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Christian RW, Hewitt SL, Roalson EH, Dhingra A. Genome-Scale Characterization of Predicted Plastid-Targeted Proteomes in Higher Plants. Sci Rep 2020; 10:8281. [PMID: 32427841 PMCID: PMC7237471 DOI: 10.1038/s41598-020-64670-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 04/20/2020] [Indexed: 12/20/2022] Open
Abstract
Plastids are morphologically and functionally diverse organelles that are dependent on nuclear-encoded, plastid-targeted proteins for all biochemical and regulatory functions. However, how plastid proteomes vary temporally, spatially, and taxonomically has been historically difficult to analyze at a genome-wide scale using experimental methods. A bioinformatics workflow was developed and evaluated using a combination of fast and user-friendly subcellular prediction programs to maximize performance and accuracy for chloroplast transit peptides and demonstrate this technique on the predicted proteomes of 15 sequenced plant genomes. Gene family grouping was then performed in parallel using modified approaches of reciprocal best BLAST hits (RBH) and UCLUST. A total of 628 protein families were found to have conserved plastid targeting across angiosperm species using RBH, and 828 using UCLUST. However, thousands of clusters were also detected where only one species had predicted plastid targeting, most notably in Panicum virgatum which had 1,458 proteins with species-unique targeting. An average of 45% overlap was found in plastid-targeted protein-coding gene families compared with Arabidopsis, but an additional 20% of proteins matched against the full Arabidopsis proteome, indicating a unique evolution of plastid targeting. Neofunctionalization through subcellular relocalization is known to impart novel biological functions but has not been described before on a genome-wide scale for the plastid proteome. Further work to correlate these predicted novel plastid-targeted proteins to transcript abundance and high-throughput proteomics will uncover unique aspects of plastid biology and shed light on how the plastid proteome has evolved to influence plastid morphology and biochemistry.
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Affiliation(s)
- Ryan W Christian
- Department of Horticulture, Washington State University, Pullman, WA, USA
- Molecular Plant Sciences Program, Washington State University, Pullman, WA, USA
| | - Seanna L Hewitt
- Department of Horticulture, Washington State University, Pullman, WA, USA
- Molecular Plant Sciences Program, Washington State University, Pullman, WA, USA
| | - Eric H Roalson
- Molecular Plant Sciences Program, Washington State University, Pullman, WA, USA
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA, USA.
- Molecular Plant Sciences Program, Washington State University, Pullman, WA, USA.
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202
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Zhu XG, Ort DR, Parry MAJ, von Caemmerer S. A wish list for synthetic biology in photosynthesis research. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2219-2225. [PMID: 32060550 PMCID: PMC7134917 DOI: 10.1093/jxb/eraa075] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 02/12/2020] [Indexed: 05/02/2023]
Abstract
This perspective summarizes the presentations and discussions at the ' International Symposium on Synthetic Biology in Photosynthesis Research', which was held in Shanghai in 2018. Leveraging the current advanced understanding of photosynthetic systems, the symposium brain-stormed about the redesign and engineering of photosynthetic systems for translational goals and evaluated available new technologies/tools for synthetic biology as well as technological obstacles and new tools that would be needed to overcome them. Four major research areas for redesigning photosynthesis were identified: (i) mining natural variations of photosynthesis; (ii) coordinating photosynthesis with pathways utilizing photosynthate; (iii) reconstruction of highly efficient photosynthetic systems in non-host species; and (iv) development of new photosynthetic systems that do not exist in nature. To expedite photosynthesis synthetic biology research, an array of new technologies and community resources need to be developed, which include expanded modelling capacities, molecular engineering toolboxes, model species, and phenotyping tools.
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Affiliation(s)
- Xin-Guang Zhu
- Institute of Plant Physiology and Ecology and Center for Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Donald R Ort
- Departments of Plant Biology and Crop Sciences, University of Illinois at Urbana Champaign, Urbana, IL, USA
| | - Martin A J Parry
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Susanne von Caemmerer
- Research School of Biological Sciences, Australian National University, Acton, Australia
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203
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Sood P, Singh RK, Prasad M. An efficient Agrobacterium-mediated genetic transformation method for foxtail millet (Setaria italica L.). PLANT CELL REPORTS 2020; 39:511-525. [PMID: 31938834 DOI: 10.1007/s00299-019-02507-w] [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: 11/21/2019] [Accepted: 12/30/2019] [Indexed: 05/25/2023]
Abstract
A simple and robust Agrobacterium-mediated gene expression system in the C4 panicoid model crop, foxtail millet has been developed with up to 27 % transformation efficiency. Foxtail millet (Setaria italica L.) is a model crop to study C4 photosynthesis, abiotic stress tolerance, and bioenergy traits. Advances in molecular genetics and genomics had identified several potential genes in this crop that would serve as candidates for imparting climate-resilient traits in related millets, cereals, and biofuel crops. However, the lack of an efficient genetic transformation system has been impeding the functional characterization of these genes in foxtail millet per se. Given this, an easy and efficient regeneration and transformation protocol was optimized using mature seeds as a choicest explant. The suitability of secondary embryogenic calli over primary calli is underlined due to their high competence. The use of perfect combinations of plant growth regulators together with the ionic strength of organic and inorganics salts was found to influence regeneration and genetic transformation. We studied and optimized various crucial factors that affect the genetic transformation of foxtail millet calli using Agrobacterium tumefaciens-mediated approach. Secondary embryogenic calli and LBA44404 strain were found to be the best targets for transformation. The use of high sucrose and glucose, together with freshly prepared tobacco leaves extract, Silwet L-77 and acetosyringone, improved the efficiency of the genetic transformation of foxtail millet. Moreover, the use of an in vitro regeneration system with 84% callusing efficiency and 70-74% regeneration frequency led to a high recovery of transformants. Altogether, the present study reports a highly efficient (~ 27%) transformation system in foxtail millet that will expedite forward and reverse genetic studies in this important crop.
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Affiliation(s)
- Priyanka Sood
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Roshan Kumar Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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204
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Lightfoot E, Ustunkaya MC, Przelomska N, O'Connell TC, Hunt HV, Jones MK, Petrie CA. Carbon and nitrogen isotopic variability in foxtail millet (Setaria italica) with watering regime. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8615. [PMID: 31658389 PMCID: PMC7050514 DOI: 10.1002/rcm.8615] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/27/2019] [Accepted: 09/27/2019] [Indexed: 06/10/2023]
Abstract
RATIONALE Carbonised plant remains are analysed for reconstruction of past climates and agricultural regimes. Several recent studies have used C4 plants to address related questions, and correlations between modern C4 plant δ13 C values and rainfall have been found. The millets were important food crops in prehistoric Eurasia, yet little is known about causes of isotopic variation within millet species. Previous research has shown there to be significant isotopic variation between millet accessions. Here we compare isotope ratios from plants grown under different watering regimes. This allows for a consideration of whether or not Setaria italica is a good proxy for environmental reconstruction. METHODS We compare stable isotope ratios of Setaria italica plants grown in a controlled environment chamber with different watering regimes. We compare the carbon isotope ratios of leaves and grains, and the nitrogen isotope ratios of grains, from 12 accessions of Setaria italica. RESULTS We find significant isotopic variability between watering regimes. Carbon isotope ratios are positively correlated with water availability, and on average vary by 1.9‰ and 1.7‰ for leaves and grains, respectively. Grain nitrogen isotope ratios also vary with watering regime; however, the highest isotope ratios are found with the 130-mL watering regime. CONCLUSIONS The carbon isotope ratios of Setaria italica are strongly correlated with water availability. However, the correlation is the opposite to that seen in studies of C3 plants. The difference in isotopic ratio due to watering regime is comparable with that seen between different accessions; thus distinguishing between changing varieties of Setaria italica and changing climate is problematic. In terms of grain nitrogen isotope ratios, the highest δ15 N values were not associated with the lowest watering regime. Again, δ15 N variation is comparable with that which would be expected from an aridity effect or a manuring effect, and thus distinguishing between these factors is probably problematic.
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Affiliation(s)
- Emma Lightfoot
- McDonald Institute for Archaeological ResearchUniversity of CambridgeDowning StreetCambridgeCB2 3ERUK
| | - M. Cemre Ustunkaya
- McDonald Institute for Archaeological ResearchUniversity of CambridgeDowning StreetCambridgeCB2 3ERUK
| | - Natalia Przelomska
- Department of Anthropology, National Museum of Natural HistorySmithsonian InstitutionWashingtonDC20560USA
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational ZooWashingtonDC20008USA
| | - Tamsin C. O'Connell
- Department of ArchaeologyUniversity of CambridgeDowning StreetCambridgeCB2 3DZUK
| | - Harriet V. Hunt
- McDonald Institute for Archaeological ResearchUniversity of CambridgeDowning StreetCambridgeCB2 3ERUK
| | - Martin K. Jones
- Department of ArchaeologyUniversity of CambridgeDowning StreetCambridgeCB2 3DZUK
| | - Cameron A. Petrie
- Department of ArchaeologyUniversity of CambridgeDowning StreetCambridgeCB2 3DZUK
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205
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Identification and profiling of microRNAs and differentially expressed genes during anther development between a genetic male-sterile mutant and its wildtype cotton via high-throughput RNA sequencing. Mol Genet Genomics 2020; 295:645-660. [PMID: 32172356 PMCID: PMC7203095 DOI: 10.1007/s00438-020-01656-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 02/19/2020] [Indexed: 11/10/2022]
Abstract
Genetic male sterility (GMS) facilitates hybrid seed production in crops including cotton (Gossypium hirsutum). However, the genetic and molecular mechanisms specifically involved in this developmental process are poorly understood. In this study, small RNA sequencing, degradome sequencing, and transcriptome sequencing were performed to analyze miRNAs and their target genes during anther development in a GMS mutant (‘Dong A’) and its fertile wildtype (WT). A total of 80 known and 220 novel miRNAs were identified, 71 of which showed differential expressions during anther development. A further degradome sequencing revealed a total of 117 candidate target genes cleaved by 16 known and 36 novel miRNAs. Based on RNA-seq, 24, 11, and 21 predicted target genes showed expression correlations with the corresponding miRNAs at the meiosis, tetrad and uninucleate stages, respectively. In addition, a large number of differentially expressed genes were identified, most of which were involved in sucrose and starch metabolism, carbohydrate metabolism, and plant hormone signal transduction based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The results of our study provide valuable information for further functional investigations of the important miRNAs and target genes involved in genetic male sterility and advance our understanding of miRNA regulatory functions during cotton anther development.
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206
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Nguyen DQ, Van Eck J, Eamens AL, Grof CPL. Robust and Reproducible Agrobacterium-Mediated Transformation System of the C 4 Genetic Model Species Setaria viridis. FRONTIERS IN PLANT SCIENCE 2020; 11:281. [PMID: 32231678 PMCID: PMC7082778 DOI: 10.3389/fpls.2020.00281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/25/2020] [Indexed: 05/04/2023]
Abstract
Setaria viridis (green foxtail) has been identified as a potential experimental model system to genetically and molecularly characterise the C4 monocotyledonous grasses due to its small physical size, short generation time and prolific seed production, together with a sequenced and annotated genome. Setaria viridis is the wild ancestor of the cropping species, foxtail millet (Setaria italica), with both Setaria species sharing a close evolutionary relationship with the agronomically important species, maize, sorghum, and sugarcane, as well as the bioenergy feedstocks, switchgrass, and Miscanthus. However, an efficient and reproducible transformation protocol is required to further advance the use of S. viridis to study the molecular genetics of C4 monocotyledonous grasses. An efficient and reproducible protocol was established for Agrobacterium tumefaciens-mediated transformation of S. viridis (Accession A10) regenerable callus material derived from mature seeds, a protocol that returned an average transformation efficiency of 6.3%. The efficiency of this protocol was the result of the: (i) use of mature embryo derived callus material; (ii) age of the seed used to induce callus formation; (iii) composition of the callus induction media, including the addition of the ethylene inhibitor, silver nitrate; (iv) use of a co-cultivation approach, and; (v) concentration of the selective agent. Our protocol furthers the use of S. viridis as an experimental model system to study the molecular genetics of C4 monocotyledonous grasses for the potential future development of improved C4 cropping species.
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Affiliation(s)
- Duc Quan Nguyen
- Centre for Plant Science, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | - Joyce Van Eck
- Boyce Thompson Institute, Ithaca, NY, United States
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Andrew L. Eamens
- Centre for Plant Science, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
| | - Christopher P. L. Grof
- Centre for Plant Science, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, Australia
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207
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Jensen SE, Charles JR, Muleta K, Bradbury PJ, Casstevens T, Deshpande SP, Gore MA, Gupta R, Ilut DC, Johnson L, Lozano R, Miller Z, Ramu P, Rathore A, Romay MC, Upadhyaya HD, Varshney RK, Morris GP, Pressoir G, Buckler ES, Ramstein GP. A sorghum practical haplotype graph facilitates genome-wide imputation and cost-effective genomic prediction. THE PLANT GENOME 2020; 13:e20009. [PMID: 33016627 DOI: 10.1002/tpg2.20009] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 01/04/2020] [Indexed: 05/22/2023]
Abstract
Successful management and utilization of increasingly large genomic datasets is essential for breeding programs to accelerate cultivar development. To help with this, we developed a Sorghum bicolor Practical Haplotype Graph (PHG) pangenome database that stores haplotypes and variant information. We developed two PHGs in sorghum that were used to identify genome-wide variants for 24 founders of the Chibas sorghum breeding program from 0.01x sequence coverage. The PHG called single nucleotide polymorphisms (SNPs) with 5.9% error at 0.01x coverage-only 3% higher than PHG error when calling SNPs from 8x coverage sequence. Additionally, 207 progenies from the Chibas genomic selection (GS) training population were sequenced and processed through the PHG. Missing genotypes were imputed from PHG parental haplotypes and used for genomic prediction. Mean prediction accuracies with PHG SNP calls range from .57-.73 and are similar to prediction accuracies obtained with genotyping-by-sequencing or targeted amplicon sequencing (rhAmpSeq) markers. This study demonstrates the use of a sorghum PHG to impute SNPs from low-coverage sequence data and shows that the PHG can unify genotype calls across multiple sequencing platforms. By reducing input sequence requirements, the PHG can decrease the cost of genotyping, make GS more feasible, and facilitate larger breeding populations. Our results demonstrate that the PHG is a useful research and breeding tool that maintains variant information from a diverse group of taxa, stores sequence data in a condensed but readily accessible format, unifies genotypes across genotyping platforms, and provides a cost-effective option for genomic selection.
