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Eragam A, Mohapatra A, Shukla V, Kadumuri RV, George AP, Putta L, Akkareddy S, Chavali S, Vemireddy LR, Ramireddy E. Panicle transcriptome of high-yield mutant indica rice reveals physiological mechanisms and novel candidate regulatory genes for yield under reproductive stage drought stress. BMC PLANT BIOLOGY 2023; 23:493. [PMID: 37833626 PMCID: PMC10571340 DOI: 10.1186/s12870-023-04507-1] [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: 03/21/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND Reproductive stage drought stress (RDS) is a major global threat to rice production. Due to climate change, water scarcity is becoming an increasingly common phenomenon in major rice-growing areas worldwide. Understanding RDS mechanisms will allow candidate gene identification to generate novel rice genotypes tolerant to RDS. RESULTS To generate novel rice genotypes that can sustain yield under RDS, we performed gamma-irradiation mediated mutation breeding in the drought stress susceptible mega rice variety, MTU1010. One of the mutant MM11 (MTU1010 derived mutant11) shows consistently increased performance in yield-related traits under field conditions consecutively for four generations. In addition, compared to MTU1010, the yield of MM11 is sustained in prolonged drought imposed during the reproductive stage under field and in pot culture conditions. A comparative emerged panicle transcriptome analysis of the MTU1010 and MM11 suggested metabolic adjustment, enhanced photosynthetic ability, and hormone interplay in regulating yield under drought responses during emerged panicle development. Regulatory network analysis revealed few putative significant transcription factor (TF)-target interactions involved in integrated signalling between panicle development, yield and drought stress. CONCLUSIONS A gamma-irradiate rice mutant MM11 was identified by mutation breeding, and it showed higher potential to sustain yield under reproductive stage drought stress in field and pot culture conditions. Further, a comparative panicle transcriptome revealed significant biological processes and molecular regulators involved in emerged panicle development, yield and drought stress integration. The study extends our understanding of the physiological mechanisms and candidate genes involved in sustaining yield under drought stress.
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Affiliation(s)
- Aparna Eragam
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
- Department of Molecular Biology and Biotechnology, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, India
| | - Ankita Mohapatra
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
| | - Vishnu Shukla
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
| | - Rajashekar Varma Kadumuri
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
| | - Abin Panackal George
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
| | - Latha Putta
- Regional Agricultural Research Station (RARS), ANGRAU, Tirupati, India
| | | | - Sreenivas Chavali
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India
| | - Lakshminarayana R Vemireddy
- Department of Molecular Biology and Biotechnology, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, India.
| | - Eswarayya Ramireddy
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, 517507, Andhra Pradesh, India.
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Sao R, Sahu PK, Patel RS, Das BK, Jankuloski L, Sharma D. Genetic Improvement in Plant Architecture, Maturity Duration and Agronomic Traits of Three Traditional Rice Landraces through Gamma Ray-Based Induced Mutagenesis. PLANTS (BASEL, SWITZERLAND) 2022; 11:3448. [PMID: 36559562 PMCID: PMC9781505 DOI: 10.3390/plants11243448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/09/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Mutation breeding offers a simple, fast and efficient way to rectify major defects without altering their original identity. The present study deployed radiation (gamma rays @ 300Gy)-induced mutation breeding for the improvement and revival of three traditional rice landraces, viz., Samundchini, Vishnubhog and Jhilli. Among the various putative mutants identified in the M2 generation, only three, ten and five rice mutants of Samundchini, Vishnubhog and Jhilli, respectively, were advanced to the M4, M5 and M6 generations, along with their parents and three checks for evaluations based on 13 agro-morphological and 16 grain quality traits. Interestingly, all the mutants of the three landraces showed a reduction in days to 50% flowering and plant height as compared to their parents in all the three generations. The reduction in days to 50% flowering ranges from 4.94% (Vishnubhog Mutant V-67) to 21.40% (Jhilli Mutant J-2-13), whereas the reduction in plant height varies from 11.28% (Vishnubhog Mutant V-45-2, Vishnubhog Mutant V-67) to 37.65% (Jhilli Mutant J-15-1). Furthermore, two, six and three mutants of Samundchini, Vishnubhog and Jhilli have increased their yield potential over their corresponding parents, respectively. Interestingly, Samundchini Mutant S-18-1 (22.45%), Vishnubhog Mutant V-74-6 (36.87%) and Jhilli Mutant J-13-5 (25.96%) showed the highest yield advantages over their parents. Further, a pooled analysis of variance based on a randomized complete block design revealed ample variations among the genotypes for the studied traits. In addition, all the traits consistently showed high to moderate PCV and GCV and a slight difference between them in all three generations indicated the negligible effect of the environment. Moreover, in the association analysis, the traits, viz., fertile spikelets/panicle, panicle length, total tillers/plant, spikelet fertility percent and 100-seed weight showed the usual grain yield/plant, whereas the traits hulling (%) and milling (%) with HRR (%) consistently showed high direct effects and significant positive correlations. The SSR marker-based genome similarity in rice mutants and corresponding parents ranged from 95.60% to 71.70% (Vishnubhog); 95.62% to 89.10% (Samundchini) and 95.62% to 80.40% (Jhilli), indicating the trueness of the mutants. Moreover, the UPGMA algorithm and Gower distance-based dendrogram, neighbour joining tree and PCA scatter diagram assured that mutants were grouped with their respective parents and fell into separate clusters showing high similarity between mutants and parents and dissimilarity among the 24 genotypes. Overall, the information and materials generated from the current study will be very useful and informative for students, researchers and plant breeders. Additionally, our results also showed that irradiation could generate a considerable amount of genetic variability and provide new avenues for crop improvement and diversification.
