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Zhang G, Ge C, Xu P, Wang S, Cheng S, Han Y, Wang Y, Zhuang Y, Hou X, Yu T, Xu X, Deng S, Li Q, Yang Y, Yin X, Wang W, Liu W, Zheng C, Sun X, Wang Z, Ming R, Dong S, Ma J, Zhang X, Chen C. The reference genome of Miscanthus floridulus illuminates the evolution of Saccharinae. NATURE PLANTS 2021; 7:608-618. [PMID: 33958777 PMCID: PMC8238680 DOI: 10.1038/s41477-021-00908-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 03/29/2021] [Indexed: 05/05/2023]
Abstract
Miscanthus, a member of the Saccharinae subtribe that includes sorghum and sugarcane, has been widely studied as a feedstock for cellulosic biofuel production. Here, we report the sequencing and assembly of the Miscanthus floridulus genome by the integration of PacBio sequencing and Hi-C mapping, resulting in a chromosome-scale, high-quality reference genome of the genus Miscanthus. Comparisons among Saccharinae genomes suggest that Sorghum split first from the common ancestor of Saccharum and Miscanthus, which subsequently diverged from each other, with two successive whole-genome duplication events occurring independently in the Saccharum genus and one whole-genome duplication occurring in the Miscanthus genus. Fusion of two chromosomes occurred during rediploidization in M. floridulus and no significant subgenome dominance was observed. A survey of cellulose synthases (CesA) in M. floridulus revealed quite high expression of most CesA genes in growing stems, which is in agreement with the high cellulose content of this species. Resequencing and comparisons of 75 Miscanthus accessions suggest that M. lutarioriparius is genetically close to M. sacchariflorus and that M. floridulus is more distantly related to other species and is more genetically diverse. This study provides a valuable genomic resource for molecular breeding and improvement of Miscanthus and Saccharinae crops.
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Affiliation(s)
- Guobin Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- College of Agronomy, Shandong Agricultural University, Taian, China
| | - Chunxia Ge
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- College of Agronomy, Shandong Agricultural University, Taian, China
| | - Pingping Xu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- College of Agronomy, Shandong Agricultural University, Taian, China
| | - Shukai Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- College of Agronomy, Shandong Agricultural University, Taian, China
| | - Senan Cheng
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- College of Agronomy, Shandong Agricultural University, Taian, China
| | - Yanbin Han
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- College of Agronomy, Shandong Agricultural University, Taian, China
| | - Yancui Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- College of Agronomy, Shandong Agricultural University, Taian, China
| | - Yongbin Zhuang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- College of Agronomy, Shandong Agricultural University, Taian, China
| | - Xinwei Hou
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- College of Agronomy, Shandong Agricultural University, Taian, China
| | - Ting Yu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- College of Agronomy, Shandong Agricultural University, Taian, China
| | - Xitong Xu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- College of Agronomy, Shandong Agricultural University, Taian, China
| | - Shuhan Deng
- Novogene Bioinformatics Institute, Beijing, China
| | - Quanquan Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- College of Agronomy, Shandong Agricultural University, Taian, China
| | - Yinqing Yang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- College of Agronomy, Shandong Agricultural University, Taian, China
| | - Xiaoru Yin
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- College of Agronomy, Shandong Agricultural University, Taian, China
| | - Weidong Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- College of Agronomy, Shandong Agricultural University, Taian, China
| | - Wenxue Liu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- College of Agronomy, Shandong Agricultural University, Taian, China
| | - Chunxiao Zheng
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- College of Agronomy, Shandong Agricultural University, Taian, China
| | - Xuezhen Sun
- College of Agronomy, Shandong Agricultural University, Taian, China
| | - Zhenlin Wang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- College of Agronomy, Shandong Agricultural University, Taian, China
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Shuting Dong
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
- College of Agronomy, Shandong Agricultural University, Taian, China
| | - Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
| | - Xiansheng Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China
| | - Cuixia Chen
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, China.
- College of Agronomy, Shandong Agricultural University, Taian, China.