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Affiliation(s)
- Sarah E Jensen
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Jean Rigaud Charles
- Chibas and Department of Agriculture and Environmental Sciences, Quisqueya University, Port-au-Prince, Haiti
| | - Kebede Muleta
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Peter J Bradbury
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
- United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
| | - Terry Casstevens
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Santosh P Deshpande
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Michael A Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Rajeev Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Daniel C Ilut
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Lynn Johnson
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Roberto Lozano
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Zachary Miller
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Punna Ramu
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - M Cinta Romay
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
| | - Geoffrey P Morris
- Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA
| | - Gael Pressoir
- Chibas and Department of Agriculture and Environmental Sciences, Quisqueya University, Port-au-Prince, Haiti
| | - Edward S Buckler
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
- United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, 14853, USA
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208
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Watson-Lazowski A, Papanicolaou A, Koller F, Ghannoum O. The transcriptomic responses of C 4 grasses to subambient CO 2 and low light are largely species specific and only refined by photosynthetic subtype. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:1170-1184. [PMID: 31651067 DOI: 10.1111/tpj.14583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 09/23/2019] [Accepted: 10/03/2019] [Indexed: 06/10/2023]
Abstract
Three subtypes of C4 photosynthesis exist (NADP-ME, NAD-ME and PEPCK), each known to be beneficial under specific environmental conditions. However, the influence of photosynthetic subtype on transcriptomic plasticity, as well as the genes underpinning this variability, remain largely unknown. Here, we comprehensively investigate the responses of six C4 grass species, spanning all three C4 subtypes, to two controlled environmental stresses: low light (200 µmol m-2 sec-1 ) and glacial CO2 (subambient; 180 ppm). We identify a susceptibility within NADP-ME species to glacial CO2 . Notably, although glacial CO2 phenotypes could be tied to C4 subtype, biochemical and transcriptomic responses to glacial CO2 were largely species specific. Nevertheless, we were able to identify subtype specific subsets of significantly differentially expressed transcripts which link resource acquisition and allocation to NADP-ME species susceptibility to glacial CO2 . Here, low light phenotypes were comparable across species with no clear subtype response, while again, transcriptomic responses to low light were largely species specific. However, numerous functional similarities were noted within the transcriptomic responses to low light, suggesting these responses are functionally relatively conserved. Additionally, PEPCK species exhibited heightened regulation of transcripts related to metabolism in response to both stresses, likely tied to their C4 metabolic pathway. These results highlight the influence that both species and subtype can have on plant responses to abiotic stress, building on our mechanistic understanding of acclimation within C4 grasses and highlighting avenues for future crop improvements.
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Affiliation(s)
- Alexander Watson-Lazowski
- Hawkesbury Institute for the Environment, University of Western Sydney, Locked Bag 1797, Penrith, NSW, 2751, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Canberra, Australia
| | - Alexie Papanicolaou
- Hawkesbury Institute for the Environment, University of Western Sydney, Locked Bag 1797, Penrith, NSW, 2751, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Canberra, Australia
| | - Fiona Koller
- Hawkesbury Institute for the Environment, University of Western Sydney, Locked Bag 1797, Penrith, NSW, 2751, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Canberra, Australia
| | - Oula Ghannoum
- Hawkesbury Institute for the Environment, University of Western Sydney, Locked Bag 1797, Penrith, NSW, 2751, Australia
- ARC Centre of Excellence for Translational Photosynthesis, Canberra, Australia
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209
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Rodríguez JP, Rahman H, Thushar S, Singh RK. Healthy and Resilient Cereals and Pseudo-Cereals for Marginal Agriculture: Molecular Advances for Improving Nutrient Bioavailability. Front Genet 2020; 11:49. [PMID: 32174958 PMCID: PMC7056906 DOI: 10.3389/fgene.2020.00049] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/16/2020] [Indexed: 11/13/2022] Open
Abstract
With the ever-increasing world population, an extra 1.5 billion mouths need to be fed by 2050 with continuously dwindling arable land. Hence, it is imperative that extra food come from the marginal lands that are expected to be unsuitable for growing major staple crops under the adverse climate change scenario. Crop diversity provides right alternatives for marginal environments to improve food, feed, and nutritional security. Well-adapted and climate-resilient crops will be the best fit for such a scenario to produce seed and biomass. The minor millets are known for their high nutritional profile and better resilience for several abiotic stresses that make them the suitable crops for arid and salt-affected soils and poor-quality waters. Finger millet (Eleucine coracana) and foxtail millet (Setaria italica), also considered as orphan crops, are highly tolerant grass crop species that grow well in marginal and degraded lands of Africa and Asia with better nutritional profile. Another category of grains, called pseudo-cereals, is considered as rich foods because of their protein quality and content, high mineral content, and healthy and balance food quality. Quinoa (Chenopodium quinoa), amaranth (Amaranthus sp.), and buckwheat (Fagopyrum esculentum) fall under this category. Nevertheless, both minor millets and pseudo-cereals are morphologically different, although similar for micronutrient bioavailability, and their grains are gluten-free. The cultivation of these millets can make dry lands productive and ensure future food as well as nutritional security. Although the natural nutrient profile of these crop plant species is remarkably good, little development has occurred in advances in molecular genetics and breeding efforts to improve the bioavailability of nutrients. Recent advances in NGS have enabled the genome and transcriptome sequencing of these millets and pseudo-cereals for the faster development of molecular markers and application in molecular breeding. Genomic information on finger millet (1,196 Mb with 85,243 genes); S. italica, a model small millet (well-annotated draft genome of 420 Mb with 38,801 protein-coding genes); amaranth (466 Mb genome and 23,059 protein-coding genes); buckwheat (genome size of 1.12 Gb with 35,816 annotated genes); and quinoa (genome size of 1.5 Gb containing 54,438 protein-coding genes) could pave the way for the genetic improvement of these grains. These genomic resources are an important first step toward genetic improvement of these crops. This review highlights the current advances and available resources on genomics to improve nutrient bioavailability in these five suitable crops for the sustained healthy livelihood.
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Affiliation(s)
| | | | | | - Rakesh K. Singh
- Crop Diversification and Genetics Program, International Center for Biosaline Agriculture, Dubai, United Arab Emirates
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210
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QTL mapping of yield component traits on bin map generated from resequencing a RIL population of foxtail millet (Setaria italica). BMC Genomics 2020; 21:141. [PMID: 32041544 PMCID: PMC7011527 DOI: 10.1186/s12864-020-6553-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 02/04/2020] [Indexed: 01/19/2023] Open
Abstract
Background Foxtail millet (Setaria italica) has been developed into a model genetical system for deciphering architectural evolution, C4 photosynthesis, nutritional properties, abiotic tolerance and bioenergy in cereal grasses because of its advantageous characters with the small genome size, self-fertilization, short growing cycle, small growth stature, efficient genetic transformation and abundant diverse germplasm resources. Therefore, excavating QTLs of yield component traits, which are closely related to aspects mentioned above, will further facilitate genetic research in foxtail millet and close cereal species. Results Here, 164 Recombinant inbreed lines from a cross between Longgu7 and Yugu1 were created and 1,047,978 SNPs were identified between both parents via resequencing. A total of 3413 bin markers developed from SNPs were used to construct a binary map, containing 3963 recombinant breakpoints and totaling 1222.26 cM with an average distance of 0.36 cM between adjacent markers. Forty-seven QTLs were identified for four traits of straw weight, panicle weight, grain weight per plant and 1000-grain weight. These QTLs explained 5.5–14.7% of phenotypic variance. Thirty-nine favorable QTL alleles were found to inherit from Yugu1. Three stable QTLs were detected in multi-environments, and nine QTL clusters were identified on Chromosome 3, 6, 7 and 9. Conclusions A high-density genetic map with 3413 bin markers was constructed and three stable QTLs and 9 QTL clusters for yield component traits were identified. The results laid a powerful foundation for fine mapping, identifying candidate genes, elaborating molecular mechanisms and application in foxtail millet breeding programs by marker-assisted selection.
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211
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Liu H, Shi J, Cai Z, Huang Y, Lv M, Du H, Gao Q, Zuo Y, Dong Z, Huang W, Qin R, Liang C, Lai J, Jin W. Evolution and Domestication Footprints Uncovered from the Genomes of Coix. MOLECULAR PLANT 2020; 13:295-308. [PMID: 31778842 DOI: 10.1016/j.molp.2019.11.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/17/2019] [Accepted: 11/13/2019] [Indexed: 05/21/2023]
Abstract
Coix lacryma-jobi, a plant species closely related to Zea and Sorghum, is an important food and medicinal crop in Asia. However, no reference genome of this species has been reported, and its exact phylogeny within the Andropogoneae remains unresolved. Here, we generated a high-quality genome assembly of coix comprising ∼1.73 Gb with 44 485 predicted protein-coding genes. We found coix to be a typical diploid plant with an overall 1-to-1 syntenic relationship with the Sorghum genome, despite its drastic genome expansion (∼2.3-fold) due mainly to the activity of transposable elements. Phylogenetic analysis revealed that coix diverged with sorghum ∼10.41 million years ago, which was ∼1.49 million years later than the divergence between sorghum and maize. Resequencing of 27 additional coix accessions revealed that they could be unambiguously separated into wild relatives and cultivars, and suggested that coix experienced a strong genetic bottleneck, resulting in the loss of about half of the genetic diversity during domestication, even though many traits have remained undomesticated. Our data not only provide novel comparative genomic and evolutionary insights into the Andropogoneae lineage, but also an important resource that will greatly benefit molecular breeding of this important crop.
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Affiliation(s)
- Hongbing Liu
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, P. R. China; Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, P. R. China
| | - Junpeng Shi
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, P. R. China; State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, P. R. China
| | - Zexi Cai
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, P. R. China; Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, P. R. China
| | - Yumin Huang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, P. R. China; Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, P. R. China
| | - Menglu Lv
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, P. R. China; State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, P. R. China
| | - Huilong Du
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, 1 Beichen West Road No. 2, Beijing 100101, P. R. China
| | - Qiang Gao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, 1 Beichen West Road No. 2, Beijing 100101, P. R. China
| | - Yi Zuo
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, P. R. China
| | - Zhaobin Dong
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, P. R. China; Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, P. R. China
| | - Wei Huang
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, P. R. China; Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, P. R. China
| | - Rui Qin
- Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of Hubei Province, South-Central University for Nationalities, Wuhan 430074, P. R. China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Innovative Academy of Seed Design, Chinese Academy of Sciences, 1 Beichen West Road No. 2, Beijing 100101, P. R. China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, P. R. China; Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, P. R. China; State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, P. R. China.
| | - Weiwei Jin
- State Key Laboratory of Plant Physiology and Biochemistry, National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, the Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, P. R. China; Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, P. R. China.
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212
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Carvalho DS, Nishimwe AV, Schnable JC. IsoSeq transcriptome assembly of C 3 panicoid grasses provides tools to study evolutionary change in the Panicoideae. PLANT DIRECT 2020; 4:e00203. [PMID: 32128472 PMCID: PMC7047018 DOI: 10.1002/pld3.203] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 01/14/2020] [Accepted: 01/16/2020] [Indexed: 06/10/2023]
Abstract
The number of plant species with genomic and transcriptomic data has been increasing rapidly. The grasses-Poaceae-have been well represented among species with published reference genomes. However, as a result the genomes of wild grasses are less frequently targeted by sequencing efforts. Sequence data from wild relatives of crop species in the grasses can aid the study of domestication, gene discovery for breeding and crop improvement, and improve our understanding of the evolution of C4 photosynthesis. Here, we used long-read sequencing technology to characterize the transcriptomes of three C3 panicoid grass species: Dichanthelium oligosanthes, Chasmanthium laxum, and Hymenachne amplexicaulis. Based on alignments to the sorghum genome, we estimate that assembled consensus transcripts from each species capture between 54.2% and 65.7% of the conserved syntenic gene space in grasses. Genes co-opted into C4 were also well represented in this dataset, despite concerns that because these genes might play roles unrelated to photosynthesis in the target species, they would be expressed at low levels and missed by transcript-based sequencing. A combined analysis using syntenic orthologous genes from grasses with published reference genomes and consensus long-read sequences from these wild species was consistent with previously published phylogenies. It is hoped that these data, targeting underrepresented classes of species within the PACMAD grasses-wild species and species utilizing C3 photosynthesis-will aid in future studies of domestication and C4 evolution by decreasing the evolutionary distance between C4 and C3 species within this clade, enabling more accurate comparisons associated with evolution of the C4 pathway.
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Affiliation(s)
- Daniel S. Carvalho
- Department of Agronomy and HorticultureCenter for Plant Science InnovationUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Aime V. Nishimwe
- Department of Agronomy and HorticultureCenter for Plant Science InnovationUniversity of Nebraska‐LincolnLincolnNEUSA
| | - James C. Schnable
- Department of Agronomy and HorticultureCenter for Plant Science InnovationUniversity of Nebraska‐LincolnLincolnNEUSA
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213
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Hunter CT, Block AK, Christensen SA, Li QB, Rering C, Alborn HT. Setaria viridis as a model for translational genetic studies of jasmonic acid-related insect defenses in Zea mays. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 291:110329. [PMID: 31928686 DOI: 10.1016/j.plantsci.2019.110329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/24/2019] [Accepted: 11/01/2019] [Indexed: 06/10/2023]
Abstract
Little is known regarding insect defense pathways in Setaria viridis (setaria), a model system for panicoid grasses, including Zea mays (maize). It is thus of interest to compare insect herbivory responses of setaria and maize. Here we use metabolic, phylogenetic, and gene expression analyses to measure a subset of jasmonic acid (JA)-related defense responses to leaf-chewing caterpillars. Phylogenetic comparisons of known defense-related maize genes were used to identify putative orthologs in setaria, and candidates were tested by quantitative PCR to determine transcriptional responses to insect challenge. Our findings show that while much of the core JA-related metabolic and genetic responses appear conserved between setaria and maize, production of downstream secondary metabolites such as benzoxazinoids and herbivore-induced plant volatiles are dissimilar. This diversity of chemical defenses and gene families involved in secondary metabolism among grasses presents new opportunities for cross species engineering. The high degree of genetic similarity and ease of orthologous gene identification between setaria and maize make setaria an excellent species for translational genetic studies, but the species specificity of downstream insect defense chemistry makes some pathways unamenable to cross-species comparisons.
