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Li Z, Wang T, Yun L, Ren X, Wang Y, Shi F. Association Analysis of Tiller-Related Traits with EST-SSR Markers in Psathyrostachys juncea. Genes (Basel) 2023; 14:1970. [PMID: 37895319 PMCID: PMC10606050 DOI: 10.3390/genes14101970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Psathyrostachys juncea is a long-lived perennial Gramineae grass with dense basal tillers and soft leaves. It is used widely in cold and dry areas of Eurasia and North America to establish grazing pasture and is even used as an ideal plant for revegetation and ecological restoration. Plant architecture, especially tillering traits, is critical for bunch grasses in breeding programs, and these traits in plants are mostly quantitative traits. In this study, the genetic diversity, population structure, and linkage disequilibrium of 480 individual lines were analyzed using 127 pairs of the EST-SSR marker, and a significant association between ten plant-architecture-related traits of P. juncea and molecular markers was found. The results of the genetic diversity analysis showed that the number of observed alleles was 1.957, the number of effective alleles was 1.682, Shannon's information index was 0.554, observed heterozygosity was 0.353, expected heterozygosity was 0.379, and the polymorphism information content was 0.300. A total of 480 individual lines were clustered into five groups based on population genetic structure, principal coordinate analysis, and unweighted pair group method with arithmetic mean analysis (UPGMA). The linkage disequilibrium coefficient (r2) was between 0.00 and 0.68, with an average of 0.04, which indicated a relatively low level of linkage disequilibrium among loci. The results of the association analysis revealed 55 significant marker-trait associations (MTA). Moreover, nine SSR markers were associated with multiple traits. This study provides tools with promising applications in the molecular selection and breeding of P. juncea germplasm.
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Affiliation(s)
- Zhen Li
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010010, China; (Z.L.)
| | - Tian Wang
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010010, China; (Z.L.)
| | - Lan Yun
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010010, China; (Z.L.)
- Key Laboratory of Grassland Resources Ministry of Education, Hohhot 010010, China
| | - Xiaomin Ren
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010010, China; (Z.L.)
| | - Yong Wang
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010010, China; (Z.L.)
| | - Fengling Shi
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010010, China; (Z.L.)
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Qu M, Zheng Y, Bi L, Yang X, Shang P, Zhou X, Zeng B, Shen B, Li W, Fan Y, Zeng B. Comparative transcriptomic analysis of the gene expression and underlying molecular mechanism of submergence stress response in orchardgrass roots. FRONTIERS IN PLANT SCIENCE 2023; 13:1104755. [PMID: 36704155 PMCID: PMC9871833 DOI: 10.3389/fpls.2022.1104755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Submergence stress creates a hypoxic environment. Roots are the first plant organ to face these low-oxygen conditions, which causes damage and affects the plant growth and yield. Orchardgrass (Dactylis glomerata L.) is one of the most important cold-season forage grasses globally. However, their submergence stress-induced gene expression and the underlying molecular mechanisms of orchardgrass roots are still unknown. METHODS Using the submergence-tolerant 'Dianbei' and submergence-sensitive 'Anba', the transcriptomic analysis of orchardgrass roots at different time points of submergence stress (0 h, 8 h, and 24 h) was performed. RESULTS We obtained 118.82Gb clean data by RNA-Seq. As compared with the control, a total of 6663 and 9857 differentially expressed genes (DEGs) were detected in Dianbei, while 7894 and 11215 DEGs were detected in Anba at 8 h and 24 h post-submergence-stress, respectively. Gene Ontology (GO) enrichment analysis obtained 986 terms, while Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis obtained 123 pathways. Among them, the DEGs in plant hormones, mitogen-activated protein kinase (MAPK) and Ca2+ signal transduction were significantly differentially expressed in Dianbei, but not in Anba. DISCUSSION This study was the first to molecularly elucidate the submergence stress tolerance in the roots of two orchardgrass cultivars. These findings not only enhanced our understanding of the orchardgrass submergence tolerance, but also provided a theoretical basis 36 for the cultivation of submergence-tolerant forage varieties.
