1
|
Nikhil S, Mohideen HS, Sella RN. Unveiling the Genomic Symphony: Identification Cultivar-Specific Genes and Enhanced Insights on Sweet Sorghum Genomes Through Comprehensive superTranscriptomic Analysis. J Mol Evol 2024:10.1007/s00239-024-10198-5. [PMID: 39261311 DOI: 10.1007/s00239-024-10198-5] [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: 12/19/2023] [Accepted: 08/20/2024] [Indexed: 09/13/2024]
Abstract
Sorghum (Sorghum bicolor (L.) Moench) is a multipurpose crop grown for food, fodder, and bioenergy production. Its cultivated varieties, along with their wild counterparts, contribute to the core genetic pool. Despite the availability of several re-sequenced sorghum genomes, a variable portion of sorghum genomes is not reported during reference genome assembly and annotation. The present analysis used 223 publicly available RNA-seq datasets from seven sweet sorghum cultivars to construct superTranscriptome. This approach yielded 45,864 Representative Transcript Assemblies (RTAs) that showcased intriguing Presence/Absence Variation (PAV) across 15 published sorghum genomes. We found 301 superTranscripts were exclusive to sweet sorghum, including 58 de novo genes encoded core and linker histones, zinc finger domains, glucosyl transferases, cellulose synthase, etc. The superTranscriptome added 2,802 new protein-coding genes to the Sweet Sorghum Reference Genome (SSRG), of which 559 code for different transcription factors (TFs). Our analysis revealed that MULE-like transposases were abundant in the sweet sorghum genome and could play a hidden role in the evolution of sweet sorghum. We observed large deletions in the D locus and terminal deletions in four other NAC encoding loci in the SSRG compared to its wild progenitor (353) suggesting non-functional NAC genes contributed to trait development in sweet sorghum. Moreover, superTranscript-based methods for Differential Exon Usage (DEU) and Differential Gene Expression (DGE) analyses were more accurate than those based on the SSRG. This study demonstrates that the superTranscriptome can enhance our understanding of fundamental sorghum mechanisms, improve genome annotations, and potentially even replace the reference genome.
Collapse
Affiliation(s)
- Shinde Nikhil
- Membrane Protein Interaction Lab, Department of Genetic Engineering, SRM Institute of Science and Technology, Chengalpattu District, Tamil Nadu, 603203, India
| | - Habeeb Shaikh Mohideen
- Entomoinformatics Lab, Department of Genetic Engineering, SRM Institute of Science and Technology, Chengalpattu District, Tamil Nadu, 603203, India
| | - Raja Natesan Sella
- Membrane Protein Interaction Lab, Department of Genetic Engineering, SRM Institute of Science and Technology, Chengalpattu District, Tamil Nadu, 603203, India.
| |
Collapse
|
2
|
Hu J, Bettembourg M, Xue L, Hu R, Schnürer A, Sun C, Jin Y, Sundström JF. A low-methane rice with high-yield potential realized via optimized carbon partitioning. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 920:170980. [PMID: 38373456 DOI: 10.1016/j.scitotenv.2024.170980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/25/2024] [Accepted: 02/13/2024] [Indexed: 02/21/2024]
Abstract
Global rice cultivation significantly contributes to anthropogenic methane emissions. The methane emissions are caused by methane-producing microorganisms (methanogenic archaea) that are favoured by the anoxic conditions of paddy soils and small carbon molecules released from rice roots. However, different rice cultivars are associated with differences in methane emission rates suggesting that there is a considerable natural variation in this trait. Starting from the hypothesis that sugar allocation within a plant is an important factor influencing both yields and methane emissions, the aim of this study was to produce high-yielding rice lines associated with low methane emissions. In this study, the offspring (here termed progeny lines) of crosses between a newly characterized low-methane rice variety, Heijing 5, and three high-yielding elite varieties, Xiushui, Huayu and Jiahua, were selected for combined low-methane and high-yield properties. Analyses of total organic carbon and carbohydrates showed that the progeny lines stored more carbon in above-ground tissues than the maternal elite varieties. Also, metabolomic analysis of rhizospheric soil surrounding the progeny lines showed reduced levels of glucose and other carbohydrates. The carbon allocation, from roots to shoots, was further supported by a transcriptome analysis using massively parallel sequencing of mRNAs that demonstrated elevated expression of the sugar transporters SUT-C and SWEET in the progeny lines as compared to the parental varieties. Furthermore, measurement of methane emissions from plants, grown in greenhouse as well as outdoor rice paddies, showed a reduction in methane emissions by approximately 70 % in the progeny lines compared to the maternal elite varieties. Taken together, we report here on three independent low-methane-emission rice lines with high yield potential. We also provide a first molecular characterisation of the progeny lines that can serve as a foundation for further studies of candidate genes involved in sugar allocation and reduced methane emissions from rice cultivation.
