwick CS, Duncan SH, Russell WR. High throughput method development and optimised production of leaf protein concentrates with potential to support the agri-industry. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2021. [DOI: 10.1007/s11694-021-01136-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractInvasive plants offer an interesting and unconventional source of protein and the considerable investment made towards their eradication can potentially be salvaged through their revalorisation. To identify viable sources, effective and high-throughput screening methods are required, as well as efficient procedures to isolate these components. Rigorous assessment of low-cost, high-throughput screening assays for total sugar, phenolics and protein was performed, and ninhydrin, Lever and Fast Blue assays were found to be most suitable owing to high reliability scores and false positive errors less than 1%. These assays were used to characterise invasive Scottish plants such as Gorse (Ulex europeans), Broom (Cystisus scoparius) and Fireweed (Chamaenerion angustifolium). Protein extraction (alkali-, heat- and enzyme assisted) were tested on these plants, and further purification (acid and ethanol precipitation, as well as ultrafiltration) procedures were tested on Gorse, based on protein recovery values. Cellulase treatment and ethanol precipitation gave the highest protein recovery (64.0 ± 0.5%) and purity (96.8 ± 0.1%) with Gorse. The amino acid profile of the purified protein revealed high levels of essential amino acids (34.8 ± 0.0%). Comparison of results with preceding literature revealed a strong association between amino acid profiles and overall protein recovery with the extraction method employed. The final purity of the protein concentrates was closely associated to the protein content of the initial plant mass. Leaf protein extraction technology can effectively raise crop harvest indices, revalorise underutilised plants and waste streams.
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21
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Sharma G, Barney JN, Westwood JH, Haak DC. Into the weeds: new insights in plant stress. TRENDS IN PLANT SCIENCE 2021; 26:1050-1060. [PMID: 34238685 DOI: 10.1016/j.tplants.2021.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 06/03/2021] [Accepted: 06/10/2021] [Indexed: 06/13/2023]
Abstract
Weeds, plants that thrive in the face of disturbance, have eluded human's attempts at control for >12 000 years, positioning them as a unique group of extreme stress tolerators. The most successful weeds have a suite of traits that enable them to rapidly adapt to environments typified by stress, growing in hostile conditions or subject to massive destruction from agricultural practices. Through their ability to persist and adapt, weeds illuminate principles of evolution and provide insights into weed management and crop improvement. Here we highlight why the time is right to move beyond traditional model systems and leverage weeds to gain a deeper understanding of the mechanisms, adaptations, and genetic and physiological bases for stress tolerance.
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Affiliation(s)
- Gourav Sharma
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - Jacob N Barney
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - James H Westwood
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA.
| | - David C Haak
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA.
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22
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Imaizumi T, Ebana K, Kawahara Y, Muto C, Kobayashi H, Koarai A, Olsen KM. Genomic divergence during feralization reveals both conserved and distinct mechanisms of parallel weediness evolution. Commun Biol 2021; 4:952. [PMID: 34376793 PMCID: PMC8355325 DOI: 10.1038/s42003-021-02484-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/23/2021] [Indexed: 12/28/2022] Open
Abstract
Agricultural weeds are the most important biotic constraints to global crop production, and chief among these is weedy rice. Despite increasing yield losses from weedy rice in recent years worldwide, the genetic basis of weediness evolution remains unclear. Using whole-genome sequence analyses, we examined the origins and adaptation of Japanese weedy rice. We find evidence for a weed origin from tropical japonica crop ancestry, which has not previously been documented in surveys of weedy rice worldwide. We further show that adaptation occurs largely through different genetic mechanisms between independently-evolved temperate japonica- and tropical japonica-derived strains; most genomic signatures of positive selection are unique within weed types. In addition, some weedy rice strains have evolved through hybridization between weedy and cultivated rice with adaptive introgression from the crop. Surprisingly, introgression from cultivated rice confers not only crop-like adaptive traits (such as shorter plant height, facilitating crop mimicry) but also weedy-like traits (such as seed dormancy). These findings reveal how hybridization with cultivated rice can promote persistence and proliferation of weedy rice.
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Affiliation(s)
- Toshiyuki Imaizumi
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Japan.
| | - Kaworu Ebana
- Research Center of Genetic Resources, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Yoshihiro Kawahara
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Chiaki Muto
- Research Center of Genetic Resources, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Hiroyuki Kobayashi
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Tsukuba, Japan
- Center for Weed and Wildlife Management, Utsunomiya University, Utsunomiya, Japan
| | - Akira Koarai
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, USA
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23
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Zhou C, Feng Y, Li G, Wang M, Jian J, Wang Y, Zhang W, Song Z, Li L, Lu B, Yang J. The New Is Old: Novel Germination Strategy Evolved From Standing Genetic Variation in Weedy Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:699464. [PMID: 34234803 PMCID: PMC8256273 DOI: 10.3389/fpls.2021.699464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/28/2021] [Indexed: 06/01/2023]
Abstract
Feralization of crop plants has aroused an increasing interest in recent years, not only for the reduced yield and quality of crop production caused by feral plants but also for the rapid evolution of novel traits that facilitate the evolution and persistence of weedy forms. Weedy rice (Oryza sativa f. spontanea) is a conspecific weed of cultivated rice, with separate and independent origins. The weedy rice distributed in eastern and northeastern China did not diverge from their cultivated ancestors by reverting to the pre-domestication trait of seed dormancy during feralization. Instead, they developed a temperature-sensing mechanism to control the timing of seed germination. Subsequent divergence in the minimum critical temperature for germination has been detected between northeastern and eastern populations. An integrative analysis was conducted using combinations of phenotypic, genomic and transcriptomic data to investigate the genetic mechanism underlying local adaptation and feralization. A dozen genes were identified, which showed extreme allele frequency differences between eastern and northeastern populations, and high correlations between allele-specific gene expression and feral phenotypes. Trancing the origin of potential adaptive alleles based on genomic sequences revealed the presence of most selected alleles in wild and cultivated rice genomes, indicating that weedy rice drew upon pre-existing, "conditionally neutral" alleles to respond to the feral selection regimes. The cryptic phenotype was exposed by activating formerly silent alleles to facilitate the transition from cultivation to wild existence, promoting the evolution and persistence of weedy forms.