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Affiliation(s)
- Charles T Hunter
- Chemistry Research Unit, USDA Agricultural Research Service, Center for Medical, Agricultural and Veterinary Entomology, Gainesville, FL, 32608, USA.
| | - Anna K Block
- Chemistry Research Unit, USDA Agricultural Research Service, Center for Medical, Agricultural and Veterinary Entomology, Gainesville, FL, 32608, USA
| | - Shawn A Christensen
- Chemistry Research Unit, USDA Agricultural Research Service, Center for Medical, Agricultural and Veterinary Entomology, Gainesville, FL, 32608, USA
| | - Qin-Bao Li
- Chemistry Research Unit, USDA Agricultural Research Service, Center for Medical, Agricultural and Veterinary Entomology, Gainesville, FL, 32608, USA
| | - Caitlin Rering
- Chemistry Research Unit, USDA Agricultural Research Service, Center for Medical, Agricultural and Veterinary Entomology, Gainesville, FL, 32608, USA
| | - Hans T Alborn
- Chemistry Research Unit, USDA Agricultural Research Service, Center for Medical, Agricultural and Veterinary Entomology, Gainesville, FL, 32608, USA
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214
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Renny-Byfield S, Baumgarten A. Repetitive DNA content in the maize genome is uncoupled from population stratification at SNP loci. BMC Genomics 2020; 21:98. [PMID: 32000670 PMCID: PMC6993463 DOI: 10.1186/s12864-020-6517-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 01/20/2020] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Repetitive DNA is a major component of plant genomes and is thought to be a driver of evolutionary novelty. Describing variation in repeat content among individuals and between populations is key to elucidating the evolutionary significance of repetitive DNA. However, the cost of producing references genomes has limited large-scale intraspecific comparisons to a handful of model organisms where multiple reference genomes are available. RESULTS We examine repeat content variation in the genomes of 94 elite inbred maize lines using graph-based repeat clustering, a reference-free and rapid assay of repeat content. We examine population structure using genome-wide repeat profiles, and demonstrate the stiff-stalk and non-stiff-stalk heterotic populations are homogenous with regard to global repeat content. In contrast, and similar to previously reported results, the same individuals show clear differentiation, and aggregate into two populations when examining population structure using genome-wide SNPs. Additionally, we develop a novel kmer based technique to examine the chromosomal distribution of repeat clusters in silico and show a cluster dependent association with gene density. CONCLUSION Our results indicate global repeat content variation in the heterotic populations of maize has not diverged, and is uncoupled from population stratification at SNP loci. We show that repeat families exhibit divergent patterns with regard to chromosomal distribution, some repeat clusters accumulate in regions of high gene density, whereas others aggregate in regions of low gene density.
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215
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Nadeem F, Ahmad Z, Ul Hassan M, Wang R, Diao X, Li X. Adaptation of Foxtail Millet ( Setaria italica L.) to Abiotic Stresses: A Special Perspective of Responses to Nitrogen and Phosphate Limitations. FRONTIERS IN PLANT SCIENCE 2020; 11:187. [PMID: 32184798 PMCID: PMC7058660 DOI: 10.3389/fpls.2020.00187] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 02/07/2020] [Indexed: 05/12/2023]
Abstract
Amongst various environmental constraints, abiotic stresses are increasing the risk of food insecurity worldwide by limiting crop production and disturbing the geographical distribution of food crops. Millets are known to possess unique features of resilience to adverse environments, especially infertile soil conditions, although the underlying mechanisms are yet to be determined. The small diploid genome, short stature, excellent seed production, C4 photosynthesis, and short life cycle of foxtail millet make it a very promising model crop for studying nutrient stress responses. Known to be a drought-tolerant crop, it responds to low nitrogen and low phosphate by respective reduction and enhancement of its root system. This special response is quite different from that shown by maize and some other cereals. In contrast to having a smaller root system under low nitrogen, foxtail millet enhances biomass accumulation, facilitating root thickening, presumably for nutrient translocation. The low phosphate response of foxtail millet links to the internal nitrogen status, which tends to act as a signal regulating the expression of nitrogen transporters and hence indicates its inherent connection with nitrogen nutrition. Altogether, the low nitrogen and low phosphate responses of foxtail millet can act as a basis to further determine the underlying molecular mechanisms. Here, we will highlight the abiotic stress responses of foxtail millet with a key note on its low nitrogen and low phosphate adaptive responses in comparison to other crops.
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Affiliation(s)
- Faisal Nadeem
- MOE Key Laboratory of Plant-Soil Interactions, Department of Plant Nutrition, China Agricultural University, Beijing, China
| | - Zeeshan Ahmad
- MOE Key Laboratory of Plant-Soil Interactions, Department of Plant Nutrition, China Agricultural University, Beijing, China
| | - Mahmood Ul Hassan
- MOE Key Laboratory of Plant-Soil Interactions, Department of Plant Nutrition, China Agricultural University, Beijing, China
| | - Ruifeng Wang
- MOE Key Laboratory of Plant-Soil Interactions, Department of Plant Nutrition, China Agricultural University, Beijing, China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuexian Li
- MOE Key Laboratory of Plant-Soil Interactions, Department of Plant Nutrition, China Agricultural University, Beijing, China
- *Correspondence: Xuexian Li,
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216
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Kang SH, Kim B, Choi BS, Lee HO, Kim NH, Lee SJ, Kim HS, Shin MJ, Kim HW, Nam K, Kang KD, Kwon SJ, Oh TJ, Lee SC, Kim CK. Genome Assembly and Annotation of Soft-Shelled Adlay ( Coix lacryma-jobi Variety ma-yuen), a Cereal and Medicinal Crop in the Poaceae Family. FRONTIERS IN PLANT SCIENCE 2020; 11:630. [PMID: 32528499 PMCID: PMC7247446 DOI: 10.3389/fpls.2020.00630] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/23/2020] [Indexed: 05/21/2023]
Abstract
Coix lacryma-jobi, also called adlay or Job's tears, is an annual herbal plant belonging to the Poaceae family that has been cultivated as a cereal and medicinal crop in Asia. Despite its importance, however, genomic resources for better understanding this plant species at the molecular level and informing improved breeding strategies remain limited. To address this, we generated a draft genome of the C. lacryma-jobi variety ma-yuen (soft-shelled adlay) Korean cultivar, Johyun, by de novo assembly, using PacBio and Illumina sequencing data. A total of 3,362 scaffold sequences, 1.28 Gb in length, were assembled, representing 82.1% of the estimated genome size (1.56 Gb). Genome completeness was confirmed by the presence of 91.4% of the BUSCO angiosperm genes and mapping ratio of 98.3% of Illumina paired-end reads. We found that approximately 77.0% of the genome is occupied by repeat sequences, most of which are Gypsy and Copia-type retrotransposons, and evidence-based genome annotation predicts 39,574 protein-coding genes, 85.5% of which were functionally annotated. We further predict that soft-shelled adlay diverged from a common ancestor with sorghum 9.0-11.2 MYA. Transcriptome profiling revealed 3,988 genes that are differentially expressed in seeds relative to other tissues, of which 1,470 genes were strongly up-regulated in seeds and the most enriched Gene Ontology terms were assigned to carbohydrate and protein metabolism. In addition, we identified 76 storage protein genes including 18 seed-specific coixin genes and 13 candidate genes involved in biosynthesis of benzoxazinoids (BXs) including coixol, a unique BX compound found in C. lacryma-jobi species. The characterization of those genes can further our understanding of unique traits of soft-shelled adlay, such as high seed protein content and medicinal compound biosynthesis. Taken together, our genome sequence data will provide a valuable resource for molecular breeding and pharmacological study of this plant species.
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Affiliation(s)
- Sang-Ho Kang
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Byeollee Kim
- Department of Life Science and Biochemical Engineering, Graduate School, Sun Moon University, Asan, South Korea
| | | | | | | | | | | | | | | | | | | | - Soo-Jin Kwon
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, Sun Moon University, Asan, South Korea
| | - Sang-Choon Lee
- Phyzen Co., Seongnam, South Korea
- *Correspondence: Sang-Choon Lee,
| | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
- Chang-Kug Kim,
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217
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Afamefule C, Raines CA. Insights Into the Regulation of the Expression Pattern of Calvin-Benson-Bassham Cycle Enzymes in C 3 and C 4 Grasses. FRONTIERS IN PLANT SCIENCE 2020; 11:570436. [PMID: 33178241 PMCID: PMC7595957 DOI: 10.3389/fpls.2020.570436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 09/23/2020] [Indexed: 05/15/2023]
Abstract
C4 photosynthesis is characterized by the compartmentalization of the processes of atmospheric uptake of CO2 and its conversion into carbohydrate between mesophyll and bundle-sheath cells. As a result, most of the enzymes participating in the Calvin-Benson-Bassham (CBB) cycle, including RubisCO, are highly expressed in bundle-sheath cells. There is evidence that changes in the regulatory sequences of RubisCO contribute to its bundle-sheath-specific expression, however, little is known about how the spatial-expression pattern of other CBB cycle enzymes is regulated. In this study, we use a computational approach to scan for transcription factor binding sites in the regulatory regions of the genes encoding CBB cycle enzymes, SBPase, FBPase, PRK, and GAPDH-B, of C3 and C4 grasses. We identified potential cis-regulatory elements present in each of the genes studied here, regardless of the photosynthetic path used by the plant. The trans-acting factors that bind these elements have been validated in A. thaliana and might regulate the expression of the genes encoding CBB cycle enzymes. In addition, we also found C4-specific transcription factor binding sites in the genes encoding CBB cycle enzymes that could potentially contribute to the pathway-specific regulation of gene expression. These results provide a foundation for the functional analysis of the differences in regulation of genes encoding CBB cycle enzymes between C3 and C4 grasses.
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218
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Rocha JRDASDC, Marçal TDS, Salvador FV, da Silva AC, Carneiro PCS, de Resende MDV, Carneiro JDC, Azevedo ALS, Pereira JF, Machado JC. Unraveling candidate genes underlying biomass digestibility in elephant grass (Cenchrus purpureus). BMC PLANT BIOLOGY 2019; 19:548. [PMID: 31822283 PMCID: PMC6905061 DOI: 10.1186/s12870-019-2180-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 12/01/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND Elephant grass [Cenchrus purpureus (Schumach.) Morrone] is used for bioenergy and animal feed. In order to identify candidate genes that could be exploited for marker-assisted selection in elephant grass, this study aimed to investigate changes in predictive accuracy using genomic relationship information and simple sequence repeats for eight traits (height, green biomass, dry biomass, acid and neutral detergent fiber, lignin content, biomass digestibility, and dry matter concentration) linked to bioenergetics and animal feeding. RESULTS We used single-step, genome-based best linear unbiased prediction and genome association methods to investigate changes in predictive accuracy and find candidate genes using genomic relationship information. Genetic variability (p < 0.05) was detected for most of the traits evaluated. In general, the overall means for the traits varied widely over the cuttings, which was corroborated by a significant genotype by cutting interaction. Knowing the genomic relationships increased the predictive accuracy of the biomass quality traits. We found that one marker (M28_161) was significantly associated with high values of biomass digestibility. The marker had moderate linkage disequilibrium with another marker (M35_202) that, in general, was detected in genotypes with low values of biomass digestibility. In silico analysis revealed that both markers have orthologous regions in other C4 grasses such as Setaria viridis, Panicum hallii, and Panicum virgatum, and these regions are located close to candidate genes involved in the biosynthesis of cell wall molecules (xyloglucan and lignin), which support their association with biomass digestibility. CONCLUSIONS The markers and candidate genes identified here are useful for breeding programs aimed at changing biomass digestibility in elephant grass. These markers can be used in marker-assisted selection to grow elephant grass cultivars for different uses, e.g., bioenergy production, bio-based products, co-products, bioactive compounds, and animal feed.
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219
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Dai Z, Li T, Li J, Han Z, Pan Y, Tang S, Diao X, Luo M. High-throughput long paired-end sequencing of a Fosmid library by PacBio. PLANT METHODS 2019; 15:142. [PMID: 31788019 PMCID: PMC6878638 DOI: 10.1186/s13007-019-0525-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/12/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Large insert paired-end sequencing technologies are important tools for assembling genomes, delineating associated breakpoints and detecting structural rearrangements. To facilitate the comprehensive detection of inter- and intra-chromosomal structural rearrangements or variants (SVs) and complex genome assembly with long repeats and segmental duplications, we developed a new method based on single-molecule real-time synthesis sequencing technology for generating long paired-end sequences of large insert DNA libraries. RESULTS A Fosmid vector, pHZAUFOS3, was developed with the following new features: (1) two 18-bp non-palindromic I-SceI sites flank the cloning site, and another two sites are present in the skeleton of the vector, allowing long DNA inserts (and the long paired-ends in this paper) to be recovered as single fragments and the vector (~ 8 kb) to be fragmented into 2-3 kb fragments by I-SceI digestion and therefore was effectively removed from the long paired-ends (5-10 kb); (2) the chloramphenicol (Cm) resistance gene and replicon (oriV), necessary for colony growth, are located near the two sides of the cloning site, helping to increase the proportion of the paired-end fragments to single-end fragments in the paired-end libraries. Paired-end libraries were constructed by ligating the size-selected, mechanically sheared pooled Fosmid DNA fragments to the Ampicillin (Amp) resistance gene fragment and screening the colonies with Cm and Amp. We tested this method on yeast and Setaria italica Yugu1. Fosmid-size paired-ends with an average length longer than 2 kb for each end were generated. The N50 scaffold lengths of the de novo assemblies of the yeast and S. italica Yugu1 genomes were significantly improved. Five large and five small structural rearrangements or assembly errors spanning tens of bp to tens of kb were identified in S. italica Yugu1 including deletions, inversions, duplications and translocations. CONCLUSIONS We developed a new method for long paired-end sequencing of large insert libraries, which can efficiently improve the quality of de novo genome assembly and identify large and small structural rearrangements or assembly errors.
