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An Y, Wang Q, Cui Y, Liu X, Wang P, Zhou Y, Kang P, Chen Y, Wang Z, Zhou Q, Wang P. Comparative physiological and transcriptomic analyses reveal genotype specific response to drought stress in Siberian wildrye (Elymus sibiricus). Sci Rep 2024; 14:21060. [PMID: 39256456 PMCID: PMC11387644 DOI: 10.1038/s41598-024-71847-9] [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: 04/11/2024] [Accepted: 08/31/2024] [Indexed: 09/12/2024] Open
Abstract
Siberian wildrye (Elymus sibiricus) is a xero-mesophytic forage grass with high nutritional quality and stress tolerance. Among its numerous germplasm resources, some possess superior drought resistance. In this study, we firstly investigated the physiological differences between the leaves of drought-tolerant (DT) and drought-sensitive (DS) genotypes under different field water contents (FWC) in soil culture. The results showed that, under drought stress, DT maintained a lower leaf water potential for water absorption, sustained higher photosynthetic efficiency, and reduced oxidative damage in leaves by efficiently maintaining the ascorbic acid-glutathione (ASA-GSH) cycle to scavenge reactive oxygen species (ROS) compared to DS. Secondly, using RNA sequencing (RNA-seq), we analyzed the gene expression profiles of DT and DS leaves under osmotic stress of hydroponics induced by PEG-6000. Through differential analysis, we identified 1226 candidate unigenes, from which we subsequently screened out 115/212 differentially expressed genes (DEGs) that were more quickly induced/reduced in DT than in DS under osmotic stress. Among them, Unigene0005863 (EsSnRK2), Unigene0053902 (EsLRK10) and Unigene0031985 (EsCIPK5) may be involved in stomatal closure induced by abscisic acid (ABA) signaling pathway. Unigene0047636 (EsCER1) may positively regulates the synthesis of very-long-chain (VLC) alkanes in cuticular wax biosynthesis, influencing plant responses to abiotic stresses. Finally, the contents of wax and cutin were measured by GC-MS under osmotic stress of hydroponics induced by PEG-6000. Corresponding to RNA-seq, contents of wax monomers, especially alkanes and alcohols, showed significant induction by osmotic stress in DT but not in DS. It is suggested that limiting stomatal and cuticle transpiration under drought stress to maintain higher photosynthetic efficiency and water use efficiency (WUE) is one of the critical mechanisms that confer stronger drought resistance to DT. This study provides some insights into the molecular mechanisms underlying drought tolerance in E. sibiricus. The identified genes may provide a foundation for the selection and breeding of drought-tolerant crops.
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Affiliation(s)
- Yongping An
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Grassland Resources, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, 610225, China
| | - Qian Wang
- Guizhou Institute of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Yannong Cui
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Xin Liu
- National Key Laboratory of Crop Genetic Improvement, Ministry of Agriculture Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ping Wang
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Grassland Resources, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, 610225, China
| | - Yue Zhou
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Grassland Resources, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, 610225, China
| | - Peng Kang
- College of Biological Science and Engineering, North Minzu University, Yinchuan, 750021, China
| | - Youjun Chen
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Grassland Resources, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, 610225, China
| | - Zhiwei Wang
- Guizhou Institute of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang, 550006, China
| | - Qingping Zhou
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Grassland Resources, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, 610225, China
| | - Pei Wang
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Grassland Resources, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, 610225, China.
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Yu Q, Xiong Y, Su X, Xiong Y, Dong Z, Zhao J, Shu X, Bai S, Lei X, Yan L, Ma X. Integrating Full-Length Transcriptome and RNA Sequencing of Siberian Wildrye ( Elymus sibiricus) to Reveal Molecular Mechanisms in Response to Drought Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:2719. [PMID: 37514333 PMCID: PMC10385362 DOI: 10.3390/plants12142719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/13/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023]
Abstract
Drought is one of the most significant limiting factors affecting plant growth and development on the Qinghai-Tibet Plateau (QTP). Mining the drought-tolerant genes of the endemic perennial grass of the QTP, Siberian wildrye (Elymus sibiricus), is of great significance to creating new drought-resistant varieties which can be used in the development of grassland livestock and restoring natural grassland projects in the QTP. To investigate the transcriptomic responsiveness of E. sibiricus to drought stress, PEG-induced short- and long-term drought stress was applied to two Siberian wildrye genotypes (drought-tolerant and drought-sensitive accessions), followed by third- and second-generation transcriptome sequencing analysis. A total of 40,708 isoforms were detected, of which 10,659 differentially expressed genes (DEGs) were common to both genotypes. There were 2107 and 2498 unique DEGs in the drought-tolerant and drought-sensitive genotypes, respectively. Additionally, 2798 and 1850 DEGs were identified in the drought-tolerant genotype only under short- and long-term conditions, respectively. DEGs numbering 1641 and 1330 were identified in the drought-sensitive genotype only under short- and long-term conditions, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that all the DEGs responding to drought stress in E. sibiricus were mainly associated with the mitogen-activated protein kinase (MAKP) signaling pathway, plant hormone signal transduction, the linoleic acid metabolism pathway, the ribosome pathway, and plant circadian rhythms. In addition, Nitrate transporter 1/Peptide transporter family protein 3.1 (NPF3.1) and Auxin/Indole-3-Acetic Acid (Aux/IAA) family protein 31(IAA31) also played an important role in helping E. sibiricus resist drought. This study used transcriptomics to investigate how E. sibiricus responds to drought stress, and may provide genetic resources and references for research into the molecular mechanisms of drought resistance in native perennial grasses and for breeding drought-tolerant varieties.
