Get 20M+ Full-Text Papers For Less Than $1.50/day. Start a 14-Day Trial for You or Your Team.

Learn More →

Analysis of genetic diversity, population structure and linkage disequilibrium in elite cotton ( Gossypium L.) germplasm in India

Analysis of genetic diversity, population structure and linkage disequilibrium in elite cotton (... An understanding of the level of genetic diversity is a prerequisite for designing efficient breeding programs. Fifty-one cultivars of four cotton species ( Gossypium hirsutum , G. barbadense , G. herbaceum and G. arboreum ) representing core collections at four major cotton research stations with a wide range of eco-geographical regions in India were examined for the level of genetic diversity, distinct subpopulations and the level of linkage disequilibrium (LD) using 1100 amplified fragment length polymorphism (AFLP) markers with 16 primer pairs combinations. The AFLP markers enabled a reliable assessment of inter- and intra-specific genetic variability with a heterogeneous genetic structure. Higher genetic diversity was noticed in G. herbaceum , followed by G. arboreum . The genetic diversity in tetraploid cotton species was found to be less than that in the diploid species. The genotypes VAGAD, RAHS14, IPS187, 221 557, Jayhellar of G. herbaceum and 551, DLSA17, 221 566 of G. arboreum were identified as the most diverse parents, useful for quantitative trait loci (QTL) analysis in diploid cotton. Similarly, LRA 5166, AS3 and MCU5 of G. hirsutum and B1, B3, Suvin of G. barbadense were most diverse to develop mapping populations for fibre quality. The internal transcribed spacer sequences were sufficient to resolve different species and subspecies of diploid cotton. Low level of genome-wide LD was detected in the entire collection ( r 2 = 0.07) as well as within the four species ( r 2 = 0.11–0.15). A strong agreement was noticed between the clusters constructed on the basis of morphological and genotyping data. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Crop and Pasture Science CSIRO Publishing

Analysis of genetic diversity, population structure and linkage disequilibrium in elite cotton ( Gossypium L.) germplasm in India

Download PDF
17 pages

Loading next page...
 
/lp/csiro-publishing/analysis-of-genetic-diversity-population-structure-and-linkage-El93JghMXH

References

References for this paper are not available at this time. We will be adding them shortly, thank you for your patience.

Publisher
CSIRO Publishing
Copyright
CSIRO
ISSN
1836-0947
eISSN
1836-5795
DOI
10.1071/CP11161
Publisher site
See Article on Publisher Site

Abstract

An understanding of the level of genetic diversity is a prerequisite for designing efficient breeding programs. Fifty-one cultivars of four cotton species ( Gossypium hirsutum , G. barbadense , G. herbaceum and G. arboreum ) representing core collections at four major cotton research stations with a wide range of eco-geographical regions in India were examined for the level of genetic diversity, distinct subpopulations and the level of linkage disequilibrium (LD) using 1100 amplified fragment length polymorphism (AFLP) markers with 16 primer pairs combinations. The AFLP markers enabled a reliable assessment of inter- and intra-specific genetic variability with a heterogeneous genetic structure. Higher genetic diversity was noticed in G. herbaceum , followed by G. arboreum . The genetic diversity in tetraploid cotton species was found to be less than that in the diploid species. The genotypes VAGAD, RAHS14, IPS187, 221 557, Jayhellar of G. herbaceum and 551, DLSA17, 221 566 of G. arboreum were identified as the most diverse parents, useful for quantitative trait loci (QTL) analysis in diploid cotton. Similarly, LRA 5166, AS3 and MCU5 of G. hirsutum and B1, B3, Suvin of G. barbadense were most diverse to develop mapping populations for fibre quality. The internal transcribed spacer sequences were sufficient to resolve different species and subspecies of diploid cotton. Low level of genome-wide LD was detected in the entire collection ( r 2 = 0.07) as well as within the four species ( r 2 = 0.11–0.15). A strong agreement was noticed between the clusters constructed on the basis of morphological and genotyping data.

Journal

Crop and Pasture Science – CSIRO Publishing

Published: Dec 6, 2011

Keywords: cotton, genetic diversity, population structure, resolving power.

