Genome Wide Association Analysis for Uniform Coleoptiles Emergence and Early Seedling Growth in Rice


Authors : Bhagyarabi Pani; G.M. Lal; Parameswaran C; Selvaraj Sabarinathan; Tejasmita Prusty; Asit Prasad Dash

Volume/Issue : Volume 9 - 2024, Issue 10 - October


Google Scholar : https://tinyurl.com/bdezspmw

Scribd : https://tinyurl.com/yubt8pf4

DOI : https://doi.org/10.38124/ijisrt/IJISRT24OCT1263

Note : A published paper may take 4-5 working days from the publication date to appear in PlumX Metrics, Semantic Scholar, and ResearchGate.


Abstract : Early seedling vigour (ESV) is a complex trait in rice. Detection of QTLs/genes controlling these traits can help us in enhancing the yield potential in rice varieties. Association mapping is a technique based on the principle of linkage disequilibrium that is used to find genes or quantitative trait loci (QTL) underlying the complex traits. In this study of haplotype breeding 281 rice genotypes were taken. ANOVA analysis showed P- value for traits and genotypes was found significant. Similarly, P-value for interaction between the traits and genotypes was also found to be highly significant (1.8663*10-208). Further, mean germination data positively correlated with mean shoot length, mean leaf number, mean culm diameter, mean shoot dry weight, and mean shoot area of 21st day among the 281 genotypes. Among the 281 number of genotypes, 111 genotypes are found to be in PCA1 and 170 genotypes are found to be in PCA2 based on the phenotypic analysis. PCA1 component constituted 29.93% and PCA2 constituted the 13.68% of total variation in the analysis. Besides, whole genome phylogenetic analysis showed three major groups of which Group 1 consists of 215 genotypes, group 2 consists of 38 genotypes and group 3 consists of 28 genotypes respectively. Especially, both the subgroups II and III comprised of the unique genotypes from the indica and aus subpopulations of rice. In this analysis, 16 significant associations (LOD Score >7) for different traits were identified using the three different models (MLM, farmCPU, and blink) for GWAS studies Especially, one major QTL was identified for the mean coleoptiles’ emergence for 10 DAS on 11th chromosome (18983591) which explained 49% of the phenotypic variance. Additionally, another major QTL contributing to the shoot length variation of 29.75% was identified in the Chr02 (32954393) for shoot length trait on 28 DAS. A candidate gene namely Os02g0778400 UMP/CMP kinase A/adenylate kinase (LOC_Os02g53790) was located in the significant SNP region of the GWAS analysis. Further characterization of this gene would assist in elucidation of the mechanism regulating the early seedling length in rice under direct seeded rice.

Keywords : ESV, GWAS, PCA, ANOVA, QTLs.

References :