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Affiliation(s)
- Minghao Qu
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yuqian Zheng
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Lei Bi
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Xingyun Yang
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Panpan Shang
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Xiaoli Zhou
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Bing Zeng
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Bingna Shen
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Wenwen Li
- College of Animal Science and Technology, Southwest University, Chongqing, China
| | - Yan Fan
- Institute of Prataculture, Chongqing Academy of Animal Science, Chongqing, China
| | - Bing Zeng
- College of Animal Science and Technology, Southwest University, Chongqing, China
- Chongqing University Herbivore Engineering Research Center, Chongqing, China
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Rai MK. Start codon targeted (SCoT) polymorphism marker in plant genome analysis: current status and prospects. PLANTA 2023; 257:34. [PMID: 36622439 DOI: 10.1007/s00425-023-04067-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
The present review illustrates a comprehensive overview of the start codon targeted (SCoT) polymorphism marker and their utilization in various applications related to genetic and genomic studies. Start codon targeted (SCoT) polymorphism marker, a targeted fingerprinting marker technique, has gained considerable importance in plant genetics, genomics, and molecular breeding due to its many desirable features. SCoT marker targets the region flanking the start codon, a highly conserved region in plant genes. Therefore, it can distinguish genetic variations in a specific gene that link to a specific trait. It is a simple, novel, cost-effective, highly polymorphic, and reproducible molecular marker for which there is no need for prior sequence information. In the recent past, SCoT markers have been employed in many commercially important and underutilized plant species for a variety of applications, including genetic diversity analysis, interspecific/generic genetic relationships, cultivar/hybrid/species identification, sex determination, construction of linkage map, association mapping/analysis, differential gene expression, and genetic fidelity analysis of tissue culture-raised plants. The main aim of this review is to provide up-to-date information on SCoT markers and their application in many commercially important and underutilized plant species, mainly progress made in the last 8-10 years.
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Affiliation(s)
- Manoj K Rai
- Department of Environmental Science, Indira Gandhi National Tribal University, Amarkantak, MP, 484887, India.
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Mavlyutov Y, Kostenko S, Shamustakimova A, Klimenko I. Genetic variability analysis of Russian cultivars of ryegrass (Lolium) based on SCoT markers. J Genet Eng Biotechnol 2022; 20:163. [PMID: 36512171 PMCID: PMC9748000 DOI: 10.1186/s43141-022-00446-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 12/04/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND Ryegrass is a promising crop for the development of meadow farming in the world. More than 1000 cultivated varieties widely used in feed production have been developed, based on the main species - perennial ryegrass (Lolium perenne L.) and annual one (Lolium multiflorum Lam.). Development and implementation of the modern methods of plant varietal and species identification are of great importance. In recent years, molecular markers have been successfully used for these purposes, which increase the accuracy of the breeding material evaluation at a significant reduction of time and labor costs. The aim of this study was to assess the discriminatory potential of the new SCoT marking technique for the identification of Russian perennial (Lolium perenne L.) and annual (Lolium multiflorum Lam.) ryegrass varieties. RESULTS Out of the total number of the tested SCoT-primers, 8 polymorphic ones were selected, which demonstrates the high stability and reproducibly amplified DNA fragments. These primers generated 107 PCR products, where 37 were found to be polymorphic. The average number of amplicons per primer was 13. The size of the PCR products varied from 349 to 2718 bp (see Table 3). The polymorphic ratio of the tested markers was 30.8%. The marker SCoT-06 was characterized by the maximum number of PCR products and the highest level of polymorphism (50%). The effective number of alleles (ne) ranged from 1.35 to 1.58 with a mean of 1.48 per locus. The average value of the PIC and Shannon index (I) were 0.35 and 0.46, respectively. The unique PCR fragments were revealed for the identification of tested varieties. Analysis of molecular variance (AMOVA) showed that the level of genetic diversity between ryegrass species (59%) was more than between varieties within a species (41%). Based on binary matrix data, clustering and PCoA analysis (see Figs. 1 and 2) of the samples were carried out that divided them into two groups according to species. CONCLUSIONS We found a set of markers that can be useful tools for ryegrass varieties identification. The level of intravarietal polymorphism turned out to be higher than the differences between varieties because of the possible significant heterogeneity of the varietal material. The information obtained can be used in breeding programs to create improved ryegrass varieties adapted to Russian climatic conditions.