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Meena MR, Kumar R, Ramaiyan K, Chhabra ML, Raja AK, Krishnasamy M, Kulshreshtha N, Pandey SK, Ram B. Biomass potential of novel interspecific and intergeneric hybrids of Saccharum grown in sub-tropical climates. Sci Rep 2020; 10:21560. [PMID: 33299008 PMCID: PMC7726553 DOI: 10.1038/s41598-020-78329-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 10/28/2020] [Indexed: 11/17/2022] Open
Abstract
Sugarcane-derived biomass is a promising source of renewable energy to meet the growing demands for biofuel. Currently, modern sugarcane cultivars are unable to provide enough biomass due to their narrow genetic base and susceptibility to abiotic and biotic stresses. We have evaluated total of 23 hybrids derived from diverse genetic backgrounds of different Saccharum spp. and allied genera, one inbred and compared with commercial checks. Intergeneric hybrids (IGHs) KGS 99-100 and GU 04-432, produced significantly higher biomass (43.37 t ha−1 and 35.24 t ha−1, respectively) than commercial sugarcane have genes derived from Erianthus arundinaceus. Interspecific hybrids (ISHs) GU 07-3704 and 99-489, also produced significantly higher amounts of biomass (37.24 t ha−1 and 33.25 t ha−1, respectively) than commercial checks have genes from S. officinarum and S. spontaneum backgrounds. ISHs recorded significantly higher biomass yield, number of stalks and total dry matter percentage whereas, IGH group recorded significantly higher fibre percent. Furthermore, the clones resistant to red rot and sugarcane borers were identified. The estimated energy value for seven hybrid clones was found to be very high. Cluster analysis of genetic traits revealed two major clusters in traits improving biomass. Our study has revealed that the genetic diversity present in these hybrids could be used for improving biomass production and tolerance to abiotic and biotic stresses in cultivated sugarcanes.
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Affiliation(s)
- Mintu Ram Meena
- ICAR-Sugarcane Breeding Institute, Regional Centre, Karnal, India.
| | - Ravinder Kumar
- ICAR-Sugarcane Breeding Institute, Regional Centre, Karnal, India
| | - Karuppaiyan Ramaiyan
- ICAR-Sugarcane Breeding Institute, Regional Centre, Karnal, India.,ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | | | | | | | | | | | - Bakshi Ram
- ICAR-Sugarcane Breeding Institute, Regional Centre, Karnal, India.,ICAR-Sugarcane Breeding Institute, Coimbatore, India
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3
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Zou G, Zhai G, Yan S, Li S, Zhou L, Ding Y, Liu H, Zhang Z, Zou J, Zhang L, Chen J, Xin Z, Tao Y. Sorghum qTGW1a encodes a G-protein subunit and acts as a negative regulator of grain size. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5389-5401. [PMID: 32497208 DOI: 10.1093/jxb/eraa277] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
Grain size is a major determinant of grain yield in sorghum and other cereals. Over 100 quantitative trait loci (QTLs) of grain size have been identified in sorghum. However, no gene underlying any grain size QTL has been cloned. Here, we describe the fine mapping and cloning of one grain size QTL. From an F8 recombinant inbred line population derived from a cross between inbred lines 654 and LTR108, we identified 44 grain size QTLs. One QTL, qTGW1a, was detected consistently on the long arm of chromosome 1 in the span of 4 years. Using the extreme recombinants from an F2:3 fine-mapping population, qTGW1a was delimited within a ~33 kb region containing three predicted genes. One of them, SORBI_3001G341700, predicted to encode a G-protein γ subunit and homologous to GS3 in rice, is likely to be the causative gene for qTGW1a. qTGW1a appears to act as a negative regulator of grain size in sorghum. The functional allele of the putatively causative gene of qTGW1a from inbred line 654 decreased grain size, plant height, and grain yield in transgenic rice. Identification of the gene underlying qTGW1a advances our understanding of the regulatory mechanisms of grain size in sorghum and provides a target to manipulate grain size through genome editing.
