Current Science

Open Access Open Access  Restricted Access Subscription Access

Marker Validation and Sequencing in Aromatic Landrace Mushk Budji


Affiliations
1 Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Jammu and Kashmir 190 025, India
 

Aroma trait imparts specialty to rice and enhances its economic value in the market. Most aromatic genotypes are known to possess a truncated version of betaine aldehyde dehydrogenase gene, imparting aroma. Temperate rice varieties of Kashmir, India, have not been assessed for allelic variants of this fragranceimparting gene. Herein we report allelic variations present in exon 7 of this gene in the popular scented rice Mushk Budji. Unlike basmati-type genotypes, Mushk Budji is a short and bold japonica rice which grows at high altitudes and is cold-tolerant. Moreover, aroma retention after cooking is better in Mushk Budji compared to Pusa Sugandh 3, a long and thin basmati- type rice adapted to low-altitude areas of the Kashmir valley. Analysis showed the presence of a deletion of 8 bps ‘GATTATGG’ and three single nucleotide polymorphism in exon 7 of aromatic rice genotypes, including Mushk Budji. No such deletion was found in non-aromatic rice varieties. Additionally, one functional marker for badh2 allele was validated in Mushk Budji. These findings can facilitate the development of short and bold fragrant rice varieties through marker assisted selection, especially for highaltitude cold regions and the temperate valley conditions of Kashmir and the rest of India.

Keywords

Aromatic Landrace, Functional Markers, Sequencing.
User
Notifications
Font Size

  • Sakthivel, K., Sundaram, R. M., Shobha-Rani, N., Balachandran, S. M. and Neeraja, C. N., Genetic and molecular basis of fragrance in rice. Biotechnol. Adv., 2009, 27, 468–473.

  • Buttery, R. G., Ling, L. C. and Juliano, B. O., 2-Acetyl-1pyrroline; an important aroma component of cooked rice. Chem. Ind. (London), 1982, 23, 958–959.

  • Kovach, M. J., Calingacion, M. N., Fitzgerald, M. A. and McCouch, S. R., The origin and evolution of fragrance in rice (Oryza sativa L.). Proc. Natl. Acad. Sci. USA, 2009, 106, 14444– 14449.

  • Parray, G. A., Shikari, A. B., Ganai, M. A. and Husaini, A. M., Local aromatic rice cultivars of North Himalayas – present status and future strategies for their sustainable improvement. Crop Resour., 2008 36, 380–381.

  • Husaini, A. M., Parray, G. A., Rather, A. G. and Sanghera, G. S., Performance of elite basmati rice varieties of subtropical India under valley temperate conditions of Kashmir. Int. Rice Res. Notes, 2009, 1–5.

  • Husaini, A. M., Parray, G. A. and Wani, S. A., Biodiversity of rice germplasm and its conservation in Kashmir: targets, accomplishments and way forward. In University Research in Kashmir Rice – A Historical Perspective, SKUAST-K University Publn, 2013.

  • Yano, M., Shimosaka, E., Sato, A. and Nakagahra, M., Linkage analysis of a gene for scent in indica rice variety, Surjamkhi, using restriction fragment length polymorphism markers (in Japanese). Jpn. J. Breed., 1991, 41, 338–339.

  • Hien, N. L., Yoshihashi, T., Sarhadi, W. A. and Hirata, Y., Sensory test for aroma and quantitative analysis of 2-acetyl-l-pyrroline in Asian aromatic varieties. Plant Prod. Sci., 2006, 9, 294–297.

  • Ahn, S. N., Bollich, C. N. and Tanksley, S. D., RFLP tagging of a gene for aroma in rice. Theor. Appl. Genet., 1992, 84, 85–828.

  • Ren, J. S., Xiao, P. C., Chen, Y., Huang, X. and Wu, X. J., Study on heredity of aroma genes in several maintainer lines of aromatic rice. Seed, 2004, 25, 778–781.

  • Wanchana, S., Kamolsukyunyong, W., Ruengphayak, S., Toojinda, T. and Tragoonrung, S., A rapid construction of a physical contig across a 4.5 cm region for rice grain aroma facilitates marker enrichment for positional cloning. Sci. Asia, 2005, 31, 299–306.

  • Bradbury, L. M., Fitzgerald, T. L., Henry, R. J., Jin, Q. and Waters, D. L., The gene for fragrance in rice. Plant Biotechnol., 2005, 3, 363–370.

  • Shi, W., Yang, Y. I., Chen, S. and Xu, M. Discovery of a new fragrance allele and the development of functional markers for the breeding of fragrant rice varieties. Mol. Breed., 2008, 22, 185– 192.

