Genome-wide characterization of genetic diversity and population structure in Secale

BMC Plant Biology

Research Article

Hanna Bolibok-Brągoszewska¹  Małgorzata Targońska¹  Monika Rakoczy-Trojanowska¹  Leszek Bolibok²  Andrzej Kilian³ 

[1] Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Warsaw, Poland;Department of Silviculture, Faculty of Forestry, Warsaw University of Life Sciences, Warsaw, Poland;Diversity Arrays Technology Pty. Ltd, Yarralumla, ACT, Australia;

关键词: Amplify Fragment Length Polymorphism;    Simple Sequence Repeat Marker;    Polymorphic Information Content;    Amplify Fragment Length Polymorphism Marker;    DArT Marker;   

DOI  :  10.1186/1471-2229-14-184

 received in 2014-03-13, accepted in 2014-06-27,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundNumerous 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.ResultsAverage 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.ConclusionsOur 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.

【 授权许可】

CC BY   
© Bolibok-Brągoszewska et al.; licensee BioMed Central Ltd. 2014