Major QTLs for eating quality of an elite Japanese rice cultivar, Koshihikari, on the short arm of chromosome 3

Abstract

To identify the chromosomal regions controlling the eating quality of Koshihikari rice, we performed a quantitative trait locus (QTL) analysis using two backcross inbred lines (BILs): N-BILs (79 lines derived from a cross of Nipponbare/Koshihikari//Nipponbare) and K-BILs (89 lines derived from a cross of Nipponbare/ Koshihikari//Koshihikari). We evaluated several components of the eating quality of cooked rice, namely glossiness, taste, stickiness, hardness, and overall evaluation, based on sensory tests by a trained panel, and amylose and protein contents. Ten QTLs for these components were detected in N-BILs (two regions of chromosome [chr.] 3 and one of chr. 11), and six in K-BILs (chr. 3 and chr. 6). Each QTL explained 11.6% to 32.0% of the total phenotypic variance. QTLs at the distal end of the short arm of chr. 3 were commonly identified in both BILs. The Koshihikari alleles at these QTLs increased eating quality. The genetic effect of the Koshihikari alleles was confirmed by analysis of a chromosome segment substitution line containing a Koshihikari segment of the short arm of chr. 3 in the Nipponbare background.

Identification of Quantitative Trait Loci Associated with Rice Eating Quality Traits Using a Population of Recombinant Inbred Lines Derived from a Cross between Two Temperate japonica Cultivars

“…Several studies have identified QTLs for such physicochemical properties and also for the eating quality of cooked rice using indica/japonica cross populations (Bao et al, 2000;Li et al, 2003;Ogata et al, 1996;Otsuki et al, 1997;Takeuchi et al, 2007;Wan et al, 2004). However, few studies have identified QTLs related to eating quality in the same manner in japonica/japonica cross populations (Kobayashi and Tomita, 2008;Takeuchi et al, 2007Takeuchi et al, , 2008Tanaka et al, 2006;Wada et al, 2006;2008). In this study, we identified 21 QTLs in seven regions on chromosomes 1, 4, 6, 7, 8 and 11 for seven traits (Table 3, Fig.…”

“…Five stable QTLs and 21 additional QTLs associated with eating quality were previously identified using chromosome segment substitution lines (CSSLs) derived from a cross of Asominori (japonica) and IR24 (indica), and by using backcross inbred lines (BILs) derived from a cross of Koshihikari/Kasalath (indica)//Koshihikari and CSSLs, respectively (Ebitani et al, 2005;Wan et al, 2004). A few studies have also identified QTLs for eating quality in doubled haploid (DH)lines or RILs derived from crosses between different japonica strains (Kobayashi and Tomita, 2008;Suh et al, 2006;Takeuchi et al, 2008;Tanaka et al, 2006;Wada et al, 2008). DNA markers closely linked to these QTLs have made it possible to more efficiently develop rice cultivars with a higher eating quality (Lestari et al, 2009).…”

Q-TARO: QTL Annotation Rice Online Database

“…These analyses have identified several unique QTLs for heading date (Matsubara et al 2008), culm length (Hori et al 2009), pre-harvest sprouting resistance (Hori et al 2010), and eating quality (Takeuchi et al 2008;Kobayashi and Tomita 2008;Wada et al 2008). The success of this approach implies that the use of a wide range of cross combinations might increase the opportunity to detect unique QTLs.…”

Validation of QTLs for Eating Quality of Japonica Rice ‘Koshihikari’ Using Backcross Inbred Lines

“…Takeuchi et al (2007) detected common QTLs on Chr 3 and Chr 6 using backcross inbred lines (BILs) and chromosome segment substitution lines (CSSLs) derived from crosses between 'Koshihikari' and indica cultivar 'Kasalath'. Takeuchi et al (2008) also detected QTLs on Chr 3 (two regions) and Chr 6 using two kinds of BILs (K-BILs; derived from a cross Nipponbare/Koshihikari// Koshihikari, and N-BILs; Nipponbare/Koshihikari// Nipponbare), and showed QTLs on Chr 3 were commonly detected regions, whose nearest marker was RM4108. identified QTLs for stickiness on Chr 1, 3, 6, 7, and 8 using recombinant inbred lines (RILs) derived from a cross, between Sakihikari, which is genetically closely related to 'Koshihikari', and Nipponbare.…”

“…Quantitative trait locus (QTL) analysis has been performed to identify the chromosome regions controlling eating quality (Tanaka et al, 2006;Takeuchi et al, 2007Takeuchi et al, , 2008; Wada et al, 2008). Although QTLs for stickiness of cooked rice were detected on chromosome (Chr) 2 (Tanaka et al, 2006;, many reports suggest that the short arm of Chr 3 has the highest effect on the eating quality of cooked rice.…”