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Magar ND, Barbadikar KM, Reddy V, Revadi P, Guha P, Gangatire D, Balakrishnan D, Sharma S, Madhav MS, Sundaram RM. Genetic mapping of regions associated with root system architecture in rice using MutMap QTL-seq. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 213:108836. [PMID: 38941724 DOI: 10.1016/j.plaphy.2024.108836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 04/04/2024] [Accepted: 06/11/2024] [Indexed: 06/30/2024]
Abstract
The root system architecture is an important complex trait in rice. With changing climatic conditions and soil nutrient deficiencies, there is an immediate need to breed nutrient-use-efficient rice varieties with robust root system architectural (RSA) traits. To map the genomic regions associated with crucial component traits of RSA viz. root length and root volume, a biparental F2 mapping population was developed using TI-128, an Ethyl Methane Sulphonate (EMS) mutant of a mega variety BPT-5204 having high root length (RL) and root volume (RV) with wild type BPT-5204. Extreme bulks having high RL and RV and low RL and RV were the whole genome re-sequenced along with parents. Genetic mapping using the MutMap QTL-Seq approach elucidated two genomic intervals on Chr.12 (3.14-3.74 Mb, 18.11-20.85 Mb), and on Chr.2 (23.18-23.68 Mb) as potential regions associated with both RL and RV. The Kompetitive Allele Specific PCR (KASP) assays for SNPs with delta SNP index near 1 were associated with higher RL and RV in the panel of sixty-two genotypes varying in root length and volume. The KASP_SNPs viz. Chr12_S4 (C→T; Chr12:3243938), located in the 3' UTR region of LOC_Os12g06670 encoding a protein kinase domain-containing protein and Chr2_S6 (C→T; Chr2:23181622) present upstream in the regulator of chromosomal condensation protein LOC_Os2g38350. Validation of these genes using qRT-PCR and in-silico studies using various online tools and databases revealed higher expression in TI-128 as compared to BPT- 5204 at the seedling and panicle initiation stages implying the functional role in enhancing RL and RV.
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Affiliation(s)
- Nakul D Magar
- ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India; Chaudhary Charan Singh University, Meerut, 250005, India
| | | | - Vishal Reddy
- ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | | | - Pritam Guha
- ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | - Dhiraj Gangatire
- ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | | | | | - M Sheshu Madhav
- ICAR-Central Tobacco Research Institute, Rajahmundry, 533106, India
| | - Raman M Sundaram
- ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
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2
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Lyu Y, Dong X, Niu S, Cao R, Shao G, Sheng Z, Jiao G, Xie L, Hu S, Tang S, Wei X, Hu P. An orchestrated ethylene-gibberellin signaling cascade contributes to mesocotyl elongation and emergence of rice direct seeding. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:1427-1439. [PMID: 38751025 DOI: 10.1111/jipb.13671] [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: 02/13/2024] [Accepted: 04/18/2024] [Indexed: 07/12/2024]
Abstract
A mechanized direct seeding of rice with less labor and water usage, has been widely adopted. However, this approach requires varieties that exhibit uniform seedling emergence. Mesocotyl elongation (ME) offers the main drive of fast emergence of rice seedlings from soils; nevertheless, its genetic basis remains unknown. Here, we identify a major rice quantitative trait locus Mesocotyl Elongation1 (qME1), an allele of the Green Revolution gene Semi-Dwarf1 (SD1), encoding GA20-oxidase for gibberellin (GA) biosynthesis. ME1 expression is strongly induced by soil depth and ethylene. When rice grains are direct-seeded in soils, the ethylene core signaling factor OsEIL1 directly promotes ME1 transcription, accelerating bioactive GA biosynthesis. The GAs further degrade the DELLA protein SLENDER RICE 1 (SLR1), alleviating its inhibition of rice PHYTOCHROME-INTERACTING FACTOR-LIKE13 (OsPIL13) to activate the downstream expansion gene OsEXPA4 and ultimately promote rice seedling ME and emergence. The ancient traits of long mesocotyl and strong emergence ability in wild rice and landrace were gradually lost in company with the Green Revolution dwarf breeding process, and an elite ME1-R allele (D349H) is found in some modern Geng varieties (long mesocotyl lengths) in northern China, which can be used in the direct seeding and dwarf breeding of Geng varieties. Furthermore, the ectopic and high expression of ME1 driven by mesocotyl-specific promoters resulted in rice plants that could be direct-seeded without obvious plant architecture or yield penalties. Collectively, we reveal the molecular mechanism of rice ME, and provide useful information for breeding new Green Revolution varieties with long mesocotyl suitable for direct-seeding practice.