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Affiliation(s)
- Yulian Mavlyutov
- grid.494809.8Federal Williams Research Center of Forage Production & Agroecology (FWRC FPA), Lobnya, Moscow region Russia
| | - Sergey Kostenko
- grid.494809.8Federal Williams Research Center of Forage Production & Agroecology (FWRC FPA), Lobnya, Moscow region Russia
| | - Anastasia Shamustakimova
- grid.494809.8Federal Williams Research Center of Forage Production & Agroecology (FWRC FPA), Lobnya, Moscow region Russia
| | - Irina Klimenko
- grid.494809.8Federal Williams Research Center of Forage Production & Agroecology (FWRC FPA), Lobnya, Moscow region Russia
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Saeidnia F, Majidi MM, Mirlohi A, Ahmadi B. Association analysis revealed loci linked to post-drought recovery and traits related to persistence of smooth bromegrass (Bromus inermis). PLoS One 2022; 17:e0278687. [PMID: 36477736 PMCID: PMC9728867 DOI: 10.1371/journal.pone.0278687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
Association analysis has been proven as a powerful tool for the genetic dissection of complex traits. This study was conducted to identify association of recovery, persistence, and summer dormancy with sequence related amplified polymorphism (SRAP) markers in 36 smooth bromegrass genotypes under two moisture conditions and find stable associations. In this study, a diverse panel of polycross-derived progenies of smooth bromegrass was phenotyped under normal and water deficit regimes for three consecutive years. Under water deficit, dry matter yield of cut 1 was approximately reduced by 36, 39, and 37% during 2013, 2014, and 2015, respectively, compared with the normal regime. For dry matter yield of cut 2, these reductions were approximately 38, 60, and 56% in the same three consecutive years relative to normal regime. Moreover, water deficit decreased the RY and PER of the genotypes by 35 and 28%, respectively. Thirty primer combinations were screened by polymerase chain reaction (PCR). From these, 541 polymorphic bands were developed and subjected to association analysis using the mixed linear model (MLM). Population structure analysis identified five main subpopulations possessing significant genetic differences. Association analysis identified 69 and 46 marker-trait associations under normal and water deficit regimes, respectively. Some of these markers were associated with more than one trait; which can be attributed to pleiotropic effects or tightly linked genes affecting several traits. In normal and water-deficit regimes, these markers could potentially be incorporated into marker-assisted selection and targeted trait introgression for the improvement of drought tolerance of smooth bromegrass.
