Abstract
Simple sequence repeat (SSR) is currently the most preferred molecular marker system owing to their highly desirable properties viz., abundance, hyper-variability, and suitability for high-throughput analysis. Hence, in present study an attempt was made to mine and analyze microsatellite dynamics in whole genome of Fusarium oxysporum f. sp. lycopersici. The distribution pattern of different SSR motifs provides the evidence of greater accumulation of tetra-nucleotide (3837) repeats followed by tri-nucleotide (3367) repeats. Maximum frequency distribution in coding region was shown by mono-nucleotide SSR motifs (34.8%), where as minimum frequency is observed for penta-nucleotide SSR (0.87%). Highest relative abundance (1023 SSR/Mb) and density of SSRs (114.46 bp/Mb) were observed on chromosome 1, while least density of SSR motifs was recorded on chromosome 11 (7.40 bp/Mb) and 12 (7.41 bp/Mb), respectively. Maximum trinucleotide (34.24%) motifs code for glutamic acid (GAA) while GT/CT were the most frequent repeat of dinucleotide SSRs. Most common and highly repeated SSR motifs were identified as (A)64, (T)48, (GT)24, (GAA)31, (TTTC)24, (TTTCT)28 and (AACCAG)27. Overall, the generated information may serve as baseline information for developing SSR markers that could find applications in genomic analysis of F. oxysporum f. sp. lycopersici for better understanding of evolution, diversity analysis, population genetics, race identification and acquisition of new virulence.
Highlights
Fusarium oxysporum f. sp. lycopersici, the cause of tomato crown and root rot is an important soil-borne fungus and reduce crop productivity by 10-50% (Borrero et al., 2004)
Total genome sequence data (59.9 Mb) of F. oxysporum f. sp. lycopersici was assembled into 423 scaffolds and used to explore mono, di, tri, tetra, penta- and hexa-nucleotide motifs with a repeat of ≥6 times
A total 13864 Simple sequence repeat (SSR) were identified from whole genome data of F. oxysporum f. sp. lycopersici (Tab. 1)
Summary
Fusarium oxysporum f. sp. lycopersici, the cause of tomato crown and root rot is an important soil-borne fungus and reduce crop productivity by 10-50% (Borrero et al., 2004). New races of pathogen have been emerged that overcome resistance in currently growing tomato cultivars (Mishra et al, 2010). Knowledge of the genetic variation within and among populations is an important component to understand the population biology of F. oxysporum f. Virulence tests are commonly used to detect the pathogen variations (Elias et al, 1991). Lycopersici have been identified (Cai et al, 2003) These tests are subjected to availability of host selection pressure, tedious, inconclusive and preclude nonpathogenic strains. To circumvent these problems, DNA based molecular markers have been used in diversity analysis, virulence evaluation and genetic structure of pathogen races (Lievens et al, 2009)
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