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Affiliation(s)
- Qingqing Yu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Sichuan Academy of Grassland Science, Chengdu 610097, China
| | - Yi Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoli Su
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yanli Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhixiao Dong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Junming Zhao
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xin Shu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Shiqie Bai
- Sichuan Academy of Grassland Science, Chengdu 610097, China
| | - Xiong Lei
- Sichuan Academy of Grassland Science, Chengdu 610097, China
| | - Lijun Yan
- Sichuan Academy of Grassland Science, Chengdu 610097, China
| | - Xiao Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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Li J, Ma S, Jiang K, Zhang C, Liu W, Chen S. Drivers of population divergence and genetic variation in Elymus breviaristatus (Keng) Keng f. (Poaceae: Triticeae), an endemic perennial herb of the Qinghai-Tibet plateau. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1068739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022] Open
Abstract
Elymus breviaristatus, a rare grass species with excellent resistance and ecological importance, is narrowly distributed on the Qinghai-Tibet plateau. Populations of E. breviaristatus are declining due to habitat fragmentation, and thus far, characteristics of genetic differentiation and adaptive responses to climate change remain poorly understood in this species. Here, we explored the genetic structure of 18 natural populations (269 individuals) in the transition zone between Tibet and the Hengduan Mountains using 15 expressed sequence tag (EST)-SSR primer pairs and identified possible barriers to gene flow that might have caused genetic discontinuities. Additional analyses were performed to identify the environmental factors affecting genetic diversity and to test whether the patterns of genetic variation among populations were more consistent with the isolation by distance (IBD) or isolation by environment (IBE) model. Multiple measures of genetic diversity revealed that intra-population genetic variation was low, while inter-population genetic variation was high. Clustering, structure, and principal coordinate analyses identified three genetic groups: (a) Eastern Qamdo, (b) Nagqu and Western Qamdo, and (c) Lhasa and Nyingchi. A clear physical barrier to gene flow was formed by the Yarlung Zangbo Grand Canyon and the Tanggula Mountains. We found that both IBD and IBE contributed to the observed patterns of genetic variation, and the IBE model played a leading role. In addition, precipitation-related variables, soil phosphorus content and soil K:P ratio significantly affected population genetic variation. Overall, our results emphasized the genetic fragility of E. breviaristatus populations and showed that this species requires attention, as future climate changes and human activities may further threaten its survival. In addition, the genetic differences among E. breviaristatus populations should be considered when formulating conservation measures for E. breviaristatus populations in the study area.
