Analysis of High-Resolution QTL Markers Associated with Rice Yields Using Data for Two Consecutive Years in Different Environmental Conditions — Oak Academic Publishing
Research ArticleOpen AccessGoogle Scholar indexed
Analysis of High-Resolution QTL Markers Associated with Rice Yields Using Data for Two Consecutive Years in Different Environmental Conditions
Division of Plant Biosciences, School of Plant Biosciences, Kyungpook National University, Daegu, Korea
,
Division of Plant Biosciences, School of Plant Biosciences, Kyungpook National University, Daegu, Korea
,
Division of Plant Biosciences, School of Plant Biosciences, Kyungpook National University, Daegu, Korea
,
Division of Plant Biosciences, School of Plant Biosciences, Kyungpook National University, Daegu, Korea; Department of Agronomy, Faculty of Agriculture, Jember University, Jember, Indonesia
,
Division of Plant Biosciences, School of Plant Biosciences, Kyungpook National University, Daegu, Korea
,
Division of Plant Biosciences, School of Plant Biosciences, Kyungpook National University, Daegu, Korea
1 Division of Plant Biosciences, School of Plant Biosciences, Kyungpook National University, Daegu, Korea
2 Division of Plant Biosciences, School of Plant Biosciences, Kyungpook National University, Daegu, Korea
3 Division of Plant Biosciences, School of Plant Biosciences, Kyungpook National University, Daegu, Korea
4 Division of Plant Biosciences, School of Plant Biosciences, Kyungpook National University, Daegu, Korea; Department of Agronomy, Faculty of Agriculture, Jember University, Jember, Indonesia
5 Division of Plant Biosciences, School of Plant Biosciences, Kyungpook National University, Daegu, Korea
6 Division of Plant Biosciences, School of Plant Biosciences, Kyungpook National University, Daegu, Korea
Previously we reported the identification of seven quantitative trait loci (QTLs) associated with the rice yield measuring five parameters including panicles per plant (PPP), spikelets per panicle (SPP), seed set percentage (SSP), 1000-grain weight (TGW) and yield in 2012. Here we report the analysis of QTLs using the same trait parameters data of the mapping population in 2013 for detecting highly conserved QTL markers. A total of 6 QTLs were identified from chromosomes 1, 7, 8, 10, 11, and 12, which were contrasted with our previous results (chromosomes 1, 2, 4, 5, 6, 8, and 11). In this comparison, three QTLs from chromosome 1, 8, and 11 were only found to be associated with the components of yield over two consecutive years indicating high sensitivity of QTL markers to the environment. Of those three QTLs, SPP-associated marker RM12285 was found to be dominantly expressed by real-time PCR (qPCR). In addition, compared to our previous report the numbers of mapping population and markers were significantly increased for higher resolution markers from 70 to 120, and from 143 to 217, respectively. We also found that the parameter SPP was dominantly correlated with the rice yield. Furthermore, the double haploid (DH) population facilitated to analyze the epistatic effects for yield and yield components in rice. Taken together, combining multiple mapping population data over years possibly enables narrowing down to the highly conserved QTL markers against diverse environmental fluctuation caused by such as drought and high temperature. Thus, these data would be critically exploited to improve for the crop breeding strategy.
Burr, B., Burr, F.A., Thompson, K.H., Albertson, M.C. and Stuber, C.W. (1998) Gene Mapping with Recombinant Inbreds in Maize. Genetics, 118, 519-526.