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Affiliation(s)
- Zhaozhao Dai
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Tong Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jiadong Li
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Zhifei Han
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yonglong Pan
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10081 China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 10081 China
| | - Meizhong Luo
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
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SiMYB3 in Foxtail Millet ( Setaria italica) Confers Tolerance to Low-Nitrogen Stress by Regulating Root Growth in Transgenic Plants. Int J Mol Sci 2019; 20:ijms20225741. [PMID: 31731735 PMCID: PMC6888739 DOI: 10.3390/ijms20225741] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/03/2019] [Accepted: 11/13/2019] [Indexed: 12/20/2022] Open
Abstract
Foxtail millet (Setaria italica), which originated in China, has a strong tolerance to low nutrition stresses. However, the mechanism of foxtail millet tolerance to low-nitrogen stress is still unknown. In this study, the transcriptome of foxtail millet under low-nitrogen stress was systematically analyzed. Expression of 1891 genes was altered, including 1318 up-regulated genes and 573 down-regulated genes. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis revealed that 3% of these genes were involved in membrane transport and 5% were involved in redox processes. There were 74 total transcription factor (TF) genes in the DEGs (differentially expressed genes), and MYB-like transcription factors accounted for one-third (25) of the TF genes. We systematically analyzed the characteristics, expression patterns, chromosome locations, and protein structures of 25 MYB-like genes. The analysis of gene function showed that Arabidopsis and rice overexpressing SiMYB3 had better root development than WT under low-nitrogen stress. Moreover, EMSA results showed that SiMYB3 protein could specifically bind MYB elements in the promoter region of TAR2, an auxin synthesis related gene and MYB3-TAR2 regulate pair conserved in rice and foxtail millet. These results suggested that SiMYB3 can regulate root development by regulating plant root auxin synthesis under low-nitrogen conditions.
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Zhao J, Yu A, Du Y, Wang G, Li Y, Zhao G, Wang X, Zhang W, Cheng K, Liu X, Wang Z, Wang Y. Foxtail millet (Setaria italica (L.) P. Beauv) CIPKs are responsive to ABA and abiotic stresses. PLoS One 2019; 14:e0225091. [PMID: 31714948 PMCID: PMC6850536 DOI: 10.1371/journal.pone.0225091] [Citation(s) in RCA: 8] [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: 01/17/2019] [Accepted: 10/29/2019] [Indexed: 11/18/2022] Open
Abstract
CBL-interacting protein kinases (CIPKs) have been shown to regulate a variety of environmental stress-related signalling pathways in plants. Foxtail millet (Setaria italica (L.) P. Beauv) is known worldwide as a relatively stress-tolerant C4 crop species. Although the foxtail millet genome sequence has been released, little is known about the functions of CIPKs in foxtail millet. Therefore, a systematic genome-wide analysis of CIPK genes in foxtail millet was performed. In total, 35 CIPK members were identified in foxtail millet and divided into four subgroups (I to IV) on the basis of their phylogenetic relationships. Phylogenetic and gene structure analyses clearly divided all SiCIPKs into intron-poor and intron-rich clades. Cis-element analysis subsequently indicated that these SiCIPKs may be involved in responses to abiotic stimuli, hormones, and light signalling during plant growth and development, and stress-induced expression profile analysis revealed that all the SiCIPKs are involved in various stress signalling pathways. These results suggest that the CIPK genes in foxtail millet exhibit the basic characteristics of CIPK family members and play important roles in response to abiotic stresses. The results of this study will contribute to future functional characterization of abiotic stress responses mediated by CIPKs in foxtail millet.
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Affiliation(s)
- Jinfeng Zhao
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, People's Republic of China
- * E-mail: (AY); (JZ)
| | - Aili Yu
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, People's Republic of China
- * E-mail: (AY); (JZ)
| | - Yanwei Du
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, People's Republic of China
| | - Gaohong Wang
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, People's Republic of China
| | - Yanfang Li
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, People's Republic of China
| | - Genyou Zhao
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, People's Republic of China
| | - Xiangdong Wang
- Tangshan Academy of Agricultural Sciences, Tangshan, Hebei, People's Republic of China
| | - Wenzhong Zhang
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, People's Republic of China
| | - Kai Cheng
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, People's Republic of China
| | - Xin Liu
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, People's Republic of China
| | - Zhenhua Wang
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, People's Republic of China
| | - Yuwen Wang
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Shanxi Key Laboratory of Genetic Resources and Breeding in Minor Crops, Changzhi, Shanxi, People's Republic of China
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Maharajan T, Ceasar SA, Krishna TPA, Ignacimuthu S. Phosphate supply influenced the growth, yield and expression of PHT1 family phosphate transporters in seven millets. PLANTA 2019; 250:1433-1448. [PMID: 31300887 DOI: 10.1007/s00425-019-03237-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 07/09/2019] [Indexed: 06/10/2023]
Abstract
Phosphate starvation altered the root morphology and phosphate uptake with the induction of PHT1 family transporter genes in root and shoot tissues of seven millets. Millets are nutrient-rich cereals majorly cultivated in Asia and Africa. Foxtail millet (FoxM), pearl millet (PeaM), finger millet (FinM), kodo millet (KodM), little millet (LitM), proso millet (ProM), and barnyard millet (BarM) were examined for the influence of external phosphorous (P) supply on phenotypic traits, P uptake, yield, and PHosphate Transporter1 (PHT1) family gene expression. Millet seedlings grown under low Pi condition (LPC) produced significantly lower mean values for all traits except for lateral root length (LRL) and lateral root number (LRN) which were increased under LPC. Under LPC, seed weight (SW) also reduced by > 75% and had significantly lower levels of total P (TP) and Pi contents in leaf and root tissues. Expression dynamics of 12 PHT1 family (PHT1;1-1;12) transporters genes were analyzed in 7 millets. PHT1;2 has been found to be a constitutive transporter gene in all millets. Under LPC, root tissues showed the overexpression of PHT1;2, 1;3, 1;4 and 1;9 in FoxM, PHT1;1, 1;2, 1;3, 1;4, 1;8 and 1;10 in PeaM, PHT1;2 and 1;3 in FinM and ProM and PHT1;3, 1;6 and 1;11 in BarM. In leaf, LPC induced the expression of PHT1;3, 1;4 and 1;6 in FoxM, PHT1;2, 1;3, 1;4 and 1;8 in PeaM, PHT1;2, 1;3 and 1;4 in FinM and KodM, PHT1;2 in LitM and PHT1;4 in ProM and BarnM. This comprehensive study on the influence of P in phenotype, physiology, and molecular responses may help to improve the P uptake and its use efficiency of millets in future.
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Affiliation(s)
- Theivanayagam Maharajan
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, 600034, India
| | - Stanislaus Antony Ceasar
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, 600034, India.
- Functional Genomics and Plant Molecular Imaging Lab, University of Liege, 4000, Liege, Belgium.
| | | | - Savarimuthu Ignacimuthu
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, 600034, India
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223
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Johnson M, Deshpande S, Vetriventhan M, Upadhyaya HD, Wallace JG. Genome-Wide Population Structure Analyses of Three Minor Millets: Kodo Millet, Little Millet, and Proso Millet. THE PLANT GENOME 2019; 12:1-9. [PMID: 33016596 DOI: 10.3835/plantgenome2019.03.0021] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 06/23/2019] [Indexed: 06/11/2023]
Abstract
Developed genome-wide SNP marker data for kodo, proso, and little millet Marker data used to analyze genetic diversity Heritability results of various traits used to validate genetic data Millets are a diverse group of small-seeded grains that are rich in nutrients but have received relatively little advanced plant breeding research. Millets are important to smallholder farmers in Africa and Asia because of their short growing season, good stress tolerance, and high nutritional content. To advance the study and use of these species, we present genome-wide marker datasets and population structure analyses for three minor millets: kodo millet (Paspalum scrobiculatum L.), little millet (Panicum sumatrense Roth), and proso millet (Panicum miliaceum L.).We generated genome-wide marker data sets for 190 accessions of each species with genotyping-by-sequencing (GBS). After filtering, we retained between 161 and 165 accessions of each species, with 3461, 2245, and 1882 single-nucleotide polymorphisms (SNPs) for kodo, little, and proso millet, respectively. Population genetic analysis revealed seven putative subpopulations of kodo millet and eight each of proso millet and little millet. To confirm the accuracy of this genetic data, we used public phenotype data on a subset of these accessions to estimate the heritability of various agronomically relevant phenotypes. Heritability values largely agree with the prior expectation for each phenotype, indicating that these SNPs provide an accurate genome-wide sample of genetic variation. These data represent one of first genome-wide population genetics analyses-and the most extensive-in these species and the first genomic analyses of any sort for little millet and kodo millet. These data will be a valuable resource for researchers and breeders trying to improve these crops for smallholder farmers.
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Affiliation(s)
- Matthew Johnson
- Johnson Institute of Plant Breeding, Genetics, and Genomics, Univ. of Georgia, 111 Riverbend Rd. Athens, GA
| | - Santosh Deshpande
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, Telangana, India
| | - Mani Vetriventhan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, Telangana, India
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502324, Telangana, India
| | - Jason G Wallace
- Johnson Institute of Plant Breeding, Genetics, and Genomics, Univ. of Georgia, 111 Riverbend Rd. Athens, GA
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224
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Matias FI, Xavier Meireles KG, Nagamatsu ST, Lima Barrios SC, Borges do Valle C, Carazzolle MF, Fritsche-Neto R, Endelman JB. Expected Genotype Quality and Diploidized Marker Data from Genotyping-by-Sequencing of Urochloa spp. Tetraploids. THE PLANT GENOME 2019; 12:1-9. [PMID: 33016594 DOI: 10.3835/plantgenome2019.01.0002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/29/2019] [Indexed: 05/08/2023]
Abstract
Introduced concept of expected genotype quality (EGQ) and software to calculate it Provided read depth guidelines for GBS in tetraploids Developed software to generate diploidized genotype calls from VCF files Demonstrated value of aligning GBS reads to a mock reference genome for SNP discovery Recommend filtering based on GQ and read depth to prevent genotype bias Although genotyping-by-sequencing (GBS) is a well-established marker technology in diploids, the development of best practices for tetraploid species is a topic of current research. We determined the theoretical relationship between read depth and the phred-scaled probability of genotype misclassification conditioned on the true genotype, which we call expected genotype quality (EGQ). If the GBS method has 0.5% allelic error, then 17 reads are needed to classify simplex tetraploids as heterozygous with 95% accuracy (EGQ = 13) vs. 61 reads to determine allele dosage. We developed an R script to convert tetraploid GBS data in variant call format (VCF) into diploidized genotype calls and applied it to 267 interspecific hybrids of the tetraploid forage grass Urochloa. When reads were aligned to a mock reference genome created from GBS data of the Urochloa brizantha (Hochst. ex A. Rich.) R. D. Webster cultivar Marandu, 25,678 biallelic single nucleotide polymorphism (SNPs) were discovered, compared with ∼3000 SNPs when aligning to the closest true reference genomes, Setaria viridis (L.) P. Beauv. and S. italica (L.) P. Beauv. Cross-validation revealed that missing genotypes were imputed by the random forest method with a median accuracy of 0.85 regardless of heterozygote frequency. Using the Urochloa spp. hybrids, we illustrated how filtering samples based only on genotype quality (GQ) creates genotype bias; a depth threshold based on EGQ is also needed regardless of whether genotypes are called using a diploidized or allele dosage model.
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Affiliation(s)
- Filipe Inácio Matias
- Genetics Dep., Luiz de Queiroz College of Agriculture, Univ. of São Paulo, Av. Pádua Dias, 11, C. P. 9, 13.418-900, Piracicaba, São Paulo, Brazil
| | | | - Sheila Tiemi Nagamatsu
- Genetics and Evolution Dep., Univ. of Campinas, Cidade Univ. Zeferino Vaz, 13.083-970, Campinas, São Paulo, Brazil
| | | | - Cacilda Borges do Valle
- Embrapa Beef Cattle, Av. Rádio Maia, 830, Zona Rural, 79.106-550, Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Roberto Fritsche-Neto
- Genetics Dep., Luiz de Queiroz College of Agriculture, Univ. of São Paulo, Av. Pádua Dias, 11, C. P. 9, 13.418-900, Piracicaba, São Paulo, Brazil
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225
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Benjelloun B, Boyer F, Streeter I, Zamani W, Engelen S, Alberti A, Alberto FJ, BenBati M, Ibnelbachyr M, Chentouf M, Bechchari A, Rezaei HR, Naderi S, Stella A, Chikhi A, Clarke L, Kijas J, Flicek P, Taberlet P, Pompanon F. An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity. Mol Ecol Resour 2019; 19:1497-1515. [PMID: 31359622 PMCID: PMC7115901 DOI: 10.1111/1755-0998.13070] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 06/30/2019] [Accepted: 07/08/2019] [Indexed: 12/12/2022]
Abstract
Whole genome sequences (WGS) greatly increase our ability to precisely infer population genetic parameters, demographic processes, and selection signatures. However, WGS may still be not affordable for a representative number of individuals/populations. In this context, our goal was to assess the efficiency of several SNP genotyping strategies by testing their ability to accurately estimate parameters describing neutral diversity and to detect signatures of selection. We analysed 110 WGS at 12× coverage for four different species, i.e., sheep, goats and their wild counterparts. From these data we generated 946 data sets corresponding to random panels of 1K to 5M variants, commercial SNP chips and exome capture, for sample sizes of five to 48 individuals. We also extracted low-coverage genome resequencing of 1×, 2× and 5× by randomly subsampling reads from the 12× resequencing data. Globally, 5K to 10K random variants were enough for an accurate estimation of genome diversity. Conversely, commercial panels and exome capture displayed strong ascertainment biases. Besides the characterization of neutral diversity, the detection of the signature of selection and the accurate estimation of linkage disequilibrium (LD) required high-density panels of at least 1M variants. Finally, genotype likelihoods increased the quality of variant calling from low coverage resequencing but proportions of incorrect genotypes remained substantial, especially for heterozygote sites. Whole genome resequencing coverage of at least 5× appeared to be necessary for accurate assessment of genomic variations. These results have implications for studies seeking to deploy low-density SNP collections or genome scans across genetically diverse populations/species showing similar genetic characteristics and patterns of LD decay for a wide variety of purposes.
