Identification and characterization of long non-coding RNAs regulating resistant starch biosynthesis in bread wheat (Triticum aestivum L.)

Akansha Madhawan; Ankita Sharma; Abhishek Bhandawat; Mohammed Saba Rahim; Prashant Kumar; Ankita Mishra; Afsana Parveen; Himanshu Sharma; Shailender Kumar Verma; Joy Roy

doi:10.1016/j.ygeno.2020.05.014

Identification and characterization of long non-coding RNAs regulating resistant starch biosynthesis in bread wheat (Triticum aestivum L.)

Genomics. 2020 Sep;112(5):3065-3074. doi: 10.1016/j.ygeno.2020.05.014. Epub 2020 May 22.

Authors

Affiliations

¹ Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India. Electronic address: akansha.m@nabi.res.in.
² Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, 176206, Himachal Pradesh, India.
³ Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India.
⁴ Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India. Electronic address: sabarahim@nabi.res.in.
⁵ Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India. Electronic address: prashant.ku@nabi.res.in.
⁶ Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India. Electronic address: ankita@nabi.res.in.
⁷ Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India. Electronic address: afsana@nabi.res.in.
⁸ Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Kangra, 176206, Himachal Pradesh, India. Electronic address: skverma@cuhimachal.ac.in.
⁹ Agri-Food Biotechnology Division, National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India. Electronic address: joykroy@nabi.res.in.

PMID: 32447006
DOI: 10.1016/j.ygeno.2020.05.014

Abstract

Resistant starch (RS) also known as healthy starch has shown several health benefits. Enhancing the RS through genetic modification approaches has huge commercial importance. Regulatory RNA like long non-coding RNA (lncRNA) plays an important role in gene regulation. In this study, we mined 63 transcriptome datasets of wheat belonging to 35 genotypes representing two seed developmental stages. Contrasting expression of a subset of lncRNAs in RS mutant lines compared to parent wheat variety 'C 306' signifies their probable role in RS biosynthesis. Further, lncRNA- TCONS_00130663 showed strong positive correlation (r² = 1) with LYPL gene and strong negative correlation with SBEIIb (r² = -0.94). We found TCONS_00130663 as positive regulator of LYPL gene through interaction with miR1128. Based on relative expression, in silico interaction and DSC analysis we hypothesize the dual role of TCONS_00130663 in RS type 2 and type 5. The study provides a useful resource for functional mechanism of lncRNAs.

Keywords: Amylose; Amylose-lipid complex; Resistant starch; lncRNA; miRNA.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Amylose / metabolism
Computer Simulation
Gene Expression Regulation, Plant
Lipids / biosynthesis
MicroRNAs / metabolism
Mutation
RNA, Long Noncoding / chemistry
RNA, Long Noncoding / metabolism*
Resistant Starch / metabolism*
Seeds / genetics
Sequence Homology, Nucleic Acid
Triticum / embryology
Triticum / genetics*
Triticum / metabolism

Substances

Lipids
MicroRNAs
RNA, Long Noncoding
Resistant Starch
Amylose