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Liu X, Wang P, An Y, Wang CM, Hao Y, Zhou Y, Zhou Q, Wang P. Endodermal apoplastic barriers are linked to osmotic tolerance in meso-xerophytic grass Elymus sibiricus. FRONTIERS IN PLANT SCIENCE 2022; 13:1007494. [PMID: 36212320 PMCID: PMC9539332 DOI: 10.3389/fpls.2022.1007494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 09/05/2022] [Indexed: 06/16/2023]
Abstract
Drought is the most serious adversity faced by agriculture and animal husbandry industries. One strategy that plants use to adapt to water deficits is modifying the root growth and architecture. Root endodermis has cell walls reinforced with apoplastic barriers formed by the Casparian strip (CS) and suberin lamellae (SL) deposits, regulates radial nutrient transport and protects the vascular cylinder from abiotic threats. Elymus sibiricus is an economically important meso-xerophytic forage grass, characterized by high nutritional quality and strong environmental adaptability. The purpose of this study was to evaluate the drought tolerance of E. sibiricus genotypes and investigate the root structural adaptation mechanism of drought-tolerant genotypes' responding to drought. Specifically, a drought tolerant (DT) and drought sensitive (DS) genotype were screened out from 52 E. sibiricus genotypes. DT showed less apoplastic bypass flow of water and solutes than DS under control conditions, as determined with a hydraulic conductivity measurement system and an apoplastic fluorescent tracer, specifically PTS trisodium-8-hydroxy-1,3,6-pyrenetrisulphonic acid (PTS). In addition, DT accumulated less Na, Mg, Mn, and Zn and more Ni, Cu, and Al than DS, regardless of osmotic stress. Further study showed more suberin deposition in DT than in DS, which could be induced by osmotic stress in both. Accordingly, the CS and SL were deposited closer to the root tip in DT than in DS. However, osmotic stress induced their deposition closer to the root tips in DS, while likely increasing the thickness of the CS and SL in DT. The stronger and earlier formation of endodermal barriers may determine the radial transport pathways of water and solutes, and contribute to balance growth and drought response in E. sibiricus. These results could help us better understand how altered endodermal apoplastic barriers in roots regulate water and mineral nutrient transport in plants that have adapted to drought environments. Moreover, the current findings will aid in improving future breeding programs to develop drought-tolerant grass or crop cultivars.
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Affiliation(s)
- Xin Liu
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
- National Key Laboratory of Crop Genetic Improvement, Ministry of Agriculture Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ping Wang
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Yongping An
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Chun-Mei Wang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yanbo Hao
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Yue Zhou
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Qingping Zhou
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Pei Wang
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
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Han M, Zhang J, Li D, Sun S, Zhang C, Zhang C, Yan L, Guan Y, Chen L, Guo Y, You M, Gou W, Li X, Yan J, Bai S, Yan X. Phylogeographical Pattern and Population Evolution History of Indigenous Elymus sibiricus L. on Qinghai-Tibetan Plateau. FRONTIERS IN PLANT SCIENCE 2022; 13:882601. [PMID: 35845670 PMCID: PMC9277506 DOI: 10.3389/fpls.2022.882601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
Elymus sibiricus L. is a perennial allotetraploid belonging to Triticeae of Poaceae, Elymus L., as the type species of genus Elymus L. The existing geographical distribution pattern and genetic spatial structure of E. sibiricus on Qinghai-Tibetan Plateau (QTP) are not yet clear. In this study, population genetic structure and demography history of 216 individuals from 44 E. sibiricus populations on QTP were studied used specific-locus amplified fragment sequencing (SLAF-seq). The result of genetic diversity showed that there was no single genetic diversity center was observed across all E. sibiricus populations. The results of genetic variation showed that 44 populations were clearly divided into the following three groups: Qinghai Plateau (Group I), South Tibet (Group II), and Hengduan Mountains (Group III). From the three analyses of AMOVA, Mantel test and Treemix, strong genetic differentiation across all populations and low genetic differentiation among populations within three groups. Molecular dating indicated that E. sibiricus diverged at 16.08 Ma (during the early Miocene) can be linked to the Himalayan Motion stage of QTP uplift. It is speculated that the reasons affecting the current phylogeographical pattern are as follows: (1) The environmental changes due to the uplift of the QTP; (2) The geographic distance between the populations (Groups I and III are close in geographic distance, and gene flow are frequent); (3) Geographical barriers (the Tanggula and Bayangela Mountains between Groups I and II). This study provides new evidence and historical perspective to the future exploration of the evolution and geographic distribution pattern of Elymus L.
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Affiliation(s)
- Mengli Han
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jingxue Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Daxu Li
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Shengnan Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | | | - Chuanjie Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Lijun Yan
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Yongzhuo Guan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Lili Chen
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Yuxia Guo
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Minghong You
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Wenlong Gou
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Xinrui Li
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Jiajun Yan
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Shiqie Bai
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Xuebing Yan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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Zhang Z, Zheng Y, Zhang J, Wang N, Wang Y, Liu W, Bai S, Xie W. High-Altitude Genetic Selection and Genome-Wide Association Analysis of Yield-Related Traits in Elymus sibiricus L. Using SLAF Sequencing. FRONTIERS IN PLANT SCIENCE 2022; 13:874409. [PMID: 35800604 PMCID: PMC9253694 DOI: 10.3389/fpls.2022.874409] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 05/26/2022] [Indexed: 05/04/2023]
Abstract
The genetic adaptations to harsh climatic conditions in high altitudes and genetic basis of important agronomic traits are poorly understood in Elymus sibiricus L. In this study, an association population of 210 genotypes was used for population structure, selective sweep analysis, and genome-wide association study (GWAS) based on 88,506 single nucleotide polymorphisms (SNPs). We found 965 alleles under the natural selection of high altitude, which included 7 hub genes involved in the response to UV, and flavonoid and anthocyanin biosynthetic process based on the protein-protein interaction (PPI) analysis. Using a mixed linear model (MLM), the GWAS test identified a total of 1,825 significant loci associated with 12 agronomic traits. Based on the gene expression data of two wheat cultivars and the PPI analysis, we finally identified 12 hub genes. Especially, in plant height traits, the top hub gene (TOPLESS protein) encoding auxins and jasmonic acid signaling pathway, shoot apical meristem specification, and xylem and phloem pattern formation was highly overexpressed. These genes might play essential roles in controlling the growth and development of E. sibiricus. Therefore, this study provides fundamental insights relevant to hub genes and will benefit molecular breeding and improvement in E. sibiricus and other Elymus species.
