Geography and end use drive the diversification of worldwide winter rye populations.

To meet the current challenges in human food production, improved understanding of the genetic diversity of crop species that maximizes the selection efficacy in breeding programs is needed. The present study offers new insights into the diversity, genetic structure and demographic history of cultivated rye (Secale cereale L.).

Multiple-trait- and selection indices-genomic predictions for grain yield and protein content in rye for feeding purposes.

Key Message: Exploiting the benefits from multiple-trait genomic selection for protein content prediction relying on additional grain yield information within training sets is a realistic genomic selection approach in rye breeding.

Abstract: Multiple-trait genomic selection (MTGS) was specially designed to benefit from the information of genetically correlated indicator traits in order to improve genomic prediction accuracies. Two segregating F3:4 rye testcross populations genotyped using diversity array technology markers and evaluated for grain yield (GY) and protein content (PC) were considered.

Diversity analysis and genomic prediction of Sclerotinia resistance in sunflower using a new 25 K SNP genotyping array.

Key Message: We have developed a SNP array for sunflower containing more than 25 K markers, representing single loci mostly in or near transcribed regions of the genome. The array was successfully applied to genotype a diversity panel of lines, hybrids, and mapping populations and represented well the genetic diversity of cultivated sunflower. Results of PCoA and population substructure analysis underlined the complexity of the genetic composition of current elite breeding material.

Multiply to conquer: Copy number variations at Ppd-B1 and Vrn-A1 facilitate global adaptation in wheat.

Background: Copy number variation was found to be a frequent type of DNA polymorphism in the human genome often associated with diseases but its importance in crops and the effects on agronomic traits are still largely unknown.

Results: Here, we employed a large worldwide panel of 1110 winter wheat varieties to assess the frequency and the geographic distribution of copy number variants at the Photoperiod-B1 (Ppd-B1) and the Vernalization-A1 (Vrn-A1) loci as well as their effects on flowering time under field conditions. We identified a novel four copy variant of Vrn-A1 and based on the phylogenetic relationships among the lines show that the higher copy variants at both loci are likely to have arisen independently multiple times.

Genetic architecture is more complex for resistance to Septoria tritici blotch than to Fusarium head blight in Central European winter wheat.

Background: Fusarium head blight (FHB) and Septoria tritici blotch (STB) severely impair wheat production. With the aim to further elucidate the genetic architecture underlying FHB and STB resistance, we phenotyped 1604 European wheat hybrids and their 135 parental lines for FHB and STB disease severities and determined genotypes at 17,372 single-nucleotide polymorphic loci.

Results: Cross-validated association mapping revealed the absence of large effect QTL for both traits.

Lutein and lutein esters in whole grain flours made from 75 genotypes of 5 triticum species grown at multiple sites.

Concentrations of lutein and lutein esters were determined in an ample collection of 75 wheat genotypes comprising bread wheat (Triticum aestivum L.), durum (Triticum durum Desf.), spelt (Triticum spelta L.

Genomic selection in wheat: optimum allocation of test resources and comparison of breeding strategies for line and hybrid breeding.

The implementation of genomic selection in breeding programs can be recommended for hybrid and line breeding in wheat. High prediction accuracies from genomic selection (GS) were reported for grain yield in wheat asking for the elaboration of efficient breeding strategies applying GS. Our objectives were therefore, (1) to optimize the number of lines, locations and testers in different multi-stage breeding strategies with and without GS, (2) to elaborate the most efficient breeding strategy based on the selection gain and its standard deviation, and (3) to investigate the potential of GS to improve the relative efficiency of hybrid versus line breeding in wheat.

First insights into the genotype-phenotype map of phenotypic stability in rye.

Improving phenotypic stability of crops is pivotal for coping with the detrimental impacts of climate change. The goal of this study was to gain first insights into the genetic architecture of phenotypic stability in cereals. To this end, we determined grain yield, thousand kernel weight, test weight, falling number, and both protein and soluble pentosan content for two large bi-parental rye populations connected through one common parent and grown in multi-environmental field trials involving more than 15 000 yield plots.

