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. 2011 Jul 28:12:380.
doi: 10.1186/1471-2164-12-380.

Detection of segregation distortion loci in triticale (x Triticosecale Wittmack) based on a high-density DArT marker consensus genetic linkage map

Katharina V Alheit  1 , Jochen C Reif, Hans Peter Maurer, Volker Hahn, Elmar A Weissmann, Thomas Miedaner, Tobias Würschum
Affiliations

Detection of segregation distortion loci in triticale (x Triticosecale Wittmack) based on a high-density DArT marker consensus genetic linkage map

Katharina V Alheit et al. BMC Genomics. .

Abstract

Background: Triticale is adapted to a wide range of abiotic stress conditions, is an important high-quality feed stock and produces similar grain yield but more biomass compared to other crops. Modern genomic approaches aimed at enhancing breeding progress in cereals require high-quality genetic linkage maps. Consensus maps are genetic maps that are created by a joint analysis of the data from several segregating populations and different approaches are available for their construction. The phenomenon that alleles at a locus deviate from the Mendelian expectation has been defined as segregation distortion. The study of segregation distortion is of particular interest in doubled haploid (DH) populations due to the selection pressure exerted on the plants during the process of their establishment.

Results: The final consensus map, constructed out of six segregating populations derived from nine parental lines, incorporated 2555 DArT markers mapped to 2602 loci (1929 unique). The map spanned 2309.9 cM with an average number of 123.9 loci per chromosome and an average marker density of one unique locus every 1.2 cM. The R genome showed the highest marker coverage followed by the B genome and the A genome. In general, locus order was well maintained between the consensus linkage map and the component maps. However, we observed several groups of loci for which the colinearity was slightly uneven. Among the 2602 loci mapped on the consensus map, 886 showed distorted segregation in at least one of the individual mapping populations. In several DH populations derived by androgenesis, we found chromosomes (2B, 3B, 1R, 2R, 4R and 7R) containing regions where markers exhibited a distorted segregation pattern. In addition, we observed evidence for segregation distortion between pairs of loci caused either by a predominance of parental or recombinant genotypes.

Conclusions: We have constructed a reliable, high-density DArT marker consensus genetic linkage map as a basis for genomic approaches in triticale research and breeding, for example for multiple-line cross QTL mapping experiments. The results of our study exemplify the tremendous impact of different DH production techniques on allele frequencies and segregation distortion covering whole chromosomes.

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Figures

Figure 1
Figure 1
Plot of the first two principal coordinates of the parents of the component populations. Principal coordinate analysis of the nine parents of the populations, based on modified Rogers' distance estimates. Crosses between parental lines are indicated by dashed lines. The numbers in parentheses refer to the percentage of variance explained by the principal coordinate.
Figure 2
Figure 2
Schematic illustration of the consensus map. Unique loci are represented on their positions by horizontal lines across the chromosome. Chromosome 2R is divided into two linkage groups as indicated by dashed lines.
Figure 3
Figure 3
Comparison of loci positions in component maps and the consensus map. DH06, DH07, EAW74, EAW78; DH_LxA, and F2_LxT are indicated by red circles, pink triangles, green crosses, light-green exes, blue diamonds and light-blue triangles, respectively.
Figure 4
Figure 4
Segregation distortion of loci in the component maps based on the consensus map. Segregation distortion in favour of one parental allele is indicated in red or blue, respectively. Populations (A) DH06, (B) DH07, (C) EAW74, (D) EAW78, (E) DH_LxA, (F) F2_LxT. The dashed horizontal line indicates the significance threshold (P > 0.01).
Figure 5
Figure 5
Segregation distortion caused by epistatic interactions. Significant segregation distortion (P < 0.01) for pairs of loci is shown in green (parental genotypes dominating) and in purple (recombinant genotypes dominating). Lines separate genomes (black) and chromosomes (grey). Both axes contain the markers segregating in the respective population, with the markers in the order of the chromosomes from 1 to 7. Populations (A) DH06, (B) DH07, (C) EAW74, (D) EAW78, (E) DH_LxA, (F) F2_LxT.
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