Identification and validation of SSR markers for Xanthomonas axonopodis pv. punicae an incitant of bacterial blight of pomegranate

P.G. Patil; J. Sharma; M. Nanjundappa; N.V. Singh; A. Bohra; R. Gunnaiah; S.M. Jamma; J. Vinayaka; V.R. Sangnure; R.A. Marathe

doi:10.1007/s13205-022-03209-z

Back

Identification and validation of SSR markers for Xanthomonas axonopodis pv. punicae an incitant of bacterial blight of pomegranate

Journal article

Peer reviewed

Identification and validation of SSR markers for Xanthomonas axonopodis pv. punicae an incitant of bacterial blight of pomegranate

P.G. Patil, J. Sharma, M. Nanjundappa, N.V. Singh, A. Bohra, R. Gunnaiah, S.M. Jamma, J. Vinayaka, V.R. Sangnure and R.A. Marathe

3 Biotech, Vol.12(7), Art. 153

2022

DOI: https://doi.org/10.1007/s13205-022-03209-z

Files and links (1)

url

Link to Published Version *Subscription may be requiredView

Abstract

This study reports genome wide characterization and development of first set of microsatellite markers through in silico analysis of eight sequenced Xanthomonas axonopodis pv. punicae strains available in the public database. SSR survey resulted in identification of ~ 4638 perfect SSRs, with mean marker frequency 901 SSRs/Mb and densitiy of 11,006 bp/Mb aross the eight genomes. Frequency distribution graphs revealed hexa-nucleotide repeats were more prominent fowllowed by tri-, tetra-, di- and penta-nucleotides in the analysed genomes. We desinged 2927 SSR primers that are specific to the strain LMG 859 and ePCR confirmed on seven other Xap genomes. This resulted in identification of 542 informative SSRs that are producing single amplicons, from which 66 primers were successfully validated through wet lab experiments on eight Xap isolates of pomegranate. Furthermore, utility of these SSRs were demostrated by analysing molecular diversity among 22 Xap isolates using 20 Xap_SSR primers. SSRs revealed moderate genetic diversity among Xap isolates (61%) and grouped 11 isolates that are repersenting six different states into one cluster. This proved the earlier evidence of wider spread of ST3 type Xap acoss India using Multi locus Sequence Typing (MLST) technique. In summary, Xap_SSR will serve as powerful genomics tools that would helps in monitoring of population dynamics, taxonomy, epidomology and quarantine aspects in bacterial blight pathogen through development of microsatellite based Multilocus Variable number of Tandem repeat analysis (MLVA) in future.

Details

Title: Identification and validation of SSR markers for Xanthomonas axonopodis pv. punicae an incitant of bacterial blight of pomegranate
Authors/Creators: P.G. Patil (Author/Creator) - Indian Council of Agricultural Research
J. Sharma (Author/Creator)
M. Nanjundappa (Author/Creator)
N.V. Singh (Author/Creator)
A. Bohra (Author/Creator)
R. Gunnaiah (Author/Creator)
S.M. Jamma (Author/Creator)
J. Vinayaka (Author/Creator)
V.R. Sangnure (Author/Creator)
R.A. Marathe (Author/Creator)
Publication Details: 3 Biotech, Vol.12(7), Art. 153
Publisher: Springer
Identifiers: 991005542571307891
Murdoch Affiliation: Centre for Crop and Food Innovation; State Agricultural Biotechnology Centre
Language: English
Resource Type: Journal article

Metrics

45 Record Views

InCites Highlights

These are selected metrics from InCites Benchmarking & Analytics tool, related to this output

Collaboration types: Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.97 Plant Pathology; 3.97.1357 Plant Bacterial Pathogens
Web Of Science research areas: Biotechnology & Applied Microbiology
ESI research areas: Biology & Biochemistry