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Jin Y, Feng G, Luo J, Yan H, Sun M, Jing T, Yang Y, Jia J, Zhu X, Wang X, Zhang X, Huang L. Combined Genome-Wide Association Study and Transcriptome Analysis Reveal Candidate Genes for Resistance to Rust ( Puccinia graminis) in Dactylis glomerata. PLANT DISEASE 2024; 108:2197-2205. [PMID: 38956749 DOI: 10.1094/pdis-02-24-0360-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Rust disease is a common plant disease that can cause wilting, slow growth of plant leaves, and even affect the growth and development of plants. Orchardgrass (Dactylis glomerata L.) is native to temperate regions of Europe, which has been introduced as a superior forage grass in temperate regions worldwide. Orchardgrass has rich genetic diversity and is widely distributed in the world, which may contain rust resistance genes not found in other crops. Therefore, we collected a total of 333 orchardgrass accessions from different regions around the world. Through a genome-wide association study (GWAS) analysis conducted in four different environments, 91 genes that overlap or are adjacent to significant single nucleotide polymorphisms (SNPs) were identified as potential rust disease resistance genes. Combining transcriptome data from susceptible (PI292589) and resistant (PI251814) accessions, the GWAS candidate gene DG5C04160.1 encoding glutathione S-transferase (GST) was found to be important for orchardgrass rust (Puccinia graminis) resistance. Interestingly, by comparing the number of GST gene family members in seven species, it was found that orchardgrass has the most GST gene family members, containing 119 GST genes. Among them, 23 GST genes showed significant differential expression after inoculation with the rust pathogen in resistant and susceptible accessions; 82% of the genes still showed significantly increased expression 14 days after inoculation in resistant accessions, while the expression level significantly decreased in susceptible accessions. These results indicate that GST genes play an important role in orchardgrass resistance to rust (P. graminis) stress by encoding GST to reduce its oxidative stress response.
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Affiliation(s)
- Yarong Jin
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jinchan Luo
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Haidong Yan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Department of Genetics, University of Georgia, Athens, GA 30602, U.S.A
| | - Min Sun
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Tingting Jing
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuchen Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiyuan Jia
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xin Zhu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoshan Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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Niu J, Shi Y, Gao Z, Sun Z, Tian S, Chen X, Luan M. The β-galactosidase gene AtrBGAL2 regulates Akebia trifoliata fruit cracking. Int J Biol Macromol 2024; 275:133313. [PMID: 38936569 DOI: 10.1016/j.ijbiomac.2024.133313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 06/09/2024] [Accepted: 06/11/2024] [Indexed: 06/29/2024]
Abstract
Cracking of Akebia trifoliata fruit at maturity is problematic for the cultivation of the horticultural crop, shortening shelf-life quality and compromising commercial value. However, the molecular mechanisms underlying this feature of A. trifoliata are not known. Genes involved in cell wall metabolism were identified by genome and transcriptome sequencing, which may play important roles in fruit cracking. One of the galactose metabolism related genes, β-galactosidase (AtrBGAL2), was identified in A. trifoliata, and overexpression (OE) of AtrBGAL2 resulted in early fruit cracking, higher water-soluble pectin contents, and lower acid-soluble pectin, cellulose, and hemicellulose content compared to the wild type. Whereas silencing of AtrBGAL2 in trifoliata by virus induced gene silencing showed opposite trends. The levels of AtrBGAL2 transcripts were 24.6 and 66.0-fold higher in OE A. trifoliata and tomato fruits, respectively, and the cell wall-related genes were also gradually greater than in control plants during fruit ripening. Whereas the expression levels of AtrBGAL2 was significantly down-regulated by 54.1 % and 73.7 % in gene silenced A. trifoliata and CRISPR/Cas9 tomato mutant plants, respectively, and cell wall-related genes were also significantly reduced. These results demonstrate that AtrBGAL2 plays important roles in regulating fruit cracking during fruit ripening.
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Affiliation(s)
- Juan Niu
- Jingdezhen University, Jingdezhen 333032, China; Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha 410205, China
| | - Yingying Shi
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha 410205, China
| | - Zexin Gao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha 410205, China
| | - Zhimin Sun
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha 410205, China
| | - Shuang Tian
- Jingdezhen University, Jingdezhen 333032, China.
| | | | - Mingbao Luan
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Key Laboratory of Stem-Fiber Biomass and Engineering Microbiology, Ministry of Agriculture, Changsha 410205, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572000, China.
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3
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Zhai X, Wu D, Chen C, Yang X, Cheng S, Sha L, Deng S, Cheng Y, Fan X, Kang H, Wang Y, Liu D, Zhou Y, Zhang H. A chromosome level genome assembly of Pseudoroegneria Libanotica reveals a key Kcs gene involves in the cuticular wax elongation for drought resistance. BMC Genomics 2024; 25:253. [PMID: 38448864 PMCID: PMC10916072 DOI: 10.1186/s12864-024-10140-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/19/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND The genus Pseudoroegneria (Nevski) Löve (Triticeae, Poaceae), whose genome symbol was designed as "St", accounts for more than 60% of perennial Triticeae species. The diploid species Psudoroegneria libanotica (2n = 14) contains the most ancient St genome, exhibited strong drought resistance, and was morphologically covered by cuticular wax on the aerial part. Therefore, the St-genome sequencing data could provide fundamental information for studies of genome evolution and reveal its mechanisms of cuticular wax and drought resistance. RESULTS In this study, we reported the chromosome-level genome assembly for the St genome of Pse. libanotica, with a total size of 2.99 Gb. 46,369 protein-coding genes annotated and 71.62% was repeat sequences. Comparative analyses revealed that the genus Pseudoroegneria diverged during the middle and late Miocene. During this period, unique genes, gene family expansion, and contraction in Pse. libanotica were enriched in biotic and abiotic stresses, such as fatty acid biosynthesis which may greatly contribute to its drought adaption. Furthermore, we investigated genes associated with the cuticular wax formation and water deficit and found a new Kcs gene evm.TU.CTG175.54. It plays a critical role in the very long chain fatty acid (VLCFA) elongation from C18 to C26 in Pse. libanotica. The function needs more evidence to be verified. CONCLUSIONS We sequenced and assembled the St genome in Triticeae and discovered a new KCS gene that plays a role in wax extension to cope with drought. Our study lays a foundation for the genome diversification of Triticeae species and deciphers cuticular wax formation genes involved in drought resistance.
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Affiliation(s)
- Xingguang Zhai
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Dandan Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Chen Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xunzhe Yang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Shaobo Cheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Lina Sha
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Shuhan Deng
- Glbizzia Biosciences Co., Ltd, Liandong U Valley, Huatuo Road 50, Daxing, Beijing, 102600, China
| | - Yiran Cheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Houyang Kang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Dengcai Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yonghong Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
| | - Haiqin Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China.
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Li L, Yang M, Wei W, Zhao J, Yu X, Impaprasert R, Wang J, Liu J, Huang F, Srzednicki G, Yu L. Characteristics of Amorphophallus konjac as indicated by its genome. Sci Rep 2023; 13:22684. [PMID: 38114626 PMCID: PMC10730839 DOI: 10.1038/s41598-023-49963-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 12/14/2023] [Indexed: 12/21/2023] Open
Abstract
Amorphophallus konjac, belonging to the genus Amorphophallus of the Araceae family, is an economically important crop widely used in health products and biomaterials. In the present work, we performed the whole-genome assembly of A. konjac based on the NovaSeq platform sequence data. The final genome assembly was 4.58 Gb with a scaffold N50 of 3212 bp. The genome includes 39,421 protein-coding genes, and 71.75% of the assemblies were repetitive sequences. Comparative genomic analysis showed 1647 gene families have expanded and 2685 contracted in the A. konjac genome. Likewise, genome evolution analysis indicated that A. konjac underwent whole-genome duplication, possibly contributing to the expansion of certain gene families. Furthermore, we identified many candidate genes involved in the tuber formation and development, cellulose and lignification synthesis. The genome of A. konjac obtained in this work provides a valuable resource for the further study of the genetics, genomics, and breeding of this economically important crop, as well as for evolutionary studies of Araceae family.
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Affiliation(s)
- Lifang Li
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - Min Yang
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - Wei Wei
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - Jianrong Zhao
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - Xuya Yu
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, China
| | - Rarisara Impaprasert
- Department of Microbiology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Jianguang Wang
- School of Life Sciences, Yunnan University, Kunming, China
| | - Jiani Liu
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - Feiyan Huang
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China
| | - George Srzednicki
- Food Science & Technology, School of Chemical Engineering, The University of New South Wales, Sydney, Australia.
| | - Lei Yu
- College of Agronomy, Yunnan Urban Agricultural Engineering and Technological Research Center, Kunming University, Kunming, China.
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Feng G, Xu X, Liu W, Hao F, Yang Z, Nie G, Huang L, Peng Y, Bushman S, He W, Zhang X. Transcriptome Profiling Provides Insights into the Early Development of Tiller Buds in High- and Low-Tillering Orchardgrass Genotypes. Int J Mol Sci 2023; 24:16370. [PMID: 38003564 PMCID: PMC10671593 DOI: 10.3390/ijms242216370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/03/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Orchardgrass (Dactylis glomerata L.) is among the most economically important perennial cool-season grasses, and is considered an excellent hay, pasture, and silage crop in temperate regions worldwide. Tillering is a vital feature that dominates orchardgrass regeneration and biomass yield. However, transcriptional dynamics underlying early-stage bud development in high- and low-tillering orchardgrass genotypes are unclear. Thus, this study assessed the photosynthetic parameters, the partially essential intermediate biomolecular substances, and the transcriptome to elaborate the early-stage profiles of tiller development. Photosynthetic efficiency and morphological development significantly differed between high- (AKZ-NRGR667) and low-tillering genotypes (D20170203) at the early stage after tiller formation. The 206.41 Gb of high-quality reads revealed stage-specific differentially expressed genes (DEGs), demonstrating that signal transduction and energy-related metabolism pathways, especially photosynthetic-related processes, influence tiller induction and development. Moreover, weighted correlation network analysis (WGCNA) and functional enrichment identified distinctively co-expressed gene clusters and four main regulatory pathways, including chlorophyll, lutein, nitrogen, and gibberellic acid (GA) metabolism pathways. Therefore, photosynthesis, carbohydrate synthesis, nitrogen efficient utilization, and phytohormone signaling pathways are closely and intrinsically linked at the transcriptional level. These findings enhance our understanding of tillering in orchardgrass and perennial grasses, providing a new breeding strategy for improving forage biomass yield.
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Affiliation(s)
- Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoheng Xu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Wen Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Feigxiang Hao
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhongfu Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Peng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Shaun Bushman
- Forage and Range Research Laboratory, United States Department of Agriculture, 695 North 1100 East, Logan, UT 84322-6300, USA
| | - Wei He
- Grassland Research Institute, Chongqing Academy of Animal Science, Chongqing 402460, China
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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Wang M, Feng G, Yang Z, Wu J, Liu B, Xu X, Nie G, Huang L, Zhang X. Genome-Wide Characterization of the Aux/IAA Gene Family in Orchardgrass and a Functional Analysis of DgIAA21 in Responding to Drought Stress. Int J Mol Sci 2023; 24:16184. [PMID: 38003372 PMCID: PMC10671735 DOI: 10.3390/ijms242216184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/06/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Drought stress is an important factor that reduces plant biomass production and quality. As one of the most important economic forage grasses, orchardgrass (Dactylis glomerata) has high drought tolerance. Auxin/indole-3-acetic acid (Aux/IAA) is one of the early responsive gene families of auxin and plays a key role in the response to drought stress. However, the characteristics of the Aux/IAA gene family in orchardgrass and their potential function in responding to drought stress remain unclear. Here, 30 Aux/IAA members were identified in orchardgrass. Segmental duplication may be an important driving force in the evolution of the Aux/IAA gene family in orchardgrass. Some Aux/IAA genes were induced by IAA, drought, salt, and temperature stresses, implying that these genes may play important roles in responding to abiotic stresses. Heterologous expression in yeast revealed that DgIAA21 can reduce drought tolerance. Similarly, the overexpression of DgIAA21 also reduced drought tolerance in transgenic Arabidopsis, which was supported by lower total chlorophyll content and relative water content as well as higher relative electrolyte leakage and malondialdehyde content (MDA) than Col-0 plants under drought conditions. The results of this study provided valuable insight into the function of DgIAAs in response to drought stress, which can be further used to improve forage grass breeding programs.
