Genetic Diversity Revealed by Single Nucleotide Polymorphism Markers in a Worldwide Germplasm Collection of Durum Wheat

Evaluation of genetic diversity and genetic structure in crops has important implications for plant breeding programs and the conservation of genetic resources. Newly developed single nucleotide polymorphism (SNP) markers are effective in detecting genetic diversity. In the present study, a worldwide durum wheat collection consisting of 150 accessions was used. Genetic diversity and genetic structure were investigated using 946 polymorphic SNP markers covering the whole genome of tetraploid wheat. Genetic structure was greatly impacted by multiple factors, such as environmental conditions, breeding methods reflected by release periods of varieties, and gene flows via human activities. A loss of genetic diversity was observed from landraces and old cultivars to the modern cultivars released during periods of the Early Green Revolution, but an increase in cultivars released during the Post Green Revolution. Furthermore, a comparative analysis of genetic diversity among the 10 mega ecogeographical regions indicated that South America, North America, and Europe possessed the richest genetic variability, while the Middle East showed moderate levels of genetic diversity.

[1]  C. Feuillet,et al.  Sequence-based marker development in wheat: advances and applications to breeding. , 2012, Biotechnology advances.

[2]  E. Nevo,et al.  Evolution of wild cereals during 28 years of global warming in Israel , 2012, Proceedings of the National Academy of Sciences.

[3]  E. Nevo,et al.  Domestication evolution, genetics and genomics in wheat , 2011, Molecular breeding.

[4]  A. Michel,et al.  Population structure and genetic differentiation associated with breeding history and selection in tomato (Solanum lycopersicum L.) , 2011, Heredity.

[5]  J. Dvorak,et al.  Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes , 2010, BMC Genomics.

[6]  J. Dvorak,et al.  Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.) , 2010, BMC Genomics.

[7]  Jean-Luc Jannink,et al.  Genomic selection in plant breeding: from theory to practice. , 2010, Briefings in functional genomics.

[8]  A. Melchinger,et al.  Population structure and genetic diversity in a commercial maize breeding program assessed with SSR and SNP markers , 2010, Theoretical and Applied Genetics.

[9]  M T Clegg,et al.  Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae , 2009, Proceedings of the National Academy of Sciences.

[10]  J. Dvorak,et al.  Single nucleotide polymorphism genotyping in polyploid wheat with the Illumina GoldenGate assay , 2009, Theoretical and Applied Genetics.

[11]  G. Barker,et al.  Multiplex single nucleotide polymorphism (SNP)-based genotyping in allohexaploid wheat using padlock probes. , 2009, Plant biotechnology journal.

[12]  Alberto Cenci,et al.  High-throughput single nucleotide polymorphism genotyping in wheat (Triticum spp.). , 2009, Plant biotechnology journal.

[13]  E. Salina,et al.  Specific features in using SNP markers developed for allopolyploid wheat , 2009, Russian Journal of Genetics.

[14]  D. Somers,et al.  Genome-Wide Reduction of Genetic Diversity in Wheat Breeding , 2009 .

[15]  Gordon Luikart,et al.  LOSITAN: A workbench to detect molecular adaptation based on a Fst-outlier method , 2008, BMC Bioinformatics.

[16]  M. C. Sanguineti,et al.  Utilization of SSR and AFLP markers for the assessment of distinctness in durum wheat , 2008, Molecular Breeding.

[17]  Wenjun Zhang,et al.  Analysis of gene-derived SNP marker polymorphism in US wheat (Triticum aestivum L.) cultivars , 2008, Molecular Breeding.

[18]  R. Varshney,et al.  EST-derived single nucleotide polymorphism markers for assembling genetic and physical maps of the barley genome , 2008, Functional & Integrative Genomics.

[19]  D. Mackill,et al.  Marker-assisted selection: an approach for precision plant breeding in the twenty-first century , 2008, Philosophical Transactions of the Royal Society B: Biological Sciences.

[20]  Junhua Peng,et al.  Molecular Mapping of the Russian Wheat Aphid Resistance Gene Dn2414 in Wheat , 2007 .

[21]  A. Brandolini,et al.  Estimating genetic diversity in durum and bread wheat cultivars from Turkey using AFLP and SAMPL markers , 2007 .

[22]  D. Bhattramakki,et al.  A comparison of simple sequence repeat and single nucleotide polymorphism marker technologies for the genotypic analysis of maize (Zea mays L.) , 2007, Theoretical and Applied Genetics.