Collapse
Affiliation(s)
- Jia Hu
- Department of Plant Biology, Sweden University of Agricultural Science, The Linnean Centre for Plant Biology, Box 7080, SE-75007 Uppsala, Sweden
| | - Mathilde Bettembourg
- Department of Plant Biology, Sweden University of Agricultural Science, The Linnean Centre for Plant Biology, Box 7080, SE-75007 Uppsala, Sweden
| | - Lihong Xue
- Key Laboratory of Agro-environment in Downstream of Yangtze plain, Ministry of Agriculture and Rural Affairs of China, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Ronggui Hu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan 43070, China
| | - Anna Schnürer
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, SE-750 07 Uppsala, Sweden
| | - Chuanxin Sun
- Department of Plant Biology, Sweden University of Agricultural Science, The Linnean Centre for Plant Biology, Box 7080, SE-75007 Uppsala, Sweden
| | - Yunkai Jin
- Department of Plant Biology, Sweden University of Agricultural Science, The Linnean Centre for Plant Biology, Box 7080, SE-75007 Uppsala, Sweden
| | - Jens F Sundström
- Department of Plant Biology, Sweden University of Agricultural Science, The Linnean Centre for Plant Biology, Box 7080, SE-75007 Uppsala, Sweden.
| |
Collapse
|
3
|
Roberts JT, McCubbin TJ, Braun DM. A Plate Growth Assay to Quantify Embryonic Root Development of Zea mays. Bio Protoc 2023; 13:e4858. [PMID: 37900110 PMCID: PMC10603264 DOI: 10.21769/bioprotoc.4858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 10/31/2023] Open
Abstract
Murashige-Skoog medium solutions have been used in a variety of plant plate growth assays, yet most research uses Arabidopsis thaliana as the study organism. For larger seeds such as maize (Zea mays), most protocols employ a paper towel roll method for experiments, which often involves wrapping maize seedlings in wet, sterile germination paper. What the paper towel roll method lacks, however, is the ability to image the roots over time without risk of contamination. Here, we describe a sterile plate growth assay that contains Murashige-Skoog medium to grow seedlings starting two days after germination. This protocol uses a section of a paper towel roll method to achieve uniform germination of maize seedlings, which are sterilely transferred onto large acrylic plates for the duration of the experiment. The media can undergo modification to include an assortment of plant hormones, exogenous sugars, and other chemicals. The acrylic plates allow researchers to freely image the plate without disturbing the seedlings and control the environment in which the seedlings are grown, such as modifications in temperature and light. Additionally, the protocol is widely adaptable for use with other cereal crops. Key features • Builds upon plate growth methods routinely used for Arabidopsis seedlings but that are inadequate for maize. • Real-time photographic analysis of seedlings up to two weeks following germination. • Allows for testing of various growth conditions involving an assortment of additives and/or modification of environmental conditions. • Samples are able to be collected for genotype screening.
Collapse
Affiliation(s)
- Jason T Roberts
- Division of Biological Sciences, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, Columbia, MO, USA
| | - Tyler J McCubbin
- Division of Plant Science and Technology, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, Columbia, MO, USA
| | - David M Braun
- Division of Biological Sciences, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, Columbia, MO, USA
- Division of Plant Science and Technology, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, Columbia, MO, USA
| |
Collapse
|
4
|
Xue X, Beuchat G, Wang J, Yu YC, Moose S, Chen J, Chen LQ. Sugar accumulation enhancement in sorghum stem is associated with reduced reproductive sink strength and increased phloem unloading activity. FRONTIERS IN PLANT SCIENCE 2023; 14:1233813. [PMID: 37767289 PMCID: PMC10519796 DOI: 10.3389/fpls.2023.1233813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023]
Abstract
Sweet sorghum has emerged as a promising source of bioenergy mainly due to its high biomass and high soluble sugar yield in stems. Studies have shown that loss-of-function Dry locus alleles have been selected during sweet sorghum domestication, and decapitation can further boost sugar accumulation in sweet sorghum, indicating that the potential for improving sugar yields is yet to be fully realized. To maximize sugar accumulation, it is essential to gain a better understanding of the mechanism underlying the massive accumulation of soluble sugars in sweet sorghum stems in addition to the Dry locus. We performed a transcriptomic analysis upon decapitation of near-isogenic lines for mutant (d, juicy stems, and green leaf midrib) and functional (D, dry stems and white leaf midrib) alleles at the Dry locus. Our analysis revealed that decapitation suppressed photosynthesis in leaves, but accelerated starch metabolic processes in stems. SbbHLH093 negatively correlates with sugar levels supported by genotypes (DD vs. dd), treatments (control vs. decapitation), and developmental stages post anthesis (3d vs.10d). D locus gene SbNAC074A and other programmed cell death-related genes were downregulated by decapitation, while sugar transporter-encoding gene SbSWEET1A was induced. Both SbSWEET1A and Invertase 5 were detected in phloem companion cells by RNA in situ assay. Loss of the SbbHLH093 homolog, AtbHLH093, in Arabidopsis led to a sugar accumulation increase. This study provides new insights into sugar accumulation enhancement in bioenergy crops, which can be potentially achieved by reducing reproductive sink strength and enhancing phloem unloading.
Collapse
Affiliation(s)
- Xueyi Xue
- Department of Energy (DOE) Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Institute for Sustainability, Energy, and Environment, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Gabriel Beuchat
- Department of Energy (DOE) Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jiang Wang
- Department of Energy (DOE) Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Ya-Chi Yu
- Department of Energy (DOE) Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Stephen Moose
- Department of Energy (DOE) Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jin Chen
- Institute for Biomedical Informatics, University of Kentucky, Lexington, KY, United States
| | - Li-Qing Chen
- Department of Energy (DOE) Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| |
Collapse
|