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Affiliation(s)
- Yusong Lyu
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xinli Dong
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Shipeng Niu
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Ruijie Cao
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Guiai Jiao
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Lihong Xie
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Shikai Hu
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Peisong Hu
- State Key Laboratory of Rice Biology and Breeding, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
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3
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Kumar S, Seem K, Kumar S, Singh A, Krishnan SG, Mohapatra T. DNA methylome analysis provides insights into gene regulatory mechanism for better performance of rice under fluctuating environmental conditions: epigenomics of adaptive plasticity. PLANTA 2023; 259:4. [PMID: 37993704 DOI: 10.1007/s00425-023-04272-3] [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: 07/02/2023] [Accepted: 10/20/2023] [Indexed: 11/24/2023]
Abstract
MAIN CONCLUSION Roots play an important role in adaptive plasticity of rice under dry/direct-sown conditions. However, hypomethylation of genes in leaves (resulting in up-regulated expression) complements the adaptive plasticity of Nagina-22 under DSR conditions. Rice is generally cultivated by transplanting which requires plenty of water for irrigation. Such a practice makes rice cultivation a challenging task under global climate change and reducing water availability. However, dry-seeded/direct-sown rice (DSR) has emerged as a resource-saving alternative to transplanted rice (TPR). Though some of the well-adapted local cultivars are used for DSR, only limited success has been achieved in developing DSR varieties mainly because of a limited knowledge of adaptability of rice under fluctuating environmental conditions. Based on better morpho-physiological and agronomic performance of Nagina-22 (N-22) under DSR conditions, N-22 and IR-64 were grown by transplanting and direct-sowing and used for whole genome methylome analysis to unravel the epigenetic basis of adaptive plasticity of rice. Comparative methylome and transcriptome analyses indicated a large number (4078) of genes regulated through DNA methylation/demethylation in N-22 under DSR conditions. Gene × environment interactions play important roles in adaptive plasticity of rice under direct-sown conditions. While genes for pectinesterase, LRK10, C2H2 zinc-finger protein, splicing factor, transposable elements, and some of the unannotated proteins were hypermethylated, the genes for regulation of transcription, protein phosphorylation, etc. were hypomethylated in CG context in the root of N-22, which played important roles in providing adaptive plasticity to N-22 under DSR conditions. Hypomethylation leading to up-regulation of gene expression in the leaf complements the adaptive plasticity of N-22 under DSR conditions. Moreover, differential post-translational modification of proteins and chromatin assembly/disassembly through DNA methylation in CHG context modulate adaptive plasticity of N-22. These findings would help developing DSR cultivars for increased water-productivity and ecological efficiency.
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Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India.
