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Ravikiran KT, Thribhuvan R, Anilkumar C, Kallugudi J, Prakash NR, Adavi B S, Sunitha NC, Abhijith KP. Harnessing the power of genomics to develop climate-smart crop varieties: A comprehensive review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2025; 373:123461. [PMID: 39622137 DOI: 10.1016/j.jenvman.2024.123461] [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: 04/12/2024] [Revised: 10/25/2024] [Accepted: 11/22/2024] [Indexed: 01/15/2025]
Abstract
Abiotic stresses arising as consequences of climate change pose a serious threat to agricultural productivity on a global scale. Most cultivated crop varieties exhibit susceptibility to such environmental pressures as drought, salinity, and waterlogging. Addressing these abiotic stresses through agronomic means is not only financially burdensome but also often impractical, particularly in the case of abiotic stresses like heat stress. Cultivating resilient varieties that can withstand such pressures emerges as an economically feasible strategy to mitigate these challenges. Nevertheless, the development of stress-tolerant cultivars is hindered by the intricate nature of abiotic stress tolerance, often characterized by low heritability values. Compounding this complexity is the dynamic and multifaceted nature of these stresses, which impede conventional breeding efforts, rendering them painstakingly slow. The identification of molecular markers has emerged as a pivotal advancement in this arena. By pinpointing genomic regions associated with tolerance to abiotic stresses, these markers serve as effective tools for selection and trait introgression. In the post-genomic era, the proliferation of high-density SNP markers has revolutionized breeding strategies. Genomic selection, leveraging these markers, has become the method of choice for addressing polygenic traits with low heritability, such as abiotic stress tolerance. With the functional characterization of many genes being done, precise manipulation through genome editing techniques is gaining significant traction. This review delves into the application of molecular markers in breeding stress-tolerant crop varieties, alongside role of recent genomic techniques in enhancing abiotic stress tolerance. It also explores success stories and identifies potential targets for marker-assisted selection.
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Affiliation(s)
- K T Ravikiran
- Indian Council of Agricultural Research-Central Soil Salinity Research Institute, Regional Research Station, Lucknow, Uttar Pradesh, India
| | - R Thribhuvan
- ICAR-Central Institute of Jute and Allied Fibres, Barrakpore, West Bengal, India
| | - C Anilkumar
- ICAR-National Rice Research Institute, Cuttak, Odisha, India; Department of Agronomy and Plant Genetics, University of Minnesota, MN, USA
| | - Jayanth Kallugudi
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Flowerdale, Shimla, Himachal Pradesh, India
| | - N R Prakash
- ICAR-CSSRI, Regional Research Station, Canning Town, West Bengal, India
| | - Sandeep Adavi B
- ICAR-National Institute of Biotic Stress Management, Raipur, Chhatisgarh, India
| | - N C Sunitha
- ICAR-National Rice Research Institute, Cuttak, Odisha, India
| | - Krishnan P Abhijith
- ICAR-Indian Agricultural Research Institute, Assam, Gogamukh, Dhemaji, Assam, India.
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James M, Tyagi W, Magudeeswari P, Neeraja CN, Rai M. Genome-Wide Association-Based Identification of Alleles, Genes and Haplotypes Influencing Yield in Rice ( Oryza sativa L.) Under Low-Phosphorus Acidic Lowland Soils. Int J Mol Sci 2024; 25:11673. [PMID: 39519225 PMCID: PMC11546970 DOI: 10.3390/ijms252111673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2024] [Revised: 10/27/2024] [Accepted: 10/28/2024] [Indexed: 11/16/2024] Open
Abstract
Rice provides poor yields in acidic soils due to several nutrient deficiencies and metal toxicities. The low availability of phosphorus (P) in acidic soils offers a natural condition for screening genotypes for grain yield and phosphorus utilization efficiency (PUE). The objective of this study was to phenotype a subset of indica rice accessions from 3000 Rice Genome Project (3K-RGP) under acidic soils and find associated genes and alleles. A panel of 234 genotypes, along with checks, were grown under low-input acidic soils for two consecutive seasons, followed by a low-P-based hydroponic screening experiment. The heritability of the agro-morphological traits was high across seasons, and Ward's clustering method identified 46 genotypes that can be used as low-P-tolerant donors in acidic soil conditions. Genotypes ARC10145, RPA5929, and K1559-4, with a higher grain yield than checks, were identified. Over 29 million SNPs were retrieved from the Rice SNP-Seek database, and after quality control, they were utilized for a genome-wide association study (GWAS) with seventeen traits. Ten quantitative trait nucleotides (QTNs) for three yield traits and five QTNs for PUE were identified. A set of 34 candidate genes for yield-related traits was also identified. An association study using this indica panel for an already reported 1.84 Mbp region on chromosome 2 identified genes Os02g09840 and Os02g08420 for yield and PUE, respectively. A haplotype analysis for the candidate genes identified favorable allelic combinations. Donors carrying the superior haplotypic combinations for the identified genes could be exploited in future breeding programs.
