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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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2
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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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3
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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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Osakina A, Jia Y. Genetic Diversity of Weedy Rice and Its Potential Application as a Novel Source of Disease Resistance. PLANTS (BASEL, SWITZERLAND) 2023; 12:2850. [PMID: 37571004 PMCID: PMC10421194 DOI: 10.3390/plants12152850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/13/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023]
Abstract
Weeds that infest crops are a primary factor limiting agricultural productivity worldwide. Weedy rice, also called red rice, has experienced independent evolutionary events through gene flow from wild rice relatives and de-domestication from cultivated rice. Each evolutionary event supplied/equipped weedy rice with competitive abilities that allowed it to thrive with cultivated rice and severely reduce yields in rice fields. Understanding how competitiveness evolves is important not only for noxious agricultural weed management but also for the transfer of weedy rice traits to cultivated rice. Molecular studies of weedy rice using simple sequence repeat (SSR), restriction fragment length polymorphism (RFLP), and whole-genome sequence have shown great genetic variations in weedy rice populations globally. These variations are evident both at the whole-genome and at the single-allele level, including Sh4 (shattering), Hd1 (heading and flowering), and Rc (pericarp pigmentation). The goal of this review is to describe the genetic diversity of current weedy rice germplasm and the significance of weedy rice germplasm as a novel source of disease resistance. Understanding these variations, especially at an allelic level, is also crucial as individual loci that control important traits can be of great target to rice breeders.
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Affiliation(s)
- Aron Osakina
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA;
- USDA ARS Dale Bumpers National Rice Research Center, Stuttgart, AR 72160, USA
| | - Yulin Jia
- USDA ARS Dale Bumpers National Rice Research Center, Stuttgart, AR 72160, USA
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5
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Horvath DP, Clay SA, Swanton CJ, Anderson JV, Chao WS. Weed-induced crop yield loss: a new paradigm and new challenges. TRENDS IN PLANT SCIENCE 2023; 28:567-582. [PMID: 36610818 DOI: 10.1016/j.tplants.2022.12.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 05/22/2023]
Abstract
Direct competition for resources is generally considered the primary mechanism for weed-induced yield loss. A re-evaluation of physiological evidence suggests weeds initially impact crop growth and development through resource-independent interference. We suggest weed perception by crops induce a shift in crop development, before resources become limited, which ultimately reduce crop yield, even if weeds are subsequently removed. We present the mechanisms by which crops perceive and respond to weeds and discuss the technologies used to identify these mechanisms. These data lead to a fundamental paradigm shift in our understanding of how weeds reduce crop yield and suggest new research directions and opportunities to manipulate or engineer crops and cropping systems to reduce weed-induced yield losses.
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Affiliation(s)
- David P Horvath
- USDA-ARS Edward T. Schafer Agricultural Research Center, Fargo, ND, USA.
| | | | | | - James V Anderson
- USDA-ARS Edward T. Schafer Agricultural Research Center, Fargo, ND, USA
| | - Wun S Chao
- USDA-ARS Edward T. Schafer Agricultural Research Center, Fargo, ND, USA
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6
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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: 4] [Impact Index Per Article: 4.0] [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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7
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Common evolutionary trajectory of short life-cycle in Brassicaceae ruderal weeds. Nat Commun 2023; 14:290. [PMID: 36653415 PMCID: PMC9849336 DOI: 10.1038/s41467-023-35966-7] [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: 05/27/2022] [Accepted: 01/10/2023] [Indexed: 01/19/2023] Open
Abstract
Weed species are detrimental to crop yield. An understanding of how weeds originate and adapt to field environments is needed for successful crop management and reduction of herbicide use. Although early flowering is one of the weed trait syndromes that enable ruderal weeds to overcome frequent disturbances, the underlying genetic basis is poorly understood. Here, we establish Cardamine occulta as a model to study weed ruderality. By genome assembly and QTL mapping, we identify impairment of the vernalization response regulator gene FLC and a subsequent dominant mutation in the blue-light receptor gene CRY2 as genetic drivers for the establishment of short life cycle in ruderal weeds. Population genomics study further suggests that the mutations in these two genes enable individuals to overcome human disturbances through early deposition of seeds into the soil seed bank and quickly dominate local populations, thereby facilitating their spread in East China. Notably, functionally equivalent dominant mutations in CRY2 are shared by another weed species, Rorippa palustris, suggesting a common evolutionary trajectory of early flowering in ruderal weeds in Brassicaceae.
