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=13 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 type 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 searched for BLASTn homology against Dabenzi genome. 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-SSRs were developed for seed type trait from 63 true pri-miRNAs, of which 46 were specific to pre-miRNAs. Through ePCR, 123 primers were validated and mapped on eight Tunisia chromosomes. Further, 80 SSRs producing specific amplicons were ePCR-confirmed on multiple genomes