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Affiliation(s)
- M. James
- School of Crop Improvement, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam 793103, Meghalaya, India; (M.J.); (W.T.); (P.M.)
| | - Wricha Tyagi
- School of Crop Improvement, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam 793103, Meghalaya, India; (M.J.); (W.T.); (P.M.)
- Research Program—Accelerated Crop Improvement (ACI), International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, Telangana, India
| | - P. Magudeeswari
- School of Crop Improvement, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam 793103, Meghalaya, India; (M.J.); (W.T.); (P.M.)
| | - C. N. Neeraja
- ICAR—Indian Institute of Rice Research, Hyderabad 500030, Telangana, India;
| | - Mayank Rai
- School of Crop Improvement, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam 793103, Meghalaya, India; (M.J.); (W.T.); (P.M.)
- Post Graduate College of Agriculture, Dr. Rajendra Prasad Central Agricultural University (RPCAU), Samastipur 848125, Bihar, India
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Guha PK, Magar ND, Kommana M, Barbadikar KM, Suneel B, Gokulan C, Lakshmi DV, Patel HK, Sonti RV, Sundaram RM, Madhav MS. Strong culm: a crucial trait for developing next-generation climate-resilient rice lines. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:665-686. [PMID: 38737321 PMCID: PMC11087419 DOI: 10.1007/s12298-024-01445-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 03/24/2024] [Accepted: 03/27/2024] [Indexed: 05/14/2024]
Abstract
Lodging, a phenomenon characterized by the bending or breaking of rice plants, poses substantial constraints on productivity, particularly during the harvesting phase in regions susceptible to strong winds. The rice strong culm trait is influenced by the intricate interplay of genetic, physiological, epigenetic, and environmental factors. Stem architecture, encompassing morphological and anatomical attributes, alongside the composition of both structural and non-structural carbohydrates, emerges as a critical determinant of lodging resistance. The adaptive response of the rice culm to various biotic and abiotic environmental factors further modulates the propensity for lodging. Advancements in next-generation sequencing technologies have expedited the genetic dissection of lodging resistance, enabling the identification of pertinent genes, quantitative trait loci, and novel alleles. Concurrently, contemporary breeding strategies, ranging from biparental approaches to more sophisticated methods such as multi-parent-based breeding, gene pyramiding, genomic selection, genome-wide association studies, and haplotype-based breeding, offer perspectives on the genetic underpinnings of culm strength. This review comprehensively delves into physiological attributes, culm histology, epigenetic determinants, and gene expression profiles associated with lodging resistance, with a specialized focus on leveraging next-generation sequencing for candidate gene discovery.
