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Huang L, Feng G, Yan H, Zhang Z, Bushman BS, Wang J, Bombarely A, Li M, Yang Z, Nie G, Xie W, Xu L, Chen P, Zhao X, Jiang W, Zhang X. Genome assembly provides insights into the genome evolution and flowering regulation of orchardgrass. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:373-388. [PMID: 31276273 PMCID: PMC6953241 DOI: 10.1111/pbi.13205] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 05/27/2019] [Accepted: 06/29/2019] [Indexed: 05/18/2023]
Abstract
Orchardgrass (Dactylis glomerata L.) is an important forage grass for cultivating livestock worldwide. Here, we report an ~1.84-Gb chromosome-scale diploid genome assembly of orchardgrass, with a contig N50 of 0.93 Mb, a scaffold N50 of 6.08 Mb and a super-scaffold N50 of 252.52 Mb, which is the first chromosome-scale assembled genome of a cool-season forage grass. The genome includes 40 088 protein-coding genes, and 69% of the assembled sequences are transposable elements, with long terminal repeats (LTRs) being the most abundant. The LTRretrotransposons may have been activated and expanded in the grass genome in response to environmental changes during the Pleistocene between 0 and 1 million years ago. Phylogenetic analysis reveals that orchardgrass diverged after rice but before three Triticeae species, and evolutionarily conserved chromosomes were detected by analysing ancient chromosome rearrangements in these grass species. We also resequenced the whole genome of 76 orchardgrass accessions and found that germplasm from Northern Europe and East Asia clustered together, likely due to the exchange of plants along the 'Silk Road' or other ancient trade routes connecting the East and West. Last, a combined transcriptome, quantitative genetic and bulk segregant analysis provided insights into the genetic network regulating flowering time in orchardgrass and revealed four main candidate genes controlling this trait. This chromosome-scale genome and the online database of orchardgrass developed here will facilitate the discovery of genes controlling agronomically important traits, stimulate genetic improvement of and functional genetic research on orchardgrass and provide comparative genetic resources for other forage grasses.
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Affiliation(s)
- Linkai Huang
- Department of Grassland ScienceAnimal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
| | - Guangyan Feng
- Department of Grassland ScienceAnimal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
| | - Haidong Yan
- Department of Grassland ScienceAnimal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
- School of Plant and Environmental SciencesVirginia TechBlacksburgVAUSA
| | | | | | - Jianping Wang
- Agronomy DepartmentUniversity of FloridaGainesvilleFLUSA
| | | | - Mingzhou Li
- Animal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
| | - Zhongfu Yang
- Department of Grassland ScienceAnimal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
| | - Gang Nie
- Department of Grassland ScienceAnimal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
| | - Wengang Xie
- State Key Laboratory of Grassland Agro‐EcosystemsCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Lei Xu
- Department of Grassland ScienceAnimal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
| | - Peilin Chen
- Department of Grassland ScienceAnimal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
| | - Xinxin Zhao
- Department of Grassland ScienceAnimal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
| | | | - Xinquan Zhang
- Department of Grassland ScienceAnimal Science and Technology CollegeSichuan Agricultural UniversityChengduChina
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Klaas M, Haiminen N, Grant J, Cormican P, Finnan J, Arojju SK, Utro F, Vellani T, Parida L, Barth S. Transcriptome characterization and differentially expressed genes under flooding and drought stress in the biomass grasses Phalaris arundinacea and Dactylis glomerata. ANNALS OF BOTANY 2019; 124:717-730. [PMID: 31241131 PMCID: PMC6821378 DOI: 10.1093/aob/mcz074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 05/09/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND AND AIMS Perennial grasses are a global resource as forage, and for alternative uses in bioenergy and as raw materials for the processing industry. Marginal lands can be valuable for perennial biomass grass production, if perennial biomass grasses can cope with adverse abiotic environmental stresses such as drought and waterlogging. METHODS In this study, two perennial grass species, reed canary grass (Phalaris arundinacea) and cocksfoot (Dactylis glomerata) were subjected to drought and waterlogging stress to study their responses for insights to improving environmental stress tolerance. Physiological responses were recorded, reference transcriptomes established and differential gene expression investigated between control and stress conditions. We applied a robust non-parametric method, RoDEO, based on rank ordering of transcripts to investigate differential gene expression. Furthermore, we extended and validated vRoDEO for comparing samples with varying sequencing depths. KEY RESULTS This allowed us to identify expressed genes under drought and waterlogging whilst using only a limited number of RNA sequencing experiments. Validating the methodology, several differentially expressed candidate genes involved in the stage 3 step-wise scheme in detoxification and degradation of xenobiotics were recovered, while several novel stress-related genes classified as of unknown function were discovered. CONCLUSIONS Reed canary grass is a species coping particularly well with flooding conditions, but this study adds novel information on how its transcriptome reacts under drought stress. We built extensive transcriptomes for the two investigated C3 species cocksfoot and reed canary grass under both extremes of water stress to provide a clear comparison amongst the two species to broaden our horizon for comparative studies, but further confirmation of the data would be ideal to obtain a more detailed picture.