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Affiliation(s)
- Guihua Zou
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guowei Zhai
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Song Yan
- Rice National Engineering Laboratory, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, China
| | - Sujuan Li
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Lengbo Zhou
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Yanqing Ding
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Heqin Liu
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhipeng Zhang
- Chinese National Sorghum Improvement Center, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Jianqiu Zou
- Chinese National Sorghum Improvement Center, Liaoning Academy of Agricultural Sciences, Shenyang, China
| | - Liyi Zhang
- Institute of Upland Food Crops, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Junping Chen
- Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, USA
| | - Zhanguo Xin
- Plant Stress & Germplasm Development Unit, Cropping Systems Research Laboratory, USDA-ARS, Lubbock, TX, USA
| | - Yuezhi Tao
- Institute of Crop and Nuclear Technology Utilization, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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4
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Maeda HA. Harnessing evolutionary diversification of primary metabolism for plant synthetic biology. J Biol Chem 2019; 294:16549-16566. [PMID: 31558606 DOI: 10.1074/jbc.rev119.006132] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Plants produce numerous natural products that are essential to both plant and human physiology. Recent identification of genes and enzymes involved in their biosynthesis now provides exciting opportunities to reconstruct plant natural product pathways in heterologous systems through synthetic biology. The use of plant chassis, although still in infancy, can take advantage of plant cells' inherent capacity to synthesize and store various phytochemicals. Also, large-scale plant biomass production systems, driven by photosynthetic energy production and carbon fixation, could be harnessed for industrial-scale production of natural products. However, little is known about which plants could serve as ideal hosts and how to optimize plant primary metabolism to efficiently provide precursors for the synthesis of desirable downstream natural products or specialized (secondary) metabolites. Although primary metabolism is generally assumed to be conserved, unlike the highly-diversified specialized metabolism, primary metabolic pathways and enzymes can differ between microbes and plants and also among different plants, especially at the interface between primary and specialized metabolisms. This review highlights examples of the diversity in plant primary metabolism and discusses how we can utilize these variations in plant synthetic biology. I propose that understanding the evolutionary, biochemical, genetic, and molecular bases of primary metabolic diversity could provide rational strategies for identifying suitable plant hosts and for further optimizing primary metabolism for sizable production of natural and bio-based products in plants.
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Affiliation(s)
- Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706
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5
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Future Perspectives of Biomass Torrefaction: Review of the Current State-Of-The-Art and Research Development. SUSTAINABILITY 2018. [DOI: 10.3390/su10072323] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Xin Z, Huang J, Smith AR, Chen J, Burke J, Sattler SE, Zhao D. Morphological Characterization of a New and Easily Recognizable Nuclear Male Sterile Mutant of Sorghum (Sorghum bicolor). PLoS One 2017; 12:e0165195. [PMID: 28052078 PMCID: PMC5215730 DOI: 10.1371/journal.pone.0165195] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 10/08/2016] [Indexed: 11/19/2022] Open
Abstract
Sorghum (Sorghum bicolor L. Moench) is one of the most important grain crops in the world. The nuclear male sterility (NMS) trait, which is caused by mutations on the nuclear gene, is valuable for hybrid breeding and genetic studies. Several NMS mutants have been reported previously, but none of them were well characterized. Here, we present our detailed morphological characterization of a new and easily recognizable NMS sorghum mutant male sterile 8 (ms8) isolated from an elite inbred BTx623 mutagenized by ethyl methane sulfonate (EMS). Our results show that the ms8 mutant phenotype was caused by a mutation on a single recessive nuclear gene that is different from all available NMS loci reported in sorghum. In fertile sorghum plants, yellow anthers appeared first during anthesis, while in the ms8 mutant, white hairy stigma emerged first and only small white anthers were observed, making ms8 plants easily recognizable when flowering. The ovary development and seed production after manual pollination are normal in the ms8 mutant, indicating it is female fertile and male sterile only. We found that ms8 anthers did not produce pollen grains. Further analysis revealed that ms8 anthers were defective in tapetum development, which led to the arrest of pollen formation. As a stable male sterile mutant across different environments, greenhouses, and fields in different locations, the ms8 mutant could be a useful breeding tool. Moreover, ms8 might be an important for elucidating male gametophyte development in sorghum and other plants.