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Affiliation(s)
| | | | | | | | | | | | | | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (M.W.); (G.F.); (Z.Y.)
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (M.W.); (G.F.); (Z.Y.)
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7
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Teng K, Guo Q, Liu L, Guo Y, Xu Y, Hou X, Teng W, Zhang H, Zhao C, Yue Y, Wen H, Wu J, Fan X. Chromosome-level reference genome assembly provides insights into the evolution of Pennisetum alopecuroides. FRONTIERS IN PLANT SCIENCE 2023; 14:1195479. [PMID: 37680353 PMCID: PMC10481962 DOI: 10.3389/fpls.2023.1195479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/28/2023] [Indexed: 09/09/2023]
Abstract
Pennisetum alopecuroides is an important forage grass resource, which plays a vital role in ecological environment improvement. Therefore, the acquisition of P. alopecuroides genome resources is conducive to the study of the adaptability of Pennisetum species in ecological remediation and forage breeding development. Here we assembled a P. alopecuroides cv. 'Liqiu' genome at the chromosome level with a size of approximately 845.71 Mb, contig N50 of 84.83Mb, and genome integrity of 99.13% as assessed by CEGMA. A total of 833.41-Mb sequences were mounted on nine chromosomes by Hi-C technology. In total, 60.66% of the repetitive sequences and 34,312 genes were predicted. The genomic evolution analysis showed that P. alopecuroides cv. 'Liqiu' was isolated from Setaria 7.53-13.80 million years ago and from Cenchrus 5.33-8.99 million years ago, respectively. The whole-genome event analysis showed that P. alopecuroides cv. 'Liqiu' underwent two whole-genome duplication (WGD) events in the evolution process, and the duplication events occurred at a similar time to that of Oryza sativa and Setaria viridis. The completion of the genome sequencing of P. alopecuroides cv. 'Liqiu' provides data support for mining high-quality genetic resources of P. alopecuroides and provides a theoretical basis for the origin and evolutionary characteristics of Pennisetum.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Yuesen Yue
- Institute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | | | | | - Xifeng Fan
- Institute of Grassland, Flowers, and Ecology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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Xing L, Wang M, He Q, Zhang H, Liang H, Zhou Q, Liu Y, Liu Z, Wang Y, Du C, Xiao Y, Liu J, Li W, Liu G, Du H. Differential subgenome expression underlies biomass accumulation in allotetraploid Pennisetum giganteum. BMC Biol 2023; 21:161. [PMID: 37480118 PMCID: PMC10362693 DOI: 10.1186/s12915-023-01643-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 06/06/2023] [Indexed: 07/23/2023] Open
Abstract
BACKGROUND Pennisetum giganteum (AABB, 2n = 4x = 28) is a C4 plant in the genus Pennisetum with origin in Africa but currently also grown in Asia and America. It is a crucial forage and potential energy grass with significant advantages in yield, stress resistance, and environmental adaptation. However, the mechanisms underlying these advantageous traits remain largely unexplored. Here, we present a high-quality genome assembly of the allotetraploid P. giganteum aiming at providing insights into biomass accumulation. RESULTS Our assembly has a genome size 2.03 Gb and contig N50 of 88.47 Mb that was further divided into A and B subgenomes. Genome evolution analysis revealed the evolutionary relationships across the Panicoideae subfamily lineages and identified numerous genome rearrangements that had occurred in P. giganteum. Comparative genomic analysis showed functional differentiation between the subgenomes. Transcriptome analysis found no subgenome dominance at the overall gene expression level; however, differentially expressed homoeologous genes and homoeolog-specific expressed genes between the two subgenomes were identified, suggesting that complementary effects between the A and B subgenomes contributed to biomass accumulation of P. giganteum. Besides, C4 photosynthesis-related genes were significantly expanded in P. giganteum and their sequences and expression patterns were highly conserved between the two subgenomes, implying that both subgenomes contributed greatly and almost equally to the highly efficient C4 photosynthesis in P. giganteum. We also identified key candidate genes in the C4 photosynthesis pathway that showed sustained high expression across all developmental stages of P. giganteum. CONCLUSIONS Our study provides important genomic resources for elucidating the genetic basis of advantageous traits in polyploid species, and facilitates further functional genomics research and genetic improvement of P. giganteum.
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Affiliation(s)
- Longsheng Xing
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
- Hebei Basic Science Center for Biotic Interaction, Baoding, 071000, China
| | - Meijia Wang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Qiang He
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
- Hebei Basic Science Center for Biotic Interaction, Baoding, 071000, China
| | - Hongyu Zhang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Hanfei Liang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Qinghong Zhou
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Yu Liu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Ze Liu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Yu Wang
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Cailian Du
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Yao Xiao
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Jianan Liu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
| | - Wei Li
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China
- Hebei Basic Science Center for Biotic Interaction, Baoding, 071000, China
| | - Guixia Liu
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China.
- Hebei Basic Science Center for Biotic Interaction, Baoding, 071000, China.
| | - Huilong Du
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071000, China.
- Hebei Basic Science Center for Biotic Interaction, Baoding, 071000, China.
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9
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Wang C, Feng G, Xu X, Huang L, Nie G, Li D, Zhang X. Genome-Wide Identification, Characterization, and Expression of TCP Genes Family in Orchardgrass. Genes (Basel) 2023; 14:genes14040925. [PMID: 37107682 PMCID: PMC10138293 DOI: 10.3390/genes14040925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Plant-specific TCP transcription factors regulate several plant growth and development processes. Nevertheless, little information is available about the TCP family in orchardgrass (Dactylis glomerata L.). This study identified 22 DgTCP transcription factors in orchardgrass and determined their structure, phylogeny, and expression in different tissues and developmental stages. The phylogenetic tree classified the DgTCP gene family into two main subfamilies, including class I and II supported by the exon-intron structure and conserved motifs. The DgTCP promoter regions contained various cis-elements associated with hormones, growth and development, and stress responses, including MBS (drought inducibility), circadian (circadian rhythms), and TCA-element (salicylic acid responsiveness). Moreover, DgTCP9 possibly regulates tillering and flowering time. Additionally, several stress treatments upregulated DgTCP1, DgTCP2, DgTCP6, DgTCP12, and DgTCP17, indicting their potential effects regarding regulating responses to the respective stress. This research offers a valuable basis for further studies of the TCP gene family in other Gramineae and reveals new ideas for increasing gene utilization.
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Affiliation(s)
- Cheng Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoheng Xu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Dandan Li
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
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10
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Integrated Transcriptomic and Metabolomics Analysis of the Root Responses of Orchardgrass to Submergence Stress. Int J Mol Sci 2023; 24:ijms24032089. [PMID: 36768412 PMCID: PMC9916531 DOI: 10.3390/ijms24032089] [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: 11/29/2022] [Revised: 01/07/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Submergence stress can severely affect plant growth. Orchardgrass (Dactylis glomerata L.) is an important forage grass, and the molecular mechanisms of orchardgrass to submergence stress are not well understood. The roots of the flood-tolerant cultivar "Dian Bei" were harvested at 0 h, 8 h and 24 h of submergence stress. The combined transcriptomic and metabolomic analyses showed that β-alanine metabolism, flavonoid biosynthesis, and biosynthesis of amino acid pathways were significantly enriched at 8 h and 24 h of submergence stress and were more pronounced at 24 h. Most of the flavonoid biosynthesis-related genes were down-regulated for the synthesis of metabolites such as naringenin, apigenin, naringin, neohesperidin, naringenin chalcone, and liquiritigenin in response to submergence stress. Metabolites such as phenylalanine, tyrosine, and tryptophan were up-regulated under stress. The predominant response of flavonoid and amino acids biosynthesis to submergence stress suggests an important role of these pathways in the submergence tolerance of orchardgrass.
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11
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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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12
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Yang Z, Nie G, Feng G, Xu X, Li D, Wang X, Huang L, Zhang X. Genome-wide identification of MADS-box gene family in orchardgrass and the positive role of DgMADS114 and DgMADS115 under different abiotic stress. Int J Biol Macromol 2022; 223:129-142. [PMID: 36356860 DOI: 10.1016/j.ijbiomac.2022.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/30/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022]
Abstract
Abiotic stress, a major factor limit growth and productivity of major crops. Orchardgrass is one of the most important cool-season forage grasses in the world, and it is highly tolerant to abiotic stress. The MADS-box transcription factor family is one of the largest families in plants, and it plays vital roles in multiple biological processes. However, MADS-box transcription factors in orchardgrass, especially those involved in abiotic stress, have not yet been elucidated. Here, 123 DgMADS-box members were identified in orchardgrass and a detailed overview has been presented. Syntenic analysis indicated that the expansion of the DgMADS-box genes in orchardgrass is mainly dependent on tandem duplication events. Some DgMADS-box genes were induced by multiple abiotic stresses, indicating that these genes may play critical regulatory roles in orchardgrass response to various abiotic stresses. Heterologous expression showed that DgMADS114 and DgMADS115 could enhance stress tolerance of transgenic Arabidopsis, as revealed by longer root length or higher survival rates under PEG, NaCl, ABA, and heat stress. The results of this study provide a scientific basis for clarifying the functional characterization of MADS-box genes in orchardgrass in response to environmental stress can be further used to improve forages and crops via breeding programs.
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Affiliation(s)
- Zhongfu Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoheng Xu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Dandan Li
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xia Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
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13
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Rohner M, Manzanares C, Yates S, Thorogood D, Copetti D, Lübberstedt T, Asp T, Studer B. Fine-Mapping and Comparative Genomic Analysis Reveal the Gene Composition at the S and Z Self-incompatibility Loci in Grasses. Mol Biol Evol 2022; 40:6882748. [PMID: 36477354 PMCID: PMC9825253 DOI: 10.1093/molbev/msac259] [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: 10/02/2022] [Revised: 11/12/2022] [Accepted: 11/21/2022] [Indexed: 12/13/2022] Open
Abstract
Self-incompatibility (SI) is a genetic mechanism of hermaphroditic plants to prevent inbreeding after self-pollination. Allogamous Poaceae species exhibit a unique gametophytic SI system controlled by two multi-allelic and independent loci, S and Z. Despite intense research efforts in the last decades, the genes that determine the initial recognition mechanism are yet to be identified. Here, we report the fine-mapping of the Z-locus in perennial ryegrass (Lolium perenne L.) and provide evidence that the pollen and stigma components are determined by two genes encoding DUF247 domain proteins (ZDUF247-I and ZDUF247-II) and the gene sZ, respectively. The pollen and stigma determinants are located side-by-side and were genetically linked in 10,245 individuals of two independent mapping populations segregating for Z. Moreover, they exhibited high allelic diversity as well as tissue-specific gene expression, matching the expected characteristics of SI determinants known from other systems. Revisiting the S-locus using the latest high-quality whole-genome assemblies revealed a similar gene composition and structure as found for Z, supporting the hypothesis of a duplicated origin of the two-locus SI system of grasses. Ultimately, comparative genomic analyses across a wide range of self-compatible and self-incompatible Poaceae species revealed that the absence of a functional copy of at least one of the six putative SI determinants is accompanied by a self-compatible phenotype. Our study provides new insights into the origin and evolution of the unique gametophytic SI system in one of the largest and economically most important plant families.