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Affiliation(s)
- Manfred Klaas
- Teagasc Crops Environment and Land Use Programme, Oak Park Crops Research Centre, Carlow, Ireland
| | - Niina Haiminen
- Computational Biology Center, IBM T. J. Watson Research Center, Yorktown Heights, NY, USA
| | - Jim Grant
- Teagasc Statistics and Applied Physics Research Operations Group, Ashtown, Dublin, Ireland
| | - Paul Cormican
- Teagasc Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland
| | - John Finnan
- Teagasc Crops Environment and Land Use Programme, Oak Park Crops Research Centre, Carlow, Ireland
| | - Sai Krishna Arojju
- Teagasc Crops Environment and Land Use Programme, Oak Park Crops Research Centre, Carlow, Ireland
| | - Filippo Utro
- Computational Biology Center, IBM T. J. Watson Research Center, Yorktown Heights, NY, USA
| | - Tia Vellani
- Teagasc Crops Environment and Land Use Programme, Oak Park Crops Research Centre, Carlow, Ireland
| | - Laxmi Parida
- Computational Biology Center, IBM T. J. Watson Research Center, Yorktown Heights, NY, USA
| | - Susanne Barth
- Teagasc Crops Environment and Land Use Programme, Oak Park Crops Research Centre, Carlow, Ireland
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Genetic Diversity and DNA Fingerprints of Three Important Aquatic Vegetables by EST-SSR Markers. Sci Rep 2019; 9:14074. [PMID: 31575997 PMCID: PMC6773842 DOI: 10.1038/s41598-019-50569-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 09/16/2019] [Indexed: 11/29/2022] Open
Abstract
Twenty-two sacred lotus (Nelumbo nucifera), 46 taros (Colocasia esculenta) and 10 arrowheads (Sagittaria trifolia) were used as materials and combined with EST-SSR (expressed sequence tag-simple sequence repeats) primers developed by our laboratory. Core primers were screened from a large number of primers that were able to distinguish all materials with a high frequency of polymorphisms. Six pairs, twenty pairs and three pairs of core primers were screened from sacred lotus, taro, and arrowhead, respectively. The SSR fingerprints of these three important aquatic vegetables, producing 17-, 87- and 14-bit binary molecular identity cards, respectively, were separately determined by using the core primers. Since there were few core primers of sacred lotus and arrowhead, 3 and 9 primer pairs with higher polymorphic information content (PIC), respectively, were selected as candidate primers. These core and candidate primers were used to identify the purities of No.36 space lotus, Shandong 8502 taro and Wuhan arrowhead, which were 93.3% (84/90), 98.9% (89/90) and 100.0% (90/90), respectively. The fingerprints, displayed as binary molecular identification cards of three important aquatic vegetables, were obtained, and their purity was successfully determined with EST-SSR labeling technology. Phylogenetic trees were also constructed to analyze the genetic diversity of 22 sacred lotus, 46 taros and 10 arrowheads. This study classifies and identifies germplasm resources and is an important reference to test the authenticity and variety purity of other aquatic vegetables in the future.