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Affiliation(s)
- Zhanguo Xin
- Plant Stress and Germplasm Development Unit, USDA-ARS, Lubbock, Texas, United States of America
| | - Jian Huang
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
| | - Ashley R. Smith
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
| | - Junping Chen
- Plant Stress and Germplasm Development Unit, USDA-ARS, Lubbock, Texas, United States of America
| | - John Burke
- Plant Stress and Germplasm Development Unit, USDA-ARS, Lubbock, Texas, United States of America
| | - Scott E. Sattler
- USDA-ARS-PA-Grain, Forage, & Bioenergy Res. Unit, 251 Filley Hall/Food Ind. Complex, Lincoln, Nebraska, United States of America
| | - Dazhong Zhao
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, United States of America
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Jiao Y, Burow G, Gladman N, Acosta-Martinez V, Chen J, Burke J, Ware D, Xin Z. Efficient Identification of Causal Mutations through Sequencing of Bulked F 2 from Two Allelic Bloomless Mutants of Sorghum bicolor. FRONTIERS IN PLANT SCIENCE 2017; 8:2267. [PMID: 29379518 PMCID: PMC5771210 DOI: 10.3389/fpls.2017.02267] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 12/27/2017] [Indexed: 05/04/2023]
Abstract
Sorghum (Sorghum bicolor Moench, L.) plant accumulates copious layers of epi-cuticular wax (EW) on its aerial surfaces, to a greater extent than most other crops. EW provides a vapor barrier that reduces water loss, and is therefore considered to be a major determinant of sorghum's drought tolerance. However, little is known about the genes responsible for wax accumulation in sorghum. We isolated two allelic mutants, bloomless40-1 (bm40-1) and bm40-2, from a mutant library constructed from ethyl methane sulfonate (EMS) treated seeds of an inbred, BTx623. Both mutants were nearly devoid of the EW layer. Each bm mutant was crossed to the un-mutated BTx623 to generated F2 populations that segregated for the bm phenotype. Genomic DNA from 20 bm F2 plants from each population was bulked for whole genome sequencing. A single gene, Sobic.001G228100, encoding a GDSL-like lipase/acylhydrolase, had unique homozygous mutations in each bulked F2 population. Mutant bm40-1 harbored a missense mutation in the gene, whereas bm40-2 had a splice donor site mutation. Our findings thus provide strong evidence that mutation in this GDSL-like lipase gene causes the bm phenotype, and further demonstrate that this approach of sequencing two independent allelic mutant populations is an efficient method for identifying causal mutations. Combined with allelic mutants, MutMap provides powerful method to identify all causal genes for the large collection of bm mutants in sorghum, which will provide insight into how sorghum plants accumulate such abundant EW on their aerial surface. This knowledge may facilitate the development of tools for engineering drought-tolerant crops with reduced water loss.