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Affiliation(s)
- Marius Rohner
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Chloé Manzanares
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Steven Yates
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Daniel Thorogood
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, United Kingdom
| | - Dario Copetti
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland,Arizona Genomics Institute, School of Plant Sciences, College of Agriculture and Life Sciences, University of Arizona, Tucson, AZ, USA
| | | | - Torben Asp
- Center for Quantitative Genetics and Genomics, Faculty of Technical Sciences, Aarhus University, Slagelse, Denmark
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14
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Su X, Liu T, Liu YP, Harris AJ, Chen JY. Adaptive radiation in Orinus, an endemic alpine grass of the Qinghai-Tibet Plateau, based on comparative transcriptomic analysis. JOURNAL OF PLANT PHYSIOLOGY 2022; 277:153786. [PMID: 35963042 DOI: 10.1016/j.jplph.2022.153786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
The species of Orinus (Poaceae) are important alpine plants with a variety of phenotypic traits and potential usages in molecular breeding toward drought-tolerant forage crops. However, the genetic basis of evolutionary adaption and diversification in the genus is still unclear. In the present study, we obtained transcriptomes for the two most divergent species, O. thoroldii and O. kokonoricus, using the Illumina platform and de novo assembly. In total, we generated 23,029 and 24,086 unigenes with N50 values of 1188 and 1203 for O. thoroldii and O. kokonoricus respectively, and identified 19,005 pairs of putative orthologs between the two species of Orinus. For these orthologs, estimations of non-synonymous/synonymous substitution rate ratios indicated that 568 pairs may be under strongly positive selection (Ka/Ks > 1), and Gene Ontogeny (GO) enrichment analysis revealed that significantly enriched pathways were in DNA repair and resistance to abiotic stress. Meanwhile, the divergence times of species between O. thoroldii and O. kokonoricus occurred 3.2 million years ago (Mya), and the recent evolutionary branch is an allotetraploid species, Cleistogenes songorica. We also detected a Ks peak of ∼0.60 for Orinus. Additionally, we identified 188 pairs of differentially expressed genes (DEGs) between the two species of Orinus, which were significantly enrich in stress resistance and lateral root development. Thus, we considered that the species diversification and evolutionary adaption of this genus was initiated by environmental selection, followed by phenotypic differentiation, finally leading to niche separation in the Qinghai-Tibet Plateau.
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Affiliation(s)
- Xu Su
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China; Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, 810016, China; Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China; Key Laboratory of Land Surface Processes and Ecological Conservation of the Qinghai-Tibet Plateau, The Ministry of Education, Qinghai Normal University, Xining, 810008, China
| | - Tao Liu
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China; School of Geographical Science, Qinghai Normal University, Xining, 810008, China
| | - Yu Ping Liu
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China; Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China.
| | - A J Harris
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Jin Yuan Chen
- School of Life Sciences, Qinghai Normal University, Xining, 810008, China; Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, 810008, China
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15
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Yang Z, Yan H, Wang J, Nie G, Feng G, Xu X, Li D, Huang L, Zhang X. DNA hypermethylation promotes the flowering of orchardgrass during vernalization. PLANT PHYSIOLOGY 2022; 190:1490-1505. [PMID: 35861426 PMCID: PMC9516772 DOI: 10.1093/plphys/kiac335] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Abstract
Vernalization, influenced by environmental factors, is an essential process associated with the productivity of temperate crops, during which epigenetic regulation of gene expression plays an important role. Although DNA methylation is one of the major epigenetic mechanisms associated with the control of gene expression, global changes in DNA methylation in the regulation of gene expression during vernalization-induced flowering of temperate plants remain largely undetermined. To characterize vernalization-associated DNA methylation dynamics, we performed whole-genome bisulfite-treated sequencing and transcriptome sequencing in orchardgrass (Dactylis glomerata) during vernalization. The results revealed that increased levels of genome DNA methylation during the early vernalization of orchardgrass were associated with transcriptional changes in DNA methyltransferase and demethylase genes. Upregulated expression of vernalization-related genes during early vernalization was attributable to an increase in mCHH in the promoter regions of these genes. Application of an exogenous DNA methylation accelerator or overexpression of orchardgrass NUCLEAR POLY(A) POLYMERASE (DgPAPS4) promoted earlier flowering, indicating that DNA hypermethylation plays an important role in vernalization-induced flowering. Collectively, our findings revealed that vernalization-induced hypermethylation is responsible for floral primordium initiation and development. These observations provide a theoretical foundation for further studies on the molecular mechanisms underlying the control of vernalization in temperate grasses.
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Affiliation(s)
| | | | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, Florida 32611, USA
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xiaoheng Xu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Dandan Li
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
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16
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Jiao Y, Feng G, Huang L, Nie G, Li Z, Peng Y, Li D, Xiong Y, Hu Z, Zhang X. Complete Chloroplast Genomes of 14 Subspecies of D. glomerata: Phylogenetic and Comparative Genomic Analyses. Genes (Basel) 2022; 13:genes13091621. [PMID: 36140789 PMCID: PMC9498378 DOI: 10.3390/genes13091621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/06/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
Orchardgrass (Dactylis glomerata L.) is a species in the Gramineae family that is highly important economically and valued for its role in ecology. However, the phylogeny and taxonomy of D. glomerata are still controversial based on current morphological and molecular evidence. The study of chloroplast (cp) genomes has developed into a powerful tool to develop molecular markers for related species and reveal the relationships between plant evolution and phylogenetics. In this study, we conducted comparative genomic analyses and phylogenetic inferences on 14 cp genomes of D. glomerata originating from the Mediterranean and Eurasia. The genome size ranged from 134,375 bp to 134,993 bp and exhibited synteny of gene organization and order. A total of 129–131 genes were identified, including 85–87 protein coding genes, 38 tRNA genes and 8 rRNA genes. The cp sequences were highly conserved, and key sequence variations were detected at the junctions of inverted repeats (IRs)/small single–copy (SSC) regions. Moreover, nine highly variable regions were identified among the subspecies based on a sequence divergence analysis. A total of 285 RNA editing sites were detected that were relevant to 52 genes, where rpoB exhibited the most abundant RNA editing sites. The phylogenetic analysis revealed that all Dactylis subspecies clustered into a monophyletic group and most branches provided a high support bootstrap. The main divergence time of D. glomerata was dated to the Miocene era, and this could have been due to changes in the climate. These findings will provide useful insights for further studies on phylogeny, the identification of subspecies and the development of hypotheses for the evolutionary history of the genus Dactylis and of the Gramineae family.
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17
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Lu X, Zhang H, Hu J, Nie G, Khan I, Feng G, Zhang X, Wang X, Huang L. Genome-wide identification and characterization of bHLH family genes from orchardgrass and the functional characterization of DgbHLH46 and DgbHLH128 in drought and salt tolerance. Funct Integr Genomics 2022; 22:1331-1344. [PMID: 35941266 DOI: 10.1007/s10142-022-00890-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 11/28/2022]
Abstract
Basic helix-loop-helix (bHLH) is the second largest family of transcription factors that widely exist in plants and animals, and plays a key role in a variety of biological processes. As an important forage crop worldwide, little information is available about the bHLH family in orchardgrass (Dactylis glomerata L.), although a huge number of bHLH family have been identified and characterized in plants. In this study, we performed genome-wide analysis of bHLH transcription factor family of orchardgrass and identified 132 DgbHLH genes. The phylogenetic tree was constructed by using bHLH proteins of orchardgrass, with Arabidopsis thaliana and Oryza sativa bHLH proteins, to elucidate their homology and classify them into 22 subfamilies. The results of conserved motifs and gene structure support the classification of DgbHLH family. In addition, chromosomal location and gene duplication events of DgbHLH genes were further studied. Transcriptome data exhibited that DgbHLH genes were differentially expressed in different tissues of orchardgrass. We analyzed the gene expression level of 12 DgbHLH genes in orchardgrass under three types of abiotic stresses (heat, salt, and drought). Finally, heterologous expression assays in yeast indicated that DgbHLH46 and DgbHLH128 may enhance the resistance to drought and salt stress. Furthermore, DgbHLH128 may also be involved in abiotic stress by binding to the MYC element. Our study provides a comprehensive assessment of DgbHLH family of orchardgrass, revealing new insights for enhancing gene utilization and improving forage performance.
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Affiliation(s)
- Xiaowen Lu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Huan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jialing Hu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Imran Khan
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xiaoshan Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China.
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18
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Callus Induction from Diverse Explants and Genotypes Enables Robust Transformation of Perennial Ryegrass (Lolium perenne L.). PLANTS 2022; 11:plants11152054. [PMID: 35956532 PMCID: PMC9370183 DOI: 10.3390/plants11152054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 07/27/2022] [Accepted: 07/27/2022] [Indexed: 11/17/2022]
Abstract
Genetic transformation of perennial ryegrass (Lolium perenne L.) is critical for fundamental and translational research in this important grass species. It often relies on Agrobacterium-mediated transformation of callus tissue. However, callus induction is restricted to a few genotypes that respond well to tissue culture. Here, we report callus induction from different perennial ryegrass genotypes and explants, such as shoot tips, seeds, and anthers, which were transformed with several plasmids for functional genomics. β-glucuronidase (GUS) histochemical staining showed the LmdsRNAbp promoter sequence was active in stigmas, spikelets, anthers, and leaves. We also transformed calli with plasmids allowing gene silencing and gene knock-out using RNA interference and CRISPR/Cas9, respectively, for which genotypic and phenotypic investigations are ongoing. Using 19 different constructs, 262 transgenic events were regenerated. Moreover, the protocol regenerated a doubled haploid transgenic event from anther-derived calli. This work provides a proof-of-concept method for expanding the range of genotypes amenable to transformation, thus, serving research and breeding initiatives to improve this important grass crop for forage and recreation.
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19
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PNGSeqR: An R Package for Rapid Candidate Gene Selection through Pooled Next-Generation Sequencing. PLANTS 2022; 11:plants11141821. [PMID: 35890455 PMCID: PMC9315718 DOI: 10.3390/plants11141821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/03/2022] [Accepted: 07/06/2022] [Indexed: 11/17/2022]
Abstract
Although bulked segregant analysis (BSA) has been used extensively in genetic mapping, user-friendly tools which can integrate current algorithms for researchers with no background in bioinformatics are scarce. To address this issue, we developed an R package, PNGSeqR, which takes single-nucleotide polymorphism (SNP) markers from next-generation sequencing (NGS) data in variant call format (VCF) as the input file, provides four BSA algorithms to indicate the magnitude of genome-wide signals, and rapidly defines the candidate region through the permutation test and fractile quantile. Users can choose the analysis methods according to their data and experimental design. In addition, it also supports differential expression gene analysis (DEG) and gene ontology analysis (GO) to prioritize the target gene. Once the analysis is completed, the plots can conveniently be exported.
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20
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Liu S, Chen H, Ouyang J, Huang M, Zhang H, Zheng S, Xi S, Tang H, Gao Y, Xiong Y, Cheng D, Chen K, Liu B, Li W, Ren J, Yan X, Mao H. A high-quality assembly reveals genomic characteristics, phylogenetic status, and causal genes for leucism plumage of Indian peafowl. Gigascience 2022; 11:6564124. [PMID: 35383847 PMCID: PMC8985102 DOI: 10.1093/gigascience/giac018] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/15/2021] [Accepted: 02/09/2022] [Indexed: 12/28/2022] Open
Abstract
Background The dazzling phenotypic characteristics of male Indian peafowl (Pavo cristatus) are attractive both to the female of the species and to humans. However, little is known about the evolution of the phenotype and phylogeny of these birds at the whole-genome level. So far, there are no reports regarding the genetic mechanism of the formation of leucism plumage in this variant of Indian peafowl. Results A draft genome of Indian peafowl was assembled, with a genome size of 1.05 Gb (the sequencing depth is 362×), and contig and scaffold N50 were up to 6.2 and 11.4 Mb, respectively. Compared with other birds, Indian peafowl showed changes in terms of metabolism, immunity, and skeletal and feather development, which provided a novel insight into the phenotypic evolution of peafowl, such as the large body size and feather morphologies. Moreover, we determined that the phylogeny of Indian peafowl was more closely linked to turkey than chicken. Specifically, we first identified that PMEL was a potential causal gene leading to the formation of the leucism plumage variant in Indian peafowl. Conclusions This study provides an Indian peafowl genome of high quality, as well as a novel understanding of phenotypic evolution and phylogeny of Indian peafowl. These results provide a valuable reference for the study of avian genome evolution. Furthermore, the discovery of the genetic mechanism for the development of leucism plumage is both a breakthrough in the exploration of peafowl plumage and also offers clues and directions for further investigations of the avian plumage coloration and artificial breeding in peafowl.
