Abstract
The present report is in continuation to our earlier reports on the identification and fine mapping of three aroma QTLs in basmati rice using a bi-parental mapping population derived from a cross between Pusa 1121, a basmati rice variety, and Pusa 1342, a non-aromatic rice variety. We used a combination of genetic mapping and transcriptome profiling to narrow down the number of differentially expressed genes in rice to identify potential candidate genes for rice grain aroma. Highly aromatic and non-aromatic recombinant inbred lines (RILs) were identified through sensory analysis of mature milled grains. RILs with similar phenotypes were bulked together using bulk segregant analysis approach which drastically reduced the number of differentially expressed genes from 4016 to 1344. The transcriptome profiles generated were analyzed through Affymetrix rice genome array containing probe sets designed from all the predicted rice gene sequences. Microarray-based transcriptome profiling revealed one down-regulated gene co-located in QTL region aro3.1 on chromosome 3, eight genes co-located in the aro4.1 region on chromosome 4 and the badh2 gene on chromosome 8 to be differentially expressed in the aromatic parent and aromatic bulk. These genes are the most suitable candidates for future validation and development of new molecular functional markers to facilitate marker assisted breeding.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Ahn, S.N., Bollich, C.N., Tanksley, S.D. 1992. RFLP tagging of a gene for aroma in rice. Theor. Appl. Genet. 84:825–828.
Aitman, T.J., Glazier, A.M., Wallace, C.A., Cooper, L.D., Norsworthy, P.J., Wahid, F.N., Al-Majali, K.M., Trembling, P.M., Mann, C.J., Shoulders, C.C., Graf, D., St. Lezin, E., Kurtz, T.W., Kren, V., Pravenec, M., Ibrahimi, A., Abumrad, N.A., Stanton, L.W., Scott, J. 1999. Identification of Cd36 fat as an insulin-resistance gene causing defective fatty acid and glucose metabolism in hypertensive rats. Nat. Genet. 21:6–83.
Amarawathi, Y., Singh, R., Singh, A.K., Singh, V.P., Mohapatra, T., Sharma, T.R., Singh, N.K. 2008. Mapping of quantitative trait loci for basmati quality traits in rice. Mol. Breed. 21:49–65.
Benjamini, Y., Hochberg, Y. 1995. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. of the Royal Statistical Soc., Series B 57:289–300.
Bradbury, L.M., Fitzgerald, T.L., Henry, R.J., Jin, Q., Waters, D.L. 2005. The gene for fragrance in rice. Plant Biotech. J. 3:363–370.
Chen, S., Wu, J., Yang, Y., Shi, W., Xu, M. 2006. The fgr gene responsible for rice fragrance was restricted within 69 kb. Plant Sci. 171:505–514.
Deshmukh, R., Singh, A., Jain, N., Anand, S., Gachche, R., Singh, A., Gaikwad, K., Sharma, T., Mohapatra, T., Singh, N. 2010. Identification of candidate genes for grain number in rice (Oryza sativa L.) Funct. Integr. Genomics 10:339–347.
Fitzgerald, M.A., Hamilton, N.R.S., Calingacion, M.N., Verhoeven, H.A., Butardo, V.M. 2008. Is there a second fragrance gene in rice? Plant Biotechnol. J. 6:416–423.
IRGSP 2005. The map based sequence of the rice genome. Nature 436:793–800.
Jodon, N.E. 1944. The inheritance of flower fragrance and other characters in rice. J. Amer. Soc. Agron. 36:844–848.
Kadam, B.S., Patankar, V.K. 1938. Inheritance of aroma in rice. Chron. Bot. 4:32.
Kathiresan, A., Lafitte, H.R., Chen, J., Mansueto, L., Bruskiewich, R., Bennett, J. 2006. Gene expression microarray and their application in drought stress research. Field Crops Res. 97:101–110.