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Zhao H, Liu Y, Jia MH, Jia Y. An Allelic Variant of the Broad-Spectrum Blast Resistance Gene Ptr in Weedy Rice Is Associated with Resistance to the Most Virulent Blast Race IB-33. PLANT DISEASE 2022; 106:1675-1680. [PMID: 34962412 DOI: 10.1094/pdis-09-21-2043-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Rice resistance (R) genes have been effectively deployed to prevent blast disease caused by the fungal pathogen Magnaporthe oryzae, one of the most serious threats for stable rice production worldwide. Weedy rice competing with cultivated rice may carry novel or lost R genes. The quantitative trait locus qBR12.3b was previously mapped between two single nucleotide polymorphism markers at the 10,633,942-bp and 10,820,033-bp genomic positions in a black-hull-awned (BHA) weed strain using a weed-crop-mapping population under greenhouse conditions. In this study, we found a portion of the known resistance gene Ptr encoding a protein with four armadillo repeats and confers a broad spectrum of blast resistance. We then analyzed the sequences of the Ptr gene from weedy rice, PtrBHA, and identified a unique amino acid glutamine at protein position 874. Minor changes of protein conformation of the PtrBHA gene were predicted through structural analysis of PtrBHA, suggesting that the product of PtrBHA is involved in disease resistance. A gene-specific codominant marker HJ17-13 from PtrBHA was then developed to distinguish alleles in weeds and crops. The PtrBHA gene existed in 207 individuals of the same mapping population, where qBR12.3b was mapped using this gene-specific marker. Disease reactions of 207 individuals and their parents to IB-33 were evaluated. The resistant individuals had PtrBHA whereas the susceptible individuals did not, suggesting that HJ17-13 is reliable to predict qBR12.3b. Taken together, this newly developed marker, and weedy rice genotypes carrying qBR12.3b, are useful for blast improvement using marker assisted selection.
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Affiliation(s)
- Haijun Zhao
- Dale Bumpers National Rice Research Center, Agricultural Research Service, U.S. Department of Agriculture, Stuttgart, AR 72160
- Noble Research Institute LLC, Ardmore, OK 73401
| | - Yan Liu
- Rice Research and Extension Center, University of Arkansas, Stuttgart, AR 72160
- Washington State University, Pullman, WA 99164
| | - Melissa H Jia
- Dale Bumpers National Rice Research Center, Agricultural Research Service, U.S. Department of Agriculture, Stuttgart, AR 72160
| | - Yulin Jia
- Dale Bumpers National Rice Research Center, Agricultural Research Service, U.S. Department of Agriculture, Stuttgart, AR 72160
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Whole-Genome Sequencing and RNA-Seq Reveal Differences in Genetic Mechanism for Flowering Response between Weedy Rice and Cultivated Rice. Int J Mol Sci 2022; 23:ijms23031608. [PMID: 35163531 PMCID: PMC8836195 DOI: 10.3390/ijms23031608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/16/2022] [Accepted: 01/26/2022] [Indexed: 02/01/2023] Open
Abstract
Flowering is a key agronomic trait that influences adaptation and productivity. Previous studies have indicated the genetic complexity associated with the flowering response in a photoinsensitive weedy rice accession PSRR-1 despite the presence of a photosensitive allele of a key flowering gene Hd1. In this study, we used whole-genome and RNA sequencing data from both cultivated and weedy rice to add further insights. The de novo assembly of unaligned sequences predicted 225 genes, in which 45 were specific to PSRR-1, including two genes associated with flowering. Comparison of the variants in PSRR-1 with the 3K rice genome (RG) dataset identified unique variants within the heading date QTLs. Analyses of the RNA-Seq result under both short-day (SD) and long-day (LD) conditions revealed that many differentially expressed genes (DEGs) colocalized with the flowering QTLs, and some DEGs such as Hd1, OsMADS56, Hd3a, and RFT1 had unique variants in PSRR-1. Ehd1, Hd1, OsMADS15, and OsMADS56 showed different alternate splicing (AS) events between genotypes and day length conditions. OsMADS56 was expressed in PSRR-1 but not in Cypress under both LD and SD conditions. Based on variations in both sequence and expression, the unique flowering response in PSRR-1 may be due to the high-impact variants of flowering genes, and OsMADS56 is proposed as a key regulator for its day-neutral flowering response.
