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Kieleczawa KA, Luke K, Gregory A. Genetic analysis of two species of Mnomen in the Kalamazoo Watershed reveal panmixia in Z. Aquatica, structure among Z. Palustris, and hybridization in areas of sympatry. PeerJ 2023; 11:e15971. [PMID: 37933259 PMCID: PMC10625758 DOI: 10.7717/peerj.15971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 08/06/2023] [Indexed: 11/08/2023] Open
Abstract
Mnomen or wild rice of the genus Zizania is an important part of Native American culture, especially in Michigan for the Ojibwe nation. An oil spill in 2010 along the Kalamazoo River and the subsequent clean-up lead to renewed interest in management of Mnomen within the Kalamazoo watershed. The affected water bodies were surveyed for Zizania species to map existing populations, determine the existing genetic diversity and species present, and to identify potential hybridization. Using Traditional Ecological Knowledge of rice beds and opportunistic sampling of encountered plants, 28 rice beds were sampled. Two species of Zizania were identified Z. palustris and Z. aquatica. Genetic diversity was measured using 11 microsatellite loci and was moderately high for both species (Z. aquatica HE = 0.669, H0 = 0.672, n = 26 and Z. palustris HE = 0.697, H0 = 0.636, n = 57). No evidence of population bottle-necking was found. Z. palustris was found to have k = 3 populations on the landscape, while Z. aquatica was found to be a single panmictic population. Several individual hybrids were confirmed using genotyping and they were all found in areas where the two species co-occurred. Additionally, Z. aquatica was found to have expanded into areas historically with only Z. palustris downstream of the oil spill, potentially due to dredging and sediment relocation as part of the clean-up effort.
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Affiliation(s)
| | - Kaylee Luke
- Bowling Green State University, Bowling Green, United States of America
- LabCorp, Colombus, United States of America
| | - Andrew Gregory
- Department of Biology, University of North Texas, Denton, TX, United States of America
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Wagutu GK, Fan X, Fu W, Tengwer MC, Li W, Chen Y. Genetic structure of wild rice Zizania latifolia in an expansive heterogeneous landscape along a latitudinal gradient. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.929944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Global aquatic habitats are undergoing rapid degradation and fragmentation as a result of climate change and changes in land use. Understanding the genetic variability and adaptive potential of aquatic plant species is thus important for conservation purposes. In this study, we investigated the genetic diversity and structure of the extant natural populations of Zizania latifolia from five river basins in China based on 46 microsatellite markers. We tested isolation by environment (IBE), isolation by resistance (IBR), and isolation by distance (IBD) patterns using a reciprocal causal model (RCM). Furthermore, we elucidated the impact of the environment on Z. latifolia genetic diversity using generalized linear models (GLMs) and spatially explicit mixed models. Low genetic diversity (HE = 0.125–0.433) and high genetic differentiation (FST = 0.641, Øpt = 0.654) were found. Higher historical gene flow (MH = 0.212–2.354) than contemporary gene flow (MC = 0.0112–0.0247) and significant bottlenecks in almost all populations were identified, highlighting the negative impact of wetland fragmentation. The IBE model was exclusively supported for all populations and in three river basins. The IBD and IBR models were supported in one river basin each. The maximum temperature of the warmest month and precipitation seasonality were the plausible environmental parameters responsible for the observed pattern of genetic diversity. Local adaptation signatures were found, with nine loci identified as outliers, four of which were gene-linked and associated with environmental variables. Based on these findings, IBE is more important than IBD and IBR in shaping the genetic structure of Z. latifolia.
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Li J, Lu Z, Yang Y, Hou J, Yuan L, Chen G, Wang C, Jia S, Feng X, Zhu S. Transcriptome Analysis Reveals the Symbiotic Mechanism of Ustilago esculenta-Induced Gall Formation of Zizania latifolia. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:168-185. [PMID: 33400553 DOI: 10.1094/mpmi-05-20-0126-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Zizania latifolia is a perennial aquatic vegetable, whose symbiosis with the fungus Ustilago esculenta (member of Basidiomycota, class Ustilaginaceae) results in the establishment of swollen gall formations. Here, we analyzed symbiotic relations of Z. latifolia and U. esculenta, using a triadimefon (TDF) treatment and transcriptome sequencing (RNA-seq). Specifically, accurately identify the whole growth cycle of Z. latifolia. Microstructure observations showed that the presence of U. esculenta could be clearly observed after gall formation but was absent after the TDF treatment. A total of 17,541 differentially expressed genes (DEGs) were identified, based on the transcriptome. According to gene ontology term and Kyoto Encyclopedia of Genes and Genomes pathway results, plant hormone signal transduction, and cell wall-loosening factors were all significantly enriched due to U. esculenta infecting Z. latifolia; relative expression levels of hormone-related genes were identified, of which downregulation of indole 3-acetic acid (IAA)-related DEGs was most pronounced in JB_D versus JB_B. The ultra-high performance liquid chromatography analysis revealed that IAA, zeatin+trans zeatin riboside, and gibberellin 3 were increased under U. esculenta infection. Based on our results, we proposed a hormone-cell wall loosening model to study the symbiotic mechanism of gall formation after U. esculenta infects Z. latifolia. Our study thus provides a new perspective for studying the physiological and molecular mechanisms of U. esculenta infection of Z. latifolia causing swollen gall formations as well as a theoretical basis for enhancing future yields of cultivated Z. latifolia.[Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law. 2021.
