Genome wide identification, characterization and validation of novel miRNA-based SSR markers in pomegranate (Punica granatum L.)

Pg, Patil; Singh, Namita Ashish; Parashuram, Shilpa; Dm, Mundewadikar; Vr, Sangnure; Kd, Babu; Sharma, Jyotsana

doi:10.1007/s12298-020-00790-6

Cited by 29 publications

(24 citation statements)

References 68 publications

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“…However, there is an urgent need to improve the efficiency of current breeding programs to deliver higher genetic gains. In this context, appropriate DNA marker technology facilitates the identification of genetic determinants (genes/QTLs) underlying various traits of economic significance ( Patil et al, 2020b , c ). Among the various marker techniques, microsatellites or simple sequence repeat (SSR) markers represent one of the most informative, abundant, and easy-to-use marker systems for genetic studies and plant breeding programs ( Bohra et al, 2011 , 2012 ; Ravishankar et al, 2013 ; Xu et al, 2013 ; Abd Ei-Moghny et al, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

Comprehensive Characterization and Validation of Chromosome-Specific Highly Polymorphic SSR Markers From Pomegranate (Punica granatum L.) cv. Tunisia Genome

et al. 2021

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The simple sequence repeat (SSR) survey of ‘Tunisia’ genome (296.85 Mb) identified a total of 365,279 perfect SSRs spanning eight chromosomes, with a mean marker density of 1,230.6 SSRs/Mb. We found a positive trend in chromosome length and the SSR abundance as marker density enhanced with a shorter chromosome length. The highest number of SSRs (60,708) was mined from chromosome 1 (55.56 Mb), whereas the highest marker density (1,294.62 SSRs/Mb) was recorded for the shortest chromosome 8 (27.99 Mb). Furthermore, we categorized all SSR motifs into three major classes based on their tract lengths. Across the eight chromosomes, the class III had maximum number of SSR motifs (301,684, 82.59%), followed by the class II (31,056, 8.50%) and the class I (5,003, 1.37%). Examination of the distribution of SSR motif types within a chromosome suggested the abundance of hexanucleotide repeats in each chromosome followed by dinucleotides, and these results are consistent with ‘Tunisia’ genome features as a whole. Concerning major repeat types, AT/AG was the most frequent (14.16%), followed by AAAAAT/AAAAAG (7.89%), A/C (7.54%), AAT/AAG (5.23%), AAAT/AAAG (4.37%), and AAAAT/AAAAG (1.2%) types. We designed and validated a total of 3,839 class I SSRs in the ‘Tunisia’ genome through electronic polymerase chain reaction (ePCR) and found 1,165 (30.34%) SSRs producing a single amplicon. Then, we selected 906 highly variable SSRs (> 40 nt) from the ePCR-verified class I SSRs and in silico validated across multiple draft genomes of pomegranate, which provided us a subset of 265 highly polymorphic SSRs. Of these, 235 primers were validated on six pomegranate genotypes through wet-lab experiment. We found 221 (94%) polymorphic SSRs on six genotypes, and 187 of these SSRs had ≥ 0.5 PIC values. The utility of the developed SSRs was demonstrated by analyzing genetic diversity of 30 pomegranate genotypes using 16 HvSSRs spanning eight pomegranate chromosomes. In summary, we developed a comprehensive set of highly polymorphic genome-wide SSRs. These chromosome-specific SSRs will serve as a powerful genomic tool to leverage future genetic studies, germplasm management, and genomics-assisted breeding in pomegranate.

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Section: Introductionmentioning

confidence: 99%

Comprehensive Characterization and Validation of Chromosome-Specific Highly Polymorphic SSR Markers From Pomegranate (Punica granatum L.) cv. Tunisia Genome

et al. 2021

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“…Plenty of sequences can be produced through NGS techniques in a very short time resulting in huge amount of data generation. This sequence data can be utilized to develop SSR markers as also developed by several workers in various crops (Zalapa et al 2012;Ravishankar et al 2017;Neophytou et al 2018;Tibihika et al 2019;Patil et al 2020). We also utilized horsegram data from public domain to develop SSR markers, specifically from the drought resistant transcripts.…”

Section: Resultsmentioning

confidence: 99%

Development of transcriptome-wide SSR markers for genetic diversity and structure analysis in Macrotyloma uniflorum (Lam.) Verdc.