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Archana Singh
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - S Gopala Krishnan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Liang C, Li Y, Zhang K, Wu Z, Liu J, Liu J, Zhou C, Wang S, Li F, Sui G. Selection and Yield Formation Characteristics of Dry Direct Seeding Rice in Northeast China. PLANTS (BASEL, SWITZERLAND) 2023; 12:3496. [PMID: 37836236 PMCID: PMC10575160 DOI: 10.3390/plants12193496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/23/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023]
Abstract
Dry direct seeding rice (DSR) is an emerging production system because of increasing labor and water scarcity in rice cultivation. The limited availability of rice cultivars suitable for dry direct seeding hampers the widespread adoption of this cultivation method in Northeast China. This study aimed to investigate grain production and plant characteristics associated with dry direct seeding rice. We conducted a field experiment on 79 japonica rice cultivars in Shenyang City, Liaoning Province, Northeast China, in 2020 and 2021. This study found that the grain yield of the tested rice cultivars ranged from 5.75-11.00 t ha-1, with a growth duration lasting between 144-161 days across the cultivars. These cultivars were then categorized into high yielding (HY), medium yielding (MY), and low yielding (LY) based on daily yield by using Ward's hierarchical clustering method. The higher grain yield for HY compared to MY and LY was attributed to more spikelets per unit area. The HY alleviated the conflict between higher panicle density and larger panicle size by improving the seedling emergence rate and productive stem rate. It also significantly increased shoot biomass at maturity. The HY reduced the period between seeding and beginning of heading (BBCH 51) and the proportion of dry matter partitioned to the leaf at the heading stage. However, it also increased the accumulation of dry matter in the grain and the proportion of dry matter partitioned to the grain at maturity. Furthermore, the HY markedly increased the harvest index and grain-leaf ratio, which are beneficial to coordinate the source-sink relationship. A quadratic function predicted that 98 days is the optimum growth duration before heading (BBCH 51) for achieving maximum yield. In conclusion, for dry direct seeding rice, it is appropriate to select high-yielding japonica inbred rice cultivars with shorter growth duration before heading (about 93-102 day), higher panicle number (about 450-500 × 104 ha-1), more spikelet number per panicle (about 110-130), higher seedling emergence rate (about 70-75%), higher productive stem rate (about 60-70%), and greater harvest index (about 50-55%).
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Affiliation(s)
- Chao Liang
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; (C.L.); (Y.L.); (K.Z.); (Z.W.); (J.L.); (J.L.); (F.L.)
| | - Yimeng Li
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; (C.L.); (Y.L.); (K.Z.); (Z.W.); (J.L.); (J.L.); (F.L.)
| | - Kunhao Zhang
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; (C.L.); (Y.L.); (K.Z.); (Z.W.); (J.L.); (J.L.); (F.L.)
| | - Zhouzhou Wu
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; (C.L.); (Y.L.); (K.Z.); (Z.W.); (J.L.); (J.L.); (F.L.)
| | - Jiaxin Liu
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; (C.L.); (Y.L.); (K.Z.); (Z.W.); (J.L.); (J.L.); (F.L.)
| | - Junfeng Liu
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; (C.L.); (Y.L.); (K.Z.); (Z.W.); (J.L.); (J.L.); (F.L.)
| | - Chanchan Zhou
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; (C.L.); (Y.L.); (K.Z.); (Z.W.); (J.L.); (J.L.); (F.L.)
| | - Shu Wang
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; (C.L.); (Y.L.); (K.Z.); (Z.W.); (J.L.); (J.L.); (F.L.)
| | - Fenghai Li
- College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China; (C.L.); (Y.L.); (K.Z.); (Z.W.); (J.L.); (J.L.); (F.L.)
| | - Guomin Sui
- Liaoning Academy of Agricultural Sciences, Shenyang 110161, China;
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Padmashree R, Barbadikar KM, Honnappa, Magar ND, Balakrishnan D, Lokesha R, Gireesh C, Siddaiah AM, Madhav MS, Ramesha YM, Bharamappanavara M, Phule AS, Senguttuvel P, Diwan JR, Subrahmanyam D, Sundaram RM. Genome-wide association studies in rice germplasm reveal significant genomic regions for root and yield-related traits under aerobic and irrigated conditions. FRONTIERS IN PLANT SCIENCE 2023; 14:1143853. [PMID: 37538056 PMCID: PMC10395336 DOI: 10.3389/fpls.2023.1143853] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/19/2023] [Indexed: 08/05/2023]
Abstract
The development of nutrient-use efficient rice lines is a priority amidst the changing climate and depleting resources viz., water, land, and labor for achieving sustainability in rice cultivation. Along with the traditional transplanted irrigated system of cultivation, the dry direct-seeded aerobic system is gaining ground nationwide. The root-related traits play a crucial role in nutrient acquisition, adaptation and need to be concentrated along with the yield-attributing traits. We phenotyped an association panel of 118 rice lines for seedling vigour index (SVI) traits at 14 and 21 days after sowing (DAS), root-related traits at panicle initiation (PI) stage in polythene bags under controlled aerobic condition, yield and yield-related traits under the irrigated condition at ICAR-IIRR, Hyderabad, Telangana; irrigated and aerobic conditions at ARS, Dhadesugur, Raichur, Karnataka. The panel was genotyped using simple sequence repeats (SSR) markers and genome-wide association studies were conducted for identifying marker-trait associations (MTAs). Significant correlations were recorded for root length, root dry weight with SVI, root volume at the PI stage, number of productive tillers per plant, spikelet fertility, the total number of grains per panicle with grain yield per plant under irrigated conditions, and the total number of grains per panicle with grain yield per plant under aerobic condition. The panel was divided into three sub-groups (K = 3) and correlated with the principal component analysis. The maximum number of MTAs were found on chromosomes 2, 3, and 12 with considerable phenotypic variability. Consistent MTAs were recorded for SVI traits at 14 and 21 DAS (RM25310, RM80, RM22961, RM1385), yield traits under irrigated conditions (RM2584, RM5179, RM410, RM20698, RM14753) across years at ICAR-IIRR, grain yield per plant (RM22961, RM1146) under the aerobic condition, grain yield per plant at irrigated ICAR-IIRR and SVI (RM5501), root traits at PI stage (RM2584, RM80, RM410, RM1146, RM18472). Functionally relevant genes near the MTAs through in-silico expression analysis in root and panicle tissues viz., HBF2 bZIP transcription factor, WD40 repeat-like domain, OsPILS6a auxin efflux carrier, WRKY108, OsSCP42, OsMADS80, nodulin-like domain-containing protein, amino acid transporter using various rice expression databases were identified. The identified MTAs and rice lines having high SVI traits (Langphou, TI-128, Mouli, TI-124, JBB-631-1), high yield under aerobic (Phouren, NPK-43, JBB-684, Ratnamudi, TI-112), irrigated conditions (KR-209, KR-262, Phouren, Keibi-Phou, TI-17), robust root traits like root length (MoirangPhou-Angouba, Wangoo-Phou, JBB-661, Dissi, NPK-45), root volume (Ratnachudi, KJ-221, Mow, Heimang-Phou, PUP-229) can be further employed in breeding programs for the targeted environments aimed at improving seedling vigour, yield-related traits under irrigated condition, aerobic condition as adaptability to water-saving technology.
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Affiliation(s)
- Revadi Padmashree
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
- University of Agricultural Sciences (UAS), Raichur, India
| | - Kalyani M. Barbadikar
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Honnappa
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
- University of Agricultural Sciences (UAS), Raichur, India
| | - Nakul D. Magar
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
- Chaudhary Charan Singh University, Meerut, India
| | - Divya Balakrishnan
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - R. Lokesha
- University of Agricultural Sciences (UAS), Raichur, India
| | - C. Gireesh
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Anantha M. Siddaiah
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Maganti Sheshu Madhav
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Y. M Ramesha
- Agricultural Research Station (ARS) Dhadesugur, University of Agricultural Sciences (UAS), Raichur, India
| | | | - Amol S. Phule
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - P. Senguttuvel
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - J. R. Diwan
- University of Agricultural Sciences (UAS), Raichur, India
| | - D. Subrahmanyam
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Raman Menakshi Sundaram
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
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6
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Ma S, Wang G, Su S, Lu J, Ren T, Cong R, Lu Z, Zhang Y, Liao S, Li X. Effects of optimized nitrogen fertilizer management on the yield, nitrogen uptake, and ammonia volatilization of direct-seeded rice. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:4553-4561. [PMID: 36852749 DOI: 10.1002/jsfa.12530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 02/22/2023] [Accepted: 02/28/2023] [Indexed: 06/06/2023]
Abstract
BACKGROUND Direct-seeded rice has been developed rapidly because of labor savings. Changes in rice cultivation methods put forward new requirements for nitrogen (N) fertilizer management practices. Field experiments with five different fertilizer ratios of basal, tillering and panicle fertilizer, namely N1 (10:0:0), N2 (6:2:2), N3 (4:3:3), N4 (2:4:4) and N5 (0:5:5), were conducted to investigate the effects of different N fertilizer management practices on yield formation, N uptakes, and ammonia (NH3 ) volatilization from paddy fields in direct-seeded rice. RESULTS The results showed that the N4 treatment improved grain yield by 5.1% while decreasing NH3 volatilization by 20.4% compared with that of conventional fertilizer treatment (N2). The panicle number per unit area was the key factor to determine the yield of direct-seeded rice (72%). Excessive N application of basal fertilizer (N1) reduced seedling emergence, N use efficiency, and yield by 45.3%, 160.6%, and 6.9% respectively and increased NH3 volatilization by 28.1% compared with that of the N4 treatment. Removal of basal N fertilizer (N5) N reduced spike number and yield by 13.0% and 6.9% respectively, minimizing NH3 volatilization while affecting the construction of high-yielding populations compared with that of the N4 treatment. CONCLUSION Optimized N fertilizer management achieved delayed senescence (maintenance of higher leaf Soil Plant Analysis Development meter values in late reproduction), higher canopy photoassimilation (suitable leaf area), higher N fertilizer use efficiency, and less N loss (lower cumulative NH3 volatilization). © 2023 Society of Chemical Industry.