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Genotyping by Sequencing and Plastome Analysis Finds High Genetic Variability and Geographical Structure in Dactylis glomerata L. in Northwest Europe Despite Lack of Ploidy Variation. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy9070342] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Large collections of the forage and bioenergy grass Dactylis glomerata were made in northwest (NW) Europe along east to west and north to south clines for genetic resource conservation and to inform breeding programmes of genetic diversity, genepools, and ploidy. Leaves were sampled for genetic analysis and seed and rhizome for ex-situ conservation. Genotyping by sequencing (GBS) was used to assay nuclear DNA diversity and plastome single nucleotide polymorphism (SNP) discovery was undertaken using a long-read PCR and MiSeq approach. Nuclear and plastid SNPs were analysed by principal component analysis (PCA) to compare genotypes. Flow cytometry revealed that all samples were tetraploid, but some genome size variation was recorded. GBS detected an average of approximately 10,000 to 15,000 SNPs per country sampled. The highest average number of private SNPs was recorded in Poland (median ca. 2000). Plastid DNA variation was also high (1466 SNPs, 17 SNPs/kbp). GBS data, and to a lesser extent plastome data, also show that genetic variation is structured geographically in NW Europe with loose clustering matching the country of plant origin. The results reveal extensive genetic diversity and genetic structuring in this versatile allogamous species despite lack of ploidy variation and high levels of human mediated geneflow via planting.
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Li J, Guo H, Wang Y, Zong J, Chen J, Li D, Li L, Wang J, Liu J. High-throughput SSR marker development and its application in a centipedegrass (Eremochloa ophiuroides (Munro) Hack.) genetic diversity analysis. PLoS One 2018; 13:e0202605. [PMID: 30133524 PMCID: PMC6105027 DOI: 10.1371/journal.pone.0202605] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 08/05/2018] [Indexed: 11/18/2022] Open
Abstract
Centipedegrass (Eremochloa ophiuroides (Munro) Hack.) is a perennial, warm-season C4 grass species that shows great potential for use as a low-maintenance turfgrass species in tropical and subtropical regions. However, limited genetic and genomic information is available for this species, which has impeded systematic studies on the enhancement of its turf quality and resistance against biotic and abiotic stress. In this study, Illumina HiSeq high-throughput sequencing technology was performed to generate centipedegrass transcriptome sequences. A total of 352,513 assembled sequences were used to search for simple sequence repeat (SSR) loci, and 64,470 SSR loci were detected in 47,638 SSR containing sequences. The tri-nucleotides were the most frequent repeat motif, followed by di-nucleotides, tetra-nucleotides hexnucleotides, and pentanucleotides. A total of 48,061 primer pairs were successfully designed in the flanking sequences of the SSRs, and 100 sets of primers were randomly selected for the initial validation in four centipedegrass accessions. In total, 56 (56.0%) of the 100 primer pairs tested successfully amplified alleles from all four centipedegrass accessions, while 50 were identified as polymorphic markers and were then used to assess the level of genetic diversity among 43 centipedegrass core collections. The genetic diversity analysis exhibited that the number of alleles (Na) per locus ranged from 3 to 13, and the observed heterozygosity (Ho) ranged from 0.17 to 0.83. The polymorphism information content (PIC) value of the markers ranged from 0.15 to 0.78, and the genetic distances (coefficient Nei72) between the accessions varied from 0.07 to 0.48. The UPGMA-based dendrogram clustered all 43 core collections into two main groups and six subgroups, which further validated the effectiveness of these newly developed SSR markers. Hence, these newly developed SSR markers will be valuable and potentially useful for future genetic and genomic studies of E. ophiuroides.
