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Fang L, Liu T, Li M, Dong X, Han Y, Xu C, Li S, Zhang J, He X, Zhou Q, Luo D, Liu Z. MODMS: a multi-omics database for facilitating biological studies on alfalfa ( Medicago sativa L.). HORTICULTURE RESEARCH 2024; 11:uhad245. [PMID: 38239810 PMCID: PMC10794946 DOI: 10.1093/hr/uhad245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/13/2023] [Indexed: 01/22/2024]
Abstract
Alfalfa (Medicago sativa L.) is a globally important forage crop. It also serves as a vegetable and medicinal herb because of its excellent nutritional quality and significant economic value. Multi-omics data on alfalfa continue to accumulate owing to recent advances in high-throughput techniques, and integrating this information holds great potential for expediting genetic research and facilitating advances in alfalfa agronomic traits. Therefore, we developed a comprehensive database named MODMS (multi-omics database of M. sativa) that incorporates multiple reference genomes, annotations, comparative genomics, transcriptomes, high-quality genomic variants, proteomics, and metabolomics. This report describes our continuously evolving database, which provides researchers with several convenient tools and extensive omics data resources, facilitating the expansion of alfalfa research. Further details regarding the MODMS database are available at https://modms.lzu.edu.cn/.
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Affiliation(s)
- Longfa Fang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Tao Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Mingyu Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - XueMing Dong
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Yuling Han
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Congzhuo Xu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Siqi Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Jia Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Xiaojuan He
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Qiang Zhou
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Dong Luo
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Zhipeng Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
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Zhou X, Li X, Zhang X, Yin D, Wang J, Zhao Y. Construction of a high-density genetic map and localization of grazing-tolerant QTLs in Medicago falcata L. FRONTIERS IN PLANT SCIENCE 2022; 13:985603. [PMID: 36262664 PMCID: PMC9574245 DOI: 10.3389/fpls.2022.985603] [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: 07/04/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Using genomic DNA from 79 F1 plants resulted from a crossing between parents with strong and weak grazing tolerance in Medicago falcata L., we generated an EcoRI restriction site-associated DNA (RAD) sequencing library. After sequencing and assembly, a high-density genetic map with high-quality SNP markers was constructed, with a total length of 1312.238 cM and an average density of 0.844 SNP/cM. METHODS The phenotypic traits of 79 F1 families were observed and the QTLS of 6 traits were analyzed by interval mapping. RESULTS Sixty three QTLs were identified for seven traits with LOD values from 3 to 6 and the contribution rates from 15% to 30%. Among the 63 QTLs, 17 were for natural shoot height, 12 for rhizome Length, 10 for Shoot canopy diameter, 9 for Basal plant diameter, 6 for stem number, 5 for absolute shoot height, and 4 for rhizome width. These QTLs were concentrated on LG2, LG4, LG5, LG7, and LG8. LG6 had only 6 QTLs. According to the results of QTL mapping, comparison of reference genomes, and functional annotation, 10 candidate genes that may be related to grazing tolerance were screened. qRT-PCR analysis showed that two candidate genes (LOC11412291 and LOC11440209) may be the key genes related to grazing tolerance of M. falcata. CONCLUSION The identified trait-associated QTLs and candidate genes in this study will provide a solid foundation for future molecular breeding for enhanced grazing-tolerance in M. falcata.
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Li Z, Yun L, Ren X, Shi F, Mi F. Analysis of controlling genes for tiller growth of Psathyrostachys juncea based on transcriptome sequencing technology. BMC PLANT BIOLOGY 2022; 22:456. [PMID: 36151542 PMCID: PMC9502641 DOI: 10.1186/s12870-022-03837-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Tillering is a complicated process in plant and is a significant trait that affects biomass and seed yield of bunch grass Psathyrostachys juncea, a typical perennial forage species. To clarify the regulatory mechanisms of tillering in P. juncea and to explore related candidate genes could be helpful to improve the seed and forage yield of perennial gramineous forages. We selected the tiller node tissues of P. juncea for transcriptome sequencing to determine the differentially expressed genes (DEG) between dense and sparse tillering genotypes. The metabolic pathway was studied, candidate genes were screened, and reference genes stability were evaluated. RESULTS The results showed that approximately 5466 DEGs were identified between the two genotypes with dense and sparse tillers of P. juncea, which significantly differed in tiller number. Tillering regulation pathways analysis suggested that DEGs closely related to the biosynthesis of three plant hormones, namely auxin (IAA), cytokinin (CTK), and strigolactones (SLs), while "biosynthesis of lignin" and "nitrogen metabolism" have remarkable differences between the dense and sparse tillering genotypes. Meanwhile, the reference gene Actin1, having the best stability, was screened from twelve genes with highest expression level and was used in verification of ten tillering related candidate genes. CONCLUSIONS The tillering mechanism of perennial grass P. juncea was expounded by transcriptome analysis of tiller node tissues. We demonstrated that dense-tillering genotypes may be distinguished by their low expression patterns of genes involved in SL, IAA, and high expression patterns of genes involved in CTK biosynthesis at the tillering stage, and nitrogen metabolism and lignin biosynthesis can also affect the number of tillers. Furthermore, the expression level of ten tillering related candidate genes were verified using Actin1 as reference gene. These candidate genes provide valuable breeding resources for marker assisted selection and yield traits improvement of P. juncea.