References

  • Genetic diversity and relationships of diploid and tetraploid cottons revealed using AFLP.
    Abdalla AM Reddy OUK El-Zik KM Pepper AE
  • Molecular characterization and genetic relationship among cotton genotypes, 2-AFLP analysis.
    Adawy SS Assem SK Ebtissam Hussein HA Hanaiya AE
  • The origin of American tetraploid Gossypium species.
    Beasley JO
  • Meiotic chromosome behavior in species, species hybrids, haploids and induced polyploids of Gossypium .
    Beasley JO
  • Genetic diversity of Rhynchosporium secalis in Tunisia as revealed by pathotype, AFLP, and microsatellite analyses.
    Bouajila A Abang MM Haouas S Rezgui SUS Baum M Yahyaoui A
  • Polymorphism and concerted evolution in a tandemly repeated gene family, 5S ribosomal DNA in diploid and allopolyploid cottons.
    Cronn RC Zhao X Paterson AH Wendel JF
  • Rapid diversification of cotton genus ( Gossypium , Malvaceae) revealed by analysis of sixteen nuclear and chloroplast genes.
    Cronn RC Small RL Haselkorn T Wendel JF
  • Genetic variation in red pine ( Pinus resinosa ) revealed by RAPD and RAPD–RFLP analysis.
    DeVerno LL Mosseler A
  • Genetics, cytogenetics, and evolution of Gossypium .
    Endrizzi JE Turcotte EL Kohel RJ
  • Genetic evidence of local adaptation of wheat yellow rust ( Puccina striiformis f. sp. tritici ) within France.
    Enjalbert J Duan X Leconte M Hovmoller MS de Vallavielle-pope C
  • Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study.
    Evanno G Regnaut S Goudet J
  • Neandertal genetic diversity, a fresh look from old samples.
    Excoffier L
  • Using allele frequencies and geographic subdivision to reconstruct gene genealogies within a species. Molecular variance parsimony.
    Excoffier L Smouse P
  • Analysis of molecular variance inferred from metric distances among DNA haplotypes, application to human mitochondrial DNA restriction data.
    Excoffier L Smouse P Quattro J
  • Extensive genome-wide linkage disequilibrium in cattle.
    Farnir F Coppieters W Arranz JJ Berzi P Cambisano N Grisart N Karim L Marcq F Moreau L Mni M Nezer C Simon P Vanmanshoven P Wagenaar D Georges M
  • Confidence limits on phylogenies, an approach using the bootstrap.
    Felsenstein J
  • PHYLIP – Phylogeny Inference Package (version 3.2).
    Felsenstein J
  • The use of ISSR and RAPD markers for detecting DNA polymorphism, genotype identification and genetic diversity among barley cultivars with known origin.
    Fernandez M Figueiras A Benito C
  • Structure of linkage disequilibrium in plants.
    Flint-Garcia SA Thornsberry JM Buckler ESIY
  • A revised taxonomic interpretation of Gossypium L. (Malvaceae).
    Fryxell PA
  • Marker-assisted sampling of the cultivated Andean potato Solanum phureja collection using RAPD markers.
    Ghislain M Zhang D Fajardo D Huaman Z Hijmans RJ
  • Fragment length distributions and collision probabilities for AFLP markers.
    Gort G Koopman WJM Stein A
  • A and D genome evolution in Gossypium revealed using SSR molecular markers.
    Guo WZ Wang K Zhang TZ
  • The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat.
    Gupta PK Varshney RK
  • Evaluation of AFLP in Beta .
    Hansen M Kraft T Christiansen M Nilsson NO
  • Genetic diversity evaluation of some elite cotton varieties by RAPD analysis.
    Iqbal MJ Aziz N Saeed NA Zafar Y Malik KA
  • A genetic bottleneck in the ‘evolution under domestication’ of upland cotton Gossypium hirsutum L. examined using DNA fingerprinting.
    Iqbal MJ Reddy OUK El-Zik KM Pepper AE
  • Nouvelles recherches sur la distribution florale.
    Jaccard P
  • Genetic mapping of a gene causing hypertensive rat.
    Jacob HJ Lindpaintner K Lincoln SE Kusumi K Bunker RK Mao YP Ganten D Dzau VJ Lander ES
  • Identification of RAPD markers, in situ DNA content and structural chromosomal diversity in some legumes of the mangrove flora of Orissa.
    Jena S Sahoo P Mohanty S Das AB
  • Reproducibility testing of RAPD, AFLP, and SSR markers in plants by a network of European laboratories.
    Jones CJ Edwards KJ Castaglione S Winfield MO Sala F van de Weil C Bredemeijer G Vosman B Mattes M Daly A Brettschneider R Bettini P Buiatti M Maestri E Malcevschi A Marmiroli N Aert R Volckaert G Rueda J Linacero R Vazquez A Karp A
  • Application of the AFLP method to differentiate Genista tinctoria microsymbionts.
    Kalita M Malek W
