1
|
Bandyopadhyay T, Maurya J, Bentley AR, Griffiths H, Swarbreck SM, Prasad M. Identification of the mechanistic basis of nitrogen responsiveness in two contrasting Setaria italica accessions. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5008-5020. [PMID: 38736217 DOI: 10.1093/jxb/erae204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/07/2024] [Indexed: 05/14/2024]
Abstract
Nitrogen (N) is a macronutrient limiting crop productivity with varied requirements across species and genotypes. Understanding the mechanistic basis of N responsiveness by comparing contrasting genotypes could inform the development and selection of varieties with lower N demands, or inform agronomic practices to sustain yields with lower N inputs. Given the established role of millets in ensuring climate-resilient food and nutrition security, we investigated the physiological and genetic basis of nitrogen responsiveness in foxtail millet (Setaria italica L.). We had previously identified genotypic variants linked to N responsiveness, and here we dissect the mechanistic basis of the trait by examining the physiological and molecular behaviour of N responsive (NRp-SI58) and non-responsive (NNRp-SI114) accessions at high and low N. Under high N, NRp-SI58 allocates significantly more biomass to nodes, internodes and roots, more N to developing grains, and is more effective at remobilizing flag leaf N compared with NNRp-SI114. Post-anthesis flag leaf gene expression suggests that differences in N induce much higher transcript abundance in NNRp-SI114 than NRp-SI58, a large proportion of which is potentially regulated by APETALA2 (AP2) transcription factors. Overall, the study provides novel insights into the regulation and manipulation of N responsiveness in S. italica.
Collapse
Affiliation(s)
| | - Jyoti Maurya
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Alison R Bentley
- NIAB, 93 Lawrence Weaver Rd, Cambridge CB3 0LE, UK
- Research School of Biology, Australian National University, Canberra, 2600, Australia
| | - Howard Griffiths
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Stéphanie M Swarbreck
- NIAB, 93 Lawrence Weaver Rd, Cambridge CB3 0LE, UK
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
- Department of Genetics, University of Delhi South Campus, Benito Juarez Marg, New Delhi 110021, India
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| |
Collapse
|
2
|
Zhou X, Li Y, Wang J, Zhao Y, Wang H, Han Y, Lin X. Genome-wide identification of U-box gene family and expression analysis in response to saline-alkali stress in foxtail millet ( Setaria italica L. Beauv). Front Genet 2024; 15:1356807. [PMID: 38435060 PMCID: PMC10904469 DOI: 10.3389/fgene.2024.1356807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 01/22/2024] [Indexed: 03/05/2024] Open
Abstract
E3 ubiquitin ligases are central modifiers of plant signaling pathways that regulate protein function, localization, degradation, and other biological processes by linking ubiquitin to target proteins. E3 ubiquitin ligases include proteins with the U-box domain. However, there has been no report about the foxtail millet (Setaria italica L. Beauv) U-box gene family (SiPUB) to date. To explore the function of SiPUBs, this study performed genome-wide identification of SiPUBs and expression analysis of them in response to saline-alkali stress. A total of 70 SiPUBs were identified, which were unevenly distributed on eight chromosomes. Phylogenetic and conserved motif analysis demonstrated that SiPUBs could be clustered into six subfamilies (I-VI), and most SiPUBs were closely related to the homologues in rice. Twenty-eight types of cis-acting elements were identified in SiPUBs, most of which contained many light-responsive elements and plant hormone-responsive elements. Foxtail millet had 19, 78, 85, 18, and 89 collinear U-box gene pairs with Arabidopsis, rice, sorghum, tomato, and maize, respectively. Tissue specific expression analysis revealed great variations in SiPUB expression among different tissues, and most SiPUBs were relatively highly expressed in roots, indicating that SiPUBs may play important roles in root development or other growth and development processes of foxtail millet. Furthermore, the responses of 15 SiPUBs to saline-alkali stress were detected by qRT-PCR. The results showed that saline-alkali stress led to significantly differential expression of these 15 SiPUBs, and SiPUB20/48/70 may play important roles in the response mechanism against saline-alkali stress. Overall, this study provides important information for further exploration of the biological function of U-box genes.
Collapse
Affiliation(s)
- Xiaoke Zhou
- Hebei Key Laboratory of Crop Stress Biology, College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yun Li
- Research Center of Rural Vitalization, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Jian Wang
- Hebei Key Laboratory of Crop Stress Biology, College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yuxue Zhao
- Hebei Key Laboratory of Crop Stress Biology, College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Huimin Wang
- Hebei Key Laboratory of Crop Stress Biology, College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Yucui Han
- Hebei Key Laboratory of Crop Stress Biology, College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Xiaohu Lin
- Hebei Key Laboratory of Crop Stress Biology, College of Agronomy and Biotechnology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| |
Collapse
|
3
|
Wang H, Li Y, Guo Z, Zhou X, Zhao Y, Han Y, Lin X. Genome-wide identification of AAAP gene family and expression analysis in response to saline-alkali stress in foxtail millet (Setaria italica L.). Sci Rep 2024; 14:3106. [PMID: 38326447 PMCID: PMC10850487 DOI: 10.1038/s41598-024-53242-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 01/30/2024] [Indexed: 02/09/2024] Open
Abstract
Amino acid/auxin permease (AAAP) genes encode a large family of protein transporters that play important roles in various aspects of plant growth and development. Here, we performed genome-wide identification of members in the foxtail millet (Setaria italica L.) AAAP family (SiAAAP) and their saline-alkali stress-induced expression patterns, resulting in the identification of 65 SiAAAP genes, which could be divided into eight subfamilies. Except for SiAAAP65, the remaining 64 genes were located on nine chromosomes of foxtail millet. Gene structure and conserved motif analyses indicated that the members in the same subfamily are highly conserved. Gene duplication event analysis suggested that tandem duplication may be the main factor driving the expansion of this gene family, and Ka/Ks analysis indicated that all the duplicated genes have undergone purifying selection. Transcriptome analysis showed differential expression of SiAAAPs in roots, stems, leaves, and tassel inflorescence. Analysis of cis-acting elements in the promoter indicated that SiAAAPs contain stress-responsive cis-acting elements. Under saline-alkali stress, qRT-PCR analysis showed that SiAAP3, SiLHT2, and SiAAP16 were differentially expressed between salt-alkali tolerant millet variety JK3 and salt-alkali sensitive millet variety B175. These results suggest that these genes may be involved in or regulate the response to saline-alkali stress, providing a theoretical basis for further studying the function of SiAAAPs.
Collapse
Affiliation(s)
- Huimin Wang
- College of Agronomy and Biotechnology/Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinhuangdao, 066000, China
| | - Yun Li
- Research Center of Rural Vitalization, Hebei Normal University of Science and Technology, Qinhuangdao, 066000, China
| | - Zhenqing Guo
- College of Agronomy and Biotechnology/Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinhuangdao, 066000, China
| | - Xiaoke Zhou
- College of Agronomy and Biotechnology/Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinhuangdao, 066000, China
| | - Yuxue Zhao
- College of Agronomy and Biotechnology/Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinhuangdao, 066000, China
| | - Yucui Han
- College of Agronomy and Biotechnology/Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinhuangdao, 066000, China.
| | - Xiaohu Lin
- College of Agronomy and Biotechnology/Hebei Key Laboratory of Crop Stress Biology, Hebei Normal University of Science and Technology, Qinhuangdao, 066000, China.
| |
Collapse
|
4
|
Liang J, Yin D, Shu X, Xiang T, Zhang C, Li H, Wang A. Integrated Genome Sequencing and Transcriptome Analysis Identifies Candidate Pathogenicity Genes from Ustilago crameri. J Fungi (Basel) 2024; 10:82. [PMID: 38276028 PMCID: PMC10821473 DOI: 10.3390/jof10010082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/12/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
Ustilago crameri is a pathogenic basidiomycete fungus that causes foxtail millet kernel smut (FMKS), a devastating grain disease in most foxtail-millet-growing regions of the world. Here, we report an assembled high-quality genome sequence of U. crameri strain SCZ-6 isolated from the diseased grains of foxtail millet in Changzhi, Shanxi Province, China. The genome size is 19.55 Mb, consisting of 73 contigs (N50 = 840,209 bp) with a G + C content of 54.09%, and encoding 6576 predicted genes and 6486 genes supported by RNA-seq. Evolutionarily, U. crameri lies close to the barley smut U. hordei, and an obvious co-linearity was observed between these two smut fungi. We annotated the genome of U. crameri strain SCZ-6 using databases, identifying 1827 pathogen-host interaction (PHI)-associated genes, 1324 genes encoding fungal virulence factors, 259 CAZy-related genes, 80 genes encoding transporters, and 206 putative cytochrome P450 genes; their expression profiles at different inoculation time points were also detected. Additionally, 70 candidate pathogen effectors were identified according to their expression patterns and predicted functions. In summary, our results provide important insights into the pathogenic mechanisms of the pathogenesis-related genes of U. crameri and a robust foundation for further investigation.
Collapse
Affiliation(s)
- Juan Liang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China; (J.L.); (X.S.); (T.X.); (C.Z.); (H.L.)
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Desuo Yin
- Food Crop Research Institute, Hubei Academy of Agriculture Sciences, Wuhan 430064, China;
| | - Xinyue Shu
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China; (J.L.); (X.S.); (T.X.); (C.Z.); (H.L.)
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Ting Xiang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China; (J.L.); (X.S.); (T.X.); (C.Z.); (H.L.)
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China
| | - Chao Zhang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China; (J.L.); (X.S.); (T.X.); (C.Z.); (H.L.)
| | - Honglian Li
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China; (J.L.); (X.S.); (T.X.); (C.Z.); (H.L.)
| | - Aijun Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China; (J.L.); (X.S.); (T.X.); (C.Z.); (H.L.)
| |
Collapse
|
5
|
Choudhary P, Shukla P, Muthamilarasan M. Genetic enhancement of climate-resilient traits in small millets: A review. Heliyon 2023; 9:e14502. [PMID: 37064482 PMCID: PMC10102230 DOI: 10.1016/j.heliyon.2023.e14502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 02/10/2023] [Accepted: 03/09/2023] [Indexed: 03/28/2023] Open
Abstract
Agriculture is facing the challenge of feeding the ever-growing population that is projected to reach ten billion by 2050. While improving crop yield and productivity can address this challenge, the increasing effects of global warming and climate change seriously threaten agricultural productivity. Thus, genomics and genome modification technologies are crucial to improving climate-resilient traits to enable sustained yield and productivity; however, significant research focuses on staple crops such as rice, wheat, and maize. Crops that are naturally climate-resilient and nutritionally superior to staple cereals, such as small millets, remain neglected and underutilized by mainstream research. The ability of small millets to grow in marginal regions having limited irrigation and poor soil fertility makes these crops a better choice for cultivation in arid and semi-arid areas. Hence, mainstreaming small millets for cultivation and using omics technologies to dissect the climate-resilient traits to identify the molecular determinants underlying these traits are imperative for addressing food and nutritional security. In this context, the review discusses the genomics and genome modification approaches for dissecting key traits in small millets and their application for improving these traits in cultivated germplasm. The review also discusses biofortification for nutritional security and machine-learning approaches for trait improvement in small millets. Altogether, the review provides a roadmap for the effective use of next-generation approaches for trait improvement in small millets. This will lead to the development of improved varieties for addressing multiple insecurities prevailing in the present climate change scenario.