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Affiliation(s)
- Yinping Jiao
- Cropping Systems Research Laboratory, Agricultural Research Service (USDA), Lubbock, TX, United States
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Gloria Burow
- Cropping Systems Research Laboratory, Agricultural Research Service (USDA), Lubbock, TX, United States
| | - Nicholas Gladman
- Cropping Systems Research Laboratory, Agricultural Research Service (USDA), Lubbock, TX, United States
| | - Veronica Acosta-Martinez
- Cropping Systems Research Laboratory, Agricultural Research Service (USDA), Lubbock, TX, United States
| | - Junping Chen
- Cropping Systems Research Laboratory, Agricultural Research Service (USDA), Lubbock, TX, United States
| | - John Burke
- Cropping Systems Research Laboratory, Agricultural Research Service (USDA), Lubbock, TX, United States
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
- USDA-ARS NAA Plant, Soil and Nutrition Laboratory Research Unit, Cornell University, Ithaca, NY, United States
- *Correspondence: Doreen Ware
| | - Zhanguo Xin
- Cropping Systems Research Laboratory, Agricultural Research Service (USDA), Lubbock, TX, United States
- Zhanguo Xin
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Jiao Y, Burke J, Chopra R, Burow G, Chen J, Wang B, Hayes C, Emendack Y, Ware D, Xin Z. A Sorghum Mutant Resource as an Efficient Platform for Gene Discovery in Grasses. THE PLANT CELL 2016; 28:1551-62. [PMID: 27354556 PMCID: PMC4981137 DOI: 10.1105/tpc.16.00373] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 06/23/2016] [Accepted: 06/23/2016] [Indexed: 05/20/2023]
Abstract
Sorghum (Sorghum bicolor) is a versatile C4 crop and a model for research in family Poaceae. High-quality genome sequence is available for the elite inbred line BTx623, but functional validation of genes remains challenging due to the limited genomic and germplasm resources available for comprehensive analysis of induced mutations. In this study, we generated 6400 pedigreed M4 mutant pools from EMS-mutagenized BTx623 seeds through single-seed descent. Whole-genome sequencing of 256 phenotyped mutant lines revealed >1.8 million canonical EMS-induced mutations, affecting >95% of genes in the sorghum genome. The vast majority (97.5%) of the induced mutations were distinct from natural variations. To demonstrate the utility of the sequenced sorghum mutant resource, we performed reverse genetics to identify eight genes potentially affecting drought tolerance, three of which had allelic mutations and two of which exhibited exact cosegregation with the phenotype of interest. Our results establish that a large-scale resource of sequenced pedigreed mutants provides an efficient platform for functional validation of genes in sorghum, thereby accelerating sorghum breeding. Moreover, findings made in sorghum could be readily translated to other members of the Poaceae via integrated genomics approaches.
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Affiliation(s)
- Yinping Jiao
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, Texas 79415 Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - John Burke
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, Texas 79415
| | - Ratan Chopra
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, Texas 79415
| | - Gloria Burow
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, Texas 79415
| | - Junping Chen
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, Texas 79415
| | - Bo Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724
| | - Chad Hayes
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, Texas 79415
| | - Yves Emendack
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, Texas 79415
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724 U.S. Department of Agriculture-Agricultural Research Service, NEA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, New York 14853
| | - Zhanguo Xin
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, Texas 79415
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9
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Ferreira SS, Hotta CT, Poelking VGDC, Leite DCC, Buckeridge MS, Loureiro ME, Barbosa MHP, Carneiro MS, Souza GM. Co-expression network analysis reveals transcription factors associated to cell wall biosynthesis in sugarcane. PLANT MOLECULAR BIOLOGY 2016; 91:15-35. [PMID: 26820137 PMCID: PMC4837222 DOI: 10.1007/s11103-016-0434-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 01/07/2016] [Indexed: 05/18/2023]
Abstract
Sugarcane is a hybrid of Saccharum officinarum and Saccharum spontaneum, with minor contributions from other species in Saccharum and other genera. Understanding the molecular basis of cell wall metabolism in sugarcane may allow for rational changes in fiber quality and content when designing new energy crops. This work describes a comparative expression profiling of sugarcane ancestral genotypes: S. officinarum, S. spontaneum and S. robustum and a commercial hybrid: RB867515, linking gene expression to phenotypes to identify genes for sugarcane improvement. Oligoarray experiments of leaves, immature and intermediate internodes, detected 12,621 sense and 995 antisense transcripts. Amino acid metabolism was particularly evident among pathways showing natural antisense transcripts expression. For all tissues sampled, expression analysis revealed 831, 674 and 648 differentially expressed genes in S. officinarum, S. robustum and S. spontaneum, respectively, using RB867515 as reference. Expression of sugar transporters might explain sucrose differences among genotypes, but an unexpected differential expression of histones were also identified between high and low Brix° genotypes. Lignin biosynthetic genes and bioenergetics-related genes were up-regulated in the high lignin genotype, suggesting that these genes are important for S. spontaneum to allocate carbon to lignin, while S. officinarum allocates it to sucrose storage. Co-expression network analysis identified 18 transcription factors possibly related to cell wall biosynthesis while in silico analysis detected cis-elements involved in cell wall biosynthesis in their promoters. Our results provide information to elucidate regulatory networks underlying traits of interest that will allow the improvement of sugarcane for biofuel and chemicals production.