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Affiliation(s)
- Jie Li
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University; Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Zhiyuan Lu
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University; Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Yang Yang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University; Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Jinfeng Hou
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University; Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Lingyun Yuan
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University; Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Guohu Chen
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University; Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Chenggang Wang
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University; Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Shaoke Jia
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University; Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Xuming Feng
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University; Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
| | - Shidong Zhu
- Vegetable Genetics and Breeding Laboratory, College of Horticulture, Anhui Agricultural University; Hefei 230036, China
- Anhui Provincial Engineering Laboratory of Horticultural Crop Breeding, Hefei 230036, China
- Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
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Zhao Y, Song Z, Zhong L, Li Q, Chen J, Rong J. Inferring the Origin of Cultivated Zizania latifolia, an Aquatic Vegetable of a Plant-Fungus Complex in the Yangtze River Basin. FRONTIERS IN PLANT SCIENCE 2019; 10:1406. [PMID: 31787995 PMCID: PMC6856052 DOI: 10.3389/fpls.2019.01406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 10/10/2019] [Indexed: 05/10/2023]
Abstract
Crop domestication is one of the essential topics in evolutionary biology. Cultivated Zizania latifolia, domesticated as the special form of a plant-fungus (the host Zizania latifolia and the endophyte Ustilago esculenta) complex, is a popular aquatic vegetable endemic in East Asia. The rapid domestication of cultivated Z. latifolia can be traced in the historical literature but still need more evidence. This study focused on deciphering the genetic relationship between wild and cultivated Z. latifolia, as well as the corresponding parasitic U. esculenta. Twelve microsatellites markers were used to study the genetic variations of 32 wild populations and 135 landraces of Z. latifolia. Model simulations based on approximate Bayesian computation (ABC) were then performed to hierarchically infer the population history. We also analyzed the ITS sequences of the smut fungus U. esculenta to reveal its genetic structure. Our results indicated a significant genetic divergence between cultivated Z. latifolia and its wild ancestors. The wild Z. latifolia populations showed significant hierarchical genetic subdivisions, which may be attributed to the joint effect of isolation by distance and hydrological unconnectedness between watersheds. Cultivated Z. latifolia was supposedly domesticated once in the low reaches of the Yangtze River. The genetic structure of U. esculenta also indicated a single domestication event, and the genetic variations in this fungus might be associated with the diversification of cultivars. These findings provided molecular evidence in accordance with the historical literature that addressed the domestication of cultivated Z. latifolia involved adaptive evolution driven by artificial selection in both the plant and fungus.
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Affiliation(s)
- Yao Zhao
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Zhiping Song
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Lan Zhong
- Institute of Vegetable, Wuhan Academy of Agriculture Science and Technology, Wuhan, China
| | - Qin Li
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Jiakuan Chen
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Jun Rong
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
- *Correspondence: Jun Rong,
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Zhao Y, Zhong L, Zhou K, Song Z, Chen J, Rong J. Seed characteristic variations and genetic structure of wild Zizania latifolia along a latitudinal gradient in China: implications for neo-domestication as a grain crop. AOB PLANTS 2018; 10:ply072. [PMID: 30595833 PMCID: PMC6304442 DOI: 10.1093/aobpla/ply072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 11/29/2018] [Indexed: 06/09/2023]
Abstract
Crop wild relatives are not only important genetic resources for crop improvement, but also domestication candidates for selecting new crops. As a close relative of American wild rice Zizania palustris, Z. latifolia is a perennial aquatic grass widely distributed in China. Although Z. latifolia has been domesticated and cultivated as an aquatic vegetable for >1000 years, a neo-domestication for grain production needs to be soundly evaluated. In this study, we investigated the seed characteristic variations and genetic structure of 15 Z. latifolia wild populations along a latitudinal gradient in China. Our results showed that Z. latifolia tended to produce relatively larger seeds with lower moisture content and lower investments in seed pericarp at lower latitudes. The width, size, shape, seed-pericarp ratio and relative water content of seeds were significantly associated with climatic variables. The seeds of Z. latifolia showed a relatively low germination percentage and strong dormancy, which might hinder the neo-domestication. In addition, high genetic differentiation had been found among Z. latifolia populations, which could be attributed to isolation by distance. This study offered preliminary information for the utilization and conservation of wild Z. latifolia. It suggested that the wild populations in the middle and lower reaches of the Yangtze River could be good candidates for grain crop domestication due to appropriate seed traits and high genetic diversity. The neo-domestication of wild Z. latifolia requires further researches on the genetic mechanism of the Domestication Syndrome and more works on artificial breeding.
