J Integr Plant Biol. ›› 2012, Vol. 54 ›› Issue (12): 979-990.DOI: 10.1111/jipb.12008

Special Issue: Rice Genomics and Agriculture

• Cell and Developmental Biology • Previous Articles     Next Articles

A Kelch Motif-Containing Serine/Threonine Protein Phosphatase Determines the Large Grain QTL Trait in Rice

Zejun Hu1,2†, Haohua He2†, Shiyong Zhang3, Fan Sun1, Xiaoyun Xin1, Wenxiang Wang2, Xi Qian1, Jingshui Yang1 and Xiaojin Luo1*   

  1. 1State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
    2Ministry of Education Key Laboratory for Crop Physiology, Ecology and Genetic Breeding, Jiangxi Agricultural University, Nanchang 330045, China; Jiangxi Super Rice Engineering Technology Research Center, Jiangxi Agricultural University, Nanchang 330045, China
    3Institute of Rice Research, Shandong Academy of Agricultural Sciences, Jinan 250100, China
  • Received:2012-11-01 Accepted:2012-11-04 Published:2012-12-11
  • About author:These authors contributed equally to this work.
    *Corresponding author Tel/Fax: +86 21 6564 3715; E-mail: luoxj@fudan.edu.cn


A thorough understanding of the genetic basis of rice grain traits is critical for the improvement of rice (Oryza sativa L.) varieties. In this study, we generated an F2 population by crossing the large-grain japonica cultivar CW23 with Peiai 64 (PA64), an elite indica small-grain cultivar. Using QTL analysis, 17 QTLs for five grain traits were detected on four different chromosomes. Eight of the QTLs were newly-identified in this study. In particular, qGL3-1, a newly-identified grain length QTL with the highest LOD value and largest phenotypic variation, was fine-mapped to the 17 kb region of chromosome 3. A serine/threonine protein phosphatase gene encoding a repeat domain containing two Kelch motifs was identified as the unique candidate gene corresponding to this QTL. A comparison of PA64 and CW23 sequences revealed a single nucleotide substitution (C→A) at position 1092 in exon 10, resulting in replacement of Asp (D) in PA64 with Glu (E) in CW23 for the 364th amino acid. This variation is located at the D position of the conserved sequence motif AVLDT of the Kelch repeat. Genetic analysis of a near-isogenic line (NIL) for qGL3-1 revealed that the allele qGL3-1 from CW23 has an additive or partly dominant effect, and is suitable for use in molecular marker-assisted selection.

Hu Z, He H, Zhang S, Sun F, Xin X, Wang W, Qian X, Yang J, Luo X (2012) A kelch motif-containing serine/threonine protein phosphatase determines the large grain QTL trait in rice. J. Integr. Plant Biol. 54(12), 979–990.

Key words: Grain shape, QTL mapping, QTL fine mapping, rice, serine/threonine protein phosphatase

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