  1. Abbai, R. Singh, V. K. Nachimuthu, V. V. Sinha, P. Selvaraj, R. Vipparla, A. K. and Kumar, A. (2019) Haplotype analysis of key genes governing grain yield and quality traits across 3K RG panel reveals scope for the development of tailor‐made rice with enhanced genetic gains. Plant biotechnology journal17(8), 1612-1622.
  2. Abe, A. Takagi, H. Fujibe, T. Aya, K. Kojima, M. Sakakibara, H. and Terauchi, R. (2012) OsGA20ox1, a candidate gene for a major QTL controlling seedling vigor in rice. Theoretical and Applied Genetics125, 647-657.
  3. Adhikary, S. Biswas, B. Chakraborty, D. Timsina, J. Pal, S. Chandra Tarafdar, J. and Roy, S. (2022) Seed priming with selenium and zinc nanoparticles modifies germination, growth, and yield of direct-seeded rice (Oryza sativa L.). Scientific Reports12(1), 7103.
  4. Anandan, A. Anumalla, M., Pradhan, S. K., and Ali, J. (2016) Population structure, diversity and trait association analysis in rice (Oryza sativa L.) germplasm for early seedling vigor (ESV) using trait linked SSR markers. PloS one11(3), e0152406.
  5. Anandan, A. Panda, S. Sabarinathan, S. Travis, A. J. Norton, G. J. and Price, A. H. (2022) Superior Haplotypes for Early Root Vigor Traits in Rice Under Dry Direct Seeded Low Nitrogen Condition Through Genome Wide Association Mapping. Frontiers in plant science13.
  6. Barik, S. R. Pandit, E. Sanghamitra, P. Mohanty, S. P. Behera, Mishra, J. and Pradhan, S. K. (2022) Unraveling the genomic regions controlling the seed vigour index, root growth parameters and germination per cent in rice. Plos one17(7), e0267303.
  7. Campbell, M. T. Du, Q. Liu, K. Brien, C. J. Berger, B. Zhang, C. and Walia, H. (2017) A comprehensive image‐based phenomic analysis reveals the complex genetic architecture of shoot growth dynamics in rice (Oryza sativa L.). The Plant Genome10(2), plantgenome 2016-07.
  8. Chamara, B. S. Marambe, B. Kumar, V. Ismail, A. M. Septiningsih, E. M. and Chauhan, B. S. (2018) Optimizing sowing and flooding depth for anaerobic germination-tolerant genotypes to enhance crop establishment, early growth, and weed management in dry-seeded rice (Oryza sativa L.). Frontiers in Plant Science9, 1654.
  9. Chen, K. Zhang, Q. Wang, C. C. Liu, Z. X. Jiang, Y. J. Zhai, L. Y. and Li, Z. K. (2019) Genetic dissection of seedling vigour in a diverse panel from the 3,000 Rice (Oryza sativa L.) Genome Project. Scientific Reports9(1), 4804.
  10. Chung, N. J. (2010) Elongation habit of mesocotyls and coleoptiles in weedy rice with high emergence ability in direct-seeding on dry paddy fields. Crop and Pasture Science61(11), 911-917.
  11. Counce, P. A. Keisling, T. C. and Mitchell, A. J. (2000) A uniform, objective, and adaptive system for expressing rice development. Crop Science40(2), 436-443.
  12. Cui, K. Peng, S. Xing, Y. Xu, C. Yu, S. & Zhang, Q. (2002) Molecular dissection of seedling-vigor and associated physiological traits in rice. Theoretical and Applied genetics105, 745-753.
  13. Dimaano, N. G. B. Ali, J. Mahender, A. Sta. Cruz, P. C. Baltazar, A. M. Diaz, M. G. Q. and Li, Z. (2020) Identification of quantitative trait loci governing early germination and seedling vigor traits related to weed competitive ability in rice. Euphytica216, 1-20.
  14. Farooq, M. K. H. M. Siddique, K. H. Rehman, H., Aziz, T. Lee, D. J. and Wahid, A. (2011). Rice direct seeding: experiences, challenges and opportunities. Soil and Tillage Research111(2), 87-98.
  15. Guo, T. Yang, J. Li, D. Sun, K. Luo, L. Xiao, W and Chen, Z. (2019) Integrating GWAS, QTL, mapping and RNA-seq to identify candidate genes for seed vigor in rice (Oryza sativa L.). Molecular Breeding39, 1-16.
  16. Jang, S. G. Park, S. Y., Lar, S. M., Zhang, H., Lee, A. R. Cao, F. Y. and Kwon, S. W. (2021). Genome-Wide Association Study (GWAS) of Mesocotyl Length for Direct Seeding in Rice. Agronomy11(12), 2527.
  17. Julius, B. T. Leach, K. A. Tran, T. M., Mertz, R. A. and Braun, D. M. (2017). Sugar transporters in plants: new insights and discoveries. Plant and Cell Physiology58(9), 1442-1460.
  18. Kalluru, S. Vemireddy, L. R. Ramireddy, E. Mohan Reddy, D. and Umamahesh, V. (2023) Identification of molecular markers and putative candidate genes associated with early seedling vigour traits in rice (Oryza sativa L.). Brazilian Journal of Botany46(1), 35-49.
