Abstract
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.
Highlights
Recent advances in genotyping with high-density markers nowadays enable genome-wide genomic analyses in crops
Modern genomic approaches such as association mapping rely on a detailed characterisation of the population structure and linkage disequilibrium (LD) present in the species under study
Population structure and kinship Our study was based on a set of 161 diverse triticale lines of worldwide origin including those used in a recent study by Badea et al [30]
Summary
Recent advances in genotyping with high-density markers nowadays enable genome-wide genomic analyses in crops. 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. Modern genomic approaches such as association mapping rely on a detailed characterisation of the population structure and linkage disequilibrium (LD) present in the species under study. LD is the non-random association of alleles at different loci and, similar to genetic diversity, is affected by several genetic factors such as recombination, mutation For this reason, it is important to assess and understand the extent and patterns of LD in the species under investigation. Diversity Arrays Technology (DArT) markers [17] have previously been identified as a valuable tool in cereals and have been employed successfully to create linkage maps of triticale [18] as well as its parents wheat [19,20,21,22] and rye [23,24]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
