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Ef-cd locus shortens rice maturity duration without yield penalty
Wednesday, 2019/09/18 | 08:18:25

Jun Fang, Fantao Zhang, Hongru Wang, Wei Wang, Fei Zhao, Zijuan Li, Changhui Sun, Faming Chen, Fan Xu, Shuoqi Chang, Liang Wu, Qingyun Bu, Pingrong Wang, Jiankun Xie, Fan Chen, Xuehui Huang, Yijing Zhang, Xinguang Zhu, Bin Han, Xiaojian Deng, and Chengcai Chu


PNAS September 10, 2019 116 (37) 18717-18722


Early maturing rice cultivars usually have a low yield, suffering from a shortening maturity duration in comparison with late-maturing ones. Here we demonstrate that shortening of maturity duration with no yield penalty of rice can be achieved by the quantitative trait locus Early flowering-completely dominant (Ef-cd). Ef-cd is a long noncoding RNA transcribed from the antisense strand of the flowering activator OsSOC1 locus, which can positively regulate the expression of OsSOC1. Physiological analysis demonstrated that Ef-cd could facilitate nitrogen utilization and also improve the photosynthesis rate. This study provides breeders with a valuable genetic resource that is useful for balancing grain yield with maturity duration for further elevating food production in the world.


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 in Ef-cd could be used to overcome the above contradictory. The Ef-cd locus gives rise to a long noncoding RNA (lncRNA) antisense transcript overlapping the OsSOC1 gene. Ef-cd lncRNA expression positively correlates with the expression of OsSOC1 and H3K36me3 deposition. Field test comparisons of early maturing Ef-cd near-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 maturing Ef-cd allele shortens maturity duration (ranging from 7 to 20 d) without a concomitant yield penalty. Ef-cd facilitates nitrogen utilization and also improves the photosynthesis rate. Analysis of 1,439 elite hybrid rice varieties revealed that the 16 homozygotes and 299 heterozygotes possessing Ef-cd matured significantly earlier. Therefore, Ef-cd could be a vital contributor of elite early maturing hybrid varieties in balancing grain yield with maturity duration.


See https://www.pnas.org/content/116/37/18717

Figure 1:

Os03g0122500 was the causal gene of Ef-cd. (A) NIL D248 headed earlier than its recurrent parent Shuhui881 (SH881). (BEf-cd was mapped in a 12.9-kb region. (C) Two T-DNA insertion mutants of Os03g0122500 headed later than the wild-type Hwayoung. (D) The insertion occurred in the first intron of Os03g0122500 in mutant ef-cd-1 and in the promoter region of Os03g0122500 in mutant ef-cd-2. The triangle represents the T-DNA insertion. The types of the binary vectors used for constructing the T-DNA insertion mutants are above the triangles. (E) Two RNAi lines of Os03g0122500 headed later than their wild-type Nipponbare. (F) Expression levels of Ef-cd and OsSOC1 were significantly decreased in the RNAi lines compared to their wild type. The P value was calculated using Student’s t test. **P < 0.01. (Scale bars, 20 cm.)

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