  19. Kumari, S. Sharma, N., and Raghuram, N. (2021) Meta-analysis of yield-related and N-responsive genes reveals chromosomal hotspots, key processes and candidate genes for nitrogen-use efficiency in rice. Frontiers in Plant Science12, 627955.
  20. Li, M. Sun, P. Zhou, H. Chen, S. and Yu, S. (2011) Identification of quantitative trait loci associated with germination using chromosome segment substitution lines of rice (Oryza sativa L.). Theoretical and Applied Genetics123, 411-420.
  21. Li, W. Yang, B. Xu, J. Peng, L. Sun, S. Huang, Z. and Wang, Z. (2021). A genome‐wide association study reveals that the 2‐oxoglutarate/malate translocator mediates seed vigor in rice. The Plant Journal108(2), 478-491.
  22. Li, X. Zheng, H. Wu, W. Liu, H. Wang, J. Jia, Y. and Zhao, H. (2020). QTL mapping and candidate gene analysis for alkali tolerance in Japonica rice at the bud stage based on linkage mapping and genome-wide association study. Rice13, 1-11.
  23. Ma, Y. Wang, J. Yang, T. Dong, J. Yang, W. Chen, L. and Zhao, J. (2022). Genome-wide association mapping and gene expression analysis identify OsCPS1 as a new candidate gene controlling early seedling length in rice. Frontiers in Plant Science13, 3014.
  24. Mahajan, G. Sarlach, R. S. Japinder, S. & Gill, M. S. (2011). Seed priming effects on germination, growth and yield of dry direct-seeded rice. Journal of Crop Improvement25(4), 409-417.
  25. Mahender, A. Anandan, A. and Pradhan, S. K. (2015). Early seedling vigour, an imperative trait for direct-seeded rice: an overview on physio-morphological parameters and molecular markers. Planta241, 1027-1050.
  26. Mei, J. Wang, W. Peng, S. and Nie, L. (2017). Seed pelleting with calcium peroxide improves crop establishment of direct-seeded rice under waterlogging conditions. Scientific Reports7(1), 1-12.
  27. Menard, G. Sandhu, N. Anderson, D. Catolos, M. Hassall, K. L. Eastmond, P. J. and Kurup, S. (2021). Laboratory phenomics predicts field performance and identifies superior indica haplotypes for early seedling vigour in dry direct-seeded rice. Genomics113(6), 4227-4236.
  28. Money, D. Gardner, K. Migicovsky, Z. Schwaninger, H., Zhong, G. Y. and Myles, S. (2015). Link Impute: fast and accurate genotype imputation for non-model organisms. G3: Genes, Genomes, Genetics. 5(11), 2383-2390.
  29. Ogiwara, H. and Terashima, K. (2001). A varietal difference in coleoptile growth is correlated with seedling establishment of direct seeded rice in submerged field under low-temperature conditions. Plant production science4(3), 166-172.
  30. Pathak, H. Tewari, A. N. Sankhyan, S. Dubey, D. S. Mina, U. Singh, V. K. and Jain, N. (2011). Direct-seeded rice: potential, performance and problems-Areview. Current Advances in Agricultural Sciences (An International Journal)3(2), 77-88.
  31. Peng, L. Sun, S. Yang, B. Zhao, J. Li, W. Huang, Z. and Wang, Z. (2022). Genome‐wide association study reveals that the cupin domain protein OsCDP3. 10 regulates seed vigour in rice. Plant Biotechnology Journal20(3), 485-498.
  32. Quilloy, F. A. Labaco, B. Casal, C. and Dixit, S. (2021). Crop establishment in direct-seeded rice: Traits, physiology, and genetics. Rice Improvement. 27(8),171-202.
  33. Rao, A. N. Johnson, D. E. Sivaprasad, B. Ladha, J. K. and Mortimer, A. M. (2007). Weed management in direct‐seeded rice. Advances in agronomy. 93, 153-255.
  34. Roy, S. K. S. Hamid, A. Miah, M. G. and Hashem, A. (1996). Seed size variation and its effects on germination and seedling vigour in rice. Journal of Agronomy and Crop Science176(2), 79-82.
  35. Sandhu, N. Torres, R. O. Sta Cruz, M. T. Maturan, P. C. Jain, R., Kumar, A. and Henry, A. (2015). Traits and QTLs for development of dry direct-seeded rainfed rice varieties. Journal of Experimental Botany66(1), 225-244.
  36. Saud, S. Wang, D., Fahad, S. Alharby, H. F. Bamagoos, A. A. Mjrashi, A. and Hassan, S. (2022). Comprehensive Impacts of Climate Change on Rice Production and Adaptive Strategies in China. Frontiers in Microbiology13.