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Affiliation(s)
- Pritam Kanti Guha
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
- Department of Microbiology, Yogi Vemana University., Y.S.R Kadapa, India
| | - Nakul D. Magar
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Madhavilatha Kommana
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Kalyani M. Barbadikar
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - B. Suneel
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - C. Gokulan
- Department of Biotechnology, CSIR-Center for Cellular and Molecular Biology, Hyderabad, India
| | - D. Vijay Lakshmi
- Department of Microbiology, Yogi Vemana University., Y.S.R Kadapa, India
| | - Hitendra Kumar Patel
- Department of Biotechnology, CSIR-Center for Cellular and Molecular Biology, Hyderabad, India
| | - Ramesh V. Sonti
- Department of Biotechnology, CSIR-Center for Cellular and Molecular Biology, Hyderabad, India
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - R. M. Sundaram
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Maganti Sheshu Madhav
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
- ICAR-Central Tobacco Research Institute, Rajahmundry, India
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Ahmad N, Ibrahim S, Kuang L, Ze T, Wang X, Wang H, Dun X. Integrating genome-wide association study with transcriptomic data to predict candidate genes influencing Brassica napus root and biomass-related traits under low phosphorus conditions. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:149. [PMID: 37789456 PMCID: PMC10548562 DOI: 10.1186/s13068-023-02403-2] [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: 07/12/2023] [Accepted: 09/21/2023] [Indexed: 10/05/2023]
Abstract
BACKGROUND Rapeseed (Brassica napus L.) is an essential source of edible oil and livestock feed, as well as a promising source of biofuel. Breeding crops with an ideal root system architecture (RSA) for high phosphorus use efficiency (PUE) is an effective way to reduce the use of phosphate fertilizers. However, the genetic mechanisms that underpin PUE in rapeseed remain elusive. To address this, we conducted a genome-wide association study (GWAS) in 327 rapeseed accessions to elucidate the genetic variability of 13 root and biomass traits under low phosphorus (LP; 0.01 mM P +). Furthermore, RNA-sequencing was performed in root among high/low phosphorus efficient groups (HP1/LP1) and high/low phosphorus stress tolerance groups (HP2/LP2) at two-time points under control and P-stress conditions. RESULTS Significant variations were observed in all measured traits, with heritabilities ranging from 0.47 to 0.72, and significant correlations were found between most of the traits. There were 39 significant trait-SNP associations and 31 suggestive associations, which integrated into 11 valid quantitative trait loci (QTL) clusters, explaining 4.24-24.43% of the phenotypic variance observed. In total, RNA-seq identified 692, 1076, 648, and 934 differentially expressed genes (DEGs) specific to HP1/LP1 and HP2/LP2 under P-stress and control conditions, respectively, while 761 and 860 DEGs common for HP1/LP1 and HP2/LP2 under both conditions. An integrated approach of GWAS, weighted co-expression network, and differential expression analysis identified 12 genes associated with root growth and development under LP stress. In this study, six genes (BnaA04g23490D, BnaA09g08440D, BnaA09g04320D, BnaA09g04350D, BnaA09g04930D, BnaA09g09290D) that showed differential expression were identified as promising candidate genes for the target traits. CONCLUSION 11 QTL clusters and 12 candidate genes associated with root and development under LP stress were identified in this study. Our study's phenotypic and genetic information may be exploited for genetic improvement of root traits to increase PUE in rapeseed.
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Affiliation(s)
- Nazir Ahmad
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Sani Ibrahim
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
- Department of Plant Biology, Faculty of Life Sciences, College of Physical and Pharmaceutical Sciences, Bayero University, P.M.B. 3011, Kano, 700006, Nigeria
| | - Lieqiong Kuang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Tian Ze
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Xinfa Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
- Hubei Hongshan Laboratory, Wuhan, 430062, China
| | - Hanzhong Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China.
- Hubei Hongshan Laboratory, Wuhan, 430062, China.
| | - Xiaoling Dun
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China.
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Comparative transcriptome analysis reveals a rapid response to phosphorus deficiency in a phosphorus-efficient rice genotype. Sci Rep 2022; 12:9460. [PMID: 35676419 PMCID: PMC9177723 DOI: 10.1038/s41598-022-13709-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/26/2022] [Indexed: 11/21/2022] Open
Abstract
Phosphorus (P) is an essential plant nutrient. Most rice growing lands lack adequate P, requiring multiple P fertiliser applications to obtain expected yields. However, P fertiliser is environmentally damaging, and already unaffordable to the marginal farmers. This warrants developing P-efficient rice varieties that require less P to produce the expected yield. However, genetic factors underlying P-use efficiency (PUE) in rice remain elusive. Here, we conducted comparative transcriptome analysis using two rice varieties with contrasting PUE; a P-efficient landrace DJ123 and a P-inefficient modern cultivar IR64. We aimed to understand the transcriptomic responses in DJ123 that allow it to achieve a high PUE under low P conditions. Our results showed that both DJ123 and IR64 had replete tissue P concentrations after 48 h of P deprivation. Yet, DJ123 strongly responded to the external low P availability by inducing P starvation-inducible genes that included SPX2, PHO1, PAPs and SQDs, while these genes were not significantly induced in IR64. We envisage that the ability of DJ123 to rapidly respond to low P conditions might be the key to its high PUE. Our findings lay a valuable foundation in elucidating PUE mechanism in rice, thus will potentially contribute to developing P-efficient modern rice variety.
