Genome-wide evaluation of genetic diversity and linkage disequilibrium in winter and spring triticale (x Triticosecale Wittmack)

BMC Genomics

Research Article

Matthew R Tucker¹  Elmar A Weissmann²  Jochen C Reif³  Volker Hahn³  Hans Peter Maurer³  Tobias Würschum³  Katharina V Alheit³ 

[1] Centre of Excellence in Plant Cell Walls, University of Adelaide, 5064, Urrbrae, SA, Australia;Saatzucht Dr. Hege GbR, Domäne Hohebuch, 74638, Waldenburg, Germany;State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany;

关键词: Linkage Disequilibrium;    Association Mapping;    Growth Habit;    Polymorphic Information Content;    DArT Marker;   

DOI  :  10.1186/1471-2164-13-235

 received in 2012-03-28, accepted in 2012-05-24,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundRecent advances in genotyping with high-density markers nowadays enable genome-wide genomic analyses in crops. A detailed characterisation of the population structure and linkage disequilibrium (LD) is essential for the application of genomic approaches and consequently for knowledge-based breeding. In this study we used the triticale-specific DArT array to analyze population structure, genetic diversity, and LD in a worldwide set of 161 winter and spring triticale lines.ResultsThe principal coordinate analysis revealed that the first principal coordinate divides the triticale population into two clusters according to their growth habit. The density distributions of the first ten principal coordinates revealed that several show a distribution indicative of population structure. In addition, we observed relatedness within growth habits which was higher among the spring types than among the winter types. The genome-wide analysis of polymorphic information content (PIC) showed that the PIC is variable among and along chromosomes and that especially the R genome of spring types possesses a reduced genetic diversity. We also found that several chromosomes showed regions of high genetic distance between the two growth habits, indicative of divergent selection. Regarding linkage disequilibrium, the A and B genomes showed a similar LD of 0.24 for closely linked markers and a decay within approximately 12 cM. LD in the R genome was lower with 0.19 and decayed within a shorter map distance of approximately 5 cM. The extent of LD was generally higher for the spring types compared to the winter types. In addition, we observed strong variability of LD along the chromosomes.ConclusionsOur results confirm winter and spring growth habit are the major contributors to population structure in triticale, and a family structure exists in both growth types. The specific patterns of genetic diversity observed within these types, such as the low diversity on some rye chromosomes of spring habits, provide a basis for targeted broadening of the available breeding germplasm. In addition, the genome-wide analysis of the extent and the pattern of LD will assist scientists and breeders alike in the implementation and the interpretation of association mapping in triticale.

【 授权许可】

Unknown   
© Alheit et al.; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.