Collapse
Affiliation(s)
- Pooja Choudhary
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Pooja Shukla
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| |
Collapse
|
6
|
SiMYBS3, Encoding a Setaria italica Heterosis-Related MYB Transcription Factor, Confers Drought Tolerance in Arabidopsis. Int J Mol Sci 2023; 24:ijms24065418. [PMID: 36982494 PMCID: PMC10049516 DOI: 10.3390/ijms24065418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/04/2023] [Accepted: 03/10/2023] [Indexed: 03/16/2023] Open
Abstract
Drought is a major limiting factor affecting grain production. Drought-tolerant crop varieties are required to ensure future grain production. Here, 5597 DEGs were identified using transcriptome data before and after drought stress in foxtail millet (Setaria italica) hybrid Zhangza 19 and its parents. A total of 607 drought-tolerant genes were screened through WGCNA, and 286 heterotic genes were screened according to the expression level. Among them, 18 genes overlapped. One gene, Seita.9G321800, encoded MYBS3 transcription factor and showed upregulated expression after drought stress. It is highly homologous with MYBS3 in maize, rice, and sorghum and was named SiMYBS3. Subcellular localization analysis showed that the SiMYBS3 protein was located in the nucleus and cytoplasm, and transactivation assay showed SiMYBS3 had transcriptional activation activity in yeast cells. Overexpression of SiMYBS3 in Arabidopsis thaliana conferred drought tolerance, insensitivity to ABA, and earlier flowering. Our results demonstrate that SiMYBS3 is a drought-related heterotic gene and it can be used for enhancing drought resistance in agricultural crop breeding.
Collapse
|
7
|
Wang L, Fu H, Zhao J, Wang J, Dong S, Yuan X, Li X, Chen M. Genome-Wide Identification and Expression Profiling of Glutathione S-Transferase Gene Family in Foxtail Millet ( Setaria italica L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:1138. [PMID: 36904001 PMCID: PMC10005783 DOI: 10.3390/plants12051138] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
Glutathione S-transferases (GSTs) are a critical superfamily of multifunctional enzymes in plants. As a ligand or binding protein, GSTs regulate plant growth and development and detoxification. Foxtail millet (Setaria italica (L.) P. Beauv) could respond to abiotic stresses through a highly complex multi-gene regulatory network in which the GST family is also involved. However, GST genes have been scarcely studied in foxtail millet. Genome-wide identification and expression characteristics analysis of the foxtail millet GST gene family were conducted by biological information technology. The results showed that 73 GST genes (SiGSTs) were identified in the foxtail millet genome and were divided into seven classes. The chromosome localization results showed uneven distribution of GSTs on the seven chromosomes. There were 30 tandem duplication gene pairs belonging to 11 clusters. Only one pair of SiGSTU1 and SiGSTU23 were identified as fragment duplication genes. A total of ten conserved motifs were identified in the GST family of foxtail millet. The gene structure of SiGSTs is relatively conservative, but the number and length of exons of each gene are still different. The cis-acting elements in the promoter region of 73 SiGST genes showed that 94.5% of SiGST genes possessed defense and stress-responsive elements. The expression profiles of 37 SiGST genes covering 21 tissues suggested that most SiGST genes were expressed in multiple organs and were highly expressed in roots and leaves. By qPCR analysis, we found that 21 SiGST genes were responsive to abiotic stresses and abscisic acid (ABA). Taken together, this study provides a theoretical basis for identifying foxtail millet GST family information and improving their responses to different stresses.
Collapse
Affiliation(s)
- Linlin Wang
- State Key Laboratory of Sustainable Dryland Agriculture (in preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan 030031, China
| | - Hongbo Fu
- Key Laboratory for Research and Utilization of Characteristic Biological Resources in Southern Yunnan, College of Biological and Agricultural Sciences, Honghe University, Mengzi 661100, China
| | - Juan Zhao
- State Key Laboratory of Sustainable Dryland Agriculture (in preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan 030031, China
| | - Jiagang Wang
- National Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding (in preparation), Shanxi Agricultural University, Taiyuan 030031, China
| | - Shuqi Dong
- State Key Laboratory of Sustainable Dryland Agriculture (in preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan 030031, China
| | - Xiangyang Yuan
- State Key Laboratory of Sustainable Dryland Agriculture (in preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan 030031, China
| | - Xiaorui Li
- State Key Laboratory of Sustainable Dryland Agriculture (in preparation), College of Agronomy, Shanxi Agricultural University, Taiyuan 030031, China
| | - Mingxun Chen
- College of Agronomy, Northwest A&F University, Yangling 712100, China
| |
Collapse
|
8
|
Liang H, He Q, Zhang H, Zhi H, Tang S, Wang H, Meng Q, Jia G, Chang J, Diao X. Identification and haplotype analysis of SiCHLI: a gene for yellow-green seedling as morphological marker to accelerate foxtail millet (Setaria italica) hybrid breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:24. [PMID: 36739566 DOI: 10.1007/s00122-023-04309-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
We cloned and developed functional markers for the SiCHLI gene, which is responsible for the yellow-green color of leaves in foxtail millet, a frequently used marker trait in the hybrid breeding of foxtail millet by using bulked segregant analysis sequencing and haplotype analysis on the F2 and core-collected nature populations. The color of leaves has been widely used as a marker for the hybrid breeding of foxtail millet; however, few related gene have been cloned to date. Here, we used two F2 populations generated from crosses between the highly male-sterile material 125A with yellow-green leaves, and CG58 and S410, which have green leaves, to identify the genes underlying the yellow-green color of the leaves of foxtail millet. The leaves of 125A seedlings were yellow-green, but they became green at the heading stage. The content of chlorophyll a and chlorophyll b was lower, the number of thylakoid lamellae and grana was reduced, and the chloroplasts was more rounded in 125A than in S410 at the yellow-green leaf stage; however, no differences were observed between 125A and S410 in these traits and photosynthetic at the heading stage. Bulked segregant analysis and map-based cloning revealed that the SiCHLI gene is responsible for the leaf colors of 125A. A nonsynonymous mutation (C/T) in exon 3 causes yellow-green leaves in 125A at the seedling stage. Haplotype analysis of the SiCHLI gene in 596 core collected accessions revealed a new haplotype associated with high photosynthetic metabolic potential at the heading and mature stages, which could be used to enhance sterile lines with yellow-green leaves. We developed a functional marker that will facilitate the identification of foxtail millet accessions with the different types of yellow-green leaves. Generally, our study provides new genetic resources to guide the future marker-assisted or target-base editing in foxtail millet hybrid breeding.
Collapse
Affiliation(s)
- Hongkai Liang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Hui Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Hui Zhi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Hailong Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Qiang Meng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China
| | - Jinhua Chang
- College of Agronomy, Agricultural University of Hebei, Baoding, 071001, China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, Haidian, China.
| |
Collapse
|
9
|
Lydia Pramitha J, Ganesan J, Francis N, Rajasekharan R, Thinakaran J. Revitalization of small millets for nutritional and food security by advanced genetics and genomics approaches. Front Genet 2023; 13:1007552. [PMID: 36699471 PMCID: PMC9870178 DOI: 10.3389/fgene.2022.1007552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 12/07/2022] [Indexed: 01/12/2023] Open
Abstract
Small millets, also known as nutri-cereals, are smart foods that are expected to dominate food industries and diets to achieve nutritional security. Nutri-cereals are climate resilient and nutritious. Small millet-based foods are becoming popular in markets and are preferred for patients with celiac and diabetes. These crops once ruled as food and fodder but were pushed out of mainstream cultivation with shifts in dietary habits to staple crops during the green revolution. Nevertheless, small millets are rich in micronutrients and essential amino acids for regulatory activities. Hence, international and national organizations have recently aimed to restore these lost crops for their desirable traits. The major goal in reviving these crops is to boost the immune system of the upcoming generations to tackle emerging pandemics and disease infestations in crops. Earlier periods of civilization consumed these crops, which had a greater significance in ethnobotanical values. Along with nutrition, these crops also possess therapeutic traits and have shown vast medicinal use in tribal communities for the treatment of diseases like cancer, cardiovascular disease, and gastrointestinal issues. This review highlights the significance of small millets, their values in cultural heritage, and their prospects. Furthermore, this review dissects the nutritional and therapeutic traits of small millets for developing sustainable diets in near future.
Collapse
Affiliation(s)
- J. Lydia Pramitha
- Karunya Institute of Technology and Sciences, Coimbatore, India,*Correspondence: J. Lydia Pramitha,
| | - Jeeva Ganesan
- Tamil Nadu Agricultural University, Coimbatore, India
| | - Neethu Francis
- Karunya Institute of Technology and Sciences, Coimbatore, India
| | | | | |
Collapse
|
10
|
Moreno-Nombela S, Romero-Parra J, Ruiz-Ojeda FJ, Solis-Urra P, Baig AT, Plaza-Diaz J. Genome Editing and Protein Energy Malnutrition. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1396:215-232. [DOI: 10.1007/978-981-19-5642-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
|
11
|
Ge W, Chen H, Zhang Y, Feng S, Wang S, Shang Q, Wu M, Li Z, Zhang L, Guo H, Jin Y, Wang X. Integrative genomics analysis of the ever-shrinking pectin methylesterase (PME) gene family in foxtail millet ( Setaria italica). FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:874-886. [PMID: 35781367 DOI: 10.1071/fp21319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 06/10/2022] [Indexed: 05/26/2023]
Abstract
Pectin methylesterase (PME) plays a vital role in the growth and development of plants. Their genes can be classified into two types, with Type-1 having an extra domain, PMEI. PME genes in foxtail millet (Setaria italica L.) have not been identified, and their sequence features and evolution have not been explored. Here, we identified 41 foxtail millet PME genes. Decoding the pro-region, containing the PMEI domain, revealed its more active nature than the DNA encoding PME domain, easier to be lost to produce Type-2 PME genes. We inferred that the active nature of the pro-region could be related to its harbouring more repetitive DNA sequences. Further, we revealed that though whole-genome duplication and tandem duplication contributed to producing new copies of PME genes, phylogenetic analysis provided clear evidence of ever-shrinking gene family size in foxtail millet and the other grasses in the past 100 million years. Phylogenetic analysis also supports the existence of two gene groups, Group I and Group II, with genes in Group II being more conservative. Our research contributes to understanding how DNA sequence structure affects the functional innovation and evolution of PME genes.
Collapse
Affiliation(s)
- Weina Ge
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Huilong Chen
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China; and School of Information Science and Technology, Yanching Institute of Technology, Langfang 065000, Hebei, China
| | - Yingchao Zhang
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Shuyan Feng
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Shuailei Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Qian Shang
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Meng Wu
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Ziqi Li
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Lan Zhang
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - He Guo
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Yongchao Jin
- College of Science, North China University of Science and Technology, Tangshan 063210, China
| | - Xiyin Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan 063210, China
| |
Collapse
|
12
|
Aggarwal PR, Pramitha L, Choudhary P, Singh RK, Shukla P, Prasad M, Muthamilarasan M. Multi-omics intervention in Setaria to dissect climate-resilient traits: Progress and prospects. FRONTIERS IN PLANT SCIENCE 2022; 13:892736. [PMID: 36119586 PMCID: PMC9470963 DOI: 10.3389/fpls.2022.892736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Millets constitute a significant proportion of underutilized grasses and are well known for their climate resilience as well as excellent nutritional profiles. Among millets, foxtail millet (Setaria italica) and its wild relative green foxtail (S. viridis) are collectively regarded as models for studying broad-spectrum traits, including abiotic stress tolerance, C4 photosynthesis, biofuel, and nutritional traits. Since the genome sequence release, the crop has seen an exponential increase in omics studies to dissect agronomic, nutritional, biofuel, and climate-resilience traits. These studies have provided first-hand information on the structure, organization, evolution, and expression of several genes; however, knowledge of the precise roles of such genes and their products remains elusive. Several open-access databases have also been instituted to enable advanced scientific research on these important crops. In this context, the current review enumerates the contemporary trend of research on understanding the climate resilience and other essential traits in Setaria, the knowledge gap, and how the information could be translated for the crop improvement of related millets, biofuel crops, and cereals. Also, the review provides a roadmap for studying other underutilized crop species using Setaria as a model.