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Affiliation(s)
| | | | - Viviane Guzzo de Carli Poelking
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
- Universidade Federal do Recôncavo da Bahia, Cruz das Almas, Brazil
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10
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Nida H, Blum S, Zielinski D, Srivastava DA, Elbaum R, Xin Z, Erlich Y, Fridman E, Shental N. Highly efficient de novo mutant identification in a Sorghum bicolor TILLING population using the ComSeq approach. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 86:349-359. [PMID: 26959378 DOI: 10.1111/tpj.13161] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/10/2016] [Accepted: 03/01/2016] [Indexed: 05/29/2023]
Abstract
Screening large populations for carriers of known or de novo rare single nucleotide polymorphisms (SNPs) is required both in Targeting induced local lesions in genomes (TILLING) experiments in plants and in screening of human populations. We previously suggested an approach that combines the mathematical field of compressed sensing with next-generation sequencing to allow such large-scale screening. Based on pooled measurements, this method identifies multiple carriers of heterozygous or homozygous rare alleles while using only a small fraction of resources. Its rigorous mathematical foundations allow scalable and robust detection, and provide error correction and resilience to experimental noise. Here we present a large-scale experimental demonstration of our computational approach, in which we targeted a TILLING population of 1024 Sorghum bicolor lines to detect carriers of de novo SNPs whose frequency was less than 0.1%, using only 48 pools. Subsequent validation confirmed that all detected lines were indeed carriers of the predicted mutations. This novel approach provides a highly cost-effective and robust tool for biologists and breeders to allow identification of novel alleles and subsequent functional analysis.
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Affiliation(s)
- Habte Nida
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shula Blum
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Dina Zielinski
- New York Genome Center, 101 Avenue of the Americas, New York, NY, USA
| | - Dhruv A Srivastava
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel
| | - Rivka Elbaum
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Zhanguo Xin
- Plant Stress and Germplasm Development Unit, US Department of Agriculture/Agricultural Research Service, Lubbock, TX, USA
| | - Yaniv Erlich
- New York Genome Center, 101 Avenue of the Americas, New York, NY, USA
- Department of Computer Science, Fu Foundation School of Engineering, Columbia University, New York, NY, USA
- Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA
| | - Eyal Fridman
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel
| | - Noam Shental
- Department of Mathematics and Computer Science, The Open University of Israel, Raanana, Israel
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Mizuno H, Kasuga S, Kawahigashi H. The sorghum SWEET gene family: stem sucrose accumulation as revealed through transcriptome profiling. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:127. [PMID: 27330561 PMCID: PMC4912755 DOI: 10.1186/s13068-016-0546-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/03/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND SWEET is a newly identified family of sugar transporters. Although SWEET transporters have been characterized by using Arabidopsis and rice, very little knowledge of sucrose accumulation in the stem region is available, as these model plants accumulate little sucrose in their stems. To elucidate the expression of key SWEET genes involved in sucrose accumulation of sorghum, we performed transcriptome profiling by RNA-seq, categorization using phylogenetic trees, analysis of chromosomal synteny, and comparison of amino acid sequences between SIL-05 (a sweet sorghum) and BTx623 (a grain sorghum). RESULTS We identified 23 SWEET genes in the sorghum genome. In the leaf, SbSWEET8-1 was highly expressed