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Islam MS, Coronejo S, Subudhi PK. Whole-genome sequencing reveals uniqueness of black-hulled and straw-hulled weedy rice genomes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2461-2475. [PMID: 32488303 DOI: 10.1007/s00122-020-03611-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 05/13/2020] [Indexed: 05/22/2023]
Abstract
Both SH and BHA weedy rice genotypes evolved independently and have distinct genomic composition. Different genetic mechanisms may be responsible for their competitiveness and adaptation to diverse environmental conditions. Two major types of weedy rice are recognized in the USA based on morphology: straw-hull (SH) and black-hull awned (BHA) weedy rice. We performed whole-genome resequencing of a SH weedy rice 'PSRR-1', a BHA weedy rice 'BHA1115', and a japonica cultivar 'Cypress' to delineate genome-wide differences and their relevance to genetics and evolution of weedy attributes. The high-quality reads were uniformly distributed with 82-88% genome coverage. The number of genotype-specific SNPs and InDels was highest in Cypress, followed by BHA1115 and PSRR-1. However, more genes were affected in BHA1115 compared with other two genotypes which is evident from the number of high-impact SNPs and InDels. Haplotype analysis of selected genes involved in domestication, adaptation, and agronomic performance not only differentiated SH from BHA weedy rice and supported evolution of weedy rice through de-domestication, but also validated the function of several genes such as qAn-1, qAn-2, Bh4, Rc, SD1, OsLG1, and OsC1. Several candidate genes were identified for previously reported seed dormancy and seed shattering QTLs. The SH and BHA weedy rice have distinct genomic composition, and the BHA weedy rice likely diverged earlier than SH weedy rice. The accumulation of plant development, reproduction, and defense-related genes in weedy rice possibly helped them to compete, survive, and spread under a wide range of environmental conditions by employing novel and diverse mechanisms. The genomic resources will be useful for both weed management and rice improvement by exploring the molecular basis of key agronomic, adaptive, and domestication attributes.
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Affiliation(s)
- Md Shofiqul Islam
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Sapphire Coronejo
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Prasanta Kumar Subudhi
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA.
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11
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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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12
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Goad DM, Jia Y, Gibbons A, Liu Y, Gealy D, Caicedo AL, Olsen KM. Identification of Novel QTL Conferring Sheath Blight Resistance in Two Weedy Rice Mapping Populations. RICE (NEW YORK, N.Y.) 2020; 13:21. [PMID: 32206941 PMCID: PMC7090113 DOI: 10.1186/s12284-020-00381-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 03/06/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Rice sheath blight (ShB) disease, caused by the pathogenic fungus Rhizoctonia solani, causes significant yield losses globally. US weedy rice populations, which are de-domesticated forms of indica and aus cultivated rice, appear to be more resistant to ShB than local japonica cultivated rice. We mapped quantitative trait loci (QTL) associated with ShB resistance using two F8 recombinant inbred line populations generated from crosses of an indica crop variety, Dee-Geo-Woo-Gen (DGWG), with individuals representing the two major US weed biotypes, straw hull (SH) and black hull awned (BHA). RESULTS We identified nine ShB resistance QTL across both mapping populations. Five were attributable to alleles that affect plant height (PH) and heading date (HD), two growth traits that are known to be highly correlated with ShB resistance. By utilizing an approach that treated growth traits as covariates in the mapping model, we were able to infer that the remaining four QTL are involved in ShB resistance. Two of these, qShB1-2 and qShB4, are different from previously identified ShB QTL and represent new candidates for further study. CONCLUSION Our findings suggest that ShB resistance can be improved through favorable plant growth traits and the combined effects of small to moderate-effect resistance QTL. Additionally, we show that including PH and HD as covariates in QTL mapping models is a powerful way to identify new ShB resistance QTL.