  • Sun, S. X., Gao, F. Y., Lu, X. J. and Wu, X. D., Genetic analysis and gene fine mapping of aroma in rice (Oryza sativa L. Cyperales, Poaceae). Genet. Mol. Biol., 2008, 31, 532–538.

  • Bourgis, F., Guyot, R., Gherbi, H., Tailliez, E. and Amabile, I., Characterization of the major fragrance gene from an aromatic japonica rice and analysis of its diversity in Asian cultivated rice. Theor. Appl. Genet., 2008, 117, 353–368.

  • Chen, S., Yang, Y., Shi, W., Jin, Q. and He, F., BADH2, encoding betaine aldehyde dehydrogenase, inhibits the biosynthesis of 2acetyl-1-pyrroline, a major component in rice fragrance. Plant Cell, 2008, 20, 1850–1861.

  • Sakthivel, K., Shobha-Rani, N., Pandey, M. K., Sivaranjani, A. K. P. and Neeraja, C. N., Development of a simple functional marker for fragrance in rice and its validation in Indian Basmati and nonBasmati fragrant rice varieties. Mol. Breed., 2009, 24, 185–190.

  • Berner, D. K. and Hoff, B. J., Inheritance of scent in American long grain rice. Crop Sci., 1986, 26, 876–878.

  • Saghai-Maroof, M. A., Biyashev, R. M., Yang, G. P., Zhang, Q. and Allard, R., Extraordinarily polymorphic microstatallite DNA in barley genome mapping: species diversity, chromosomal location and population dynamics. Proc. Natl. Acad. Sci. USA, 1994, 91, 5466–5470.

  • Wettewa, W. and Kottearahchi, N. S., Sequence analysis of the mutation in the 7th exon of BADH2 gene in traditional aromatic rice varieties in Sri Lanka. J. Agric. Sci., 2014, 9, 1.

  • Zhang, Z., Schwartz, S., Wagner, L. and Miller, W., A greedy algorithm for aligning DNA sequences. J. Comput. Biol., 2000, 7, 203–214.

  • Morgulis, A., Coulouris, G., Raytselis, Y., Madden, T. L., Agarwala, R. and Schäffer, A. A., Database indexing for production MegaBLAST searches. Bioinformatics, 2008, 24, 1757–1764.

  • Siddiq, E. A., Vemireddy, L. R. and Nagaraju, J., Basmati rices: genetics, breeding and trade. Agric. Resour., 2012, 1, 25–36.

  • Bradbury, L. M. T., Gillies, S. A., Brushett, D. J., Waters, D. L. E. and Henry, R. J., Inactivation of an aminoaldehyde dehydrogenase is responsible for fragrance in rice. Plant Mol. Biol., 2008, 68, 439–449.

  • Niu, X., Tang, W., Huang, W., Ren, G. and Wang, Q., RNAidirected downregulation of OsBADH2 results in aroma (2-acetyl1-pyrroline) production in rice (Oryza sativa L.). BMC Plant Biol., 2008, 8, 100.


Abstract Views: 412

PDF Views: 130




  • Marker Validation and Sequencing in Aromatic Landrace Mushk Budji

Abstract Views: 412  |  PDF Views: 130

Authors

Aafreen Sakina
Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Jammu and Kashmir 190 025, India
Amjad M. Husaini
Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Jammu and Kashmir 190 025, India

Abstract


Aroma trait imparts specialty to rice and enhances its economic value in the market. Most aromatic genotypes are known to possess a truncated version of betaine aldehyde dehydrogenase gene, imparting aroma. Temperate rice varieties of Kashmir, India, have not been assessed for allelic variants of this fragranceimparting gene. Herein we report allelic variations present in exon 7 of this gene in the popular scented rice Mushk Budji. Unlike basmati-type genotypes, Mushk Budji is a short and bold japonica rice which grows at high altitudes and is cold-tolerant. Moreover, aroma retention after cooking is better in Mushk Budji compared to Pusa Sugandh 3, a long and thin basmati- type rice adapted to low-altitude areas of the Kashmir valley. Analysis showed the presence of a deletion of 8 bps ‘GATTATGG’ and three single nucleotide polymorphism in exon 7 of aromatic rice genotypes, including Mushk Budji. No such deletion was found in non-aromatic rice varieties. Additionally, one functional marker for badh2 allele was validated in Mushk Budji. These findings can facilitate the development of short and bold fragrant rice varieties through marker assisted selection, especially for highaltitude cold regions and the temperate valley conditions of Kashmir and the rest of India.

Keywords


Aromatic Landrace, Functional Markers, Sequencing.

References





DOI: https://doi.org/10.18520/cs%2Fv118%2Fi4%2F625-629