University of Adelaide Library

Adelaide Research and Scholarship : Schools and Disciplines : School of Agriculture, Food and Wine : Agriculture, Food and Wine publications

Please use this identifier to cite or link to this item: http://hdl.handle.net/2440/74379

Type: Journal article
Title: Genome-wide evaluation of genetic diversity and linkage disequilibrium in winter and spring triticale (x Triticosecale Wittmack)
Author: Alheit, K.
Maurer, H.
Reif, J.
Tucker, M.
Hahn, V.
Weissmann, E.
Wurschum, T.
Citation: BMC Genomics, 2012; 13(1):1-10
Publisher: BioMed Central Ltd.
Issue Date: 2012
ISSN: 1471-2164
Statement of
Responsibility: 
Katharina V Alheit, Hans P Maurer, Jochen C Reif, Matthew R Tucker, Volker Hahn, Elmar A Weissmann and Tobias Würschum
Abstract: Background: Recent 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. Results: The 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. Conclusions: Our 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.
Description: Extent: 10p.
Rights: © 2012 Alheit et al.; licensee 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.
RMID: 0020122071
DOI: 10.1186/1471-2164-13-235
Appears in Collections:Agriculture, Food and Wine publications
View citing articles in: Web of Science
Google Scholar
Scopus

Files in This Item:

File Description SizeFormat
hdl_74379.pdfPublished version1.88 MBAdobe PDFView/Open

Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.

 

© 2008 The University of Adelaide
library@adelaide.edu.au
CRICOS Provider Number 00123M
Service Charter | Copyright | Privacy | Disclaimer