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Affiliation(s)
- David M Goad
- Department of Biology, Washington University in St. Louis, 1 Brookings Drive, Campus Box 1137, St. Louis, MO, 63110, USA
| | - Yulin Jia
- United States Department of Agriculture-Agricultural Research Service, Dale Bumpers National Rice Research Center, 2890 HWY 130 E, Stuttgart, AR, 72160, USA.
| | - Andrew Gibbons
- University of Arkansas Rice Research and Extension Center, 2900 AR-130, Stuttgart, AR, 72160, USA
- Present address: Arkansas Department of Health, Little Rock, AR, 72205, USA
| | - Yan Liu
- Present address: Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA
| | - David Gealy
- United States Department of Agriculture-Agricultural Research Service, Dale Bumpers National Rice Research Center, 2890 HWY 130 E, Stuttgart, AR, 72160, USA
| | - Ana L Caicedo
- Department of Biology, University of Massachusetts, Amherst, USA
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, 1 Brookings Drive, Campus Box 1137, St. Louis, MO, 63110, USA
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13
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Chai C, Shankar R, Jain M, Subudhi PK. Genome-wide discovery of DNA polymorphisms by whole genome sequencing differentiates weedy and cultivated rice. Sci Rep 2018; 8:14218. [PMID: 30242197 PMCID: PMC6155081 DOI: 10.1038/s41598-018-32513-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 09/10/2018] [Indexed: 12/13/2022] Open
Abstract
Analyzing the genome level DNA polymorphisms between weedy and cultivated rice is crucial to elucidate the molecular basis of weedy and agronomic traits, which in turn can enhance our ability to control weedy rice and its utilization for rice improvement. Here, we presented the genome-wide genetic variations between a weedy rice accession PSRR-1 and two cultivated rice accessions, Bengal and Nona Bokra, belonging to japonica and indica subspecies, respectively. The total number of SNPs and InDels in PSRR/Bengal was similar to that of Nona Bokra/Bengal, but was three times greater than that of PSRR/Nona Bokra. There were 11546 large-effect SNPs/InDels affecting 5673 genes, which most likely differentiated weedy rice from cultivated rice. These large effect DNA polymorphisms were mostly resulted in stop codon gain and least by start codon loss. Analysis of the molecular functions and biological processes of weedy rice specific SNPs/InDels indicated that most of these genes were involved in protein modification/phosphorylation, protein kinase activity, and protein/nucleotide binding. By integrating previous QTL mapping results with the DNA polymorphisms data, the candidate genes for seed dormancy and seed shattering were narrowed down. The genomic resource generated in this study will facilitate discovery of functional variants for weedy and agronomic traits.
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Affiliation(s)
- Chenglin Chai
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Rama Shankar
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Prasanta K Subudhi
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA.
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Zhao C, Xu W, Song X, Dai W, Dai L, Zhang Z, Qiang S. Early flowering and rapid grain filling determine early maturity and escape from harvesting in weedy rice. PEST MANAGEMENT SCIENCE 2018; 74:465-476. [PMID: 28902454 DOI: 10.1002/ps.4730] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/25/2017] [Accepted: 09/08/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Early maturity is an important trait that is essential to the survival of weedy rice. To explore the mechanism of early maturity in weedy rice, the reproductive development of a large sample of weedy rice accessions and cultivars was compared in a common garden study. A selected sample of both weedy and cultivated rice was sown at different dates in two years to study in more detail their flowering and grain-filling patterns. RESULTS The weedy rice from three major cropping regions matured 7-8 days earlier than their associated cultivars. Representative weedy rice accessions planted on conventional sowing dates flowered 3-26 days earlier than cultivars; delayed sowing caused divergence in the flowering regimes in weedy rice. However, regardless of the sowing date, weedy rice filled its grain 7-21 days faster than cultivars in both study years. Vegetative and reproductive traits of weedy and cultivated rice have different patterns of variation with delayed planting. CONCLUSION Early maturity is an essential factor determining the persistence of weedy rice by contributing to the escape of its seed from being harvested with the rice crop. Both early flowering and shorter grain-filling stages determine early maturity, and flowering is more plastic than grain filling. © 2017 Society of Chemical Industry.
