Genomic prediction with haplotype blocks in wheat.

Haplotype blocks might carry additional information compared to single SNPs and have therefore been suggested for use as independent variables in genomic prediction. Studies in different species resulted in more accurate predictions than with single SNPs in some traits but not in others. In addition, it remains unclear how the blocks should be built to obtain the greatest prediction accuracies. Our objective was to compare the results of genomic prediction with different types of haplotype blocks to prediction with single SNPs in 11 traits in winter wheat. We built haplotype blocks from marker data from 361 winter wheat lines based on linkage disequilibrium, fixed SNP numbers, fixed lengths in cM and with the R package HaploBlocker. We used these blocks together with data from single-year field trials in a cross-validation study for predictions with RR-BLUP, an alternative method (RMLA) that allows for heterogeneous marker variances, and GBLUP performed with the software GVCHAP. The greatest prediction accuracies for resistance scores for B. graminis, P. triticina, and F. graminearum were obtained with LD-based haplotype blocks while blocks with fixed marker numbers and fixed lengths in cM resulted in the greatest prediction accuracies for plant height. Prediction accuracies of haplotype blocks built with HaploBlocker were greater than those of the other methods for protein concentration and resistances scores for S. tritici, B. graminis, and P. striiformis. We hypothesize that the trait-dependence is caused by properties of the haplotype blocks that have overlapping and contrasting effects on the prediction accuracy. While they might be able to capture local epistatic effects and to detect ancestral relationships better than single SNPs, prediction accuracy might be reduced by unfavorable characteristics of the design matrices in the models that are due to their multi-allelic nature.

Deciphering the complex nature of bolting time regulation in Beta vulgaris.

KEY MESSAGE: Only few genetic loci are sufficient to increase the variation of bolting time in Beta vulgaris dramatically, regarding vernalization requirement, seasonal bolting time and reproduction type. Beta species show a wide variation of bolting time regarding the year of first reproduction, seasonal bolting time and the number of reproduction cycles. To elucidate the genetics of bolting time control, we used three F3 mapping populations that were produced by crossing a semelparous, annual sugar beet with iteroparous, vernalization-requiring wild beet genotypes. The semelparous plants died after reproduction, whereas iteroparous plants reproduced at least twice. All populations segregated for vernalization requirement, seasonal bolting time and the number of reproduction cycles. We found that vernalization requirement co-segregated with the bolting locus B on chromosome 2 and was inherited independently from semel- or iteroparous reproduction. Furthermore, we found that seasonal bolting time is a highly heritable trait (h 2 > 0.84), which is primarily controlled by two major QTL located on chromosome 4 and 9. Late bolting alleles of both loci act in a partially recessive manner and were identified in both iteroparous pollinators. We observed an additive interaction of both loci for bolting delay. The QTL region on chromosome 4 encompasses the floral promoter gene BvFT2, whereas the QTL on chromosome 9 co-localizes with the BR 1 locus, which controls post-winter bolting resistance. Our findings are applicable for marker-assisted sugar beet breeding regarding early bolting to accelerate generation cycles and late bolting to develop bolting-resistant spring and winter beets. Unexpectedly, one population segregated also for dwarf growth that was found to be controlled by a single locus on chromosome 9.

Hybrid wheat: quantitative genetic parameters and consequences for the design of breeding programs.

KEY MESSAGE: Commercial heterosis for grain yield is present in hybrid wheat but long-term competiveness of hybrid versus line breeding depends on the development of heterotic groups to improve hybrid prediction. Detailed knowledge of the amount of heterosis and quantitative genetic parameters are of paramount importance to assess the potential of hybrid breeding. Our objectives were to (1) examine the extent of midparent, better-parent and commercial heterosis in a vast population of 1,604 wheat (Triticum aestivum L.) hybrids and their parental elite inbred lines and (2) discuss the consequences of relevant quantitative parameters for the design of hybrid wheat breeding programs. Fifteen male lines were crossed in a factorial mating design with 120 female lines, resulting in 1,604 of the 1,800 potential single-cross hybrid combinations. The hybrids, their parents, and ten commercial wheat varieties were evaluated in multi-location field experiments for grain yield, plant height, heading time and susceptibility to frost, lodging, septoria tritici blotch, yellow rust, leaf rust, and powdery mildew at up to five locations. We observed that hybrids were superior to the mean of their parents for grain yield (10.7 %) and susceptibility to frost (-7.2 %), leaf rust (-8.4 %) and septoria tritici blotch (-9.3 %). Moreover, 69 hybrids significantly (P < 0.05) outyielded the best commercial inbred line variety underlining the potential of hybrid wheat breeding. The estimated quantitative genetic parameters suggest that the establishment of reciprocal recurrent selection programs is pivotal for a successful long-term hybrid wheat breeding.

EcoTILLING in Beta vulgaris reveals polymorphisms in the FLC-like gene BvFL1 that are associated with annuality and winter hardiness.

BACKGROUND: Sugar beet (Beta vulgaris ssp. vulgaris L.) is an important crop for sugar and biomass production in temperate climate regions. Currently sugar beets are sown in spring and harvested in autumn. Autumn-sown sugar beets that are grown for a full year have been regarded as a cropping system to increase the productivity of sugar beet cultivation. However, for the development of these "winter beets" sufficient winter hardiness and a system for bolting control is needed. Both require a thorough understanding of the underlying genetics and its natural variation. RESULTS: We screened a diversity panel of 268 B. vulgaris accessions for three flowering time genes via EcoTILLING. This panel had been tested in the field for bolting behaviour and winter hardiness. EcoTILLING identified 20 silent SNPs and one non-synonymous SNP within the genes BTC1, BvFL1 and BvFT1, resulting in 55 haplotypes. Further, we detected associations of nucleotide polymorphisms in BvFL1 with bolting before winter as well as winter hardiness. CONCLUSIONS: These data provide the first genetic indication for the function of the FLC homolog BvFL1 in beet. Further, it demonstrates for the first time that EcoTILLING is a powerful method for exploring genetic diversity and allele mining in B. vulgaris.