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Affiliation(s)
- Jianjian Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Hailin Guo
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Yi Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Junqin Zong
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Jingbo Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Dandan Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Ling Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Jingjing Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
| | - Jianxiu Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing, Jiangsu, China
- * E-mail:
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Zhao X, Bushman BS, Zhang X, Robbins MD, Larson SR, Robins JG, Thomas A. Association of candidate genes with heading date in a diverse Dactylis glomerata population. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 265:146-153. [PMID: 29223336 DOI: 10.1016/j.plantsci.2017.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 09/29/2017] [Accepted: 10/03/2017] [Indexed: 06/07/2023]
Abstract
Flowering occurs in response to cues from both temperature and photoperiod elicitors in cool-season, long-day forage grasses, and genes involved in sensing the elicitors and inducing downstream flowering responses have been associated with heading date and flowering time in perennial forage grasses as well as cereal grasses. In this study we test for association between orchardgrass (Dactylis glomerata L.) heading date and polymorphisms in the CONSTANS (DgCO1), FLOWERING TIME (DgFT1), a VRN1 like MADS-box (DgMADS), and PHOTOPERIOD (DgPPD1-like) containing genes. A diverse population of 150 genotypes was measured for heading date across three years, genotyped, and candidate genes sequenced. Although pairwise population kinship values were generally low, the genotypes fit into a two-group structure model. Linkage disequilibrium decayed rapidly, reaching r2 levels below 0.2 within the 500bp of each gene. SNPs significantly associated with heading date were detected in equal-dose and tetraploid dosage models. The DgCO1 gene had the most significant polymorphisms and those with the largest effects, while DgMADS had several significant polymorphisms in its first intron with smaller effects. These polymorphisms can be used for further validation, selection, and development of breeding lines of orchardgrass.
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Affiliation(s)
- Xinxin Zhao
- USDA-ARS Forage and Range Research Laboratory, 695 North 1100 East, Logan, UT 84322-6300, USA; Department of Grassland Science, Sichuan Agricultural University, Chengdu, China
| | - B Shaun Bushman
- USDA-ARS Forage and Range Research Laboratory, 695 North 1100 East, Logan, UT 84322-6300, USA.
| | - Xinquan Zhang
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, China
| | - Matthew D Robbins
- USDA-ARS Forage and Range Research Laboratory, 695 North 1100 East, Logan, UT 84322-6300, USA
| | - Steven R Larson
- USDA-ARS Forage and Range Research Laboratory, 695 North 1100 East, Logan, UT 84322-6300, USA
| | - Joseph G Robins
- USDA-ARS Forage and Range Research Laboratory, 695 North 1100 East, Logan, UT 84322-6300, USA
| | - Aaron Thomas
- Utah State University, Center for Integrated Biosystems, Logan, UT, USA
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Zhao X, Huang L, Zhang X, Wang J, Yan D, Li J, Tang L, Li X, Shi T. Construction of high-density genetic linkage map and identification of flowering-time QTLs in orchardgrass using SSRs and SLAF-seq. Sci Rep 2016; 6:29345. [PMID: 27389619 PMCID: PMC4937404 DOI: 10.1038/srep29345] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/17/2016] [Indexed: 11/09/2022] Open
Abstract
Orchardgrass (Dactylis glomerata L.) is one of the most economically important perennial, cool-season forage species grown and pastured worldwide. High-density genetic linkage mapping is a valuable and effective method for exploring complex quantitative traits. In this study, we developed 447,177 markers based on SLAF-seq and used them to perform a comparative genomics analysis. Perennial ryegrass sequences were the most similar (5.02%) to orchardgrass sequences. A high-density linkage map of orchardgrass was constructed using 2,467 SLAF markers and 43 SSRs, which were distributed on seven linkage groups spanning 715.77 cM. The average distance between adjacent markers was 0.37 cM. Based on phenotyping in four environments, 11 potentially significant quantitative trait loci (QTLs) for two target traits–heading date (HD) and flowering time (FT)–were identified and positioned on linkage groups LG1, LG3, and LG5. Significant QTLs explained 8.20–27.00% of the total phenotypic variation, with the LOD ranging from 3.85–12.21. Marker167780 and Marker139469 were associated with FT and HD at the same location (Ya’an) over two different years. The utility of SLAF markers for rapid generation of genetic maps and QTL analysis has been demonstrated for heading date and flowering time in a global forage grass.
