Journal article
Novel miRNA-SSRs for Improving Seed Hardness Trait of Pomegranate (Punica granatum L.)
Frontiers in Genetics, Vol.13, Art. 866504
2022
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 i.e. Dabenzi, Taishanhong, AG2017 and Tunisia, yielding a set of 63 polymorphic SSRs (polymorphism information content ≥0.5). Of these, 32 miRNA-SSRs revealed higher polymorphism level (89.29%) when assayed on six pomegranate genotypes. Furthermore, target prediction and network analysis suggested a possible association of miRNA-SSRs i.e. miRNA_SH_SSR69, miRNA_SH_SSR36, miRNA_SH_SSR103, miRNA_SH_SSR35 and miRNA_SH_SSR53 with seed type trait. These miRNA-SSRs would serve as important genomic resource for rapid and targeted improvement of seed type trait of pomegranate.
Details
- Title
- Novel miRNA-SSRs for Improving Seed Hardness Trait of Pomegranate (Punica granatum L.)
- Authors/Creators
- P.G. Patil (Author/Creator)N.V. Singh (Author/Creator)A. Bohra (Author/Creator)S. Jamma (Author/Creator)N. Manjunatha (Author/Creator)C.S. Venkatesh (Author/Creator)D.B. Karuppannan (Author/Creator)J. Sharma (Author/Creator)R.A. Marathe (Author/Creator)
- Publication Details
- Frontiers in Genetics, Vol.13, Art. 866504
- Publisher
- Frontiers
- Identifiers
- 991005543552207891
- Copyright
- © 2022 Patil et al.
- Murdoch Affiliation
- Murdoch University
- Language
- English
- Resource Type
- Journal article
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