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Affiliation(s)
- Can Zhao
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing, P. R. China
| | - Wenrong Xu
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing, P. R. China
| | - Xiaoling Song
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing, P. R. China
| | - Weimin Dai
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing, P. R. China
| | - Lei Dai
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing, P. R. China
- College of Life Science and Technology, Henan Institute Science and Technology, Xinxiang, P. R. China
| | - Zheng Zhang
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing, P. R. China
| | - Sheng Qiang
- Weed Research Laboratory, Nanjing Agricultural University, Nanjing, P. R. China
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15
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Qiu J, Zhou Y, Mao L, Ye C, Wang W, Zhang J, Yu Y, Fu F, Wang Y, Qian F, Qi T, Wu S, Sultana MH, Cao YN, Wang Y, Timko MP, Ge S, Fan L, Lu Y. Genomic variation associated with local adaptation of weedy rice during de-domestication. Nat Commun 2017; 8:15323. [PMID: 28537247 PMCID: PMC5477509 DOI: 10.1038/ncomms15323] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 03/17/2017] [Indexed: 11/09/2022] Open
Abstract
De-domestication is a unique evolutionary process by which domesticated crops are converted into ‘wild predecessor like' forms. Weedy rice (Oryza sativa f. spontanea) is an excellent model to dissect the molecular processes underlying de-domestication. Here, we analyse the genomes of 155 weedy and 76 locally cultivated rice accessions from four representative regions in China that were sequenced to an average 18.2 × coverage. Phylogenetic and demographic analyses indicate that Chinese weedy rice was de-domesticated independently from cultivated rice and experienced a strong genetic bottleneck. Although evolving from multiple origins, critical genes underlying convergent evolution of different weedy types can be found. Allele frequency analyses suggest that standing variations and new mutations contribute differently to japonica and indica weedy rice. We identify a Mb-scale genomic region present in weedy rice but not cultivated rice genomes that shows evidence of balancing selection, thereby suggesting that there might be more complexity inherent to the process of de-domestication. De-domestication is the process by which cultivated plants adopt characteristics similar to that of their wild predecessors. Here Qiu et al. re-sequence de-domesticated weedy rice and matched cultivated varieties and identify genetic variants indicative of convergent evolution across multiple de-domestication events.
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Affiliation(s)
- Jie Qiu
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yongjun Zhou
- China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Lingfeng Mao
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chuyu Ye
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Weidi Wang
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jianping Zhang
- China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Yongyi Yu
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Fei Fu
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yunfei Wang
- Zhejiang Sheng Ting Biotechnology Co., Ltd., Taizhou 318020, China
| | - Feijian Qian
- Zhejiang Sheng Ting Biotechnology Co., Ltd., Taizhou 318020, China
| | - Ting Qi
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Sanling Wu
- Analysis Center of Agrobiology and Environmental Sciences, Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University, Hangzhou 310058, China
| | - Most Humaira Sultana
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ya-Nan Cao
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, Zhejiang University, Hangzhou 310058, China
| | - Yu Wang
- Department of Biology, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Longjiang Fan
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yongliang Lu
- China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
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16
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Huang Z, Young ND, Reagon M, Hyma KE, Olsen KM, Jia Y, Caicedo AL. All roads lead to weediness: Patterns of genomic divergence reveal extensive recurrent weedy rice origins from South Asian
Oryza. Mol Ecol 2017; 26:3151-3167. [DOI: 10.1111/mec.14120] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 01/21/2017] [Accepted: 03/10/2017] [Indexed: 01/28/2023]
Affiliation(s)
- Zhongyun Huang
- Department of Biology University of Massachusetts Amherst MA USA
| | - Nelson D. Young
- Department of Biology University of Massachusetts Amherst MA USA
| | - Michael Reagon
- Department of Biology Ohio State University Lima Lima OH USA
| | - Katie E. Hyma
- Department of Biology University of Massachusetts Amherst MA USA
| | | | - Yulin Jia
- Dale Bumpers National Rice Research Center USDA‐ARS Stuttgart AR USA
| | - Ana L. Caicedo
- Department of Biology University of Massachusetts Amherst MA USA
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17
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Kanapeckas KL, Vigueira CC, Ortiz A, Gettler KA, Burgos NR, Fischer AJ, Lawton-Rauh AL. Escape to Ferality: The Endoferal Origin of Weedy Rice from Crop Rice through De-Domestication. PLoS One 2016; 11:e0162676. [PMID: 27661982 PMCID: PMC5035073 DOI: 10.1371/journal.pone.0162676] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 08/26/2016] [Indexed: 11/30/2022] Open
