MARKER-ASSISTED DEVELOPMENT OF AN EXTRA-LONG GRAIN AND HIGH YIELDING BASMATI RICE LINE WITH SEMI-ERECT AND DENSE PANICLES

Abstract

In light of the rapidly growing global population, there is an urgent need to develop high-yielding and climateresilient rice varieties. The productivity of traditional basmati cultivars is limiting due to region-specific cultivation, and genetic improvements are direly needed to enhance their productivity without compromising quality attributes. This study aimed to develop high yielding basmati advance line with good quality attributes through a marker-assisted selection approach. A cross was attempted between Basmati 515 and IRBB 66, followed by pedigree selection up to the F5 generation. A uniform recombinant inbred line was identified then backcrossed with PK 1121 Aromatic and again followed by pedigree selection up to BC3F5 for desirable genotype development. Genes pyramiding for aroma (BADEX7-5), dense and erect panicles (DEP1), grain length (FMGS7) and grain width (GW8-indel) were achieved using gene-linked markers. The identified line “BLB 18-5001”, predominately harbored agronomic and quality characteristics of Basmati 515, panicle architecture, and grain dimension traits of IRBB 66 and PK 1121 Aromatic, respectively. The BLB 18-5001 outperformed in thousandgrain weight (28.5 g), grain yield (4.7 t ha-1), average grain length (9.22 mm), and cooked grain length (19.5 mm) compared to parents. A two-year field evaluation revealed superior agronomic and quality attributes of BLB 18-5001, suggesting an unprecedented genetic potential to meet future varietal demands. This study concludes that the BLB 18-5001 line has overcome the negative correlation between grain quality and yield to some extent and is expected to serve as a valuable breeding source to improve basmati productivity to meet the growing demand for food.

Keywords

• Aromatic rice
• Gene pyramiding
• Food security
• Molecular breeding
• Rice quality
• Varietal development

References

1. Akhter, M. and Z. Haider. 2020. Basmati Rice Production and Research in Pakistan. Springer, Cham, pp 119–136.
2. Ashikari, M., H. Sakakibara, S. Lin, T. Yamamoto, T. Takashi, A. Nishimura, E.R. Angeles, Q. Qian, H. Kitano and M. Matsuoka. 2005. Cytokinin oxidase regulates rice grain production. Science 309 (5735): 741-745.
3. Babu, N.N., S.G. Krishnan, K.K. Vinod, S.L. Krishnamurthy, V.K. Singh, M.P. Singh, R. Singh, R.K. Ellur, V. Rai, H. Bollinedi and P.K. Bhowmick. 2017. Marker aided incorporation of saltol, a major QTL associated with seedling stage salt tolerance, into Oryza sativa ‘pusa basmati 1121. Frontior in Plant Science 8:41.
4. Bradbury, L.M., R.J. Henry, Q. Jin, R.F. Reinke and D.L. Waters. 2005. A perfect marker for fragrance genotyping in rice. Molecular Breeding 16:279–283.
5. Bryant, R.J. and A.M. McClung. 2011. Volatile profiles of aromatic and non-aromatic rice cultivars using SPME/GC– MS. Food Chemistry 124(2): 501-513.
6. Doyle, J.J and J.L. Doyle. 1987. A rapid DNA isolation procedure from small quantities of fresh leaf material. Phytochemical Bulletin 19:11–15
7. Ellur, R.K., A. Khanna, A. Yadav, S. Pathania, H. Rajashekara, V. K. Singh, S. G. Krishnan, P.K. Bhowmick, M., Nagarajan, K.K. Vinod and G. Prakash. 2016. Improvement of Basmati rice varieties for resistance to blast and bacterial blight diseases using marker assisted backcross breeding. Plant Science 242:330–341.
8. Garris, A.J., T.H. Tai, J. Coburn, S. Kresovich and S. McCouch. 2005. Genetic structure and diversity in Oryza sativa L. Genetics 169(3): 1631-1638.