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Affiliation(s)
- Shaojuan Liu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Hao Chen
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Jing Ouyang
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Min Huang
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Hui Zhang
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Sumei Zheng
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Suwang Xi
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Hongbo Tang
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Yuren Gao
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Yanpeng Xiong
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Di Cheng
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Kaifeng Chen
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
| | - Bingbing Liu
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Wanbo Li
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen 361021, China
| | - Jun Ren
- College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xueming Yan
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang 330013, China
| | - Huirong Mao
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, China
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21
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Zhang S, Xia Z, Li C, Wang X, Lu X, Zhang W, Ma H, Zhou X, Zhang W, Zhu T, Liu P, Liu G, Wang W, Xia T. Chromosome-Scale Genome Assembly Provides Insights into Speciation of Allotetraploid and Massive Biomass Accumulation of Elephant Grass (Pennisetum purpureum Schum.). Mol Ecol Resour 2022; 22:2363-2378. [PMID: 35347881 DOI: 10.1111/1755-0998.13612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 03/02/2022] [Accepted: 03/23/2022] [Indexed: 11/29/2022]
Abstract
Elephant grass (Pennisetum purpureum Schum) is an important forage, biofuels and industrial plant widely distributed in tropical and subtropical areas globally. It is characterized with robust growth and high biomass. We sequenced its allopolyploid genome and assembled 2.07 Gb into A' and B sub-genomes of 14 chromosomes with scaffold N50 of 8.47 Mb, yielding a total of 77,139 genes. The allotetraploid speciation occurred approximately 15 MYA after the divergence between Setaria italica and Pennisetum glaucum, according to a phylogenetic analysis of Pennisetum species. Double whole-genome duplication (WGD) and polyploidization events resulted in large scale gene expansion, especially in the key steps of growth and biomass accumulation. Integrated transcriptome profiling revealed the functional divergence between sub-genomes A' and B. A' sub-genome mainly contributed to plant growth, development and photosynthesis, whereas the B sub-genome was primarily responsible for effective transportation and resistance to stimulation. Some key gene families related to cellulose biosynthesis were expanded and highly expressed in stems, which could explain the high cellulose content in elephant grass. Our findings provide deep insights into genetic evolution of elephant grass and will aid future biological research and breeding, even for other grasses in the family Poaceae.
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Affiliation(s)
- Shengkui Zhang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, 250353, Shandong, PR China.,School of Bioengineering, Qilu University of Technology, Jinan, 250353, Shandong, PR China
| | - Zhiqiang Xia
- College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, PR China
| | - Can Li
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, 250353, Shandong, PR China.,School of Bioengineering, Qilu University of Technology, Jinan, 250353, Shandong, PR China
| | - Xiaohan Wang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, 250353, Shandong, PR China.,School of Bioengineering, Qilu University of Technology, Jinan, 250353, Shandong, PR China
| | - Xianqin Lu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, 250353, Shandong, PR China.,School of Bioengineering, Qilu University of Technology, Jinan, 250353, Shandong, PR China
| | - Wenqing Zhang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, 250353, Shandong, PR China.,School of Bioengineering, Qilu University of Technology, Jinan, 250353, Shandong, PR China
| | - Haizhen Ma
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, 250353, Shandong, PR China.,School of Bioengineering, Qilu University of Technology, Jinan, 250353, Shandong, PR China
| | - Xincheng Zhou
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haiko, 571101, Hainan, PR China
| | - Weixiong Zhang
- Department of Computer Science and Engineering, Department of Genetics, Washington University, St. Louis, MO, USA
| | - Tingting Zhu
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Pandao Liu
- Institute of Tropical Crops Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571700, Hainan, PR China
| | - Guodao Liu
- Institute of Tropical Crops Genetic Resources, Chinese Academy of Tropical Agricultural Sciences, Danzhou, 571700, Hainan, PR China
| | - Wenquan Wang
- College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, PR China.,Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haiko, 571101, Hainan, PR China
| | - Tao Xia
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Jinan, 250353, Shandong, PR China.,School of Bioengineering, Qilu University of Technology, Jinan, 250353, Shandong, PR China
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22
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Chang D, Gao S, Zhou G, Deng S, Jia J, Wang E, Cao W. The chromosome-level genome assembly of Astragalus sinicus and comparative genomic analyses provide new resources and insights for understanding legume-rhizobial interactions. PLANT COMMUNICATIONS 2022; 3:100263. [PMID: 35529952 PMCID: PMC9073321 DOI: 10.1016/j.xplc.2021.100263] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 05/20/2023]
Abstract
The legume species Astragalus sinicus (Chinese milk vetch [CMV]) has been widely cultivated for centuries in southern China as one of the most important green manures/cover crops for improving rice productivity and preventing soil degeneration. In this study, we generated the first chromosome-scale reference genome of CMV by combining PacBio and Illumina sequencing with high-throughput chromatin conformation capture (Hi-C) technology. The CMV genome was 595.52 Mb in length, with a contig N50 size of 1.50 Mb. Long terminal repeats (LTRs) had been amplified and contributed to genome size expansion in CMV. CMV has undergone two whole-genome duplication (WGD) events, and the genes retained after the WGD shared by Papilionoideae species shaped the rhizobial symbiosis and the hormonal regulation of nodulation. The chalcone synthase (CHS) gene family was expanded and was expressed primarily in the roots of CMV. Intriguingly, we found that resistance genes were more highly expressed in roots than in nodules of legume species, suggesting that their expression may be increased to bolster plant immunity in roots to cope with pathogen infection in legumes. Our work sheds light on the genetic basis of nodulation and symbiosis in CMV and provides a benchmark for accelerating genetic research and molecular breeding in the future.
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Affiliation(s)
- Danna Chang
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Songjuan Gao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Guopeng Zhou
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuhan Deng
- Glbizzia Biological Science and Technology, Co, Ltd, Beijing, China
| | - Jizeng Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Corresponding author
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Corresponding author
| | - Weidong Cao
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Corresponding author
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23
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Li Z, Xu Y. Bulk segregation analysis in the NGS era: a review of its teenage years. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1355-1374. [PMID: 34931728 DOI: 10.1111/tpj.15646] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/27/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Bulk segregation analysis (BSA) utilizes a strategy of pooling individuals with extreme phenotypes to conduct economical and rapidly linked marker screening or quantitative trait locus (QTL) mapping. With the development of next-generation sequencing (NGS) technology in the past 10 years, BSA methods and technical systems have been gradually developed and improved. At the same time, the ever-decreasing costs of sequencing accelerate NGS-based BSA application in different species, including eukaryotic yeast, grain crops, economic crops, horticultural crops, trees, aquatic animals, and insects. This paper provides a landscape of BSA methods and reviews the BSA development process in the past decade, including the sequencing method for BSA, different populations, different mapping algorithms, associated region threshold determination, and factors affecting BSA mapping. Finally, we summarize related strategies in QTL fine mapping combining BSA.
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Affiliation(s)
- Zhiqiang Li
- Adsen Biotechnology Co., Ltd., Urumchi, 830022, China
| | - Yuhui Xu
- Adsen Biotechnology Co., Ltd., Urumchi, 830022, China
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24
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Zhang L, Zhu X, Zhao Y, Guo J, Zhang T, Huang W, Huang J, Hu Y, Huang CH, Ma H. Phylotranscriptomics Resolves the Phylogeny of Pooideae and Uncovers Factors for Their Adaptive Evolution. Mol Biol Evol 2022; 39:6521033. [PMID: 35134207 PMCID: PMC8844509 DOI: 10.1093/molbev/msac026] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Adaptation to cool climates has occurred several times in different angiosperm groups. Among them, Pooideae, the largest grass subfamily with ∼3,900 species including wheat and barley, have successfully occupied many temperate regions and play a prominent role in temperate ecosystems. To investigate possible factors contributing to Pooideae adaptive evolution to cooling climates, we performed phylogenetic reconstruction using five gene sets (with 1,234 nuclear genes and their subsets) from 157 transcriptomes/genomes representing all 15 tribes and 24 of 26 subtribes. Our phylogeny supports the monophyly of all tribes (except Diarrheneae) and all subtribes with at least two species, with strongly supported resolution of their relationships. Molecular dating suggests that Pooideae originated in the late Cretaceous, with subsequent divergences under cooling conditions first among many tribes from the early middle to late Eocene and again among genera in the middle Miocene and later periods. We identified a cluster of gene duplications (CGD5) shared by the core Pooideae (with 80% Pooideae species) near the Eocene–Oligocene transition, coinciding with the transition from closed to open habitat and an upshift of diversification rate. Molecular evolutionary analyses homologs of CBF for cold resistance uncovered tandem duplications during the core Pooideae history, dramatically increasing their copy number and possibly promoting adaptation to cold habitats. Moreover, duplication of AP1/FUL-like genes before the Pooideae origin might have facilitated the regulation of the vernalization pathway under cold environments. These and other results provide new insights into factors that likely have contributed to the successful adaptation of Pooideae members to temperate regions.
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Affiliation(s)
- Lin Zhang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Xinxin Zhu
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China
| | - Yiyong Zhao
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Jing Guo
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Taikui Zhang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Weichen Huang
- Department of Biology, the Huck Institutes of Life Sciences, the Pennsylvania State University, University Park, PA, USA
| | - Jie Huang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Yi Hu
- Department of Biology, the Huck Institutes of Life Sciences, the Pennsylvania State University, University Park, PA, USA
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Hong Ma
- Department of Biology, the Huck Institutes of Life Sciences, the Pennsylvania State University, University Park, PA, USA
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25
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Shuai Y, Feng G, Yang Z, Liu Q, Han J, Xu X, Nie G, Huang L, Zhang X. Genome-wide identification of C2H2-type zinc finger gene family members and their expression during abiotic stress responses in orchardgrass ( Dactylis glomerata). Genome 2022; 65:189-203. [PMID: 35104149 DOI: 10.1139/gen-2020-0201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The C2H2-type zinc finger protein (ZFP) family is one of the largest transcription factor families in the plant kingdom and its members are involved in plant growth, development, and stress responses. As an economically valuable perennial graminaceous forage crop, orchardgrass (Dactylis glomerata) is an important feedstuff resource owing to its high yield and quality. In this study, 125 C2H2-type ZFPs in orchardgrass (Dg-ZFPs) were identified and further classified by phylogenetic analysis. The members with similar gene structures were generally clustered into the same groups, with proteins containing the conserved QALGGH motif being concentrated in groups VIII and IX. Gene ontology and miRNA target analyses indicated that Dg-ZFPs likely perform diverse biological functions through their gene interactions. The RNA-seq data revealed differentially expressed genes across tissues and development phases, suggesting that some Dg-ZFPs might participate in growth and development regulation. Abiotic stress responses of Dg-ZFP genes were verified by qPCR and Saccharomyces cerevisiae transformation, revealing that Dg-ZFP125 could enhance the tolerance of yeasts to osmotic and salt stresses. Our study performed a novel systematic analysis of Dg-ZFPs in orchardgrass, providing a reference for this gene family in other grasses and revealing new insights for enhancing gene utilization.
