IC4R006-lncRNA-2015-26387578

Project Title

Analysis of non-coding transcriptome in rice and maize uncovers roles of conserved lncRNAs associated with agriculture traits

Long non-coding RNAs (lncRNAs) have recently been found to widely exist in eukaryotes and play important roles in key biological processes. To extend the knowledge of lncRNAs in crop plants, the researchers performed both non-directional and strand-specific RNA-sequencing experiments to profile non-coding transcriptomes of various rice and maize organs at different developmental stages.

Seeds from the cultivated rice subspecies Oryza sativa L. ssp. Japonica cultivar Nipponbare were grown in a greenhouse in Singapore under natural light conditions. Flower buds were collected before flowering and flowers were collected at the flowering day. Flag leaves and roots were collected at both the before- and afterflowering stage. The before-flowering sample was defined as a mixture of different stages in a period from panicle initiation to 1 day before flowering. The after-flowering sample was defined as a mixture of different stages after the flowering day. Milk grains and mature seeds were also collected. Maize (Zea mays L. ssp. mays) B73 seeds were germinated on wetted paper towel in plates for 2 days and then transferred to soil and grown for 2 weeks under 26°C and 16 h light and 8 h dark condition in a growth chamber at The Rockefeller University. Shoot and root tissues were separately collected. All samples were frozen in liquid nitrogen.

Analysis of more than 3 billion reads identified 22 334 long intergenic non-coding RNAs (lincRNAs) and 6673 pairs of sense and natural antisense transcript (NAT).

Many lincRNA genes were associated with epigenetic marks. Expression of rice lincRNA genes was significantly correlated with that of nearby protein-coding genes. A set of NAT genes also showed expression correlation with their sense genes.

More than 200 rice lincRNA genes had homologous non-coding sequences in the maize genome. Much more lincRNA and NAT genes were derived from conserved genomic regions between the two cereals presenting positional conservation. Protein-coding genes flanking or having a sense-antisense relationship to these conserved lncRNA genes were mainly involved in development and stress responses, suggesting that the associated lncRNAs might have similar functions.

Integrating previous genome-wide association studies (GWAS), we found that hundreds of lincRNAs contain trait-associated SNPs (single nucleotide polymorphisms [SNPs]) suggesting their putative contributions to developmental and agriculture traits.

Laboratory of Plant Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA, and
Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore City 117604, Singapore