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Affiliation(s)
- Fatemeh Saeidnia
- Assistant Professor of Agricultural and Horticultural Science Research Department, Khorasan Razavi Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization, Mashhad, Iran
- * E-mail:
| | - Mohammad Mahdi Majidi
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Aghafakhr Mirlohi
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Benyamin Ahmadi
- Department of Horticulture, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
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Cai Z, Lim D, Liu G, Chen C, Jin L, Duan W, Ding C, Sun Q, Peng J, Dong C, Zhang F, Feng Z. Valproic Acid-Like Compounds Enhance and Prolong the Radiotherapy Effect on Breast Cancer by Activating and Maintaining Anti-Tumor Immune Function. Front Immunol 2021; 12:646384. [PMID: 34054811 PMCID: PMC8149798 DOI: 10.3389/fimmu.2021.646384] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 04/16/2021] [Indexed: 12/12/2022] Open
Abstract
Inadequate sustained immune activation and tumor recurrence are major limitations of radiotherapy (RT), sustained and targeted activation of the tumor microenvironment can overcome this obstacle. Here, by two models of a primary rat breast cancer and cell co-culture, we demonstrated that valproic acid (VPA) and its derivative (HPTA) are effective immune activators for RT to inhibit tumor growth by inducing myeloid-derived macrophages and polarizing them toward the M1 phenotype, thus elevate the expression of cytokines such as IL-12, IL-6, IFN-γ and TNF-α during the early stage of the combination treatment. Meanwhile, activated CD8+ T cells increased, angiogenesis of tumors is inhibited, and the vasculature becomes sparse. Furthermore, it was suggested that VPA/HPTA can enhance the effects of RT via macrophage-mediated and macrophage-CD8+ T cell-mediated anti-tumor immunity. The combination of VPA/HPTA and RT treatment slowed the growth of tumors and prolong the anti-tumor effect by continuously maintaining the activated immune response. These are promising findings for the development of new effective, low-cost concurrent cancer therapy.
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Affiliation(s)
- Zuchao Cai
- Department of Occupational Health and Occupational Medicine, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - David Lim
- School of Health Sciences, Western Sydney University, Campbelltown, NSW, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Guochao Liu
- Department of Occupational Health and Occupational Medicine, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Chen Chen
- Department of Occupational Health and Occupational Medicine, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Liya Jin
- Department of Occupational Health and Occupational Medicine, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Wenhua Duan
- Department of Occupational Health and Occupational Medicine, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Chenxia Ding
- Department of Occupational Health and Occupational Medicine, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Qingjie Sun
- Department of Occupational Health and Occupational Medicine, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Junxuan Peng
- Department of Occupational Health and Occupational Medicine, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Chao Dong
- Department of Occupational Health and Occupational Medicine, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Fengmei Zhang
- Department of Occupational Health and Occupational Medicine, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Zhihui Feng
- Department of Occupational Health and Occupational Medicine, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
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Zarei A, Rezaei A, Esmailpour M, Ebrahimi A. A comparative assessment of morphological and molecular characterization among three Ziziphus species. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1007-1025. [PMID: 34092949 PMCID: PMC8140020 DOI: 10.1007/s12298-021-01000-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
UNLABELLED Genetic variability of 84 accessions of three Ziziphus species including Z. spina-christi, Z. nummularia and Z. mauritiana were analyzed using a combination of morphological traits and translation initiation codon (ATG) polymorphism. Both morphological and molecular data revealed a high level of inter and intra specific variations among the accessions. Accordingly, 90.49% of amplified fragments were polymorphic among the accessions with the mean values of 0.37 for polymorphic information content (PIC), 3.31 for resolving power (RP), and 1.95 for marker index (MI). The phylogenetic clustering clearly delineated the entire germplasm into three well supported distinct clusters according to the species sources. According to the Nei's genetic identity, Z. spina-christi and Z. nummularia were the most similar species and had high differentiation with Z. mauritiana. Moreover, the highest values for Shannon's information index (I = 0.505) and gene diversity (h = 0.347) were recorded in Z. spina-christi indicating there is higher genetic diversity compared with two other species. Four private alleles were identified in two species which could be beneficial for accessions authentication in argumentative situations. Moreover, results of the Mantel test showed there were moderate correlation between molecular and morphological matrices. In addition, estimation of bivariate correlations revealed there were significant positive and negative correlations between different variables, which offer a practical application of this information during phenotype based selection in ber improvement programs. The results of this investigation highlight the efficiency of translation initiation codon polymorphism for genetic characterization and accurate authentication of Ziziphus accessions as well as detecting and tagging morphologically important traits in this genus that would be helpful for implementation of effective conservation strategies and even broaden current genetic diversity. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01000-7.
