Breeding Science 61: 338–346 (2011) doi:10.1270/jsbbs.61.338 Fine mapping of stable QTLs related to eating quality in rice (Oryza sativa L.) by CSSLs harboring small target chromosomal segments Jingjing Li1), Wenwei Zhang1), Hongkai Wu1), Tao Guo1), Xiaolu Liu2), Xiangyuan Wan3), Jiansheng Jin1), Than Thi Thu Hanh1), Nguyen Thi Nhu Thoa1), Mingjiang Chen1), Shijia Liu1), Liangming Chen1), Xi Liu1), Jiankang Wang2), Huqu Zhai2) and Jianmin Wan*1,2) 1) Key Laboratory of Crop Genetics and Germplasm Enhancement/ Jiangsu Plant Gene Engineering Research Center, Nanjing Agri- cultural University, Nanjing 210095, Jiangsu, China 2) Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China 3) National Engineering Research Center for Crop Molecular Design, Beijing 100085, China Amylose content (AC) and viscosity profile are primary indices for evaluating eating and cooking qualities of rice grain. Using chromosome segment substitution lines (CSSLs), previous studies identified a QTL clus- ter of genes for rice eating and cooking quality in the interval R727–G1149 on chromosome 8. In this study we report two QTLs for viscosity parameters, respectively controlling setback viscosity (SBV) and consis- tency viscosity (CSV), located in the same interval using rapid viscosity analyzer (RVA) profile as an indi- cator of eating quality. Previously reported QTL for AC was dissected into two components with opposite genetic effects. Of four QTLs, qCSV-8 and qAC-8-2 had stable genetic effects across three and four environ- ments, respectively. qSBV-8, qCSV-8 and qAC-8-1 partly overlapped, but were separated from qAC-8-2. Based on data from an Affymetrix rice GeneChip, two genes related to starch biosynthesis at the qAC-8-2 locus were chosen for further quantitative expression analysis. Both genes showed enhanced expression in sub-CSSLs carrying the target qAC-8-2 allele, but not in sub-CSSLs without the target qAC-8-2 allele, indi- cating their possible role in rice quality determination. Molecular markers closely linked to the two stable QTL provide the opportunity for marker-assisted selection (MAS) in breeding high quality rice. Key Words: Eating and cooking quality, Rapid viscosity analyzer profiles, QTL, Chromosome segment sub- situtution lines. Introduction Rice is the staple food for almost half of the world’s popula- tion. Improvement of grain quality has become a major ob- jective in rice breeding, particularly cooking and eating quality. However, selection for cooking and eating quality is difficult because of the complicated sensory analysis and limited quantities of grain in early generations of a breeding program. Marker-assisted selection (MAS) has proved to be efficient for improving traits where heritabilities are high and phenotyping costs are expensive (Wang et al. 2007, 2009b). To apply MAS to quality traits, marker and quality gene associations need to be identified. The most important determinant of cooking and eating quality is well recognized as amylose content (AC) (Juliano 1998), which is under the control of the waxy (Wx) gene on chromosome 6 (Aluko et al. 2004, Bao et al. 2000, He et al. 1999, Septiningsih et al. 2003, Tan et al. 1999). It encodes Communicated by M. Yano Received April 12, 2011. Accepted August 5, 2011. *Corresponding author (e-mail: wanjm@njau.edu.cn) the enzyme granule bound starch synthase (GBSS) (Tian et al. 2004, Wang et al. 1990, Zhou et al. 2003). The Wx gene alone does not explain all of the variation among rice culti- vars and some minor genes might also be involved (Ayres et al. 1997). To this end, secondary measurements, such as starch paste viscosity, were developed to measure cooking and eating quality. Application of other QTL-marker associ- ations among rice quality genes, in addition to the Wx gene, will facilitate further genetic studies and cultivar develop- ment by MAS. Conventional mapping populations, such as DH or RIL, derived from two parental lines, have limitations in the accu- rate identification and fine mapping of QTL. Some QTLs of minor effect and those having epistatic interactions might be missed in QTL analysis, making selection of favorable QTL alleles alone incapable of reaching its full genetic potential (Wang et al. 2006). Wan et al. (2004) and Liu et al. (2011) conducted genetic analyses of cooking and eating quality using chromosome segment subsitutution lines (CSSLs) de- rived from the crosses between indica rice cv. IR24 as donor parent, and japonica rice cv. Asominori as a genetic back- ground parent, developed by Tsunematsu et al. (1996). They