Beavis, W.D., Grant, D., Albertsen, M. and Fincher, R. (1991) Quantitative Trait Loci for Plant Height in Four Maize Populations and Their Associations with Qualitative Genetic Loci. Theoretical and Applied Genetics, 83, 141-145. http://dx.doi.org/10.1007/BF00226242
Veldboom, L.R. and Lee, M. (1994) Molecular-Marker-Facilitated Studies of Morphological Traits in Maize. II: Determination of QTLs for Grain Yield and Yield Components. Theoretical and Applied Genetics, 89, 451-458. http://dx.doi.org/10.1007/BF00225380
Paterson, A.H., Lander, E.S., Hewitt, J.D., Peterson, S., Lincoln, S.E. and Tanksley, S.D. (1988) Resolution of Quantitative Traits into Mendelian Factors by Using a Complete Linkage Map of Restriction Fragment Length Polymorphisms. Nature, 335, 721-726. http://dx.doi.org/10.1038/335721a0
Tanksley, S.D. and Nelson, J. (1996) Advanced Backcross QTL Analysis: A Method for the Simultaneous Discovery and Transfer of Valuable QTLs from Unadapted Germplasm into Elite Breeding Lines. Theoretical and Applied Genetics, 92, 191-203. http://dx.doi.org/10.1007/BF00223376
Frary, A., Nesbitt, T.C., Grandillo, S., Knaap, E., Cong, B., Liu, J., Meller, J., Elber, R., Alpert, K.B. and Tanksley, S.D. (2000) fw2.2: A Quantitative Trait Locus Key to the Evolution of Tomato Fruit Size. Science, 289, 85-88. http://dx.doi.org/10.1126/science.289.5476.85
Kato, K., Miura, H. and Sawada, S. (2000) Mapping QTLs Controlling Grain Yield and Its Components on Chromosome 5A of Wheat. Theoretical and Applied Genetics, 101, 1114-1121. http://dx.doi.org/10.1007/s001220051587
Roeder, M.I.S., Huang, X.Q. and Boerner, A. (2008) Fine Mapping of the Region on Wheat Chromosome 7D Controlling Grain Weight. Functional & integrative genomics, 8, 79-86. http://dx.doi.org/10.1007/s10142-007-0053-8
Yu, S.B., Li, J.X., Xu, C.G., Tan, Y.F., Gao, Y.J., Li, X.H., Zhang, Q.F. and Saghai Maroof, M.A. (1997) Importance of Epistasis as the Genetic Basis of Heterosis in an Elite Rice Hybrid. Proceedings of the National Academy of Sciences of the United States of America, 94, 9226-9231. http://dx.doi.org/10.1073/pnas.94.17.9226
Xing, Y.Z., Tan, Y.F., Hua, J.P., Sun, X.L., Xu, C.G. and Zhang, Q.F. (2002) Characterization of the Main Effects, Epistatic Effects and Their Environmental Interactions of QTLs on the Genetic Basis of Yield Traits in Rice. Theoretical and applied genetics, 105, 248-257. http://dx.doi.org/10.1007/s00122-002-0952-y
Yoon, D.B., Kang, K.H., Kim, H.J., Ju, H.G., Kwon, S.J., Suh, J.P., Jeong, O.Y. and Ahn, S.N. (2006) Mapping Quantitative Trait Loci for Yield Components and Morphological Traits in an Advanced Backcross Population between Oryza grandiglumis and the O. sativa Japonica Cultivar Hwaseongbyeo. Theoretical and applied genetics, 112, 1052-1062. http://dx.doi.org/10.1007/s00122-006-0207-4
McCouch, S.R. and Doerge, R.W. (1995) QTL Mapping in Rice. Trends in Genetics, 11,482-487. http://dx.doi.org/10.1016/S0168-9525(00)89157-X
Xiao, J., Li, J., Grandillo, S., Ahn, S.N., Yuan, L., Tanksley, S.D. and McCouch, S.R. (1998) Identification of Trait-Improving Quantitative Trait Loci Alleles from a Wild Rice Relative Oryza rufipogon. Genetics, 150, 899-909.
Thomson, M.J., Tai, T.H., McClung, A.M., Lai, X.H., Hinga, M.E., Lobos, K.B., Xu, Y., Martinez, C.P. and McCouch, S.R. (2003) Mapping Quantitative Trait Loci for Yield, Yield Components and Morphological Traits in an Advanced Backcross Population between Oryza rufipogon and the Oryza sativa Cultivar Jefferson. Theoretical and Applied Genetics, 107, 479-493. http://dx.doi.org/10.1007/s00122-003-1270-8
Ashikari, M., Sakakibara, H., Lin, S., Yamamoto, T., Takashi, T., Nishimura, A., Angeles, E.R., Qian, Q., Kitano, H. and Matsuoka, M. (2005) Cytokinin Oxidaseregulates Rice Grain Production. Science, 309, 741-745. http://dx.doi.org/10.1126/science.1113373
Chu, S.H., Jiang, W., Lee, J., Chin, J.H., Koh, H.J., Song, X.J., Huang, W., Shi, M., Zhu, M.Z. and Lin, H.X. (2007) A QTL for Rice Grain Width and Weight Encodes a Previously Unknown RING-Type E3 Ubiquitin Ligase. Nature Genetics, 39, 623-630. http://dx.doi.org/10.1038/ng2014
Fasoulas, A.C. and Allard, R.W. (1962) Nonallelic Gene Interactions in the Inheritance of Quantitative Characters in Barley. Genetics, 47, 899-907.
