Fine mapping of a QTL for the number of spikelets per panicle by using near-isogenic lines derived from an interspecific cross between Oryza sativa and Oryza minuta S ANGSHETTY B ALKUNDE 1 ,H UNG -L INH L E 2 ,H YUN -S OOK L EE 1 ,D ONG -M IN K IM 1 ,J U -W ON K ANG 1 and S ANG -N AG A HN 1,3 1 Department of Agronomy, College of Agriculture and Life Sciences, Chungnam National University, Daejeon, 305-764, Korea; 2 Agricultural Genetics Institute, Pham Van Dong Road, Tuliem, Hanoi, Vietnam; 3 Corresponding author, E-mail: ahnsn@cnu.ac.kr With 3 figures and 2 tables Received July 30, 2012/Accepted September 29, 2012 Communicated by M. Yano Abstract We constructed a high-resolution physical map for the qSPP7 QTL for spikelets per panicle (SPP) on rice chromosome 7 across a 28.6-kb region containing four predicted genes. Using a series of BC 7 F 4 near- isogenic lines (NILs) derived from a cross between the Korean japonica cultivar ‘Hwaseongbyeo’ and Oryza minuta (IRGC Acc. No. 101144), three QTLs for the number of SPP, grains per panicle and primary branches were identified in the cluster (P  0.01). All three QTLs were additive, and alleles from the O. minuta parent were beneficial in the ‘Hwaseongbyeo’ background. qSPP7 was mapped to a 28.6-kb region between the two simple sequence repeat (SSR) markers RM4952 and RM21605. The additive effect of the O. minuta allele at qSPP7 was 23 SPP, and 43.6% of the phenotypic variance was explained by the segre- gation of the SSR marker RM4952. Colocalization of the three QTLs suggested that this locus was associated with panicle structure and had pleiotropic effects. The NIL populations and molecular markers are use- ful for cloning qspp7. Key words: rice — spikelet per panicle — QTL — near- isogenic line — fine mapping Rice is a staple food for nearly half of the world’s population and is likely to be the most important grain with regard to human nutrition and caloric intake, providing almost one-quarter of the global dietary energy supply per capita (Miura et al. 2010). The global population has increased by 30% in the last two decades, and within the next four decades, it is predicted to increase further by >50% (http://www.un.org/). To support such a population explosion, rice production has to be increased by at least 70% over the next three decades to meet growing demand (Xing et al. 2008). Wild rice has been recognized as a natural gene bank that conserves many specific genes that are not cur- rently found in cultivated rice. There is an urgent need to dis- cover useful genes hidden in the wild rice genome and apply these findings to improve agricultural traits in crop breeding. Identifying QTLs represents the first step towards dissecting the molecular basis of naturally occurring genetic variation for complex traits of agronomic importance. Many studies have been performed to detect the genes underlying genetically complex traits in rice (Yano and Sasaki 1997). The number of spikelets per rice panicle is very important in determining the yield, which is defined as the product of spikelet yield (or sink) and ripening ability (or source) (Hua et al. 2002). Therefore, elucidation of the genetic basis of the number of spikelets per panicle (SPP) would be of great value in breeding a high-yield variety. SPP is inherited in a quantitative manner, is typically controlled by many major and minor QTLs and is also affected by the environment, all of which present a challenge in characterizing it (Xing et al. 2002). Previous studies have shown that epistasis and genotype 9 environment (G 9 E) interaction also frequently have considerable effects on SPP, although their contribution to SPP is less than that of the main genetic effect (Xing et al. 2002). QTLs for SPP have been detected using various segre- gating populations (Kobayashi et al. 2004, Suh et al. 2005, Zou et al. 2005). In addition, five QTLs for SPP have been mapped as a single Mendelian factor (Zhang et al. 2006, 2009). Several QTLs for SPP have also been identified from wild relatives (Thomson et al. 2003, Linh et al. 2006, Onishi et al. 2007). These QTLs, which are located across different chromosomes, provide valuable information on the genes that control SPP in different populations. A few QTLs controlling SPP have been cloned, including Gn1a, APO1, Gdh7, and OsSPL14. Gn1a, which controls grain productivity in rice, was found to encode cytokinin oxidase/ dehydrogenase (OsCKX2), an enzyme that degrades cytokinins (Ashikari et al. 2005). Increased expression of OsSPL14 in the reproductive stage promotes panicle branching and is associated with an increase in grain numbers and primary branches (PBs) in ST-2 (Miura et al. 2010). Ghd7, isolated from an elite rice hybrid and encoding a CCT domain protein, has major effects on an array of traits in rice, including SPP, plant height and heading date (Xue et al. 2008). Ikeda et al. (2007) identified rice aberrant panicle organization 1 (APO1) mutants that positively control spikelet number by suppressing the precocious conver- sion of inflorescence meristems to spikelet meristems. Terao et al. (2010) also reported that APO1 overexpression at the PBN6 QTL increased both the number of PRBs and the number of grains per panicle. In our previous study, we detected the qSPP7 QTL in the O. min- uta segment on chromosome 7 introgressed into the ‘Hwaseongb- yeo’ background by using an introgression line, WH29001 (Linh et al. 2008). In this study, we characterized and fine mapped qSPP7 as a step towards map-based cloning of this gene. Materials and Methods Mapping population and field experiment: Development and field testing of the introgression line (WH29001) constructed for QTL mapping has been described previously (Linh et al. 2006, 2008); an Oryza sativa ssp. japonica cultivar, ‘Hwaseongbyeo’, was used as the recurrent parent and a wild accession of O. minuta (2n=48, BBCC, Acc. wileyonlinelibrary.com Plant Breeding 132, 70–76 (2013) doi:10.1111/pbr.12020 © 2012 Blackwell Verlag GmbH