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Affiliation(s)
- Xinxin Zhao
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linkai Huang
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xinquan Zhang
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jianping Wang
- Agronomy Department, University of Florida, FL, 32610, USA
| | - Defei Yan
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ji Li
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lu Tang
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaolong Li
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Tongwei Shi
- Biomarker Technologies Corporation, Beijing, 101300, China
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Ahmed S, Zhan C, Yang Y, Wang X, Yang T, Zhao Z, Zhang Q, Li X, Hu X. The Transcript Profile of a Traditional Chinese Medicine, Atractylodes lancea, Revealing Its Sesquiterpenoid Biosynthesis of the Major Active Components. PLoS One 2016; 11:e0151975. [PMID: 26990438 PMCID: PMC4798728 DOI: 10.1371/journal.pone.0151975] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Accepted: 03/07/2016] [Indexed: 11/18/2022] Open
Abstract
Atractylodes lancea (Thunb.) DC., named “Cangzhu” in China, which belongs to the Asteraceae family. In some countries of Southeast Asia (China, Thailand, Korea, Japan etc.) its rhizome, commonly called rhizoma atractylodis, is used to treat many diseases as it contains a variety of sesquiterpenoids and other components of medicinal importance. Despite its medicinal value, the information of the sesquiterpenoid biosynthesis is largely unknown. In this study, we investigated the transcriptome analysis of different tissues of non-model plant A. lancea by using short read sequencing technology (Illumina). We found 62,352 high quality unigenes with an average sequence length of 913 bp in the transcripts of A. Lancea. Among these, 43,049 (69.04%), 30,264 (48.53%), 26,233 (42.07%), 17,881 (28.67%) and 29,057(46.60%) unigenes showed significant similarity (E-value<1e-5) to known proteins in Nr, KEGG, SWISS-PROT, GO, and COG databases, respectively. Of the total 62,352 unigenes, 43,049 (Nr Database) open reading frames were predicted. On the basis of different bioinformatics tools we identify all the enzymes that take part in the terpenoid biosynthesis as well as five different known sesquiterpenoids via cytosolic mevalonic acid (MVA) pathway and plastidal methylerythritol phosphate (MEP) pathways. In our study, 6, 864 Simple Sequence Repeats (SSRs) were also found as great potential markers in A. lancea. This transcriptomic resource of A. lancea provides a great contribution in advancement of research for this specific medicinal plant and more specifically for the gene mining of different classes of terpenoids and other chemical compounds that have medicinal as well as economic importance.
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Affiliation(s)
- Shakeel Ahmed
- Department of Medicinal Plant, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Center for Plant Functional Components, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Engineering Research Center for Medicinal Plants, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Chuansong Zhan
- Department of Medicinal Plant, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Center for Plant Functional Components, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Engineering Research Center for Medicinal Plants, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Yanyan Yang
- Department of Medicinal Plant, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Engineering Research Center for Medicinal Plants, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Xuekui Wang
- Department of Medicinal Plant, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Engineering Research Center for Medicinal Plants, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Tewu Yang
- Department of Medicinal Plant, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Engineering Research Center for Medicinal Plants, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Zeying Zhao
- Department of Medicinal Plant, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Engineering Research Center for Medicinal Plants, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Qiyun Zhang
- Department of Medicinal Plant, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Center for Plant Functional Components, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Engineering Research Center for Medicinal Plants, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Xiaohua Li
- Department of Medicinal Plant, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Center for Plant Functional Components, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Engineering Research Center for Medicinal Plants, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Xuebo Hu