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Affiliation(s)
- Chengchuan Zhou
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Yang Feng
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Gengyun Li
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Mengli Wang
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Jinjing Jian
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Yuguo Wang
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Wenju Zhang
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Zhiping Song
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Linfeng Li
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Baorong Lu
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Ji Yang
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
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24
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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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25
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Shukla K, Laursen AE, Benavides J, Ejbari N, Campbell LG. Growth and fecundity of colonizing hybrid Raphanus populations are environmentally dependent. AMERICAN JOURNAL OF BOTANY 2021; 108:580-597. [PMID: 33855711 DOI: 10.1002/ajb2.1640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Hybrid gene pools harbor more genetic variation than progenitor populations. Thus, we expect hybrid populations to exhibit more dynamic evolutionary responses to environmental variation. We ask how environmental variation experienced by adapted and transplanted populations influence the success of late-generation hybrid populations during invasion. METHODS For four generations, 20 wild (Raphanus raphanistrum) and 20 hybrid radish (R. sativus × R. raphanistrum) plant populations evolved under experimentally manipulated moisture conditions (dry, wet, control-sheltered, or control-unsheltered plots; i.e., evolutionary environment) in old fields near Toronto, Canada. We planted advanced-generation wild and hybrid radishes in sheltered plots and exposed them to either an evolutionary or a novel watering environment. To determine how soil moisture would influence invasion success, we compared the phenotype and fecundity of plants grown in these various environments. RESULTS Hybridization produced larger plants. In wet environments, hybrid seedlings emerged more frequently and expressed higher photosynthetic activity. Low-moisture, novel conditions delayed and reduced seedling emergence frequency. Hybrid plants and those that evolved under relatively wet environments exhibited higher aboveground biomass. Hybrid plants from control-sheltered plots colonizing novel moisture environments were more fecund than comparable wild plants. CONCLUSIONS Dry environments are less likely than other evolutionary environments to contribute colonists. However, relatively wet locations support the evolution of relatively fecund plants, especially crop-wild hybrid populations. Thus, our results provide a strong mechanistic explanation for variation in the relative success of crop-wild hybrids among study locations and a new standard for studies that assess the risk of crop-wild hybridization events.
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Affiliation(s)
- Kruti Shukla
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, M5B 2K3, Canada
| | - Andrew E Laursen
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, M5B 2K3, Canada
| | - Jessica Benavides
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, M5B 2K3, Canada
| | - Neda Ejbari
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, M5B 2K3, Canada
| | - Lesley G Campbell
- Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, M5B 2K3, Canada
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26
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Shergill LS, Schwartz-Lazaro LM, Leon R, Ackroyd VJ, Flessner ML, Bagavathiannan M, Everman W, Norsworthy JK, VanGessel MJ, Mirsky SB. Current outlook and future research needs for harvest weed seed control in North American cropping systems. PEST MANAGEMENT SCIENCE 2020; 76:3887-3895. [PMID: 32633078 DOI: 10.1002/ps.5986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
Harvest weed seed control (HWSC) comprises a set of tools and tactics that prevents the addition of weed seed to the soil seed bank, attenuating weed infestations and providing a method to combat the development and spread of herbicide-resistant weed populations. Initial HWSC research efforts in North America are summarized and, combined with the vast area of crops suitable for HWSC, clearly indicate strong potential for this technology. However, potential limitations exist that are not present in Australian cropping systems where HWSC was developed. These include rotations with crops that are not currently amenable to HWSC (e.g. corn), high moisture content at harvest, untimely harvest, and others. Concerns about weeds becoming resistant to HWSC (i.e. adapting) exist, as do shifts in weed species composition, particularly with the diversity of weeds in North America. Currently the potential of HWSC vastly outweighs any drawbacks, necessitating further research. Such expanded efforts should foremost include chaff lining and impact mill commercial scale evaluation, as this will address potential limitations as well as economics. Growers must be integrated into large-scale, on-farm research and development activities aimed at alleviating the problems of using HWSC systems in North America and drive greater adoption subsequently. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Lovreet S Shergill
- Southern Agricultural Research Center, Montana State University, Huntley, MT, USA
- Beltsville Agricultural Research Center, USDA-ARS, Beltsville, MD, USA
- Carvel Research and Education Center, University of Delaware, Georgetown, DE, USA
| | - Lauren M Schwartz-Lazaro
- School of Plant, Environmental, and Soil Sciences, Louisiana State University AgCenter, Baton Rouge, LA, USA
| | - Ramon Leon
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, USA
| | - Victoria J Ackroyd
- Sustainable Agricultural Systems Laboratory, Beltsville Agricultural Research Center, USDA-ARS, Beltsville, MD, USA
| | - Michael L Flessner
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | | | - Wesley Everman
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, USA
| | - Jason K Norsworthy
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Mark J VanGessel
- Carvel Research and Education Center, University of Delaware, Georgetown, DE, USA
| | - Steven B Mirsky
- Sustainable Agricultural Systems Laboratory, Beltsville Agricultural Research Center, USDA-ARS, Beltsville, MD, USA
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27
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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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28
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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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29