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Affiliation(s)
- Shihao Ma
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Guibing Wang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Sumiao Su
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Jianwei Lu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Tao Ren
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Rihuan Cong
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Zhifeng Lu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Yangyang Zhang
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Shipeng Liao
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Xiaokun Li
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Wuhan, China
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7
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Song X, Chen Z, Du X, Li B, Fei Y, Tao Y, Wang F, Xu Y, Li W, Wang J, Liang G, Zhou Y, Tan X, Li Y, Yang J. Generation of new rice germplasms with low amylose content by CRISPR/CAS9-targeted mutagenesis of the FLOURY ENDOSPERM 2 gene. FRONTIERS IN PLANT SCIENCE 2023; 14:1138523. [PMID: 36993856 PMCID: PMC10040805 DOI: 10.3389/fpls.2023.1138523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
FLOURY ENDOSPERM 2 (FLO2), encoding a tetratricopeptide repeat domain (TPR)-containing protein located in the nucleus, is considered to be a regulatory protein that controls the biosynthesis of seed storage substances. The diversity of flo2 allele is attributable for the variations in grain appearance, amylose content (AC), and physicochemical properties, influencing the eating and cooking quality (ECQ) of rice. In this study, we used CRISPR/Cas9 to introduce loss-of-function mutations into the FLOURY ENDOSPERM 2 gene in Suken118 (SK118), a widely cultivated elite japonica rice variety in Jiangsu, China. Physiochemical analyses of the flo2 mutants were congruent with previous studies, exhibiting lowered AC and viscosity, risen gel consistency (GC) and gelatinization temperature (GT) values, which were all instrumental to the improvement of ECQ. However, the wrinkled opaque appearance and the decrease in grain width, grain thickness and grain weight imply trade-offs in grain yield. Despite the ex-ante estimation for low yielding, the superior ECQ in these novel genotypes generated by using genome editing approach may have the potential for formulating high value specialty food.
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Affiliation(s)
- Xiaohong Song
- School of Life Science, Jiangsu University, Zhenjiang, Jiangsu, China
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Key Laboratory of Germplasm Innovation in Downstream of Huaihe River Ministry of Agriculture and Rural Affairs, Nanjing, Jiangsu, China
| | - Zhihui Chen
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Key Laboratory of Germplasm Innovation in Downstream of Huaihe River Ministry of Agriculture and Rural Affairs, Nanjing, Jiangsu, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Xi Du
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Key Laboratory of Germplasm Innovation in Downstream of Huaihe River Ministry of Agriculture and Rural Affairs, Nanjing, Jiangsu, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Bin Li
- School of Life Science, Jiangsu University, Zhenjiang, Jiangsu, China
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Key Laboratory of Germplasm Innovation in Downstream of Huaihe River Ministry of Agriculture and Rural Affairs, Nanjing, Jiangsu, China
| | - Yunyan Fei
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Key Laboratory of Germplasm Innovation in Downstream of Huaihe River Ministry of Agriculture and Rural Affairs, Nanjing, Jiangsu, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Yajun Tao
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Key Laboratory of Germplasm Innovation in Downstream of Huaihe River Ministry of Agriculture and Rural Affairs, Nanjing, Jiangsu, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Fangquan Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Key Laboratory of Germplasm Innovation in Downstream of Huaihe River Ministry of Agriculture and Rural Affairs, Nanjing, Jiangsu, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Yang Xu
