Literature DB >> 30956421

Genetic diversity and population structure analysis of Indian garlic (Allium sativum L.) collection using SSR markers.

Mukesh Kumar1, V Rakesh Sharma2, Vipin Kumar1, Ujjawal Sirohi3, Veena Chaudhary4, Shiveta Sharma5, Gautam Saripalli5, R K Naresh6, Hemant Kumar Yadav2, Shailendra Sharma5.   

Abstract

Genetic diversity was assessed among 53 Indian garlic accessions using SSR markers. Initially, 24 SSR primer pairs were used for screening three selected garlic accessions. Out of 24 SSR primer pairs, 10 primer pairs which consistently showed good amplification and polymorphism were selected for DNA profiling. SSR primer pairs showed PIC values ranging from 0.30 to 0.99. Based on AMOVA we found that the greater part of the genetic diversity was expected due to intra population with 84% variation and only 16% of variation was due to among populations suggesting presence of genetic structure. The results of cluster analysis and principal component analysis largely correspond to each other. Population structure analysis revealed genetic differentiation of accessions. The results of present study revealed existence of significant variability in Indian garlic germplasm.

Entities:  

Keywords:  Allium sativum; Garlic; PCA; Population structure; SSR; UPGMA

Year:  2018        PMID： 30956421      PMCID： PMC6419858          DOI： 10.1007/s12298-018-0628-y

Source DB:  PubMed          Journal:  Physiol Mol Biol Plants        ISSN： 0974-0430


  13 in total

1.  Inference of population structure using multilocus genotype data.

Authors:  J K Pritchard; M Stephens; P Donnelly
Journal:  Genetics       Date:  2000-06       Impact factor: 4.562

2.  Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies.

Authors:  Daniel Falush; Matthew Stephens; Jonathan K Pritchard
Journal:  Genetics       Date:  2003-08       Impact factor: 4.562

3.  Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study.

Authors:  G Evanno; S Regnaut; J Goudet
Journal:  Mol Ecol       Date:  2005-07       Impact factor: 6.185

4.  Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data.

Authors:  L Excoffier; P E Smouse; J M Quattro
Journal:  Genetics       Date:  1992-06       Impact factor: 4.562

5.  New microsatellite markers for garlic, Allium sativum (Alliaceae).

Authors:  Camila P Cunha; Eulália S S Hoogerheide; Maria I Zucchi; Mariza Monteiro; José B Pinheiro
Journal:  Am J Bot       Date:  2011-12-27       Impact factor: 3.844

6.  Demonstration of linkage and development of the first low-density genetic map of garlic, based on AFLP markers.

Authors:  M Ipek; A Ipek; S G Almquist; P W Simon
Journal:  Theor Appl Genet       Date:  2004-11-24       Impact factor: 5.699

7.  SSR-based genetic diversity and structure of garlic accessions from Brazil.

Authors:  Camila Pinto da Cunha; Francisco Vilela Resende; Maria Imaculada Zucchi; José Baldin Pinheiro
Journal:  Genetica       Date:  2014-09-02       Impact factor: 1.082

8.  GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research--an update.

Authors:  Rod Peakall; Peter E Smouse
Journal:  Bioinformatics       Date:  2012-07-20       Impact factor: 6.937

Review 9.  A review of microsatellite markers and their applications in rice breeding programs to improve blast disease resistance.

Authors:  Gous Miah; Mohd Y Rafii; Mohd R Ismail; Adam B Puteh; Harun A Rahim; Kh Nurul Islam; Mohammad Abdul Latif
Journal:  Int J Mol Sci       Date:  2013-11-14       Impact factor: 5.923

Review 10.  Simple sequence repeat polymorphisms (SSRPs) for evaluation of molecular diversity and germplasm classification of minor crops.

Authors:  Yong-Jin Park; Ju Kyong Lee; Nam-Soo Kim
Journal:  Molecules       Date:  2009-11-10       Impact factor: 4.411
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  4 in total

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Authors:  Weijie Tang; Jing Lin; Yanping Wang; Hongzhou An; Haiyuan Chen; Gen Pan; Suobing Zhang; Baowei Guo; Kun Yu; Huayong Li; Xianwen Fang; Yunhui Zhang
Journal:  Rice (N Y)       Date:  2022-09-24       Impact factor: 5.638

2.  De novo assembly, transcriptome characterization, and simple sequence repeat marker development in duckweed Lemna gibba.

Authors:  Lili Fu; Zehong Ding; Anuwat Kumpeangkeaw; Deguan Tan; Bingying Han; Xuepiao Sun; Jiaming Zhang
Journal:  Physiol Mol Biol Plants       Date:  2019-12-09

3.  The landscape of microsatellites in the enset (Ensete ventricosum) genome and web-based marker resource development.

Authors:  Manosh Kumar Biswas; Jaypal N Darbar; James S Borrell; Mita Bagchi; Dhiman Biswas; Gizachew Woldesenbet Nuraga; Sebsebe Demissew; Paul Wilkin; Trude Schwarzacher; J S Heslop-Harrison
Journal:  Sci Rep       Date:  2020-09-17       Impact factor: 4.379

4.  Genome-wide mining of microsatellites in king cobra (Ophiophagus hannah) and cross-species development of tetranucleotide SSR markers in Chinese cobra (Naja atra).

Authors:  Wencong Liu; Yongtao Xu; Zekun Li; Jun Fan; Yi Yang
Journal:  Mol Biol Rep       Date:  2019-09-09       Impact factor: 2.316
  4 in total

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