title: Genome-wide characterization of genetic diversity and population structure in Secale.
abstract: BACKGROUND
  Numerous rye accessions are stored in ex situ genebanks worldwide. Little is known about the extent of genetic diversity contained in any of them and its relation to contemporary varieties, since to date rye genetic diversity studies had a very limited scope, analyzing few loci and/ or few accessions. Development of high throughput genotyping methods for rye opened the possibility for genome wide characterizations of large accessions sets. In this study we used 1054 Diversity Array Technology (DArT) markers with defined chromosomal location to characterize genetic diversity and population structure in a collection of 379 rye accessions including wild species, landraces, cultivated materials, historical and contemporary rye varieties.
  
  
  RESULTS
  Average genetic similarity (GS) coefficients and average polymorphic information content (PIC) values varied among chromosomes. Comparison of chromosome specific average GS within and between germplasm sub-groups indicated regions of chromosomes 1R and 4R as being targeted by selection in current breeding programs. Bayesian clustering, principal coordinate analysis and Neighbor Joining clustering demonstrated that source and improvement status contributed significantly to the structure observed in the analyzed set of Secale germplasm. We revealed a relatively limited diversity in improved rye accessions, both historical and contemporary, as well as lack of correlation between clustering of improved accessions and geographic origin, suggesting common genetic background of rye accessions from diverse geographic regions and extensive germplasm exchange. Moreover, contemporary varieties were distinct from the remaining accessions.
  
  
  CONCLUSIONS
  Our results point to an influence of reproduction methods on the observed diversity patterns and indicate potential of ex situ collections for broadening the genetic diversity in rye breeding programs. Obtained data show that DArT markers provide a realistic picture of the genetic diversity and population structure present in the collection of 379 rye accessions and are an effective platform for rye germplasm characterization and association mapping studies.
authors.affiliation: Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Warsaw, Poland. hanna_bolibok_bragoszewska@sggw.pl.
authors.forename: Hanna
authors.initials: H
authors.lastname: Bolibok-Brągoszewska
authors.forename: Małgorzata
authors.initials: M
authors.lastname: Targońska
authors.forename: Leszek
authors.initials: L
authors.lastname: Bolibok
authors.forename: Andrzej
authors.initials: A
authors.lastname: Kilian
authors.forename: Monika
authors.initials: M
authors.lastname: Rakoczy-Trojanowska
mesh_terms: D001499:Bayes Theorem; D001947:Breeding; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D016000:Cluster Analysis; D018744:DNA, Plant / Q000235:genetics; D005819:Genetic Markers; D014644:Genetic Variation; D005828:Genetics, Population; D060005:Genotyping Techniques; D025341:Principal Component Analysis; D012434:Secale / Q000145:classification / Q000235:genetics*
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers
references.citation: Theor Appl Genet. 2003 Nov;107(8):1469-76
references.pmid: 12898026
references.citation: Mol Ecol. 2005 Jul;14(8):2611-20
references.pmid: 15969739
references.citation: Genome. 2007 Aug;50(8):724-34
references.pmid: 17893732
references.citation: J Nutr. 2010 Mar;140(3):534-41
references.pmid: 20089780
references.citation: PLoS One. 2012;7(11):e49488
references.pmid: 23145179
references.citation: J Nutr. 2000 Sep;130(9):2215-21
references.pmid: 10958815
references.citation: PLoS One. 2013 May 28;8(5):e64062
references.pmid: 23724020
references.citation: PLoS One. 2013 Nov 25;8(11):e81267
references.pmid: 24282578
references.citation: BMC Plant Biol. 2011 Sep 28;11:131
references.pmid: 21951788
references.citation: Theor Appl Genet. 2010 Jan;120(2):291-9
references.pmid: 19669632
references.citation: BMC Genomics. 2008 Jan 22;9:26
references.pmid: 18208620
references.citation: PLoS One. 2008 Feb 27;3(2):e1682
references.pmid: 18301759
references.citation: BMC Plant Biol. 2013 May 06;13:78
references.pmid: 23647851
references.citation: Genetics. 2000 Jun;155(2):945-59
references.pmid: 10835412
references.citation: Bioinformatics. 2012 Oct 1;28(19):2537-9
references.pmid: 22820204
references.citation: BMC Genomics. 2012 Jun 12;13:235
references.pmid: 22691168
references.citation: Theor Appl Genet. 2011 May;122(8):1547-60
references.pmid: 21394532
references.citation: Theor Appl Genet. 2008 Feb;116(3):439-53
references.pmid: 18060539
references.citation: Mol Biol Evol. 2010 Nov;27(11):2534-47
references.pmid: 20558595
references.citation: PLoS One. 2011;6(12):e28495
references.pmid: 22163026
references.citation: BMC Plant Biol. 2013 Mar 12;13:41
references.pmid: 23497122
references.citation: Theor Appl Genet. 2008 Aug;117(4):641-52
references.pmid: 18535814
references.citation: BMC Plant Biol. 2011 Jan 10;11:6
references.pmid: 21219606
references.citation: Hereditas. 2002;136(1):29-38
references.pmid: 12184486
references.citation: BMC Genomics. 2008 May 21;9:237
references.pmid: 18495015
references.citation: Mol Genet Genomics. 2005 Dec;274(5):515-27
references.pmid: 16244872
references.citation: BMC Genomics. 2009 Sep 30;10:458
references.pmid: 19788762
references.citation: Nucleic Acids Res. 2001 Feb 15;29(4):E25
references.pmid: 11160945
references.citation: BMC Genomics. 2013 Nov 27;14:835
references.pmid: 24279304
references.citation: BMC Plant Biol. 2013 Mar 07;13:39
references.pmid: 23497049
references.citation: PLoS Biol. 2004 Oct;2(10):e347
references.pmid: 15486582
references.citation: Mol Biol Evol. 2011 Oct;28(10):2731-9
references.pmid: 21546353
references.citation: Genome. 2005 Oct;48(5):792-801
references.pmid: 16391685
references.citation: PLoS One. 2012;7(10):e46919
references.pmid: 23071663
references.citation: Hereditas. 2004;140(3):210-21
references.pmid: 15198711
references.citation: Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9915-20
references.pmid: 15192146
references.citation: BMC Genet. 2011 May 11;12:42
references.pmid: 21569312
references.citation: Chromosoma. 1991 Oct;101(1):1-10
references.pmid: 1769268
references.citation: PLoS Genet. 2013 Mar;9(3):e1003378
references.pmid: 23555290
references.citation: New Phytol. 2012 Apr;194(1):116-128
references.pmid: 22309312
references.citation: BMC Genomics. 2009 Dec 03;10:578
references.pmid: 19958552
references.citation: Theor Appl Genet. 2005 Apr;110(6):1092-8
references.pmid: 15742202
references.citation: Curr Opin Plant Biol. 2002 Apr;5(2):94-100
references.pmid: 11856602
references.citation: PLoS One. 2013 Jun 27;8(6):e67280
references.pmid: 23826256
references.citation: Plant Sci. 2012 Mar;184:54-62
references.pmid: 22284710
references.citation: J Appl Genet. 2005;46(4):371-3
references.pmid: 16278509
references.citation: Bioinformatics. 2007 Jul 15;23(14):1801-6
references.pmid: 17485429
references.citation: Hereditas. 2001;134(3):237-43
references.pmid: 11833287