- Department of Medicinal Plant, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Center for Plant Functional Components, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- Engineering Research Center for Medicinal Plants, Huazhong Agricultural University, Wuhan, 430070, P.R. China
- * E-mail:
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9
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Kallida R, Zhouri L, Volaire F, Guerin A, Julier B, Shaimi N, Fakiri M, Barre P. Combining Drought Survival via Summer Dormancy and Annual Biomass Productivity in Dactylis glomerata L. FRONTIERS IN PLANT SCIENCE 2016; 7:82. [PMID: 26904054 PMCID: PMC4746912 DOI: 10.3389/fpls.2016.00082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 01/17/2016] [Indexed: 06/05/2023]
Abstract
Under Mediterranean climates, the best strategy to produce rain-fed fodder crops is to develop perennial drought resistant varieties. Summer dormancy present in native germplasm has been shown to confer a high level of survival under severe drought. Nevertheless it has also been shown to be negatively correlated with annual biomass productivity. The aim of this study was to analyze the correlations between summer dormancy and annual biomass productivity related traits and to identify quantitative trait loci (QTL) for these traits in a progeny of a summer dormant cocksfoot parent (Kasbah) and a summer active parent (Medly). A total of 283 offspring and the parents were phenotyped for summer dormancy, plant growth rate (PGR) and heading date in Morocco and for maximum leaf elongation rate (LERm) in France. The individuals were genotyped with a total of 325 markers including 59 AFLP, 64 SSR, and 202 DArT markers. The offspring exhibited a large quantitative variation for all measured traits. Summer dormancy showed a negative correlation with both PGR (-0.34 p < 0.005) and LERm (-0.27 p < 0.005). However, genotypes with both a high level of summer dormancy and a high level of PGR were detected in the progeny. One genetic map per parent was built with a total length of 377 and 423 cM for Kasbah and Medly, respectively. Both different and co-localized QTL for summer dormancy and PGR were identified. These results demonstrate that it should be possible to create summer dormant cocksfoot varieties with a high annual biomass productivity.
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Affiliation(s)
- Rajae Kallida
- Unité de Recherche de Production Animales et Fourrage, INRA Maroc, Centre Régional de la Recherche Agronomique de RabatRabat, Morocco
| | - Latifa Zhouri
- Unité de Recherche de Production Animales et Fourrage, INRA Maroc, Centre Régional de la Recherche Agronomique de RabatRabat, Morocco
- Laboratoire d’agroalimentaire et santé, Faculté des Sciences Techniques de Settat, Université Hassan 1erSettat, Morocco
| | - Florence Volaire
- USC 1338, Centre d’Ecologie Fonctionnelle et Evolutive, UMR 5175, Institut National de la Recherche AgronomiqueMontpellier, France
| | - Adrien Guerin
- UR4 Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères, Institut National de la Recherche AgronomiqueLusignan, France
| | - Bernadette Julier
- UR4 Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères, Institut National de la Recherche AgronomiqueLusignan, France
| | - Naima Shaimi
- Unité de Recherche d’Amélioration des Plantes Valorisation et Conservation des Ressources Phytogénétiques, INRA Maroc, Centre Régional de la Recherche Agronomique de RabatRabat, Morocco
| | - Malika Fakiri
- Laboratoire d’agroalimentaire et santé, Faculté des Sciences Techniques de Settat, Université Hassan 1erSettat, Morocco
| | - Philippe Barre
- UR4 Unité de Recherche Pluridisciplinaire Prairies et Plantes Fourragères, Institut National de la Recherche AgronomiqueLusignan, France
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10
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Huang LK, Yan HD, Zhao XX, Zhang XQ, Wang J, Frazier T, Yin G, Huang X, Yan DF, Zang WJ, Ma X, Peng Y, Yan YH, Liu W. Identifying differentially expressed genes under heat stress and developing molecular markers in orchardgrass (Dactylis glomerataL.) through transcriptome analysis. Mol Ecol Resour 2015; 15:1497-509. [DOI: 10.1111/1755-0998.12418] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 04/08/2015] [Accepted: 04/15/2015] [Indexed: 11/29/2022]
Affiliation(s)
- L. K. Huang
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - H. D. Yan
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - X. X. Zhao
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - X. Q. Zhang
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - J. Wang
- Agronomy Department; University of Florida; Gainesville FL 32611 USA
| | - T. Frazier
- Department of Horticulture; Virginia Tech; Blacksburg VA 24061 USA
| | - G. Yin
- Department of Crop, Soil, and Environmental Sciences; University of Arkansas; Fayetteville AR 72704 USA
| | - X. Huang
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - D. F. Yan
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - W. J. Zang
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - X. Ma