Abstract
Domestication is the hallmark of evolution and civilization and harnesses biodiversity through selection for specific traits. In regions where domesticated lines are grown near wild relatives, congeneric sources of aggressive weedy genotypes cause major economic losses. Thus, the origins of weedy genotypes where no congeneric species occur raise questions regarding management effectiveness and evolutionary mechanisms responsible for weedy population success. Since eradication in the 1970s, California growers avoided weedy rice through continuous flood culture and zero-tolerance guidelines, preventing the import, presence, and movement of weedy seeds. In 2003, after decades of no reported presence in California, a weedy rice population was confirmed in dry-seeded fields. Our objectives were to identify the origins and establishment of this population and pinpoint possible phenotypes involved. We show that California weedy rice is derived from a different genetic source among a broad range of AA genome Oryzas and is most recently diverged from O. sativa temperate japonica cultivated in California. In contrast, other weedy rice ecotypes in North America (Southern US) originate from weedy genotypes from China near wild Oryza, and are derived through existing crop-wild relative crosses. Analyses of morphological data show that California weedy rice subgroups have phenotypes like medium-grain or gourmet cultivars, but have colored pericarp, seed shattering, and awns like wild relatives, suggesting that reversion to non-domestic or wild-like traits can occur following domestication, despite apparent fixation of domestication alleles. Additionally, these results indicate that preventive methods focused on incoming weed sources through contamination may miss burgeoning weedy genotypes that rapidly adapt, establish, and proliferate. Investigating the common and unique evolutionary mechanisms underlying global weed origins and subsequent interactions with crop relatives sheds light on how weeds evolve and addresses broader questions regarding the stability of selection during domestication and crop improvement.
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Affiliation(s)
- Kimberly L. Kanapeckas
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
- South Carolina Department of Natural Resources, Marine Resources Research Institute, Charleston, South Carolina, United States of America
| | - Cynthia C. Vigueira
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
- Department of Biology, High Point University, High Point, North Carolina, United States of America
| | - Aida Ortiz
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Kyle A. Gettler
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Nilda R. Burgos
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Albert J. Fischer
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Amy L. Lawton-Rauh
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
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18
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Wei FJ, Tsai YC, Wu HP, Huang LT, Chen YC, Chen YF, Wu CC, Tseng YT, Hsing YIC. Both Hd1 and Ehd1 are important for artificial selection of flowering time in cultivated rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:187-194. [PMID: 26566836 DOI: 10.1016/j.plantsci.2015.09.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 07/31/2015] [Accepted: 09/04/2015] [Indexed: 05/04/2023]
Abstract
Rice is a facultative short-day plant, and it requires a photoperiod shorter than the critical day length to get flowering. Sensitivity to photoperiod has been suggested as a major selection target in cultivated or weedy rice. The modern rice varieties in Taiwan may be cultivated twice a year. These varieties contain loss-of-function of two important flowering-time related genes, Heading date 1 (Hd1) and Early heading date 1 (Ehd1), and are mainly from a mega variety, Taichung 65. However, the parental lines of this variety were sensitive to photoperiod, thus, how Taichung 65 loss its sensitivity is a mystery. In this study, we used accession-specific single nucleotide polymorphism analysis to reveal the gene flow that occurred between different rice accessions decades ago and demonstrate that two landraces introgressed during the breeding process, which led to the loss of photoperiod sensitivity. Both Hd1 and Ehd1 may be important during artificial selection for flowering time, especially in a subtropical region such as Taiwan. This is a good example of introgression playing important roles during rice domestication.
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Affiliation(s)
- Fu-Jin Wei
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan; Department of Agronomy, National Taiwan University, Taipei 106, Taiwan.
| | - Yuan-Ching Tsai
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan.
| | - Hshin-Ping Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan.
| | - Lin-Tzu Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan.
| | - Yu-Chi Chen
- Taiwan International Cooperation and Development Fund, Taipei 111, Taiwan.
| | - Yi-Fang Chen
- Soil and Water Conservation Bureau, Council of Agriculture, Nantou 540, Taiwan.
| | - Cheng-Chieh Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan; Institute of Botany, National Taiwan University, Taipei 106, Taiwan.
| | - Yi-Tzu Tseng
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan; Institute of Botany, National Taiwan University, Taipei 106, Taiwan.
| | - Yue-Ie C Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 115, Taiwan.