9. Gopalakrishnan, S., R.K. Sharma, K.A. Rajkumar, M. Joseph, V.P. Singh, A.K. Singh, K.V. Bhat, N.K. Singh and T. Mohapatra. 2008. Integrating marker assisted background analysis with foreground selection for identification of superior bacterial blight resistant recombinants in Basmati rice. Plant Breeding 127(2): 131-139.
10. Huang, X., Q. Qian, Z. Liu, H. Sun, S. He, D. Luo, G. Xia, C. Chu, J. Li and X. Fu. 2009. Natural variation at the DEP1 locus enhances grain yield in rice. Nature Genetics 41(4): 494-497.
11. Hussain, B., Q. Raza, R.M. Atif and M.Q. Ahmad. 2022. New Breeding Techniques (NBTs) and Biotechnology for Boosting Rice Grain Yield to Feed 5 Billion in 2050. In:Modoern Techology in Rice Crop Production, 681–700. Singapore: Springer Singapore.
12. Immanuel, S.C., N. Pothiraj, K. Thiyagarajan, M. Bharathi, Rabindran, R. 2011. Genetic parameters of variability, correlation and pathcoefficient studies for grain yield and other yield attributes among rice blast disease resistant genotypes of rice (Oryza sativa L.). African Journal of Biotechnology 10: 3322–3334.
13. Kondo, S. and Y. Futsuhara. 1980. Genetical studies on the panicle formation in rice. 1. Analysis of component characters of panicle density. Japanese Journal of Breeding 30:335–343
14. Lee, C.M., J. Park, B. Kim, J. Seo, G. Lee, S. Jang and H.J. Koh. 2015. Influence of multi-gene allele combinations on grain size of rice and development of a regression equation model to predict grain parameters. Rice 8(1): 1-10.
15. Nan, J., X. Feng, C. Wang, X. Zhang, R. Wang, J. Liu, Q. Yuan, G. Jiang and S. Lin. 2018. Improving rice grain length through updating the GS3 locus of an elite variety Kongyu 131. Rice 11: 1-9.
16. Ngangkham, U., S. Samantaray, M.K. Yadav, A. Kumar, P. Chidambaranathan and J.L. Katara. 2018. Effect of multiple allelic combinations of genes on regulating grain size in rice. PLoS One, 13(1):e0190684.
17. Popat, R., R. Patel and D. Parmar. 2022. Variability: Genetic Variability Analysis for Plant Breeding Research: R package version 0.1.0. https://CRAN.R-project.
18. org/package=variability. (Accessed 02 February 2023). Roy, S.C. and P. Shil. 2020. Assessment of Genetic Heritability in Rice Breeding Lines Based on Morphological Traits and Caryopsis Ultrastructure. Scientific Report, 10, 7830
19. Sabar, M., M. Akhter, T. Bibi, A. Riaz, Z. Haider, A.R. Khan and A. Bibi. 2019. Basmati rice lines development carrying multiple bacterial blight resistance genes pyramided using the marker-assisted backcross breeding approach. Molecular Breeding 39(10-11): 155.
20. Sakthivel, K., N. S. Rani, M.K. Pandey, A.K.P. Sivaranjani, C.N. Neeraja, S.M. Balachandran, M.S. Madhav, B.C. Viraktamath, G.S.V. Prasad and R.M. Sundaram. 2009. Development of a simple functional marker for fragrance in rice and its validation in Indian Basmati and non-Basmati fragrant rice varieties. Molecular breeding 24: 185-190.
21. SES, I. 2013. Standard evaluation system for rice. International Rice Research Institute, Philippines.
22. Shao, G., X. Wei, M. Chen, S. Tang, J. Luo, G. Jiao, L. Xie and P. Hu. 2012. Allelic variation for a candidate gene for GS7, responsible for grain shape in rice. Theoretical and Applied Genetics 125: 1303-1312.
23. Singh, A., V.K. Singh, S.P. Singh, R.T.P. Pandian, R.K. Ellur, D., Singh, P.K. Bhowmick, S. G. Krishnan, M. Nagarajan, K.K. Vinod and U.D. Singh. 2012. Molecular breeding for the development of multiple disease resistance in Basmati rice. AoB Plants 2012:pls02.
24. Singh, V., A.K. Singh, T. Mohapatra, and R.K. Ellur. 2018. Pusa Basmati 1121–a rice variety with exceptional kernel elongation and volume expansion after cooking. Rice 11: 1- 10.
25. Singh, V.K., A. Singh, S.P. Singh, R.K. Ellur, D. Singh, S.G. Krishnan, P.K. Bhowmick, M. Nagarajan, K.K. Vinod, U.D. Singh and T. Mohapatra. 2013. Marker‐assisted simultaneous but stepwise backcross breeding for pyramiding blast resistance genes Piz5 and Pi54 into an elite Basmati rice restorer line ‘PRR 78’. Plant Breeding 132(5): 486-495.
26. Taguchi-Shiobara, F., Y. Kawagoe, H. Kato, H. Onodera, A. Tagiri, N. Hara, A. Miyao, H. Hirochika, H. Kitano, M. Yano and S. Toki. 2011. A loss-of-function mutation of rice DENSE PANICLE 1 causes semi-dwarfness and slightly increased number of spikelets. Breeding Science 61(1): 17-25.
27. Takeda, S. and M. Matsuoka. 2008. Genetic approaches to crop improvement: Responding to environmental and population changes. Nature. Review of Genetics 9:444–457
28. Wakte, K., R. Zanan, V. Hinge, K. Khandagale, A. Nadaf and R. Henry. 2017. Thirty‐three years of 2‐acetyl‐1‐pyrroline, a principal basmati aroma compound in scented rice (Oryza sativa L.): a status review. Journal of the Science of Food and Agriculture 97(2): 384-395.
29. Wang, C.H., X.M. Zheng, Q. Xu, X.P. Yuan, L. Huang, H.F. Zhou, X.H Wei and S. Ge. 2014. Genetic diversity and classification of Oryza sativa with emphasis on Chinese rice germplasm. Heredity 112(5): 489-496.
30. Wang, S., K. Wu, Q. Yuan, X. Liu, Z. Liu, X. Lin, R. Zeng, H. Zhu, G. Dong, Q. Qian and G. Zhang. 2012. Control of grain size, shape and quality by OsSPL16 in rice. Nature Genetics 44(8): 950-954.
31. Wang, S., S. Li, Q. Liu, K. Wu, J. Zhang, S. Wang, Y. Wang, X. Chen, Y. Zhang, C. Gao and F. Wang. 2015. The OsSPL16- GW7 regulatory module determines grain shape and simultaneously improves rice yield and grain quality. Nature Genetics 47(8): 949-954.
32. Xi, Z.Y., F.H. He, R.Z. Zeng, Z.M. Zhang, X.H. Ding, W.T. Li and G.Q. Zhang. 2006. Development of a wide population of chromosome single-segment substitution lines in the genetic background of an elite cultivar of rice (Oryza sativa L.). Genome 49(5): 476-484.
33. Xu, Q., M. Zhao, K. Wu, X. Fu and Q. Liu. 2016. Emerging insights into heterotrimeric G protein signaling in plants. Journal of Genetics and Genomics 43(8): 495-502.
34. Yan, C.J., J.H. Zhou, S. Yan, F. Chen, M. Yeboah, S.Z. Tang, G.H. Liang and M.H. Gu. 2007. Identification and characterization of a major QTL responsible for erect panicle trait in japonica rice (Oryza sativa L.). Theoretical and Applied Genetics 115(8): 1093-1100.