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Affiliation(s)
- Yang Shuai
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhongfu Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiuxu Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiating Han
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaoheng Xu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
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26
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Ren G, Jiang Y, Li A, Yin M, Li M, Mu W, Wu Y, Liu J. The genome sequence provides insights into salt tolerance of Achnatherum splendens (Gramineae), a constructive species of alkaline grassland. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:116-128. [PMID: 34487631 PMCID: PMC8710827 DOI: 10.1111/pbi.13699] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 08/18/2021] [Accepted: 09/01/2021] [Indexed: 05/02/2023]
Abstract
Achnatherum splendens Trin. (Gramineae) is a constructive species of the arid grassland ecosystem in Northwest China and is a major forage grass. It has good tolerance of salt and drought stress in alkaline habitats. Here, we report its chromosome-level genome, determined through a combination of Illumina HiSeq sequencing, PacBio sequencing and Hi-C technology. The final assembly of the ~1.17 Gb genome sequence had a super-scaffold N50 of 40.3 Mb. A total of 57 374 protein-coding genes were annotated, of which 54 426 (94.5%) genes have functional protein annotations. Approximately 735 Mb (62.37%) of the assembly were identified as repetitive elements, and among these, LTRs (40.53%) constitute the highest proportion, having made a major contribution to the expansion of genome size in A. splendens. Phylogenetic analysis revealed that A. splendens diverged from the Brachypodium distachyon-Hordeum vulgare-Aegilops tauschii subclade around 37 million years ago (Ma) and that a clade comprising these four species diverged from the Phyllostachys edulis clade ~47 Ma. Genomic synteny indicates that A. splendens underwent an additional species-specific whole-genome duplication (WGD) 18-20 Ma, which further promoted an increase in copies of numerous saline-alkali-related gene families in the A. splendens genome. By transcriptomic analysis, we further found that many of these duplicated genes from this extra WGD exhibited distinct functional divergence in response to salt stress. This WGD, therefore, contributed to the strong resistance to salt stress and widespread arid adaptation of A. splendens.
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Affiliation(s)
- Guangpeng Ren
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Yanyou Jiang
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Ao Li
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Mou Yin
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Minjie Li
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Wenjie Mu
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Ying Wu
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro‐EcosystemsInstitute of Innovation Ecology & School of Life SciencesLanzhou UniversityLanzhouChina
- Key Laboratory of Bio‐Resources and Eco‐Environment of the Ministry of Education & State Key Lab of Hydraulics & Mountain River EngineeringCollege of Life SciencesSichuan UniversityChengduChina
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27
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Song T, Zhou M, Yuan Y, Yu J, Cai H, Li J, Chen Y, Bai Y, Zhou G, Cui G. Chromosome-Scale Reference Genome of Amphicarpaea edgeworthii: A New Resource for Amphicarpic Plants Research and Complex Flowering Pattern. FRONTIERS IN PLANT SCIENCE 2021; 12:770660. [PMID: 34868169 PMCID: PMC8637744 DOI: 10.3389/fpls.2021.770660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
Amphicarpaea edgeworthii, an annual twining herb, is a widely distributed species and an attractive model for studying complex flowering types and evolutionary mechanisms of species. Herein, we have generated a high-quality assembly of A. edgeworthii by using a combination of PacBio, 10× Genomics libraries, and Hi-C mapping technologies. The final 11 chromosome-level scaffolds covered 90.61% of the estimated genome (343.78Mb), which is a chromosome-scale assembled genome of an amphicarpic plant. Subsequently, we characterized the genetic diversity and population structure of A. edgeworthii species by resequencing individuals collected from their natural area of distribution. Using transcriptome profiling, we observed that specific phenotypes are regulated by a complex network of light, hormones, and MADS-box gene families. These data are beneficial for the discovery of genes that control major agronomic traits and spur genetic improvement of and functional genetic studies in legumes, as well as supply comparative genetic resources for other amphicarpic plants.
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Affiliation(s)
- Tingting Song
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Mengyan Zhou
- Novogene Bioinformatics Institute, Beijing, China
| | - Yuying Yuan
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Jinqiu Yu
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Hua Cai
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Jiawei Li
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yajun Chen
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yan Bai
- Novogene Bioinformatics Institute, Beijing, China
| | - Gang Zhou
- Novogene Bioinformatics Institute, Beijing, China
| | - Guowen Cui
- Department of Grassland Science, College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
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28
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Nie G, Yang Z, He J, Liu A, Chen J, Wang S, Wang X, Feng G, Li D, Peng Y, Huang L, Zhang X. Genome-Wide Investigation of the NAC Transcription Factor Family in Miscanthus sinensis and Expression Analysis Under Various Abiotic Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:766550. [PMID: 34804100 PMCID: PMC8600139 DOI: 10.3389/fpls.2021.766550] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
The NAC transcription factor family is deemed to be a large plant-specific gene family that plays important roles in plant development and stress response. Miscanthus sinensis is commonly planted in vast marginal land as forage, ornamental grass, or bioenergy crop which demand a relatively high resistance to abiotic stresses. The recent release of a draft chromosome-scale assembly genome of M. sinensis provided a basic platform for the genome-wide investigation of NAC proteins. In this study, a total of 261 M. sinensis NAC genes were identified and a complete overview of the gene family was presented, including gene structure, conserved motif compositions, chromosomal distribution, and gene duplications. Results showed that gene length, molecular weights (MW), and theoretical isoelectric points (pI) of NAC family were varied, while gene structure and motifs were relatively conserved. Chromosomal mapping analysis found that the M. sinensis NAC genes were unevenly distributed on 19 M. sinensis chromosomes, and the interchromosomal evolutionary analysis showed that nine pairs of tandem duplicates genes and 121 segmental duplications were identified, suggesting that gene duplication, especially segmental duplication, is possibly associated with the amplification of M. sinensis NAC gene family. The expression patterns of 14 genes from M. sinensis SNAC subgroup were analyzed under high salinity, PEG, and heavy metals, and multiple NAC genes could be induced by the treatment. These results will provide a very useful reference for follow-up study of the functional characteristics of NAC genes in the mechanism of stress-responsive and potential roles in the development of M. sinensis.
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29
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Ren J, Hu J, Zhang A, Ren S, Jing T, Wang X, Sun M, Huang L, Zeng B. The whole-genome and expression profile analysis of WRKY and RGAs in Dactylis glomerata showed that DG6C02319.1 and Dg WRKYs may cooperate in the immunity against rust. PeerJ 2021; 9:e11919. [PMID: 34466285 PMCID: PMC8380429 DOI: 10.7717/peerj.11919] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/16/2021] [Indexed: 02/01/2023] Open
Abstract
Orchardgrass (Dactylis glomerata) is one of the top four perennial forages worldwide and, despite its large economic advantages, often threatened by various environmental stresses. WRKY transcription factors (TFs) can regulate a variety of plant processes, widely participate in plant responses to biotic and abiotic stresses, and are one of the largest gene families in plants. WRKYs can usually bind W-box elements specifically. In this study, we identified a total of 93 DgWRKY genes and 281 RGAs, including 65, 169 and 47 nucleotide-binding site-leucine-rich repeats (NBS-LRRs), leucine-rich repeats receptor-like protein kinases (LRR-RLKs), and leucine-rich repeats receptor-like proteins (LRR-RLPs), respectively. Through analyzing the expression of DgWRKY genes in orchardgrass under different environmental stresses, it was found that many DgWRKY genes were differentially expressed under heat, drought, submergence, and rust stress. In particular, it was found that the greatest number of genes were differentially expressed under rust infection. Consistently, GO and KEGG enrichment analysis of all genes showed that 78 DgWRKY TFs were identified in the plant–pathogen interaction pathway, with 59 of them differentially expressed. Through cis-acting element prediction, 154 RGAs were found to contain W-box elements. Among them, DG6C02319.1 (a member of the LRR-RLK family) was identified as likely to interact with 14 DGWRKYs. Moreover, their expression levels in susceptible plants after rust inoculation were first up-regulated and then down-regulated, while those in the resistant plants were always up-regulated. In general, DgWRKYs responded to both biotic stress and abiotic stress. DgWRKYs and RGAs may synergistically respond to the response of orchardgrass to rust. This study provides meaningful insight into the molecular mechanisms of WRKY proteins in orchardgrass.
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Affiliation(s)
- Juncai Ren
- College of Animal Science and Technology, Southwest University, Chongqing, Chongqing, China
| | - Jialing Hu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ailing Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shuping Ren
- College of Animal Science and Technology, Southwest University, Chongqing, Chongqing, China
| | - Tingting Jing
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaoshan Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Min Sun
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bing Zeng
- College of Animal Science and Technology, Southwest University, Chongqing, Chongqing, China
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30
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Frei D, Veekman E, Grogg D, Stoffel-Studer I, Morishima A, Shimizu-Inatsugi R, Yates S, Shimizu KK, Frey JE, Studer B, Copetti D. Ultralong Oxford Nanopore Reads Enable the Development of a Reference-Grade Perennial Ryegrass Genome Assembly. Genome Biol Evol 2021; 13:evab159. [PMID: 34247248 PMCID: PMC8358221 DOI: 10.1093/gbe/evab159] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2021] [Indexed: 12/24/2022] Open
Abstract
Despite the progress made in DNA sequencing over the last decade, reconstructing telomere-to-telomere genome assemblies of large and repeat-rich eukaryotic genomes is still difficult. More accurate basecalls or longer reads could address this issue, but no current sequencing platform can provide both simultaneously. Perennial ryegrass (Lolium perenne L.) is an example of an important species for which the lack of a reference genome assembly hindered a swift adoption of genomics-based methods into breeding programs. To fill this gap, we optimized the Oxford Nanopore Technologies' sequencing protocol, obtaining sequencing reads with an N50 of 62 kb-a very high value for a plant sample. The assembly of such reads produced a highly complete (2.3 of 2.7 Gb), correct (QV 45), and contiguous (contig N50 and N90 11.74 and 3.34 Mb, respectively) genome assembly. We show how read length was key in determining the assembly contiguity. Sequence annotation revealed the dominance of transposable elements and repeated sequences (81.6% of the assembly) and identified 38,868 protein coding genes. Almost 90% of the bases could be anchored to seven pseudomolecules, providing the first high-quality haploid reference assembly for perennial ryegrass. This protocol will enable producing longer Oxford Nanopore Technology reads for more plant samples and ushering forage grasses into modern genomics-assisted breeding programs.
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Affiliation(s)
- Daniel Frei
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland
| | | | - Daniel Grogg
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Ingrid Stoffel-Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Aki Morishima
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Steven Yates
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Kentaro K Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Kihara Institute for Biological Research, Yokohama City University, Maioka, Totsuka-ward, Yokohama, Japan
| | - Jürg E Frey
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics, Wädenswil, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Dario Copetti
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
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Awan SA, Khan I, Rizwan M, Zhang X, Brestic M, Khan A, El-Sheikh MA, Alyemeni MN, Ali S, Huang L. Exogenous abscisic acid and jasmonic acid restrain polyethylene glycol-induced drought by improving the growth and antioxidative enzyme activities in pearl millet. PHYSIOLOGIA PLANTARUM 2021; 172:809-819. [PMID: 33094486 DOI: 10.1111/ppl.13247] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 05/04/2023]
Abstract
Drought stress is one of the most immense and permanent constraints in agriculture, which leads to a massive loss of crop productivity. However, little is known about the mitigation role of exogenously applied abscisic acid (ABA) and jasmonic acid (JA) in pearl millet (Pennisetum glaucum L.) under PEG-induced drought stress. Therefore, the current study investigated the putative role of exogenous ABA and JA in improving drought stress tolerance in pearl millet. Thirteen-day-old seedlings were exposed to six different treatments as follow; control (ck), PEG-600 (20%), JA (100 μM), ABA (100 μM), PEG+JA, and PEG+ABA, and data were collected at 7 and 14 days after treatment (DAT). Results showed that PEG decreased plant growth while the oxidative damage increased due to over production of H2 O2 and MDA content as a result of decreased activities of the antioxidative enzymes including APX, CAT, and SOD in the leaves. However, exogenous ABA and JA positively enhanced the growth profile of seedlings by improving chlorophyll and relative water content under PEG treatment. A significant improvement was observed in the plant defense system resulting from increased activities of antioxidative enzymes due to exogenous ABA and JA under PEG. Overall, the performance of JA was found better than ABA under PEG-induced drought stress, and future investigations are needed to explore the potential effects of these phytohormones on the long-term crop management and productivity under drought stress.
