Background The genetic diversity and gene pool characteristics must be clarified for efficient genome-wide association studies, genomic selection, and hybrid breeding. The aim of this study was to evaluate the genetic structure of 509 wheat accessions representing registered varieties and advanced breeding lines via the high-density genotyping-by-sequencing approach. Results More than 30% of 13,499 SNP markers representing 2162 clusters were mapped to genes, whereas 22.50% of 26,369 silicoDArT markers overlapped with coding sequences and were linked in 3527 blocks. Regarding hexaploidy, perfect sequence matches following BLAST searches were not sufficient for the unequivocal mapping to unique loci. Moreover, allelic variations in homeologous loci interfered with heterozygosity calculations for some markers. Analyses of the major genetic changes over the last 27 years revealed the selection pressure on orthologs of the gibberellin biosynthesis-related GA2 gene and the senescence-associated SAG12 gene. A core collection representing the wheat population was generated for preserving germplasm and optimizing breeding programs. Conclusions Our results confirmed considerable differences among wheat subgenomes A, B and D, with D characterized by the lowest diversity but the highest LD. They revealed genomic regions that have been targeted by breeding.

We present a reliable, visual method for evaluation of the level of male fertility during flowering, that is indispensable for breeding of hybrid cultivars of winter triticale based on the cms-T.timopheevi system. Detailed observations of anther development were performed on 20 F 2 and BC 1 plants derived from crosses between male-sterile and fertility restoring lines. Variation of anther development within florets, spikelets, spikes, and among spikes of the same plant was examined. Hierarchic analysis showed significant role of these factors in determination of anther development, irrespective of the level of plant fertility. The sterilizing effect of cytoplasm was always better visible in the tip and base spikelets of the spike, in the third floret, and the anther adjacent to the floret axis. Our data indicate that during selection toward male-sterile plants at anthesis, at least 5 spikes should be evaluated. Special attention should be paid to the development of the anthers at the 2 nd and 7 th spikelet of the spike along with the variability in anther development within spikelet and floret. The anthers in the tip and base spikelets of the spike must be precisely evaluated during selection toward restorer lines.

Increased grain yield (GY) is the primary breeding target of wheat breeders. We performed the genome-wide association study (GWAS) on 168 elite winter wheat lines from an ongoing breeding program to identify the main determinants of grain yield. Sequencing of Diversity Array Technology fragments (DArTseq) resulted in 19,350 single-nucleotide polymorphism (SNP) and presence-absence variation (PAV) markers. We identified 15 main genomic regions located in ten wheat chromosomes (1B, 2B, 2D, 3A, 3D, 5A, 5B, 6A, 6B, and 7B) that explained from 7.9 to 20.3% of the variation in grain yield and 13.3% of the yield stability. Loci identified in the reduced genepool are important for wheat improvement using marker-assisted selection. We found marker-trait associations between three genes involved in starch biosynthesis and grain yield. Two starch synthase genes (TraesCS2B03G1238800 and TraesCS2D03G1048800) and a sucrose synthase gene (TraesCS3D03G0024300) were found in regions of QGy.rut-2B.2, QGy.rut-2D.1, and QGy.rut-3D, respectively. These loci and other significantly associated SNP markers found in this study can be used for pyramiding favorable alleles in high-yielding varieties or to improve the accuracy of prediction in genomic selection.