[23]  K. Chase,et al.  A Soybean Transcript Map: Gene Distribution, Haplotype and Single-Nucleotide Polymorphism Analysis , 2007, Genetics.

[24]  W. Powell,et al.  Methods for linkage disequilibrium mapping in crops. , 2007, Trends in plant science.

[25]  Laurent Excoffier,et al.  Arlequin (version 3.0): An integrated software package for population genetics data analysis , 2005, Evolutionary bioinformatics online.

[26]  K. Hammer,et al.  Simple sequence repeats marker polymorphism in emmer wheat (Triticum dicoccon Schrank): Analysis of genetic diversity and differentiation , 2007, Genetic Resources and Crop Evolution.

[27]  J. Dvorak,et al.  The structure of wild and domesticated emmer wheat populations, gene flow between them, and the site of emmer domestication , 2007, Theoretical and Applied Genetics.

[28]  C. Royo,et al.  Dispersal of durum wheat [Triticum turgidum L. ssp. turgidum convar. durum (Desf.) MacKey] landraces across the Mediterranean basin assessed by AFLPs and microsatellites , 2007, Genetic Resources and Crop Evolution.

[29]  J. Jia,et al.  Impact of plant breeding on genetic diversity of the Canadian hard red spring wheat germplasm as revealed by EST-derived SSR markers , 2006, Theoretical and Applied Genetics.

[30]  M. Giovannetti,et al.  The introduction of Old World crops (wheat, barley and peach) in Andean Argentina during the 16th century a.d.: archaeobotanical and ethnohistorical evidence , 2005 .

[31]  G. Evanno,et al.  Detecting the number of clusters of individuals using the software structure: a simulation study , 2005, Molecular ecology.

[32]  Kejun Liu,et al.  PowerMarker: an integrated analysis environment for genetic marker analysis , 2005, Bioinform..

[33]  J. Clarke,et al.  Allelic reduction and genetic shift in the Canadian hard red spring wheat germplasm released from 1845 to 2004 , 2005, Theoretical and Applied Genetics.

[34]  J. David,et al.  Estimation of Long-Term Effective Population Sizes Through the History of Durum Wheat Using Microsatellite Data , 2005, Genetics.

[35]  M. Baum,et al.  Analysis of genetic diversity in Tunisian durum wheat cultivars and related wild species by SSR and AFLP markers , 2005, Genetic Resources and Crop Evolution.

[36]  C. Royo,et al.  Using AFLPs to determine phylogenetic relationships and genetic erosion in durum wheat cultivars released in Italy and Spain throughout the 20th century , 2005 .

[37]  Michael L. Morris,et al.  Impacts of International Wheat Breeding Research in the Developing World, 1988-2002 , 2005 .

[38]  M. Arabi,et al.  Genetic Diversity among Syrian Cultivated and Landraces Wheat Revealed by AFLP Markers , 2006, Genetic Resources and Crop Evolution.

[39]  N. Zencirci,et al.  Variation in Wheat (Triticum spp.) Landraces from Different Altitudes of Three Regions of Turkey , 2005, Genetic Resources and Crop Evolution.

[40]  N. Zencirci,et al.  Effect of Developmental Stages Length on Yield and some Quality Traits of Turkish Durum Wheat (Triticum turgidum L. Convar. durum (Desf.) Mackey) Landraces: Influence of Developmental Stages Length on Yield and Quality of Durum Wheat , 2005, Genetic Resources and Crop Evolution.

[41]  J. Reif,et al.  Wheat genetic diversity trends during domestication and breeding , 2005, Theoretical and Applied Genetics.

[42]  Lydia Zapata,et al.  Early Neolithic Agriculture in the Iberian Peninsula , 2004 .

[43]  M. Hanafey,et al.  Insertion-deletion polymorphisms in 3′ regions of maize genes occur frequently and can be used as highly informative genetic markers , 2002, Plant Molecular Biology.

[44]  M. Akkaya,et al.  Assessment of genetic relationships in durum wheat cultivars using AFLP markers , 2001, Genetic Resources and Crop Evolution.

[45]  J. Dvorak,et al.  Structural evolution of wheat chromosomes 4A, 5A, and 7B and its impact on recombination , 1995, Theoretical and Applied Genetics.

[46]  H. Nguyen,et al.  Use of RAPD markers to determine the genetic diversity of diploid, wheat genotypes , 1992, Theoretical and Applied Genetics.

[47]  C. Chinoy,et al.  Nonhomoeologous translocations between group 4, 5 and 7 chromosomes within wheat and rye , 2004, Theoretical and Applied Genetics.