Lorieux, M., Petrov, M., Huang, N., Guiderdoni, E., Ghesquière, A. 1996. Aroma in rice: Genetic analysis of quantitative trait. Theor. Appl. Genet. 93:1145–1151.
Marino, R., Ponnaiah, M., Krajewski, P., Frova, C., Gianfranceschi, L., Pe, E.M., Gorla, S.M. 2009. Addressing drought tolerance in maize by transcriptional profiling and mapping. Mol. Genet. Genomics 218:163–179.
Murray, M.G., Thompson, W.F. 1980. Rapid isolation of high molecular weight plant DNA. Nucleic Acid Res. 8:4321–4325.
Pachauri, V., Singh, M.K., Singh, A.K., Singh, S., Shakeel, N.A., Singh, V.P., Singh, N.K. 2010. Origin and genetic diversity of aromatic rice varieties, molecular breeding and chemical and genetic basis of rice aroma. J. Pl. Biochem. Biotechnol. 19:127–143.
Pandit, A., Rai, V., Bal, S., Sinha, S., Kumar, V., Chauhan, M., Gautam, R.K., Singh, R., Sharma, P.C., Singh, A.K., Gaikwad, K., Sharma, T.R., Mohapatra, T., Singh, N.K. 2010. Combining QTL mapping and transcriptome profiling of bulked RILs for identification of functional polymorphism for salt tolerance genes in rice (Oryza sativa L.) Mol. Genet. Genomics 284:121–136.
Pinson, S.R.M. 1994. Inheritance of aroma in six rice cultivars. Crop Sci. 34:1151–1157.
Price, A. 2006. Believe it or not, QTLs are accurate! Trends Plant Sci. 11:213–216.
Salvi, S., Tuberosa, R. 2005. To clone or not to clone plant QTLs: Present and future challenges. Trends Plant Sci. 10:297–304.
Senadheera, P., Tirimanne, S., Maathuis, F.J.M. 2012. Long term salinity stress reveals cultivar specific differences in root oxidative stress response. Rice Sci. 19:212–221.
Singh, V.P., Singh, A.K., Atwal, S.S., Joseph, M., Mohapatra, T. 2002. Pusa 1121: A rice line with exceptionally high cooked kernel elongation and basmati quality. Int. Rice Res. Notes 27:25–26.
Singh, R., Singh, A.K., Sharma, T.R., Singh, A., Singh, N.K. 2007. Fine mapping of aroma QTLs in Basmati rice (Oryza sativa) on chromosomes 3, 4 and 8. J. Pl. Biochem. Biotechnol. 16:75–82.
Singh, A., Singh, P.K., Singh, R., Pandit, A., Mahato, A.K., Gupta, D.K., Tyagi, K., Singh, A.K., Singh, N.K, Sharma, T.R. 2010. SNP haplotypes of the BADH1 gene and their association with aroma in rice (Oryza sativa L.). Mol. Breed. 26:325–338.
Sood, B.C., Sidiq, E.A. 1978. A rapid technique for scent determination in rice. Indian J. Genet. Pl. Breed. 38:268–271.
Wanchana, S., Kamolsukyunyong, W., Ruengphayak, S., Toojinda, T., Tragoonrung, S., Vanavichit, A. 2005. A rapid construction of a physical contig across a 4.5cM region for rice grain aroma facilitates marker enrichment for positional cloning. Sci. Asia 31:299–306.
Wayne, M.L., McIntyre, L.M. 2002. Combining mapping and arraying: An approach to candidate gene identification. Proc. Natl Acad. Sci. USA 99:14903–14906.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by V.G. Horváth
Rights and permissions
This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
About this article
Cite this article
Pachauri, V., Mishra, V., Mishra, P. et al. Identification of Candidate Genes for Rice Grain Aroma by Combining QTL Mapping and Transcriptome Profiling Approaches. CEREAL RESEARCH COMMUNICATIONS 42, 376–388 (2014). https://doi.org/10.1556/CRC.42.2014.3.2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1556/CRC.42.2014.3.2