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Debnath S, Dey A, Khanam R, Saha S, Sarkar D, Saha JK, Coumar MV, Patra BC, Biswas T, Ray M, Radhika MS, Mandal B. Historical shifting in grain mineral density of landmark rice and wheat cultivars released over the past 50 years in India. Sci Rep 2023; 13:21164. [PMID: 38036556 PMCID: PMC10689764 DOI: 10.1038/s41598-023-48488-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 11/27/2023] [Indexed: 12/02/2023] Open
Abstract
The 'Green Revolution (GR)' has been successful in meeting food sufficiency in India, but compromising its nutritional security. In a first, we report altered grain nutrients profile of modern-bred rice and wheat cultivars diminishing their mineral dietary significance to the Indian population. To substantiate, we evaluated grain nutrients profile of historical landmark high-yielding cultivars of rice and wheat released in succeeding decades since the GR and its impacts on mineral diet quality and human health, with a prediction for decades ahead. Analysis of grain nutrients profile shows a downward trend in concentrations of essential and beneficial elements, but an upward in toxic elements in past 50 y in both rice and wheat. For example, zinc (Zn) and iron (Fe) concentration in grains of rice decreased by ~ 33.0 (P < 0.001) and 27.0% (P < 0.0001); while for wheat it decreased by ~ 30.0 (P < 0.0001) and 19.0% (P < 0.0001) in past more than 50 y, respectively. A proposed mineral-diet quality index (M-DQI) significantly (P < 0.0001) decreased ~ 57.0 and 36.0% in the reported time span (1960-2010) in rice and wheat, respectively. The impoverished M-DQI could impose hostile effects on non-communicable diseases (NCDs) like iron-deficiency anemia, respiratory, cardiovascular, and musculoskeletal among the Indian population by 2040. Our research calls for an urgency of grain nutrients profiling before releasing a cultivar of staples like rice and wheat in the future.
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Affiliation(s)
- Sovan Debnath
- Directorate of Research, Bidhan Chandra Krishi Viswavidyalaya, Kalyani, West Bengal, 741 235, India
- Department of Agricultural Chemistry and Soil Science, Faculty of Agriculture, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, West Bengal, 741 252, India
- Indian Council of Agricultural Research (ICAR)-Central Institute of Temperate Horticulture, Regional Station Mukteshwar, Nainital, Uttarakhand, 263 138, India
- ICAR-Central Agroforestry Research Institute, Jhansi, Uttar Pradesh, 284 003, India
| | - Ahana Dey
- Department of Agricultural Chemistry and Soil Science, Faculty of Agriculture, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, West Bengal, 741 252, India
| | - Rubina Khanam
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753 006, India
| | - Susmit Saha
- College of Agriculture, Bidhan Chandra Krishi Viswavidyalaya, Burdwan Sadar, West Bengal, 713 101, India
| | - Dibyendu Sarkar
- Directorate of Research, Bidhan Chandra Krishi Viswavidyalaya, Kalyani, West Bengal, 741 235, India
- Department of Agricultural Chemistry and Soil Science, Faculty of Agriculture, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, West Bengal, 741 252, India
| | - Jayanta K Saha
- Division of Environmental Soil Science, ICAR-Indian Institute of Soil Science, Bhopal, Madhya Pradesh, 462 038, India
| | - Mounissamy V Coumar
- Division of Environmental Soil Science, ICAR-Indian Institute of Soil Science, Bhopal, Madhya Pradesh, 462 038, India
| | - Bhaskar C Patra
- ICAR-National Rice Research Institute, Cuttack, Odisha, 753 006, India
| | - Tufleuddin Biswas
- Department of Agricultural Statistics, Faculty of Agriculture, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, West Bengal, 741 252, India
- Department of Agricultural Economics and Statistics, M.S. Swaminathan School of Agriculture, Centurion University of Technology and Management, Bhubaneswar, Odisha, 761 211, India
| | - Mrinmoy Ray
- Division of Forecasting and Agricultural Systems Modeling, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110 012, India
| | - Madhari S Radhika
- Department of Dietetics, Indian Council of Medical Research-National Institute of Nutrition, Hyderabad, Telangana, 500 007, India
| | - Biswapati Mandal
- Directorate of Research, Bidhan Chandra Krishi Viswavidyalaya, Kalyani, West Bengal, 741 235, India.
- Department of Agricultural Chemistry and Soil Science, Faculty of Agriculture, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, West Bengal, 741 252, India.