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Affiliation(s)
- Zongyu Zhang
- The State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yuying Zheng
- The State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Junchao Zhang
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
| | - Na Wang
- The State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yanrong Wang
- The State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Wenhui Liu
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibetan Plateau, Qinghai Academy of Animal Science and Veterinary Medicine, Xining, China
| | - Shiqie Bai
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Wengang Xie
- The State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- *Correspondence: Wengang Xie,
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Energetic Value of Elymus elongatus L. and Zea mays L. Grown on Soil Polluted with Ni2+, Co2+, Cd2+, and Sensitivity of Rhizospheric Bacteria to Heavy Metals. ENERGIES 2021. [DOI: 10.3390/en14164903] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Plants, and microorganisms associated with them, offer an effective tool for removing pollutants, such as heavy metals, from the soil environment. The aim of this study was to determine changes caused by Ni2+, Co2+, and Cd2+ in the genetic diversity of soil-populating bacteria and the effect these heavy metals on the heating value of elongated coach grass (Elymus elongatus L.) and maize (Zea mays L.). Microorganisms support plants in removing heavy metals from soil. These plants can then be used for energetic purposes. The study aim was accomplished by determining counts of microorganisms and their resistance (RS) to Ni2+, Co2+, Cd2+, their colony development index (CD), ecophysiological diversity index (EP), and diversity established with the next generation sequencing (NGS) method. Further analyses aimed to establish test plants resistance to pollution with heavy metals and their heating value. Organotrophic bacteria turned out to be the most resistant to Co2+, whereas actinobacteria—to Cd2+ effects. At all taxonomic levels, the genetic diversity of bacteria was most adversely influenced by Cd2+ in the soil sown with Zea mays L. Bacteria belonging to Arthrobacter, Rhodoplanes, Kaistobacter, Devosia, Phycicoccus, and Thermomonas genera showed high tolerance to soil pollution with Ni2+, Co2+, and Cd2+, hence they should be perceived as potential sources of microorganisms useful for bioaugmentation of soils polluted with these heavy metals. Ni2+, Co2+, and Cd2+ had no effect on the heating value of Elymus elongatus L. and Zea mays L. The heating value of 1 kg of air-dry biomass of the tested plants was relatively high and ranged from 14.6 to 15.1 MJ. Elymus elongatus L. proved more useful in phytoremediation than Zea mays L.
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Xie J, Zhao Y, Yu L, Liu R, Dou Q. Molecular karyotyping of Siberian wild rye (Elymus sibiricus L.) with oligonucleotide fluorescence in situ hybridization (FISH) probes. PLoS One 2020; 15:e0227208. [PMID: 31951623 PMCID: PMC6968859 DOI: 10.1371/journal.pone.0227208] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 12/14/2019] [Indexed: 12/01/2022] Open
Abstract
Siberian wild rye (Elymus sibiricus L.), an allotetraploid species, is a potentially high-quality perennial forage crop native to temperate regions. We used fluorescently conjugated oligonucleotides, representing ten repetitive sequences, including 6 microsatellite repeats, two satellite repeats, and two ribosomal DNAs, to characterize E. sibiricus chromosomes, using sequential fluorescence in situ hybridization and genomic in situ hybridization assays. Our results showed that microsatellite repeats (AAG)10 or (AGG)10, satellite repeats pAs1 and pSc119.2, and ribosomal 5S rDNA and 45S rDNA are specific markers for unique chromosomes. A referable karyotype ideogram was suggested, by further polymorphism screening, across different E. sibiricus cultivars with a probe mixture of (AAG)10, Oligo-pAs1, and Oligo-pSc119.2. Chromosomal polymorphisms vary between different genomes and between different individual chromosomes. In particular, two distinct forms of chromosome E in H genome were identified in intra- and inter-populations. Here, the significance of these results, for E. sibiricus genome research and breeding, and novel approaches to improve fluorescence in situ hybridization-based karyotyping are discussed.
