QTL detection for stickiness of cooked rice using recombinant inbred lines derived from crosses between japonica rice cultivars

Abstract

To establish a marker-assisted selection system for the eating quality of cooked rice, we performed quantitative trait locus (QTL) analysis using 188 recombinant inbred lines (RILs) derived from crosses of two japonica cultivars, 'Sakihikari' and 'Nipponbare'. The former has excellent eating quality with strong stickiness whereas the latter is less sticky. We evaluated the stickiness of cooked rice using a sensory test, as well as amylose content (AC), amylographic characteristics (AM), and days-to-heading of RILs, which affect stickiness, in 2005, 2006 and 2007, and used them for QTL analysis. Six QTLs for stickiness were identified on chromosomes 1, 3 (two QTLs), 6, 7 and 8. Of these, qST3-1 on the short arm of chromosome 3 was detected throughout the three-year experiments but the others were detected in one year only. We also mapped two QTLs for AC, 19 QTLs for AM, and three QTLs for days-to-heading. Stickiness of RILs was significantly correlated with AM, and several QTLs for AM were detected in the same QTL regions for stickiness. These results thus suggested that AM was important for the stickiness of RILs. The obtained QTL information is useful to identify DNA markers tightly linked to genes controlling eating quality.

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

“…Three QTLs, qADV6, qAC6.1 and qGCR6 mapped to the terminal region of the short arm of chromosome 6, corresponding to the wx locus (Harushima et al, 1998;Tan et al, 1999;Wan et al, 2004). This region includes important genes for good eating quality as revealed by several previous studies which have identified QTLs for eating quality near this region (Bao et al, 2000;Kobayashi and Tomita, 2008;Li et al, 2003;Suh et al, 2004;Takeuchi et al, 2007;Tanaka et al, 2006;Wada et al, 2006;Wan et al, 2004). In addition, there are several starch synthase-related genes on the short arm of chromosome 6, including waxy (Juliano, 1985;Sano, 1984), starch synthase I (Baba et al, 1993;Tanaka et al, 1995), and starch synthase IIa (Umemoto et al, 2002).…”

“…However, this trait is usually evaluated using a sensory test and needs to be done in advanced breeding generations (F 6 or later), which is both time consuming and labor intensive. Other selection methods, using as the measurement of physicochemical properties such as the ADV, AC, PC and gel consistency, have been used to evaluate eating quality indirectly (Bao et al, 2000;Kobayashi and Tomita, 2008;Li et al, 2003;Tanaka et al, 2006;Wada et al, 2006). 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).…”

“…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).…”

Identification of QTLs controlling heading date on the short arm of chromosome 3 in rice (Oryza sativa L.)

“…The results of this study revealed that a QTL for heading date, qDTH3, was linked to qLTG3-1. Furthermore, QTLs for agronomically important traits, eating quality (Kobayashi et al 2008, Takeuchi et al 2008, Wada et al 2008) and pre-harvest sprouting resistance (Hori et al 2010), have been identified in this chromosomal region. For the manipulation of these traits, targeted recombination within this chromosomal region should be useful for creating novel genotypes, which may provide novel advantages for adaptation for local environmental conditions.…”