Collapse
Affiliation(s)
- Pooja Rani Aggarwal
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Lydia Pramitha
- School of Agriculture and Biosciences, Karunya Institute of Technology and Sciences, Coimbatore, Tamil Nadu, India
| | - Pooja Choudhary
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | | | - Pooja Shukla
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Manoj Prasad
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| |
Collapse
|
13
|
Nadeem F, Mahmood R, Sabir M, Khan WUD, Haider MS, Wang R, Zhong Y, Ishfaq M, Li X. Foxtail millet [Setaria italica (L.) Beauv.] over-accumulates ammonium under low nitrogen supply. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 185:35-44. [PMID: 35660775 DOI: 10.1016/j.plaphy.2022.05.031] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/22/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Nitrogen (N) deficiency is a primary limiting factor for crop production worldwide. Previously, we reported root system architectural modifications of hydroponically cultured foxtail millet [Setaria italica (L.) Beauv.] to facilitate N translocation under N limitation. Here, we investigated foxtail millet for its shoot adaptation to low N in terms of internal N regulation under hydroponic culture. The results of this study revealed that the shoot N and nitrate (NO3-) concentrations significantly declined as compared to control (CK); however, the shoot over-accumulated ammonium (NH4+) under low N (LN). N shortage resulted in down-regulation of expressions of SiPetA, SiccsA, SipsbA, SirpoB, SipsaA, SiatpA, Sirps16, and SiPEPC which, undermined chloroplast functioning and CO2 assimilation for the provision of carbon skeleton. Carbon deficiency and lower activities of GS decelerated ammonia assimilation and led to over-accumulation of NH4+ in the LN-shoot, as indicated by lower concentrations of total amino acids. Thus, enhanced GOGAT activity was to assimilate NH4+ while, those of catalase (CAT), superoxide dismutase (SOD) and peroxidase (POD) were to scavenge reactive oxygen species (ROS) of NH4+ toxicity framework. The weakened chloroplast factory eventually minimized photosynthesis and reduced dry mass of the LN shoot. Such regulation of N by the shoot, perhaps, resurrected physiological functions which maintained internal mineral status under nitrogen limitation in foxtail millet.
Collapse
Affiliation(s)
- Faisal Nadeem
- MOE Key Laboratory of Plant-Soil Interactions, Department of Plant Nutrition, China Agricultural University, Beijing, 100193, China; Department of Soil Science, University of the Punjab, Lahore, 54590, Pakistan
| | - Rashid Mahmood
- Department of Soil Science, University of the Punjab, Lahore, 54590, Pakistan
| | - Muhammad Sabir
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad, 38040, Pakistan
| | - Waqas-Ud-Din Khan
- Sustainable Development Study Centre, Government College University, Lahore, 54000, Pakistan
| | | | - Ruifeng Wang
- MOE Key Laboratory of Plant-Soil Interactions, Department of Plant Nutrition, China Agricultural University, Beijing, 100193, China
| | - Yanting Zhong
- Department of Vegetable Sciences, China Agricultural University, Beijing, 100193, China
| | - Muhammad Ishfaq
- MOE Key Laboratory of Plant-Soil Interactions, Department of Plant Nutrition, China Agricultural University, Beijing, 100193, China
| | - Xuexian Li
- MOE Key Laboratory of Plant-Soil Interactions, Department of Plant Nutrition, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
14
|
Li C, Ma J, Wang G, Li H, Wang H, Wang G, Jiang Y, Liu Y, Liu G, Liu G, Cheng R, Wang H, Wei J, Yao L. Exploring the SiCCT Gene Family and Its Role in Heading Date in Foxtail Millet. FRONTIERS IN PLANT SCIENCE 2022; 13:863298. [PMID: 35755676 PMCID: PMC9218912 DOI: 10.3389/fpls.2022.863298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
CCT transcription factors are involved in the regulation of photoperiod and abiotic stress in Arabidopsis and rice. It is not clear that how CCT gene family expand and regulate heading date in foxtail millet. In this study, we conducted a systematic analysis of the CCT gene family in foxtail millet. Thirty-nine CCT genes were identified and divided into four subfamilies based on functional motifs. Analysis showed that dispersed duplication played a predominant role in the expansion of CCT genes during evolution. Nucleotide diversity analysis suggested that genes in CONSTANS (COL)-like, CCT MOTIF FAMILY (CMF)-like, and pseudoresponse response regulator (PRR)-like subfamilies were subjected to selection. Fifteen CCT genes were colocalized with previous heading date quantitative trait loci (QTL) and genome-wide association analysis (GWAS) signals. Transgenic plants were then employed to confirm that overexpression of the CCT gene SiPRR37 delayed the heading date and increased plant height. Our study first investigated the characterization and expansion of the CCT family in foxtail millet and demonstrated the role of SiPRR37. These results lay a significant foundation for further research on the function of CCT genes and provide a cue for the regulation of heading date.
Collapse
Affiliation(s)
- Congcong Li
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Biotechnology Research, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Ma
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Vegetable Research, Beijing Key Laboratory of Vegetable Germplasm Improvement, National Engineering Research Center for Vegetables, Beijing, China
| | - Genping Wang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Haiquan Li
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Hailong Wang
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Biotechnology Research, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, China
| | - Guoliang Wang
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Biotechnology Research, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, China
| | - Yanmiao Jiang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Yanan Liu
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Guiming Liu
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Biotechnology Research, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, China
| | - Guoqing Liu
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Ruhong Cheng
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Huan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianhua Wei
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Biotechnology Research, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, China
| | - Lei Yao
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Institute of Biotechnology Research, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, China
| |
Collapse
|
15
|
Lai D, Fan Y, Xue G, He A, Yang H, He C, Li Y, Ruan J, Yan J, Cheng J. Genome-wide identification and characterization of the SPL gene family and its expression in the various developmental stages and stress conditions in foxtail millet (Setaria italica). BMC Genomics 2022; 23:389. [PMID: 35596144 PMCID: PMC9122484 DOI: 10.1186/s12864-022-08633-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 05/10/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Among the major transcription factors, SPL plays a crucial role in plant growth, development, and stress response. Foxtail millet (Setaria italica), as a C4 crop, is rich in nutrients and is beneficial to human health. However, research on the foxtail millet SPL (SQUAMOSA PROMOTER BINDING-LIKE) gene family is limited. RESULTS: In this study, a total of 18 SPL genes were identified for the comprehensive analysis of the whole genome of foxtail millet. These SiSPL genes were divided into seven subfamilies (I, II, III, V, VI, VII, and VIII) according to the classification of the Arabidopsis thaliana SPL gene family. Structural analysis of the SiSPL genes showed that the number of introns in subfamilies I and II were much larger than others, and the promoter regions of SiSPL genes were rich in different cis-acting elements. Among the 18 SiSPL genes, nine genes had putative binding sites with foxtail millet miR156. No tandem duplication events were found between the SiSPL genes, but four pairs of segmental duplications were detected. The SiSPL genes expression were detected in different tissues, which was generally highly expressed in seeds development process, especially SiSPL6 and SiSPL16, which deserve further study. The results of the expression levels of SiSPL genes under eight types of abiotic stresses showed that many stress responsive genes, especially SiSPL9, SiSPL10, and SiSPL16, were highly expressed under multiple stresses, which deserves further attention. CONCLUSIONS In this research, 18 SPL genes were identified in foxtail millet, and their phylogenetic relationships, gene structural features, duplication events, gene expression and potential roles in foxtail millet development were studied. The findings provide a new perspective for the mining of the excellent SiSPL gene and the molecular breeding of foxtail millet.
Collapse
Affiliation(s)
- Dili Lai
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, 550025, Guizhou Province, People's Republic of China
- School of Food and Biological Engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, People's Republic of China
| | - Yue Fan
- College of Food Science and Engineering, Xinjiang Institute of Technology, Aksu, 843100, People's Republic of China
| | - Guoxing Xue
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Ailing He
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Hao Yang
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Chunlin He
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524000, People's Republic of China
| | - Yijing Li
- Henan Cancer Hospital, Zhengzhou, 450001, People's Republic of China
| | - Jingjun Ruan
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Jun Yan
- School of Food and Biological Engineering, Chengdu University, Longquanyi District, Chengdu, 610106, Sichuan Province, People's Republic of China.
| | - Jianping Cheng
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, 550025, Guizhou Province, People's Republic of China.
| |
Collapse
|
16
|
Bandyopadhyay T, Swarbreck SM, Jaiswal V, Maurya J, Gupta R, Bentley AR, Griffiths H, Prasad M. GWAS identifies genetic loci underlying nitrogen responsiveness in the climate resilient C 4 model Setaria italica (L.). J Adv Res 2022; 42:249-261. [PMID: 36513416 PMCID: PMC9788950 DOI: 10.1016/j.jare.2022.01.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/21/2022] [Accepted: 01/23/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION N responsiveness is the capacity to perceive and induce morpho-physiological adaptation to external and internal Nitrogen (N). Crop productivity is propelled by N fertilizer and requires the breeding/selection of cultivars with intrinsically high N responsiveness. This trait has many advantages in being more meaningful in commercial/environmental context, facilitating in-season N management and not being inversely correlated with N availability over processes regulating NUE. Current lack of its understanding at the physio-genetic basis is an impediment to select for cultivars with a predictably high N response. OBJECTIVES To dissect physio-genetic basis of N responsiveness in 142 diverse population of foxtail millet, Setaria italica (L.) by employing contrasting N fertilizer nutrition regimes. METHODS We phenotyped S. italica accessions for major yield related traits under low (N10, N25) and optimal (N100) growth conditions and genotyped them to subsequently perform a genome-wide association study to identify genetic loci associated with nitrogen responsiveness trait. Groups of accessions showing contrasting trait performance and allelic forms of specific linked genetic loci (showing haplotypes) were further accessed for N dependent transcript abundances of their proximal genes. RESULTS Our study show that N dependent yield rise in S. italica is driven by grain number whose responsiveness to N availability is genetically underlined. We identify 22 unique SNP loci strongly associated with this trait out of which six exhibit haplotypes and consistent allelic variation between lines with contrasting N dependent grain number response and panicle architectures. Furthermore, differential transcript abundances of specific genes proximally linked to these SNPs in same lines is indicative of their N dependence in a genotype specific manner. CONCLUSION The study demonstrates the value/ potential of N responsiveness as a selection trait and identifies key genetic components underlying the trait in S. italica. This has major implications for improving crop N sustainability and food security.
Collapse
Affiliation(s)
| | - Stéphanie M Swarbreck
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Rd, Cambridge CB3 0LE, United Kingdom,Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, United Kingdom
| | - Vandana Jaiswal
- CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh 176061, India
| | - Jyoti Maurya
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Rajeev Gupta
- Cereal Crops Research Unit, US Department of Agriculture (USDA) Agricultural Research Service (ARS), Fargo, ND, United States,International Crop Research Institute for the Semi -arid Tropics, Patancheru, Hyderabad, Telangana 502324, India
| | - Alison R. Bentley
- The John Bingham Laboratory, NIAB, 93 Lawrence Weaver Rd, Cambridge CB3 0LE, United Kingdom,International Maize and Wheat Improvement Center, Texcoco, México
| | - Howard Griffiths
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, United Kingdom
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India,Corresponding author at: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.
| |
Collapse
|
17
|
Hou S, Man X, Lian B, Ma G, Sun Z, Han L, Yan L, Gao H, Du W, Wang X, Zhang Y, Li H, Han Y. Folate metabolic profiling and expression of folate metabolism-related genes during panicle development in foxtail millet (Setaria italica (L.) P. Beauv). JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:268-279. [PMID: 34109642 DOI: 10.1002/jsfa.11355] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 04/16/2021] [Accepted: 06/09/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Foxtail millet grain has higher folate content than other cereal crops. However, the folate metabolite content and the expression patterns of folate metabolite-related genes are unknown. RESULTS Liquid chromatography-mass spectrometry was used to investigate 12 folate metabolites in a foxtail millet panicle. The content of total folate and derivatives gradually decreased during panicle development. Polyglutamate 5-formyl-tetrahydrofolate was the major form. Twenty-eight genes involved in the folate metabolic pathway were identified through bioinformatic analysis. These genes in Setaria italica, S. viridis and Zea mays showed genomic collinearity. Phylogenetic analysis revealed that the folate-related genes were closely related among the C4 plants compared to C3 plants. The gene expressions were then studied at three panicle development stages. The gene expression patterns were classified into two groups, namely SiADCL1 and SiGGH as two key enzymes, which are responsible for folate synthesis and degradation; their expression levels were highest at the early panicle development stage, up to 179.11- and 163.88-fold, respectively. Their expression levels had a similar downward trend during panicle development and were significantly positively correlated with the concentration of total folate and folate derivatives. However, SiSHMT3 expression levels were significantly negatively correlated with total folate concentration. CONCLUSION Besides being the major determinants of folate and folate derivatives accumulation, SiADCL1 and SiGGH expression levels are key limiting factors in the foxtail millet panicle. Therefore, SiADCL1 and SiGGH expression levels can be targeted in genetic modification studies to improve folate content in foxtail millet seeds in the future. © 2021 Society of Chemical Industry.