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Affiliation(s)
- Richa Sao
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya (IGKV), Raipur 492012, India
| | - Parmeshwar K. Sahu
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya (IGKV), Raipur 492012, India
| | - Raviraj Singh Patel
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya (IGKV), Raipur 492012, India
| | - Bikram K. Das
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre (BARC), Mumbai 400085, India
| | - Ljupcho Jankuloski
- Plant Breeding and Genetics Section, Joint FAO/IAEA Centre, International Atomic Energy Agency, 1400 Vienna, Austria
| | - Deepak Sharma
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya (IGKV), Raipur 492012, India
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Thangwana A, Gwata ET, Zhou MM. Impact of chemical mutagenesis using ethyl methane sulphonate on tepary bean seedling vigour and adult plant performance. Heliyon 2021; 7:e06103. [PMID: 33553760 PMCID: PMC7848653 DOI: 10.1016/j.heliyon.2021.e06103] [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: 10/10/2020] [Revised: 11/20/2020] [Accepted: 01/22/2021] [Indexed: 11/30/2022] Open
Abstract
Tepary bean is an important food legume. The genetic improvement of the crop is limited by a narrow genetic base but this genetic base can be broadened through induced mutagenesis. This study was designed to determine the (i) effects of chemical mutagenesis using ethyl methane sulfonate (EMS) on M1 seedlings (ii) the adult plant performance of M2 - M4 generations and (iii) the relationships between growth attributes at the seedling and adult plant stage. Mutagenized seed with varying doses of EMS was germinated at room temperature in order to raise M1 seedlings. There were highly significant (P < 0.01) differences due to dose effects among the seedlings. The highest LD50 (3.37 % EMS v/v) was observed for ‘Genotype 3’. Under field conditions, all the three factors influenced the plant performance. The results demonstrated the potential of EMS to induce genotypic variation and desirable agronomic traits in tepary bean.
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Affiliation(s)
- Andries Thangwana
- University of Venda, School of Agriculture, Department of Plant Production, P. Bag X5050, Thohoyandou, 0950, South Africa
| | - Eastonce T Gwata
- University of Venda, School of Agriculture, Department of Plant Production, P. Bag X5050, Thohoyandou, 0950, South Africa
| | - Marvelous M Zhou
- South African Sugarcane Research Institute, P. Bag X02, Mount Edgecombe, 4300, South Africa
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Li Y, Xiong H, Zhang J, Guo H, Zhou C, Xie Y, Zhao L, Gu J, Zhao S, Ding Y, Fang Z, Liu L. Genome-Wide and Exome-Capturing Sequencing of a Gamma-Ray-Induced Mutant Reveals Biased Variations in Common Wheat. FRONTIERS IN PLANT SCIENCE 2021; 12:793496. [PMID: 35095966 PMCID: PMC8790116 DOI: 10.3389/fpls.2021.793496] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/09/2021] [Indexed: 05/13/2023]
Abstract
Induced mutagenesis is a powerful approach for the creation of novel germplasm and the improvement of agronomic traits. The evaluation of mutagenic effects and functional variations in crops is needed for breeding mutant strains. To investigate the mutagenic effects of gamma-ray irradiation in wheat, this study characterized genomic variations of wheat early heading mutant (eh1) as compared to wild-type (WT) Zhongyuan 9 (ZY9). Whole-genome resequencing of eh1 and ZY9 produced 737.7 Gb sequencing data and identified a total of 23,537,117 homozygous single nucleotide polymorphism (SNP) and 1,608,468 Indel. Analysis of SNP distribution across the chromosome suggests that mutation hotspots existed in certain chromosomal regions. Among the three subgenomes, the variation frequency in subgenome D was significantly lower than in subgenomes A and B. A total of 27.8 Gb data were obtained by exome-capturing sequencing, while 217,948 SNP and 13,554 Indel were identified. Variation annotation in the gene-coding sequences demonstrated that 5.0% of the SNP and 5.3% of the Indel were functionally important. Characterization of exomic variations in 12 additional gamma-ray-induced mutant lines further provided additional insights into the mutagenic effects of this approach. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) analysis suggested that genes with functional variations were enriched in several metabolic pathways, including plant-pathogen interactions and ADP binding. Kompetitive allele-specific PCR (KASP) genotyping with selected SNP within functional genes indicated that 85.7% of the SNPs were polymorphic between the eh1 and wild type. This study provides a basic understanding of the mechanism behind gamma-ray irradiation in hexaploid wheat.
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Affiliation(s)
- Yuting Li
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongchun Xiong
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiazi Zhang
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huijun Guo
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunyun Zhou
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongdun Xie
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Linshu Zhao
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiayu Gu
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shirong Zhao
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuping Ding
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhengwu Fang
- Hubei Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
- Zhengwu Fang,
| | - Luxiang Liu
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Luxiang Liu,
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