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Wu DH, Gealy DR, Jia MH, Edwards JD, Lai MH, McClung AM. Phylogenetic origin and dispersal pattern of Taiwan weedy rice. PEST MANAGEMENT SCIENCE 2020; 76:1639-1651. [PMID: 31714668 DOI: 10.1002/ps.5683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 10/11/2019] [Accepted: 11/07/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Knowledge of the genetic diversity and spatial structure of Taiwan weedy red rice (WRR) populations, which adapted in a transplanting system, will facilitate the design of effective methods to control this weed by tracing its origins and dispersal patterns in a given region. RESULTS Taiwan WRR is genetically most similar to Taiwan indica cultivars and landraces according to genetic distance. The inbreeding coefficient of the Taiwan WRR population is greater than 0.8, which is similar to the inbred cultivars. The ancestry coefficients map suggests a dispersal pattern of long-distance and seed-mediated contamination across Taiwan, often from warmer, earlier-planted regions to cooler, later-planted regions. Parentage analysis of Taiwan WRR revealed that mostly early indica landraces and indica cultivars were present in the genetic pool; in rare cases temperate japonica was present. Based on the above results, the phylogenetic origin of most Taiwan weedy rice appears to be from hybrid progenies of old cultivated red rice accessions crossed with 'DGWG'. The inbreeding coefficient trend of the six TWR clusters suggests a temporal shift from 'old' indica landraces with red bran (high inbreeding coefficient) to modern indica varieties (low inbreeding coefficient). CONCLUSION Although there were sustained efforts to remove these old red rice accessions from paddy fields before 1945, some farmers continued to use low purity seed. This practice, along with volunteer cultivation of these old varieties in the second cropping season, apparently has facilitated the long-distance, seed-mediated contamination of rice seed, and the increase in weedy rice seed in paddy soil. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Dong-Hong Wu
- Crop Science Division, Taiwan Agricultural Research Institute, Council of Agriculture, Taichung City, Taiwan
| | - David R Gealy
- Dale Bumpers National Rice Research Center, United States Department of Agriculture - Agricultural Research Service, Stuttgart, AR, USA
| | - Melissa H Jia
- Dale Bumpers National Rice Research Center, United States Department of Agriculture - Agricultural Research Service, Stuttgart, AR, USA
| | - Jeremy D Edwards
- Dale Bumpers National Rice Research Center, United States Department of Agriculture - Agricultural Research Service, Stuttgart, AR, USA
| | - Ming-Hsin Lai
- Crop Science Division, Taiwan Agricultural Research Institute, Council of Agriculture, Taichung City, Taiwan
| | - Anna M McClung
- Dale Bumpers National Rice Research Center, United States Department of Agriculture - Agricultural Research Service, Stuttgart, AR, USA
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30
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Czuryszkiewicz D, Maćkowiak A, Marcinkowska K, Borkowski A, Chrzanowski Ł, Pernak J. Herbicidal Ionic Liquids Containing the Acetylcholine Cation. Chempluschem 2020; 84:268-276. [PMID: 31950757 DOI: 10.1002/cplu.201800651] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/05/2019] [Indexed: 12/22/2022]
Abstract
This study presents a new group of herbicidal ionic liquids (HILs) based on a cation occurs commonly in nature-acetylcholine. The HILs were obtained with a high yield through ion exchange between acetylcholine chloride and potassium or sodium salts of selected acids with herbicidal activity. The results of the herbicidal activity measurement against common oilseed rape (Brassica napus L.) exceeded those of the commercial products. Spray solutions of the synthesized HILs revealed high surface activity and wetting properties which further manifested as higher herbicidal activity. The reduction of surface tension and low contact angles together with the specific action of acetylcholine allowed for better penetration of synthesized HILs into plant tissues. In addition, OECD 301F tests confirmed high mineralization of the HILs. The simple transformation of commercial herbicides into acetylcholine HILs proved to be a very effective method of increasing their activity, and constitutes an interesting solution to the problem of weed infestation with the use of a substance commonly found in nature.
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Affiliation(s)
- Daria Czuryszkiewicz
- Department of Chemical Technology, Poznan University of Technology, Berdychowo 4, Poznan, 60-965, Poland
| | - Adam Maćkowiak
- Department of Chemical Technology, Poznan University of Technology, Berdychowo 4, Poznan, 60-965, Poland
| | - Katarzyna Marcinkowska
- Institute of Plant Protection, National Research Institute, Węgorka 20, Poznan, 60-318, Poland
| | - Andrzej Borkowski
- Faculty of Geology, University of Warsaw, Żwirki i Wigury 93, Warsaw, 02-089, Poland
| | - Łukasz Chrzanowski
- Department of Chemical Technology, Poznan University of Technology, Berdychowo 4, Poznan, 60-965, Poland
| | - Juliusz Pernak
- Department of Chemical Technology, Poznan University of Technology, Berdychowo 4, Poznan, 60-965, Poland
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31
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Isolation and characterization of microfibrillated cellulose and nanofibrillated cellulose with “biomechanical hotspots”. Carbohydr Polym 2020; 234:115827. [DOI: 10.1016/j.carbpol.2020.115827] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 12/17/2019] [Accepted: 01/02/2020] [Indexed: 01/27/2023]
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32
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D’Onofrio C. Introgression Among Cultivated and Wild Grapevine in Tuscany. FRONTIERS IN PLANT SCIENCE 2020; 11:202. [PMID: 32184799 PMCID: PMC7058638 DOI: 10.3389/fpls.2020.00202] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/11/2020] [Indexed: 05/06/2023]
Abstract
Wild grapevine, Vitis vinifera L. subsp. sylvestris (Gmelin, Hegi) is spontaneous to Europe and common in Tuscany. In this study, wild grapevines were identified in 22 populations from eight locations in Tuscan Maremma (Grosseto and Siena province). The plants were propagated by cuttings, collected in a vineyard, genotyped by nuclear simple sequence repeats (SSRs), chloroplast SSRs and single nucleotide polymorphisms (SNPs), and compared to locally cultivated varieties (Vitis vinifera L. subsp. sativa) and to non-vinifera and non-vitis genotypes. The identity analysis revealed that some individuals were redundant genotypes, suggesting natural vegetative propagation. In addition, four of the supposed V.v. sylvestris were in fact naturalized V.v. sativa. The majority of putative sylvestris genotypes had chlorotype A, while the remainder had chlorotype D, as the majority of Vitis vinifera subsp. sativa cultivated in Italy. Some of the recovered sylvestris genotypes appeared to be natural crosses with cultivated grapevine varieties in Tuscany, and their chlorotype suggests a higher pollen flow from sativa to the sylvestris genotypes than in the opposite direction. In addition, other genotypes appeared to be crosses within sylvestris, sylvestris-sativa or sylvestris-sylvestris siblings, or equivalent relationships. These relationships suggest a noticeably level of sexual reproductive activities among sylvestris and sylvestris-sativa genotypes. A cluster and structure analysis clearly differentiated the true sylvestris from the sativa, and the non-vinifera or non-vitis genotypes, and also highlighted a possible introgression of sylvestris into some Italian and French cultivated varieties. The results therefore suggest that, in addition to the primary ancient center of domestication from the Near East to Central Asia, the introgression among cultivated and wild grapevine occurred in other centers of diversification along the migration routes, contributing to the domestication processes, and suggesting that these processes are still ongoing despite the reduction in populations of sylvestris. The results also highlight that the GrapeReSeq 18K Vitis genotyping chip are suitable for non-vitis genotyping and that the range of SNPs heterozygosity in sylvestris appears to be up to 6% less and does not overlap the heterozygosity range of sativa genotypes.