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Affiliation(s)
- Samrah A Awan
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Imran Khan
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Muhammad Rizwan
- Department of Environmental Sciences and Engineering, Government College University, Faisalabad, Pakistan
| | - Xinquan Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
| | - Marian Brestic
- Department of Plant Physiology, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, Nitra, Slovakia
| | - Aaqil Khan
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Mohamed A El-Sheikh
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammed N Alyemeni
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Shafaqat Ali
- Department of Environmental Sciences and Engineering, Government College University, Faisalabad, Pakistan
- Department of Biological Sciences and Technology, China Medical University, Taichung, Taiwan
| | - Linkai Huang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, China
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Feng G, Han J, Yang Z, Liu Q, Shuai Y, Xu X, Nie G, Huang L, Liu W, Zhang X. Genome-wide identification, phylogenetic analysis, and expression analysis of the SPL gene family in orchardgrass (Dactylis glomerata L.). Genomics 2021; 113:2413-2425. [PMID: 34058273 DOI: 10.1016/j.ygeno.2021.05.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 05/20/2021] [Accepted: 05/25/2021] [Indexed: 02/06/2023]
Abstract
SPL (SQUAMOSA promoter binding protein-like) is a plant-specific transcription factor family that contains the conserved SBP domain, which plays a vital role in the vegetative-to-reproductive phase transition, flowering development and regulation, tillering/branching, and stress responses. Although the SPL family has been identified and characterized in various plant species, limited information about it has been obtained in orchardgrass, which is a critical forage crop worldwide. In this study, 17 putative DgSPL genes were identified among seven chromosomes, and seven groups that share similar gene structures and conserved motifs were determined by phylogenetic analysis. Of these, eight genes have potential target sites for miR156. cis-Element and gene ontology annotation analysis indicated DgSPLs may be involved in regulating development and abiotic stress responses. The expression patterns of eight DgSPL genes at five developmental stages, in five tissues, and under three stress conditions were determined by RNA-seq and qRT-PCR. These assays indicated DgSPLs are involved in vegetative-to-reproductive phase transition, floral development, and stress responses. The transient expression analysis in tobacco and heterologous expression assays in yeast indicated that miR156-targeted DG1G01828.1 and DG0G01071.1 are nucleus-localized proteins, that may respond to drought, salt, and heat stress. Our study represents the first systematic analysis of the SPL family in orchardgrass. This research provides a comprehensive assessment of the DgSPL family, which lays the foundation for further examination of the role of miR156/DgSPL in regulating development and stress responses in forages grasses.
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Affiliation(s)
- Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Jiating Han
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Zhongfu Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Qiuxu Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Yang Shuai
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Xiaoheng Xu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Wei Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
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Liu Y, Zhang X, Han K, Li R, Xu G, Han Y, Cui F, Fan S, Seim I, Fan G, Li G, Wan S. Insights into amphicarpy from the compact genome of the legume Amphicarpaea edgeworthii. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:952-965. [PMID: 33236503 PMCID: PMC8131047 DOI: 10.1111/pbi.13520] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/13/2020] [Accepted: 11/18/2020] [Indexed: 05/04/2023]
Abstract
Amphicarpy (seed heteromorphy) is a unique and fascinating reproductive strategy wherein a single plant produces both aerial and subterranean fruits. This strategy is believed to be an adaptation to life under stressful or uncertain environments. Here, we sequenced and de novo assembled a chromosome-level genome assembly of the legume Amphicarpaea edgeworthii Benth. The 299-Mb A. edgeworthii genome encodes 27 899 protein-coding genes and is the most compact sequenced legume genome reported until date. Its reduced genome size may be attributed to the reduced long-terminal repeat retrotransposon content, which stems from the unequal homologous recombination. Gene families related to immunity and stress resistance have been contracted in A. edgeworthii, which is consistent with the notion that the amphicarpic reproductive strategy may be a complementary mechanism for its weak environmental-adaptation ability. We demonstrated the 'ABCE' model for the differentiation of chasmogamous and cleistogamous flowers. In addition, the characteristics of aerial and subterranean seeds in hard-seededness were explored. Thus, we suggest that the A. edgeworthii genome, which is the first of an amphicarpic plant, offers significant insights into its unusual reproductive strategy that is a key resource towards comprehending the evolution of angiosperms.
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Affiliation(s)
- Yiyang Liu
- Bio‐technology Research CenterShandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyShandong Academy of Agricultural SciencesJi’nanChina
| | - Xuejie Zhang
- College of Life SciencesShandong Normal UniversityJi’nanChina
| | - Kai Han
- BGI‐QingdaoBGI‐ShenzhenQingdaoChina
| | - Rongchong Li
- Bio‐technology Research CenterShandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyShandong Academy of Agricultural SciencesJi’nanChina
| | - Guoxin Xu
- Shandong Rice Research InstituteShandong Academy of Agricultural SciencesJi’nanChina
| | - Yan Han
- College of Life SciencesShandong Normal UniversityJi’nanChina
| | - Feng Cui
- Bio‐technology Research CenterShandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyShandong Academy of Agricultural SciencesJi’nanChina
| | - Shoujin Fan
- College of Life SciencesShandong Normal UniversityJi’nanChina
| | - Inge Seim
- Integrative Biology LaboratoryCollege of Life SciencesNanjing Normal UniversityNanjingChina
| | - Guangyi Fan
- BGI‐QingdaoBGI‐ShenzhenQingdaoChina
- BGI‐ShenzhenShenzhenChina
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
| | - Guowei Li
- Bio‐technology Research CenterShandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyShandong Academy of Agricultural SciencesJi’nanChina
| | - Shubo Wan
- Bio‐technology Research CenterShandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyShandong Academy of Agricultural SciencesJi’nanChina
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Guo R, Zhao L, Zhang K, Lu H, Bhanbhro N, Yang C. Comparative Genomics and Transcriptomics of the Extreme Halophyte Puccinellia tenuiflora Provides Insights Into Salinity Tolerance Differentiation Between Halophytes and Glycophytes. FRONTIERS IN PLANT SCIENCE 2021; 12:649001. [PMID: 33968105 PMCID: PMC8100201 DOI: 10.3389/fpls.2021.649001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 04/06/2021] [Indexed: 05/25/2023]
Abstract
Halophytes and glycophytes exhibit clear differences in their tolerance to high levels of salinity. The genetic mechanisms underlying this differentiation, however, remain unclear. To unveil these mechanisms, we surveyed the evolution of salinity-tolerant gene families through comparative genomic analyses between the model halophyte Puccinellia tenuiflora and glycophytic Gramineae plants, and compared their transcriptional and physiological responses to salinity stress. Under salinity stress, the K+ concentration in the root was slightly enhanced in P. tenuiflora, but it was greatly reduced in the glycophytic Gramineae plants, which provided a physiological explanation for differences in salinity tolerance between P. tenuiflora and these glycophytes. Interestingly, several K+ uptake gene families from P. tenuiflora experienced family expansion and positive selection during evolutionary history. This gene family expansion and the elevated expression of K+ uptake genes accelerated K+ accumulation and decreased Na+ toxicity in P. tenuiflora roots under salinity stress. Positively selected P. tenuiflora K+ uptake genes may have evolved new functions that contributed to development of P. tenuiflora salinity tolerance. In addition, the expansion of the gene families involved in pentose phosphate pathway, sucrose biosynthesis, and flavonoid biosynthesis assisted the adaptation of P. tenuiflora to survival under high salinity conditions.
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Affiliation(s)
- Rui Guo
- Key Laboratory of Dryland Agriculture, Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Long Zhao
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Kaijian Zhang
- Beijing Novogene Bioinformatics Technology Ltd., Beijing, China
| | - Huiying Lu
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Nadeem Bhanbhro
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Chunwu Yang
- Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University, Changchun, China
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Yang Z, Nie G, Feng G, Han J, Huang L, Zhang X. Genome-wide identification, characterization, and expression analysis of the NAC transcription factor family in orchardgrass (Dactylis glomerata L.). BMC Genomics 2021; 22:178. [PMID: 33711917 PMCID: PMC7953825 DOI: 10.1186/s12864-021-07485-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 02/25/2021] [Indexed: 01/07/2023] Open
Abstract
Background Orchardgrass (Dactylis glomerata L.) is one of the most important cool-season perennial forage grasses that is widely cultivated in the world and is highly tolerant to stressful conditions. However, little is known about the mechanisms underlying this tolerance. The NAC (NAM, ATAF1/2, and CUC2) transcription factor family is a large plant-specific gene family that actively participates in plant growth, development, and response to abiotic stress. At present, owing to the absence of genomic information, NAC genes have not been systematically studied in orchardgrass. The recent release of the complete genome sequence of orchardgrass provided a basic platform for the investigation of DgNAC proteins. Results Using the recently released orchardgrass genome database, a total of 108 NAC (DgNAC) genes were identified in the orchardgrass genome database and named based on their chromosomal location. Phylogenetic analysis showed that the DgNAC proteins were distributed in 14 subgroups based on homology with NAC proteins in Arabidopsis, including the orchardgrass-specific subgroup Dg_NAC. Gene structure analysis suggested that the number of exons varied from 1 to 15, and multitudinous DgNAC genes contained three exons. Chromosomal mapping analysis found that the DgNAC genes were unevenly distributed on seven orchardgrass chromosomes. For the gene expression analysis, the expression levels of DgNAC genes in different tissues and floral bud developmental stages were quite different. Quantitative real-time PCR analysis showed distinct expression patterns of 12 DgNAC genes in response to different abiotic stresses. The results from the RNA-seq data revealed that orchardgrass-specific NAC exhibited expression preference or specificity in diverse abiotic stress responses, and the results indicated that these genes may play an important role in the adaptation of orchardgrass under different environments. Conclusions In the current study, a comprehensive and systematic genome-wide analysis of the NAC gene family in orchardgrass was first performed. A total of 108 NAC genes were identified in orchardgrass, and the expression of NAC genes during plant growth and floral bud development and response to various abiotic stresses were investigated. These results will be helpful for further functional characteristic descriptions of DgNAC genes and the improvement of orchardgrass in breeding programs. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07485-6.
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Affiliation(s)
- Zhongfu Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China
| | - Gang Nie
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China
| | - Guangyan Feng
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China
| | - Jiating Han
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China
| | - Linkai Huang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China
| | - Xinquan Zhang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan Province, China.
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Zhang J, Wu F, Yan Q, John UP, Cao M, Xu P, Zhang Z, Ma T, Zong X, Li J, Liu R, Zhang Y, Zhao Y, Kanzana G, Lv Y, Nan Z, Spangenberg G, Wang Y. The genome of Cleistogenes songorica provides a blueprint for functional dissection of dimorphic flower differentiation and drought adaptability. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:532-547. [PMID: 32964579 PMCID: PMC7955882 DOI: 10.1111/pbi.13483] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 09/13/2020] [Indexed: 05/24/2023]
Abstract
Cleistogenes songorica (2n = 4x = 40) is a desert grass with a unique dimorphic flowering mechanism and an ability to survive extreme drought. Little is known about the genetics underlying drought tolerance and its reproductive adaptability. Here, we sequenced and assembled a high-quality chromosome-level C. songorica genome (contig N50 = 21.28 Mb). Complete assemblies of all telomeres, and of ten chromosomes were derived. C. songorica underwent a recent tetraploidization (~19 million years ago) and four major chromosomal rearrangements. Expanded genes were significantly enriched in fatty acid elongation, phenylpropanoid biosynthesis, starch and sucrose metabolism, and circadian rhythm pathways. By comparative transcriptomic analysis we found that conserved drought tolerance related genes were expanded. Transcription of CsMYB genes was associated with differential development of chasmogamous and cleistogamous flowers, as well as drought tolerance. Furthermore, we found that regulation modules encompassing miRNA, transcription factors and target genes are involved in dimorphic flower development, validated by overexpression of CsAP2_9 and its targeted miR172 in rice. Our findings enable further understanding of the mechanisms of drought tolerance and flowering in C. songorica, and provide new insights into the adaptability of native grass species in evolution, along with potential resources for trait improvement in agronomically important species.
