DEVELOPMENT AND CHARACTERIZATION OF ESTSSR MARKERS IN Rubus ellipticus SMITH AND THEIR TRANSFERABILITY IN RELATED SPECIES/GENERA
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Date
2018-03
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UHF,NAUNI
Abstract
ABSTRACT
Rubus ellipticus Smith. commonly known as ‘Yellow Himalayan raspberry’ is an important
member of Rosaceae family with antioxidant and antibacterial properties. In the present study EST-SSR
markers were developed for R. ellipticus and were used for polymorphism/transferability studies. EST
sequences of R. ellipticus were generated from cDNA clones using Paired-End sequencing method on
NextSeq 500. The raw data were assembled using DNASTAR (https://www.dnastar.com/ ) software. A
total of 7777 EST sequences for R. ellipticus were obtained. ESTs containing SSR motifs were extracted
out using an online tool, MISA (http://pgrc.ipk-gatersleben.de/misa). 704 ESTs were used for SSR
extraction. SSR primers were designed from the SSR containing EST sequences using Websat software
(http:/www.wsmartins.net/websat) and 68 randomly selected primer pairs were custom synthesized.
Polymorphism study was carried out using 68 SSR primer pairs among 21 collections of Rubus ellipticus
and 31 members of Rosaceae family. For polymorphism studies, DNA was isolated from young leaves
using CTAB method (Doyle and Doyle, 1987). The EST-SSR primers revealed 95.3% and 93.6%
polymorphism in diversity and cross transferability analysis. Jaccard’s similarity matrix was developed
and dendrograms were generated using NTSYSpc ver.2.02h to establish the percent similarity among the
21 collections of Rubus ellipticus and 31 members of Rosaceae family. With EST-SSR primers, two
clusters were obtained. Maximum similarity i.e 69% was found between ‘Kharkog-1’ and ‘Majhgaon’ of
Rubus ellipticus and 87 % betweenn‘High and magic’ and ‘Chaubattia ambrose’ of Rosaceae family. Thus
EST-SSRs used in the present study revealed a high level of polymorphism in the 21 colllections of Rubus
ellipticus and 31 members of Rosaceae family, revealing their efficiency in fingerprinting analysis.
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