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Presotto A, Hernández F, Vercellino RB, Kruger RD, Fontana ML, Ureta MS, Crepy M, Auge G, Caicedo A. Introgression from local cultivars is a driver of agricultural adaptation in Argentinian weedy rice. Mol Ecol 2024; 33:e17368. [PMID: 38676602 DOI: 10.1111/mec.17368] [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: 09/30/2023] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/29/2024]
Abstract
Weedy rice, a pervasive and troublesome weed found across the globe, has often evolved through fertilization of rice cultivars with little importance of crop-weed gene flow. In Argentina, weedy rice has been reported as an important constraint since the early 1970s, and, in the last few years, strains with herbicide-resistance are suspected to evolve. Despite their importance, the origin and genetic composition of Argentinian weedy rice as well its adaptation to agricultural environments has not been explored so far. To study this, we conducted genotyping-by-sequencing on samples of Argentinian weedy and cultivated rice and compared them with published data from weedy, cultivated and wild rice accessions distributed worldwide. In addition, we conducted a phenotypic characterization for weedy-related traits, a herbicide resistance screening and genotyped accessions for known mutations in the acetolactate synthase (ALS) gene, which confers herbicide resistance. Our results revealed large phenotypic variability in Argentinian weedy rice. Most strains were resistant to ALS-inhibiting herbicides with a high frequency of the ALS mutation (A122T) present in Argentinian rice cultivars. Argentinian cultivars belonged to the three major genetic groups of rice: japonica, indica and aus while weeds were mostly aus or aus-indica admixed, resembling weedy rice strains from the Southern Cone region. Phylogenetic analysis supports a single origin for aus-like South American weeds, likely as seed contaminants from the United States, and then admixture with local indica cultivars. Our findings demonstrate that crop to weed introgression can facilitate rapid adaptation to agriculture environments.
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Affiliation(s)
- Alejandro Presotto
- Departamento de Agronomía, CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | - Fernando Hernández
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Román Boris Vercellino
- Departamento de Agronomía, CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | | | | | - María Soledad Ureta
- Departamento de Agronomía, CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | - María Crepy
- EEA INTA Concepción del Uruguay-CONICET, Concepción del Uruguay, Entre Ríos, Argentina
| | - Gabriela Auge
- Centro de Investigaciones en Ciencias Agronómicas y Veterinarias (CICVyA), Instituto de Agrobiotecnología y Biología Molecular (IABIMO) - (INTA-CONICET), Instituto de Biotecnología, Hurlingham, Buenos Aires, Argentina
| | - Ana Caicedo
- Deparment of Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
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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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Deng XL, Li JQ, Yi JM, Lian RJ, Zhang ZY, Li JH, He S, Bai LY. A pH-responsive MOF-functionalized hollow mesoporous silica controlled herbicide delivery system exhibits enhanced activity against ACCase-herbicide-resistant weeds. PEST MANAGEMENT SCIENCE 2023; 79:5237-5249. [PMID: 37595063 DOI: 10.1002/ps.7729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 08/20/2023]
Abstract
BACKGROUND Weeds grow aggressively in agricultural fields, leading to reduced crop yields and an inability to meet the growing demand for food. Herbicides are currently the most effective method for weed control. However, the overuse of herbicides has resulted in the evolution of resistance mutants and has caused environmental pollution. Therefore, new technologies are urgently required to address this global challenge. RESULTS We report a copper-benzene-1,4-dicarboxylate metal organic framework (Cu-BDC MOF)-functionalized carboxyl hollow mesoporous silica (HMS-COOH) delivery system for the pH-controlled release of the acetyl-CoA carboxylase (ACCase)-inhibiting herbicide quizalofop-p-ethyl (QE). The delivery system (QE@HMS@Cu-BDC) enabled the efficient control of barnyard grasses that are susceptible and resistant to ACCase-inhibiting herbicides, which showed 93.33% and 88.33% FW control efficacy at 67.5 g ha-1 , respectively. With the lowest pH value (3), QE and copper ion were released slowly to total 70.30% and 78.55% levels (respectively) from QE@HMS@Cu-BDC after 89 h. QE@HMS@Cu-BDC showed better absorption, conduction, transportation and ACCase activity inhibition performance than that of QE emulsifiable concentrate (EC) in both susceptible and ACCase-herbicide resistant barnyard grasses. In addition, with the safener effect of carrier HMS@Cu-BDC and the aid of the safener fenchlorazole-ethyl (FE), the application of QE@HMS@Cu-BDC was shown to mitigate the damage caused by QE to rice plants. CONCLUSION This work found that the new material HMS-COOH@Cu-BDC can be used to mitigate herbicide-induced oxidative stress and improve rice plant safety. Futhermore, the QE@HMS-COOH@Cu-BDC constructed in this research might be used as an efficient nanopesticide formulation for weed controls in paddy rice fields. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Xi-le Deng
- Key Laboratory for Biology and Control of Weeds, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Jia-Qing Li
- The Center of Crop Nanobiotechnology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ji-Ming Yi
- College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Ren-Jie Lian
- The Center of Crop Nanobiotechnology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhao-Yang Zhang
- The Center of Crop Nanobiotechnology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jian-Hong Li
- The Center of Crop Nanobiotechnology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shun He
- The Center of Crop Nanobiotechnology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Lian-Yang Bai
- Key Laboratory for Biology and Control of Weeds, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
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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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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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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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