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Affiliation(s)
- Abdolkarim Zarei
- Department of Plant Production and Genetic (Biotechnology), College of Agriculture, Jahrom University, PO BOX 74135-111, Jahrom, Iran
| | - Asma Rezaei
- Department of Plant Production and Genetic (Biotechnology), College of Agriculture, Jahrom University, PO BOX 74135-111, Jahrom, Iran
| | - Mohammad Esmailpour
- Department of Plant Production and Genetic (Biotechnology), College of Agriculture, Jahrom University, PO BOX 74135-111, Jahrom, Iran
| | - Aziz Ebrahimi
- Department of Forestry and Natural Resources, Purdue University, 715 State Street, West Lafayette, IN 47907 USA
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Saeidnia F, Majidi MM, Mirlohi A. Marker-trait association analysis for drought tolerance in smooth bromegrass. BMC PLANT BIOLOGY 2021; 21:116. [PMID: 33632123 PMCID: PMC7908751 DOI: 10.1186/s12870-021-02891-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 02/13/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Little information is available on the application of marker-trait association (MTA) analysis for traits related to drought tolerance in smooth bromegrass. The objectives of this study were to identify marker loci associated with important agronomic traits and drought tolerance indices as well as fining stable associations in a diverse panel of polycross derived genotypes of smooth bromegrass. Phenotypic evaluations were performed at two irrigation regimes (normal and deficit irrigation) during 2 years; and association analysis was done with 626 SRAP markers. RESULTS The results of population structure analysis identified three main subpopulations possessing significant genetic differences. Under normal irrigation, 68 and 57 marker-trait associations were identified using general linear model (GLM) and mixed linear mode1 (MLM), respectively. While under deficit irrigation, 61 and 54 markers were associated with the genes controlling the studied traits, based on these two models, respectively. Some of the markers were associated with more than one trait. It was revealed that markers Me1/Em5-11, Me1/Em3-15, and Me5/Em4-7 were consistently linked with drought-tolerance indices. CONCLUSION Following marker validation, the MTAs reported in this panel could be useful tools to initiate marker-assisted selection (MAS) and targeted trait introgression of smooth bromegrass under normal and deficit irrigation regimes, and possibly fine mapping and cloning of the underlying genes and QTLs.
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Affiliation(s)
- F. Saeidnia
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111 Iran
| | - M. M. Majidi
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111 Iran
| | - A. Mirlohi
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111 Iran
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Qiao D, Zhang Y, Xiong X, Li M, Cai K, Luo H, Zeng B. Transcriptome analysis on responses of orchardgrass (Dactylis glomerata L.) leaves to a short term flooding. Hereditas 2020; 157:20. [PMID: 32418541 PMCID: PMC7232843 DOI: 10.1186/s41065-020-00134-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/30/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Orchardgrass (Dactylis glomerata L.) is a popular cool-season perennial grass with a high production value, and orchardgrass seed is the fourth top-selling forage grass seed in the world. However, its yield and quality are often affected by flooding. To date, the molecular responses of orchardgrass to flooding were poorly understood. RESULTS Here, we performed mRNA-seq to explore the transcriptomic responses of orchardgrass to a short term flooding (8 h and 24 h). There were 1454 and 565 differentially expressed genes identified in the 8 h and 24 h of flooding, respectively, compared to well control. GO functional enrichment analysis showed that oxidoreductase activity and oxidation-reduction process were highly present, suggesting that flooding induced the response to oxygen stress. Pathways enrichment analysis highlights the importance of glutathione metabolism, peroxidase, glycolysis and plant hormone signal transduction in response to flooding acclimation. Besides, the ROS clearance system is activated by significantly expressed glutathione S-transferase and genes encoding SOD and CAT (CAT1 and CDS2). The significant positive correlation between RNA sequencing data and a qPCR analysis indicated that the identified genes were credible. CONCLUSION In the process of orchardgrass response to flooding stress, multiple differential genes and biological processes have participated in its acclimation to flooding, especially the biological processes involved in the removal of ROS. These results provide a basis for further research on the adaptation mechanism of orchardgrass to flood tolerance.