Paterson, A.H., Damon, S., Hewitt, J.D, Zamir, D., Rabinowitch, H.D., Lincoln, S.E., Lander, E.S. and Tanksley, S.D. (1991) Mendelian Factors Underlying Quantitative Traits in Tomato: Comparison across Species, Generations, and Environments. Genetics, 127, 181-197.
Zhuang, J.Y., Lin, H.X., Lu, J., Qian, H.R., Hittalmani, S., Huang, N. and Zheng, K.L. (1997) Analysis of QTL×Environment Interaction for Yield Components and Plant Height in Rice. Theoretical and Applied Genetics, 779, 799-808. http://dx.doi.org/10.1007/s001220050628
Campbell, T., Baenziger, P.S., Gill, K.S., Eskridge, K.M., Budak, H., Erayman, M., Dweikat, I. and Yen, Y. (2003) Identification of QTLs and Environmental Interactions Associated with Agronomic Traits on Chromosome 3A of Wheat. Crop Science, 43, 1493-1505. http://dx.doi.org/10.2135/cropsci2003.1493
Lincoln, S., Daley, M. and Lander, E. (1992) Constructing Genetic Maps with MAPMAKER/EXP 3.0. Whitehead Institute Technical Report, 3rd Edition.
Zeng, Z.B. (1994) Precision Mapping of Quantitative Trait Loci. Genetics, 136, 1457-1468.
Basten, J., Weir, B.S. and Zeng, Z.B. (2005) QTL Cartographer, Version 1.17. Department of Statistics, North Carolina State University, Raleigh.
Wang, L., Zhu, J., Li, Z.K. and Paterson, A.H. (1999) Mapping QTLs with Epistatic Effects and QTL×Environment Interactions by Mixed Linear Model Approaches. Theoretical and Applied Genetics, 99, 1255-1264. http://dx.doi.org/10.1007/s001220051331
Yano, M., Kojima, S., Takahashi, Y., Lin, H. and Sasaki, T. (2001) Genetic Control of Flowering Time in Rice, a Short-Day Plant. Plant Physiology, 127, 1425-1429. http://dx.doi.org/10.1104/pp.010710
Tan, L.B., Zhang, P.J., Liu, F.X., Wang, G.J., Ye, S., Zhu, Z.F., Fu, Y.C., Cai, H.W. and Sun, C.Q. (2008) Quantitative Trait Loci Underlying Domestication- and yield-Related Traits in an Oryza sativa × Oryza rufipogon Advanced Backcross Population. Genome, 51, 692-704. http://dx.doi.org/10.1139/G08-054
Cho, Y.G., Kang, H.J., Lee, J.S., Lee, Y.T., Lim, S.J., Gauch, H., Eun, M.Y. and McCouch, S.R. (2007) Identification of Quantitative Trait Loci in Rice for Yield, Yield Components, and Agronomic Traits across Years and Locations. Crop Science, 47, 2403-2417. http://dx.doi.org/10.2135/cropsci2006.08.0509
Zhao, X., Qin, Y. and Sohn, J.K. (2010) Identification of Main Effects, Epistatic Effects and Their Environmental Interactions of QTLs for Yield Traits in Rice. Genomics, 32, 37-45.
Zhang, Z.H., Li, P., Wang, L.X., Hu, Z.L., Zhu, L.H. and Zhu, Y.G. (2004) Genetic Dissection of the Relationships of Biomass Production and Partitioning with Yield and Yield Related Traits in Rice. Plant Science, 167, 1-8. http://dx.doi.org/10.1016/j.plantsci.2004.01.007
You, A., Lu, X., Jin, H., Ren, X., Liu, K., Yang, G., Yang, H., Zhu, L. and He, G. (2006) Identification of Quantitative Trait Loci across Recombinant Inbred Lines and Testcross Populations for Traits of Agronomic Importance in Rice. Genetics, 172, 1287-1300. http://dx.doi.org/10.1534/genetics.105.047209
Lin, H.X., Qian, H.R., Zhuang, J.Y., Lu, J., Min, S.K., Xiong, Z.M., Huang, N. and Zheng, K.L. (1996) RFLP Mapping of QTLs for Yield and Related Characters in Rice (Oryza sativa L.). Theoretical and Applied Genetics, 92, 920-927. http://dx.doi.org/10.1007/BF00224031