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Anilkumar C, Sah RP, Muhammed Azharudheen TP, Behera S, Singh N, Prakash NR, Sunitha NC, Devanna BN, Marndi BC, Patra BC, Nair SK. Understanding complex genetic architecture of rice grain weight through QTL-meta analysis and candidate gene identification. Sci Rep 2022; 12:13832. [PMID: 35974066 PMCID: PMC9381546 DOI: 10.1038/s41598-022-17402-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 07/25/2022] [Indexed: 11/17/2022] Open
Abstract
Quantitative trait loci (QTL) for rice grain weight identified using bi-parental populations in various environments were found inconsistent and have a modest role in marker assisted breeding and map-based cloning programs. Thus, the identification of a consistent consensus QTL region across populations is critical to deploy in marker aided breeding programs. Using the QTL meta-analysis technique, we collated rice grain weight QTL information from numerous studies done across populations and in diverse environments to find constitutive QTL for grain weight. Using information from 114 original QTL in meta-analysis, we discovered three significant Meta-QTL (MQTL) for grain weight on chromosome 3. According to gene ontology, these three MQTL have 179 genes, 25 of which have roles in developmental functions. Amino acid sequence BLAST of these genes indicated their orthologue conservation among core cereals with similar functions. MQTL3.1 includes the OsAPX1, PDIL, SAUR, and OsASN1 genes, which are involved in grain development and have been discovered to play a key role in asparagine biosynthesis and metabolism, which is crucial for source-sink regulation. Five potential candidate genes were identified and their expression analysis indicated a significant role in early grain development. The gene sequence information retrieved from the 3 K rice genome project revealed the deletion of six bases coding for serine and alanine in the last exon of OsASN1 led to an interruption in the synthesis of α-helix of the protein, which negatively affected the asparagine biosynthesis pathway in the low grain weight genotypes. Further, the MQTL3.1 was validated using linked marker RM7197 on a set of genotypes with extreme phenotypes. MQTL that have been identified and validated in our study have significant scope in MAS breeding and map-based cloning programs for improving rice grain weight.
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Affiliation(s)
- C Anilkumar
- ICAR-National Rice Research Institute, Cuttack, India.
| | | | | | | | - Namita Singh
- Indira Gandhi Krishi Vishwavidyalaya, Raipur, India
| | - Nitish Ranjan Prakash
- ICAR-Central Soil Salinity Research Institute, Regional Research Station, Canning Town, India
| | - N C Sunitha
- University of Agricultural Sciences, Bangalore, India
| | - B N Devanna
- ICAR-National Rice Research Institute, Cuttack, India
| | - B C Marndi
- ICAR-National Rice Research Institute, Cuttack, India
| | - B C Patra
- ICAR-National Rice Research Institute, Cuttack, India
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Kumar A, Daware A, Kumar A, Kumar V, Gopala Krishnan S, Mondal S, Patra BC, Singh AK, Tyagi AK, Parida SK, Thakur JK. Genome-wide analysis of polymorphisms identified domestication-associated long low-diversity region carrying important rice grain size/weight quantitative trait loci. Plant J 2020; 103:1525-1547. [PMID: 32432802 DOI: 10.1111/tpj.14845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 05/01/2020] [Accepted: 05/12/2020] [Indexed: 05/02/2023]
Abstract
Rice grain size and weight are major determinants of grain quality and yield and so have been under rigorous selection since domestication. However, the genetic basis for contrasting grain size/weight trait among Indian germplasms and their association with domestication-driven evolution is not well understood. In this study, two long (LGG) and two short grain (SGG) genotypes were resequenced. LGG (LGR and PB 1121) differentiated from SGG (Sonasal and Bindli) by 504 439 single nucleotide polymorphisms (SNPs) and 78 166 insertion-and-deletion polymorphisms. The LRK gene cluster was different and a truncation mutation in the LRK8 kinase domain was associated with LGG. Phylogeny with 3000 diverse rice accessions revealed that the four sequenced genotypes belonged to the japonica group and were at the edge of the clades indicating them to be the potential source of genetic diversity available in Indian rice germplasm. Six SNPs were significantly associated with grain size/weight and the top four of these could be validated in mapping a population, suggesting this study as a valuable resource for high-throughput genotyping. A contiguous long low-diversity region (LDR) of approximately 6 Mb carrying a major grain weight quantitative trait loci (harbouring OsTOR gene) was identified on Chromosome 5. This LDR was identified as an evolutionary important site with significant positive selection and multiple selection sweeps, and showed association with many domestication-related traits, including grain size/weight. The aus population retained more allelic variations in the LDR than the japonica and indica populations, suggesting it to be one of the divergence loci. All the data and analyses can be accessed from the RiceSzWtBase database.
