Development and characterization of genomic and expressed SSRs for levant cotton (Gossypium herbaceum L.)

Satya Narayan Jena; Anukool Srivastava; Krishan Mohan Rai; Alok Ranjan; Sunil K Singh; Tarannum Nisar; Meenal Srivastava; Sumit K Bag; Shrikant Mantri; Mehar Hasan Asif; Hemant Kumar Yadav; Rakesh Tuli; Samir V Sawant

doi:10.1007/s00122-011-1729-y

Development and characterization of genomic and expressed SSRs for levant cotton (Gossypium herbaceum L.)

Satya Narayan Jena, Anukool Srivastava, Krishan Mohan Rai, Alok Ranjan, Sunil K Singh, Tarannum Nisar, Meenal Srivastava, Sumit K Bag, Shrikant Mantri, Mehar Hasan Asif, Hemant Kumar Yadav, Rakesh Tuli, Samir V Sawant

Agronomy and Plant Genetics

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41 Scopus citations

Abstract

Four microsatellite-enriched genomic libraries for CA(15), GA(15), AAG(8) and ATG(8) repeats and transcriptome sequences of five cDNA libraries of Gossypium herbaceum were explored to develop simple sequence repeat (SSR) markers. A total of 428 unique clones from repeat enriched genomic libraries were mined for 584 genomic SSRs (gSSRs). In addition, 99,780 unigenes from transcriptome sequencing were explored for 8,900 SSR containing sequences with 12,471 expressed SSRs. The present study adds 1,970 expressed SSRs and 263 gSSRs to the public domain for the use of genetic studies of cotton. When 150 gSSRs and 50 expressed SSRs were tested on a panel of four species of cotton, 68 gSSRs and 12 expressed SSRs revealed polymorphism. These 200 SSRs were further deployed on 15 genotypes of levant cotton for the genetic diversity assessment. This is the first report on the successful use of repeat enriched genomic library and expressed sequence database for microsatellite markers development in G. herbaceum.

Original language	English (US)
Pages (from-to)	565-76
Number of pages	12
Journal	TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Volume	124
Issue number	3
DOIs	https://doi.org/10.1007/s00122-011-1729-y
State	Published - Feb 2012

Keywords

Base Sequence
Cluster Analysis
Computational Biology
Data Mining
Gene Library
Genomics/methods
Gossypium/genetics
Microsatellite Repeats/genetics
Molecular Sequence Data
Phenotype
Polymorphism, Genetic
Sequence Analysis, DNA

PubMed: MeSH publication types

Journal Article
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10.1007/s00122-011-1729-y

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Jena, S. N., Srivastava, A., Rai, K. M., Ranjan, A., Singh, S. K., Nisar, T., Srivastava, M., Bag, S. K., Mantri, S., Asif, M. H., Yadav, H. K., Tuli, R., & Sawant, S. V. (2012). Development and characterization of genomic and expressed SSRs for levant cotton (Gossypium herbaceum L.). TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 124(3), 565-76. https://doi.org/10.1007/s00122-011-1729-y

Jena, SN, Srivastava, A, Rai, KM, Ranjan, A, Singh, SK, Nisar, T, Srivastava, M, Bag, SK, Mantri, S, Asif, MH, Yadav, HK, Tuli, R & Sawant, SV 2012, 'Development and characterization of genomic and expressed SSRs for levant cotton (Gossypium herbaceum L.)', TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, vol. 124, no. 3, pp. 565-76. https://doi.org/10.1007/s00122-011-1729-y

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abstract = "Four microsatellite-enriched genomic libraries for CA(15), GA(15), AAG(8) and ATG(8) repeats and transcriptome sequences of five cDNA libraries of Gossypium herbaceum were explored to develop simple sequence repeat (SSR) markers. A total of 428 unique clones from repeat enriched genomic libraries were mined for 584 genomic SSRs (gSSRs). In addition, 99,780 unigenes from transcriptome sequencing were explored for 8,900 SSR containing sequences with 12,471 expressed SSRs. The present study adds 1,970 expressed SSRs and 263 gSSRs to the public domain for the use of genetic studies of cotton. When 150 gSSRs and 50 expressed SSRs were tested on a panel of four species of cotton, 68 gSSRs and 12 expressed SSRs revealed polymorphism. These 200 SSRs were further deployed on 15 genotypes of levant cotton for the genetic diversity assessment. This is the first report on the successful use of repeat enriched genomic library and expressed sequence database for microsatellite markers development in G. herbaceum.",

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AU - Jena, Satya Narayan

AU - Srivastava, Anukool

AU - Rai, Krishan Mohan

AU - Ranjan, Alok

AU - Singh, Sunil K

AU - Nisar, Tarannum

AU - Srivastava, Meenal

AU - Bag, Sumit K

AU - Mantri, Shrikant

AU - Asif, Mehar Hasan

AU - Yadav, Hemant Kumar

AU - Tuli, Rakesh

AU - Sawant, Samir V

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N2 - Four microsatellite-enriched genomic libraries for CA(15), GA(15), AAG(8) and ATG(8) repeats and transcriptome sequences of five cDNA libraries of Gossypium herbaceum were explored to develop simple sequence repeat (SSR) markers. A total of 428 unique clones from repeat enriched genomic libraries were mined for 584 genomic SSRs (gSSRs). In addition, 99,780 unigenes from transcriptome sequencing were explored for 8,900 SSR containing sequences with 12,471 expressed SSRs. The present study adds 1,970 expressed SSRs and 263 gSSRs to the public domain for the use of genetic studies of cotton. When 150 gSSRs and 50 expressed SSRs were tested on a panel of four species of cotton, 68 gSSRs and 12 expressed SSRs revealed polymorphism. These 200 SSRs were further deployed on 15 genotypes of levant cotton for the genetic diversity assessment. This is the first report on the successful use of repeat enriched genomic library and expressed sequence database for microsatellite markers development in G. herbaceum.

AB - Four microsatellite-enriched genomic libraries for CA(15), GA(15), AAG(8) and ATG(8) repeats and transcriptome sequences of five cDNA libraries of Gossypium herbaceum were explored to develop simple sequence repeat (SSR) markers. A total of 428 unique clones from repeat enriched genomic libraries were mined for 584 genomic SSRs (gSSRs). In addition, 99,780 unigenes from transcriptome sequencing were explored for 8,900 SSR containing sequences with 12,471 expressed SSRs. The present study adds 1,970 expressed SSRs and 263 gSSRs to the public domain for the use of genetic studies of cotton. When 150 gSSRs and 50 expressed SSRs were tested on a panel of four species of cotton, 68 gSSRs and 12 expressed SSRs revealed polymorphism. These 200 SSRs were further deployed on 15 genotypes of levant cotton for the genetic diversity assessment. This is the first report on the successful use of repeat enriched genomic library and expressed sequence database for microsatellite markers development in G. herbaceum.

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KW - Gene Library

KW - Genomics/methods

KW - Gossypium/genetics

KW - Microsatellite Repeats/genetics

KW - Molecular Sequence Data

KW - Phenotype

KW - Polymorphism, Genetic

KW - Sequence Analysis, DNA

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IS - 3

ER -

Development and characterization of genomic and expressed SSRs for levant cotton (Gossypium herbaceum L.)

Abstract

Keywords

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