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Affiliation(s)
- Claudio D’Onofrio
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
- Nutraceuticals and Food for Health – Nutrafood, University of Pisa, Pisa, Italy
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Zhang SJ, Wang GD, Ma P, Zhang LL, Yin TT, Liu YH, Otecko NO, Wang M, Ma YP, Wang L, Mao B, Savolainen P, Zhang YP. Genomic regions under selection in the feralization of the dingoes. Nat Commun 2020; 11:671. [PMID: 32015346 PMCID: PMC6997406 DOI: 10.1038/s41467-020-14515-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 12/16/2019] [Indexed: 12/30/2022] Open
Abstract
Dingoes are wild canids living in Australia, originating from domestic dogs. They have lived isolated from both the wild and the domestic ancestor, making them a unique model for studying feralization. Here, we sequence the genomes of 10 dingoes and 2 New Guinea Singing Dogs. Phylogenetic and demographic analyses show that dingoes originate from dogs in southern East Asia, which migrated via Island Southeast Asia to reach Australia around 8300 years ago, and subsequently diverged into a genetically distinct population. Selection analysis identifies 50 positively selected genes enriched in digestion and metabolism, indicating a diet change during feralization of dingoes. Thirteen of these genes have shifted allele frequencies compared to dogs but not compared to wolves. Functional assays show that an A-to-G mutation in ARHGEF7 decreases the endogenous expression, suggesting behavioral adaptations related to the transitions in environment. Our results indicate that the feralization of the dingo induced positive selection on genomic regions correlated to neurodevelopment, metabolism and reproduction, in adaptation to a wild environment.
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Affiliation(s)
- Shao-Jie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming, 650091, China
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
| | - Pengcheng Ma
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Liang-Liang Zhang
- KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, Science for Life Laboratory, SE-171 65, Solna, Sweden
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Yan-Hu Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Newton O Otecko
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Meng Wang
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming, 650091, China
| | - Ya-Ping Ma
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming, 650091, China
| | - Lu Wang
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming, 650091, China
| | - Bingyu Mao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Peter Savolainen
- KTH Royal Institute of Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Gene Technology, Science for Life Laboratory, SE-171 65, Solna, Sweden.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, Yunnan University, Kunming, 650091, China.
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Page A, Gibson J, Meyer RS, Chapman MA. Eggplant Domestication: Pervasive Gene Flow, Feralization, and Transcriptomic Divergence. Mol Biol Evol 2020; 36:1359-1372. [PMID: 31039581 DOI: 10.1093/molbev/msz062] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In the context of food security, examining the genomics of domestication will help identify genes underlying adaptive and economically important phenotypes, for example, larger fruit, improved taste, and loss of agronomically inferior phenotypes. Examination of genome-scale single nucleotide polymorphisms demonstrates the relationships between wild ancestors of eggplant (Solanum melongena L.), confirming that Solanum insanum L. is the wild progenitor. This species is split roughly into an Eastern (Malaysian, Thai, and Vietnamese) and Western (Indian, Madagascan, and Sri Lankan) group, with domesticates derived from the former. Additional "wild" accessions from India appear to be feral escapes, derived multiple times from domesticated varieties through admixture. Accessions with small egg-shaped fruit are generally found intermixed with East Asian Solanum insanum confirming they are primitive relative to the large-fruited domesticates. Comparative transcriptomics was used to track the loci under selection. Sequence analysis revealed a genetic bottleneck reducing variation by almost 50% in the primitive accessions relative to the wild species and a further 10% in the landraces. We also show evidence for selection on genes with a role in response to wounding and apoptosis. Genes showing a significant difference in expression between wild and primitive or between primitive and landrace genepools were mostly (>75%) downregulated in the derived populations and enriched for gene ontologies related to defense, flowering, signaling, and response to biotic and abiotic stimuli. This work reveals genomic changes involved in crop domestication and improvement, and the population genetics work explains why defining the eggplant domestication trajectory has been so challenging.
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Affiliation(s)
- Anna Page
- Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Jane Gibson
- Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Rachel S Meyer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Southampton, United Kingdom
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Raybould A. Problem formulation and phenotypic characterisation for the development of novel crops. Transgenic Res 2020; 28:135-145. [PMID: 31321696 DOI: 10.1007/s11248-019-00147-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Phenotypic characterisation provides important information about novel crops that helps their developers to make technical and commercial decisions. Phenotypic characterisation comprises two activities. Product characterisation checks that the novel crop has the qualities of a viable product-the intended traits have been introduced and work as expected, and no unintended changes have been made that will adversely affect the performance of the final product. Risk assessment evaluates whether the intended and unintended changes are likely to harm human health or the environment. Product characterisation follows the principles of problem formulation, namely that the characteristics required in the final product are defined and criteria to decide whether the novel crop will have these properties are set. The hypothesis that the novel crop meets the criteria are tested during product development. If the hypothesis is corroborated, development continues, and if the hypothesis is falsified, the product is redesigned or its development is halted. Risk assessment should follow the same principles. Criteria that indicate the crop poses unacceptable risk should be set, and the hypothesis that the crop does not possess those properties should be tested. However, risk assessment, particularly when considering unintended changes introduced by new plant breeding methods such as gene editing, often ignores these principles. Instead, phenotypic characterisation seeks to catalogue all unintended changes by profiling methods and then proceeds to work out whether any of the changes are important. This paper argues that profiling is an inefficient and ineffective method of phenotypic characterisation for risk assessment. It discusses reasons why profiling is favoured and corrects some misconceptions about problem formulation.
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Affiliation(s)
- Alan Raybould
- Syngenta Crop Protection AG, Rosentalstrasse 67, 4002, Basel, Switzerland.