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Affiliation(s)
- Jihong Xie
- Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Yan Zhao
- College of Grassland, Resource and Environmental Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Linqing Yu
- Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Ruijuan Liu
- Key Laboratory of Crop Molecular Breeding, Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining, China
| | - Quanwen Dou
- Key Laboratory of Crop Molecular Breeding, Qinghai Province, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Plateau Institute of Biology, Chinese Academy of Sciences, Xining, China
- * E-mail:
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Zhang Z, Xie W, Zhang J, Wang N, Zhao Y, Wang Y, Bai S. Construction of the first high-density genetic linkage map and identification of seed yield-related QTLs and candidate genes in Elymus sibiricus, an important forage grass in Qinghai-Tibet Plateau. BMC Genomics 2019; 20:861. [PMID: 31726988 PMCID: PMC6857239 DOI: 10.1186/s12864-019-6254-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 10/31/2019] [Indexed: 11/28/2022] Open
Abstract
Background Elymus sibiricus is an ecologically and economically important perennial, self-pollinated, and allotetraploid (StStHH) grass, widely used for forage production and animal husbandry in Western and Northern China. However, it has low seed yield mainly caused by seed shattering, which makes seed production difficult for this species. The goals of this study were to construct the high-density genetic linkage map, and to identify QTLs and candidate genes for seed-yield related traits. Results An F2 mapping population of 200 individuals was developed from a cross between single genotype from “Y1005” and “ZhN06”. Specific-locus amplified fragment sequencing (SLAF-seq) was applied to construct the first genetic linkage map. The final genetic map included 1971 markers on the 14 linkage groups (LGs) and was 1866.35 cM in total. The length of each linkage group varied from 87.67 cM (LG7) to 183.45 cM (LG1), with an average distance of 1.66 cM between adjacent markers. The marker sequences of E. sibiricus were compared to two grass genomes and showed 1556 (79%) markers mapped to wheat, 1380 (70%) to barley. Phenotypic data of eight seed-related traits (2016–2018) were used for QTL identification. A total of 29 QTLs were detected for eight seed-related traits on 14 linkage groups, of which 16 QTLs could be consistently detected for two or three years. A total of 6 QTLs were associated with seed shattering. Based on annotation with wheat and barley genome and transcriptome data of abscission zone in E. sibiricus, we identified 30 candidate genes for seed shattering, of which 15, 7, 6 and 2 genes were involved in plant hormone signal transcription, transcription factor, hydrolase activity and lignin biosynthetic pathway, respectively. Conclusion This study constructed the first high-density genetic linkage map and identified QTLs and candidate genes for seed-related traits in E. sibiricus. Results of this study will not only serve as genome-wide resources for gene/QTL fine mapping, but also provide a genetic framework for anchoring sequence scaffolds on chromosomes in future genome sequence assembly of E. sibiricus.
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Affiliation(s)
- Zongyu Zhang
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Wengang Xie
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China.
| | - Junchao Zhang
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Na Wang
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Yongqiang Zhao
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Yanrong Wang
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China.
| | - Shiqie Bai
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, 611731, People's Republic of China
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Borowik A, Wyszkowska J, Kucharski M, Kucharski J. Implications of Soil Pollution with Diesel Oil and BP Petroleum with ACTIVE Technology for Soil Health. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:E2474. [PMID: 31336741 PMCID: PMC6678237 DOI: 10.3390/ijerph16142474] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 07/06/2019] [Accepted: 07/09/2019] [Indexed: 12/18/2022]
Abstract
Grass Elymus elongatus has a potential in phytoremediation and was used in this study in a potted experiment, which was performed to determine the effect of polluting soil (Eutric Cambisol) with diesel oil (DO) and unleaded petroleum (P) on the diversity of soil microorganisms, activity of soil enzymes, physicochemical properties of soil, and on the resistance of Elymus elongatus to DO and P, which altogether allowed evaluating soil health. Both petroleum products were administered in doses of 0 and 7 cm3 kg-1 soil d.m. Vegetation of Elymus elongatus spanned for 105 days. Grasses were harvested three times, i.e., on day 45, 75, and 105 of the experiment. The study results demonstrated a stronger toxic effect of DO than of P on the growth and development of Elymus elongatus. Diesel oil caused greater changes in soil microbiome compared to unleaded petroleum. This hypothesis was additionally confirmed by Shannon and Simpson indices computed based on operational taxonomic unit (OTU) abundance, whose values were the lowest in the DO-polluted soil. Soil pollution with DO reduced the counts of all bacterial taxa and stimulated the activity of soil enzymes, whereas soil pollution with P diminished the diversity of bacteria only at the phylum, class, order, and family levels, but significantly suppressed the enzymatic activity. More polycyclic aromatic hydrocarbons (PAHs) were degraded in the soil polluted with P compared to DO, which may be attributed to the stimulating effect of Elymus elongatus on this process, as it grew better in the soil polluted with P than in that polluted with DO.
