Table 1.
List of Piper nigrum accessions used for validation of SSRs and diversity analysis.
Table 2.
List of accessions in different Piper species used for cross species amplification.
Fig 1.
Distribution of simple sequence repeats in the draft genome sequence of black pepper (Piper nigrum).
Fig 2.
Abundance of specific SSR motifs in di- to hexanucleotides repeats in the Piper nigrum genome.
Fig 3.
Distribution of SSRs identified in genic and intergenic regions of Piper nigrum.
Fig 4.
Distribution of SSRs identified in regions with transposable elements in Piper nigrum.
Fig 5.
Validation of SSR markers in germplasm accessions of black pepper (Piper nigrum).
Gel image of PCR amplification of SSR marker BPSSR27 on 30 germplasm accessions of P. nigrum as captured on QIAxcel ScreenGel software is shown on the left side. Numbers refer to accession numbers as mentioned in Table 1. The lane marked ‘M’ is DNA molecular weight standard 50-800bp v2.0 Qx DNA size marker. A representative electropherogram showing allele sizes of 234 bp (sample 25) and 234, 243 and 249bp (sample 26) has been shown on right side of the figure.
Fig 6.
Genetic relationship of germplasm accessions as revealed by SSR markers in black pepper.
Dendrogram was constructed using SSR profiles for 30 black pepper (Piper nigrum) accessions. The pairwise Jaccard’s similarity coefficients was used for construction of phylogenetic tree.
Table 3.
List of 74 validated SSR primer pairs from black pepper used for diversity analysis and cross species transferability.
Fig 7.
Cross-species transferability of SSR from P. nigrum in other species of Piper.
A. Amplification profile of SSRs in different Piper species with primer BPSSR17 and BPSSR25. Name of the species have been mentioned in the top of the gel image. The numbers under the species name indicate different accessions from the species. M is the DNA molecular weight standard, 50bp ladder (MBI Fermentas). Primer names have been indicated at the bottom of each gel. B. Species wise transferability of SSRs from P. nigrum in nine different Piper species.
Table 4.
Cross species amplification of 50 SSRs from P. nigrum in 9 other Piper species.
Numbers in the first row indicate species name and TCR number as given below. 1: P. nigrum (TCR419), 2: P. nigrum (TCR8), 3: P. longum (P25), 4: P. longum (TCR267), 5: P. arboreum (TCR267), 6: P. arboreum (P. arboreum), 7: P. argyrophyllum (TCR302), 8: P. argyrophyllum (TCR365), 9: P attenuatum (TCR171), 10: P betel (TCR166), 11: P betel (TCR357), 12: P betel (Lakshdweep), 13: P chaba (TCR149), 14: P. chaba (TCR265), 15: P. hymenophyllum (TCR345), 16: P. trichostachyon (TCR363), 17: P. trichostachyon (CR279), 18: P. wallichi (P. wallichi). Plus (+) and minus (-) sign indicate cross species transferability. Monomorhic/polymorphic indicate amplification of same/different allele as P. nigrum.