Biology, genetics, and management of ergot (Claviceps spp.) in rye, sorghum, and pearl millet.

Ergot is a disease of cereals and grasses caused by fungi in the genus Claviceps. Of particular concern are Claviceps purpurea in temperate regions, C. africana in sorghum (worldwide), and C.

Genetic control of plant height in European winter wheat cultivars.

Plant height variation in European winter wheat cultivars is mainly controlled by the Rht - D1 and Rht - B1 semi-dwarfing genes, but also by other medium- or small-effect QTL and potentially epistatic QTL enabling fine adjustments of plant height. Plant height is an important goal in wheat (Triticum aestivum L.) breeding as it affects crop performance and thus yield and quality.

Yield performance and stability of CMS-based triticale hybrids.

CMS-based triticale hybrids showed only marginal midparent heterosis for grain yield and lower dynamic yield stability compared to inbred lines. Hybrids of triticale (×Triticosecale Wittmack) are expected to possess outstanding yield performance and increased dynamic yield stability. The objectives of the present study were to (1) examine the optimum choice of the biometrical model to compare yield stability of hybrids versus lines, (2) investigate whether hybrids exhibit a more pronounced grain yield performance and yield stability, and (3) study optimal strategies to predict yield stability of hybrids.

Evaluation of multi-locus models for genome-wide association studies: a case study in sugar beet.

Association mapping has become a widely applied genomic approach to dissect the genetic architecture of complex traits. A major issue for association mapping is the need to control for the confounding effects of population structure, which is commonly done by mixed models incorporating kinship information. In this case study, we employed experimental data from a large sugar beet population to evaluate multi-locus models for association mapping.

Flowering time control in European winter wheat.

Flowering time is an important trait in wheat breeding as it affects adaptation and yield potential. The aim of this study was to investigate the genetic architecture of flowering time in European winter bread wheat cultivars. To this end a population of 410 winter wheat varieties was evaluated in multi-location field trials and genotyped by a genotyping-by-sequencing approach and candidate gene markers.

Adult plant development in triticale (× triticosecale wittmack) is controlled by dynamic genetic patterns of regulation.

Many biologically and agronomically important traits are dynamic and show temporal variation. In this study, we used triticale (× Triticosecale Wittmack) as a model crop to assess the genetic dynamics underlying phenotypic plasticity of adult plant development. To this end, a large mapping population with 647 doubled haploid lines derived from four partially connected families from crosses among six parents was scored for developmental stage at three different time points.

Optimum allocation of test resources and comparison of breeding strategies for hybrid wheat.

The use of a breeding strategy combining the evaluation of line per se with testcross performance maximizes annual selection gain for hybrid wheat breeding. Recent experimental studies confirmed a high commercial potential for hybrid wheat requiring the design of optimum breeding strategies. Our objectives were to (1) determine the optimum allocation of the type and number of testers, the number of test locations and the number of doubled haploid lines for different breeding strategies, (2) identify the best breeding strategy and (3) elaborate key parameters for an efficient hybrid wheat breeding program.

Exploitation of yield stability in barley.

Analyses of registration trials of winter barley suggested that yield and yield stability can be enhanced by developing hybrid instead of line varieties. Yield stability is central to cope with the expected increased frequency of extreme weather conditions. The objectives of our study were to (1) examine the dimensioning of field trials needed to precisely portray yield stability of individual winter barley (Hordeum vulgare L.

Redesigning the exploitation of wheat genetic resources.

More than half a million wheat genetic resources are resting in gene banks worldwide. Unlocking their hidden favorable genetic diversity for breeding is pivotal for enhancing grain yield potential, and averting future food shortages. Here, we propose exploiting recent advances in hybrid wheat technology to uncover the masked breeding values of wheat genetic resources.

Genetic architecture of winter hardiness and frost tolerance in triticale.

