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Gnanapragasam N, Prasanth VV, Sundaram KT, Kumar A, Pahi B, Gurjar A, Venkateshwarlu C, Kalia S, Kumar A, Dixit S, Kohli A, Singh UM, Singh VK, Sinha P. Extreme trait GWAS (Et-GWAS): Unraveling rare variants in the 3,000 rice genome. Life Sci Alliance 2024; 7:e202302352. [PMID: 38148113 PMCID: PMC10751245 DOI: 10.26508/lsa.202302352] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/28/2023] Open
Abstract
Identifying high-impact, rare genetic variants associated with specific traits is crucial for crop improvement. The 3,010 rice genome (3K RG) dataset offers a valuable resource for discovering genomic regions with potential applications in crop breeding. We used Extreme Trait GWAS (Et-GWAS), employing bulk pooling and allele frequency measurement to efficiently extract rare variants from the 3K RG. This innovative approach facilitates the detection of associations between genetic variants and target traits, concentrating and quantifying rare alleles. In our study, on grain yield under drought stress, Et-GWAS successfully identified five key genes (OsPP2C11, OsK5.2, OsIRO2, OsPEX1, and OsPWA1) known for enhancing yield under drought. In addition, we examined the overlap of our results with previously reported qDTY-QTLs and observed that OsUCH1 and OsUCH2 genes were located within qDTY2.2 We compared Et-GWAS with conventional GWAS, finding it effectively capturing most candidate genes associated with the target trait. Validation with resistant starch showed similar results. To enhance user-friendliness, we developed a GUI for Et-GWAS; https://et-gwas.shinyapps.io/Et-GWAS/.
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Affiliation(s)
| | | | | | - Ajay Kumar
- International Rice Research Institute, South Asia Hub, Patancheru, India
| | - Bandana Pahi
- International Rice Research Institute, South Asia Hub, Patancheru, India
| | - Anoop Gurjar
- International Rice Research Institute, South-Asia Regional Centre, Varanasi, India
| | | | - Sanjay Kalia
- Department of Biotechnology, CGO Complex, New Delhi, India
| | - Arvind Kumar
- International Rice Research Institute, South-Asia Regional Centre, Varanasi, India
| | - Shalabh Dixit
- International Rice Research Institute, Los Banos, Philippines
| | - Ajay Kohli
- International Rice Research Institute, Los Banos, Philippines
| | - Uma Maheshwer Singh
- International Rice Research Institute, South-Asia Regional Centre, Varanasi, India
| | - Vikas Kumar Singh
- International Rice Research Institute, South Asia Hub, Patancheru, India
| | - Pallavi Sinha
- International Rice Research Institute, South Asia Hub, Patancheru, India
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Nirgude M, Babu BK, Shambhavi Y, Singh UM, Upadhyaya HD, Kumar A. Development and molecular characterization of genic molecular markers for grain protein and calcium content in finger millet (Eleusine coracana (L.) Gaertn.). Mol Biol Rep 2014; 41:1189-200. [PMID: 24477581 DOI: 10.1007/s11033-013-2825-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Accepted: 10/25/2013] [Indexed: 11/29/2022]
Abstract
Finger millet (Eleusine coracana (L.) Gaertn), holds immense agricultural and economic importance for its high nutraceuticals quality. Finger millets seeds are rich source of calcium and its proteins are good source of essential amino acids. In the present study, we developed 36 EST-SSR primers for the opaque2 modifiers and 20 anchored-SSR primers for calcium transporters and calmodulin for analysis of the genetic diversity of 103 finger millet genotypes for grain protein and calcium contents. Out of the 36 opaque2 modifiers primers, 15 were found polymorphic and were used for the diversity analysis. The highest PIC value was observed with the primer FMO2E33 (0.26), while the lowest was observed FMO2E27 (0.023) with an average value of 0.17. The gene diversity was highest for the primer FMO2E33 (0.33), however it was lowest for FMO2E27 (0.024) at average value of 0.29. The percentage polymorphism shown by opaque2 modifiers primers was 68.23%. The diversity analysis by calcium transporters and calmodulin based anchored SSR loci revealed that the highest PIC was observed with the primer FMCA8 (0.30) and the lowest was observed for FMCA5 (0.023) with an average value of 0.18. The highest gene diversity was observed for primer FMCA8 (0.37), while lowest for FMCA5 (0.024) at an average of 0.21. The opaque2 modifiers specific EST-SSRs could able to differentiate the finger millet genotypes into high, medium and low protein containing genotypes. However, calcium dependent candidate gene based EST-SSRs could broadly differentiate the genotypes based on the calcium content with a few exceptions. A significant negative correlation between calcium and protein content was observed. The present study resulted in identification of highly polymorphic primers (FMO2E30, FMO2E33, FMO2-18 and FMO2-14) based on the parameters such as percentage of polymorphism, PIC values, gene diversity and number of alleles.
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Affiliation(s)
- M Nirgude
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences & Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, 263 145, India
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Griffiths GL, Singh UM, Hopkins D, Wilcox GE. Nutritional stress as a cause of thymic atrophy in broiler chickens. Avian Dis 1985; 29:103-6. [PMID: 3985868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A study was conducted to examine the effect of nutritional stress on the development of the thymus, bursa, and pancreas of 7-to-14-day-old commercial meat-type chickens. One group of 7-day-old chickens was given access to food for only 30 minutes daily for 7 days. The birds were necropsied, and the thymus, pancreas, and bursa were compared with those of the control chickens fed ad libitum and necropsied at 7 and 14 days of age. The thymuses from birds on the restricted diet were atrophied (0.45 +/- 0.08 g) and congested compared with the thymuses from chickens fed ad libitum (1.32 +/- 0.31 g). The bursae from chickens on a restricted diet were also smaller (0.26 +/- 0.08 g) than the bursae from birds with free access to food (0.74 +/- 0.11 g). The restricted diet did not appear to cause any gross or histological pancreatic changes. The thymic lesions produced by nutritional stress were similar to those observed in the runting/stunting syndrome.
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Singh UM, Doig PA, Ruhnke HL. Mycoplasma arthritis in calves. Can Vet J 1971; 12:183-5. [PMID: 5151524 PMCID: PMC1695434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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