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Affiliation(s)
- Badr Benjelloun
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
- National Institute of Agronomic Research (INRA Maroc), Regional Centre of Agronomic Research, 23000 Beni-Mellal, Morocco
| | - Frédéric Boyer
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - Ian Streeter
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Wahid Zamani
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
- Department of Environmental Sciences, Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, 46417-76489 Noor, Mazandaran, Iran
| | - Stefan Engelen
- CEA - Institut de biologie François-Jacob, Genoscope, 2 Rue Gaston Cremieux 91057 Evry Cedex, France
| | - Adriana Alberti
- CEA - Institut de biologie François-Jacob, Genoscope, 2 Rue Gaston Cremieux 91057 Evry Cedex, France
| | - Florian J. Alberto
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - Mohamed BenBati
- National Institute of Agronomic Research (INRA Maroc), Regional Centre of Agronomic Research, 23000 Beni-Mellal, Morocco
| | - Mustapha Ibnelbachyr
- National Institute of Agronomic Research (INRA Maroc), CRRA Errachidia, 52000 Errachidia, Morocco
| | - Mouad Chentouf
- National Institute of Agronomic Research (INRA Maroc), CRRA Tangier, 90010 Tangier, Morocco
| | - Abdelmajid Bechchari
- National Institute of Agronomic Research (INRA Maroc), CRRA Oujda, 60000 Oujda, Morocco
| | - Hamid R. Rezaei
- Department of Environmental Sci, Gorgan University of Agricultural Sciences & Natural Resources, 41996-13776 Gorgan, Iran
| | - Saeid Naderi
- Environmental Sciences Department, Natural Resources Faculty, University of Guilan, 49138-15749 Guilan, Iran
| | - Alessandra Stella
- PTP Science Park, Bioinformatics Unit, Via Einstein-Loc. Cascina Codazza, 26900 Lodi, Italy
| | - Abdelkader Chikhi
- National Institute of Agronomic Research (INRA Maroc), CRRA Errachidia, 52000 Errachidia, Morocco
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - James Kijas
- Commonwealth Scientific and Industrial Research Organisation Animal Food and Health Sciences, St Lucia, QLD 4067, Australia
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Pierre Taberlet
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - François Pompanon
- Univ. Grenoble-Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
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226
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Ruan JJ, Weng WF, Yan J, Zhou YX, Chen H, Ren MJ, Cheng JP. Coix lacryma-jobi chymotrypsin inhibitor displays antifungal activity. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2019; 160:49-57. [PMID: 31519257 DOI: 10.1016/j.pestbp.2019.06.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 06/24/2019] [Accepted: 06/26/2019] [Indexed: 06/10/2023]
Abstract
A novel chymotrypsin inhibitor, named ClCI, was purified from coix seed (Coix lacryma-jobi L.) by aqueous two-phase extraction, chymotrypsin-Sepharose 4B affinity chromatography and centrifugal ultrafiltration. ClCI was a 7.9 kDa competitive inhibitor with pI 6.54. The inhibition constants (Ki) for bovine pancreatic chymotrypsin and bacterial subtilisin were 1.27 × 10-10 M and 1.57 × 10-9 M respectively. ClCI had no inhibitory activity against bovine trypsin and porcine elastase. ClCI had wide pH stability and good heat resistance. It can maintain >90% inhibition activity against chymotrypsin at 20-80 °C for 1 h. The primary structure of ClCI was highly similar (57%-92%) to those of several inhibitors belonging to the Gramineae crop potato protease inhibitor- I superfamily and showed the typical sequence motif of the protease inhibitor of the seed storage protein group. ClCI (12.5 mg) inhibited mycelial growth of the phytopathogenic fungi Mycosphaerella melonis, Helminthosporium turcicum, Alternaria solani, Phytophthora capsici, Isariopsis griseola, and Colletotrichum gloeosporioides, and caused 89% inhibition of the proteases from spore germination of plant-pathogenic fungi. The results of the present study indicate that ClCI had biotechnological potential as an alternative agent to combat the important phytopathogenic fungi.
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Affiliation(s)
- Jing-Jun Ruan
- College of Agricultural Sciences, Guizhou University, Guiyang 550025, Guizhou, China
| | - Wen-Feng Weng
- College of Agricultural Sciences, Guizhou University, Guiyang 550025, Guizhou, China
| | - Jun Yan
- School of Pharmacy and Bioengineering, Chengdu University, Chengdu, Sichuan 610106, China
| | - Yue-Xia Zhou
- College of Agricultural Sciences, Guizhou University, Guiyang 550025, Guizhou, China
| | - Hui Chen
- College of Life Sciences, Sichuan Agricultural University, Yaan 625014, Sichuan, China
| | - Ming-Jian Ren
- College of Agricultural Sciences, Guizhou University, Guiyang 550025, Guizhou, China
| | - Jian-Ping Cheng
- College of Agricultural Sciences, Guizhou University, Guiyang 550025, Guizhou, China.
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227
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Yan L, Kenchanmane Raju SK, Lai X, Zhang Y, Dai X, Rodriguez O, Mahboub S, Roston RL, Schnable JC. Parallels between natural selection in the cold-adapted crop-wild relative Tripsacum dactyloides and artificial selection in temperate adapted maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:965-977. [PMID: 31069858 DOI: 10.1111/tpj.14376] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/25/2019] [Accepted: 04/01/2019] [Indexed: 06/09/2023]
Abstract
Artificial selection has produced varieties of domesticated maize that thrive in temperate climates around the world. However, the direct progenitor of maize, teosinte, is indigenous only to a relatively small range of tropical and subtropical latitudes and grows poorly or not at all outside of this region. Tripsacum, a sister genus to maize and teosinte, is naturally endemic to the majority of areas in the western hemisphere where maize is cultivated. A full-length reference transcriptome for Tripsacum dactyloides generated using long-read Iso-Seq data was used to characterize independent adaptation to temperate climates in this clade. Genes related to phospholipid biosynthesis, a critical component of cold acclimation in other cold-adapted plant lineages, were enriched among those genes experiencing more rapid rates of protein sequence evolution in T. dactyloides. In contrast with previous studies of parallel selection, we find that there is a significant overlap between the genes that were targets of artificial selection during the adaptation of maize to temperate climates and those that were targets of natural selection in temperate-adapted T. dactyloides. Genes related to growth, development, response to stimulus, signaling, and organelles were enriched in the set of genes identified as both targets of natural and artificial selection.
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Affiliation(s)
- Lang Yan
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Laboratory of Functional Genome and Application of Potato, Xichang University, Liangshan, 615000, China
- College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | | | - Xianjun Lai
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Laboratory of Functional Genome and Application of Potato, Xichang University, Liangshan, 615000, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Zhang
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Xiuru Dai
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Oscar Rodriguez
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, 68588, NE, USA
| | - Samira Mahboub
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Rebecca L Roston
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - James C Schnable
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, 68588, NE, USA
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228
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Seymour DK, Gaut BS. Phylogenetic Shifts in Gene Body Methylation Correlate with Gene Expression and Reflect Trait Conservation. Mol Biol Evol 2019; 37:31-43. [DOI: 10.1093/molbev/msz195] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Abstract
A subset of genes in plant genomes are labeled with DNA methylation specifically at CG residues. These genes, known as gene-body methylated (gbM), have a number of associated characteristics. They tend to have longer sequences, to be enriched for intermediate expression levels, and to be associated with slower rates of molecular evolution. Most importantly, gbM genes tend to maintain their level of DNA methylation between species, suggesting that this trait is under evolutionary constraint. Given the degree of conservation in gbM, we still know surprisingly little about its function in plant genomes or whether gbM is itself a target of selection. To address these questions, we surveyed DNA methylation across eight grass (Poaceae) species that span a gradient of genome sizes. We first established that genome size correlates with genome-wide DNA methylation levels, but less so for genic levels. We then leveraged genomic data to identify a set of 2,982 putative orthologs among the eight species and examined shifts of methylation status for each ortholog in a phylogenetic context. A total of 55% of orthologs exhibited a shift in gbM, but these shifts occurred predominantly on terminal branches, indicating that shifts in gbM are rarely conveyed over time. Finally, we found that the degree of conservation of gbM across species is associated with increased gene length, reduced rates of molecular evolution, and increased gene expression level, but reduced gene expression variation across species. Overall, these observations suggest a basis for evolutionary pressure to maintain gbM status over evolutionary time.
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Affiliation(s)
- Danelle K Seymour
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA
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229
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de C Lara LA, Santos MF, Jank L, Chiari L, Vilela MDM, Amadeu RR, Dos Santos JPR, Pereira GDS, Zeng ZB, Garcia AAF. Genomic Selection with Allele Dosage in Panicum maximum Jacq. G3 (BETHESDA, MD.) 2019; 9:2463-2475. [PMID: 31171567 PMCID: PMC6686918 DOI: 10.1534/g3.118.200986] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/23/2019] [Indexed: 12/21/2022]
Abstract
Genomic selection is an efficient approach to get shorter breeding cycles in recurrent selection programs and greater genetic gains with selection of superior individuals. Despite advances in genotyping techniques, genetic studies for polyploid species have been limited to a rough approximation of studies in diploid species. The major challenge is to distinguish the different types of heterozygotes present in polyploid populations. In this work, we evaluated different genomic prediction models applied to a recurrent selection population of 530 genotypes of Panicum maximum, an autotetraploid forage grass. We also investigated the effect of the allele dosage in the prediction, i.e., considering tetraploid (GS-TD) or diploid (GS-DD) allele dosage. A longitudinal linear mixed model was fitted for each one of the six phenotypic traits, considering different covariance matrices for genetic and residual effects. A total of 41,424 genotyping-by-sequencing markers were obtained using 96-plex and Pst1 restriction enzyme, and quantitative genotype calling was performed. Six predictive models were generalized to tetraploid species and predictive ability was estimated by a replicated fivefold cross-validation process. GS-TD and GS-DD models were performed considering 1,223 informative markers. Overall, GS-TD data yielded higher predictive abilities than with GS-DD data. However, different predictive models had similar predictive ability performance. In this work, we provide bioinformatic and modeling guidelines to consider tetraploid dosage and observed that genomic selection may lead to additional gains in recurrent selection program of P. maximum.
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Affiliation(s)
- Letícia A de C Lara
- Luiz de Queiroz College of Agriculture / University of São Paulo (ESALQ/USP), Piracicaba, SP, Brazil
| | | | - Liana Jank
- Embrapa Beef Cattle, Campo Grande, MS, Brazil, and
| | | | | | - Rodrigo R Amadeu
- Luiz de Queiroz College of Agriculture / University of São Paulo (ESALQ/USP), Piracicaba, SP, Brazil
| | - Jhonathan P R Dos Santos
- Luiz de Queiroz College of Agriculture / University of São Paulo (ESALQ/USP), Piracicaba, SP, Brazil
| | | | | | - Antonio Augusto F Garcia
- Luiz de Queiroz College of Agriculture / University of São Paulo (ESALQ/USP), Piracicaba, SP, Brazil
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Shameer K, Naika MB, Shafi KM, Sowdhamini R. Decoding systems biology of plant stress for sustainable agriculture development and optimized food production. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 145:19-39. [DOI: 10.1016/j.pbiomolbio.2018.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 10/23/2018] [Accepted: 12/06/2018] [Indexed: 12/13/2022]
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231
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Li P, Li B, Seneweera S, Zong Y, Li FY, Han Y, Hao X. Photosynthesis and yield response to elevated CO 2, C 4 plant foxtail millet behaves similarly to C 3 species. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 285:239-247. [PMID: 31203889 DOI: 10.1016/j.plantsci.2019.05.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/28/2019] [Accepted: 05/08/2019] [Indexed: 05/14/2023]
Abstract
Foxtail millet (Setaria italica) is a nutrient-rich food source traditionally grown in arid and semi-arid areas, as it is well adapted to drought climate. Yet there is limited information as how the crop responses to the changing climate. In order to investigate the response of foxtail millet to elevated [CO2] and the underlying mechanism, the crop was grown at ambient [CO2] (400 μmol mol-1) and elevated [CO2] (600 μmol mol-1) in an open-top chamber (OTC) experimental facility in North China. The changes in leaf photosynthesis, chlorophyll fluorescence, biomass, yield and global gene expression in response to elevated [CO2] were determined. Despite foxtail millet being a C4 photosynthetic crop, photosynthetic rates (PN) and intrinsic water-use efficiency (WUEi), were increased under elevated [CO2]. Similarly, grain yield and above-ground biomass also significantly increased (P < 0.05) for the two years of experimentation under elevated [CO2]. Increases in seeds and tiller number, spike and stem weight were the main contributors to the increased grain yield and biomass. Using transcriptomic analyses, this study further identified some genes which play a role in cell wall reinforcement, shoot initiation, stomatal conductance, carbon fixation, glycolysis / gluconeogenesis responsive to elevated [CO2]. Changes in these genes reduced plant height, increased stem diameters, and promote CO2 fixation. Higher photosynthetic rates at elevated [CO2] demonstrated that foxtail millet was not photosynthetically saturated at elevated [CO2] and its photosynthesis response to elevated [CO2] were analogous to C3 plants.