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Key Laboratory of Germplasm Innovation in Downstream of Huaihe River Ministry of Agriculture and Rural Affairs, Nanjing, Jiangsu, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Wenqi Li
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Key Laboratory of Germplasm Innovation in Downstream of Huaihe River Ministry of Agriculture and Rural Affairs, Nanjing, Jiangsu, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Jun Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Key Laboratory of Germplasm Innovation in Downstream of Huaihe River Ministry of Agriculture and Rural Affairs, Nanjing, Jiangsu, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Guohua Liang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Key Laboratory of Germplasm Innovation in Downstream of Huaihe River Ministry of Agriculture and Rural Affairs, Nanjing, Jiangsu, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Yong Zhou
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Key Laboratory of Germplasm Innovation in Downstream of Huaihe River Ministry of Agriculture and Rural Affairs, Nanjing, Jiangsu, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Xiaoli Tan
- School of Life Science, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yulong Li
- School of Life Science, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jie Yang
- School of Life Science, Jiangsu University, Zhenjiang, Jiangsu, China
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences/Key Laboratory of Germplasm Innovation in Downstream of Huaihe River Ministry of Agriculture and Rural Affairs, Nanjing, Jiangsu, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
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8
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Kumar S, Kumar S, Krishnan GS, Mohapatra T. Molecular basis of genetic plasticity to varying environmental conditions on growing rice by dry/direct-sowing and exposure to drought stress: Insights for DSR varietal development. FRONTIERS IN PLANT SCIENCE 2022; 13:1013207. [PMID: 36352870 PMCID: PMC9638133 DOI: 10.3389/fpls.2022.1013207] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 09/28/2022] [Indexed: 06/01/2023]
Abstract
Rice requires plenty of water for its cultivation by transplanting. This poses several challenges to its cultivation due to erratic rainfall resulting in drought, flood, and other abiotic stresses of varying intensity. Dry/direct-sown rice (DSR) has emerged as a water-saving/climate-smart alternative to transplanted rice (TPR). The performance of a rice cultivar on growing by different methods of planting under varying environmental conditions varies considerably. However, the molecular basis of the observed phenotypic plasticity of rice to varying environmental conditions is still elusive. Resilience to various environmental fluctuations is important to ensure sustainable rice production in the present era of global climate change. Our observations on exclusively up-regulated genes in leaf of Nagina 22 (N 22) grown by dry/direct-sowing and subjected to drought stress at panicle initiation stage (compared to that in leaf of IR 64), and another set of genes exclusively down-regulated in leaf of N 22 (compared to that in leaf of IR 64) indicate important roles of leaf in stress resilience. A large number of genes down-regulated exclusively in root of N 22 on dry/direct-sowing subjected to drought stress indicates a major contribution of roots in stress tolerance. The genes for redox-homeostasis, transcription factors, stress signaling, carbohydrate metabolism, and epigenetic modifications play important roles in making N 22 better adapted to DSR conditions. More importantly, the involvement of genes in rendering genetic plasticity to N 22 under changing environmental conditions was confirmed by reversal of the method of planting. To the best of our knowledge, this is the first report on decoding the molecular basis of genetic plasticity of rice grown by two different methods of planting subjected to drought stress at the reproductive stage of plant growth. This might help in DSR varietal development program to enhance water-productivity, conserve natural resources, and minimize the emission of greenhouse gases, thus achieving the objectives of negative-emission agriculture.