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Shin NH, Han JH, Vo KTX, Seo J, Navea IP, Yoo SC, Jeon JS, Chin JH. Development of a Temperate Climate-Adapted indica Multi-stress Tolerant Rice Variety by Pyramiding Quantitative Trait Loci. RICE (NEW YORK, N.Y.) 2022; 15:22. [PMID: 35397732 PMCID: PMC8994804 DOI: 10.1186/s12284-022-00568-2] [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: 07/12/2021] [Accepted: 03/27/2022] [Indexed: 06/14/2023]
Abstract
Successful cultivation of rice (Oryza sativa L.) in many Asian countries requires submergence stress tolerance at the germination and early establishment stages. Two quantitative trait loci, Sub1 (conferring submergence tolerance) and AG1 (conferring anaerobic germination), were recently pyramided into a single genetic background, without compromising any desirable agronomic traits, leading to the development of Ciherang-Sub1 + AG1 (CSA). However, little research has been conducted to enhance plant tolerance to abiotic stress (submergence) and biotic stress (rice blast), which occur in a damp climate following flooding. The BC2F5 breeding line was phenotypically characterized using the AvrPi9 isolate. The biotic and abiotic stress tolerance of selected lines was tested under submergence stress and anaerobic germination conditions, and lines tolerant to each stress condition were identified through phenotypic and gene expression analyses. The Ciherang-Sub1 + AG1 + Pi9 (CSA-Pi9) line showed similar agronomic performance to its recurrent parent, CSA, but had significantly reduced chalkiness in field trials conducted in temperate regions. Unexpectedly, the CSA-Pi9 line also showed salinity tolerance. Thus, the breeding line newly developed in this study, CSA-Pi9, functioned under stress conditions, in which Sub1, AG1, and Pi9 play a role and had superior grain quality traits compared to its recurrent parent in temperate regions. We speculate that CSA-Pi9 will enable the establishment of climate-resilient rice cropping systems, particularly in East Asia.
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Affiliation(s)
- Na-Hyun Shin
- Department of Integrative Biological Sciences and Industry, College of Life Sciences, Sejong University, Seoul, 05006, Korea
| | - Jae-Hyuk Han
- Department of Integrative Biological Sciences and Industry, College of Life Sciences, Sejong University, Seoul, 05006, Korea
| | - Kieu Thi Xuan Vo
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Gyeonggi-do, 17104, Korea
| | - Jeonghwan Seo
- Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, 50463, Korea
- Life and Industry Convergence Research Institute, Pusan National University, Miryang, 50463, Korea
| | - Ian Paul Navea
- Department of Integrative Biological Sciences and Industry, College of Life Sciences, Sejong University, Seoul, 05006, Korea
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Banos, Philippines
| | - Soo-Cheul Yoo
- Department of Plant Life and Environmental Science, Hankyong National University, Anseong, Gyeonggi-do, 17579, Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Gyeonggi-do, 17104, Korea.
| | - Joong Hyoun Chin
- Department of Integrative Biological Sciences and Industry, College of Life Sciences, Sejong University, Seoul, 05006, Korea.
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Hibbert L, Taylor G. Improving phosphate use efficiency in the aquatic crop watercress (Nasturtium officinale). HORTICULTURE RESEARCH 2022; 9:uhac011. [PMID: 35147194 PMCID: PMC8969064 DOI: 10.1093/hr/uhac011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
Watercress is a nutrient-dense leafy green crop, traditionally grown in aquatic outdoor systems and increasingly seen as well-suited for indoor hydroponic systems. However, there is concern that this crop has a detrimental impact on the environment through direct phosphate additions causing environmental pollution. Phosphate-based fertilisers are supplied to enhanced crop yield, but their use may contribute to eutrophication of waterways downstream of traditional watercress farms. One option is to develop a more phosphate use efficient (PUE) crop. This review identifies the key traits for this aquatic crop (the ideotype), for future selection, marker development and breeding. Traits identified as important for PUE are (i) increased root surface area through prolific root branching and adventitious root formation, (ii) aerenchyma formation and root hair growth. Functional genomic traits for improved PUE are (iii) efficacious phosphate remobilisation and scavenging strategies and (iv) the use of alternative metabolic pathways. Key genomic targets for this aquatic crop are identified as: PHT phosphate transporter genes, global transcriptional regulators such as those of the SPX family and genes involved in galactolipid and sulfolipid biosynthesis such as MGD2/3, PECP1, PSR2, PLDζ1/2 and SQD2. Breeding for enhanced PUE in watercress will be accelerated by improved molecular genetic resources such as a full reference genome sequence that is currently in development.