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Affiliation(s)
- Zhen Li
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Lan Yun
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, 010018, China.
- Key Laboratory of Grassland Resources of the Ministry of Education and Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of the Ministry of Agriculture, Hohhot, 010018, China.
| | - Xiaomin Ren
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Fengling Shi
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Fugui Mi
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, 010018, China
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Wang Y, Zhu W, Ren F, Zhao N, Xu S, Sun P. Transcriptional Memory in Taraxacum mongolicum in Response to Long-Term Different Grazing Intensities. PLANTS 2022; 11:plants11172251. [PMID: 36079633 PMCID: PMC9460496 DOI: 10.3390/plants11172251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 12/02/2022]
Abstract
Grazing, as an important land use method in grassland, has a significant impact on the morphological and physiological traits of plants. However, little is known about how the molecular mechanism of plant responds to different grazing intensities. Here, we investigated the response of Taraxacum mongolicum to light grazing and heavy grazing intensities in comparison with a non-grazing control. Using de novo transcriptome assembly, T. mongolicum leaves were compared for the expression of the different genes under different grazing intensities in natural grassland. In total, 194,253 transcripts were de novo assembled and comprised in nine leaf tissues. Among them, 11,134 and 9058 genes were differentially expressed in light grazing and heavy grazing grassland separately, with 5867 genes that were identified as co-expression genes in two grazing treatments. The Nr, SwissProt, String, GO, KEGG, and COG analyses by BLASTx searches were performed to determine and further understand the biological functions of those differentially expressed genes (DEGs). Analysis of the expression patterns of 10 DEGs by quantitative real-time RT-PCR (qRT-PCR) confirmed the accuracy of the RNA-Seq results. Based on a comparative transcriptome analysis, the most significant transcriptomic changes that were observed under grazing intensity were related to plant hormone and signal transduction pathways, carbohydrate and secondary metabolism, and photosynthesis. In addition, heavy grazing resulted in a stronger transcriptomic response compared with light grazing through increasing the of the secondary metabolism- and photosynthesis-related genes. These changes in key pathways and related genes suggest that they may synergistically respond to grazing to increase the resilience and stress tolerance of T. mongolicum. Our findings provide important clues for improving grassland use and protection and understanding the molecular mechanisms of plant response to grazing.
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Affiliation(s)
- Yalin Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Wenyan Zhu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471003, China
| | - Fei Ren
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Na Zhao
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471003, China
| | - Shixiao Xu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471003, China
- Correspondence: (S.X.); (P.S.); Tel.: +86-13997163501 (S.X.); +86-13525415882 (P.S.)
| | - Ping Sun
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- Correspondence: (S.X.); (P.S.); Tel.: +86-13997163501 (S.X.); +86-13525415882 (P.S.)
