Novel QTLs for photoperiodic flowering revealed by using reciprocal backcross inbred lines from crosses between japonica rice cultivars

Abstract

The rice japonica cultivars Nipponbare and Koshihikari differ in heading date and response of heading to photoperiod (photoperiod sensitivity). Using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers, we conducted quantitative trait locus (QTL) analyses for heading date in a set of reciprocal backcross inbred lines (BILs) from crosses between Nipponbare and Koshihikari. Under natural-day conditions, transgressive segregation in days to heading (DTH) toward both early and late heading was observed in both BIL populations. QTL analyses revealed that two QTLs--on chromosomes 3 and 6--were involved in the difference in heading date between the parental cultivars. The Nipponbare allele at the QTLs on chromosomes 3 and 6 showed, respectively, increasing and decreasing effects on DTH in both BIL populations. The transgressive segregation observed in the BILs could be accounted for mainly by the complementary action of a set of alleles with opposing effects. Both QTLs were finely mapped as single Mendelian factors in secondary mapping populations (BC2F2 plants/BC2F3 lines). The QTL on chromosome 3 was mapped in the 1,140-kb interval between 94O03-4 (SSR) and OJ21G19-4 (SNP) and was designated Hd16. The QTL on chromosome 6 was mapped in the 328-kb interval between P548D347 (SSR) and 0007O20 (SSR) and was designated Hd17. Both Hd16 and Hd17 were involved in photoperiod sensitivity, as revealed by observation of the DTH of nearly isogenic lines of Nipponbare under short- and long-day conditions, suggesting that allelic differences in both Hd16 and Hd17 account for most of the difference in photoperiod sensitivity between the parental cultivars.

Core single-nucleotide polymorphisms-a tool for genetic analysis of the Japanese rice population

“…Recently, biparental populations of Japanese rice cultivars have been used for genetic analysis of the natural variation in several agronomic traits, such as heading date (Fujino et al 2005, Matsubara et al 2008, culm length (Hori et al 2009), pre-harvest sprouting resistance (Hori et al 2010), eating quality (Kobayashi and Tomita 2008, Takeuchi et al 2008, Wada et al 2008) and grain quality (Kobayashi et al 2007, Tabata et al 2007). These studies have demonstrated that a relatively large allelic difference at a particular locus could be detected despite extremely low sequence diversity in Japanese cultivars.…”

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.…”

Mapping of Quantitative Trait Loci Associated with Concentrations of Five Trace Metal Elements in Rice (Oryza sativa)

“…QTLs were called where their logarithm of the odds (LOD) values exceeded 2.0, and the proportion of phenotypic variation was estimated from the coefficient of determination (R 2 ). Parameter settings for the QTL mapping were as described by Matsubara (Matsubara et al, 2008). The QTL was named following the nomenclature recommended by McCouch and CGSNL (McCouch and CGSNL, 2008).…”