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Affiliation(s)
- Ping Li
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China; Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Taigu 030801, Shanxi, China
| | - Bingyan Li
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Saman Seneweera
- National Institute of Fundamental Studies, Kandy 20000, Sri Lanka
| | - Yuzheng Zong
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China
| | - Frank Yonghong Li
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China; Ecology, College of Life Sciences, Inner Mongolia University, Huhehot 010021, China
| | - Yuanhuai Han
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China; Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Taigu 030801, Shanxi, China; Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Taiyuan 030031, Shanxi, China
| | - Xingyu Hao
- College of Agriculture, Shanxi Agricultural University, Taigu 030801, China.
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Zhang Y, Guo M, Shen J, Song X, Dong S, Wen Y, Yuan X, Guo P. Comparative Genomics Analysis in Grass Species Reveals Two Distinct Evolutionary Strategies Adopted by R Genes. Sci Rep 2019; 9:10735. [PMID: 31341223 PMCID: PMC6656885 DOI: 10.1038/s41598-019-47121-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 07/05/2019] [Indexed: 12/04/2022] Open
Abstract
Resistance genes play an important role in the defense of plants against the invasion of pathogens. In Setaria italica and closely related grass species, R genes have been identified through genetic mapping and genome-wide homologous/domain searching. However, there has been to date no systematic analysis of the evolutionary features of R genes across all sequenced grass genomes. Here, we determined and comprehensively compared R genes in all 12 assembled grass genomes and an outgroup species (Arabidopsis thaliana) through synteny and selection analyses of multiple genomes. We found that the two groups of nucleotide binding site (NBS) domains containing R genes—R tandem duplications (TD) and R singletons—adopted different strategies and showed different features in their evolution. Based on Ka/Ks analysis between syntenic R loci pairs of TDs or singletons, we conclude that R singletons are under stronger purifying selection to be conserved among different grass species than R TDs, while R genes located at TD arrays have evolved much faster through diversifying selection. Furthermore, using the variome datasets of S. italica populations, we scanned for selection signals on genes and observed that a part of R singleton genes have been under purifying selection in populations of S. italica, which is consistent with the pattern observed in syntenic R singletons among different grass species. Additionally, we checked the synteny relationships of reported R genes in grass species and found that the functionally mapped R genes for novel resistance traits are prone to appear in TDs and are heavily divergent from their syntenic orthologs in other grass species, such the black streak R gene Rxo1 in Z. mays and the blast R gene Pi37 in O. sativa. These findings indicate that the R genes from TDs adopted tandem duplications to evolve faster and accumulate more mutations to facilitate functional innovation to cope with variable threats from a fluctuating environment, while R singletons provide a way for R genes to maintain sequence stability and retain conservation of function.
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Affiliation(s)
- Yinan Zhang
- Agronomy College, Shanxi Agricultural University, Taigu, 030801, China
| | - Meijun Guo
- Agronomy College, Shanxi Agricultural University, Taigu, 030801, China
| | - Jie Shen
- Agronomy College, Shanxi Agricultural University, Taigu, 030801, China
| | - Xie Song
- Agronomy College, Shanxi Agricultural University, Taigu, 030801, China
| | - Shuqi Dong
- Agronomy College, Shanxi Agricultural University, Taigu, 030801, China
| | - Yinyuan Wen
- Agronomy College, Shanxi Agricultural University, Taigu, 030801, China
| | - Xiangyang Yuan
- Agronomy College, Shanxi Agricultural University, Taigu, 030801, China
| | - Pingyi Guo
- Agronomy College, Shanxi Agricultural University, Taigu, 030801, China.
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233
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Liu D, Li J, Lu J, Tian B, Liu X, Yang G, Pei Y. Cloning and functional analysis of four O-Acetylserine (thiol) lyase family genes from foxtail millet. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 139:325-332. [PMID: 30947063 DOI: 10.1016/j.plaphy.2019.03.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 03/20/2019] [Indexed: 06/09/2023]
Abstract
Cysteine is the first organic molecule generated during the assimilation of sulfate. As such, cysteine and its derivatives are always essential signal molecules and thus have important roles in the regulation of many plant processes. O-acetylserine (thiol) lyase (OASTL) catalyzes the last step of the biosynthesis of cysteine. At present, detailed and comprehensive work about these enzymes has only been reported from the plant Arabidopsis thaliana, though sporadic studies on OASTL have been conducted on other dicots, such as spinach and soybean. However, few reports on the functions of OASTLs in monocots have been found in the literature. Here in this study, we obtained four SiOASTL genes (SiOASTL7, SiOASTL8, SiOASTL9 and SiOASTL10) from foxtail millet and analyzed their potential functions. Phylogenetically, the four SiOASTL genes did not belong to any published subfamily of the OASTL genes; instead they constituted a new subfamily specific to the OASTL genes from monocots. In sequencing, we found that with the exception of the pseudogene SiOASTL8, proteins encoded by the other three genes exhibited high similarity with OASTL proteins from Arabidopsis, though the critical PLP-binding sites of both SiOASTL7 and SiOASTL10 were missing. The enzymatic activity assays demonstrated that SiOASTL9 has the ability to catalyze the biosynthesis of both cysteine and S-sulfocysteine, while SiOASTL7 and SiOASTL10 did not possess any previously reported catalyzing abilities. In addition, the gene expression pattern analysis showed that all four genes were widely expressed in various tissues of foxtail millet, and all had a preference in the leaves. Under abiotic stresses, the expression of these genes could be induced by salt and drought stress. Our finding that cadmium could only up-regulate the transcription of SlOASTL8 and SlOASTL9, further indicates the diversified responses of SiOASTLs to abiotic stresses.
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Affiliation(s)
- Danmei Liu
- College of Life Science, Shanxi University, Taiyuan, 030006, China; Shanxi Key Laboratory for Research and Development of Regional Plants, Taiyuan, 030006, China
| | - Juan Li
- College of Life Science, Shanxi University, Taiyuan, 030006, China; Shanxi Key Laboratory for Research and Development of Regional Plants, Taiyuan, 030006, China
| | - Juanjuan Lu
- College of Life Science, Shanxi University, Taiyuan, 030006, China; Shanxi Key Laboratory for Research and Development of Regional Plants, Taiyuan, 030006, China
| | - Baohua Tian
- Taiyuan University of Technology, Taiyuan, 030024, China
| | - Xin Liu
- Key Lab of Plant Biotechnology in Universities of Shandong Province, College of Life Science, Qingdao Agricultural University, Qingdao, 266109, China
| | - Guangdong Yang
- Department of Chemistry and Biochemistry, Laurentian University, Canada
| | - Yanxi Pei
- College of Life Science, Shanxi University, Taiyuan, 030006, China; Shanxi Key Laboratory for Research and Development of Regional Plants, Taiyuan, 030006, China.
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234
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Zhang L, Zhou D, Hu H, Li W, Hu Y, Xie J, Huang S, Wang W. Genome-wide characterization of a SRO gene family involved in response to biotic and abiotic stresses in banana (Musa spp.). BMC PLANT BIOLOGY 2019; 19:211. [PMID: 31113386 PMCID: PMC6530135 DOI: 10.1186/s12870-019-1807-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/26/2019] [Indexed: 05/29/2023]
Abstract
BACKGROUND Banana (Musa spp.) is one of the world's most important fruits and its production is largely limited by diverse stress conditions. SROs (SIMILAR TO RCD-ONE) have important functions in abiotic stress resistance and development of plants. They contain a catalytic core of the poly(ADP-ribose) polymerase (PARP) domain and a C-terminal RST (RCD-SRO-TAF4) domain. In addition, partial SROs also include an N-terminal WWE domain. Although a few of SROs have been characterized in some model plants, little is known about their functions in banana, especially in response to biotic stress. RESULTS Six MaSRO genes in banana genome were identified using the PARP and RST models as a query. Phylogenetic analysis showed that 77 SROs from 15 species were divided into two structurally distinct groups. The SROs in the group I possessed three central regions of the WWE, PARP and RST domains. The WWE domain was lacking in the group II SROs. In the selected monocots, only MaSROs of banana were present in the group II. Most of MaSROs expressed in more than one banana tissue. The stress- and hormone-related cis-regulatory elements (CREs) in the promoter regions of MaSROs supported differential transcripts of MaSROs in banana roots treated with abiotic and biotic stresses. Moreover, expression profiles of MaSROs in the group I were clearly distinct with those observed in the group II after hormone treatment. Notably, the expression of MaSRO4 was significantly upregulated by the multiple stresses and hormones. The MaSRO4 protein could directly interact with MaNAC6 and MaMYB4, and the PARP domain was required for the protein-protein interaction. CONCLUSIONS Six MaSROs in banana genome were divided into two main groups based on the characteristics of conserved domains. Comprehensive expression analysis indicated that MaSROs had positive responses to biotic and abiotic stresses via a complex interaction network with hormones. MaSRO4 could interact directly with MaNAC6 and MaMYB4 through the PARP domain to regulate downstream signaling pathway.
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Affiliation(s)
- Lu Zhang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006 China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101 China
| | - Dengbo Zhou
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101 China
| | - Huigang Hu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of China Southern Subtropical Crop Research, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091 China
| | - Weiming Li
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of China Southern Subtropical Crop Research, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091 China
| | - Yulin Hu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of China Southern Subtropical Crop Research, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091 China
| | - Jianghui Xie
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101 China
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of China Southern Subtropical Crop Research, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, 524091 China
| | - Shangzhi Huang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006 China
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275 Guangdong China
| | - Wei Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101 China
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235
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Suguiyama VF, Vasconcelos LAB, Rossi MM, Biondo C, de Setta N. The population genetic structure approach adds new insights into the evolution of plant LTR retrotransposon lineages. PLoS One 2019; 14:e0214542. [PMID: 31107873 PMCID: PMC6527191 DOI: 10.1371/journal.pone.0214542] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/14/2019] [Indexed: 12/30/2022] Open
Abstract
Long terminal repeat retrotransposons (LTR-RTs) in plant genomes differ in abundance, structure and genomic distribution, reflecting the large number of evolutionary lineages. Elements within lineages can be considered populations, in which each element is an individual in its genomic environment. In this way, it would be reasonable to apply microevolutionary analyses to understand transposable element (TE) evolution, such as those used to study the genetic structure of natural populations. Here, we applied a Bayesian method to infer genetic structure of populations together with classical phylogenetic and dating tools to analyze LTR-RT evolution using the monocot Setaria italica as a model species. In contrast to a phylogeny, the Bayesian clusterization method identifies populations by assigning individuals to one or more clusters according to the most probabilistic scenario of admixture, based on genetic diversity patterns. In this work, each LTR-RT insertion was considered to be one individual and each LTR-RT lineage was considered to be a single species. Nine evolutionary lineages of LTR-RTs were identified in the S. italica genome that had different genetic structures with variable numbers of clusters and levels of admixture. Comprehensive analysis of the phylogenetic, clusterization and time of insertion data allowed us to hypothesize that admixed elements represent sequences that harbor ancestral polymorphic sequence signatures. In conclusion, application of microevolutionary concepts in genome evolution studies is suitable as a complementary approach to phylogenetic analyses to address the evolutionary history and functional features of TEs.
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Affiliation(s)
- Vanessa Fuentes Suguiyama
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil
| | | | - Maria Magdalena Rossi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Cibele Biondo
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil
| | - Nathalia de Setta
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil
- * E-mail:
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236
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Kong W, Gong Z, Zhong H, Zhang Y, Zhao G, Gautam M, Deng X, Liu C, Zhang C, Li Y. Expansion and Evolutionary Patterns of Glycosyltransferase Family 8 in Gramineae Crop Genomes and Their Expression under Salt and Cold Stresses in Oryza sativa ssp. japonica. Biomolecules 2019; 9:E188. [PMID: 31096659 PMCID: PMC6571792 DOI: 10.3390/biom9050188] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/13/2019] [Accepted: 05/14/2019] [Indexed: 12/13/2022] Open
Abstract
Plant cell walls play a fundamental role in several ways, providing structural support for cells, resistance against pathogens and facilitating the communication between cells. The glycosyltransferase family 8 (GT8) is involved in the formation of the plant cell wall. However, the evolutionary relationship and the functional differentiation of this important gene family remain obscure in Gramineae crop genomes. In the present investigation, we identified 269 GT8 genes in the seven Gramineae representative crop genomes, namely, 33 in Hordeum vulgare, 37 in Brachypodium distachyon, 40 in Oryza sativa ssp. japonica, 41 in Oryza rufipogon, 36 in Setaria italica, 37 in Sorghum bicolor, and 45 in Zea mays. Phylogenetic analysis suggested that all identified GT8 proteins belonged to seven subfamilies: galacturonosyltransferase (GAUT), galacturonosyltransferase-like (GATL), GATL-related (GATR), galactinol synthase (GolS), and plant glycogenin-like starch initiation proteins A (PGSIP-A), PGSIP-B, and PGSIP-C. We estimated that the GAUT subfamily might be further divided into four subgroups (I-IV) due to differentiation of gene structures and expression patterns. Our orthogroup analysis identified 22 orthogroups with different sizes. Of these orthogroups, several orthogroups were lost in some species, such as S. italica and Z. mays. Moreover, lots of duplicate pairs and collinear pairs were discovered among these species. These results indicated that multiple duplication modes led to the expansion of this important gene family and unequal loss of orthogroups and subfamilies might have happened during the evolutionary process. RNA-seq, microarray analysis, and qRT-PCR analyses indicated that GT8 genes are critical for plant growth and development, and for stresses responses. We found that OsGolS1 was significantly up-regulated under salt stress, while OsGAUT21, OsGATL2, and OsGATL5 had remarkable up-regulation under cold stress. The current study highlighted the expansion and evolutionary patterns of the GT8 gene family in these seven Gramineae crop genomes and provided potential candidate genes for future salt- and cold- resistant molecular breeding studies in O. sativa.
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Affiliation(s)
- Weilong Kong
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Ziyun Gong
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Hua Zhong
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Yue Zhang
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China. Yue.Zhang-@whu.edu.cn
| | - Gangqing Zhao
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Mayank Gautam
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Xiaoxiao Deng
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Chang Liu
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Chenhao Zhang
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Yangsheng Li
- State Key Laboratory for Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China.
