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Alheit K.V.,University of Hohenheim | Maurer H.P.,University of Hohenheim | Reif J.C.,University of Hohenheim | Tucker M.R.,University of Adelaide | And 3 more authors.
BMC Genomics | Year: 2012

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. © 2012 Alheit et al.; licensee BioMed Central Ltd.


Liu W.,China Agricultural University | Leiser W.L.,University of Hohenheim | Maurer H.P.,University of Hohenheim | Li J.,China Agricultural University | And 3 more authors.
Plant Breeding | Year: 2015

Lodging tolerance is an important agronomic trait as it can have a severe negative impact on grain yield and quality. Here, we used a large mapping population of 647 doubled haploid triticale lines derived from four families to dissect the genetic architecture underlying lodging tolerance and to assess different approaches for a genomics-based improvement of the trait. The plants were evaluated for lodging in two environments and genotyped with 1710 genomewide DArT markers. We observed a large genotypic variation for lodging and transgressive segregation in all families. Employing two complementary QTL mapping approaches, we identified both main effect and epistatic QTL. Using cross-validation, we showed that the proportion of genotypic variance explained by the detected QTL is low, thus limiting the efficiency of marker-assisted selection to improve this trait. By contrast, the cross-validated predictive ability of genomic prediction was approximately twice as high as that of the QTL-based selection approaches. In conclusion, our results show that lodging tolerance is a complex trait that can be improved by classical breeding but also assisted by marker-based approaches. © 2015 Blackwell Verlag GmbH.


Boeven P.H.G.,University of Hohenheim | Wurschum T.,University of Hohenheim | Weissmann S.,Saatzucht Dr. Hege GbR | Miedaner T.,University of Hohenheim | Maurer H.P.,University of Hohenheim
Euphytica | Year: 2015

Like other small grain cereals, triticale (×Triticosecale Wittmack) is also affected by Fusarium head blight (FHB) which is a serious plant disease leading to yield losses and to a contamination of feed and food by harmful mycotoxins. Use of resistant varieties is the most effective way to manage FHB infections. More recently, commercial hybrid breeding in autogamous cereals has received increased interest. Therefore, we built a bridge between hybrid and resistance breeding and conducted a multi-environmental field trial using deliberate inoculation with Fusarium culmorum to: (i) evaluate different hybrid prediction approaches based on phenotypic and/or genomic data; (ii) compare the effect of cytoplasmic male sterility (CMS) inducing cytoplasm and normal (N) cytoplasm on FHB resistance. We evaluated 226 single cross hybrids, their paternal and maternal lines in both CMS- and N-cytoplasm. Our analysis revealed a large genetic variation for FHB resistance. Single cross hybrids tended to be more resistant than their parental lines. We observed a close association between N-lines and CMS-lines for FHB resistance. We found a predominance of σGCA2over σSCA2for FHB resistance. Correlation between the sum of general combining ability (GCA) effects and hybrid performance was high for FHB resistance. Mid-parent performance served as a moderate indicator for FHB resistance of single crosses. Best linear unbiased prediction of hybrid performance based on relatedness between tested and untested genotypes estimated by marker data showed great potential for hybrid prediction when no reliable per se information or GCA estimates are available. © 2015 Springer Science+Business Media Dordrecht


Gowda M.,University of Hohenheim | Zhao Y.,University of Hohenheim | Maurer H.P.,University of Hohenheim | Weissmann E.A.,Saatzucht Dr. Hege GbR | And 2 more authors.
Euphytica | Year: 2013

Predicting single-cross performance is of special interest in hybrid breeding of triticale. We used molecular and phenotypic data of factorial triticale crosses and compared several approaches to predict their single-cross performance. Twenty-three inbred lines and their 76 incomplete factorial crosses were field evaluated for grain yield, plant height, and heading time at five locations in Central Europe. In addition, the parental lines were genotyped with 52 SSR markers. Plant height and heading time were predicted with high accuracy based on mid-parent performance. In contrast, prediction of hybrid performance based on mid-parent value was not accurate for grain yield. Using general combining ability effects led to an enhanced prediction accuracy of hybrid grain yield performance. This accuracy could be slightly improved using best linear unbiased prediction approaches. The prediction accuracy was considerably high even if the number of tested hybrids was small. Consequently, best linear unbiased prediction of hybrid performance is a promising tool for hybrid triticale breeding programs. © 2012 Springer Science+Business Media B.V.

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