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - Y. Peng
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - Y. H. Yan
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - W. Liu
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
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11
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Last L, Widmer F, Fjellstad W, Stoyanova S, Kölliker R. Genetic diversity of natural orchardgrass (Dactylis glomerata L.) populations in three regions in Europe. BMC Genet 2013; 14:102. [PMID: 24165514 PMCID: PMC4231346 DOI: 10.1186/1471-2156-14-102] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 10/08/2013] [Indexed: 11/29/2022] Open
Abstract
Background Dactylis glomerata (orchardgrass or cocksfoot) is a forage crop of agronomic importance comprising high phenotypic plasticity and variability. Although the genus Dactylis has been studied quite well within the past century, little is known about the genetic diversity and population patterns of natural populations from geographically distinct grassland regions in Europe. The objectives of this study were to test the ploidy level of 59 natural and semi-natural populations of D. glomerata, to investigate genetic diversity, differentiation patterns within and among the three geographic regions, and to evaluate selected populations for their value as genetic resources. Results Among 1861 plants from 20 Swiss, 20 Bulgarian and 19 Norwegian populations of D. glomerata, exclusively tetraploid individuals were identified based on 29 SSR markers. The average expected heterozygosity (HE,C) ranged from 0.44 to 0.59 and was highest in the Norwegian region. The total number of rare alleles was high, accounting for 59.9% of the amplified alleles. 80.82% of the investigated individuals could be assigned to their respective geographic region based on allele frequencies. Average genetic distances were low despite large geographic distances and ranged from D = 0.09 to 0.29 among populations. Conclusions All three case study regions revealed high genetic variability of tetraploid D. glomerata within selected populations and numerous rare and localized alleles which were geographically unique. The large, permanent grassland patches in Bulgaria provided a high genetic diversity, while fragmented, semi-natural grassland in the Norwegian region provided a high amount of rare, localized alleles, which have to be considered in conservation and breeding strategies. Therefore, the selected grassland populations investigated conserve a large pool of genetic resources and provide valuable sources for forage crop breeding programs.
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Affiliation(s)
| | | | | | | | - Roland Kölliker
- Agroscope Reckenholz-Tänikon Research Station ART, Reckenholzstrasse 191, Zurich 8046, Switzerland.
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12
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Jiang B, Xie D, Liu W, Peng Q, He X. De novo assembly and characterization of the transcriptome, and development of SSR markers in wax gourd (Benicasa hispida). PLoS One 2013; 8:e71054. [PMID: 23951078 PMCID: PMC3738631 DOI: 10.1371/journal.pone.0071054] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 06/26/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Wax gourd is a widely used vegetable of Cucuribtaceae, and also has important medicinal and health values. However, the genomic resources of wax gourd were scarcity, and only a few nucleotide sequences could be obtained in public databases. METHODOLOGY/PRINCIPAL FINDINGS In this study, we examined transcriptome in wax gourd. More than 44 million of high quality reads were generated from five different tissues of wax gourd using Illumina paired-end sequencing technology. Approximately 4 Gbp data were generated, and de novo assembled into 65,059 unigenes, with an N50 of 1,132 bp. Based on sequence similarity search with known protein database, 36,070 (55.4%) showed significant similarity to known proteins in Nr database, and 24,969 (38.4%) had BLAST hits in Swiss-Prot database. Among the annotated unigenes, 14,994 of wax gourd unigenes were assigned to GO term annotation, and 23,977 were found to have COG classifications. In addition, a total of 18,713 unigenes were assigned to 281 KEGG pathways. Furthermore, 6,242 microsatellites (simple sequence repeats) were detected as potential molecular markers in wax gourd. Two hundred primer pairs for SSRs were designed for validation of the amplification and polymorphism. The result showed that 170 of the 200 primer pairs were successfully amplified and 49 (28.8%) of them exhibited polymorphisms. CONCLUSION/SIGNIFICANCE Our study enriches the genomic resources of wax gourd and provides powerful information for future studies. The availability of this ample amount of information about the transcriptome and SSRs in wax gourd could serve as valuable basis for studies on the physiology, biochemistry, molecular genetics and molecular breeding of this important vegetable crop.