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Affiliation(s)
- Agata Borowik
- Department of Microbiology, University of Warmia and Mazury in Olsztyn, 10-727 Olsztyn, Poland
| | - Jadwiga Wyszkowska
- Department of Microbiology, University of Warmia and Mazury in Olsztyn, 10-727 Olsztyn, Poland.
| | - Mirosław Kucharski
- Department of Microbiology, University of Warmia and Mazury in Olsztyn, 10-727 Olsztyn, Poland
| | - Jan Kucharski
- Department of Microbiology, University of Warmia and Mazury in Olsztyn, 10-727 Olsztyn, Poland
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Phenotype- and SSR-Based Estimates of Genetic Variation between and within Two Important Elymus Species in Western and Northern China. Genes (Basel) 2018. [PMID: 29518961 PMCID: PMC5867868 DOI: 10.3390/genes9030147] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Elymus nutans and Elymus sibiricus are two important perennial forage grasses of the genus Elymus, widely distributed in high altitude regions of Western and Northern China, especially on the Qinghai-Tibetan Plateau. Information on phenotypic and genetic diversity is limited, but necessary for Elymus germplasm collection, conservation, and utilization. In the present study, the phenotypic and genetic differentiation of 73 accessions of the two species were evaluated using 15 phenotypic traits and 40 expressed sequence tag derived simple sequence repeat markers (EST-SSRs). The results showed that only 7.23% phenotypic differentiation (Pst) existed between the two Elymus species based on fifteen quantitative traits. Principal component analysis (PCA) revealed that leaf traits, spike traits, and some seed traits were dominant factors in phenotypic variation. Moreover, 396 (97.8%) and 331 (87.1%) polymorphic bands were generated from 40 EST-SSR primers, suggesting high levels of genetic diversity for the two species. The highest genetic diversity was found in the Northeastern Qinghai-Tibetan Plateau groups. Clustering analysis based on molecular data showed that most accessions of each Elymus species tended to group together. Similar results were described by principal coordinates analysis (PCoA) and structure analysis. The molecular variance analysis (AMOVA) revealed that 81.47% and 89.32% variation existed within the geographical groups for the two species, respectively. Pearson’s correlation analyses showed a strong positive correlation between Nei’s genetic diversity and annual mean temperature. These results could facilitate Elymus germplasm collection, conservation, and future breeding.
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Zhao X, Zhang J, Zhang Z, Wang Y, Xie W. Hybrid identification and genetic variation of Elymus sibiricus hybrid populations using EST-SSR markers. Hereditas 2017; 154:15. [PMID: 29255380 PMCID: PMC5727920 DOI: 10.1186/s41065-017-0053-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 11/28/2017] [Indexed: 11/10/2022] Open
Abstract
Background Elymus sibiricus is an important native grass in Qinghai-Tibetan Plateau. Seed shattering is a serious problem for E. sibiricus, especially at harvest time. Cross breeding is an effective way to create new varieties with beneficial characteristic or improved traits, and to broaden genetic base. Results In this study, we created five hybrid populations by crossing seven E. sibiricus genotypes that have seed shattering variation. Then, nine EST-SSR primers were used for hybrid identification based on DNA fingerprinting, and genetic diversity analysis of hybrid populations and their respective parents. A total of 15 hybrids were identified. An analysis of amplified polymorphic bands among genuine hybrids and their respective parents revealed mainly two types of markers: 1) hybrids shared bands exclusively amplified in both parents; 2)hybrids shared bands exclusively amplified in male parents. For each hybrid population, the total number of amplified bands ranged from 37 to 57, the percentage of polymorphism varied from 65.12% to 75.68%, with an average of 70.51%. Novel bands found in each hybrid population varied from 0 to 9 bands, suggesting an occurrence of rearrangements in the hybrid population. The structure analysis revealed that all hybrid populations and parents were assigned to eight groups. The principal coordinate analysis (PCoA) showed similar results. Conclusions In general, this study proved EST-SSR markers are efficient for hybrid identification, and suggested more genetic variation could be captured in hybrid populations by crossing breeding.