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Affiliation(s)
- Dandan Qiao
- College of Animal Science, Southwest University, Rongchang District, Chongqing, 402460 China
| | - Yajie Zhang
- College of Animal Science, Southwest University, Rongchang District, Chongqing, 402460 China
| | - Xuemei Xiong
- College of Animal Science, Southwest University, Rongchang District, Chongqing, 402460 China
| | - Mingyang Li
- College of Animal Science, Southwest University, Rongchang District, Chongqing, 402460 China
| | - Kai Cai
- College of Animal Science, Southwest University, Rongchang District, Chongqing, 402460 China
| | - Hui Luo
- College of Animal Science, Southwest University, Rongchang District, Chongqing, 402460 China
| | - Bing Zeng
- College of Animal Science, Southwest University, Rongchang District, Chongqing, 402460 China
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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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Hao J, Jiao K, Yu C, Guo H, Zhu Y, Yang X, Zhang S, Zhang L, Feng S, Song Y, Dong M, Wang H, Shen C. Development of SCoT-Based SCAR Marker for Rapid Authentication of Taxus Media. Biochem Genet 2018; 56:255-266. [DOI: 10.1007/s10528-018-9842-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/19/2018] [Indexed: 10/18/2022]
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Dai Y, Su W, Yang C, Song B, Li Y, Fu Y. Development of Novel Polymorphic EST-SSR Markers in Bailinggu (Pleurotus tuoliensis) for Crossbreeding. Genes (Basel) 2017; 8:genes8110325. [PMID: 29149037 PMCID: PMC5704238 DOI: 10.3390/genes8110325] [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: 10/16/2017] [Revised: 10/16/2017] [Accepted: 11/08/2017] [Indexed: 01/02/2023] Open
Abstract
Identification of monokaryons and their mating types and discrimination of hybrid offspring are key steps for the crossbreeding of Pleurotus tuoliensis (Bailinggu). However, conventional crossbreeding methods are troublesome and time consuming. Using RNA-seq technology, we developed new expressed sequence tag-simple sequence repeat (EST-SSR) markers for Bailinggu to easily and rapidly identify monokaryons and their mating types, genetic diversity and hybrid offspring. We identified 1110 potential EST-based SSR loci from a newly-sequenced Bailinggu transcriptome and then randomly selected 100 EST-SSRs for further validation. Results showed that 39, 43 and 34 novel EST-SSR markers successfully identified monokaryons from their parent dikaryons, differentiated two different mating types and discriminated F1 and F2 hybrid offspring, respectively. Furthermore, a total of 86 alleles were detected in 37 monokaryons using 18 highly informative EST-SSRs. The observed number of alleles per locus ranged from three to seven. Cluster analysis revealed that these monokaryons have a relatively high level of genetic diversity. Transfer rates of the EST-SSRs in the monokaryons of closely-related species Pleurotuseryngii var. ferulae and Pleurotus ostreatus were 72% and 64%, respectively. Therefore, our study provides new SSR markers and an efficient method to enhance the crossbreeding of Bailinggu and closely-related species.
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Affiliation(s)
- Yueting Dai
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
| | - Wenying Su
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
| | - Chentao Yang
- China National GeneBank, Environmental Genomics, Beijing Genomics Institute, Shenzhen 518083, China.
| | - Bing Song
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
| | - Yu Li
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
| | - Yongping Fu
- Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China.
