Identification of Novel Microsatellite Markers to Assess the Population Structure and Genetic Differentiation of Causing Covered Smut of Barley

Overview

Journal Front Microbiol

Specialty Microbiology

Date 2020 Feb 4

PMID 32010068

Citations 3

Authors

Prem Lal Kashyap

Sudheer Kumar

Ravi Shekhar Kumar

Rahul Tripathi

Palika Sharma

Anju Sharma

Poonam Jasrotia

Gyanendra Pratap Singh

Affiliations

Soon will be listed here.

Abstract

Barley covered smut (CS) pathogen genome was mined for microsatellite distribution and their application in defining population structure and genetic variation. To dissect the molecular variation and genetic structure of , 59 fungal isolates representing two distinct agro-ecological zones of India were analyzed by employing simple sequence repeats (SSRs). Using bioinformatic approaches, a total of 100,239 and 137,442 microsatellites were identified from 20.13 and 26.94 Mb of assembled genomic sequences of Uh364 and Uh4857-4 isolates of , respectively. Penta-nucleotides (31.29 and 29.75%) followed by tri-nucleotide (28.27 and 29.88%) were most prevalent in both the genomes. Out of them, 15 polymorphic microsatellites showing conservancies in both the genomes were selected for exploring population genetic structure of . An average of two alleles per microsatellite marker was generated with band size ranging from 180 to 850 bp. Polymorphic information content (PIC) varied between 0.095 and 0.37. Fifty-nine isolates were distributed in two distinct groups with about 65% genetic similarity according to UPGMA clustering and population structure analysis ( = 2). Gene flow analysis (Nm = 1.009) reflected moderate gene flow among the analyzed population. An analysis of molecular variance (AMOVA) displayed high level of genetic variation within population (87%) and low variation among populations (13%). Linkage disequilibrium (LD) analysis indicated positively significant but relatively low standardized index of association (SIA) value in both the population sets (SIA = 0.181), advocating a state of LD with epidemic population structure. In conclusion, the newly developed neutral SSR markers are highly polymorphic within and will be useful for revealing evolutionary history and providing deep insight into the population dynamics of in India as well as facilitating developing management strategies for CS of barley.

Citing Articles

Comparative analysis of nine genomes for the development of novel microsatellite markers for genetic diversity and population structure analysis.

Kashyap P, Kumar S, Kumar R, Sharma A, Khanna A, Kajal Front Microbiol. 2023; 14:1227750.

PMID: 37520344 PMC: 10374028. DOI: 10.3389/fmicb.2023.1227750.

Virulence and pathogenicity determinants in whole genome sequence of causing wilt of pigeon pea.

Srivastava A, Srivastava R, Yadav J, Singh A, Tiwari P, Srivastava A Front Microbiol. 2023; 14:1066096.

PMID: 36876067 PMC: 9981795. DOI: 10.3389/fmicb.2023.1066096.

Molecular diversity, haplotype distribution and genetic variation flow of Bipolaris sorokiniana fungus causing spot blotch disease in different wheat-growing zones.

Kashyap P, Kumar S, Sharma A, Kumar R, Mahapatra S, Kaul N J Appl Genet. 2022; 63(4):793-803.

PMID: 35931929 DOI: 10.1007/s13353-022-00716-w.

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