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Dong S, Pang W, Liu Z, Li H, Zhang K, Cong L, Yang G, Wang ZY, Xie H. Transcriptome Analysis of Leaf Senescence Regulation Under Alkaline Stress in Medicago truncatula. FRONTIERS IN PLANT SCIENCE 2022; 13:881456. [PMID: 35574123 PMCID: PMC9096890 DOI: 10.3389/fpls.2022.881456] [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: 02/22/2022] [Accepted: 04/01/2022] [Indexed: 06/15/2023]
Abstract
In plants, the leaf is an essential photosynthetic organ, and is the primary harvest in forage crops such as alfalfa (Medicago sativa). Premature leaf senescence caused by environmental stress can result in significant yield loss and quality reduction. Therefore, the stay-green trait is important for improving the economic value of forage crops. Alkaline stress can severely damage leaf cells and, consequently, cause leaf senescence. To understand the molecular regulatory mechanisms and identify vital senescence-associated genes under alkaline stress, we used high-throughput sequencing to study transcriptional changes in Medicago truncatula, a model plant for forage crops. We identified 2,165 differentially expressed genes, 985 of which were identical to those in the dark-induced leaf senescence group. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses showed that the 985 genes were mainly enriched in nutrient cycling processes such as cellular amino acid metabolic processes and organic substance catabolic processes, indicating nutrient redistribution. The other 1,180 differentially expressed genes were significantly enriched in the oxidoreductase complex, aerobic respiration, and ion transport. Our analysis showed the two gene sets guiding the coupled physiological and biochemical alterations play different roles under alkaline stress with a coordinated and integrated way. Many transcription factor families were identified from these differentially expressed genes, including MYB, WRKY, bHLH, and NAC which have particular preference involved in stress resistance and regulation of senescence. Our results contribute to the exploration of the molecular regulatory mechanisms of leaf senescence in M. truncatula under alkaline stress and provide new candidate genes for future breeding to improve the biomass and quality of forage crops.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Hongli Xie
- *Correspondence: Hongli Xie, , orcid.org/0000-0001-6392-0494
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Dang Z, Jia Y, Tian Y, Li J, Zhang Y, Huang L, Liang C, Lockhart PJ, Matthew C, Li FY. Transcriptome-Wide Gene Expression Plasticity in Stipa grandis in Response to Grazing Intensity Differences. Int J Mol Sci 2021; 22:ijms222111882. [PMID: 34769324 PMCID: PMC8611654 DOI: 10.3390/ijms222111882] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 01/15/2023] Open
Abstract
Organisms have evolved effective and distinct adaptive strategies to survive. Stipa grandis is a representative species for studying the grazing effect on typical steppe plants in the Inner Mongolia Plateau. Although phenotypic (morphological and physiological) variations in S. grandis in response to long-term grazing have been identified, the molecular mechanisms underlying adaptations and plastic responses remain largely unknown. Here, we performed a transcriptomic analysis to investigate changes in gene expression of S. grandis under four different grazing intensities. As a result, a total of 2357 differentially expressed genes (DEGs) were identified among the tested grazing intensities, suggesting long-term grazing resulted in gene expression plasticity that affected diverse biological processes and metabolic pathways in S. grandis. DEGs were identified in RNA-Seq and qRT-PCR analyses that indicated the modulation of the Calvin–Benson cycle and photorespiration metabolic pathways. The key gene expression profiles encoding various proteins (e.g., ribulose-1,5-bisphosphate carboxylase/oxygenase, fructose-1,6-bisphosphate aldolase, glycolate oxidase, etc.) involved in these pathways suggest that they may synergistically respond to grazing to increase the resilience and stress tolerance of S. grandis. Our findings provide scientific clues for improving grassland use and protection and identifying important questions to address in future transcriptome studies.
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Affiliation(s)
- Zhenhua Dang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Y.J.); (J.L.); (Y.Z.); (L.H.); (C.L.); (F.Y.L.)
- Correspondence: ; Tel.: +86-1514-802-6396
| | - Yuanyuan Jia
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Y.J.); (J.L.); (Y.Z.); (L.H.); (C.L.); (F.Y.L.)
| | - Yunyun Tian
- Ministry of Education Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot 010021, China;
| | - Jiabin Li
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Y.J.); (J.L.); (Y.Z.); (L.H.); (C.L.); (F.Y.L.)
| | - Yanan Zhang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Y.J.); (J.L.); (Y.Z.); (L.H.); (C.L.); (F.Y.L.)
| | - Lei Huang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Y.J.); (J.L.); (Y.Z.); (L.H.); (C.L.); (F.Y.L.)
| | - Cunzhu Liang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Y.J.); (J.L.); (Y.Z.); (L.H.); (C.L.); (F.Y.L.)
| | - Peter J. Lockhart
- School of Fundamental Sciences, College of Sciences, Massey University, Palmerston North 4442, New Zealand;
| | - Cory Matthew
- School of Agriculture and Environment, Massey University, Palmerston North 4442, New Zealand;
| | - Frank Yonghong Li
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China; (Y.J.); (J.L.); (Y.Z.); (L.H.); (C.L.); (F.Y.L.)
