AUTHOR=Patil Prakash Goudappa , Singh Nripendra Vikram , Bohra Abhishek , Jamma Shivani , N Manjunatha , C Venkatesh S. , Karuppannan Dhinesh Babu , Sharma Jyotsana , Marathe Rajiv A. 

TITLE=Novel miRNA-SSRs for Improving Seed Hardness Trait of Pomegranate (Punica granatum L.)

JOURNAL=Frontiers in Genetics

VOLUME=Volume 13 - 2022

YEAR=2022

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2022.866504

DOI=10.3389/fgene.2022.866504

ISSN=1664-8021

ABSTRACT=Present research discovered novel miRNA-SSRs for seed harness trait from 761 potential precursor miRNA sequences of pomegranate. SSR mining and BLASTx of the unique sequences identified 69 non-coding pre-miRNA sequences, which were then selected as query sequences for BLASTn homology search against pomegranate genome cv. Dabenzi. Sixty three true pri-miRNA contigs encoding 213 pre-miRNAs were predicted. Analysis of the resulting sequences enabled discovery of SSRs within pri-miRNA (227) and pre-miRNA sequences (79). A total of 132 miRNA-SSR were developed for seed hardness traits using 63 true pri-miRNAs, of which 46 were specific to pre-miRNAs. Through ePCR, 123 primers were validated and mapped on 8 Tunisia chromosomes. Further, 80 SSRs producing specific amplicons were ePCR-confirmed on multiple genomes i.e. Dabenzi, Taishanhong, AG2017 and Tunisia, resulting in identification of 63 polymorphic SSR markers (PIC ≥ 0.5). A subset of miRNA-SSRs (32) when assayed on six pomegranate genotypes, revealed their ability to detect higher polymorphism (89.29%). Furthermore, target prediction and network analysis suggested a possible association of miRNA-SSRs i.e. miRNA_SH69, miRNA_SH36, miRNA_SH103, miRNA_SH35 and miRNA_SH53 with seed hardness trait. These miRNA-SSRs would serve as important genomic resource for rapid and targeted improvement of seed hardness trait of pomegranate.