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Muktar MS, Teshome A, Hanson J, Negawo AT, Habte E, Domelevo Entfellner JB, Lee KW, Jones CS. Genotyping by sequencing provides new insights into the diversity of Napier grass (Cenchrus purpureus) and reveals variation in genome-wide LD patterns between collections. Sci Rep 2019; 9:6936. [PMID: 31061417 PMCID: PMC6502793 DOI: 10.1038/s41598-019-43406-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 04/24/2019] [Indexed: 12/12/2022] Open
Abstract
Napier grass is an important tropical forage-grass and of growing potential as an energy crop. One-hundred-five Napier grass accessions, encompassing two independent collections, were subjected to genotyping by sequencing which generated a set of high-density genome-wide markers together with short sequence reads. The reads, averaging 54 nucleotides, were mapped to the pearl millet genome and the closest genes and annotation information were used to select candidate genes linked to key forage traits. 980 highly polymorphic SNP markers, distributed across the genome, were used to assess population structure and diversity with seven-subgroups identified. A few representative accessions were selected with the objective of distributing subsets of a manageable size for further evaluation. Genome-wide linkage disequilibrium (LD) analyses revealed a fast LD-decay, on average 2.54 kbp, in the combined population with a slower LD-decay in the ILRI collection compared with the EMBRAPA collection, the significance of which is discussed. This initiative generated high-density markers with a good distribution across the genome. The diversity analysis revealed the existence of a substantial amount of variation in the ILRI collection and identified some unique materials from the EMBRAPA collection, demonstrating the potential of the overall population for further genetic and marker-trait-association studies.
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Affiliation(s)
- Meki S Muktar
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Abel Teshome
- Teagasc
- CELUP Crop Research, Oak Park, Carlow, R93 XE12, Ireland
| | - Jean Hanson
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Alemayehu T Negawo
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Ermias Habte
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa, Ethiopia
| | | | - Ki-Won Lee
- Grassland and Forages Division, National Institute of Animal Science, Rural Development Administration, Cheonan, 31000, Republic of Korea
| | - Chris S Jones
- Feed and Forage Development, International Livestock Research Institute, Nairobi, Kenya.
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238
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Miao C, Yang J, Schnable JC. Optimising the identification of causal variants across varying genetic architectures in crops. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:893-905. [PMID: 30320953 PMCID: PMC6587547 DOI: 10.1111/pbi.13023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 09/28/2018] [Accepted: 10/10/2018] [Indexed: 05/11/2023]
Abstract
Association studies use statistical links between genetic markers and the phenotype variation across many individuals to identify genes controlling variation in the target phenotype. However, this approach, particularly conducted on a genome-wide scale (GWAS), has limited power to identify the genes responsible for variation in traits controlled by complex genetic architectures. In this study, we employ real-world genotype datasets from four crop species with distinct minor allele frequency distributions, population structures and linkage disequilibrium patterns. We demonstrate that different GWAS statistical approaches provide favourable trade-offs between power and accuracy for traits controlled by different types of genetic architectures. FarmCPU provides the most favourable outcomes for moderately complex traits while a Bayesian approach adopted from genomic prediction provides the most favourable outcomes for extremely complex traits. We assert that by estimating the complexity of genetic architectures for target traits and selecting an appropriate statistical approach for the degree of complexity detected, researchers can substantially improve the ability to dissect the genetic factors controlling complex traits such as flowering time, plant height and yield component.
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Affiliation(s)
- Chenyong Miao
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
- Center for Plant Science InnovationUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Jinliang Yang
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
- Center for Plant Science InnovationUniversity of Nebraska‐LincolnLincolnNEUSA
| | - James C. Schnable
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
- Center for Plant Science InnovationUniversity of Nebraska‐LincolnLincolnNEUSA
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Liu TY, Ye N, Song T, Cao Y, Gao B, Zhang D, Zhu F, Chen M, Zhang Y, Xu W, Zhang J. Rhizosheath formation and involvement in foxtail millet (Setaria italica) root growth under drought stress. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:449-462. [PMID: 30183129 DOI: 10.1111/jipb.12716] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/03/2018] [Indexed: 06/08/2023]
Abstract
The rhizosheath, a layer of soil particles that adheres firmly to the root surface by a combination of root hairs and mucilage, may improve tolerance to drought stress. Setaria italica (L.) P. Beauv. (foxtail millet), a member of the Poaceae family, is an important food and fodder crop in arid regions and forms a larger rhizosheath under drought conditions. Rhizosheath formation under drought conditions has been studied, but the regulation of root hair growth and rhizosheath size in response to soil moisture remains unclear. To address this question, in this study we monitored root hair growth and rhizosheath development in response to a gradual decline in soil moisture. Here, we determined that a soil moisture level of 10%-14% (w/w) stimulated greater rhizosheath production compared to other soil moisture levels. Root hair density and length also increased at this soil moisture level, which was validated by measurement of the expression of root hair-related genes. These findings contribute to our understanding of rhizosheath formation in response to soil water stress.
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Affiliation(s)
- Tie-Yuan Liu
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Nenghui Ye
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha 410128, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Tao Song
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Yunying Cao
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
- College of Life Sciences, Nantong University, Nantong 226019, China
| | - Bei Gao
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Di Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Fuyuan Zhu
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Moxian Chen
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
| | - Yingjiao Zhang
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weifeng Xu
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jianhua Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China
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Jaiswal V, Gupta S, Gahlaut V, Muthamilarasan M, Bandyopadhyay T, Ramchiary N, Prasad M. Genome-Wide Association Study of Major Agronomic Traits in Foxtail Millet (Setaria italica L.) Using ddRAD Sequencing. Sci Rep 2019; 9:5020. [PMID: 30903013 PMCID: PMC6430830 DOI: 10.1038/s41598-019-41602-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 03/05/2019] [Indexed: 12/17/2022] Open
Abstract
Foxtail millet (Setaria italica), the second largest cultivated millet crop after pearl millet, is utilized for food and forage globally. Further, it is also considered as a model crop for studying agronomic, nutritional and biofuel traits. In the present study, a genome-wide association study (GWAS) was performed for ten important agronomic traits in 142 foxtail millet core eco-geographically diverse genotypes using 10 K SNPs developed through GBS-ddRAD approach. Number of SNPs on individual chromosome ranged from 844 (chromosome 5) to 2153 (chromosome 8) with an average SNP frequency of 25.9 per Mb. The pairwise linkage disequilibrium (LD) estimated using the squared-allele frequency correlations was found to decay rapidly with the genetic distance of 177 Kb. However, for individual chromosome, LD decay distance ranged from 76 Kb (chromosome 6) to 357 Kb (chromosome 4). GWAS identified 81 MTAs (marker-trait associations) for ten traits across the genome. High confidence MTAs for three important agronomic traits including FLW (flag leaf width), GY (grain yield) and TGW (thousand-grain weight) were identified. Significant pyramiding effect of identified MTAs further supplemented its importance in breeding programs. Desirable alleles and superior genotypes identified in the present study may prove valuable for foxtail millet improvement through marker-assisted selection.
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Affiliation(s)
- Vandana Jaiswal
- School of Life Science, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sarika Gupta
- School of Life Science, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Vijay Gahlaut
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Mehanathan Muthamilarasan
- National Institute of Plant Genome Research, New Delhi, 110067, India
- ICAR-National Research Centre on Plant Biotechnology, LBS Centre, Pusa Campus, New Delhi, 110012, India
| | | | - Nirala Ramchiary
- School of Life Science, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi, 110067, India.
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Genome-Wide Analysis of LIM Family Genes in Foxtail Millet ( Setaria italica L.) and Characterization of the Role of SiWLIM2b in Drought Tolerance. Int J Mol Sci 2019; 20:ijms20061303. [PMID: 30875867 PMCID: PMC6470693 DOI: 10.3390/ijms20061303] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/10/2019] [Accepted: 03/11/2019] [Indexed: 12/12/2022] Open
Abstract
LIM proteins have been found to play important roles in many life activities, including the regulation of gene expression, construction of the cytoskeleton, signal transduction and metabolic regulation. Because of their important roles in many aspects of plant development, LIM genes have been studied in many plant species. However, the LIM gene family has not yet been characterized in foxtail millet. In this study, we analyzed the whole genome of foxtail millet and identified 10 LIM genes. All LIM gene promoters contain MYB and MYC cis-acting elements that are related to drought stress. Based on the presence of multiple abiotic stress-related cis-elements in the promoter of SiWLIM2b, we chose this gene for further study. We analyzed SiWLIM2b expression under abiotic stress and hormone treatments using qRT-PCR. We found that SiWLIM2b was induced by various abiotic stresses and hormones. Under drought conditions, transgenic rice of SiWLIM2b-overexpression had a higher survival rate, higher relative water content and less cell damage than wild type (WT) rice. These results indicate that overexpression of the foxtail millet SiWLIM2b gene enhances drought tolerance in transgenic rice, and the SiWLIM2b gene can potentially be used for molecular breeding of crops with increased resistance to abiotic stress.
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Duarte KE, de Souza WR, Santiago TR, Sampaio BL, Ribeiro AP, Cotta MG, da Cunha BADB, Marraccini PRR, Kobayashi AK, Molinari HBC. Identification and characterization of core abscisic acid (ABA) signaling components and their gene expression profile in response to abiotic stresses in Setaria viridis. Sci Rep 2019; 9:4028. [PMID: 30858491 PMCID: PMC6411973 DOI: 10.1038/s41598-019-40623-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 02/19/2019] [Indexed: 12/21/2022] Open
Abstract
Abscisic acid (ABA) is an essential phytohormone that regulates growth, development and adaptation of plants to environmental stresses. In Arabidopsis and other higher plants, ABA signal transduction involves three core components namely PYR/PYL/RCAR ABA receptors (PYLs), type 2C protein phosphatases (PP2Cs) and class III SNF-1-related protein kinase 2 (SnRK2s). In the present study, we reported the identification and characterization of the core ABA signaling components in Setaria viridis, an emerging model plant for cereals and feedstock crops presenting C4 metabolism, leading to the identification of eight PYL (SvPYL1 to 8), twelve PP2C (SvPP2C1 to 12) and eleven SnRK2 (SvSnRK2.1 through SvSnRK2.11) genes. In order to study the expression profiles of these genes, two different S. viridis accessions (A10.1 and Ast-1) were submitted to drought, salinity and cold stresses, in addition to application of exogenous ABA. Differential gene expression profiles were observed in each treatment and plant genotype, demonstrating variations of ABA stress responses within the same species. These differential responses to stresses were also assessed by physiological measurements such as photosynthesis, stomatal conductance and transpiration rate. This study allows a detailed analysis of gene expression of the core ABA signaling components in Setaria viridis submitted to different treatments and provides suitable targets for genetic engineering of C4 plants aiming tolerance to abiotic stresses.
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Affiliation(s)
- Karoline Estefani Duarte
- Plant Biotechnology Program, Federal University of Lavras (UFLA), Lavras, MG, 37200-000, Brazil.,Genetics and Biotechnology Laboratory, Embrapa Agroenergy (CNPAE), Brasilia, DF, 70770-901, Brazil
| | - Wagner Rodrigo de Souza
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy (CNPAE), Brasilia, DF, 70770-901, Brazil.,Centro de Ciências Naturais e Humanas, Universidade Federal do ABC (UFABC), São Bernardo do Campo, Santo André, SP, 09606-045, Brazil
| | - Thaís Ribeiro Santiago
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy (CNPAE), Brasilia, DF, 70770-901, Brazil
| | - Bruno Leite Sampaio
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy (CNPAE), Brasilia, DF, 70770-901, Brazil
| | - Ana Paula Ribeiro
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy (CNPAE), Brasilia, DF, 70770-901, Brazil
| | - Michelle Guitton Cotta
- Department of Cell Biology, University of Brasília (UnB), Brasília, DF, 70910-900, Brazil
| | | | - Pierre Roger René Marraccini
- Plant Biotechnology Program, Federal University of Lavras (UFLA), Lavras, MG, 37200-000, Brazil.,CIRAD, UMR AGAP (University Montpellier, CIRAD, IRD, INRA), Montpellier, 34398, France.,CIRAD, UMR IPME (University Montpellier, CIRAD, IRD, Montpellier), Agricultural Genetics Institute, LMI RICE2, Hanoi, Vietnam
| | - Adilson Kenji Kobayashi
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy (CNPAE), Brasilia, DF, 70770-901, Brazil
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Ceasar SA. Genome-wide Identification and in silico Analysis of PHT1 Family Genes and Proteins in Setaria viridis: The Best Model to Study Nutrient Transport in Millets. THE PLANT GENOME 2019; 12:180019. [PMID: 30951094 DOI: 10.3835/plantgenome2018.04.0019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Millets are small-seeded cereals predominantly cultivated and consumed by millions of poor people living in developing countries in Asia and Africa. Limited availability of genomic resources hinders studies of nutrient transport in millets. Two species, foxtail millet [ (L.) P. Beauv.] and its wild relative green foxtail [ (L.) P. Beauv.], are considered to be suitable models to study the genomics of other millets. Understanding the nutrient mobilization of millets is essential for improving nutrient use efficiency and biofortification in millets and other cereal crops. Millets are adapted for low-input agriculture, so understanding and improving the phosphate use efficiency of these plants is important because (i) subsistence farmers cannot afford to buy expensive phosphate fertilizers and (ii) the phosphate rock used for phosphate fertilizer production is depleting quickly. In this minireview, I discuss various studies on nutrient transport in millets and highlight phosphate transport studies. I report the identification and phylogenetic and multiple sequence analyses of 12 PHosphate Transporter1 (PHT1) family genes and proteins of green foxtail for the first time. With the exception of PHT1;5, all other green foxtail PHT1 transporters are closely clustered with foxtail millet PHT1 transporters. The multiple sequence analysis of SvPHT1s revealed that the key residues involved in phosphate and H-binding and transport are well conserved, as in other PHT1 transporters. Efforts need to be undertaken to understand and improve phosphate uptake and utilization in millets to strengthen food security in the developing world.