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Affiliation(s)
- Jiyu Zhang
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Fan Wu
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Qi Yan
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Ulrik P John
- Agriculture Victoria Research, Department of Jobs, Precincts and RegionsAgriBio, Centre for AgriBioscience, La Trobe UniversityVictoriaAustralia
| | - Mingshu Cao
- AgResearch Limited, Grasslands Research CentrePalmerston NorthNew Zealand
| | - Pan Xu
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Zhengshe Zhang
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Tiantian Ma
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Xifang Zong
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Jie Li
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Ruijuan Liu
- Key Laboratory of Adaptation and Evolution of Plateau BiotaNorthwest Institute of Plateau BiologyChinese Academy of SciencesXiningChina
| | - Yufei Zhang
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Yufeng Zhao
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Gisele Kanzana
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Yanyan Lv
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - Zhibiao Nan
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
| | - German Spangenberg
- Agriculture Victoria Research, Department of Jobs, Precincts and RegionsAgriBio, Centre for AgriBioscience, La Trobe UniversityVictoriaAustralia
| | - Yanrong Wang
- State Key Laboratory of Grassland Agro‐ecosystemsKey Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural AffairsEngineering Research Center of Grassland Industry, Ministry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouChina
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Hu Y, Wu X, Jin G, Peng J, Leng R, Li L, Gui D, Fan C, Zhang C. Rapid Genome Evolution and Adaptation of Thlaspi arvense Mediated by Recurrent RNA-Based and Tandem Gene Duplications. FRONTIERS IN PLANT SCIENCE 2021; 12:772655. [PMID: 35058947 PMCID: PMC8764390 DOI: 10.3389/fpls.2021.772655] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/09/2021] [Indexed: 05/21/2023]
Abstract
Retrotransposons are the most abundant group of transposable elements (TEs) in plants, providing an extraordinarily versatile source of genetic variation. Thlaspi arvense, a close relative of the model plant Arabidopsis thaliana with worldwide distribution, thrives from sea level to above 4,000 m elevation in the Qinghai-Tibet Plateau (QTP), China. Its strong adaptability renders it an ideal model system for studying plant adaptation in extreme environments. However, how the retrotransposons affect the T. arvense genome evolution and adaptation is largely unknown. We report a high-quality chromosome-scale genome assembly of T. arvense with a scaffold N50 of 59.10 Mb. Long terminal repeat retrotransposons (LTR-RTs) account for 56.94% of the genome assembly, and the Gypsy superfamily is the most abundant TEs. The amplification of LTR-RTs in the last six million years primarily contributed to the genome size expansion in T. arvense. We identified 351 retrogenes and 303 genes flanked by LTRs, respectively. A comparative analysis showed that orthogroups containing those retrogenes and genes flanked by LTRs have a higher percentage of significantly expanded orthogroups (SEOs), and these SEOs possess more recent tandem duplicated genes. All present results indicate that RNA-based gene duplication (retroduplication) accelerated the subsequent tandem duplication of homologous genes resulting in family expansions, and these expanded gene families were implicated in plant growth, development, and stress responses, which were one of the pivotal factors for T. arvense's adaptation to the harsh environment in the QTP regions. In conclusion, the high-quality assembly of the T. arvense genome provides insights into the retroduplication mediated mechanism of plant adaptation to extreme environments.
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Affiliation(s)
- Yanting Hu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaopei Wu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guihua Jin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Junchu Peng
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Rong Leng
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ling Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Daping Gui
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Chuanzhu Fan
- Department of Biological Sciences, Wayne State University, Detroit, MI, United States
- Chuanzhu Fan,
| | - Chengjun Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Haiyan Engineering & Technology Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- *Correspondence: Chengjun Zhang,
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Zheng Y, Zhang Z, Wan Y, Tian J, Xie W. Development of EST-SSR Markers Linked to Flowering Candidate Genes in Elymus sibiricus L. Based on RNA Sequencing. PLANTS 2020; 9:plants9101371. [PMID: 33076513 PMCID: PMC7650638 DOI: 10.3390/plants9101371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/05/2020] [Accepted: 10/14/2020] [Indexed: 01/08/2023]
Abstract
Elymus sibiricus L. is an important cold-season grass with excellent cold and drought tolerance, good palatability, and nutrition. Flowering time is a key trait that affects forage and seed yield. Development of EST-SSR (expressed sequence tag simple sequence repeat) markers based on flowering genes contributes to the improvement of flowering traits. In the study, we detected 155 candidate genes related to flowering traits from 10,591 unigenes via transcriptome sequencing in early- and late-flowering genotypes. These candidate genes were mainly involved in the photoperiodic pathway, vernalization pathway, central integrator, and gibberellin pathway. A total of 125 candidate gene-based EST-SSRs were developed. Further, 15 polymorphic EST-SSRs closely associated to 13 candidate genes were used for genetic diversity and population structure analysis among 20 E. sibiricus accessions, including two contrasting panels (early-flowering and late-flowering). Among them, primer 28366, designed from heading date 3a (HD3a), effectively distinguished early- and late-flowering genotypes using a specifically amplified band of 175 bp. The polymorphic information content (PIC) value ranged from 0.12 to 0.48, with an average of 0.25. The unweighted pair group method analysis (UPGMA) cluster and structure analysis showed that the 20 E. sibiricus genotypes with similar flowering times tended to group together. These newly developed EST-SSR markers have the potential to be used for molecular markers assisted selection and germplasm evaluation of flowering traits in E. sibiricus.
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Yin X, Yi K, Zhao Y, Hu Y, Li X, He T, Liu J, Cui G. Revealing the full-length transcriptome of caucasian clover rhizome development. BMC PLANT BIOLOGY 2020; 20:429. [PMID: 32938399 PMCID: PMC7493993 DOI: 10.1186/s12870-020-02637-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 09/03/2020] [Indexed: 06/02/2023]
Abstract
BACKGROUND Caucasian clover (Trifolium ambiguum M. Bieb.) is a strongly rhizomatous, low-crowned perennial leguminous and ground-covering grass. The species may be used as an ornamental plant and is resistant to cold, arid temperatures and grazing due to a well-developed underground rhizome system and a strong clonal reproduction capacity. However, the posttranscriptional mechanism of the development of the rhizome system in caucasian clover has not been comprehensively studied. Additionally, a reference genome for this species has not yet been published, which limits further exploration of many important biological processes in this plant. RESULT We adopted PacBio sequencing and Illumina sequencing to identify differentially expressed genes (DEGs) in five tissues, including taproot (T1), horizontal rhizome (T2), swelling of taproot (T3), rhizome bud (T4) and rhizome bud tip (T5) tissues, in the caucasian clover rhizome. In total, we obtained 19.82 GB clean data and 80,654 nonredundant transcripts were analysed. Additionally, we identified 78,209 open reading frames (ORFs), 65,227 coding sequences (CDSs), 58,276 simple sequence repeats (SSRs), 6821 alternative splicing (AS) events, 2429 long noncoding RNAs (lncRNAs) and 4501 putative transcription factors (TFs) from 64 different families. Compared with other tissues, T5 exhibited more DEGs, and co-upregulated genes in T5 are mainly annotated as involved in phenylpropanoid biosynthesis. We also identified betaine aldehyde dehydrogenase (BADH) as a highly expressed gene-specific to T5. A weighted gene co-expression network analysis (WGCNA) of transcription factors and physiological indicators were combined to reveal 11 hub genes (MEgreen-GA3), three of which belong to the HB-KNOX family, that are up-regulated in T3. We analysed 276 DEGs involved in hormone signalling and transduction, and the largest number of genes are associated with the auxin (IAA) signalling pathway, with significant up-regulation in T2 and T5. CONCLUSIONS This study contributes to our understanding of gene expression across five different tissues and provides preliminary insight into rhizome growth and development in caucasian clover.
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Affiliation(s)
- Xiujie Yin
- College of Animal Science and Technology, Northeast Agricultural University, No.600 Changjiang Street, Xiangfang District, Harbin, 150030, Heilongjiang, China
| | - Kun Yi
- College of Animal Science and Technology, Northeast Agricultural University, No.600 Changjiang Street, Xiangfang District, Harbin, 150030, Heilongjiang, China
| | - Yihang Zhao
- College of Animal Science and Technology, Northeast Agricultural University, No.600 Changjiang Street, Xiangfang District, Harbin, 150030, Heilongjiang, China
| | - Yao Hu
- College of Animal Science and Technology, Northeast Agricultural University, No.600 Changjiang Street, Xiangfang District, Harbin, 150030, Heilongjiang, China
| | - Xu Li
- College of Animal Science and Technology, Northeast Agricultural University, No.600 Changjiang Street, Xiangfang District, Harbin, 150030, Heilongjiang, China
| | - Taotao He
- College of Animal Science and Technology, Northeast Agricultural University, No.600 Changjiang Street, Xiangfang District, Harbin, 150030, Heilongjiang, China
| | - Jiaxue Liu
- College of Animal Science and Technology, Northeast Agricultural University, No.600 Changjiang Street, Xiangfang District, Harbin, 150030, Heilongjiang, China
| | - Guowen Cui
- College of Animal Science and Technology, Northeast Agricultural University, No.600 Changjiang Street, Xiangfang District, Harbin, 150030, Heilongjiang, China.
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Zhang J, Lei Y, Wang B, Li S, Yu S, Wang Y, Li H, Liu Y, Ma Y, Dai H, Wang J, Zhang Z. The high-quality genome of diploid strawberry (Fragaria nilgerrensis) provides new insights into anthocyanin accumulation. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1908-1924. [PMID: 32003918 PMCID: PMC7415782 DOI: 10.1111/pbi.13351] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 05/11/2023]
Abstract
Fragaria nilgerrensis is a wild diploid strawberry species endemic to east and southeast region in Asia and provides a rich source of genetic variations for strawberry improvement. Here, we present a chromosome-scale assembly of F. nilgerrensis using single-molecule real-time (SMRT) Pacific Biosciences sequencing and chromosome conformation capture (Hi-C) genome scaffolding. The genome assembly size was 270.3 Mb, with a contig N50 of ∼8.5 Mb. A total of 28 780 genes and 117.2 Mb of transposable elements were annotated for this genome. Next, detailed comparative genomics with the high-quality F. vesca reference genome was conducted to obtain the difference among transposable elements, SNPs, Indels, and so on. The genome size of F. nilgerrensis was enhanced by around 50 Mb relatively to F. vesca, which is mainly due to expansion of transposable elements. In comparison with the F. vesca genome, we identified 4 561 825 SNPs, 846 301 Indels, 4243 inversions, 35 498 translocations and 10 099 relocations. We also found a marked expansion of genes involved in phenylpropanoid biosynthesis, starch and sucrose metabolism, cyanoamino acid metabolism, plant-pathogen interaction, brassinosteroid biosynthesis and plant hormone signal transduction in F. nilgerrensis, which may account for its specific phenotypes and considerable environmental adaptability. Interestingly, we found sequence variations in the upstream regulatory region of FnMYB10, a core transcriptional activator of anthocyanin biosynthesis, resulted in the low expression level of the FnMYB10 gene, which is likely responsible for white fruit phenotype of F. nilgerrensis. The high-quality F. nilgerrensis genome will be a valuable resource for biological research and comparative genomics research.