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36
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Cronin D, Kron P, Husband BC. The origins and evolutionary history of feral apples in southern Canada. Mol Ecol 2019; 29:1776-1790. [PMID: 31622503 DOI: 10.1111/mec.15277] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 09/30/2019] [Accepted: 10/03/2019] [Indexed: 12/11/2022]
Abstract
Feral populations of domesticated crops can establish through two nonmutually exclusive pathways: hybridization with native relatives and recruitment of and recombination between known cultivars. The extent and relative importance of these pathways is not known, especially for woody fruit crops. Here, we examined the evolutionary origins of feral populations of Malus domestica (domestic apple) in southern Canada using a population genetic analysis. We characterized genotypes of 578 putative feral apple trees and evaluated them in relation to genotypes of 156 commercial cultivars, 28 non-native, ornamental crabapples and 47 native Malus coronaria trees using 14 microsatellite markers. No feral trees were genetic admixtures between domestic and native Malus; however, a minority of trees were admixed with introduced ornamental Malus. Feral trees and commercial cultivars both occurred in two major genetic groups and seven subgroups distributed throughout all commercial growing regions. A total of 42 cultivars, both heritage and currently grown, occurred in probable parental pairs for feral trees, with nine heritage varieties accounting for 72% of parental assignments. We conclude that feral apples in southern Canada are not products of hybridization with native M. coronaria but we cannot exclude ornamental apple species as contributing to the naturalization process. Nonhybrid feral domestic apples have multiple origins, with a prominent signature of early heritage cultivars. These lineages have spread and coexist throughout Ontario, rather than being derived strictly from local sources.
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Affiliation(s)
- Dane Cronin
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Paul Kron
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Brian C Husband
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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Gering E, Incorvaia D, Henriksen R, Conner J, Getty T, Wright D. Getting Back to Nature: Feralization in Animals and Plants. Trends Ecol Evol 2019; 34:1137-1151. [PMID: 31488326 PMCID: PMC7479514 DOI: 10.1016/j.tree.2019.07.018] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 07/23/2019] [Accepted: 07/25/2019] [Indexed: 11/24/2022]
Abstract
Formerly domesticated organisms and artificially selected genes often escape controlled cultivation, but their subsequent evolution is not well studied. In this review, we examine plant and animal feralization through an evolutionary lens, including how natural selection, artificial selection, and gene flow shape feral genomes, traits, and fitness. Available evidence shows that feralization is not a mere reversal of domestication. Instead, it is shaped by the varied and complex histories of feral populations, and by novel selection pressures. To stimulate further insight we outline several future directions. These include testing how 'domestication genes' act in wild settings, studying the brains and behaviors of feral animals, and comparative analyses of feral populations and taxa. This work offers feasible and exciting research opportunities with both theoretical and practical applications.
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Affiliation(s)
- Eben Gering
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA; Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Davie, FL, USA.
| | - Darren Incorvaia
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Rie Henriksen
- IIFM Biology and AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Jeffrey Conner
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA; Kellogg Biological Station and Dept. of Plant Biology, Michigan State University, Hickory Corners, MI, USA
| | - Thomas Getty
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Dominic Wright
- IIFM Biology and AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
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38
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Ellstrand NC. The evolution of crops that do not need us anymore. THE NEW PHYTOLOGIST 2019; 224:550-551. [PMID: 31545886 DOI: 10.1111/nph.16145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- Norman C Ellstrand
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521-0124, USA
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39
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Jiang YF, Chen Q, Wang Y, Guo ZR, Xu BJ, Zhu J, Zhang YZ, Gong X, Luo CH, Wu W, Liu CH, Kong L, Deng M, Jiang QT, Lan XJ, Wang JR, Chen GY, Zheng YL, Wei YM, Qi PF. Re-acquisition of the brittle rachis trait via a transposon insertion in domestication gene Q during wheat de-domestication. THE NEW PHYTOLOGIST 2019; 224:961-973. [PMID: 31168798 DOI: 10.1111/nph.15977] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 05/28/2019] [Indexed: 05/18/2023]
Abstract
De-domestication is a unique evolutionary process during which crops re-acquire wild-like traits to survive and persist in agricultural fields without the need for human cultivation. The re-acquisition of seed dispersal mechanisms is crucial for crop de-domestication. Common wheat is an important cereal crop worldwide. Tibetan semi-wild wheat is a potential de-domesticated common wheat subspecies. However, the crucial genes responsible for its brittle rachis trait have not been identified. Genetic mapping, functional analyses and phylogenetic analyses were completed to identify the gene associated with Qbr.sau-5A, which is a major locus for the brittle rachis trait of Tibetan semi-wild wheat. The cloned Qbr.sau-5A gene is a new Q allele (Qt ) with a 161-bp transposon insertion in exon 5. Although Qt is expressed normally, its encoded peptide lacks some key features of the APETALA2 family. The abnormal functions of Qt in developing wheat spikes result in brittle rachises. Phylogenetic and genotyping analyses confirmed that Qt originated from Q in common wheat and is naturally distributed only in Tibetan semi-wild wheat populations. The identification of Qt provides new evidence regarding the origin of Tibetan semi-wild wheat, and new insights into the re-acquisition of wild traits during crop de-domestication.
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Affiliation(s)
- Yun-Feng Jiang
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Qing Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yan Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Zhen-Ru Guo
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Bin-Jie Xu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Jing Zhu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Ya-Zhou Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xi Gong
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Cui-Hua Luo
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Wang Wu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Cai-Hong Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Li Kong
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Qian-Tao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xiu-Jin Lan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Ji-Rui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Guo-Yue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - You-Liang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yu-Ming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Peng-Fei Qi
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
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40
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Martin SL, Parent JS, Laforest M, Page E, Kreiner JM, James T. Population Genomic Approaches for Weed Science. PLANTS (BASEL, SWITZERLAND) 2019; 8:E354. [PMID: 31546893 PMCID: PMC6783936 DOI: 10.3390/plants8090354] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/12/2019] [Accepted: 09/14/2019] [Indexed: 12/16/2022]
Abstract
Genomic approaches are opening avenues for understanding all aspects of biological life, especially as they begin to be applied to multiple individuals and populations. However, these approaches typically depend on the availability of a sequenced genome for the species of interest. While the number of genomes being sequenced is exploding, one group that has lagged behind are weeds. Although the power of genomic approaches for weed science has been recognized, what is needed to implement these approaches is unfamiliar to many weed scientists. In this review we attempt to address this problem by providing a primer on genome sequencing and provide examples of how genomics can help answer key questions in weed science such as: (1) Where do agricultural weeds come from; (2) what genes underlie herbicide resistance; and, more speculatively, (3) can we alter weed populations to make them easier to control? This review is intended as an introduction to orient weed scientists who are thinking about initiating genome sequencing projects to better understand weed populations, to highlight recent publications that illustrate the potential for these methods, and to provide direction to key tools and literature that will facilitate the development and execution of weed genomic projects.
