A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice

Abstract

Hybrid rice has greatly contributed to the global increase of rice productivity. A major component that facilitated the development of hybrids was a mutant showing photoperiod-sensitive male sterility (PSMS) with its fertility regulated by day length. Transcriptome studies have shown that large portions of the eukaryotic genomic sequences are transcribed to long noncoding RNAs (lncRNAs). However, the potential roles for only a few lncRNAs have been brought to light at present. Thus, great efforts have to be invested to understand the biological functions of lncRNAs. Here we show that a lncRNA of 1,236 bases in length, referred to as long-dayspecific male-fertility-associated RNA (LDMAR), regulates PSMS in rice. We found that sufficient amount of the LDMAR transcript is required for normal pollen development of plants grown under long-day conditions. A spontaneous mutation causing a single nucleotide polymorphism (SNP) between the wild-type and mutant altered the secondary structure of LDMAR. This change brought about increased methylation in the putative promoter region of LDMAR, which reduced the transcription of LDMAR specifically under long-day conditions, resulting in premature programmed cell death (PCD) in developing anthers, thus causing PSMS. Thus, a lncRNA could directly exert a major effect on a trait like a structure gene, and a SNP could alter the function of a lncRNA similar to amino acid substitution in structural genes. Molecular elucidating of PSMS has important implications for understanding molecular mechanisms of photoperiod regulation of many biological processes and also for developing male sterile germplasms for hybrid crop breeding.epigenetics | Oryza sativa

Construction of a male sterility system for hybrid rice breeding and seed production using a nuclear male sterility gene

“…Photoperiod-sensitive and thermo-sensitive lines are the two major types of rice PTGMS germplasm resources (5)(6)(7)(8). Two widely used PTGMS genes have been cloned: one is a noncoding RNA gene (6,7), and the other codes for RNase Z S1 (8).…”

“…Two widely used PTGMS genes have been cloned: one is a noncoding RNA gene (6,7), and the other codes for RNase Z S1 (8). The male fertility of PTGMS lines is reversible in response to environmental conditions, which enables the PTGMS lines to propagate via selfpollination under environmental conditions restoring the male fertility and to outcross with restorer lines for hybrid seed production under conditions suppressing male fertility (5)(6)(7)(8). Because PTGMS traits are controlled by nuclear recessive genes and male fertility can be restored by any normal rice cultivars (5-8), broader genetic resources can be explored for strong heterosis (1,5).…”

RNase ZS1 processes UbL40 mRNAs and controls thermosensitive genic male sterility in rice

“…Male reproduction is very sensitive to alterations in environmental conditions. A long non-coding RNA (lncRNA), the longday-specific male-fertility-associated RNA, causes a PGMS trait and was identified in Nongken58S 11 . At the same locus in the indica line Pei'ai64S, a non-coding RNA producing small RNAs was shown to confer a P/TGMS trait 10 .…”

“…The two-line breeding system uses thermosensitive genic male sterility (TGMS) lines or photoperiod-sensitive genic male sterility (PGMS) lines as maternal parents to produce hybrid seeds. TGMS and PGMS lines are male-sterile under restrictive conditions (high temperatures for TGMS and long-day for PGMS) but convert to male-fertile under permissive conditions (low temperatures for TGMS and short-day for PGMS); thus, they can self-pollinate under permissive conditions 10,11 . The TGMS and PGMS traits are controlled by nuclear, recessive genes and most normal rice cultivars can restore male fertility, thus providing broader genetic resources for rice breeding to produce hybrids with strong hybrid vigour [10][11][12] .…”

A stable tRNA-like molecule is generated from the long noncoding RNA GUT15 in Arabidopsis

“…Photomorphogenesis in Arabidopsis seedlings is regulated by the HID3 lncRNA, which is known to associate with PIF3 locus chromatin and repress its transcription [10]. In rice, the LDMAR noncoding transcript is required for normal male fertility under long-day conditions [11]. Plant lncRNAs are also involved in root nodule organogenesis; for example, the ENOD40 lncRNA plays a role in the cytoplasmic re-location of the nuclear protein RBP1 during nodulation in Medicago truncatula [12].…”