  • Assessing genetic diversity in Gossypium arboreum L. cultivars using genomic and EST-derived microsatellites.
    Kantartzi SK Ulloa M Sacks E Stewart JM
  • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences.
    Kimura M
  • Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars.
    Kraakman ATW Niks RE Berg PMMM Stam P Eeuwijk FA
  • Microsatellite diversity in tetraploid Gossypium germplasm, assembling a highly informative genotyping set of cotton SSRs.
    Lacape JM Dessauw D Rajab M Noyer JL Hau B
  • The apportionment of human diversity.
    Lewontin RC
  • Assessment of genetic diversity in glandless cotton germplasm resources by using agronomic traits and molecular markers.
    Li Z Wang X Yan Z Guiyin Z Wu L Jina C Ma Z
  • The detection of disease clustering and a generalized regression approach.
    Mantel N
  • Comparative genetic diversity of Triticum aestivum–Triticum polonicum introgression lines with long glume and Triticum petropavlovskyi by AFLP-based assessment.
    Masum Akond ASMG Watanabe N Furuta Y
  • AFLP genotyping and fingerprinting.
    Mueller UG Wolfenbarger LL
  • Analysis of gene diversity in subdivided populations.
    Nei M
  • Mathematical model for studying genetic variation in terms of restriction endonucleases.
    Nei N Li W
  • Effects of life history traits and sampling strategies on genetic diversity estimates obtained with RAPD markers in plants.
    Nybom N Bartish I
  • Genetic diversity assessed by variation in ribosomal RNA genes and AFLP markers.
    Pillay M Myers GO
  • The comparison of RFLP, RAPD, AFLP and
    Powell W Morgante M Andre C Hanafey M Vogel J Tingey S Rafalski A
  • A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars.
    Prevost A Wilkinson MJ
  • Inference of population structure using multilocus genotype data.
    Pritchard K Stephens M Donnelly PJ
  • Assessment of genetic diversity in Upland cotton ( Gossypium hirsutum L.) breeding lines by using amplified fragment length
    Rana MK Singh VP Bhat KV
  • Genetic map-based studies of reticulate evolution in plants.
    Rieseberg LH Noyes RD
  • Extraordinarily polymorphic microsatellite DNA in barley: species diversity, chromosomal locations and population dynamics.
    Saghai-Maroof MA Biyashev RM Yang GP Zhang Q Allard RW
  • The neighbor-joining method: A new method for reconstructing phylogenetic trees.
    Saitou N Nei M
  • Congruence and consensus in the cotton tribe.
    Seelanan T Schnabel A Wendel JF
  • Organization and evolution of highly repeated satellite DNA sequences in plant chromosomes.
    Sharma S Raina SN
  • Genome-wide linkage disequilibrium analysis in bread wheat and durum wheat.
    Somers DJ Banks T DePauw R Fox S Clarke J
  • MEGA4, Molecular Evolutionary Genetics
    Tamura K Dudley J Nei M Kumar S
  • AFLP-based molecular characterization of an elite germplasm collection of Jatropha curcas L., a biofuel plant.
    Tatikonda L Wani SP Kannan S Beerelli N Sreedevi TK Hoisington DA Prathibha Devi P Varshney RK
  • Genetic diversity in elite cotton germplasm determined by morphological characteristics and RAPD.
    Tatineni V Cantrell RG Davis DD
  • Simple sequence repeats are ubiquitous repetitive components of eukaryotic genomes.
    Tautz D Renz M
  • Comparative assessment of EST-SSR, EST-SNP and AFLP markers for evaluation of genetic diversity and conservation of genetic resources using wild, cultivated and elite barleys.
    Varshney RK Chabane K Hendre PS Aggarwal RK Graner A
  • AFLP, a new technique for DNA finger printing.
    Vos P Hogers R Bleeker M Reijans M van de Lee T Hornes M Frijters A Pot J Peleman J Kuiper M Zabeau M
  • Genetic diversity in Gossypium hirsutum and the origin of upland cotton.
    Wendel JF Brubaker CL Percival AE
  • Bidirectional interlocus concerted evolution following allopolyploid speciation in cotton ( Gossypium ).
    Wendel JF Schnabel A Seelanan T
  • An unusual ribosomal DNA sequence from Gossypium gossypioides reveals ancient, cryptic, inter-genomic introgression.
    Wendel JF Schnabel A Seelanan T
  • AFLP analysis of genetic diversity of the endangered species Sinopodophyllum hexandrum in the Tibetan region of Sichuan province.
    Xiao M Li Q Guo L Luo T Duan WX He WX Wang L Chen F
  • Population genetic analysis of co-dominant and dominant markers and quantitative traits.
    Yeh FC Boyle TJB