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Affiliation(s)
- Sara L Martin
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
| | - Jean-Sebastien Parent
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
| | - Martin Laforest
- Saint-Jean-sur-Richelieu Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Jean-sur-Richelieu, QC J3B 3E6, Canada.
| | - Eric Page
- Harrow Research and Development Centre, Agriculture and Agri-Food Canada, Harrow, ON N0R 1G0, Canada.
| | - Julia M Kreiner
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.
| | - Tracey James
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada.
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When West Meets East: The Origins and Spread of Weedy Rice Between Continental and Island Southeast Asia. G3-GENES GENOMES GENETICS 2019; 9:2941-2950. [PMID: 31292156 PMCID: PMC6723143 DOI: 10.1534/g3.119.400021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Weedy crop relatives are among the world’s most problematic agricultural weeds, and their ability to rapidly evolve can be enhanced by gene flow from both domesticated crop varieties and wild crop progenitor species. In this study, we examined the role of modern commercial crop cultivars, traditional landraces, and wild relatives in the recent emergence and proliferation of weedy rice in East Malaysia on the island of Borneo. This region of Malaysia is separated from the Asian continent by the South China Sea, and weedy rice has become a major problem there more recently than on the Malaysian peninsular mainland. Using 24 polymorphic SSR loci and genotype data from the awn-length domestication gene An-1, we assessed the genetic diversity, population structure and potential origins of East Malaysian weeds; 564 weedy, cultivated and wild rice accessions were analyzed from samples collected in East Malaysia, Peninsular Malaysia and neighboring countries. While there is considerable evidence for contributions of Peninsular Malaysian weed ecotypes to East Malaysian populations, we find that local crop cultivars and/or landraces from neighboring countries are also likely contributors to the weedy rice infestations. These findings highlight the implications of genetic admixture from different cultivar source populations in the spread of weedy crop relatives and the urgent need for preventive measurements to maintain sustainable crop yields.
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Mabhaudhi T, Chimonyo VGP, Hlahla S, Massawe F, Mayes S, Nhamo L, Modi AT. Prospects of orphan crops in climate change. PLANTA 2019; 250:695-708. [PMID: 30868238 PMCID: PMC6667417 DOI: 10.1007/s00425-019-03129-y] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 02/22/2019] [Indexed: 05/22/2023]
Abstract
MAIN CONCLUSION Orphan crops can contribute to building resilience of marginal cropping systems as a climate chnage adaptation strategy. Orphan crops play an important role in global food and nutrition security, and may have potential to contribute to sustainable food systems under climate change. Owing to reports of their potential under water scarcity, there is an argument to promote them to sustainably address challenges such as increasing drought and water scarcity, food and nutrition insecurity, environmental degradation, and employment creation under climate change. We conducted a scoping review using online databases to identify the prospects of orphan crops to contribute to (1) sustainable and healthy food systems, (2) genetic resources for future crop improvement, and (3) improving agricultural sustainability under climate change. The review found that, as a product of generations of landrace agriculture, several orphan crops are nutritious, resilient, and adapted to niche marginal agricultural environments. Including such orphan crops in the existing monocultural cropping systems could support more sustainable, nutritious, and diverse food systems in marginalised agricultural environments. Orphan crops also represent a broad gene pool for future crop improvement. The reduction in arable land due to climate change offers opportunities to expand the area under their production. Their suitability to marginal niche and low-input environments offers opportunities for low greenhouse gas (GHG) emissions from an agro-ecosystems, production, and processing perspective. This, together with their status as a sub-set of agro-biodiversity, offers opportunities to address socio-economic and environmental challenges under climate change. With research and development, and policy to support them, orphan crops could play an important role in climate-change adaptation, especially in the global south.
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Affiliation(s)
- Tafadzwanashe Mabhaudhi
- Centre for Transformative Agricultural and Food Systems, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, P/Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa.
| | - Vimbayi Grace Petrova Chimonyo
- Centre for Transformative Agricultural and Food Systems, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, P/Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa
- Department of Plant, Soil and Microbial Sciences, Michigan State University, 1066 Bogue St., Rm. A286, East Lansing, MI, 48824, USA
| | - Sithabile Hlahla
- Centre for Transformative Agricultural and Food Systems, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, P/Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Festo Massawe
- School of Biosciences, University of Nottingham Malaysia, Jalan Broga, Seminyih, Selangor Darul Ehsan, Malaysia
| | - Sean Mayes
- Crops for the Future, Jalan Broga, Semenyih, Selangor Darul Ehsan, Malaysia
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire, LE12 5RD, UK
| | - Luxon Nhamo
- International Water Management Institute, Southern Africa (IWMI-SA), 141 Cresswell Street, Silverton, Pretoria, 0184, South Africa
| | - Albert Thembinkosi Modi
- Centre for Transformative Agricultural and Food Systems, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, P/Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa
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Pipatpongpinyo W, Korkmaz U, Wu H, Kena A, Ye H, Feng J, Gu XY. Assembling seed dormancy genes into a system identified their effects on seedbank longevity in weedy rice. Heredity (Edinb) 2019; 124:135-145. [PMID: 31391557 DOI: 10.1038/s41437-019-0253-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 11/09/2022] Open
Abstract
Seed dormancy (SD) and longevity (SL) may share developmental and genetic mechanisms, as both traits are developed in the same maternal environment and evolved to coordinate the timing of germination and the life span of seedbanks. To test the hypothesis, allelic variants at the SD1-2, 7-1, 7-2, and 12 loci from weedy and cultivated rice (Oryza sativa) were assembled into the same genetic background, and 16 homozygous lines selected as a tetragenic system. These lines were evaluated for SD measured by germination at 7, 21, 35, and 150 days of after-ripening (DAR), and for SL measured by the seed decay rate and survivability in the soil of a rice field for 7 months. Pyramiding the alleles from weedy rice lengthened the dormancy duration, and seeds survived in the soil remained dormant at the excavation. Germination levels at 7 to 150 DAR were correlated positively with the seed decay rate (r = 0.41-0.53) and negatively with the survivability (r = -0.45 to -0.28) in the tetragenic system. All four loci contributed to genotypic variation for each of the SD and SL measurements through main and/or epistatic (two- to four-order interactions) effects. SD7-1 (identical to the pericarp color gene Rc) played a major role in regulating seedbank longevity when interacted with the other SD gene(s). This research provided evidence that natural genes controlling SD are involved in regulation of soil seedbank longevity. Thus, accumulation of SD genes in a population could result in persistence of wild plants and weeds in conventional tillage systems.
