Ef-cd locus shortens rice maturity duration without yield penalty

Abstract

The contradiction between “high yielding” and “early maturing” hampers further improvement of annual rice yield. Here we report the positional cloning of a major maturity duration regulatory gene,Early flowering-completely dominant(Ef-cd), and demonstrate that natural variation inEf-cdcould be used to overcome the above contradictory. TheEf-cdlocus gives rise to a long noncoding RNA (lncRNA) antisense transcript overlapping theOsSOC1gene.Ef-cdlncRNA expression positively correlates with the expression ofOsSOC1and H3K36me3 deposition. Field test comparisons of early maturingEf-cdnear-isogenic lines with their wild types as well as of the derivative early maturing hybrids with their wild-type hybrids conducted under different latitudes determined that the early maturingEf-cdallele shortens maturity duration (ranging from 7 to 20 d) without a concomitant yield penalty.Ef-cdfacilitates nitrogen utilization and also improves the photosynthesis rate. Analysis of 1,439 elite hybrid rice varieties revealed that the 16 homozygotes and 299 heterozygotes possessingEf-cdmatured significantly earlier. Therefore,Ef-cdcould be a vital contributor of elite early maturing hybrid varieties in balancing grain yield with maturity duration.

Long non-coding RNAs in plants: emerging modulators of gene activity in development and stress responses

“…Other flowering time-related lncRNAs, including FLOWERING LONG INTERGENIC NON CODING RNA ( FLINC ), CDF5 LONG NONCODING RNA ( FLORE ), LDMAR , PHOTOPERIOD-SENSITIVE GENIC MALE STERILITY 1 ( PMS1T ) and Ef-cd , have been recently discovered in Arabidopsis or rice (Ding et al 2012a , b ; Fan et al 2016 ; Henriques et al 2017 ; Severing et al 2018 ; Fang et al 2019 ). FLINC regulates ambient temperature-mediated flowering.…”

“…After floral transition, the inflorescence meristem starts to produce floral meristems, which in turn give rise to different types of floral organs. Nowadays, a number of lncRNAs such as LINC-AP2 (Gao et al 2016 ), LONG-DAY SPECIFIC MALE-FERTILITY-ASSOCIATED RNA (LDMAR) (Ding et al 2012a , b ), PHOTOPERIOD-SENSITIVE GENIC MALE STERILITY T ( PMS1T ; Fan et al 2016 ), and EARLY FLOWERING-COMPLETELY DOMINANT ( Ef-cd ; Fang et al 2019 ) have been found to regulate diverse aspects of flower and reproductive development (see Supplemental table S1 for a more comprehensive list of examples). LINC-AP2 is an intergenic lincRNA close to the flower developmental regulatory TF gene APETALA2 ( AP2) .…”

“…2 f). Ef-cd is an antisense RNA in the OsSOC1 locus and positively regulates OsSOC1 activity by deposition of H3K36me3, thereby reducing the time-span that is needed to reach plant maturity without yield penalty (Fang et al 2019 ). Together, these findings highlight important functions for lncRNAs in reproductive growth via different molecular mechanisms.…”

Rice Breeding: A Long Noncoding Locus with Great Potential

“…6442S-7 showed a completely dominant earlymaturing phenotype, and a dominant earliness gene, designated Early flowering-completely dominant (Ef-cd), was roughly mapped to the short arm of rice chromosome 3 (Deng et al, 2001). After 18 years of effort, Ef-cd was finally cloned by map-based cloning (Fang et al, 2019). Interestingly, Ef-cd encodes a long noncoding RNA (lncRNA) that is transcribed from the antisense strand of OsSOC1, which encodes a flowering activator in rice.…”

A Comprehensive Transcriptomics Analysis Reveals Long Non-Coding RNA to Be Involved in the Key Metabolic Pathway in Response to Waterlogging Stress in Maize

“…Recent studies have demonstrated that lncRNAs participate in diversified biological functions in different organisms [23,24]. Nevertheless, only a few lncRNAs have been well characterized in plants, including COOLAIR and COLDAIR in the regulation of flowering in Arabidopsis [25,26], INDUCED BY PHOSPHATE STARVATION1, which is involved in phosphate uptake [27,28]; Enod40, which is involved in nodulation [29,30]; LDMAR, which is required for pollen development in rice [31]; LAIR, which increases rice grain yield [32]; and Ef-cd, which shortens rice maturity duration without a yield penalty [33]. Remarkably, accumulated evidence has demonstrated the involvement of lncRNAs in biotic and abiotic stress responses in plants [34].…”