Detection of quantitative trait loci controlling pre-harvest sprouting resistance by using backcrossed populations of japonica rice cultivars

Abstract

Backcrossed inbred lines (BILs) and a set of reciprocal chromosome segment substitution lines (CSSLs) derived from crosses between japonica rice cultivars Nipponbare and Koshihikari were used to detect quantitative trait loci (QTLs) for pre-harvest sprouting resistance. In the BILs, we detected one QTL on chromosome 3 and one QTL on chromosome 12. The QTL on the short arm of chromosome 3 accounted for 45.0% of the phenotypic variance and the Nipponbare allele of the QTL increased germination percentage by 21.3%. In the CSSLs, we detected seven QTLs, which were located on chromosomes 2, 3 (two), 5, 8 and 11 (two). All Nipponbare alleles of the QTLs were associated with an increased rate of germination. The major QTL for pre-harvest sprouting resistance on the short arm of chromosome 3 was localized to a 474-kbp region in the Nipponbare genome by the SSR markers RM14240 and RM14275 by using 11 substitution lines to replace the different short chromosome segments on chromosome 3. This QTL co-localized with the low-temperature germinability gene qLTG3-1. The level of germinability under low temperature strongly correlated with the level of pre-harvest sprouting resistance in the substitution lines. Sequence analyses revealed a novel functional allele of qLTG3-1 in Nipponbare and a loss-of-function allele in Koshihikari. The allelic difference in qLTG3-1 between Nipponbare and Koshihikari is likely to be associated with differences in both pre-harvest sprouting resistance and low-temperature germinability.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-010-1275-z) contains supplementary material, which is available to authorized users.

Multiple functional polymorphisms in a single disease resistance gene in rice enhance durable resistance to blast

“…To confirm the effect of each haplotype on resistance to M. oryzae, we used 6 backcrossed lines, each carrying the target chromosome from 1 of 6 donors: Hokkai 188 (BC 4 F 4 ), Padi Kuning (BC 2 F 2 ), LAC23 (BC 4 F 4 ), IR64 (BC 4 F 4 ), Bleiyo (BC 4 F 3 ), or Nipponbare (BC 4 F 4 ). The lines for LAC23 (SL2207), IR64 (SL2003), and Nipponbare (SL602) were used in previous studies [52][53][54] .…”

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.…”

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.…”