Collapse
Affiliation(s)
- Siyu Hou
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, China
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Taiyuan, China
| | - Xiaxia Man
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, China
| | - Boying Lian
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, China
| | - Guifang Ma
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, China
| | - Zhaoxia Sun
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, China
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Taiyuan, China
| | - Lida Han
- Biotechnology Research Institute, Chinese Academy of Agricultural Science, Beijing, China
| | - Lufei Yan
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, China
| | - Hao Gao
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, China
| | - Wei Du
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, China
| | - Xinfang Wang
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, China
| | - Yijuan Zhang
- College of Life science, Shanxi Agricultural University, Taigu, China
| | - Hongying Li
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, China
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Taiyuan, China
| | - Yuanhuai Han
- College of Agriculture, Institute of Agricultural Bioengineering, Shanxi Agricultural University, Taigu, China
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, Taiyuan, China
| |
Collapse
|
18
|
Xu C, Luo M, Sun X, Yan J, Shi H, Yan H, Yan R, Wang S, Tang W, Zhou Y, Wang C, Xu Z, Chen J, Ma Y, Jiang Q, Chen M, Sun D. SiMYB19 from Foxtail Millet ( Setaria italica) Confers Transgenic Rice Tolerance to High Salt Stress in the Field. Int J Mol Sci 2022; 23:ijms23020756. [PMID: 35054940 PMCID: PMC8775554 DOI: 10.3390/ijms23020756] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/05/2022] [Accepted: 01/08/2022] [Indexed: 12/24/2022] Open
Abstract
Salt stress is a major threat to crop quality and yield. Most experiments on salt stress-related genes have been conducted at the laboratory or greenhouse scale. Consequently, there is a lack of research demonstrating the merit of exploring these genes in field crops. Here, we found that the R2R3-MYB transcription factor SiMYB19 from foxtail millet is expressed mainly in the roots and is induced by various abiotic stressors such as salt, drought, low nitrogen, and abscisic acid. SiMYB19 is tentatively localized to the nucleus and activates transcription. It enhances salt tolerance in transgenic rice at the germination and seedling stages. SiMYB19 overexpression increased shoot height, grain yield, and salt tolerance in field- and salt pond-grown transgenic rice. SiMYB19 overexpression promotes abscisic acid (ABA) accumulation in transgenic rice and upregulates the ABA synthesis gene OsNCED3 and the ABA signal transduction pathway-related genes OsPK1 and OsABF2. Thus, SiMYB19 improves salt tolerance in transgenic rice by regulating ABA synthesis and signal transduction. Using rice heterologous expression analysis, the present study introduced a novel candidate gene for improving salt tolerance and increasing yield in crops grown in saline-alkali soil.
Collapse
Affiliation(s)
- Chengjie Xu
- Key Laboratory of Sustainable Dryland Agriculture, College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (C.X.); (H.S.); (H.Y.); (R.Y.); (S.W.)
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; (M.L.); (X.S.); (W.T.); (Y.Z.); (C.W.); (Z.X.); (J.C.); (Y.M.); (Q.J.)
| | - Mingzhao Luo
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; (M.L.); (X.S.); (W.T.); (Y.Z.); (C.W.); (Z.X.); (J.C.); (Y.M.); (Q.J.)
| | - Xianjun Sun
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; (M.L.); (X.S.); (W.T.); (Y.Z.); (C.W.); (Z.X.); (J.C.); (Y.M.); (Q.J.)
| | - Jiji Yan
- College of Life Sciences, Shanxi Normal University, Taiyuan 030006, China;
| | - Huawei Shi
- Key Laboratory of Sustainable Dryland Agriculture, College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (C.X.); (H.S.); (H.Y.); (R.Y.); (S.W.)
| | - Huishu Yan
- Key Laboratory of Sustainable Dryland Agriculture, College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (C.X.); (H.S.); (H.Y.); (R.Y.); (S.W.)
| | - Rongyue Yan
- Key Laboratory of Sustainable Dryland Agriculture, College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (C.X.); (H.S.); (H.Y.); (R.Y.); (S.W.)
| | - Shuguang Wang
- Key Laboratory of Sustainable Dryland Agriculture, College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (C.X.); (H.S.); (H.Y.); (R.Y.); (S.W.)
| | - Wensi Tang
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; (M.L.); (X.S.); (W.T.); (Y.Z.); (C.W.); (Z.X.); (J.C.); (Y.M.); (Q.J.)
| | - Yongbin Zhou
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; (M.L.); (X.S.); (W.T.); (Y.Z.); (C.W.); (Z.X.); (J.C.); (Y.M.); (Q.J.)
| | - Chunxiao Wang
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; (M.L.); (X.S.); (W.T.); (Y.Z.); (C.W.); (Z.X.); (J.C.); (Y.M.); (Q.J.)
| | - Zhaoshi Xu
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; (M.L.); (X.S.); (W.T.); (Y.Z.); (C.W.); (Z.X.); (J.C.); (Y.M.); (Q.J.)
| | - Jun Chen
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; (M.L.); (X.S.); (W.T.); (Y.Z.); (C.W.); (Z.X.); (J.C.); (Y.M.); (Q.J.)
| | - Youzhi Ma
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; (M.L.); (X.S.); (W.T.); (Y.Z.); (C.W.); (Z.X.); (J.C.); (Y.M.); (Q.J.)
| | - Qiyan Jiang
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; (M.L.); (X.S.); (W.T.); (Y.Z.); (C.W.); (Z.X.); (J.C.); (Y.M.); (Q.J.)
| | - Ming Chen
- Institute of Crop Sciences, National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; (M.L.); (X.S.); (W.T.); (Y.Z.); (C.W.); (Z.X.); (J.C.); (Y.M.); (Q.J.)
- Correspondence: or (D.S.); (M.C.)
| | - Daizhen Sun
- Key Laboratory of Sustainable Dryland Agriculture, College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China; (C.X.); (H.S.); (H.Y.); (R.Y.); (S.W.)
- Correspondence: or (D.S.); (M.C.)
| |
Collapse
|
19
|
Dhaka A, Singh RK, Muthamilarasan M, Prasad M. Genetics and Genomics Interventions for Promoting Millets as Functional Foods. Curr Genomics 2021; 22:154-163. [PMID: 34975288 PMCID: PMC8640850 DOI: 10.2174/1389202922666210225084212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/05/2021] [Accepted: 01/21/2021] [Indexed: 11/22/2022] Open
Abstract
Several crops, including millets with immense nutritional and therapeutic values, were once a part of our regular diet. However, due to domestication and selection pressures, many of them have become marginally cultivated crops confined to a particular region, race, or locality. Millets are a perfect example of neglected species that have the potential to address both food and nutritional insecurities prevalent among the ever-growing global population. Starvation and malnutrition contribute to a large number of health-related issues, being the main reason behind the occurrence of most of the severe diseases worldwide. These constraints are repeatedly disturbing both the social and economic health of global society. Naturally, millets are rich in minerals, nutrients, and bioactive compounds, and these crops are less dependent on synthetic fertilizers, systemic irrigation, and pest/weed control. Given this, the review emphasizes the nutritional values, health benefits, processing techniques, and genomic advancements of millets. In addition, it proposes a roadmap for enhancing the utility and commercialization of millets.
Collapse
Affiliation(s)
- Annvi Dhaka
- 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
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| |
Collapse
|
20
|
Wang T, Lu Q, Song H, Hu N, Wei Y, Li P, Liu Y, Zhao Z, Liu J, Zhang B, Peng R. DNA Methylation and RNA-Sequencing Analysis Show Epigenetic Function During Grain Filling in Foxtail Millet ( Setaria italica L.). FRONTIERS IN PLANT SCIENCE 2021; 12:741415. [PMID: 34512708 PMCID: PMC8429616 DOI: 10.3389/fpls.2021.741415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 08/06/2021] [Indexed: 06/13/2023]
Abstract
Grain filling is a crucial process for crop yield and quality. Certain studies already gained insight into the molecular mechanism of grain filling. However, it is unclear whether epigenetic modifications are associated with grain filling in foxtail millet. Global DNA methylation and transcriptome analysis were conducted in foxtail millet spikelets during different stages to interpret the epigenetic effects of the grain filling process. The study employed the whole-genome bisulfite deep sequencing and advanced bioinformatics to sequence and identify all DNA methylation during foxtail millet grain filling; the DNA methylation-mediated gene expression profiles and their involved gene network and biological pathway were systematically studied. One context of DNA methylation, namely, CHH methylation, was accounted for the largest percentage, and it was gradually increased during grain filling. Among all developmental stages, the methylation levels were lowest at T2, followed by T4, which mainly occurred in CHG. The distribution of differentially methylated regions (DMR) was varied in the different genetic regions for three contexts. In addition, gene expression was negatively associated with DNA methylation. Evaluation of the interconnection of the DNA methylome and transcriptome identified some stage-specific differentially expressed genes associated with the DMR at different stages compared with the T1 developmental stage, indicating the potential function of epigenetics on the expression regulation of genes related to the specific pathway at different stages of grain development. The results demonstrated that the dynamic change of DNA methylation plays a crucial function in gene regulation, revealing the potential function of epigenetics in grain development in foxtail millet.
Collapse
Affiliation(s)
- Tao Wang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
- Innovation and Practice Base for Postdoctors, Anyang Institute of Technology, Anyang, China
| | - Quanwei Lu
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Hui Song
- Anyang Academy of Agriculture Sciences, Anyang, China
| | - Nan Hu
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Yangyang Wei
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Pengtao Li
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Yuling Liu
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Zilin Zhao
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Jinrong Liu
- Anyang Academy of Agriculture Sciences, Anyang, China
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, United States
| | - Renhai Peng
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| |
Collapse
|
21
|
Xie H, Hou J, Fu N, Wei M, Li Y, Yu K, Song H, Li S, Liu J. Identification of QTL related to anther color and hull color by RAD sequencing in a RIL population of Setaria italica. BMC Genomics 2021; 22:556. [PMID: 34281524 PMCID: PMC8290542 DOI: 10.1186/s12864-021-07882-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 06/30/2021] [Indexed: 11/13/2022] Open
Abstract
Background Foxtail millet (Setaria italica) is one of the oldest domesticated crops and has been considered as an ideal model plant for C4 grasses. It has abundant type of anther and hull colors which is not only a most intuitive morphological marker for color selection in seed production, but also has very important biological significance for the study of molecular mechanism of regulating the synthesis and metabolism of flavonoids and lignin. However, only a few genetic studies have been reported for anther color and hull color in foxtail millet. Results Quantitative trait loci (QTL) analysis for anther color and hull color was conducted using 400 F6 and F7 recombinant inbreed lines (RILs) derived from a cross between parents Yugu18 and Jigu19. Using restriction-site associated DNA sequencing, 43,001 single-nucleotide polymorphisms (SNPs) and 3,022 indels were identified between both the parents and the RILs. A total of 1,304 bin markers developed from the SNPs and indels were used to construct a genetic map that spanned 2196 cM of the foxtail millet genome with an average of 1.68 cM/bin. Combined with this genetic map and the phenotypic data observed in two locations for two years, two QTL located on chromosome 6 (Chr6) in a 1.215-Mb interval (33,627,819–34,877,940 bp) for anther color (yellow - white) and three QTL located on Chr1 in a 6.23-Mb interval (1–6,229,734 bp) for hull color (gold-reddish brown) were detected. To narrow the QTL regions identified from the genetic map and QTL analysis, we developed a new method named “inconsistent rate analysis” and efficiently narrowed the QTL regions of anther color into a 60-kb interval (34.13–34.19 Mb) in Chr6, and narrowed the QTL regions of hull color into 70-kb (5.43–5.50 Mb) and 30-kb (5.69–5.72 Mb) intervals in Chr1. Two genes (Seita.6G228600.v2.2 and Seita.6G228700.v2.2) and a cinnamyl alcohol dehydrogenase (CAD) gene (Seita.1G057300.v2.2) with amino acid changes between the parents detected by whole-genome resequencing were identified as candidate genes for anther and hull color, respectively. Conclusions This work presents the related QTL and candidate genes of anther and hull color in foxtail millet and developed a new method named inconsistent rate analysis to detect the chromosome fragments linked with the quality trait in RILs. This is the first study of the QTL related to hull color in foxtail millet and clarifying that the CAD gene (Seita.1G057300.v2.2) is the key gene responsible for this trait. It lays the foundation for further cloning of the functional genes and provides a powerful tool to detect the chromosome fragments linked with quality traits in RILs. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07882-x.