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Qiao Y, Cheng Q, Zhang Y, Yan W, Yi F, Shi F. Transcriptomic and chemical analyses to identify candidate genes involved in color variation of sainfoin flowers. BMC PLANT BIOLOGY 2021; 21:61. [PMID: 33482728 PMCID: PMC7825240 DOI: 10.1186/s12870-021-02827-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 01/05/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND Sainfoin (Onobrychis viciifolia Scop) is not only a high-quality legume forage, but also a nectar-producing plant. Therefore, the flower color of sainfoin is an important agronomic trait, but the factors affecting its flower phenotype are still unclear. To gain insights into the regulatory networks associated with metabolic pathways of coloration compounds (flavonoids or anthocyanins) and identify the key genes, we conducted a comprehensive analysis of the phenotype, metabolome and transcriptome of WF and AF of sainfoin. RESULTS Delphinidin, petunidin and malvidin derivatives were the main anthocyanin compounds in the AF of sainfoin. These substances were not detected in the WF of sainfoin. The transcriptomes of WF and AF in sainfoin at the S1 and S3 stages were obtained using the Illumina HiSeq4000 platform. Overall, 10,166 (4273 upregulated and 5893 downregulated) and 15,334 (8174 upregulated and 7160 downregulated) DEGs were identified in flowers at S1 and S3 stages, respectively (WF-VS-AF). KEGG pathway annotations showed that 6396 unigenes were annotated to 120 pathways and contained 866 DEGs at S1 stages, and 6396 unigenes were annotated to 131 pathways and included 1546 DEGs at the S3 stage. Nine DEGs belonging to the "flavonoid biosynthesis"and "phenylpropanoid biosynthesis" pathways involved in flower color formation were identified and verified by RT-qPCR analyses. Among these DEGs, 4CL3, FLS, ANS, CHS, DFR and CHI2 exhibited downregulated expression, and F3H exhibited upregulated expression in the WF compared to the AF, resulting in a decrease in anthocyanin synthesis and the formation of WF in sainfoin. CONCLUSIONS This study is the first to use transcriptome technology to study the mechanism of white flower formation in sainfoin. Our transcriptome data will be a great enrichment of the genetic information for sainfoin. In addition, the data presented herein will provide valuable molecular information for genetic breeding and provide insight into the future study of flower color polymorphisms in sainfoin.
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Affiliation(s)
- Yu Qiao
- College of Grassland Resources and Environment, Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of the Ministry of Agriculture and Key Laboratory of Grassland Resources of the Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010011, China
| | - Qiming Cheng
- College of Grassland Resources and Environment, Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of the Ministry of Agriculture and Key Laboratory of Grassland Resources of the Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010011, China
| | - Yutong Zhang
- College of Grassland Resources and Environment, Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of the Ministry of Agriculture and Key Laboratory of Grassland Resources of the Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010011, China
| | - Wei Yan
- College of Grassland Resources and Environment, Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of the Ministry of Agriculture and Key Laboratory of Grassland Resources of the Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010011, China
| | - Fengyan Yi
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Fengling Shi
- College of Grassland Resources and Environment, Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of the Ministry of Agriculture and Key Laboratory of Grassland Resources of the Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010011, China.
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Yan D, Ren J, Liu J, Ding Y, Niu J. De novo assembly, annotation, marker discovery, and genetic diversity of the Stipa breviflora Griseb. (Poaceae) response to grazing. PLoS One 2020; 15:e0244222. [PMID: 33351838 PMCID: PMC7755183 DOI: 10.1371/journal.pone.0244222] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 12/04/2020] [Indexed: 12/04/2022] Open
Abstract
Grassland is one of the most widely-distributed ecosystems on Earth and provides a variety of ecosystem services. Grasslands, however, currently suffer from severe degradation induced by human activities, overgrazing pressure and climate change. In the present study, we explored the transcriptome response of Stipa breviflora, a dominant species in the desert steppe, to grazing through transcriptome sequencing, the development of simple sequence repeat (SSR) markers, and analysis of genetic diversity. De novo assembly produced 111,018 unigenes, of which 88,164 (79.41%) unigenes were annotated. A total of 686 unigenes showed significantly different expression under grazing, including 304 and 382 that were upregulated and downregulated, respectively. These differentially expressed genes (DEGs) were significantly enriched in the “alpha-linolenic acid metabolism” and “plant-pathogen interaction” pathways. Based on transcriptome sequencing data, we developed eight SSR molecular markers and investigated the genetic diversity of S. breviflora in grazed and ungrazed sites. We found that a relatively high level of S. breviflora genetic diversity occurred under grazing. The findings of genes that improve resistance to grazing are helpful for the restoration, conservation, and management of desert steppe.