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Affiliation(s)
- Wirat Pipatpongpinyo
- Agronomy, Horticulture and Plant Science Department, South Dakota State University, Brookings, SD, USA
| | - Ugur Korkmaz
- Agronomy, Horticulture and Plant Science Department, South Dakota State University, Brookings, SD, USA
| | - Hao Wu
- Agronomy, Horticulture and Plant Science Department, South Dakota State University, Brookings, SD, USA
| | - Alexander Kena
- Agronomy, Horticulture and Plant Science Department, South Dakota State University, Brookings, SD, USA
| | - Heng Ye
- Agronomy, Horticulture and Plant Science Department, South Dakota State University, Brookings, SD, USA
| | - Jiuhuan Feng
- Agronomy, Horticulture and Plant Science Department, South Dakota State University, Brookings, SD, USA
| | - Xing-You Gu
- Agronomy, Horticulture and Plant Science Department, South Dakota State University, Brookings, SD, USA.
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44
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Luo Y, Bai R, Li J, Yang W, Li R, Wang Q, Zhao G, Duan D. The transcription factor MYB15 is essential for basal immunity (PTI) in Chinese wild grape. PLANTA 2019; 249:1889-1902. [PMID: 30864013 DOI: 10.1007/s00425-019-03130-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 03/05/2019] [Indexed: 05/14/2023]
Abstract
MYB15 promoter of Vitis quinquangularis has potential as a target for disease resistance breeding, and its involvement in PTI is associated with a range of defense mechanisms. China is a center of origin for Vitis and is home to diverse wild Vitis genotypes, some of which show superior pathogen resistance, although the underlying molecular basis for this has not yet been elucidated. In the current study, we identified a transcription factor, MYB15, from the Chinese wild grape, Vitis quinquangularis, whose promoter region (pVqMYB15) was shown to be induced by basal immunity (also called PAMP-triggered immunity, PTI) triggered by flg22, following heterologous expression in Nicotiana benthamiana and homologous expression in grapevine. By analyzing the promoter structure and activity, we identified a unique 283 bp sequence that plays a key role in the activation of basal immunity. In addition, we showed that activation of the MYB15 promoter correlates with differences in the expression of MYB15 and RESVERATROL SYNTHASE (RS) induced by the flg22 elicitor. We further tested whether the MYB15 induction triggered by flg22 was consistent with MYB15 and RS expression following inoculation with Plasmopara viticola in grape (V. quinquangularis and Vitis vinifera) leaves. Mapping upstream signals, we found that calcium influx, an RboH-dependent oxidative burst, an MAPK cascade, and jasmonate and salicylic acid co-contributed to flg22-triggered pVqMYB15 activation. Our data suggest that the MYB15 promoter has potential as a target for disease resistance breeding, and its involvement in PTI is associated with a range of defense mechanisms.
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Affiliation(s)
- Yangyang Luo
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Ru Bai
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Jing Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Weidong Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Ruixiang Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Qingyang Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Guifang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Dong Duan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China.
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Discordant Patterns of Introgression Suggest Historical Gene Flow into Thai Weedy Rice from Domesticated and Wild Relatives. J Hered 2019; 110:601-609. [DOI: 10.1093/jhered/esz030] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/04/2019] [Indexed: 12/12/2022] Open
Abstract
Abstract
Weedy relatives of crop species infest agricultural fields worldwide, reducing harvests and threatening global food security. These weeds can potentially evolve and adapt through gene flow from both domesticated crop varieties and reproductively compatible wild relatives. We studied populations of weedy rice in Thailand to investigate the role of introgression from cultivated and wild rice in their evolution. We examined 2 complementary sources of genetic data: allelic variation at 3 rice domestication genes (Bh4, controlling hull color; Rc, controlling pericarp color and seed dormancy; and sh4, controlling seed shattering), and 12 previously published SSR markers. Sampling spanned 3 major rice growing regions in Thailand (Lower North, North East, and Central Plain) and included 124 cultivated rice accessions, 166 weedy rice accessions, and 98 wild rice accessions. Weedy rice strains were overall closely related to the cultivated varieties with which they co-occur. Domestication gene data revealed potential adaptive introgression of sh4 shattering alleles from wild rice. Introgression of potentially maladaptive rc crop alleles (conferring reduced dormancy) was also detected, with the frequency of the crop allele highest in northern populations. Although SSR markers also indicated introgression into weed populations from wild and cultivated rice, there was little overlap with domestication genes in the accessions showing admixed ancestry. This suggests that much of the introgression we detected at domestication genes most likely reflects past introgression rather than recent gene flow. This finding has implications for understanding long-term gene flow dynamics between rice and its weedy and wild relatives, including potential risks of transgene escape.
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Sun J, Ma D, Tang L, Zhao M, Zhang G, Wang W, Song J, Li X, Liu Z, Zhang W, Xu Q, Zhou Y, Wu J, Yamamoto T, Dai F, Lei Y, Li S, Zhou G, Zheng H, Xu Z, Chen W. Population Genomic Analysis and De Novo Assembly Reveal the Origin of Weedy Rice as an Evolutionary Game. MOLECULAR PLANT 2019; 12:632-647. [PMID: 30710646 DOI: 10.1016/j.molp.2019.01.019] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 01/23/2019] [Accepted: 01/23/2019] [Indexed: 05/27/2023]
Abstract
Crop weediness, especially that of weedy rice (Oryza sativa f. spontanea), remains mysterious. Weedy rice possesses robust ecological adaptability; however, how this strain originated and gradually formed proprietary genetic features remains unclear. Here, we demonstrate that weedy rice at Asian high latitudes (WRAH) is phylogenetically well defined and possesses unselected genomic characteristics in many divergence regions between weedy and cultivated rice. We also identified novel quantitative trait loci underlying weedy-specific traits, and revealed that a genome block on the end of chromosome 1 is associated with rice weediness. To identify the genomic modifications underlying weedy rice evolution, we generated the first de novo assembly of a high-quality weedy rice genome (WR04-6), and conducted a comparative genomics study between WR04-6 with other rice reference genomes. Multiple lines of evidence, including the results of demographic scenario comparisons, suggest that differentiation between weedy rice and cultivated rice was initiated by genetic improvement of cultivated rice and that the essence of weediness arose through semi-domestication. A plant height model further implied that the origin of WRAH can be modeled as an evolutionary game and indicated that strategy-based selection driven by fitness shaped its genomic diversity.
