QTL Analysis of Yield Components in Rice Using a Cheongcheong/Nagdong Doubled Haploid Genetic Map

Gyu Hwan Park, Jin-Hee Kim, Kyung-Min Kim

Department of Plant Resources, College of Life Science and Natural Resources, Kyungpook National University, Sangju, Korea.
Division of Plant Biosciences, School of Plant Biosciences, Kyungpook National University, Daegu, Korea.

DOI: 10.4236/ajps.2014.59130                

Abstract

In this study, only two of 12 quantitative trait loci (QTLs) affecting yield and yield components were identified in a single year, indicating that individual QTLs are probably sensitive to the environment. A rice growth survey of “Cheongcheong” and “Nag dong” in a doubled haploid population in 2012 revealed that yield capacity was influenced by climate change. Analysis of yield and yield components indicated that five average traits are high in “Cheongcheong”. Frequency distribution tables indicated that panicles per plant (PPP), spike lets per panicle (SPP), and 1000-grain weight (TGW) were normally distributed. The strongest relationship was identified between SPP and seed set percentage (SSP) among phenotypic correlations related to yield and yield components found on chromosomes 2, 3, 6, 8 in 2012. SPP and SSP was a very relevant requisite about quantity. Analysis of QTL about quantity was total 9. In the present study, a doubled haploid population was used to analyze the epistatic effects on yield and yield components in rice. Although other epistatic QTLs were not included in any of the main-effect QTLs, they significantly influenced the traits. These results indicated that epistatic interaction plays an important role in controlling the expression of complex traits. Thus, the utilization of marker-assisted selection in rice breeding programs should take epistatic effects into consideration. Hence, the QTLs responsible for major effects are more suitable for marker-assisted selection programs to improve yield and related traits across different environments.

Keywords

Rice; QTL; Yield; Epistatic

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	Burr, B., Burr, F.A., Thompson, K.H., Albertson, M.C. and Stuber, C.W. (1988) Gene Mapping with Recombinant Inbreds in Maize. Genetics, 118, 519-526.
[2]	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
[3]	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
[4]	Paterson, A.H. and Lander, E.S., Hewitt, J.D., Peterson, S., Lincoln, S.E. andTanksley, 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
[5]	Tanksley, S.D. and Nelson, J.C. (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
[6]	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
[7]	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
[8]	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
[9]	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
[10]	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
[11]	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 Oryzagrandiglumis and the O. sativa Japonica Cultivar Hwaseongbyeo. Theoretical and Applied Genetics, 112, 1052-1062. http://dx.doi.org/10.1007/s00122-006-0207-4
[12]	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
[13]	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, Oryzarufipogon. Genetics, 150, 899-909.
[14]	Thomson, M.J., Tai, T.H., McClung, A.M., Lai, X.H., Hinga, M.E., Lobos, K.B., Xu, Y., Martinez, C.P., McCouch, S.R. (2003) Mapping Quantitative Trait Loci for Yield, Yield Components and Morphological Traits in an Advanced Backcross Population between Oryzarufipogon and the Oryza Sativa Cultivar Jefferson. Theoretical and Applied Genetics, 107, 479-493. http://dx.doi.org/10.1007/s00122-003-1270-8
[15]	Ashikari, M., Sakakibara, H., Lin, S., Yamamoto, T., Takashi, T., Nishimura, A., Angeles, E.R., Qian, Q., Kitano, H. and Matsuoka, M. (2005) Cytokinin Oxidase Regulates Rice Grain Production. Science, 309, 741-745. http://dx.doi.org/10.1126/science.1113373
[16]	Fasoulas, A.C. and Allard, R.W. (1962) Nonallelic Gene Interactions in the Inheritance of Quantitative Characters in Barley. Genetics, 47, 899-907.
[17]	Paterson, A., Damon, S., Hewitt, J., Zamir, D., Rabinowitch, H., Lincoln, S., Lander, E. and Tanksley, S.D. (1991) Mendelian Factors Underlying Quantitative Traits in Tomato: Comparison across Species, Generations, and Environments. Genetics, 127, 181-197.
[18]	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
[19]	Campbell, B.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
[20]	Zeng, Z.B. (1994) Precision Mapping of Quantitative Trait Loci. Genetics, 136, 1457-1468.
[21]	Basten, C.J., Weir, B.S. and Zeng, Z.B. (2005) QTL Cartographer. Version 1.17.
[22]	Wang, D.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
[23]	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 Oryzasativa × Oryzarufipogon Advanced Backcross Population. Genome, 51, 692-704. http://dx.doi.org/10.1139/G08-054
[24]	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
[25]	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
[26]	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