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Affiliation(s)
- Biao Jiang
- Vegetable Research Institute, Guangdong Academy of Agricultural Science, Guangzhou, China
- Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou, China
| | - Dasen Xie
- Vegetable Research Institute, Guangdong Academy of Agricultural Science, Guangzhou, China
- Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou, China
- * E-mail:
| | - Wenrui Liu
- Vegetable Research Institute, Guangdong Academy of Agricultural Science, Guangzhou, China
- Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou, China
| | - Qingwu Peng
- Vegetable Research Institute, Guangdong Academy of Agricultural Science, Guangzhou, China
| | - Xiaoming He
- Vegetable Research Institute, Guangdong Academy of Agricultural Science, Guangzhou, China
- Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou, China
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13
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Peanut (Arachis hypogaea) Expressed Sequence Tag Project: Progress and Application. Comp Funct Genomics 2012; 2012:373768. [PMID: 22745594 PMCID: PMC3382957 DOI: 10.1155/2012/373768] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 04/26/2012] [Indexed: 12/12/2022] Open
Abstract
Many plant ESTs have been sequenced as an alternative to whole genome sequences, including peanut because of the genome size and complexity. The US peanut research community had the historic 2004 Atlanta Genomics Workshop and named the EST project as a main priority. As of August 2011, the peanut research community had deposited 252,832 ESTs in the public NCBI EST database, and this resource has been providing the community valuable tools and core foundations for various genome-scale experiments before the whole genome sequencing project. These EST resources have been used for marker development, gene cloning, microarray gene expression and genetic map construction. Certainly, the peanut EST sequence resources have been shown to have a wide range of applications and accomplished its essential role at the time of need. Then the EST project contributes to the second historic event, the Peanut Genome Project 2010 Inaugural Meeting also held in Atlanta where it was decided to sequence the entire peanut genome. After the completion of peanut whole genome sequencing, ESTs or transcriptome will continue to play an important role to fill in knowledge gaps, to identify particular genes and to explore gene function.
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14
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Xie W, Robins JG, Bushman BS. A genetic linkage map of tetraploid orchardgrass (Dactylis glomerata L.) and quantitative trait loci for heading date. Genome 2012; 55:360-9. [PMID: 22551303 DOI: 10.1139/g2012-026] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Orchardgrass (Dactylis glomerata L.), or cocksfoot, is indigenous to Eurasia and northern Africa, but has been naturalized on nearly every continent and is one of the top perennial forage grasses grown worldwide. To improve the understanding of genetic architecture of orchardgrass and provide a template for heading date candidate gene search in this species, the goals of the present study were to construct a tetraploid orchardgrass genetic linkage map and identify quantitative trait loci associated with heading date. A combination of SSR markers derived from an orchardgrass EST library and AFLP markers were used to genotype an F1 population of 284 individuals derived from a very late heading Dactylis glomerata subsp. himalayensis parent and an early to mid-heading Dactylis glomerata subsp. aschersoniana parent. Two parental maps were constructed with 28 cosegregation groups and seven consensus linkage groups each, and homologous linkage groups were tied together by 38 bridging markers. Linkage group lengths varied from 98 to 187 cM, with an average distance between markers of 5.5 cM. All but two mapped SSR markers had homologies to physically mapped rice (Oryza sativa L.) genes, and six of the seven orchardgrass linkage groups were assigned based on this putative synteny with rice. Quantitative trait loci were detected for heading date on linkage groups 2, 5, and 6 in both parental maps, explaining between 12% and 24% of the variation.
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Affiliation(s)
- Wengang Xie
- United States Department of Agriculture, Agricultural Research Service, Forage and Range Research Laboratory, Logan, UT 84322-6300, USA
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