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19
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Qi X, Liu Y, Vigueira CC, Young ND, Caicedo AL, Jia Y, Gealy DR, Olsen KM. More than one way to evolve a weed: parallel evolution of US weedy rice through independent genetic mechanisms. Mol Ecol 2015; 24:3329-44. [PMID: 26031196 DOI: 10.1111/mec.13256] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/26/2015] [Accepted: 05/27/2015] [Indexed: 02/06/2023]
Abstract
Many different crop species were selected for a common suite of 'domestication traits', which facilitates their use for studies of parallel evolution. Within domesticated rice (Oryza sativa), there has also been independent evolution of weedy strains from different cultivated varieties. This makes it possible to examine the genetic basis of parallel weed evolution and the extent to which this process occurs through shared genetic mechanisms. We performed comparative QTL mapping of weediness traits using two recombinant inbred line populations derived from crosses between an indica crop variety and representatives of each of the two independently evolved weed strains found in US rice fields, strawhull (S) and blackhull awned (B). Genotyping-by-sequencing provided dense marker coverage for linkage map construction (average marker interval <0.25 cM), with 6016 and 13 730 SNPs mapped in F5 lines of the S and B populations, respectively. For some weediness traits (awn length, hull pigmentation and pericarp pigmentation), QTL mapping and sequencing of underlying candidate genes confirmed that trait variation was largely attributable to individual loci. However, for more complex quantitative traits (including heading date, panicle length and seed shattering), we found multiple QTL, with little evidence of shared genetic bases between the S and B populations or across previous studies of weedy rice. Candidate gene sequencing revealed causal genetic bases for 8 of 27 total mapped QTL. Together these findings suggest that despite the genetic bottleneck that occurred during rice domestication, there is ample genetic variation in this crop to allow agricultural weed evolution through multiple genetic mechanisms.
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Affiliation(s)
- Xinshuai Qi
- Department of Biology, Washington University, St. Louis, MO, 63130, USA
| | - Yan Liu
- Dale Bumpers National Rice Research Center, USDA-ARS, Stuttgart, AR, 72160, USA
| | - Cynthia C Vigueira
- Department of Biology, Washington University, St. Louis, MO, 63130, USA.,Department of Biology, High Point University, High Point, NC, 27268, USA
| | - Nelson D Young
- Department of Biology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Ana L Caicedo
- Department of Biology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Yulin Jia
- Dale Bumpers National Rice Research Center, USDA-ARS, Stuttgart, AR, 72160, USA
| | - David R Gealy
- Dale Bumpers National Rice Research Center, USDA-ARS, Stuttgart, AR, 72160, USA
| | - Kenneth M Olsen
- Department of Biology, Washington University, St. Louis, MO, 63130, USA
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20
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Burgos NR, Singh V, Tseng TM, Black H, Young ND, Huang Z, Hyma KE, Gealy DR, Caicedo AL. The impact of herbicide-resistant rice technology on phenotypic diversity and population structure of United States weedy rice. PLANT PHYSIOLOGY 2014; 166:1208-20. [PMID: 25122473 PMCID: PMC4226343 DOI: 10.1104/pp.114.242719] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Accepted: 08/03/2014] [Indexed: 05/20/2023]
Abstract
The use of herbicide-resistant (HR) Clearfield rice (Oryza sativa) to control weedy rice has increased in the past 12 years to constitute about 60% of rice acreage in Arkansas, where most U.S. rice is grown. To assess the impact of HR cultivated rice on the herbicide resistance and population structure of weedy rice, weedy samples were collected from commercial fields with a history of Clearfield rice. Panicles from each weedy type were harvested and tested for resistance to imazethapyr. The majority of plants sampled had at least 20% resistant offspring. These resistant weeds were 97 to 199 cm tall and initiated flowering from 78 to 128 d, generally later than recorded for accessions collected prior to the widespread use of Clearfield rice (i.e. historical accessions). Whereas the majority (70%) of historical accessions had straw-colored hulls, only 30% of contemporary HR weedy rice had straw-colored hulls. Analysis of genotyping-by-sequencing data showed that HR weeds were not genetically structured according to hull color, whereas historical weedy rice was separated into straw-hull and black-hull populations. A significant portion of the local rice crop genome was introgressed into HR weedy rice, which was rare in historical weedy accessions. Admixture analyses showed that HR weeds tend to possess crop haplotypes in the portion of chromosome 2 containing the ACETOLACTATE SYNTHASE gene, which confers herbicide resistance to Clearfield rice. Thus, U.S. HR weedy rice is a distinct population relative to historical weedy rice and shows modifications in morphology and phenology that are relevant to weed management.