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Affiliation(s)
- Jian Sun
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Dianrong Ma
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Liang Tang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Minghui Zhao
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Guangchen Zhang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Wenjia Wang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Jiayu Song
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Xiang Li
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Zimeng Liu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Wenxing Zhang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Quan Xu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Yuncheng Zhou
- College of Information and Electrical Engineering, Shenyang Agricultural University, Shenyang, China
| | - Jianzhong Wu
- Institute of Crop Science, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Toshio Yamamoto
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Fei Dai
- Department of Agronomy, Zhejiang Key Lab of Crop Germplasm, Zhejiang University, Hangzhou, China
| | - Yan Lei
- Biomarker Technologies Corporation, Beijing, China
| | - Song Li
- Biomarker Technologies Corporation, Beijing, China
| | - Gang Zhou
- Biomarker Technologies Corporation, Beijing, China
| | | | - Zhengjin Xu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Wenfu Chen
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China.
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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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Chen E, Huang X, Tian Z, Wing RA, Han B. The Genomics of Oryza Species Provides Insights into Rice Domestication and Heterosis. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:639-665. [PMID: 31035826 DOI: 10.1146/annurev-arplant-050718-100320] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Here, we review recent progress in genetic and genomic studies of the diversity of Oryza species. In recent years, unlocking the genetic diversity of Oryza species has provided insights into the genomics of rice domestication, heterosis, and complex traits. Genome sequencing and analysis of numerous wild rice (Oryza rufipogon) and Asian cultivated rice (Oryza sativa) accessions have enabled the identification of genome-wide signatures of rice domestication and the unlocking of the origin of Asian cultivated rice. Moreover, similar studies on genome variations of African rice (Oryza glaberrima) cultivars and their closely related wild progenitor Oryza barthii accessions have provided strong evidence to support a theory of independent domestication in African rice. Integrated genomic approaches have efficiently investigated many heterotic loci in hybrid rice underlying yield heterosis advantages and revealed the genomic architecture of rice heterosis. We conclude that in-depth unlocking of genetic variations among Oryza species will further enhance rice breeding.
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Affiliation(s)
- Erwang Chen
- National Center of Plant Gene Research; Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences; and CAS Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200233, China;
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Xuehui Huang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China;
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA;
| | - Bin Han
- National Center of Plant Gene Research; Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences; and CAS Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200233, China;
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49
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Seabra SG, Silva SE, Nunes VL, Sousa VC, Martins J, Marabuto E, Rodrigues ASB, Pina‐Martins F, Laurentino TG, Rebelo MT, Figueiredo E, Paulo OS. Genomic signatures of introgression between commercial and native bumblebees, Bombus terrestris, in western Iberian Peninsula-Implications for conservation and trade regulation. Evol Appl 2019; 12:679-691. [PMID: 30976302 PMCID: PMC6439495 DOI: 10.1111/eva.12732] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 10/24/2018] [Accepted: 10/27/2018] [Indexed: 01/02/2023] Open
Abstract
Human-mediated introductions of species may have profound impacts on native ecosystems. One potential impact with largely unforeseen consequences is the potential admixture of introduced with autochthonous species through hybridization. Throughout the world, bumblebees have been deliberately introduced for crop pollination with known negative impacts on native pollinators. Given the likely allochthonous origin of commercial bumblebees used in Portugal (subspecies Bombus terrestris terrestris and B. t. dalmatinus), our aim was to assess their putative introgression with the native Iberian subspecies B. terrestris lusitanicus. We analysed one mitochondrial gene, cytochrome c oxidase subunit I (COX1) and genomic data involving thousands of genome-wide restriction-site-associated DNA markers (RAD-seq). In the mitochondrial COX1 analyses, we detected one relatively common haplotype in commercial bumblebees, also present in wild samples collected nearby the greenhouses where the commercial hives are used. In the RAD-seq analysis, we found a clear genetic differentiation between native and commercial lineages. Furthermore, we detected candidate hybrids in the wild, as well as putatively escaped commercial bumblebees, some of which being potentially fertile males. Although we cannot assess directly the fitness effects of introgressed alleles, there is a risk of maladaptive allele introgression to the local bumblebee subspecies, which can negatively impact autochthon populations. One immediate recommendation to farmers is for the proper disposal of hive boxes, after their use in greenhouses, so as to minimize the risk of escapees contaminating native populations. On the other hand, the feasibility of using local subspecies B. t. lusitanicus, preferably with local production, should be evaluated.
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Affiliation(s)
- Sofia G. Seabra
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Sara E. Silva
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Vera L. Nunes
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Vitor C. Sousa
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Joana Martins
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de AgronomiaUniversidade de LisboaLisboaPortugal
- Present address:
SAPEC AgroLisboaPortugal
| | - Eduardo Marabuto
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Ana S. B. Rodrigues
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Natural History and Systematics (NHS) Research Group /MUHNAC ‐ Museu Nacional de História Natural e da CiênciaUniversidade de LisboaLisboaPortugal
| | - Francisco Pina‐Martins
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | | | - Maria Teresa Rebelo
- Centre for Environmental and Marine Studies (CESAM), Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Elisabete Figueiredo
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de AgronomiaUniversidade de LisboaLisboaPortugal
| | - Octávio S. Paulo
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
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50
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Yan Y, Chao J, Wang Y, Mo S, Kong M, Shi Z, Song X, Qiang S, Dai W.
WA
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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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