Natural variation in Early flowering1 contributes to early flowering in japonica rice under long days

Abstract

Natural variation in heading-date genes enables rice, a shortday (SD) plant, to flower early under long-day (LD) conditions at high latitudes. Through analysis of heading-date quantitative trait loci (QTL) with F7 recombinant inbred lines from the cross of early heading 'H143' and late heading 'Milyang23 (M23)', we found a minor-effect Early Heading3 (EH3) QTL in the Hd16 region on chromosome 3. We found that Early flowering1 (EL1), encoding casein kinase I (CKI), is likely to be responsible for the EH3/Hd16 QTL, because a missense mutation occurred in the highly conserved serine/ threonine kinase domain of EL1 in H143. A different missense mutation was found in the EL1 kinase domain in Koshihikari. In vitro kinase assays revealed that EL1/ CKI in H143 and Koshihikari are non-functional. In F7:9 heterogeneous inbred family-near isogenic lines (HNILs), HNIL(H143) flowered 13 days earlier than HNIL(M23) in LD, but not in SD, in which EL1 mainly acts as a LD-dependent flowering repressor, down-regulating Ehd1 expression. In the world rice collection, two types of nonfunctional EL1 variants were found in japonica rice generally cultivated at high latitudes. These results indicate that natural variation in EL1 contributes to early heading for rice adaptation to LD in temperate and cooler regions.

QTL mapping for heading date, leaf area and chlorophyll content under cold and drought stress in two related recombinant inbred line populations (Japonica rice) and meta‐analysis

“…Heading dates (HD) under field conditions was measured just after the emergence of the first panicle (Kwon et al., ), the number of days required from sowing to heading. After the completion of heading stage, flag leaf area was calculated using the formula: leaf length × leaf width × 0.75 (Pommel et al., ).…”

Heat-induced inhibition of phosphorylation of the stress-protective transcription factor DREB2A promotes thermotolerance of Arabidopsis thaliana

“…CK1 functions in various plant biological processes, such as flowering (40,41), light signaling (42), hormone biosynthesis and signaling (43,44), and organization of the cytoskeleton (45,46). With regard to the regulation of stress responses, one report has shown the involvement of CK1 in the osmoticstress-induced phosphorylation of histone H3, which may positively regulate drought tolerance (47).…”

Cloning of quantitative trait genes from rice reveals conservation and divergence of photoperiod flowering pathways in Arabidopsis and rice

“…Another missense mutation was found in the kinase domain of Hd16 in the early-heading Korean cultivar “H143” (Kwon et al, 2014). In vitro kinase assays revealed that the “H143” Hd16 allele is also defective.…”

“…Thus, there are two defective natural variants of Hd16 . The “Koshihikari” and “H143” alleles were found only among japonica cultivars in temperate areas (Hori et al, 2013; Kwon et al, 2014). …”

“…To introduce rice at high latitudes, breeders have selected lines with a weaker response to photoperiod to produce early-flowering cultivars and to ensure maturation during the optimal period (e.g., Izawa, 2007; Ebana et al, 2011). The weak allele of Hd16 may have permitted the extension of the rice cultivation area into northern regions (Hori et al, 2013; Kwon et al, 2014). Deficient or weak alleles of Hd1 , Ghd7 , DTH8 , DTH2 , and OsPRR37 are also distributed in northern rice cultivation areas at high latitudes (Xue et al, 2008; Takahashi et al, 2009; Wei et al, 2010; Koo et al, 2013; Wu et al, 2013), strongly suggesting that such alleles are involved in the expansion of rice cultivation areas.…”