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Affiliation(s)
- Nilda Roma Burgos
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72704 (N.R.B., V.S., T.M.T.);United States Department of Agriculture Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160 (H.B., D.R.G.); andBiology Department, University of Massachusetts, Amherst, Massachusetts 01003 (N.D.Y., Z.H., K.E.H., A.L.C.)
| | - Vijay Singh
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72704 (N.R.B., V.S., T.M.T.);United States Department of Agriculture Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160 (H.B., D.R.G.); andBiology Department, University of Massachusetts, Amherst, Massachusetts 01003 (N.D.Y., Z.H., K.E.H., A.L.C.)
| | - Te Ming Tseng
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72704 (N.R.B., V.S., T.M.T.);United States Department of Agriculture Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160 (H.B., D.R.G.); andBiology Department, University of Massachusetts, Amherst, Massachusetts 01003 (N.D.Y., Z.H., K.E.H., A.L.C.)
| | - Howard Black
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72704 (N.R.B., V.S., T.M.T.);United States Department of Agriculture Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160 (H.B., D.R.G.); andBiology Department, University of Massachusetts, Amherst, Massachusetts 01003 (N.D.Y., Z.H., K.E.H., A.L.C.)
| | - Nelson D Young
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72704 (N.R.B., V.S., T.M.T.);United States Department of Agriculture Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160 (H.B., D.R.G.); andBiology Department, University of Massachusetts, Amherst, Massachusetts 01003 (N.D.Y., Z.H., K.E.H., A.L.C.)
| | - Zhongyun Huang
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72704 (N.R.B., V.S., T.M.T.);United States Department of Agriculture Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160 (H.B., D.R.G.); andBiology Department, University of Massachusetts, Amherst, Massachusetts 01003 (N.D.Y., Z.H., K.E.H., A.L.C.)
| | - Katie E Hyma
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72704 (N.R.B., V.S., T.M.T.);United States Department of Agriculture Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160 (H.B., D.R.G.); andBiology Department, University of Massachusetts, Amherst, Massachusetts 01003 (N.D.Y., Z.H., K.E.H., A.L.C.)
| | - David R Gealy
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72704 (N.R.B., V.S., T.M.T.);United States Department of Agriculture Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160 (H.B., D.R.G.); andBiology Department, University of Massachusetts, Amherst, Massachusetts 01003 (N.D.Y., Z.H., K.E.H., A.L.C.)
| | - Ana L Caicedo
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72704 (N.R.B., V.S., T.M.T.);United States Department of Agriculture Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160 (H.B., D.R.G.); andBiology Department, University of Massachusetts, Amherst, Massachusetts 01003 (N.D.Y., Z.H., K.E.H., A.L.C.)
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Gross BL, Kellogg EA, Miller AJ. Speaking of food: connecting basic and applied plant science. AMERICAN JOURNAL OF BOTANY 2014; 101:1597-600. [PMID: 25326609 DOI: 10.3732/ajb.1400409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The Food and Agriculture Organization (FAO) predicts that food production must rise 70% over the next 40 years to meet the demands of a growing population that is expected to reach nine billion by the year 2050. Many facets of basic plant science promoted by the Botanical Society of America are important for agriculture; however, more explicit connections are needed to bridge the gap between basic and applied plant research. This special issue, Speaking of Food: Connecting Basic and Applied Plant Science, was conceived to showcase productive overlaps of basic and applied research to address the challenges posed by feeding billions of people and to stimulate more research, fresh connections, and new paradigms. Contributions to this special issue thus illustrate some interactive areas of study in plant science-historical and modern plant-human interaction, crop and weed origins and evolution, and the effects of natural and artificial selection on crops and their wild relatives. These papers provide examples of how research integrating the basic and applied aspects of plant science benefits the pursuit of knowledge and the translation of that knowledge into actions toward sustainable production of crops and conservation of diversity in a changing climate.
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Affiliation(s)
- Briana L Gross
- Department of Biology, University of Minnesota Duluth, 207 Swenson Science Building, 1035 Kirby Drive, Duluth Minnesota 55812 USA
| | - Elizabeth A Kellogg
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, Missouri 63132 USA
| | - Allison J Miller
- Department of Biology, Saint Louis University, 3507 Laclede Avenue, St. Louis, Missouri 63103-2010 USA
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