Genome-wide identification and characterization of novel non-coding RNA-derived SSRs in wheat
- PDF / 1,438,384 Bytes
- 15 Pages / 595.276 x 790.866 pts Page_size
- 105 Downloads / 164 Views
ORIGINAL ARTICLE
Genome‑wide identification and characterization of novel non‑coding RNA‑derived SSRs in wheat Abhishek Bhandawat1 · Himanshu Sharma1 · Neha Pundir1 · Akansha Madhawan1 · Joy Roy1 Received: 22 April 2020 / Accepted: 26 July 2020 © Springer Nature B.V. 2020
Abstract Expression of eukaryotic genes is largely regulated by non-coding RNAs (ncRNA). Sequence variations in the regulatory RNAs may have critical biological consequences including transcriptional and post-transcriptional gene regulation. ncRNAderived markers thus can be proved useful in molecular breeding, QTL mapping and association studies for trait dissection. In present study, we identified a total of 661 SSRs dwelling in pre-miRNA (15), small nuclear RNA (25) and lncRNA (621). Of these, 46 were validated and 100% amplification success was observed in selected wheat genotypes. A set of 36 ncRNASSRs markers was utilized for genetic variability assessment in forty-eight Indian wheat genotypes (which includes bread wheat, durum wheat and relatives). Number of alleles ranged from 1 to 4 with an average of two alleles per SSR locus. Mean PIC, observed heterozygosity and Shannon information index were found to be 0.258, 0.37 and 0.476 which suggests ncRNA-SSRs show higher polymorphism compared to genic SSRs but lower polymorphism compared to genomic SSRs. Thirty-six ncRNA-SSRs showed transferability ranging from 42.1% to 100%. Average genetic dissimilarity among wheat genotypes was found to be 0.29 based on Jaccard’s dissimilarity. This is the first report of ncRNA-SSRs in wheat which will be useful for molecular breeding and genetic improvement of wheat. Keywords Long non-coding RNA · miRNA · Non-coding RNA · snRNA · SSRs · Wheat
Introduction
Abhishek Bhandawat and Himanshu Sharma are contributed equally. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11033-020-05687-x) contains supplementary material, which is available to authorized users. * Joy Roy [email protected] Abhishek Bhandawat [email protected] Himanshu Sharma [email protected] Neha Pundir [email protected] Akansha Madhawan [email protected] 1
National Agri-Food Biotechnology Institute, Sector‑81, Mohali‑140306, Punjab, India
Wheat is among the most popular staple crop worldwide. Wheat consumption exceeds that of rice, especially in India and China [1]. Besides a major calorie source (due to abundance of storage starch), wheat is a rich source of proteins, iron, calcium, vitamin B6 and fibers, thus contributing additional health benefits [2]. Wheat has a long and complex history of hybridization and cultivation. Selection of varieties focusing mainly for traits like early maturing, higher yield, disease resistance and easy harvesting has narrowed down the genetic base of present-day wheat [3]. Genetic diversity associated with diverse gene and allelic variants provide a rich resource for various approaches of molecular breeding, genomic selection, genome-wide association studies, genetic mappin
Data Loading...