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Affiliation(s)
- Dongqing Yan
- School of Ecology and Environment, Inner Mongolia University, Hohhot, People’s Republic of China
| | - Jing Ren
- School of Ecology and Environment, Inner Mongolia University, Hohhot, People’s Republic of China
| | - Jiamei Liu
- School of Ecology and Environment, Inner Mongolia University, Hohhot, People’s Republic of China
| | - Yu Ding
- School of Ecology and Environment, Inner Mongolia University, Hohhot, People’s Republic of China
| | - Jianming Niu
- School of Ecology and Environment, Inner Mongolia University, Hohhot, People’s Republic of China
- Inner Mongolia Key Laboratory of Grassland Ecology and the Candidate State Key Laboratory of Ministry of Science and Technology, Hohhot, People’s Republic of China
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Hohhot, People’s Republic of China
- * E-mail:
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Chao Y, Yuan J, Guo T, Xu L, Mu Z, Han L. Analysis of transcripts and splice isoforms in Medicago sativa L. by single-molecule long-read sequencing. PLANT MOLECULAR BIOLOGY 2019; 99:219-235. [PMID: 30600412 DOI: 10.1007/s11103-018-0813-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 12/14/2018] [Indexed: 05/20/2023]
Abstract
The full-length transcriptome of alfalfa was analyzed with PacBio single-molecule long-read sequencing technology. The transcriptome data provided full-length sequences and gene isoforms of transcripts in alfalfa, which will improve genome annotation and enhance our understanding of the gene structure of alfalfa. As an important forage, alfalfa (Medicago sativa L.) is world-wide planted. For its complexity of genome and unfinished whole genome sequencing, the sequences and complete structure of mRNA transcripts remain unclear in alfalfa. In this study, single-molecule long-read sequencing was applied to investigate the alfalfa transcriptome using the Pacific Biosciences platform, and a total of 113,321 transcripts were obtained from young, mature and senescent leaves. We identified 72,606 open reading frames including 46,616 full-length ORFs, 1670 transcription factors from 54 TF families and 44,040 simple sequence repeats from 30,797 sequences. A total of 7568 alternative splicing events was identified and the majority of alternative splicing events in alfalfa was intron retention. In addition, we identified 17,740 long non-coding RNAs. Our results show the feasibility of deep sequencing full-length RNA from alfalfa transcriptome on a single-molecule level.
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Affiliation(s)
- Yuehui Chao
- Turfgrass Research Institute, Beijing Forestry University, Beijing, 100083, China
| | - Jianbo Yuan
- Turfgrass Research Institute, Beijing Forestry University, Beijing, 100083, China
| | - Tao Guo
- Turfgrass Research Institute, Beijing Forestry University, Beijing, 100083, China
| | - Lixin Xu
- Turfgrass Research Institute, Beijing Forestry University, Beijing, 100083, China
| | - Zhiyuan Mu
- Turfgrass Research Institute, Beijing Forestry University, Beijing, 100083, China
| | - Liebao Han
- Turfgrass Research Institute, Beijing Forestry University, Beijing, 100083, China.
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Singer SD, Hannoufa A, Acharya S. Molecular improvement of alfalfa for enhanced productivity and adaptability in a changing environment. PLANT, CELL & ENVIRONMENT 2018; 41:1955-1971. [PMID: 29044610 DOI: 10.1111/pce.13090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/29/2017] [Accepted: 10/04/2017] [Indexed: 05/09/2023]
Abstract
Due to an expanding world population and increased buying power, the demand for ruminant products such as meat and milk is expected to grow substantially in coming years, and high levels of forage crop production will therefore be a necessity. Unfortunately, urbanization of agricultural land, intensive agricultural practices, and climate change are all predicted to limit crop production in the future, which means that the development of forage cultivars with improved productivity and adaptability will be essential. Because alfalfa (Medicago sativa L.) is one of the most widely cultivated perennial forage crops, it has been the target of much research in this field. In this review, we discuss progress that has been made towards the improvement of productivity, abiotic stress tolerance, and nutrient-use efficiency, as well as disease and pest resistance, in alfalfa using biotechnological techniques. Furthermore, we consider possible future priorities and avenues for attaining further enhancements in this crop as a means of contributing to the realization of food security in a changing environment.
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Affiliation(s)
- Stacy D Singer
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta, T1J 4B1, Canada
| | - Abdelali Hannoufa
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, Ontario, N5V 4T3, Canada
| | - Surya Acharya
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta, T1J 4B1, Canada
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