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Affiliation(s)
- Yao Zhao
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Lan Zhong
- Institute of Vegetable, Wuhan Academy of Agriculture Science and Technology, Wuhan, Hubei Province, China
| | - Kai Zhou
- Institute of Vegetable, Wuhan Academy of Agriculture Science and Technology, Wuhan, Hubei Province, China
| | - Zhiping Song
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Jiakuan Chen
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Jun Rong
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
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Chen Y, Liu Y, Fan X, Li W, Liu Y. Landscape-Scale Genetic Structure of Wild Rice Zizania latifolia: The Roles of Rivers, Mountains and Fragmentation. Front Ecol Evol 2017. [DOI: 10.3389/fevo.2017.00017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Yu J, Zhang Y, Cui H, Hu P, Yu X, Ye Z. An efficient genetic manipulation protocol for Ustilago esculenta. FEMS Microbiol Lett 2015; 362:fnv087. [PMID: 26038251 DOI: 10.1093/femsle/fnv087] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2015] [Indexed: 11/14/2022] Open
Abstract
Ustilago esculenta grows within the flowering stem of the aquatic grass Zizania latifolia, resembling a fungal endophyte. The fungus colonizes Z. latifolia and induces swelling which results in the formation of galls near the base of the plant. Due to their unique flavor and textures these galls are considered as a delicacy in southern China. Efficient genetic manipulation is required to determine the relationship between U. esculenta and Z. latifolia. In this study, we report a protoplast-based transformation system for this unique fungal species. We have explored various factors (enzyme digesting conditions, osmotic pressure stabilizers, vectors and selection agents) that might impact protoplast yield and high frequencies of transformation. A haploid strain (UeT55) of U. esculenta was found to produce higher yields of protoplasts when treating with 15 mg mL(-1) lywallzyme in a sucrose-containing solution at 30°C for 3 h. The transformation frequencies were higher when fungal strain was transformed with a linear plasmid harboring hygromycin or carboxin resistance gene and regenerated on a sucrose-containing medium. A UeICL gene (coding isocitrate lyase) was disrupted and an EGFP (coding enhanced green fluorescent protein) gene was overexpressed successfully in the UeT55 strain using the developed conditions. The genetic manipulation system reported in this study will open up new opportunities for forward and reverse genetics in U. esculenta.
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Affiliation(s)
- Jiajia Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang 310018, China
| | - Yafen Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang 310018, China
| | - Haifeng Cui
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang 310018, China
| | - Peng Hu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang 310018, China
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang 310018, China
| | - Zihong Ye
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang 310018, China
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Xu XW, Wu JW, Qi MX, Lu QX, Lee PF, Lutz S, Ge S, Wen J. Comparative phylogeography of the wild-rice genus Zizania (Poaceae) in eastern Asia and North America. AMERICAN JOURNAL OF BOTANY 2015; 102:239-47. [PMID: 25667077 DOI: 10.3732/ajb.1400323] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
PREMISE OF THE STUDY Comparative phylogeography of intercontinental disjunct taxa allowed us not only to elucidate their diversification and evolution following geographic isolation, but also to understand the effect of climatic and geological histories on the evolutionary processes of closely related species. A phylogeographic analysis was conducted on the eastern Asian-North American disjunct genus Zizania to compare intracontinental phylogeographic patterns between different continents. METHODS Surveys were conducted of 514 individuals using three chloroplast DNA fragments and three nuclear microsatellite loci. These individuals included 246 from 45 populations of Zizania latifolia in eastern Asia, and the following from North America: 154 individuals from 26 populations of Z. aquatica, 84 individuals from 14 populations of Z. palustris, and 30 individuals from one population of Z. texana. KEY RESULTS The genetic diversity of North American Zizania was significantly higher than that of eastern Asian Zizania. High levels of genetic differentiation among populations and no signal of population expansion were detected in three widespread species. No phylogeographic structure was observed in Z. latifolia, and discordant patterns of cpDNA and microsatellite markers were observed in North American Zizania. CONCLUSIONS Reduced variation in Zizania latifolia likely reflects its perennial life history, the North American origin of Zizania, and the relative homogeneity of aquatic environments. High levels of genetic differentiation suggest limited dispersal among populations in all Zizania species. The more complex patterns of diversification and evolution in North American Zizania may be driven by the greater impact of glaciation in North America relative to eastern Asia.
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Affiliation(s)
- Xin-Wei Xu
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Jin-Wei Wu
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Mei-Xia Qi
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Qi-Xiang Lu
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Peter F Lee
- Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, Ontario P7B 5E1, Canada
| | - Sue Lutz
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, District of Columbia 20013-7012 USA
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, District of Columbia 20013-7012 USA
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