Kumar

Kaundal

Sharma³

et al. 2020

Physiol Mol Biol Plants

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Horsegram is an important drought resistant pulse crop from Fabaceae and can be easily grown in dry lands with no irrigation facilities. However, it remained neglected since long and has been considered as orphan legume which requires immediate attention for its improvement and for the development of new promising varieties in future. In the present study, 7352 simple sequence repeat (SSR) markers were developed from the transcriptome data and 150 SSR were randomly synthesized for validation and diversity analysis in a panel of 58 horsegram genotypes. The synthesized primers included all types of repeats spanning direpeats to hexarepeats. Of the validated SSR markers, 33 markers were polymorphic and produced 40 loci which were used to analyze the genetic diversity and structure of horsegram. In total, 130 alleles were produced in a range of 2-9 alleles with maximum alleles produced by primer HTSSR 155. Expected heterozygosity (He) ranged from 0.03 to 1.00 and observed heterozygosity (Ho) ranged from 0.13 to 0.81. Polymorphism information content value ranged from 0.065 to 0.78. Dendrogram based on UPGMA and principal component analysis showed four groups of the 58 genotypes of horsegram. Structure analysis showed three genetic stocks for the analyzed germplasm. Thus, the developed SSRs can be useful in future population genetics analysis, molecular breeding studies and mapping works in horsegram germplasm as well as in related legume species.

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“…The miRNA targeted regulation over the 63, expression has already been reported in different plant species [ 62 , 63 , 64 ], hence, the putative miRNA of jute might exhibit regulatory roles over the important cellular expression through in vivo and in vitro validation. EST based miRNA prediction is getting more prioritized in different crops as the regulatory profile of targeted miRNAs could impact on the better crop production as well as significant improvement in the desired characteristics of the economically important crop plants [ 65 , 66 , 67 , 68 ]. That is why, the above study could have significant importance in the fibre industry as the contributory roles of putative miRNAs of C. capsularis have been identified in the lignin biosynthesis process.…”

Section: Discussionmentioning

confidence: 99%

In silico identification of conserved miRNAs in the genome of fibre biogenesis crop Corchorus capsularis

Ahmed

et al. 2021

Heliyon

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Corchorus capsularis, commonly known as jute occupies the leading position in the production of natural fibre alongside lower environmental threat. Small noncoding ~21 to 24 nucleotides long microRNAs play significant roles in regulating the gene expression as well as different functions in cellular growth and development. Here, the study adopted a comprehensive in silico approach to identify and characterize the conserved miRNAs in the genome of C. capsularis including functional annotation of specific gene targets. Expressed Sequence Tags (ESTs) based homology search of 3350 known miRNAs of dicotyledons were allowed against 763 non-redundant ESTs of jute genome, resulted in the prediction of 5 potential miRNA candidates belonging five different miRNA families (miR1536, miR9567-3p, miR4391, miR11300, and miR8689). The putative miRNAs were composed of 18 nucleotides having a range of -0.49 to -1.56 MFEI values and 55%–61% of (A + U) content in their pre-miRNAs. A total of 1052 gene targets of putative miRNAs were identified and their functions were extensively analyzed. Most of the gene targets were involved in plant growth, cell cycle regulation, organelle synthesis, developmental process and environmental responses. Five gene targets, namely, NAC Domain Containing Protein, WRKY DNA binding protein, 3-dehydroquinate synthase, S-adenosyl-L-Met–dependent methyl transferase and Vascular-related NAC-Domain were found to be involved in the lignin biosynthesis, phenylpropanoid pathways and secondary wall formation. The present study might accelerate the more miRNA discovery, strengthening the complete understanding of miRNAs association in the cellular basis of lignin biosynthesis towards the production of high standard jute products.

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Genome wide identification, characterization and validation of novel miRNA-based SSR markers in pomegranate (Punica granatum L.)

Cited by 29 publications

References 68 publications

Comprehensive Characterization and Validation of Chromosome-Specific Highly Polymorphic SSR Markers From Pomegranate (Punica granatum L.) cv. Tunisia Genome

Comprehensive Characterization and Validation of Chromosome-Specific Highly Polymorphic SSR Markers From Pomegranate (Punica granatum L.) cv. Tunisia Genome

Development of transcriptome-wide SSR markers for genetic diversity and structure analysis in Macrotyloma uniflorum (Lam.) Verdc.

In silico identification of conserved miRNAs in the genome of fibre biogenesis crop Corchorus capsularis

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