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Affiliation(s)
- Xuhong Zhao
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020 People's Republic of China
| | - Junchao Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020 People's Republic of China
| | - Zongyu Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020 People's Republic of China
| | - Yanrong Wang
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020 People's Republic of China
| | - Wengang Xie
- The State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020 People's Republic of China
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Xie W, Zhang J, Zhao X, Zhang Z, Wang Y. Transcriptome profiling of Elymus sibiricus, an important forage grass in Qinghai-Tibet plateau, reveals novel insights into candidate genes that potentially connected to seed shattering. BMC PLANT BIOLOGY 2017; 17:78. [PMID: 28431567 PMCID: PMC5399857 DOI: 10.1186/s12870-017-1026-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/06/2017] [Indexed: 05/12/2023]
Abstract
BACKGROUND Elymus sibiricus is an important forage grass in semi-arid regions, but it is difficult to grow for commercial seed production due to high seed shattering. To better understand the underlying mechanism and explore the putative genes related to seed shattering, we conducted a combination of morphological, histological, physiochemical and transcriptome analysis on two E. sibiricus genotypes (XH09 and ZhN03) that have contrasting seed shattering. RESULTS The results show that seed shattering is generally caused by a degradation of the abscission layer. Early degradation of abscission layers was associated with the increased seed shattering in high seed shattering genotype XH09. Two cell wall degrading enzymes, cellulase (CE) and polygalacturonase (PG), had different activity in the abscission zone, indicating their roles in differentiation of abscission layer. cDNA libraries from abscission zone tissue of XH09 and ZhN03 at 7 days, 21 days and 28 days after heading were constructed and sequenced. A total of 86,634 unigenes were annotated and 7110 differentially expressed transcripts (DETs) were predicted from "XH09-7 vs ZhN03-7", "XH09-21 vs ZhN03-21" and "XH09-28 vs ZhN03-28", corresponding to 2058 up-regulated and 5052 down-regulated unigenes. The expression profiles of 10 candidate transcripts involved in cell wall-degrading enzymes, lignin biosynthesis and phytohormone activity were validated using quantitative real-time PCR (qRT-PCR), 8 of which were up-regulated in low seed shattering genotype ZhN03, suggesting these genes may be associated with reduction of seed shattering. CONCLUSIONS The expression data generated in this study provides an important resource for future molecular biological research in E. sibiricus.
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Affiliation(s)
- Wengang Xie
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Junchao Zhang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xuhong Zhao
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Zongyu Zhang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yanrong Wang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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Development and cross-species transferability of EST-SSR markers in Siberian wildrye (Elymus sibiricus L.) using Illumina sequencing. Sci Rep 2016; 6:20549. [PMID: 26853106 PMCID: PMC4744933 DOI: 10.1038/srep20549] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 01/06/2016] [Indexed: 11/09/2022] Open
Abstract
Siberian wildrye (Elymus sibiricus L.) is a perennial, self-fertilizing grass that plays an important role in animal husbandry and environmental sustenance. However, the transcriptomic and genomic information on this species is very limited, which hinders genetic and breeding studies. In the present study, 76,686,804 clean reads were generated from 11 different tissue samples of E. sibiricus by Illumina paired-end sequencing, and the reads were deposited into the NCBI SRA database (SRX574376). A total of 8,769 EST-SSRs were identified from 94,458 unigene sequences, which were obtained by de novo assembly. Moreover, 1,078 primer pairs were successfully designed, and 500 pairs were randomly selected to assess polymorphisms in 15 E. sibiricus accessions. A total of 112 primer pairs were polymorphic, and the polymorphism information content (PIC) values ranged from 0.39 to 0.81, indicating a high level of informativeness. Furthermore, these 112 polymorphic primer pairs were used to evaluate the transferability to 13 other related species, and 55 EST-SSR markers were found to be polymorphic among these 13 Elymus species. This study collected the global sequence data for E. sibiricus, and the newly developed markers will prove valuable in facilitating genetic diversity in E. sibiricus and related Elymus species.