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Affiliation(s)
- Lauren Hibbert
- School of Biological Sciences, University of Southampton, Southampton, Hampshire, SO17 1BJ, UK
- Department of Plant Sciences, UC Davis, Davis, CA, 95616, USA
| | - Gail Taylor
- School of Biological Sciences, University of Southampton, Southampton, Hampshire, SO17 1BJ, UK
- Department of Plant Sciences, UC Davis, Davis, CA, 95616, USA
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Kale RR, Durga Rani CV, Anila M, Mahadeva Swamy HK, Bhadana VP, Senguttuvel P, Subrahmanyam D, Ayyappa Dass M, Swapnil K, Anantha MS, Punniakotti E, Prasanna BL, Rekha G, Sinha P, Kousik MBVN, Dilip T, Hajira SK, Brajendra P, Mangrauthia SK, Gireesh C, Tuti M, Mahendrakumar R, Giri J, Singh P, Sundaram RM. Novel major QTLs associated with low soil phosphorus tolerance identified from the Indian rice landrace, Wazuhophek. PLoS One 2021; 16:e0254526. [PMID: 34264991 PMCID: PMC8282084 DOI: 10.1371/journal.pone.0254526] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/28/2021] [Indexed: 11/21/2022] Open
Abstract
With an objective of mapping novel low soil P (Phosphorus) tolerance loci in the non-Pup1 type donor rice line, Wazuhophek, we screened a recombinant inbred line (RIL) mapping population consisting of 330 lines derived from the cross Wazuhophek x Improved Samba Mahsuri (which is highly sensitive to low soil P) in a plot with low soil P for tolerance associated traits. Molecular mapping with SSR markers revealed a total of 16 QTLs (seven major and nine minor QTLs), which are associated with low soil P tolerance related traits. Interestingly, a QTL hotspot, harbouring 10 out of 16 QTLs were identified on the short arm of chromosome 8 (flanked by the makers RM22554 and RM80005). Five major QTLs explaining phenotypic variance to an extent of 15.28%, 17.25%, 21.84%, 20.23%, and 18.50%, associated with the traits, plant height, shoot length, the number of productive tillers, panicle length and yield, respectively, were located in the hotspot. Two major QTLs located on chromosome 1, associated with the traits, total biomass and root to shoot ratio, explaining 15.44% and 15.44% phenotypic variance, respectively were also identified. Complex epistatic interactions were observed among the traits, grain yield per plant, days to 50% flowering, dry shoot weight, and P content of the seed. In-silico analysis of genomic regions flanking the major QTLs revealed the presence of key putative candidate genes, possibly associated with tolerance.
