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Gene actions at loci underlying several quantitative traits in two elite rice hybrids

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Abstract

To understand the gene activities controlling nine important agronomic quantitative traits in rice, we applied a North Carolina design 3 (NC III design) analysis to recombinant inbred lines (RILs) in highly heterotic inter- (IJ) and intra-subspecific (II) hybrids by performing the following tasks: (1) investigating the relative contribution of additive, dominant, and epistatic effects for performance traits by generation means analysis and variance component estimates; (2) detecting the number, genomic positions, and genetic effects of QTL for phenotypic traits; and (3) characterizing their mode of gene action. Under an F∞-metric, generation means analysis and variance components estimates revealed that epistatic effects prevailed for the majority of traits in the two hybrids. QTL analysis identified 48 and 66 main-effect QTL (M-QTL) for nine traits in IJ and II hybrids, respectively. In IJ hybrids, 20 QTL (41.7%) showed an additive effect of gene actions, 20 (41.7%) showed partial-to-complete dominance, and 8 (16.7%) showed overdominance. In II hybrids, 34 QTL (51.5%) exhibited additive effects, 14 (21.2%) partial-to-complete dominance, and 18 (27.3%) overdominance. There were 153 digenic interactions (E-QTL) in the IJ hybrid and 252 in the II hybrid. These results suggest that additive effects, dominance, overdominance, and particularly epistasis attribute to the genetic basis of the expression of traits in the two hybrids. Additionally, we determined that the genetic causes of phenotypic traits and their heterosis are different. In the plants we studied, the phenotypic traits investigated and their heterosis were conditioned by different M-QTL and E-QTL, respectively, and were mainly due to non-allelic interactions (epistasis).

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Acknowledgments

We gratefully acknowledge the expert technical assistance of Prof. Qifa Zhang in trial design and analysis and the skillful assistance of Prof. Yingguo Zhu in field trials. We are indebted to Prof. Jinhua Xiao and Prof. Yunchun Song for valuable suggestions for improving the manuscript. This work was financially supported by the 973 Program (No. 2006CB101707), the 863 Program (No. 2003AA207160), the National Natural Science Foundation of China (No. 30270760 and No. 31000666), the Key grant Project of the Chinese Ministry of Education (No. 307018), and the Youth Science Foundation of Hunan Agricultural University (No. 09QN16).

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Authors and Affiliations

  1. College of Bio-Safety Science and Technology, Hunan Agricultural University, Changsha, 410128, China

    Lanzhi Li

  2. Key Lab of the Ministry of Education for Plant Developmental Biology, College of Life Science, Wuhan University, Wuhan, 430072, Hubei, People’s Republic of China

    Lanzhi Li, Zhaoming Chen & Zhongli Hu

  3. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, No. 1 Shizishan Road, Hongshan District, Wuhan, 430070, Hubei, People’s Republic of China

    Kaiyang Lu & Tongmin Mou

  4. Department of Breeding, China National Hybrid Rice Research and Development Center, Changsha, 410125, China

    Xinqi Li

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  1. Lanzhi Li
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  2. Kaiyang Lu
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  4. Tongmin Mou
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Correspondence to Tongmin Mou or Zhongli Hu.

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Communicated by S. Omholt.

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Li, L., Lu, K., Chen, Z. et al. Gene actions at loci underlying several quantitative traits in two elite rice hybrids. Mol Genet Genomics 284, 383–397 (2010). https://doi.org/10.1007/s00438-010-0575-y

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  • DOI: https://doi.org/10.1007/s00438-010-0575-y

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