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Sun M, Zhang C, Zhang X, Fan Y, Fu K, Wu W, Bai S, Zhang J, Peng Y, Huang L, Yan Y, Ma X. AFLP assessment of genetic variability and relationships in an Asian wild germplasm collection of Dactylis glomerata L. C R Biol 2017; 340:145-155. [PMID: 28215522 DOI: 10.1016/j.crvi.2016.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 12/29/2016] [Accepted: 12/29/2016] [Indexed: 11/29/2022]
Abstract
Orchardgrass (Dactylis glomerata L.), an excellent perennial and cool season forage species distributed in most temperate regions, has been cultivated widely in Western China. Amplified fragment length polymorphism markers were employed to determine the genetic variability and population structure among 41 indigenous orchardgrass accessions from Central Asia and Western China. On the basis of 531 polymorphic fragments resulted from eight primer combinations, polymorphic information content (PIC), marker index (MI) and resolving power (RP) averaged 0.252, 16.34 and 25.27 per primer combination, respectively, demonstrating the high efficiency and reliability of the markers used. We found relatively low differentiation (Fst=0.135) for three geographical groups, where Central Asia (CA) and Southwest China (SWC) group exhibited higher intra-population diversity (He=0.20 and 0.21) than that of the Xinjiang (XJ) group (He=0.14). We also did not detect a clear pattern of isolation by distance with a low value of r=0.301 in the Mantel test. STRUCTURE, FLOCK, UPGMA clustering and PCoA analyses showed that CA group is more related to the SWC Group rather than to the XJ Group. In addition, this study strongly suggests that geographical and ecological environmental factors together could better explain the genetic differentiation between different geographical regions than geographic isolation alone, especially for Xinjiang accessions. The present study also could support that Southwest China might be the internal diversity center of D. glomerata in China. The knowledge about the genetic variability of the Asian accessions examined contributes to rapid characterization, defining gene pools of wild accessions, and selecting appropriate germplasms for plant improvement.
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Affiliation(s)
- Ming Sun
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Chenglin Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - XinQuan Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yan Fan
- Chongqing Municipal Institute of Animal Husbandry, Chongqing 400039, China
| | - Kaixin Fu
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Wendan Wu
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Shiqie Bai
- Sichuan Academy of Grassland Science, Chengdu, Sichuan 611731, China
| | - Jianbo Zhang
- Sichuan Academy of Grassland Science, Chengdu, Sichuan 611731, China
| | - Yan Peng
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Linkai Huang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yanhong Yan
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xiao Ma
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
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Yan D, Zhao X, Cheng Y, Ma X, Huang L, Zhang X. Phylogenetic and Diversity Analysis of Dactylis glomerata Subspecies Using SSR and IT-ISJ Markers. Molecules 2016; 21:molecules21111459. [PMID: 27809251 PMCID: PMC6272990 DOI: 10.3390/molecules21111459] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/13/2016] [Accepted: 10/26/2016] [Indexed: 11/16/2022] Open
Abstract
The genus Dactylis, an important forage crop, has a wide geographical distribution in temperate regions. While this genus is thought to include a single species, Dactylis glomerata, this species encompasses many subspecies whose relationships have not been fully characterized. In this study, the genetic diversity and phylogenetic relationships of nine representative Dactylis subspecies were examined using SSR and IT-ISJ markers. In total, 21 pairs of SSR primers and 15 pairs of IT-ISJ primers were used to amplify 295 polymorphic bands with polymorphic rates of 100%. The average polymorphic information contents (PICs) of SSR and IT-ISJ markers were 0.909 and 0.780, respectively. The combined data of the two markers indicated a high level of genetic diversity among the nine D. glomerata subspecies, with a Nei’s gene diversity index value of 0.283 and Shannon’s diversity of 0.448. Preliminarily phylogenetic analysis results revealed that the 20 accessions could be divided into three groups (A, B, C). Furthermore, they could be divided into five clusters, which is similar to the structure analysis with K = 5. Phylogenetic placement in these three groups may be related to the distribution ranges and the climate types of the subspecies in each group. Group A contained eight accessions of four subspecies, originating from the west Mediterranean, while Group B contained seven accessions of three subspecies, originating from the east Mediterranean.
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Affiliation(s)
- Defei Yan
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China.
| | - Xinxin Zhao
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China.
| | - Yajuan Cheng
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China.
| | - Xiao Ma
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China.
| | - Linkai Huang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China.
| | - Xinquan Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China.
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