and was grouped in the same clade as AtSWEET11 and AtSWEET12 that play a role in the efflux of photosynthesized sucrose. The key genes in sucrose synthesis (SPS3) and that in another step of sugar transport (SbSUT1 and SbSUT2) were also highly expressed, suggesting that sucrose is newly synthesized and actively exported from the leaf. In the stem, SbSWEET4-3 was uniquely highly expressed. SbSWEET4-1, SbSWEET4-2, and SbSWEET4-3 were categorized into the same clade, but their tissue specificities were different, suggesting that SbSWEET4-3 is a sugar transporter with specific roles in the stem. We found a putative SWEET4-3 ortholog in the corresponding region of the maize chromosome, but not the rice chromosome, suggesting that SbSWEET4-3 was copied after the branching of sorghum and maize from rice. In the panicle from the heading through to 36 days afterward, SbSWEET2-1 and SbSWEET7-1 were expressed and grouped in the same clade as rice OsSWEET11/Xa13 that is essential for seed development. SbSWEET9-3 was highly expressed in the panicle only just after heading and was grouped into the same clade as AtSWEET8/RPG1 that is essential for pollen viability. Five of 23 SWEET genes had SNPs that caused nonsynonymous amino acid substitutions between SIL-05 and BTx623. CONCLUSIONS We determined the key SWEET genes for technological improvement of sorghum in the production of biofuels: SbSWEET8-1 for efflux of sucrose from the leaf; SbSWEET4-3 for unloading sucrose from the phloem in the stem; SbSWEET2-1 and SbSWEET7-1 for seed development; SbSWEET9-3 for pollen nutrition.
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Affiliation(s)
- Hiroshi Mizuno
- />Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), 2-1-2, Kannondai, Tsukuba, Ibaraki 305-8602 Japan
- />Institute of Crop Science (NICS), National Agriculture and Food Research Organization, 1-2, Owashi, Tsukuba, Ibaraki 305-8602 Japan
| | - Shigemitsu Kasuga
- />Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Nagano, 399-4598 Japan
| | - Hiroyuki Kawahigashi
- />Agrogenomics Research Center, National Institute of Agrobiological Sciences (NIAS), 2-1-2, Kannondai, Tsukuba, Ibaraki 305-8602 Japan
- />Institute of Crop Science (NICS), National Agriculture and Food Research Organization, 1-2, Owashi, Tsukuba, Ibaraki 305-8602 Japan
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Hoang NV, Furtado A, Botha FC, Simmons BA, Henry RJ. Potential for Genetic Improvement of Sugarcane as a Source of Biomass for Biofuels. Front Bioeng Biotechnol 2015; 3:182. [PMID: 26636072 PMCID: PMC4646955 DOI: 10.3389/fbioe.2015.00182] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 10/26/2015] [Indexed: 11/13/2022] Open
Abstract
Sugarcane (Saccharum spp. hybrids) has great potential as a major feedstock for biofuel production worldwide. It is considered among the best options for producing biofuels today due to an exceptional biomass production capacity, high carbohydrate (sugar + fiber) content, and a favorable energy input/output ratio. To maximize the conversion of sugarcane biomass into biofuels, it is imperative to generate improved sugarcane varieties with better biomass degradability. However, unlike many diploid plants, where genetic tools are well developed, biotechnological improvement is hindered in sugarcane by our current limited understanding of the large and complex genome. Therefore, understanding the genetics of the key biofuel traits in sugarcane and optimization of sugarcane biomass composition will advance efficient conversion of sugarcane biomass into fermentable sugars for biofuel production. The large existing phenotypic variation in Saccharum germplasm and the availability of the current genomics technologies will allow biofuel traits to be characterized, the genetic basis of critical differences in biomass composition to be determined, and targets for improvement of sugarcane for biofuels to be established. Emerging options for genetic improvement of sugarcane for the use as a bioenergy crop are reviewed. This will better define the targets for potential genetic manipulation of sugarcane biomass composition for biofuels.