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Affiliation(s)
- Ravindra Ramrao Kale
- Institute of Biotechnology, The Professor Jayashankar Telangana State Agricultural University, Rajendranagar, Hyderabad, India
- Indian Council of Agricultural Research -Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - Ch. V. Durga Rani
- Institute of Biotechnology, The Professor Jayashankar Telangana State Agricultural University, Rajendranagar, Hyderabad, India
| | - M. Anila
- Indian Council of Agricultural Research -Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - H. K. Mahadeva Swamy
- Indian Council of Agricultural Research—Sugarcane Breeding Institute, Coimbatore, India
| | - V. P. Bhadana
- Indian Council of Agricultural Research -Indian Institute of Agricultural Biotechnology, Ranchi, India
| | - P. Senguttuvel
- Indian Council of Agricultural Research -Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - D. Subrahmanyam
- Indian Council of Agricultural Research -Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - M. Ayyappa Dass
- Indian Council of Agricultural Research -Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - K. Swapnil
- Indian Council of Agricultural Research -Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - M. S. Anantha
- Indian Council of Agricultural Research -Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - E. Punniakotti
- Indian Council of Agricultural Research -Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - B. Laxmi Prasanna
- Institute of Biotechnology, The Professor Jayashankar Telangana State Agricultural University, Rajendranagar, Hyderabad, India
| | - G. Rekha
- Indian Council of Agricultural Research -Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - P. Sinha
- Indian Council of Agricultural Research -Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - M. B. V. N. Kousik
- Indian Council of Agricultural Research -Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - T. Dilip
- Indian Council of Agricultural Research -Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - S. K. Hajira
- Indian Council of Agricultural Research -Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - P. Brajendra
- Indian Council of Agricultural Research -Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - S. K. Mangrauthia
- Indian Council of Agricultural Research -Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - C. Gireesh
- Indian Council of Agricultural Research -Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - Mangaldeep Tuti
- Indian Council of Agricultural Research -Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - R. Mahendrakumar
- Indian Council of Agricultural Research -Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - Jitendra Giri
- Department of Biotechnology - National Institute of Plant Genome Research, New Delhi, India
| | - Pawandeep Singh
- Department of Biotechnology - National Institute of Plant Genome Research, New Delhi, India
| | - R. M. Sundaram
- Indian Council of Agricultural Research -Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
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9
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Ramalingam J, Palanisamy S, Alagarasan G, Renganathan VG, Ramanathan A, Saraswathi R. Improvement of Stable Restorer Lines for Blast Resistance through Functional Marker in Rice ( Oryza sativa L.). Genes (Basel) 2020; 11:genes11111266. [PMID: 33121205 PMCID: PMC7692511 DOI: 10.3390/genes11111266] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/21/2020] [Accepted: 08/26/2020] [Indexed: 11/16/2022] Open
Abstract
Two popular stable restorer lines, CB 87 R and CB 174 R, were improved for blast resistance through marker-assisted back-cross breeding (MABB). The hybrid rice development program in South India extensively depends on these two restorer lines. However, these restorer lines are highly susceptible to blast disease. To improve the restorer lines for resistance against blasts, we introgressed the broad-spectrum dominant gene Pi54 into these elite restorer lines through two independent crosses. Foreground selection for Pi54 was done by using gene-specific functional marker, Pi54 MAS, at each back-cross generation. Back-crossing was continued until BC3 and background analysis with seventy polymorphic SSRs covering all the twelve chromosomes to recover the maximum recurrent parent genome was done. At BC3F2, closely linked gene-specific/SSR markers, DRRM-RF3-10, DRCG-RF4-8, and RM 6100, were used for the identification of fertility restoration genes, Rf3 and Rf4, along with target gene (Pi54), respectively, in the segregating population. Subsequently, at BC3F3, plants, homozygous for the Pi54 and fertility restorer genes (Rf3 and Rf4), were evaluated for blast disease resistance under uniform blast nursery (UBN) and pollen fertility status. Stringent phenotypic selection resulted in the identification of nine near-isogenic lines in CB 87 R × B 95 and thirteen in CB 174 R × B 95 as the promising restorer lines possessing blast disease resistance along with restoration ability. The improved lines also showed significant improvement in agronomic traits compared to the recurrent parents. The improved restorer lines developed through the present study are now being utilized in our hybrid development program.
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Affiliation(s)
- Jegadeesan Ramalingam
- Department of Biotechnology, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai 625104, India;
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.P.); (G.A.)
- Correspondence:
| | - Savitha Palanisamy
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.P.); (G.A.)
| | - Ganesh Alagarasan
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.P.); (G.A.)
| | | | - Ayyasamy Ramanathan
- Department of Rice, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore 641003, India; (A.R.); (R.S.)
| | - Ramasamy Saraswathi
- Department of Rice, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore 641003, India; (A.R.); (R.S.)