Collapse
Affiliation(s)
- Huifang Xie
- Anyang Academy of Agriculture Sciences, 455000, Anyang, Henan, China
| | - Junliang Hou
- BGI Institute of Applied Agriculture, BGI-Shenzhen, 518120, Shenzhen, Guangdong, China
| | - Nan Fu
- Anyang Academy of Agriculture Sciences, 455000, Anyang, Henan, China
| | - Menghan Wei
- Anyang Academy of Agriculture Sciences, 455000, Anyang, Henan, China
| | - Yunfei Li
- BGI Institute of Applied Agriculture, BGI-Shenzhen, 518120, Shenzhen, Guangdong, China
| | - Kang Yu
- BGI Institute of Applied Agriculture, BGI-Shenzhen, 518120, Shenzhen, Guangdong, China
| | - Hui Song
- Anyang Academy of Agriculture Sciences, 455000, Anyang, Henan, China
| | - Shiming Li
- BGI Institute of Applied Agriculture, BGI-Shenzhen, 518120, Shenzhen, Guangdong, China.
| | - Jinrong Liu
- Anyang Academy of Agriculture Sciences, 455000, Anyang, Henan, China.
| |
Collapse
|
22
|
Huangfu Y, Pan J, Li Z, Wang Q, Mastouri F, Li Y, Yang S, Liu M, Dai S, Liu W. Genome-wide identification of PTI1 family in Setaria italica and salinity-responsive functional analysis of SiPTI1-5. BMC PLANT BIOLOGY 2021; 21:319. [PMID: 34217205 PMCID: PMC8254068 DOI: 10.1186/s12870-021-03077-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 05/27/2021] [Indexed: 05/18/2023]
Abstract
BACKGROUND PTI1 (Pto-interacting 1) protein kinase belongs to the receptor-like cytoplasmic kinase (RLCK) group of receptor-like protein kinases (RLK), but lack extracellular and transmembrane domains. PTI1 was first identified in tomato (Solanum lycopersicum) and named SlPTI1, which has been reported to interact with bacterial effector Pto, a serine/threonine protein kinase involved in plant resistance to bacterial disease. Briefly, the host PTI1 specifically recognizes and interacts with the bacterial effector AvrPto, which triggers hypersensitive cell death to inhibit the pathogen growth in the local infection site. Previous studies have demonstrated that PTI1 is associated with oxidative stress and hypersensitivity. RESULTS We identified 12 putative PTI1 genes from the genome of foxtail millet (Setaria italica) in this study. Gene replication analysis indicated that both segmental replication events played an important role in the expansion of PTI1 gene family in foxtail millet. The PTI1 family members of model plants, i.e. S. italica, Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), maize (Zea mays), S. lycopersicum, and soybean (Glycine max), were classified into six major categories according to the phylogenetic analysis, among which the PTI1 family members in foxtail millet showed higher degree of homology with those of rice and maize. The analysis of a complete set of SiPTI1 genes/proteins including classification, chromosomal location, orthologous relationships and duplication. The tissue expression characteristics revealed that SiPTI1 genes are mainly expressed in stems and leaves. Experimental qRT-PCR results demonstrated that 12 SiPTI1 genes were induced by multiple stresses. Subcellular localization visualized that all of foxtail millet SiPTI1s were localized to the plasma membrane. Additionally, heterologous expression of SiPTI1-5 in yeast and E. coli enhanced their tolerance to salt stress. CONCLUSIONS Our results contribute to a more comprehensive understanding of the roles of PTI1 protein kinases and will be useful in prioritizing particular PTI1 for future functional validation studies in foxtail millet.
Collapse
Affiliation(s)
- Yongguan Huangfu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, Heilongjiang, China
| | - Jiaowen Pan
- Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China
| | - Zhen Li
- Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China
| | - Qingguo Wang
- Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China
| | - Fatemeh Mastouri
- Bota Bioscience, 325 Vassar st. Suite 2a, Cambridge, MA, 02139, USA
| | - Ying Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, 150040, Heilongjiang, China
| | - Stephen Yang
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Dr, Rockville, MD, 20850, USA
| | - Min Liu
- Shandong Agriculture and Engineering University, Jinan, 250100, Shandong, China
| | - Shaojun Dai
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China.
| | - Wei Liu
- Shandong Academy of Agricultural Sciences, Jinan, 250100, Shandong, China.
- College of Life Sciences, Shandong Normal University, Jinan, 250014, Shandong, China.
| |
Collapse
|
23
|
Metal based nanoparticles trigger the differential expression of key regulatory genes which regulate iron and zinc homeostasis mechanism in finger millet. J Cereal Sci 2021. [DOI: 10.1016/j.jcs.2021.103235] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
24
|
Li C, Wang G, Li H, Wang G, Ma J, Zhao X, Huo L, Zhang L, Jiang Y, Zhang J, Liu G, Liu G, Cheng R, Wei J, Yao L. High-depth resequencing of 312 accessions reveals the local adaptation of foxtail millet. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1303-1317. [PMID: 33566123 DOI: 10.1007/s00122-020-03760-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 12/30/2020] [Indexed: 05/20/2023]
Abstract
Based on the high-density variation map, we identified genome-level evidence for local adaptation and demonstrated that Siprr37 with transposon insertion contributes to the fitness of foxtail millet in the northeastern ecoregion. Adaptation is a robust way through which plants are able to overcome environmental constraints. The mechanisms of adaptation in heterogeneous natural environments are largely unknown. Deciphering the genomic basis of local adaptation will contribute to further improvement in domesticated plants. To this end, we describe a high-depth (19.4 ×) haplotype map of 3.02 million single nucleotide polymorphisms in foxtail millet (Setaria italica) from whole-genome resequencing of 312 accessions. In the genome-wide scan, we identified a set of improvement signals (including the homologous gene of OsIPA1, a key gene controlling ideal plant architecture) related to the geographical adaptation to four ecoregions in China. In particular, based on the genome-wide association analysis results, we identified the contribution of a pseudo-response regulator gene, SiPRR37, to heading date adaptation in foxtail millet. We observed the expression changes of SiPRR37 resulted from a key Tc1-Mariner transposon insertion in the first intron. Positive selection analyses revealed that SiPRR37 mainly contributed to the adaptation of northeastern ecoregions. Taken together, foxtail millet adapted to the northeastern region by regulating the function of SiPRR37, which sheds lights on genome-level evidence for adaptive geographical divergence. Besides, our data provide a nearly complete catalog of genomic variation aiding the identification of functionally important variants.
Collapse
Affiliation(s)
- Congcong Li
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Genping Wang
- Institute of Millet Crops, Key Laboratory of Minor Crops in Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Haiquan Li
- Institute of Millet Crops, Key Laboratory of Minor Crops in Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Guoliang Wang
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Jian Ma
- Beijing Vegetable Research Center, Beijing Key Laboratory of Vegetable Germplasms Improvement, National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xin Zhao
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Linhe Huo
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Liquan Zhang
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yanmiao Jiang
- Institute of Millet Crops, Key Laboratory of Minor Crops in Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Jiewei Zhang
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Guiming Liu
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Guoqing Liu
- Institute of Millet Crops, Key Laboratory of Minor Crops in Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Ruhong Cheng
- Institute of Millet Crops, Key Laboratory of Minor Crops in Hebei Province, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Jianhua Wei
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Lei Yao
- Beijing Agro-Biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| |
Collapse
|
25
|
Pankievicz VCS, do Amaral FP, Ané JM, Stacey G. Diazotrophic Bacteria and Their Mechanisms to Interact and Benefit Cereals. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:491-498. [PMID: 33543986 DOI: 10.1094/mpmi-11-20-0316-fi] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Plant-growth-promoting bacteria (PGPB) stimulate plant growth through diverse mechanisms. In addition to biological nitrogen fixation, diazotrophic PGPB can improve nutrient uptake efficiency from the soil, produce and release phytohormones to the host, and confer resistance against pathogens. The genetic determinants that drive the success of biological nitrogen fixation in nonlegume plants are understudied. These determinants include recognition and signaling pathways, bacterial colonization, and genotype specificity between host and bacteria. This review presents recent discoveries of how nitrogen-fixing PGPB interact with cereals and promote plant growth. We suggest adopting an experimental model system, such as the Setaria-diazotrophic bacteria association, as a reliable way to better understand the associated mechanisms and, ultimately, increase the use of PGPB inoculants for sustainable agriculture.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
| | - Fernanda Plucani do Amaral
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Science Center, University of Missouri, Columbia, MO, U.S.A
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, U.S.A
| | - Gary Stacey
- Divisions of Plant Sciences and Biochemistry, C. S. Bond Life Science Center, University of Missouri, Columbia, MO, U.S.A
| |
Collapse
|
26
|
Hunt HV, Przelomska NAS, Campana MG, Cockram J, Bligh HFJ, Kneale CJ, Romanova OI, Malinovskaya EV, Jones MK. Population genomic structure of Eurasian and African foxtail millet landrace accessions inferred from genotyping-by-sequencing. THE PLANT GENOME 2021; 14:e20081. [PMID: 33543599 PMCID: PMC8638668 DOI: 10.1002/tpg2.20081] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 10/15/2020] [Indexed: 05/11/2023]
Abstract
Foxtail millet [Setaria italica (L.) P. Beauv.] is the second most important millet species globally and is adapted to cultivation in diverse environments. Like its wild progenitor, green foxtail [S. viridis (L.) P. Beauv.], it is a model species for C4 photosynthetic pathways and stress tolerance genes in related bioenergy crops. We addressed questions regarding the evolution and spread of foxtail millet through a population genomic study of landraces from across its cultivated range in Europe, Asia, and Africa. We sought to determine population genomic structure and the relationship of domesticated lineages relative to green foxtail. Further, we aimed to identify genes involved in environmental stress tolerance that have undergone differential selection between geographical and genetic groups. Foxtail millet landrace accessions (n = 328) and green foxtail accessions (n = 12) were sequenced by genotyping-by-sequencing (GBS). After filtering, 5,677 single nucleotide polymorphisms (SNPs) were retained for the combined foxtail millet-green foxtail dataset and 5,020 for the foxtail millet dataset. We extended geographic coverage of green foxtail by including previously published GBS sequence tags, yielding a 4,515-SNP dataset for phylogenetic reconstruction. All foxtail millet samples were monophyletic relative to green foxtail, suggesting a single origin of foxtail millet, although no group of foxtail millet was clearly the most ancestral. Four genetic clusters were found within foxtail millet, each with a distinctive geographical distribution. These results, together with archaeobotanical evidence, suggest plausible routes of spread of foxtail millet. Selection scans identified nine candidate genes potentially involved in environmental adaptations, particularly to novel climates encountered, as domesticated foxtail millet spread to new altitudes and latitudes.