Abiotic stress experienced by autumn-sown crops during winter is of great economic importance as it can have a severe negative impact on yield. In this study, we investigated the genetic architecture of winter hardiness and frost tolerance in triticale. To this end, we used a large mapping population of 647 DH lines phenotyped for both traits in combination with genome-wide marker data.

Genetic dynamics underlying phenotypic development of biomass yield in triticale.

Background: The nature of dynamic traits with their phenotypic plasticity suggests that they are under the control of a dynamic genetic regulation. We employed a precision phenotyping platform to non-invasively assess biomass yield in a large mapping population of triticale at three developmental stages.

Results: Using multiple-line cross QTL mapping we identified QTL for each of these developmental stages which explained a considerable proportion of the genotypic variance.

Mapping dynamic QTL for plant height in triticale.

Background: Plant height is a prime example of a dynamic trait that changes constantly throughout adult development. In this study we utilised a large triticale mapping population, comprising 647 doubled haploid lines derived from 4 families, to phenotype for plant height by a precision phenotyping platform at multiple time points.

Results: Using multiple-line cross QTL mapping we identified main effect and epistatic QTL for plant height for each of the time points.

Effect of a rye dwarfing gene on plant height, heading stage, and Fusarium head blight in triticale (×Triticosecale Wittmack).

The rye-derived dwarfing gene Ddw1 on chromosome 5R acts in triticale in considerably reducing plant height, increasing FHB severity and delaying heading stage. Triticale, an amphiploid hybrid between durum wheat and rye, is an European cereal mainly grown in Germany, France, Poland, and Belarus for feeding purposes. Dwarfing genes might further improve the genetic potential of triticale concerning lodging resistance and yield.

Long-term perspective of hybrid versus line breeding in wheat based on quantitative genetic theory.

The predicted future yield potential of hybrids was competitive with lines in the near future, but on a long term the competitiveness of hybrids depends on a number of factors. The change from line to hybrid breeding in autogamous crops is a recent controversial discussion among scientists and breeders. Our objectives were to employ wheat as a model to: (1) deliver a theoretical framework for the comparison of the selection gain of hybrid versus line breeding; (2) elaborate key parameters affecting selection gain in this comparison; (3) and evaluate the potential to modify these parameters in applied breeding programs.

Bridging the gap between marker-assisted and genomic selection of heading time and plant height in hybrid wheat.

Based on data from field trials with a large collection of 135 elite winter wheat inbred lines and 1604 F1 hybrids derived from them, we compared the accuracy of prediction of marker-assisted selection and current genomic selection approaches for the model traits heading time and plant height in a cross-validation approach. For heading time, the high accuracy seen with marker-assisted selection severely dropped with genomic selection approaches RR-BLUP (ridge regression best linear unbiased prediction) and BayesCπ, whereas for plant height, accuracy was low with marker-assisted selection as well as RR-BLUP and BayesCπ. Differences in the linkage disequilibrium structure of the functional and single-nucleotide polymorphism markers relevant for the two traits were identified in a simulation study as a likely explanation for the different trends in accuracies of prediction.

Relatedness severely impacts accuracy of marker-assisted selection for disease resistance in hybrid wheat.

The accuracy of genomic selection depends on the relatedness between the members of the set in which marker effects are estimated based on evaluation data and the types for which performance is predicted. Here, we investigate the impact of relatedness on the performance of marker-assisted selection for fungal disease resistance in hybrid wheat. A large and diverse mapping population of 1739 elite European winter wheat inbred lines and hybrids was evaluated for powdery mildew, leaf rust and stripe rust resistance in multi-location field trials and fingerprinted with 9 k and 90 k SNP arrays.

Cross-validation in association mapping and its relevance for the estimation of QTL parameters of complex traits.

Association mapping has become a widely applied genomic approach to identify quantitative trait loci (QTL) and dissect the genetic architecture of complex traits. However, approaches to assess the quality of the obtained QTL results are lacking. We therefore evaluated the potential of cross-validation in association mapping based on a large sugar beet data set.