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Joshi JB, Arul L, Ramalingam J, Uthandi S. Advances in the Xoo-rice pathosystem interaction and its exploitation in disease management. J Biosci 2020. [DOI: 10.1007/s12038-020-00085-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ramalingam J, Alagarasan G, Savitha P, Lydia K, Pothiraj G, Vijayakumar E, Sudhagar R, Singh A, Vedna K, Vanniarajan C. Improved host-plant resistance to Phytophthora rot and powdery mildew in soybean (Glycine max (L.) Merr.). Sci Rep 2020; 10:13928. [PMID: 32811867 PMCID: PMC7434881 DOI: 10.1038/s41598-020-70702-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 07/10/2020] [Indexed: 11/08/2022] Open
Abstract
Soybean is an important oilseed cum vegetable crop, susceptible to various biotic stresses which is attributed to recent decline in crop productivity. The emergence of virulent biotypes/strains of different plant pathogens necessitates the development of new crop varieties with enhanced host resistance mechanisms. Pyramiding of multiple disease-resistant genes is one of the strategies employed to develop durable disease-resistant cultivars to the prevailing and emerging biotypes of pathogens. The present study, reports the successful introgression of two major R-genes, including Rps2 (Phytophthora rot resistance), Rmd-c (complete-powdery mildew resistance) and effective nodulating gene (rj2) through functional Marker-Assisted Backcross Breeding (MABB) in the genetic background of well-adapted and high yielding soybean varieties, CO 3 and JS 335. We have identified several promising introgressed lines with enhanced resistance to Phytophthora rot and powdery mildew. The improved soybean lines have exhibited medium to high level of resistance against powdery mildew and Phytophthora rot as well as displayed effective nodulation capacity. Our study has proven the generation of resistant genotypes to realize the potential of MABB for achieving host plant resistance in soybean. The improved lines developed can greatly assist the soybean breeding programs in India and other soybean growing countries for evolving disease-resistant varieties.
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Affiliation(s)
- Jegadeesan Ramalingam
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India.
- Department of Biotechnology, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, India.
| | - Ganesh Alagarasan
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Palanisamy Savitha
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Kelsey Lydia
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Govindan Pothiraj
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India
| | - Eswaramoorthy Vijayakumar
- Department of Plant Breeding and Genetics, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | - Rajaprakasam Sudhagar
- Centre for Plant Breeding and Genetics, Department of Pulses, Tamil Nadu Agricultural University, Coimbatore, India
| | - Amar Singh
- Department of Plant Pathology, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, India
| | - Kumari Vedna
- Department of Plant Breeding and Genetics, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, India
| | - Chockalingam Vanniarajan
- Department of Plant Breeding and Genetics, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, India
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Jyoti A, Kaushik S, Srivastava VK, Datta M, Kumar S, Yugandhar P, Kothari SL, Rai V, Jain A. The potential application of genome editing by using CRISPR/Cas9, and its engineered and ortholog variants for studying the transcription factors involved in the maintenance of phosphate homeostasis in model plants. Semin Cell Dev Biol 2019; 96:77-90. [PMID: 30951893 DOI: 10.1016/j.semcdb.2019.03.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 12/26/2022]
Abstract
Phosphorus (P), an essential macronutrient, is pivotal for growth and development of plants. Availability of phosphate (Pi), the only assimilable P, is often suboptimal in rhizospheres. Pi deficiency triggers an array of spatiotemporal adaptive responses including the differential regulation of several transcription factors (TFs). Studies on MYB TF PHR1 in Arabidopsis thaliana (Arabidopsis) and its orthologs OsPHRs in Oryza sativa (rice) have provided empirical evidence of their significant roles in the maintenance of Pi homeostasis. Since the functional characterization of PHR1 in 2001, several other TFs have now been identified in these model plants. This raised a pertinent question whether there are any likely interactions across these TFs. Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system has provided an attractive paradigm for editing genome in plants. Here, we review the applications and challenges of this technique for genome editing of the TFs for deciphering the function and plausible interactions across them. This technology could thus provide a much-needed fillip towards engineering TFs for generating Pi use efficient plants for sustainable agriculture. Furthermore, we contemplate whether this technology could be a viable alternative to the controversial genetically modified (GM) rice or it may also eventually embroil into a limbo.
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Affiliation(s)
- Anupam Jyoti
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Sanket Kaushik
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | | | - Manali Datta
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Shailesh Kumar
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Poli Yugandhar
- ICAR-Indian Institute of Rice Research, Hyderabad, 500030, India
| | - Shanker L Kothari
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
| | - Vandna Rai
- National Research Centre on Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Campus, New Delhi, 110012, India
| | - Ajay Jain
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India.
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