[48]  R. Tuberosa,et al.  Microsatellite analysis reveals a progressive widening of the genetic basis in the elite durum wheat germplasm , 2003, Theoretical and Applied Genetics.

[49]  A. Walsh,et al.  Mining single-nucleotide polymorphisms from hexaploid wheat ESTs. , 2003, Genome.

[50]  R. Evenson,et al.  Assessing the Impact of the Green Revolution, 1960 to 2000 , 2003, Science.

[51]  Peter Hedden,et al.  The genes of the Green Revolution. , 2003, Trends in genetics : TIG.

[52]  J. Rafalski.  Novel genetic mapping tools in plants: SNPs and LD-based approaches , 2002 .

[53]  B. Baum,et al.  AFLP and pedigree-based genetic diversity estimates in modern cultivars of durum wheat [Triticum turgidum L. subsp. durum (Desf.) Husn.] , 2002, Theoretical and Applied Genetics.

[54]  Virander S. Chauhan,et al.  Novel genetic mapping tools in plants , 2002 .

[55]  A. Shalom,et al.  Pharmacogenetics of Psychotropic Drugs: High-throughput single nucleotide polymorphism genotyping , 2002 .

[56]  Y. Minobe,et al.  Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza sativa, Oryza rufipogon) and establishment of SNP markers. , 2002, DNA research : an international journal for rapid publication of reports on genes and genomes.

[57]  A B Korol,et al.  Molecular genetic maps in wild emmer wheat, Triticum dicoccoides: genome-wide coverage, massive negative interference, and putative quasi-linkage. , 2000, Genome research.

[58]  A. Beiles,et al.  Microsatellite diversity correlated with ecological-edaphic and genetic factors in three microsites of wild emmer wheat in North Israel. , 2000, Molecular biology and evolution.

[59]  P. Donnelly,et al.  Inference of population structure using multilocus genotype data. , 2000, Genetics.

[60]  R. Koebner,et al.  Temporal trends in the diversity of UK wheat , 2000, Theoretical and Applied Genetics.

[61]  Earl Hubbell,et al.  Genome-wide mapping with biallelic markers in Arabidopsis thaliana , 1999, Nature Genetics.

[62]  M. Warburton,et al.  Plant genetic resources: what can they contribute toward increased crop productivity? , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[63]  Junhua Peng,et al.  Microsatellite tagging of the stripe-rust resistance gene YrH52 derived from wild emmer wheat, Triticum dicoccoides, and suggestive negative crossover interference on chromosome 1B , 1999, Theoretical and Applied Genetics.

[64]  Hans-Joachim Braun,et al.  New wheats for a secure, sustainable future , 1999 .

[65]  M. Ganal,et al.  A microsatellite map of wheat. , 1998, Genetics.

[66]  A. Myburg,et al.  Development of RAPD and SCAR markers linked to the Russian wheat aphid resistance gene Dn2 in wheat , 1998, Theoretical and Applied Genetics.

[67]  J. Ott.  Genetic data analysis II , 1997 .

[68]  W. G. Hill,et al.  Genetic Data Analysis II . By Bruce S. Weir, Sunderland, Massachusetts. Sinauer Associates, Inc.445 pages. ISBN 0-87893-902-4. , 1996 .

[69]  S. Tanksley,et al.  Genetic diversity in durum wheat based on RFLPs, morphophysiological traits, and coefficient of parentage , 1996 .

[70]  G. Hettel,et al.  Wheat breeding at CIMMYT: Commemorating 50 years of research in Mexico for global wheat improvement; Ciudad Obregon, Sonora, Mexico; 21-25 Mar 1994 , 1995 .

[71]  P. Moya,et al.  Impacts of international wheat breeding research in the developing world , 1993 .

[72]  E. Saari,et al.  Durum wheats : challenges and opportunities , 1992 .

[73]  K. Tsunewaki,et al.  Restriction fragment length polymorphism (RFLP) analysis in wheat. II. Linkage maps of the RFLP sites in common wheat. , 1991, Idengaku zasshi.

[74]  D. Crawford.  Food: tradition and change in Hellenistic Egypt. , 1979, World archaeology.

[75]  Alfred W. Crosby,et al.  The Columbian exchange : biological and cultural consequences of 1492 , 1973 .

[76]  J. Harlan,et al.  Agricultural Origins: Centers and Noncenters , 1971, Science.

[77]  A. A. Hanson.  The Origin, Variation, Immunity, and Breeding of Cultivated Plants , 1952 .

[78]  K. Shadan,et al.  Available online: , 2012 .