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Affiliation(s)
- Junxiang Zhang
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Yingying Lei
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Baotian Wang
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Song Li
- Biomarker Technologies CorporationBeijingChina
| | - Shuang Yu
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Yan Wang
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
| | - He Li
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Yuexue Liu
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Yue Ma
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Hongyan Dai
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
| | | | - Zhihong Zhang
- Liaoning Key Laboratory of Strawberry Breeding and CultivationCollege of HorticultureShenyang Agricultural UniversityShenyangChina
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Duan J, Li Y, Du J, Duan E, Lei Y, Liang S, Zhang X, Zhao X, Kan Y, Yao L, Yang X, Zhang X, Wu X. A chromosome‐scale genome assembly of
Antheraea pernyi
(Saturniidae, Lepidoptera). Mol Ecol Resour 2020; 20:1372-1383. [DOI: 10.1111/1755-0998.13199] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Jianping Duan
- Henan Key Laboratory of Funiu Mountain Insect Biology, Henan Engineering Lab of Insects Bio‐reactor College of Agricultural Engineering, Nanyang Normal University Nanyang China
| | - Ying Li
- Henan Key Laboratory of Funiu Mountain Insect Biology, Henan Engineering Lab of Insects Bio‐reactor College of Agricultural Engineering, Nanyang Normal University Nanyang China
| | - Jie Du
- Henan Key Laboratory of Funiu Mountain Insect Biology, Henan Engineering Lab of Insects Bio‐reactor College of Agricultural Engineering, Nanyang Normal University Nanyang China
| | - Erzhen Duan
- College of Biological Engineering Henan University of Technology Zhengzhou China
| | - Yuyu Lei
- Henan Key Laboratory of Funiu Mountain Insect Biology, Henan Engineering Lab of Insects Bio‐reactor College of Agricultural Engineering, Nanyang Normal University Nanyang China
| | - Shimei Liang
- Henan Key Laboratory of Funiu Mountain Insect Biology, Henan Engineering Lab of Insects Bio‐reactor College of Agricultural Engineering, Nanyang Normal University Nanyang China
| | - Xian Zhang
- Henan Key Laboratory of Funiu Mountain Insect Biology, Henan Engineering Lab of Insects Bio‐reactor College of Agricultural Engineering, Nanyang Normal University Nanyang China
| | - Xin Zhao
- Henan Key Laboratory of Funiu Mountain Insect Biology, Henan Engineering Lab of Insects Bio‐reactor College of Agricultural Engineering, Nanyang Normal University Nanyang China
| | - Yunchao Kan
- Henan Key Laboratory of Funiu Mountain Insect Biology, Henan Engineering Lab of Insects Bio‐reactor College of Agricultural Engineering, Nanyang Normal University Nanyang China
| | - Lunguang Yao
- Henan Key Laboratory of Funiu Mountain Insect Biology, Henan Engineering Lab of Insects Bio‐reactor College of Agricultural Engineering, Nanyang Normal University Nanyang China
| | - Xinfeng Yang
- Henan Institute of Sericulture Science Zhengzhou China
| | - Xingtan Zhang
- Fujian Provincial Key Lab of Haixia Applied Plant Systems Biology Fujian Agriculture and Forestry University Fuzhou China
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Xu X, Feng G, Liang Y, Shuai Y, Liu Q, Nie G, Yang Z, Hang L, Zhang X. Comparative transcriptome analyses reveal different mechanism of high- and low-tillering genotypes controlling tiller growth in orchardgrass (Dactylis glomerata L.). BMC PLANT BIOLOGY 2020; 20:369. [PMID: 32758131 PMCID: PMC7409468 DOI: 10.1186/s12870-020-02582-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/27/2020] [Indexed: 05/12/2023]
Abstract
BACKGROUND Tillering is an important agronomic trait underlying the yields and reproduction of orchardgrass (Dactylis glomerata), an important perennial forage grass. Although some genes affecting tiller initiation have been identified, the tillering regulatory network is still largely unknown, especially in perennial forage grasses. Thus, unraveling the regulatory mechanisms of tillering in orchardgrass could be helpful in developing selective strategies for high-yield perennial grasses. In this study, we generated high-throughput RNA-sequencing data from multiple tissues of tillering stage plants to identify differentially expressed genes (DEGs) between high- and low-tillering orchardgrass genotypes. Gene Ontology and pathway enrichment analyses connecting the DEGs to tillering number diversity were conducted. RESULTS In the present study, approximately 26,282 DEGs were identified between two orchardgrass genotypes, AKZ-NRGR667 (a high-tillering genotype) and D20170203 (a low-tillering genotype), which significantly differed in tiller number. Pathway enrichment analysis indicated that DEGs related to the biosynthesis of three classes of phytohormones, i.e., strigolactones (SLs), abscisic acid (ABA), and gibberellic acid (GA), as well as nitrogen metabolism dominated such differences between the high- and low-tillering genotypes. We also confirmed that under phosphorus deficiency, the expression level of the major SL biosynthesis genes encoding DWARF27 (D27), 9-cis-beta-carotene 9',10'-cleaving dioxygenase (CCD7), carlactone synthase (CCD8), and more axillary branching1 (MAX1) proteins in the high-tillering orchardgrass genotype increased more slowly relative to the low-tillering genotype. CONCLUSIONS Here, we used transcriptomic data to study the tillering mechanism of perennial forage grasses. We demonstrated that differential expression patterns of genes involved in SL, ABA, and GA biosynthesis may differentiate high- and low-tillering orchardgrass genotypes at the tillering stage. Furthermore, the core SL biosynthesis-associated genes in high-tillering orchardgrass were more insensitive than the low-tillering genotype to phosphorus deficiency which can lead to increases in SL biosynthesis, raising the possibility that there may be distinct SL biosynthesis way in tillering regulation in orchardgrass. Our research has revealed some candidate genes involved in the regulation of tillering in perennial grasses that is available for establishment of new breeding resources for high-yield perennial grasses and will serve as a new resource for future studies into molecular mechanism of tillering regulation in orchardgrass.
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Affiliation(s)
- Xiaoheng Xu
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Guangyan Feng
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yueyang Liang
- Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yang Shuai
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qiuxu Liu
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Gang Nie
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Zhongfu Yang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Linkai Hang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xinquan Zhang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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43
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Sun M, Huang D, Zhang A, Khan I, Yan H, Wang X, Zhang X, Zhang J, Huang L. Transcriptome analysis of heat stress and drought stress in pearl millet based on Pacbio full-length transcriptome sequencing. BMC PLANT BIOLOGY 2020; 20:323. [PMID: 32640987 PMCID: PMC7346438 DOI: 10.1186/s12870-020-02530-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 06/26/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Heat and drought are serious threats for crop growth and development. As the sixth largest cereal crop in the world, pearl millet can not only be used for food and forage but also as a source of bioenergy. Pearl millet is highly tolerant to heat and drought. Given this, it is considered an ideal crop to study plant stress tolerance and can be used to identify heat-resistant genes. RESULTS In this study, we used Pacbio sequencing data as a reference sequence to analyze the Illumina data of pearl millet that had been subjected to heat and drought stress for 48 h. By summarizing previous studies, we found 26,299 new genes and 63,090 new transcripts, and the number of gene annotations increased by 20.18%. We identified 2792 transcription factors and 1223 transcriptional regulators. There were 318 TFs and 149 TRs differentially expressed under heat stress, and 315 TFs and 128 TRs were differentially expressed under drought stress. We used RNA sequencing to identify 6920 genes and 6484 genes differentially expressed under heat stress and drought stress, respectively. CONCLUSIONS Through Pacbio sequencing, we have identified more new genes and new transcripts. On the other hand, comparing the differentially expressed genes under heat tolerance with the DEGs under drought stress, we found that even in the same pathway, pearl millet responds with a different protein.
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Affiliation(s)
- Min Sun
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, 6111130 China
| | - Dejun Huang
- Herbivorous Livestock Research Institute, Chongqing Academy of Animal Sciences, Chongqing, China
| | - Ailing Zhang
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, 6111130 China
| | - Imran Khan
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, 6111130 China
| | - Haidong Yan
- Department of Horticulture, Virginia Tech, Blacksburg, VA 24061 USA
| | - Xiaoshan Wang
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, 6111130 China
| | - Xinquan Zhang
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, 6111130 China
| | - Jian Zhang
- Herbivorous Livestock Research Institute, Chongqing Academy of Animal Sciences, Chongqing, China
| | - Linkai Huang
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, 6111130 China
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Xu L, Feng G, Yang Z, Xu X, Huang L, Yang Q, Zhang X. Genome-wide AP2/ERF gene family analysis reveals the classification, structure, expression profiles and potential function in orchardgrass (Dactylis glomerata). Mol Biol Rep 2020; 47:5225-5241. [PMID: 32577992 DOI: 10.1007/s11033-020-05598-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 06/17/2020] [Indexed: 11/29/2022]
Abstract
The AP2/ERF transcription factor (TF) family is of great importance in developmental regulation and responses to stress and pathogenic stimuli. Orchardgrass (Dactylis glomerata), a perennial cold-season forage of high quality in the world's temperate zones, contributes to grazing land through mixed sowing with alfalfa (Medicago sativa) and white clover (Trifolium repens). However, little is known about AP2/ERF TFs in orchardgrass. In this study, 193 AP2/ERF genes were classified into five subfamilies and 13 subgroups through phylogenetic analysis. Chromosome structure analysis showed that AP2/ERF family genes in orchardgrass were distributed on seven chromosomes and specific conservative sequences were found in each subgroup. Exon-intron structure and motifs in the same subgroup were almost identical, and the unique motifs contributed to the classification and functional annotation of DgERFs. Expression analysis showed tissue-specific expression of DgERFs in roots and flowers, with most DgERFs widely expressed in roots. The expression levels of each subgroup (subgroups Vc, VIIa, VIIIb, IXa, and XIa) were high at the before-heading and heading stages (BH_DON and H_DON). In addition, 12 DgERFs in various tissues and five DgERFs associated with abiotic stresses were selected for qRT-PCR analysis showed that four dehydration-responsive element binding (DREB) genes and one ERF subfamily gene in orchardgrass were regulated with PEG, heat and salt stresses. DgERF056 belonged to ERF subfamily was involved in the processes of flowering and development stage. This study systematic explored the DgERFs at the genome level for the first time, which lays a foundation for a better understanding of AP2/ERF gene function in Dactylis glomerata and other types of forage.
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Affiliation(s)
- Lei Xu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.,The State Key Laboratory of Grassland Farming Systems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Guangyan Feng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhongfu Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaoheng Xu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linkai Huang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qingchuan Yang
- The State Key Laboratory of Grassland Farming Systems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.,Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100000, China
| | - Xinquan Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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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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Xu X, Feng G, Huang L, Yang Z, Liu Q, Shuai Y, Zhang X. Genome-wide identification, structural analysis and expression profiles of GRAS gene family in orchardgrass. Mol Biol Rep 2020; 47:1845-1857. [PMID: 32026320 DOI: 10.1007/s11033-020-05279-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Accepted: 01/24/2020] [Indexed: 11/24/2022]
Abstract
The GRAS gene family is a family of transcription factors that regulates plant growth and development. Despite being well-studied in many plant species, little is known about this gene family in orchardgrass (Dactylis glomerata L.), one of the top four economically important perennial forage grasses cultivated worldwide. We identified 46 GRAS genes in orchardgrass and analyzed their characteristics by phylogenetic, gene structural, motifs and expression patterns analysis. The phylogenetic analysis of eight species revealed that DgGRAS family had the evolutional conservation and closer homology relationship with the GRAS family of rice, barley and Brachypodium distachyon. Moreover, 46 DgGRAS proteins were divided into eight subfamilies based on the tree topology and rice or Arabidopsis classification, and LISCL subfamily was the largest one. Besides, we found that the motif 15 may be unique to the orchardgrass LISCL subfamily, and the motif 6 and motif 17 had indispensable functions in the orchardgrass LISCL subfamily. We further analyzed the expression profiles of DgGRAS genes at mature and seeding stage. And we found that DgGRAS17 played an important role in the growth and development no matter what stage it was at. DgGRAS5, DgGRAS28, DgGRAS31, DgGRAS42 and DgGRAS44 got involved in processes of the growth and development at seeding stage instead of mature stage. These results indicated that the major expression patterns and detailed functions of the DgGRAS genes varied with developmental stages. Taken together, this is the first systematic analysis of the GRAS gene family in the orchardgrass genome and the results provide insights into the potential functions of GRAS genes.
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Affiliation(s)
- Xiaoheng Xu
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guangyan Feng
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Linkai Huang
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhongfu Yang
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qiuxu Liu
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yang Shuai
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xinquan Zhang
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, Sichuan, China.
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