  37. Scofield, G. N. Aoki, N. Hirose, T. Takano, M. Jenkins, C. L. and Furbank, R. T. (2007). The role of the sucrose transporter, OsSUT1, in germination and early seedling growth and development of rice plants. Journal of Experimental Botany58(3), 483-495.
  38. Singh, U. M. Yadav, S. Dixit, S. Ramayya, P. J. Devi, M. N. Raman, K. A. and Kumar, A. (2017). QTL hotspots for early vigor and related traits under dry direct-seeded system in rice (Oryza sativa L.). Frontiers in plant science8, 286.
  39. Singh, U. M., Yadav, S. Dixit, S. Ramayya, P. J. Devi, M. N. Raman, K. A. and Kumar, A. (2017). QTL hotspots for early vigor and related traits under dry direct-seeded system in rice (Oryza sativa L.). Frontiers in plant science8, 286.
  40. Su, L. Yang, J. Li, D. Peng, Z. Xia, A. Yang, M. and Guo, T. (2021). Dynamic genome-wide association analysis and identification of candidate genes involved in anaerobic germination tolerance in rice. Rice14, 1-22.
  41. Subedi, S. R. Sandhu, N. Singh, V. K. Sinha, P. Kumar, S. Singh, S. P. and Kumar, A. (2019). Genome-wide association study reveals significant genomic regions for improving yield, adaptability of rice under dry direct seeded cultivation condition. BMC genomics20(1), 1-20.
  42. Thapa, R. and Septiningsih, E. M. (2021). Genome‐wide association study for traits related to seedling vigor in rice. Crop Science61(6), 3931-3946.
  43. Tyagi, W. Rai, M. and Dohling, A. (2012). Haplotype analysis for Pup1 locus in rice genotypes of North-Eastern and Eastern India to identify suitable donors tolerant to low phosphorus. SABRAO Journal of Breeding and Genetics44(2), 398-405.
  44. Wang, F. Longkumer, T. Catausan, S. C. Calumpang, C. L. F. Tarun, J. A. Cattin‐Ortola, J, Kretzschmar, T. (2018). Genome‐wide association and gene validation studies for early root vigour to improve direct seeding of rice. Plant, Cell & Environment41(12), 2731-2743.
  45. Wang, J. and Zhang, Z. (2021). GAPIT version 3: boosting power and accuracy for genomic association and prediction. Genomics, proteomics & bioinformatics. 19(4), 6.
  46. Wang, M. Chen, J. Zhou, F. Yuan, J. Chen, L. Wu, R. and Zhang, Q. (2021). The ties of brotherhood between japonica and indica rice for regional adaptation. Science China Life Sciences. 1-11.
  47. Wu, J. Feng, F. Lian, X. Teng, X. Wei, H. Yu, H. and Mei, H. (2015). Genome-wide Association Study (GWAS) of mesocotyl elongation based on re-sequencing approach in rice. BMC plant biology15(1), 1-10.
  48. Xie, L. Tan, Z. Zhou, Y. Xu, R. Feng, L. Xing, Y. and Qi, X. (2014). Identification and fine mapping of quantitative trait loci for seed vigor in germination and seedling establishment in rice. Journal of Integrative Plant Biology56(8), 749-759.
  49. Xu, L. Li, X. Wang, X. Xiong, D. and Wang, F. (2019). Comparing the grain yields of direct-seeded and transplanted rice: A meta-analysis. Agronomy9(11), 767.
  50. Yadav, S. Singh, U. M. Naik, S. M. Venkateshwarlu, C., Ramayya, P. J. Raman, K. A. and Kumar, A. (2017). Molecular mapping of QTLs associated with lodging resistance in dry direct-seeded rice (Oryza sativa L.). Frontiers in plant science8, 1431.
  51. Yang, B. Chen, M., Zhan, C., Liu, K. Cheng, Y. Xie, T. and Cheng, J. (2022). Identification of OsPK5 involved in rice glycolytic metabolism and GA/ABA balance for improving seed germination via genome-wide association study. Journal of Experimental Botany73(11), 3446-3461.
  52. Yang, J. Guo, Z. Luo, L. Gao, Q. Xiao, W. Wang, J. and Guo, T. (2021). Identification of QTL and candidate genes involved in early seedling growth in rice via high-density genetic mapping and RNA-seq. The Crop Journal9(2), 360-371.
  53. Yonemaru, J. I. Yamamoto, T. Ebana, K. Yamamoto, E. Nagasaki, H. Shibaya, T. and Yano, M. (2012). Genome-wide haplotype changes produced by artificial selection during modern rice breeding in Japan. Plosone7(3), e32982.
  54. Zeng, M. Yang, J. Wu, K. Wang, H. Sun, K. Chen, Z. and Chen, C. (2021). Genome-wide association study reveals early seedling vigour-associated quantitative trait loci in indica rice. Euphytica217, 1-16.
  55. Zhang, J. Guo, T. Yang, J. Hu, M. Wang, H. Sun, K. and Wang, H. (2020). QTL mapping and haplotype analysis revealed candidate genes for grain thickness in rice (Oryza sativa L.). Molecular Breeding40, 1-12.