Collapse
Affiliation(s)
- Harriet V. Hunt
- McDonald Institute for Archaeological ResearchUniversity of CambridgeDowning StreetCambridgeCB2 3ERUK
| | - Natalia A. S. Przelomska
- Comparative Plant and Fungal BiologyRoyal Botanic GardensKewRichmondTW9 3AEUK
- Department of AnthropologyNational Museum of Natural HistorySmithsonian InstitutionWashingtonDC20560USA
- Center for Conservation GenomicsSmithsonian's National Zoo and Conservation Biology InstituteSmithsonian InstitutionWashingtonDC20008USA
- Department of ArchaeologyUniversity of CambridgeDowning StreetCambridgeCB2 3DZUK
| | - Michael G. Campana
- Center for Conservation GenomicsSmithsonian's National Zoo and Conservation Biology InstituteSmithsonian InstitutionWashingtonDC20008USA
| | - James Cockram
- The John Bingham LaboratoryNIAB93 Lawrence Weaver RoadCambridgeCB3 0LEUK
| | | | - Catherine J. Kneale
- McDonald Institute for Archaeological ResearchUniversity of CambridgeDowning StreetCambridgeCB2 3ERUK
| | - Olga I. Romanova
- N.I. Vavilov Institute of Plant Genetic Resources (VIR)St. Petersburg190000Russia
| | | | - Martin K. Jones
- Department of ArchaeologyUniversity of CambridgeDowning StreetCambridgeCB2 3DZUK
| |
Collapse
|
27
|
Gururani K, Sood S, Kumar A, Joshi DC, Pandey D, Sharma AR. Mainstreaming Barahnaja cultivation for food and nutritional security in the Himalayan region. BIODIVERSITY AND CONSERVATION 2021; 30:551-574. [PMID: 33526962 PMCID: PMC7838019 DOI: 10.1007/s10531-021-02123-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 01/09/2021] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
Selective production of input intensive crops in the present scenario have resulted in productivity stagnation or even decline due to excessive usage of chemicals, affecting the farmers economically. Sustainable agriculture is the way to increase agricultural productivity and economic prosperity by protecting all natural resources. It maintains a balance of soil fertility with crop productivity and nutritional quality. The mixed cropping systems followed earlier in different regions according to their tradition, climatic zone, soil and water conditions were climate-smart approaches to sustainable food production based on practical experiences over the years of old generations. The life style changes, imbalance in farming system in last 70 years and demand for more food as well as declining land resources resulted in intensive agriculture. Besides, least returns and less demand of ethnic crops gave more preference to major staple food crops. Barahnaja is a traditional orphan crops based mixed cropping system practiced in Himalayan region due to its sustainability and assured crop harvest during erratic weather conditions. This traditional farming method is an exemplary scientific approach to derive innovations with respect to productivity, quality, plant soil interactions and organic agriculture. The main focus of the review is to substantiate the characteristics of the traditional mixed cropping system by describing the advantages of the system and opportunities for scientific innovation towards new knowledge and sustainability.
Collapse
Affiliation(s)
- Kavita Gururani
- Department of Molecular Biology & Genetic Engineering, G.B. Pant Univ. of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Salej Sood
- Division of Crop Improvement, ICAR-Central Potato Research Institute Shimla, Shimla, Himachal Pradesh 171001 India
| | - Anil Kumar
- Central Agricultural University, Jhanshi, UP India
| | - Dinesh C. Joshi
- ICAR-Vivekanada Institute of Hill Agriculture, Almora, Uttarakhand 263601 India
| | - Dinesh Pandey
- Department of Molecular Biology & Genetic Engineering, G.B. Pant Univ. of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - A. R. Sharma
- Central Agricultural University, Jhanshi, UP India
| |
Collapse
|
28
|
Singh RK, Muthamilarasan M, Prasad M. Biotechnological approaches to dissect climate-resilient traits in millets and their application in crop improvement. J Biotechnol 2021; 327:64-73. [PMID: 33422569 DOI: 10.1016/j.jbiotec.2021.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/21/2020] [Accepted: 01/02/2021] [Indexed: 10/22/2022]
Abstract
'Small millets' is a generic term that includes all the millets except pearl millet and sorghum. These small or minor millets constitute eleven species that are marginally cultivated and consumed worldwide. These small millets possess excellent agronomic-, climate-resilient, and nutritional traits, although they lack popularity. Small millets withstand a broad spectrum of environmental stresses and possess better water-use and nitrogen-use efficiencies. Of note, small millets are five- to seven-fold nutritionally rich in terms of protein, bioactive compounds, micro- and macro-nutrients as compared to major cereals. Irrespective of these merits, small millets have received little research attention compared to major millets and cereals. However, the knowledge generated from such studies is significant for the improvement of millets per se and for translating the information to improve major cereals through breeding and transgene-based approaches. Given this, the review enumerates the efforts invested in dissecting the climate-resilient traits in small millets and provides a roadmap for deploying the information in crop improvement of millets as well as cereals in the scenario of climate change.
Collapse
Affiliation(s)
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi 110067, India.
| |
Collapse
|
29
|
A comprehensive study on core enzymes involved in starch metabolism in the model nutricereal, foxtail millet (Setaria italica L.). J Cereal Sci 2021. [DOI: 10.1016/j.jcs.2020.103153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
30
|
Chandra AK, Pandey D, Tiwari A, Sharma D, Agarwal A, Sood S, Kumar A. An Omics Study of Iron and Zinc Homeostasis in Finger Millet: Biofortified Foods for Micronutrient Deficiency in an Era of Climate Change? ACTA ACUST UNITED AC 2020; 24:688-705. [DOI: 10.1089/omi.2020.0095] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ajay Kumar Chandra
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, India
| | - Dinesh Pandey
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, India
| | - Apoorv Tiwari
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, India
- Department of Computational Biology and Bioinformatics, Sam Higginbottom University of Agriculture, Technology and Sciences (SHUATS), Allahabad, India
| | - Divya Sharma
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, India
- Department of Botany, Delhi University, Delhi, India
| | - Aparna Agarwal
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, India
- Department of Microbiology, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, India
| | - Salej Sood
- Department of Crop Improvement, Central Potato Research Institute, Shimla, India
| | - Anil Kumar
- Director of Education, Rani Lakshmi Bai Central Agricultural University, Jhansi, India
| |
Collapse
|
31
|
Zhao Z, Liu D, Cui Y, Li S, Liang D, Sun D, Wang J, Liu Z. Genome-wide identification and characterization of long non-coding RNAs related to grain yield in foxtail millet [Setaria italica (L.) P. Beauv.]. BMC Genomics 2020; 21:853. [PMID: 33261549 PMCID: PMC7709324 DOI: 10.1186/s12864-020-07272-9] [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: 04/04/2020] [Accepted: 11/23/2020] [Indexed: 12/05/2022] Open
Abstract
Background Long noncoding RNAs (lncRNAs) have been reported to play critical roles in diverse growth and development processes in plants. However, the systematic identification and characterization of lncRNAs in foxtail millet is nearly blank. Results In this study, we performed high-throughput sequencing of young spikelets from four foxtail millet varieties in different yield levels at booting stage. As a result, a total of 12,378 novel lncRNAs were identified, and 70 were commonly significantly differentially expressed in comparisons between high-yield varieties and conventional varieties, suggesting that they involved in yield formation and regulation in foxtail millet. Functional analysis revealed that among the 70 significantly differentially expressed lncRNAs, 67 could transcriptionally modulate target genes in cis and in trans. Moreover, 18 lncRNAs related to grain yield in foxtail millet were predicted to function as miRNA target mimics and regulate gene expression by competing for the interaction between miRNAs and their target mRNAs. Conclusion Our results will provide materials for elucidation of the molecular mechanisms of lncRNAs participate in yield regulation, and will contribute to high yield foxtail millet breeding. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07272-9.
Collapse
Affiliation(s)
- Zilong Zhao
- College of Agronomy, Shanxi Agricultural University, Taigu, China.,Department of Life Sciences, Tangshan Normal University, Tangshan, China
| | - Dan Liu
- Tianjin Key Laboratory of Crop Genetics and Breeding, Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Yanjiao Cui
- Department of Life Sciences, Tangshan Normal University, Tangshan, China
| | - Suying Li
- Department of Life Sciences, Tangshan Normal University, Tangshan, China
| | - Dan Liang
- Tianjin Key Laboratory of Crop Genetics and Breeding, Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Daizhen Sun
- College of Agronomy, Shanxi Agricultural University, Taigu, China.
| | - Jianhe Wang
- Tianjin Key Laboratory of Crop Genetics and Breeding, Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, China.
| | - Zhengli Liu
- Department of Life Sciences, Tangshan Normal University, Tangshan, China.
| |
Collapse
|
32
|
Essemine J, Qu M, Lyu MJA, Song Q, Khan N, Chen G, Wang P, Zhu XG. Photosynthetic and transcriptomic responses of two C 4 grass species with different NaCl tolerance. JOURNAL OF PLANT PHYSIOLOGY 2020; 253:153244. [PMID: 32818766 DOI: 10.1016/j.jplph.2020.153244] [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: 03/30/2020] [Revised: 07/16/2020] [Accepted: 07/16/2020] [Indexed: 05/15/2023]
Abstract
This report reveals the effects of salt on the photosynthetic electron transport and transcriptome of the glycophyte Setaria viridis (S. viridis) and its salt-tolerant close relative halophyte Spartina alterniflora (S. alterniflora). S. viridis was unable to survive exposed to sodium chloride (NaCl) levels higher than 100 mM, in contrast, S. alterniflora could tolerate NaCl up to 550 mM, with negligible effect on gas exchange related parameters and conductance of electrons transport chain (gETC). Under salt, the prompt fluorescence (OJIP-curves) exhibits an increase in the O- and J-steps in S. viridis and much less for S. alterniflora. Flowing NaCl stress, a dramatic decline in the photosystem II (PSII) primary photochemistry was observed for S. viridis, as reflected by the drastic drop in Fv/Fm, Fv/Fo and ΦPSII; however, no substantial change was recorded for these parameters in S. alterniflora. Interestingly, we found an increase in the primary PSII photochemistry (ΦPSII) for S. alterniflora with increasing either NaCl concentration or NaCl treatment duration. The NPQ magnitude was strongly enhanced for S. viridis even at a low NaCl (50 mM); however, it remains unchangeable or slightly increased for S. alterniflora at NaCl levels above 400 mM. After NaCl treatment, we found an increase in both the proportion of oxidized P700 and the amount of active P700 in S. viridis and almost no change for S. alterniflora. Under salt, the net photosynthetic rate (A) and stomatal conductance (gs) measurements demonstrate that A decreases earlier in S. viridis, even after one week exposure to only 50 mM NaCl; in contrast, in S. alterniflora, the effect of NaCl on A and gs was minor even after exposure for two weeks to high NaCl levels. For S. viridis exposed to 50 mM NaCl for 12 d, carbon dioxide (CO2) at a concentration of 2000 μL L-1 could not fully restore A to the control (Ctrl) level. Conversely, in S. alterniflora, high CO2 can fully restore A for all NaCl treatments except at 550 mM. RNA-seq data shows a major impact of NaCl on metabolic pathways in S. viridis and we found a number of transcription factors potentially related to NaCl responses. For S. alterniflora, no major changes in the transcriptomic levels were recorded under NaCl stress. To confirm our data analysis of RNA-seq, we performed quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis for randomly selected four genes for each species (8 genes in total) and we found that our results (up- and/or down-regulated genes) are fully consistent and match well our RNA-seq data. Overall, this study showed drastically different photosynthetic and transcriptomic responses of a salt-tolerant C4 grass species and one salt-sensitive C4 grass species to NaCl stress, which suggests that S. alterniflora could be used as a promising model species to study salt tolerance in C4 or monocot species.
