QTLs related to eating quality in rice 343 Fig. 3. Substitution mapping of QTL for rice quality and phenotype (AC and RVA profile) for sub-CSSLs located in the interval G1149–R727 on chromosome 8 in four environments. Blocks represent chromosomes. Horizontal lines show the positions of SSR markers investigated. To graph- ically represent the genotypes of CSSLs, the recombination point was arbitrarily determined at the mid-point between markers. Black and white blocks denote homozygous IR24 alleles and Asominori alleles, respectively. NJ and HN, Naijing and Hainan, respectively. ** and * represent significant differences from Asominori at P = 0.001 and P = 0.01, respectively by t-tests. A: Substitution mapping of QTL for SBV, CSV and AC located in the interval RM5351–RM5485 on the left. Phenotype means for 4 sub-CSSLs (Lines 1, 2, 3 and 4) and Asominori are shown on the right table. B: Substitution mapping of QTL for AC located in the interval RM5485–RM23653 on the left. Phenotypic means for 5 sub-CSSLs (Lines 10, 11, 12, 13 and 14) and Asominori are shown on the right Table. The serial numbers for sub-CSSLs corresponded to the final sub- CSSLs. ND, no data. Os08g0536000 was not expressed until a relatively late stage in endosperm development (Fig. 5B). At 15 DAF, the amount of Os08g0536000 transcript in sub-CSSLs carrying the target qAC-8-2 allele was markedly higher than that in sub-CSSLs not carrying the target qAC-8-2 allele and CSSL50-1. Discussion To date, whole-genome chromosome substitution segments lines (CSSLs) or near isogenic lines (NILs) have been suc- cessfully constructed in rice (Ebitani et al. 2005, Kubo et al. 2002, Xi et al. 2006), tomato (Bernacchi et al. 1998, Chetelat and Meglic 2000), and maize (Graham et al. 1997, Koester et al. 1993). Many major QTLs have been precisely mapped and map-based cloned; for example, genes in rice affecting heading date QTL, Hd2, were map-based cloned using NILs (Lin et al. 2002); and genes in tomato controlling fruit shape QTL, fw2.2, were cloned using introgression lines of wild type chromosome segments in a genetic back- ground of a cultivated variety (Frary et al. 2000). Thus, the usefulness of CSSLs and NILs for QTL identification was already demonstrated. Fig. 4. Ten bacterial artificial chromosome (BAC) clones and two up- regulated genes in the interval RM23510–RM23579. The two up- regulated genes with higher expression ratios are marked by the arrows. To dissect the stable gene cluster for the AC and RVA profiles on chromosome 8 that have been identified in previ- ous study (Wan et al. 2004, shown in Fig. 2A), we stepwise constructed sub-CSSLs harboring small segments of Asominori in which IR24 target segments were introduced. After several generations using SSR markers to select the background and foreground, we eventually developed 14 sub- CSSLs spanning R727–G1149 (Fig. 2B). All the agronomic characters of the sub-CSSLs were not different from those of Asominori, especially heading date (See Supplemental Table 1). Therefore, we decided that these sub-CSSLs were nearly isogenic to Asominori and could be used to evaluate