Early seedling vigour (ESV) is a complex trait in rice. Detection of QTLs/genes controlling these traits can help us in enhancing the yield potential in rice varieties. Association mapping is a technique based on the principle of linkage disequilibrium that is used to find genes or quantitative trait loci (QTL) underlying the complex traits. In this study of haplotype breeding 281 rice genotypes were taken. ANOVA analysis showed P- value for traits and genotypes was found significant. Similarly, P-value for interaction between the traits and genotypes was also found to be highly significant (1.8663*10-208). Further, mean germination data positively correlated with mean shoot length, mean leaf number, mean culm diameter, mean shoot dry weight, and mean shoot area of 21st day among the 281 genotypes. Among the 281 number of genotypes, 111 genotypes are found to be in PCA1 and 170 genotypes are found to be in PCA2 based on the phenotypic analysis. PCA1 component constituted 29.93% and PCA2 constituted the 13.68% of total variation in the analysis. Besides, whole genome phylogenetic analysis showed three major groups of which Group 1 consists of 215 genotypes, group 2 consists of 38 genotypes and group 3 consists of 28 genotypes respectively. Especially, both the subgroups II and III comprised of the unique genotypes from the indica and aus subpopulations of rice. In this analysis, 16 significant associations (LOD Score >7) for different traits were identified using the three different models (MLM, farmCPU, and blink) for GWAS studies Especially, one major QTL was identified for the mean coleoptiles’ emergence for 10 DAS on 11th chromosome (18983591) which explained 49% of the phenotypic variance. Additionally, another major QTL contributing to the shoot length variation of 29.75% was identified in the Chr02 (32954393) for shoot length trait on 28 DAS. A candidate gene namely Os02g0778400 UMP/CMP kinase A/adenylate kinase (LOC_Os02g53790) was located in the significant SNP region of the GWAS analysis. Further characterization of this gene would assist in elucidation of the mechanism regulating the early seedling length in rice under direct seeded rice.

Keywords : ESV, GWAS, PCA, ANOVA, QTLs.

Never miss an update from Papermashup

Get notified about the latest tutorials and downloads.

Subscribe by Email

Get alerts directly into your inbox after each post and stay updated.
Subscribe
OR

Subscribe by RSS

Add our RSS to your feedreader to get regular updates from us.
Subscribe