Collapse
Affiliation(s)
- Jemaa Essemine
- National Key Laboratory of Plant Molecular Genetics, CAS-Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Mingnan Qu
- National Key Laboratory of Plant Molecular Genetics, CAS-Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Ming-Ju Amy Lyu
- National Key Laboratory of Plant Molecular Genetics, CAS-Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Qingfeng Song
- National Key Laboratory of Plant Molecular Genetics, CAS-Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Naveed Khan
- National Key Laboratory of Plant Molecular Genetics, CAS-Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Genyun Chen
- National Key Laboratory of Plant Molecular Genetics, CAS-Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Peng Wang
- CAS-Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Xin-Guang Zhu
- National Key Laboratory of Plant Molecular Genetics, CAS-Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200032, Shanghai, China.
| |
Collapse
|
33
|
Singh RK, Prasad A, Muthamilarasan M, Parida SK, Prasad M. Breeding and biotechnological interventions for trait improvement: status and prospects. PLANTA 2020; 252:54. [PMID: 32948920 PMCID: PMC7500504 DOI: 10.1007/s00425-020-03465-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/12/2020] [Indexed: 05/06/2023]
Abstract
Present review describes the molecular tools and strategies deployed in the trait discovery and improvement of major crops. The prospects and challenges associated with these approaches are discussed. Crop improvement relies on modulating the genes and genomic regions underlying key traits, either directly or indirectly. Direct approaches include overexpression, RNA interference, genome editing, etc., while breeding majorly constitutes the indirect approach. With the advent of latest tools and technologies, these strategies could hasten the improvement of crop species. Next-generation sequencing, high-throughput genotyping, precision editing, use of space technology for accelerated growth, etc. had provided a new dimension to crop improvement programmes that work towards delivering better varieties to cope up with the challenges. Also, studies have widened from understanding the response of plants to single stress to combined stress, which provides insights into the molecular mechanisms regulating tolerance to more than one stress at a given point of time. Altogether, next-generation genetics and genomics had made tremendous progress in delivering improved varieties; however, the scope still exists to expand its horizon to other species that remain underutilized. In this context, the present review systematically analyses the different genomics approaches that are deployed for trait discovery and improvement in major species that could serve as a roadmap for executing similar strategies in other crop species. The application, pros, and cons, and scope for improvement of each approach have been discussed with examples, and altogether, the review provides comprehensive coverage on the advances in genomics to meet the ever-growing demands for agricultural produce.
Collapse
Affiliation(s)
- Roshan Kumar Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ashish Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - Swarup K Parida
- 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.
| |
Collapse
|
34
|
Genomic dissection and expression analysis of stress-responsive genes in C4 panicoid models, Setaria italica and Setaria viridis. J Biotechnol 2020; 318:57-67. [DOI: 10.1016/j.jbiotec.2020.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/23/2020] [Accepted: 05/11/2020] [Indexed: 02/02/2023]
|
35
|
Renganathan VG, Vanniarajan C, Karthikeyan A, Ramalingam J. Barnyard Millet for Food and Nutritional Security: Current Status and Future Research Direction. Front Genet 2020; 11:500. [PMID: 32655612 PMCID: PMC7325689 DOI: 10.3389/fgene.2020.00500] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 04/22/2020] [Indexed: 01/09/2023] Open
Abstract
Barnyard millet (Echinochloa species) has become one of the most important minor millet crops in Asia, showing a firm upsurge in world production. The genus Echinochloa comprises of two major species, Echinochloa esculenta and Echinochloa frumentacea, which are predominantly cultivated for human consumption and livestock feed. They are less susceptible to biotic and abiotic stresses. Barnyard millet grain is a good source of protein, carbohydrate, fiber, and, most notably, contains more micronutrients (iron and zinc) than other major cereals. Despite its nutritional and agronomic benefits, barnyard millet has remained an underutilized crop. Over the past decades, very limited attempts have been made to study the features of this crop. Hence, more concerted research efforts are required to characterize germplasm resources, identify trait-specific donors, develop mapping population, and discover QTL/gene (s). The recent release of genome and transcriptome sequences of wild and cultivated Echinochloa species, respectively has facilitated in understanding the genetic architecture and decoding the rapport between genotype and phenotype of micronutrients and agronomic traits in this crop. In this review, we highlight the importance of barnyard millet in the current scenario and discuss the up-to-date status of genetic and genomics research and the research gaps to be worked upon by suggesting directions for future research to make barnyard millet a potential crop in contributing to food and nutritional security.
Collapse
Affiliation(s)
- Vellaichamy Gandhimeyyan Renganathan
- Department of Plant Breeding and Genetics, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
- Department of Biotechnology, Centre of Innovation, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Chockalingam Vanniarajan
- Department of Plant Breeding and Genetics, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Adhimoolam Karthikeyan
- Department of Biotechnology, Centre of Innovation, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Jegadeesan Ramalingam
- Department of Biotechnology, Centre of Innovation, Agricultural College & Research Institute, Tamil Nadu Agricultural University, Madurai, India
| |
Collapse
|
36
|
Yu A, Zhao J, Wang Z, Cheng K, Zhang P, Tian G, Liu X, Guo E, Du Y, Wang Y. Transcriptome and metabolite analysis reveal the drought tolerance of foxtail millet significantly correlated with phenylpropanoids-related pathways during germination process under PEG stress. BMC PLANT BIOLOGY 2020; 20:274. [PMID: 32539796 PMCID: PMC7296958 DOI: 10.1186/s12870-020-02483-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 06/04/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Foxtail millet [Setaria italica (L.) P. Beauv.] is an excellent crop known for its superior level of drought tolerance across the world. Especially, less water is needed during its germination period than the other cereal crops. However, the knowledge of the mechanisms underlying the abiotic stress effects on seed germination of foxtail millet is largely unknown. RESULTS The water uptake pattern of foxtail millet seeds was ploted during germination period, according to which the germination time course of millet was separated into three phases. We sequenced the transcriptome of foxtail millet seeds, which were treated by PEG during different germination phases after sowing. The transcriptional studies revealed that more DEGs were identified during the further increase in water uptake period (phase III) than during the rapid initial uptake period (phase I) and the plateau period (phase II) under PEG stress. The pathway analysis of DEGs showed that the highly enriched categories were related to phenylpropanoid biosynthesis, plant hormone signal transduction and phenylalanine metabolism during phase III. The 20 phenylpropanoids-related genes of germinating foxtail millet were found to be down-regulated during the further increase in water uptake period under PEG stress. Further expression analysis identified 4 genes of phenylalanine ammonia-lyase, 4-coumarate-CoA ligase 3, cinnamoyl-CoA reductase 1, cationic peroxidase SPC4 in phenylpropanoids-related pathway, which played important roles in foxtail millet in response to PEG stress during different germination periods. The studies of metabolites in phenylpropanoid biosynthesis pathway revealed that higher amount of cinnamic acid was accumulated in germinating seeds under PEG stress, while the contents of p-coumaric acid, caffeic acid, ferulic acid and sinapic acid were decreased. And the effects of five phenolic compounds on germination and growth of foxtail millet showed that 1 mM concentration of cinnamic acid inhibited shoot and root growth, especially root development. Ferulic acid, caffeic acid, sinapic acid and p-coumaric acid could increase the root length and root/sprout in lower concentration. CONCLUSIONS These findings suggest that key genes and metabolites of foxtail millet related with phenylpropanoids pathway may play prominent roles in the regulation of resistance to drought during germination. Foxtail millet can probably avoid drought by regulating the levels of endogenous allelochemicals.
Collapse
Affiliation(s)
- Aili Yu
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, 046011, China
| | - Jinfeng Zhao
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, 046011, China.
| | - Zhenhua Wang
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, 046011, China
| | - Kai Cheng
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, 046011, China
| | - Peng Zhang
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, 046011, China
| | - Gang Tian
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, 046011, China
| | - Xin Liu
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, 046011, China
| | - Erhu Guo
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, 046011, China
| | - Yanwei Du
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, 046011, China
| | - Yuwen Wang
- Millet Research Institute, Shanxi Academy of Agricultural Sciences, Changzhi, 046011, China
| |
Collapse
|
37
|
Ceasar SA, Ramakrishnan M, Vinod KK, Roch GV, Upadhyaya HD, Baker A, Ignacimuthu S. Phenotypic responses of foxtail millet (Setaria italica) genotypes to phosphate supply under greenhouse and natural field conditions. PLoS One 2020; 15:e0233896. [PMID: 32492057 PMCID: PMC7269269 DOI: 10.1371/journal.pone.0233896] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 05/14/2020] [Indexed: 01/12/2023] Open
Abstract
Food insecurity is a looming threat for the burgeoning world population. Phosphorus (P), which is absorbed from soil as inorganic phosphate (Pi), is an essential macronutrient for the growth of all agricultural crops. This study reports phenotype analysis for P responses in natural field and greenhouse conditions, using 54 genotypes of foxtail millet (Setaria italica) representing wide geographic origins. The genotype responses were assessed in natural field conditions in two different seasons (monsoon and summer) under Pi-fertilized (P+) and unfertilized (P-) soil for eight above-ground traits. Enormous variations were seen among the genotypes in phenotypic responses for all the measured parameters under low P stress conditions. Variations were significant for plant height, leaf number and length, tillering ability and seed yield traits. Genotypes ISe 1234 and ISe 1541 were P+ responders, and the genotypes ISe 1181, ISe 1655, ISe 783 and ISe 1892 showed tolerance to low P for total seed yield. Genotypes that performed well under P- conditions were almost as productive as genotypes that performed well under P+ conditions suggesting some genotypes are well adapted to nutrient-poor soils. In the greenhouse, most of the genotypes produced changes in root architecture that are characteristic of P- stress, but to differing degrees. Significant variation was seen in root hair density and root hair number and in fresh and dry weight of shoot and root under P- stress. However, there was not much difference in the shoot and root total P and Pi levels of five selected high and low responding genotypes. We noticed contrasting responses in the greenhouse and natural field experiments for most of these genotypes. The leads from the study form the basis for breeding and improvement of foxtail millet for better Pi-use efficiency.
Collapse
Affiliation(s)
- S. Antony Ceasar
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, India
- Centre for Plant Sciences, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - M. Ramakrishnan
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, India
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - K. K. Vinod
- Division of Genetics, ICAR—Indian Agricultural Research Institute, New Delhi, India
| | - G. Victor Roch
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, India
| | | | - Alison Baker
- Centre for Plant Sciences, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - S. Ignacimuthu
- Xavier Research Foundation, St. Xavier’s College, Palayamkottai, India
| |
Collapse
|
38
|
Bai H, Song Z, Zhang Y, Li Z, Wang Y, Liu X, Ma J, Quan J, Wu X, Liu M, Zhou J, Dong Z, Li D. The bHLH transcription factor PPLS1 regulates the color of pulvinus and leaf sheath in foxtail millet (Setaria italica). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1911-1926. [PMID: 32157354 DOI: 10.1007/s00122-020-03566-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/15/2020] [Indexed: 05/20/2023]
Abstract
The bHLH transcription factor, PPLS1, interacts with SiMYB85 to control the color of pulvinus and leaf sheath by regulating anthocyanin biosynthesis in foxtail millet (Setaria italica). Foxtail millet (Setaria italica), a self-pollinated crop with numerous small florets, is difficult for cross-pollination. The color of pulvinus and leaf sheath with purple being dominant to green is an indicative character and often used for screening authentic hybrids in foxtail millet crossing. Deciphering molecular mechanism controlling this trait would greatly facilitate genetic improvement of cultivars in foxtail millet. Here, using the F2 bulk specific-locus amplified fragment sequencing approach, we mapped the putative causal gene for the purple color of pulvinus and leaf sheath (PPLS) trait to a 100 Kb region on chromosome 7. Expression analyses of the 15 genes in this region revealed that Seita.7G195400 (renamed here as PPLS1) was differentially expressed between purple and green cultivars. PPLS1 encodes a bHLH transcription factor and is localized in the nucleus with a transactivation activity. Furthermore, we observed that expression of a MYB transcription factor gene, SiMYB85 (Seita.4G086300) involved in anthocyanin biosynthesis, shows a totally positive association with that of PPLS1. Heterologous co-expression of both PPLS1 and SiMYB85 in tobacco leaves led to elevated anthocyanin accumulation and expression of some anthocyanin-related genes. Furthermore, PPLS1 physically interacts with SiMYB85. Taken together, our results suggest that PPLS1 interacts with SiMYB85 to control the color of pulvinus and leaf sheath by regulating anthocyanin biosynthesis in foxtail millet.