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Xie W, Zhang J, Zhao X, Zhang J, Wang Y. Siberian wild rye (Elymus sibiricus L.): Genetic diversity of germplasm determined using DNA fingerprinting and SCoT markers. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.04.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Zhang J, Xie W, Wang Y, Zhao X. Potential of Start Codon Targeted (SCoT) markers to estimate genetic diversity and relationships among Chinese Elymus sibiricus accessions. Molecules 2015; 20:5987-6001. [PMID: 25853316 PMCID: PMC6272172 DOI: 10.3390/molecules20045987] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 03/28/2015] [Accepted: 04/01/2015] [Indexed: 11/16/2022] Open
Abstract
Elymus sibiricus as an important forage grass and gene pool for improving cereal crops, that is widely distributed in West and North China. Information on its genetic diversity and relationships is limited but necessary for germplasm collection, conservation and future breeding. Start Codon Targeted (SCoT) markers were used for studying the genetic diversity and relationships among 53 E. sibiricus accessions from its primary distribution area in China. A total of 173 bands were generated from 16 SCoT primers, 159 bands of which were polymorphic with the percentage of polymorphic bands (PPB) of 91.91%. Based upon population structure analysis five groups were formed. The cluster analysis separated the accessions into two major clusters and three sub-clusters, similar to results of principal coordinate analysis (PCoA). The molecular variance analysis (AMOVA) showed that genetic variation was greater within geographical regions (50.99%) than between them (49.01%). Furthermore, the study also suggested that collecting and evaluating E. sibiricus germplasm for major geographic regions and special environments broadens the available genetic base and illustrates the range of variation. The results of the present study showed that SCoT markers were efficient in assessing the genetic diversity among E. sibiricus accessions.
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Affiliation(s)
- Junchao Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Wengang Xie
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Yanrong Wang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
| | - Xuhong Zhao
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China.
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Xie W, Zhao X, Zhang J, Wang Y, Liu W. Assessment of genetic diversity of Siberian wild rye (Elymus sibiricus L.) germplasms with variation of seed shattering and implication for future genetic improvement. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2014.12.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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18
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Nie G, Zhang XQ, Huang LK, Xu WZ, Wang JP, Zhang YW, Ma X, Yan YH, Yan HD. Genetic variability and population structure of the potential bioenergy crop Miscanthus sinensis (Poaceae) in Southwest China based on SRAP markers. Molecules 2014; 19:12881-97. [PMID: 25153884 PMCID: PMC6271393 DOI: 10.3390/molecules190812881] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Revised: 08/12/2014] [Accepted: 08/13/2014] [Indexed: 11/16/2022] Open
Abstract
The genus Miscanthus has great potential as a biofuel feedstock because of its high biomass, good burning quality, environmental tolerance, and good adaptability to marginal land. In this study, the genetic diversity and the relationship of 24 different natural Miscanthus sinensis populations collected from Southwestern China were analyzed by using 33 pairs of Sequence Related Amplified Polymorphism (SRAP) primers. A total of 688 bands were detected with 646 polymorphic bands, an average of 19.58 polymorphic bands per primer pair. The average percentage of polymorphic loci (P), gene diversity (H), and Shannon's diversity index (I) among the 24 populations are 70.59%, 0.2589, and 0.3836, respectively. The mean value of total gene diversity (HT) was 0.3373±0.0221, while the allelic diversity within populations (HS) was 0.2589±0.0136 and the allelic diversity among populations (DST) was 0.0784. The mean genetic differentiation coefficient (Gst=0.2326) estimated from the detected 688 loci indicated that there was 76.74% genetic differentiation within the populations, which is consistent with the results from Analysis of Molecular Variance (AMOVA) analysis. Based upon population structure and phylogenetic analysis, five groups were formed and a special population with mixed ancestry was inferred indicating that human-mediated dispersal may have had a significant effect on population structure of M. sinensis. Evaluating the genetic structure and genetic diversity at morphological and molecular levels of the wild M. sinensis in Southwest China is critical to further utilize the wild M. sinensis germplasm in the breeding program. The results in this study will facilitate the biofuel feedstock breeding program and germplasm conservation.
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Affiliation(s)
- Gang Nie
- Grassland Science Department, Sichuan Agricultural University, Ya'an 625014, China.
| | - Xin-Quan Zhang
- Grassland Science Department, Sichuan Agricultural University, Ya'an 625014, China.
| | - Lin-Kai Huang
- Grassland Science Department, Sichuan Agricultural University, Ya'an 625014, China.
| | - Wen-Zhi Xu
- Grassland Science Department, Sichuan Agricultural University, Ya'an 625014, China.
| | - Jian-Ping Wang
- Agronomy Department, University of Florida, Gainesville, FL 32610, USA.
| | - Yun-Wei Zhang
- Grassland Institute, China Agricultural University, Beijing 100193, China.
| | - Xiao Ma
- Grassland Science Department, Sichuan Agricultural University, Ya'an 625014, China.
| | - Yan-Hong Yan
- Grassland Science Department, Sichuan Agricultural University, Ya'an 625014, China.
| | - Hai-Dong Yan
- Grassland Science Department, Sichuan Agricultural University, Ya'an 625014, China.
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