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Galla G, Siena LA, Ortiz JPA, Baumlein H, Barcaccia G, Pessino SC, Bellucci M, Pupilli F. A Portion of the Apomixis Locus of Paspalum Simplex is Microsyntenic with an Unstable Chromosome Segment Highly Conserved Among Poaceae. Sci Rep 2019; 9:3271. [PMID: 30824748 PMCID: PMC6397161 DOI: 10.1038/s41598-019-39649-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 01/16/2019] [Indexed: 01/04/2023] Open
Abstract
The introgression of apomixis in major seed crops, would guarantee self-seeding of superior heterotic seeds over generations. In the grass species Paspalum simplex, apomixis is controlled by a single locus in which recombination is blocked. In the perspective of isolating the genetic determinants of apomixis, we report data on sequencing, in silico mapping and expression analysis of some of the genes contained in two cloned genomic regions of the apomixis locus of P. simplex. In silico mapping allowed us to identify a conserved synteny group homoeologous to the apomixis locus, located on a telomeric position of chromosomes 12, 8, 3 and 4 of rice, Sorghum bicolor, Setaria italica and Brachypodium distachyum, respectively, and on a more centromeric position of maize chromosome 1. Selected genes of the apomixis locus expressed sense and antisense transcripts in reproductively committed cells of sexual and apomictic ovules. Some of the genes considered here expressed apomixis-specific allelic variants which showed partial non-overlapping expression patterns with alleles shared by sexual and apomictic reproductive phenotypes. Our findings open new routes for the isolation of the genetic determinants of apomixis and, in perspective, for its introgression in crop grasses.
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Affiliation(s)
- Giulio Galla
- Department of Agriculture Food Natural resources Animals and Environment (DAFNAE), University of Padova, 35020, Legnaro (PD), Italy
| | - Lorena A Siena
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR), CONICET-UNR, Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, S2125ZAA, Zavalla, Argentina
| | - Juan Pablo A Ortiz
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR), CONICET-UNR, Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, S2125ZAA, Zavalla, Argentina
| | - Helmut Baumlein
- The Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Gianni Barcaccia
- Department of Agriculture Food Natural resources Animals and Environment (DAFNAE), University of Padova, 35020, Legnaro (PD), Italy
| | - Silvina C Pessino
- Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR), CONICET-UNR, Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, S2125ZAA, Zavalla, Argentina
| | - Michele Bellucci
- Institute of Biosciences and Bioresources (IBBR), National Research Council (CNR), 06128, Perugia, Italy
| | - Fulvio Pupilli
- Institute of Biosciences and Bioresources (IBBR), National Research Council (CNR), 06128, Perugia, Italy.
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245
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Herbgenomics: A stepping stone for research into herbal medicine. SCIENCE CHINA-LIFE SCIENCES 2019; 62:913-920. [DOI: 10.1007/s11427-018-9472-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 12/21/2018] [Indexed: 12/31/2022]
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246
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Qiao X, Li Q, Yin H, Qi K, Li L, Wang R, Zhang S, Paterson AH. Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants. Genome Biol 2019; 20:38. [PMID: 30791939 PMCID: PMC6383267 DOI: 10.1186/s13059-019-1650-2] [Citation(s) in RCA: 463] [Impact Index Per Article: 92.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 02/08/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences of gene duplication in a range of taxa, and unravel common principles underlying duplicate gene retention. RESULTS We survey 141 sequenced plant genomes to elucidate consequences of gene and genome duplication, processes central to the evolution of biodiversity. We develop a pipeline named DupGen_finder to identify different modes of gene duplication in plants. Genes derived from whole-genome, tandem, proximal, transposed, or dispersed duplication differ in abundance, selection pressure, expression divergence, and gene conversion rate among genomes. The number of WGD-derived duplicate genes decreases exponentially with increasing age of duplication events-transposed duplication- and dispersed duplication-derived genes declined in parallel. In contrast, the frequency of tandem and proximal duplications showed no significant decrease over time, providing a continuous supply of variants available for adaptation to continuously changing environments. Moreover, tandem and proximal duplicates experienced stronger selective pressure than genes formed by other modes and evolved toward biased functional roles involved in plant self-defense. The rate of gene conversion among WGD-derived gene pairs declined over time, peaking shortly after polyploidization. To provide a platform for accessing duplicated gene pairs in different plants, we constructed the Plant Duplicate Gene Database. CONCLUSIONS We identify a comprehensive landscape of different modes of gene duplication across the plant kingdom by comparing 141 genomes, which provides a solid foundation for further investigation of the dynamic evolution of duplicate genes.
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Affiliation(s)
- Xin Qiao
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Qionghou Li
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Hao Yin
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Kaijie Qi
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Leiting Li
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Runze Wang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shaoling Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605 USA
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247
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Muthamilarasan M, Singh NK, Prasad M. Multi-omics approaches for strategic improvement of stress tolerance in underutilized crop species: A climate change perspective. ADVANCES IN GENETICS 2019; 103:1-38. [PMID: 30904092 DOI: 10.1016/bs.adgen.2019.01.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
For several decades, researchers are working toward improving the "major" crops for better adaptability and tolerance to environmental stresses. However, little or no research attention is given toward neglected and underutilized crop species (NUCS) which hold the potential to ensure food and nutritional security among the ever-growing global population. NUCS are predominantly climate resilient, but their yield and quality are compromised due to selective breeding. In this context, the importance of omics technologies namely genomics, transcriptomics, proteomics, phenomics and ionomics in delineating the complex molecular machinery governing growth, development and stress responses of NUCS is underlined. However, gaining insights through individual omics approaches will not be sufficient to address the research questions, whereas integrating these technologies could be an effective strategy to decipher the gene function, genome structures, biological pathways, metabolic and regulatory networks underlying complex traits. Given this, the chapter enlists the importance of NUCS in food and nutritional security and provides an overview of deploying omics approaches to study the NUCS. Also, the chapter enumerates the status of crop improvement programs in NUCS and suggests implementing "integrating omics" for gaining a better understanding of crops' response to abiotic and biotic stresses.
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Affiliation(s)
- Mehanathan Muthamilarasan
- National Institute of Plant Genome Research, New Delhi, India; ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Nagendra Kumar Singh
- ICAR-National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi, India.
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248
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Abstract
A fundamental tenet of multicellular eukaryotic evolution is that vertical inheritance is paramount, with natural selection acting on genetic variants transferred from parents to offspring. This lineal process means that an organism's adaptive potential can be restricted by its evolutionary history, the amount of standing genetic variation, and its mutation rate. Lateral gene transfer (LGT) theoretically provides a mechanism to bypass many of these limitations, but the evolutionary importance and frequency of this process in multicellular eukaryotes, such as plants, remains debated. We address this issue by assembling a chromosome-level genome for the grass Alloteropsis semialata, a species surmised to exhibit two LGTs, and screen it for other grass-to-grass LGTs using genomic data from 146 other grass species. Through stringent phylogenomic analyses, we discovered 57 additional LGTs in the A. semialata nuclear genome, involving at least nine different donor species. The LGTs are clustered in 23 laterally acquired genomic fragments that are up to 170 kb long and have accumulated during the diversification of Alloteropsis. The majority of the 59 LGTs in A. semialata are expressed, and we show that they have added functions to the recipient genome. Functional LGTs were further detected in the genomes of five other grass species, demonstrating that this process is likely widespread in this globally important group of plants. LGT therefore appears to represent a potent evolutionary force capable of spreading functional genes among distantly related grass species.
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249
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Cao X, Hu L, Chen X, Zhang R, Cheng D, Li H, Xu Z, Li L, Zhou Y, Liu A, Song J, Liu C, Liu J, Zhao Z, Chen M, Ma Y. Genome-wide analysis and identification of the low potassium stress responsive gene SiMYB3 in foxtail millet (Setariaitalica L.). BMC Genomics 2019; 20:136. [PMID: 30767761 PMCID: PMC6377754 DOI: 10.1186/s12864-019-5519-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 02/07/2019] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Potassium (K) is essential to plant growth and development. Foxtail millet (Setaria italic L.) is an important fodder grain crop in arid and semi-arid regions of Asia and Africa because of its strong tolerance to drought and barren stresses. The molecular mechanisms of physiological and biochemical responses and regulations to various abiotic stresses such as low potassium conditions in foxtail millet are not fully understood, which hinders the research and exploitation of this valuable resource. RESULTS In this research, we demonstrated that the millet variety Longgu 25 was the most insensitive variety to low potassium stress among other five varieties. The transcriptome analysis of Longgu 25 variety revealed a total of 26,192 and 26,849 genes from the K+-deficient and normal transcriptomic libraries by RNA-seq, respectively. A total of 1982 differentially expressed genes (DEGs) were identified including 866 up-regulated genes and 1116 down-regulated genes. We conducted a comparative analysis of these DEGs under low-K+ stress conditions and discovered 248 common DEGs for potassium deprivation among foxtail millet, rice and Arabidopsis. Further Gene Ontology (GO) enrichment analysis identified a series of candidate genes that may involve in K+-deficient response and in intersection of molecular functions among foxtail millet, rice and Arabidopsis. The expression profiles of randomly selected 18 candidate genes were confirmed as true DEGs with RT-qPCR. Furthermore, one of the 18 DEGs, SiMYB3, is specifically expressed only in the millet under low-K+ stress conditions. Overexpression of SiMYB3 promoted the main root elongation and improved K+ deficiency tolerance in transgenic Arabidopsis plants. The fresh weight of the transgenic plants was higher, the primary root length was longer and the root surface-area was larger than those of control plants after K+ deficiency treatments. CONCLUSIONS This study provides a global view of transcriptomic resources relevant to the K+-deficient tolerance in foxtail millet, and shows that SiMYB3 is a valuable genetic resource for the improvement of K+ deficiency tolerance in foxtail millet.
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Affiliation(s)
- Xinyou Cao
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat and Maize/Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture, Jinan, 250100, People's Republic of China
| | - Liqin Hu
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Xueyan Chen
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences/Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China
| | - Rongzhi Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat and Maize/Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture, Jinan, 250100, People's Republic of China
| | - Dungong Cheng
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat and Maize/Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture, Jinan, 250100, People's Republic of China
| | - Haosheng Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat and Maize/Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture, Jinan, 250100, People's Republic of China
| | - Zhaoshi Xu
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Liancheng Li
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Yongbin Zhou
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Aifeng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat and Maize/Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture, Jinan, 250100, People's Republic of China
| | - Jianming Song
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat and Maize/Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture, Jinan, 250100, People's Republic of China
| | - Cheng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat and Maize/Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture, Jinan, 250100, People's Republic of China
| | - Jianjun Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat and Maize/Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture, Jinan, 250100, People's Republic of China
| | - Zhendong Zhao
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat and Maize/Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow and Huai River Valley, Ministry of Agriculture, Jinan, 250100, People's Republic of China
| | - Ming Chen
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
| | - Youzhi Ma
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.
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Zou C, Li L, Miki D, Li D, Tang Q, Xiao L, Rajput S, Deng P, Peng L, Jia W, Huang R, Zhang M, Sun Y, Hu J, Fu X, Schnable PS, Chang Y, Li F, Zhang H, Feng B, Zhu X, Liu R, Schnable JC, Zhu JK, Zhang H. The genome of broomcorn millet. Nat Commun 2019; 10:436. [PMID: 30683860 PMCID: PMC6347628 DOI: 10.1038/s41467-019-08409-5] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 12/04/2018] [Indexed: 01/05/2023] Open
Abstract
Broomcorn millet (Panicum miliaceum L.) is the most water-efficient cereal and one of the earliest domesticated plants. Here we report its high-quality, chromosome-scale genome assembly using a combination of short-read sequencing, single-molecule real-time sequencing, Hi-C, and a high-density genetic map. Phylogenetic analyses reveal two sets of homologous chromosomes that may have merged ~5.6 million years ago, both of which exhibit strong synteny with other grass species. Broomcorn millet contains 55,930 protein-coding genes and 339 microRNA genes. We find Paniceae-specific expansion in several subfamilies of the BTB (broad complex/tramtrack/bric-a-brac) subunit of ubiquitin E3 ligases, suggesting enhanced regulation of protein dynamics may have contributed to the evolution of broomcorn millet. In addition, we identify the coexistence of all three C4 subtypes of carbon fixation candidate genes. The genome sequence is a valuable resource for breeders and will provide the foundation for studying the exceptional stress tolerance as well as C4 biology.
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Affiliation(s)
- Changsong Zou
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, 85 Minglun Street, 475001, Kaifeng, Henan, China
| | - Leiting Li
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Daisuke Miki
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Delin Li
- Data2Bio LLC, Ames, IA, 50011-3650, USA
- Dryland Genetics LLC, Ames, IA, 50010, USA
- China Agricultural University, 100193, Beijing, China
| | - Qiming Tang
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Lihong Xiao
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | | | - Ping Deng
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Li Peng
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Wei Jia
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Ru Huang
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Meiling Zhang
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Yidan Sun
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Jiamin Hu
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Xing Fu
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Patrick S Schnable
- Data2Bio LLC, Ames, IA, 50011-3650, USA
- Dryland Genetics LLC, Ames, IA, 50010, USA
- China Agricultural University, 100193, Beijing, China
- Department of Agronomy, Iowa State University, Ames, IA, 50011-3650, USA
| | - Yuxiao Chang
- Agricultural Genomes Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Feng Li
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - Hui Zhang
- Key Laboratory of Plant Stress Research, Shandong Normal University, No. 88 Wenhua East Rd, Jinan, 250014, Shandong, China
| | - Baili Feng
- School of Agronomy, Northwest Agriculture & Forestry University, 3 Weihui Rd, 712100, Yangling, China
| | - Xinguang Zhu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Rd, 200032, Shanghai, China
| | - Renyi Liu
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China
| | - James C Schnable
- Data2Bio LLC, Ames, IA, 50011-3650, USA
- Dryland Genetics LLC, Ames, IA, 50010, USA
- Department of Agriculture and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China.
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA.
| | - Heng Zhang
- Shanghai Center for Plant Stress Biology and CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China.
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 3888 Chenhua Rd, 201602, Shanghai, China.
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