Collapse
Affiliation(s)
- Hui Bai
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, National Foxtail Millet Improvement Center, Minor Cereal Crops Laboratory of Hebei Province, Shijiazhuang, 050035, China
| | - Zhenjun Song
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, National Foxtail Millet Improvement Center, Minor Cereal Crops Laboratory of Hebei Province, Shijiazhuang, 050035, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Yan Zhang
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Zhiyong Li
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, National Foxtail Millet Improvement Center, Minor Cereal Crops Laboratory of Hebei Province, Shijiazhuang, 050035, China
| | - Yongfang Wang
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, National Foxtail Millet Improvement Center, Minor Cereal Crops Laboratory of Hebei Province, Shijiazhuang, 050035, China
| | - Xue Liu
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing Key Laboratory of Vegetable Germplasms Improvement, National Engineering Research Center for Vegetables, Beijing, 100097, China
| | - Jifang Ma
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, National Foxtail Millet Improvement Center, Minor Cereal Crops Laboratory of Hebei Province, Shijiazhuang, 050035, China
| | - Jianzhang Quan
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, National Foxtail Millet Improvement Center, Minor Cereal Crops Laboratory of Hebei Province, Shijiazhuang, 050035, China
| | - Xianghong Wu
- Rice Research Institute of Sichuan Agricultural University, Chengdu, 611130, China
| | - Min Liu
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Jun Zhou
- College of Life Sciences, Nankai University, Tianjin, 300071, China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Zhiping Dong
- Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, National Foxtail Millet Improvement Center, Minor Cereal Crops Laboratory of Hebei Province, Shijiazhuang, 050035, China.
| | - Dayong Li
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing Key Laboratory of Vegetable Germplasms Improvement, National Engineering Research Center for Vegetables, Beijing, 100097, China.
| |
Collapse
|
39
|
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.
Collapse
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.
| |
Collapse
|
40
|
Santos CM, Romeiro D, Silva JP, Basso MF, Molinari HBC, Centeno DC. An improved protocol for efficient transformation and regeneration of Setaria italica. PLANT CELL REPORTS 2020; 39:501-510. [PMID: 31915913 DOI: 10.1007/s00299-019-02505-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 12/23/2019] [Indexed: 06/10/2023]
Abstract
An efficient and improved transformation method for functional genetics studies in S. italica, being a boon for the Setaria scientific community and for crop improvement. Foxtail millet (Setaria italica) is a short life cycle C4 plant, with sequenced genome, and a potential model plant for C4 species. S. italica is also important on a global food security and healthiness context due to its importance in arid and semi-arid areas. However, despite its importance, there are just few transformation protocols directed to this species. The current protocols reached about 5.5-9% of efficiency, which do not make it a valuable model organism. Different types of explants were used in the above mentioned methods, such as immature and mature inflorescence and shoot apex. However, these techniques have many limitations, such as unavailability of explants throughout the year and a crucial, laborious and considerable time-consuming selection. Aiming a simplified and efficient methodology, we adopted dry mature seeds as explants, which are available in abundance, are constant along the year and well responsive to tissue culture, in addition to a differentiated approach that reaches on an average 19.2% transformation efficiency of S. italica. Thus, we propose a protocol that optimizes the transformation efficiency of this cereal crop allowing a high increase on transformation and regeneration rates. Our transformation protocol provides an interesting tool for Setaria community research as well as enables new strategies for breeding enhanced productivity in the species.
Collapse
Affiliation(s)
- C M Santos
- Universidade Federal Do ABC, São Bernardo Do Campo, SP, Brazil
| | - D Romeiro
- Universidade Federal Do ABC, São Bernardo Do Campo, SP, Brazil
| | - J P Silva
- Universidade Federal Do ABC, São Bernardo Do Campo, SP, Brazil
| | - M F Basso
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy, Brasília, DF, Brazil
| | - H B C Molinari
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy, Brasília, DF, Brazil
| | - D C Centeno
- Universidade Federal Do ABC, São Bernardo Do Campo, SP, Brazil.
| |
Collapse
|
41
|
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.
Collapse
Affiliation(s)
| | | | | | - Rakesh K. Singh
- Crop Diversification and Genetics Program, International Center for Biosaline Agriculture, Dubai, United Arab Emirates
| |
Collapse
|
42
|
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.
Collapse
|
43
|
Xu W, Tang W, Wang C, Ge L, Sun J, Qi X, He Z, Zhou Y, Chen J, Xu Z, Ma YZ, Chen M. SiMYB56 Confers Drought Stress Tolerance in Transgenic Rice by Regulating Lignin Biosynthesis and ABA Signaling Pathway. FRONTIERS IN PLANT SCIENCE 2020; 11:785. [PMID: 32625221 PMCID: PMC7314972 DOI: 10.3389/fpls.2020.00785] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 05/18/2020] [Indexed: 05/19/2023]
Abstract
Foxtail millet (Setaria italica) originated in China and is generally cultivated in arid and barren soil. Through long-term harsh environmental selection, foxtail millet has acquired significant drought resistance. However, the molecular mechanism of foxtail millet drought resistance is still unknown. Here, we identified a drought-induced R2R3-MYB transcription factor SiMYB56 in foxtail millet. Overexpression of SiMYB56 significantly enhances tolerance to drought stress in transgenic rice plants at both the vegetative and the reproductive stage and has no adverse effect on its normal growth. Compared with wild-type controls, SiMYB56-overexpressing rice plants had lower MDA content and higher lignin content under drought conditions. Quantitative real-time PCR and Transcriptional activity assays demonstrated that SiMYB56 could activate expression of lignin biosynthesis genes under drought conditions. Also, we found that overexpression of SiMYB56 can led to ABA accumulation in the seeds transgenic rice plants. Further experiments showed that Overexpression of SiMYB56 can upregulate the expression of ABA synthesis and response related genes under drought conditions. In conclusion, SiMYB56 may enhance the drought resistance of transgenic rice plants by regulating lignin biosynthesis and ABA signaling pathway, making SiMYB56 a candidate gene for drought resistance improvement in gramineous crops.
Collapse
Affiliation(s)
- Weiya Xu
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wensi Tang
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunxiao Wang
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Linhao Ge
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianchang Sun
- Institute of Crop Sciences, Ningxia Academy of Agriculture and Forestry Sciences, Yongning, China
| | - Xin Qi
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhang He
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 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 Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jun Chen
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 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 Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - You-Zhi Ma
- National Key Facility for Crop Genetic Resources and Genetic Improvement, Key Laboratory of Crop Genetics and Breeding, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: You-Zhi Ma,
| | - 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 Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Ming Chen,
| |
Collapse
|
44
|
Chandra AK, Kumar A, Bharati A, Joshi R, Agrawal A, Kumar S. Microbial-assisted and genomic-assisted breeding: a two way approach for the improvement of nutritional quality traits in agricultural crops. 3 Biotech 2020; 10:2. [PMID: 31824813 DOI: 10.1007/s13205-019-1994-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 11/18/2019] [Indexed: 12/19/2022] Open
Abstract
Both human and animals, for their nutritional requirements, mainly rely on the plant-based foods, which provide a wide range of nutrients. Minerals, proteins, vitamins are among the nutrients which are essential and need to be available in adequate amount in edible portion of the staple crops. Increasing nutritional content in staple crops either through agronomic biofortification or through conventional plant-breeding strategies continue to be a huge task for scientists around the globe. Although some success has been achieved in recent past, in most cases, we have fallen short of expected targets. To maximize the nutrient uptake and partitioning to different economic part of plants, scientists have employed and tailored several biofortification strategies. But in present agricultural and environmental concerns, these approaches are not much effective. Henceforth, we are highlighting the recent developments and promising aspects of microbial-assisted and genomic-assisted breeding as candidate biofortification approach, that have contributed significantly in increasing nutritional content in grains of different crops. The methods used to date to accomplish nutrient enrichment with recently emerging strategies that we believe could be the most promising and holistic approach for future biofortification program. Results are encouraging, but for future perspective, the existing knowledge about the strategies needs to be confined. Concerted scientific investment are required to widen up these biofortification strategies, so that it could play an important role in ensuring nutritional security of ever-growing population in growing agricultural and environmental constraints.
Collapse
|
45
|
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.
Collapse
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
| |
Collapse
|
46
|
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.
Collapse
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.
| |
Collapse
|
47
|
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.
Collapse
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
| | | |
Collapse
|
48
|
Singh RK, Shweta S, Muthamilarasan M, Rani R, Prasad M. Study on aquaporins of Setaria italica suggests the involvement of SiPIP3;1 and SiSIP1;1 in abiotic stress response. Funct Integr Genomics 2019; 19:587-596. [PMID: 30759293 DOI: 10.1007/s10142-018-00653-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 12/17/2018] [Accepted: 12/26/2018] [Indexed: 11/26/2022]
Abstract
Aquaporins are versatile proteins involved in several biological as well as molecular functions, and they have been extensively studied in various plant systems. Increasing evidences indicate their role in biotic and abiotic stresses, and therefore, studying these proteins in a naturally stress-tolerant crop would provide further insights into the roles of this important protein family. Given this, the present study was performed in foxtail millet (Setaria italica), a model plant for studying biofuel, stress tolerance, and C4 photosynthetic traits. The study identified 12 plasma membrane intrinsic proteins (PIPs), 11 tonoplast intrinsic proteins (TIPs), 13 NOD26-like intrinsic proteins (NIPs), and 3 small basic intrinsic proteins (SIPs) in foxtail millet. The identified proteins and their corresponding genes were characterized using in silico approaches such as chromosomal localization, analysis of gene and protein properties, phylogenetic analysis, promoter analysis, and RNA-seq-derived expression profiling. The candidate genes identified through these analyses were studied for their expression in response to abiotic stresses (dehydration, salinity, and heat) as well as hormone treatments (abscisic acid, methyl jasmonate, and salicylic acid) in two contrasting cultivars of foxtail millet. The study showed that SiPIP3;1 and SiSIP1;1 were differentially expressed in both the cultivars in response to stress and hormone treatments. Overexpression of these genes in a heterologous yeast system also demonstrated that the transgenic cells were able to tolerate dehydration as well as salt stress which suggests the involvement of these proteins in the tolerance mechanism. Overall, the present study provides insights into structure and organization of the aquaporin gene family in foxtail millet and highlights the potential candidate genes for further functional characterizations.
Collapse
Affiliation(s)
- Roshan Kumar Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Shweta Shweta
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | | | - Rekha Rani
- 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.
| |
Collapse
|
49
|
Jaiswal V, Bandyopadhyay T, Gahlaut V, Gupta S, Dhaka A, Ramchiary N, Prasad M. Genome-wide association study (GWAS) delineates genomic loci for ten nutritional elements in foxtail millet (Setaria italica L.). J Cereal Sci 2019. [DOI: 10.1016/j.jcs.2018.11.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
50
|
Sun J, Luu NS, Chen Z, Chen B, Cui X, Wu J, Zhang Z, Lu T. Generation and Characterization of a Foxtail Millet ( Setaria italica) Mutant Library. FRONTIERS IN PLANT SCIENCE 2019; 10:369. [PMID: 31001298 PMCID: PMC6455083 DOI: 10.3389/fpls.2019.00369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 03/11/2019] [Indexed: 05/20/2023]
Abstract
Foxtail millet (Setaria italica) is attractive to plant scientists as a model plant because of several distinct characteristics, such as its short stature, rapid life cycle, sufficient seed production per plant, self-compatibility, true diploid nature, high photosynthetic efficiency, small genome size, and tolerance to abiotic and biotic stress. However, the study on the genetic resources of foxtail millet largely lag behind those of the other model plants such as Arabidopsis, rice and maize. Mutagenized populations cannot only create new germplasm resources, but also provide materials for gene function research. In this manuscript, an ethyl methanesulfonate (EMS)-induced foxtail millet population comprising ∼15,000 individual M1 lines was established. Total 1353 independent lines with diverse abnormal phenotypes of leaf color, plant morphologies and panicle shapes were identified in M2. Resequencing of sixteen randomly selected M2 plants showed an average estimated mutation density of 1 loci/213 kb. Moreover, we provided an example for rapid cloning of the WP1 gene by a map-based cloning method. A white panicle mutant, named as wp1.a, exhibited significantly reduced chlorophyll (Chl) and carotenoid contents in leaf and panicle. Map-based cloning results showed an eight-base pair deletion located at the sixth exon of wp1.a in LOC101786849, which caused the premature termination. WP1 encoded phytoene synthase. Moreover, the sequencing analysis and cross test verified that a white panicle mutant wp1.b was an allelic mutant of wp1.a. The filed phenotypic observation and gene cloning example showed that our foxtail millet EMS-induced mutant population would be used as an important resource for functional genomics studies of foxtail millet.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Tiegang Lu
- *Correspondence: Zhiguo Zhang, Tiegang Lu,
| |
Collapse
|