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Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Gopala S. Krishnan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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9
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Kumar S, Seem K, Kumar S, Mohapatra T. RNA-seq analysis reveals the genes/pathways responsible for genetic plasticity of rice to varying environmental conditions on direct-sowing and transplanting. Sci Rep 2022; 12:2241. [PMID: 35145168 PMCID: PMC8831524 DOI: 10.1038/s41598-022-06009-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/21/2022] [Indexed: 01/23/2023] Open
Abstract
Rice cultivation by transplanting requires plenty of water. It might become a challenging task in future to grow rice by transplanting due to the climatic change, water and labor scarcities. Direct-sown rice (DSR) is emerging as a resource-conserving and climate-smart alternative to transplanted rice (TPR). However, no specific variety has been bred for dry/direct-sown conditions. The present study was undertaken to decipher the molecular basis of genetic plasticity of rice under different planting methods. Comparative RNA-seq analysis revealed a number (6133) of genes exclusively up-regulated in Nagina-22 (N-22) leaf under DSR conditions, compared to that (3538) in IR64 leaf. Several genes up-regulated in N-22 were down-regulated in IR64. Genes for growth-regulation and nutrient-reservoir activities, transcription factors, translational machinery, carbohydrate metabolism, cell cycle/division, and chromatin organization/epigenetic modifications were considerably up-regulated in the leaf of N-22 under DSR conditions. Complementary effects of these factors in rendering genetic plasticity were confirmed by the agronomic/physiological performance of rice cultivar. Thus, growth-regulation/nutrient-reservoir activities, transcription factors, and translational machinery are important molecular factors responsible for the observed genetic plasticity/adaptability of Nagina-22 to different planting methods. This might help to develop molecular markers for DSR breeding, replacing TPR with DSR for better water-productivity, and minimizing greenhouse-gas emission necessary for negative emission agriculture.
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Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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Heredia MC, Kant J, Prodhan MA, Dixit S, Wissuwa M. Breeding rice for a changing climate by improving adaptations to water saving technologies. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:17-33. [PMID: 34218290 DOI: 10.1007/s00122-021-03899-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 06/25/2021] [Indexed: 06/13/2023]
Abstract
Climate change is expected to increasingly affect rice production through rising temperatures and decreasing water availability. Unlike other crops, rice is a main contributor to greenhouse gas emissions due to methane emissions from flooded paddy fields. Climate change can therefore be addressed in two ways in rice: through making the crop more climate resilient and through changes in management practices that reduce methane emissions and thereby slow global warming. In this review, we focus on two water saving technologies that reduce the periods lowland rice will be grown under fully flooded conditions, thereby improving water use efficiency and reducing methane emissions. Rice breeding over the past decades has mostly focused on developing high-yielding varieties adapted to continuously flooded conditions where seedlings were raised in a nursery and transplanted into a puddled flooded soil. Shifting cultivation to direct-seeded rice or to introducing non-flooded periods as in alternate wetting and drying gives rise to new challenges which need to be addressed in rice breeding. New adaptive traits such as rapid uniform germination even under anaerobic conditions, seedling vigor, weed competitiveness, root plasticity, and moderate drought tolerance need to be bred into the current elite germplasm and to what extent this is being addressed through trait discovery, marker-assisted selection and population improvement are reviewed.
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Affiliation(s)
| | | | - M Asaduzzaman Prodhan
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
| | - Shalabh Dixit
- International Rice Research Institute (IRRI), Los Baños, The Philippines
| | - Matthias Wissuwa
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan.
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11
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Proofing Direct-Seeded Rice with Better Root Plasticity and Architecture. Int J Mol Sci 2021; 22:ijms22116058. [PMID: 34199720 PMCID: PMC8199995 DOI: 10.3390/ijms22116058] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022] Open
Abstract
The underground reserve (root) has been an uncharted research territory with its untapped genetic variation yet to be exploited. Identifying ideal traits and breeding new rice varieties with efficient root system architecture (RSA) has great potential to increase resource-use efficiency and grain yield, especially under direct-seeded rice, by adapting to aerobic soil conditions. In this review, we tried to mine the available research information on the direct-seeded rice (DSR) root system to highlight the requirements of different root traits such as root architecture, length, number, density, thickness, diameter, and angle that play a pivotal role in determining the uptake of nutrients and moisture at different stages of plant growth. RSA also faces several stresses, due to excess or deficiency of moisture and nutrients, low or high temperature, or saline conditions. To counteract these hindrances, adaptation in response to stress becomes essential. Candidate genes such as early root growth enhancer PSTOL1, surface rooting QTL qSOR1, deep rooting gene DRO1, and numerous transporters for their respective nutrients and stress-responsive factors have been identified and validated under different circumstances. Identifying the desired QTLs and transporters underlying these traits and then designing an ideal root architecture can help in developing a suitable DSR cultivar and aid in further advancement in this direction.
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