Theor Appl Genet (2009) 118:1509–1517 DOI 10.1007/s00122-009-0999-0 123 ORIGINAL PAPER Fine mapping SPP1, a QTL controlling the number of spikelets per panicle, to a BAC clone in rice (Oryza sativa) Touming Liu · Donghai Mao · Shengpeng Zhang · Caiguo Xu · Yongzhong Xing Received: 26 June 2008 / Accepted: 17 February 2009 / Published online: 6 March 2009  Springer-Verlag 2009 Abstract Near isogenic lines (NILs) can be used to eYciently handle a target quantitative trait locus (QTL) by blocking genetic background noise. One QTL, SPP1, which controls the number of spikelets per panicle (SPP), was located on chromosome 1, near Gn1a, a cloned gene for rice production in a recombinant inbred line population. NILs of the SPP1 regions were quickly obtained by self- crossing recombinant inbred line 30 which is heterozygous around SPP1. Using a random NIL-F 2 population of 210 individuals, we mapped SPP1 to a 2.2-cM interval between RM1195 and RM490, which explained 51.1% of SPP vari- ation. The diVerence in SPP between the two homozygotes was 44. F 2 -1456, one NIL-F 2 plant, was heterozygous in the SPP1 region but was Wxed in the region of Gn1a gene. This plant F 3 family showed a very wide variation in SPP, which suggested that it was SPP1 but Gn1a aVected the variation of SPP in this population. In a word, SPP1 is a novel gene distinct from Gn1a. Four newly developed InDel markers were used for high-resolution mapping of SPP1 with a large NIL-F 2 population. Finally, it was narrowed down to a bacterial artiWcial chromosome clone spanning 107 kb; 17 open reading frames have been identiWed in the region. Of them, LOC_Os01g12160, which encodes an IAA synthetase, is the most interesting candidate gene. Introduction Grain yield is one of the most valuable traits in crop pro- duction. Pursuing high grain yield is one of the most impor- tant goals in rice (Oryza sativa L.) production. Grain yield is frequently replaced with grain yield per plant in quantita- tive trait locus (QTL) mapping owing to control of Weld experimental scale (Zhuang et al. 2002; Hittalmani et al. 2003). Grain yield per plant is determined by its three com- ponents, panicles per plant, 1,000-grain weight, and spik- elets per panicle (SPP). Among the three components, SPP frequently makes the greatest contribution to grain yield and has received the most attention in genetic analysis. However, this trait is inherited in a quantitative manner and typically controlled by a number of major and minor QTL and is also aVected by environment, which present a chal- lenge in characterizing SPP. With QTL analysis based on molecular markers, SPP has been studied, and hundreds of QTL have been reported (Yu et al. 1997; Zhuang et al. 1997; Xing et al. 2002; Septiningsih et al. 2003). Many reports have provided evidence for a very complicated genetic basis of yield traits, which are aVected simulta- neously by QTL, epistasis, and environment in primary mapping populations (Li et al. 1997; Xing et al. 2002; Zhu- ang et al. 2002). Currently, QTL Wne mapping and cloning are still diYcult although many QTL for SPP have been mapped to chromosome regions. In a primary mapping population with simultaneous seg- regation of multiple genetic factors, a given trait value is contributed not only by a given QTL but also by other QTL. For Wne mapping of a QTL, genetic background noise should be avoided. Hence, QTL analysis in advanced popu- lations is necessary for a good understanding of their char- acteristics. Near isogenic lines (NILs) has been proven to be an ideal population for QTL Wne mapping and cloning. Communicated by H. H. Geiger. T. Liu · D. Mao · S. Zhang · C. Xu · Y. Xing (&) National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, 430070 Wuhan, China e-mail: yzxing@mail.hzau.edu.cn; yzhxing@hotmail.com