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Affiliation(s)
- Nam V. Hoang
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
- College of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| | - Frederik C. Botha
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
- Sugar Research Australia, Indooroopilly, QLD, Australia
| | - Blake A. Simmons
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
- Joint BioEnergy Institute, Emeryville, CA, USA
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
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Furtado A, Lupoi JS, Hoang NV, Healey A, Singh S, Simmons BA, Henry RJ. Modifying plants for biofuel and biomaterial production. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:1246-58. [PMID: 25431201 DOI: 10.1111/pbi.12300] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 08/28/2014] [Accepted: 10/23/2014] [Indexed: 05/08/2023]
Abstract
The productivity of plants as biofuel or biomaterial crops is established by both the yield of plant biomass per unit area of land and the efficiency of conversion of the biomass to biofuel. Higher yielding biofuel crops with increased conversion efficiencies allow production on a smaller land footprint minimizing competition with agriculture for food production and biodiversity conservation. Plants have traditionally been domesticated for food, fibre and feed applications. However, utilization for biofuels may require the breeding of novel phenotypes, or new species entirely. Genomics approaches support genetic selection strategies to deliver significant genetic improvement of plants as sources of biomass for biofuel manufacture. Genetic modification of plants provides a further range of options for improving the composition of biomass and for plant modifications to assist the fabrication of biofuels. The relative carbohydrate and lignin content influences the deconstruction of plant cell walls to biofuels. Key options for facilitating the deconstruction leading to higher monomeric sugar release from plants include increasing cellulose content, reducing cellulose crystallinity, and/or altering the amount or composition of noncellulosic polysaccharides or lignin. Modification of chemical linkages within and between these biomass components may improve the ease of deconstruction. Expression of enzymes in the plant may provide a cost-effective option for biochemical conversion to biofuel.
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Affiliation(s)
- Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Qld, Australia
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Nishiyama MY, Ferreira SS, Tang PZ, Becker S, Pörtner-Taliana A, Souza GM. Full-length enriched cDNA libraries and ORFeome analysis of sugarcane hybrid and ancestor genotypes. PLoS One 2014; 9:e107351. [PMID: 25222706 PMCID: PMC4164538 DOI: 10.1371/journal.pone.0107351] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 08/14/2014] [Indexed: 11/18/2022] Open
Abstract
Sugarcane is a major crop used for food and bioenergy production. Modern cultivars are hybrids derived from crosses between Saccharum officinarum and Saccharum spontaneum. Hybrid cultivars combine favorable characteristics from ancestral species and contain a genome that is highly polyploid and aneuploid, containing 100–130 chromosomes. These complex genomes represent a huge challenge for molecular studies and for the development of biotechnological tools that can facilitate sugarcane improvement. Here, we describe full-length enriched cDNA libraries for Saccharum officinarum, Saccharum spontaneum, and one hybrid genotype (SP803280) and analyze the set of open reading frames (ORFs) in their genomes (i.e., their ORFeomes). We found 38,195 (19%) sugarcane-specific transcripts that did not match transcripts from other databases. Less than 1.6% of all transcripts were ancestor-specific (i.e., not expressed in SP803280). We also found 78,008 putative new sugarcane transcripts that were absent in the largest sugarcane expressed sequence tag database (SUCEST). Functional annotation showed a high frequency of protein kinases and stress-related proteins. We also detected natural antisense transcript expression, which mapped to 94% of all plant KEGG pathways; however, each genotype showed different pathways enriched in antisense transcripts. Our data appeared to cover 53.2% (17,563 genes) and 46.8% (937 transcription factors) of all sugarcane full-length genes and transcription factors, respectively. This work represents a significant advancement in defining the sugarcane ORFeome and will be useful for protein characterization, single nucleotide polymorphism and splicing variant identification, evolutionary and comparative studies, and sugarcane genome assembly and annotation.
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Affiliation(s)
| | | | - Pei-Zhong Tang
- ThermoFisher Scientific, Carlsbad, California, United States of America
| | - Scott Becker
- ThermoFisher Scientific, Carlsbad, California, United States of America
| | | | - Glaucia Mendes Souza
- Departamento de Bioquímica, Universidade de São Paulo, São Paulo, SP, Brazil
- * E-mail:
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