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Affiliation(s)
- Angad Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Anurag Daware
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Arvind Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Vinay Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - S Gopala Krishnan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, 110012, India
| | - Subhasish Mondal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Bhaskar C Patra
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, 753006, India
| | - Ashok K Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, 110012, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Swarup K Parida
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Jitendra K Thakur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
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Das S, Nayak M, Patra BC, Ramakrishnan B, Krishnan P. Characterization of seeds of selected wild species of rice (Oryza) stored under high temperature and humidity conditions. Indian J Biochem Biophys 2010; 47:178-184. [PMID: 20653290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Wild progenitors of rice (Oryza) are an invaluable resource for restoring genetic diversity and incorporating useful traits back into cultivars. Studies were conducted to characterize the biochemical changes, including SDS-PAGE banding pattern of storage proteins in seeds of six wild species (Oryza alta, O. grandiglumis, O. meridionalis, O. nivara, O. officinalis and O. rhizomatis) of rice stored under high temperature (45 degrees C) and humidity (approixmately 100%) for 15 days, which facilitated accelerated deterioration. Under the treated conditions, seeds of different wild rice species showed decrease in per cent germination and concentrations of protein and starch, but increase in conductivity of leachate and content of sugar. The SDS-PAGE analysis of seed proteins showed that not only the total number of bands, but also their intensity in terms of thickness differed for each species under storage. The total number of bands ranged from 11 to 22, but none of the species showed all the bands. Similarity index for protein bands between the control and treated seeds was observed to be least in O. rhizomatis and O. alta, while the indices were 0.7 and 0.625 for O. officinalis and O. nivara, respectively. This study clearly showed that seed deterioration led to distinctive biochemical changes, including the presence or absence as well as altered levels of intensity of proteins. Hence, SDS-PAGE protein banding pattern can be used effectively to characterize deterioration of seeds of different wild species of rice.
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Affiliation(s)
- Smruti Das
- Division of Biochemistry, Plant Physiology and Environmental Sciences, Central Rice Research Institute, Cuttack 753006
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Nanda PK, Swain P, Nayak SK, Dash S, Routray P, Swain SK, Patra BC. Goat serum as an alternative to establish cell culture from Indian major carp, Cirrhinus mrigala. In Vitro Cell Dev Biol Anim 2009; 45:148-51. [PMID: 19118441 DOI: 10.1007/s11626-008-9160-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Accepted: 11/10/2008] [Indexed: 11/27/2022]
Abstract
Serum from goat, calf, and chicken sources were evaluated in terms of attachment, growth, and proliferation of explants of Indian major carp, Cirrhinus mrigala. The attachment of explants viz. heart, liver, and kidney was directly proportional to the concentration of the serum. Among these sera, the highest percentage of attachment, growth, and proliferation was recorded for 10% goat serum and 15% newborn calf serum without affecting their cell morphology. On contrary to these sera, chicken serum at 15% concentration was found to be mildly toxic for all the explants. The cell count was significantly high for the kidney, liver, and heart at 10% goat serum among all the tested sera as well as concentration. Similarly, the liver, heart, and kidney explants were found to survive up to the tenth, seventh, and ninth passage, respectively. Therefore, the goat serum at 10% concentration can be used as effectively as newborn calf serum for routine culture of fish cells.
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Affiliation(s)
- P K Nanda
- Central Institute of Freshwater Aquaculture, Bhubaneswar, India
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Patra BC, Aditya AK. Circular form of regeneration in an unidentified species of land planarians, Bipalium sp. Indian J Exp Biol 2001; 39:496-9. [PMID: 11510140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
The communication describes an interesting and possibly novel finding regarding a species of land planarians (Bipalium sp.) from a high altitude of Himalayan range. The regeneration in Bipalium sp. is highly interesting and the process takes about a fortnight for the completion. Accumulation of numerous basophilic cells in parenchyma at the blastema region occurs within 5 days after excision and in 7 to 9 days the head and tail regions become reorganized with the formation of functional pharynx in the tail piece. The neoblast cells in the mesenchyme and the gastrodermis cells proliferate continuously replenishing the population of stem cell for growth, reproduction, and regeneration. Many undifferentiated cells are present even in completely regenerated specimens. Sometimes middle piece regenerates apparently fuse at the blastema surface forming a peculiar circular form of Bipalium sp. where both the head and tail cut ends join completely. These regenerated individuals excepting the middle piece regenerate behave in a normal fashion within 12-14 days.
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Affiliation(s)
- B C Patra
- Department of Zoology (DSA-UGC), Visva Bharati, Santiniketan, India
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Mohanty B, Patra BC. Role of mitomycin C in malignant tumours of gastro-intestinal tract. J Indian Med Assoc 1979; 72:201-3. [PMID: 544689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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