The presented red clover genomic data constitute a resource for improvement through molecular breeding and for comparison to other sequenced plant species.

The genus clover (Trifolium sp.) is one of the most economically important genera in the Fabaceae family. More than 10 species are grown as manure plants or forage legumes. Red clover’s (T. pratense) genome size is one of the smallest in the Trifolium genus, while many clovers with potential breeding value have much larger genomes. Zigzag clover (T. medium) is closely related to the sequenced red clover; however, its genome is approximately 7.5x larger. Currently, almost nothing is known about the architecture of this large genome and differences between these two clover species. We sequenced the T. medium genome (2n = 8x = 64) with ∼23× coverage and managed to partially assemble 492.7 Mbp of its genomic sequence. A thorough comparison between red clover and zigzag clover sequencing reads resulted in the successful validation of 7 T. pratense- and 45 T. medium-specific repetitive elements. The newly discovered repeats led to the set-up of the first partial T. medium karyotype. Newly discovered red clover and zigzag clover tandem repeats were summarized. The structure of centromere-specific satellite repeat resembling that of T. repens was inferred in T. pratense. Two repeats, TrM300 and TrM378, showed a specific localization into centromeres of a half of all zigzag clover chromosomes; TrM300 on eight chromosomes and TrM378 on 24 chromosomes. A comparison with the red clover draft sequence was also used to mine more than 105,000 simple sequence repeats (SSRs) and 1,170,000 single nucleotide variants (SNVs). The presented data obtained from the sequencing of zigzag clover represent the first glimpse on the genomic sequence of this species. Centromeric repeats indicated its allopolyploid origin and naturally occurring homogenization of the centromeric repeat motif was somehow prevented. Using various repeats, highly uniform 64 chromosomes were separated into eight types of chromosomes. Zigzag clover genome underwent substantial chromosome rearrangements and cannot be counted as a true octoploid. The resulting data, especially the large number of predicted SSRs and SNVs, may have great potential for further research of the legume family and for rapid advancements in clover breeding.

Four newly detected accessions of wild barley (Hordeum vulgare ssp. spontaneum) resistant to powdery mildew caused by Blumeria graminis f. sp. hordei were studied with the aim of finding the number of genes/loci conferring the resistance of individual accessions, the type of inheritance of the genes and their relationships to the Mla locus. F 2 populations after crosses between the winter variety 'Tiffany' and four wild barley accessions and use of microsatellite DNA markers were focused on the identification of individual resistance genes/loci by means of their chromosomal locations. In PI466495, one locus conferring powdery mildew resistance was identified in highly significant linkage with the marker Bmac0213. This location is consistent with the known locus Mla on chromosome 1HS. In the other three accessions the resistance was determined by two independent loci. In PI466197, PI466297 and PI466461, one locus was identified on chromosome 1HS and three new loci were revealed on chromosomes 2HS (highly significant linkage with Bmac0134), 7HS (highly significant linkage with Bmag0021) and 7HL (significant linkage with EBmac0755). Our prospective aim is identification of further linked DNA markers and the exact location of the resistance genes on the barley chromosomes.

Dynamics of crop growth and photosynthesis are two main processes that are of major importance for adaptation of plants to their environment. Two experiments were carried out during 2005 and 2006 with sun and shaded barley plants. The results showed that leaf area increased with leaf position on the main stem up to leaf position 5 for sun and leaf position 6 for shaded plants, and then declined towards flag leaves. Air temperature affected leaf appearance, mainly at the beginning of the growing season. A positive correlation between leaf expansion duration (LED) and accumulated temperature sum was measured for both variants, LED linearly increased with temperature sum. Leaf expansion rate (LER) showed a similar dependence on accumulated air temperatures in both light variants. A strong relation was found between soil temperature and LER for the first four leaves of the main stem of shaded plants in 2006. In shaded environment the higher LER was associated with lower accumulated irradiance sum when light restriction supported an increase of leaf elongation and final leaf length.

Red clover (Trifolium pratense) is an important forage plant worldwide. This study was directed to broadening current knowledge of red clover's coding regions and enhancing its utilization in practice by specific reanalysis of previously published assembly. A total of 42,996 genes were characterized using Illumina paired-end sequencing after manual revision of Blast2GO annotation. Genes were classified into metabolic and biosynthetic pathways in response to biological processes, with 7,517 genes being assigned to specific pathways. Moreover, 17,727 enzymatic nodes in all pathways were described. We identified 6,749 potential microsatellite loci in red clover coding sequences, and we characterized 4,005 potential simple sequence repeat (SSR) markers as generating polymerase chain reaction products preferentially within 100-350 bp. Marker density of 1 SSR marker per 12.39 kbp was achieved. Aligning reads against predicted coding sequences resulted in the identification of 343,027 single nucleotide polymorphism (SNP) markers, providing marker density of one SNP marker per 144.6 bp. Altogether, 95 SSRs in coding sequences were analyzed for 50 red clover varieties and a collection of 22 highly polymorphic SSRs with pooled polymorphism information content >0.9 was generated, thus obtaining primer pairs for application to diversity studies in T. pratense. A set of 8,623 genome-wide distributed SNPs was developed and used for polymorphism evaluation in individual plants. The polymorphic information content ranged from 0 to 0.375. Temperature switch PCR was successfully used in single-marker SNP genotyping for targeted coding sequences and for heterozygosity or homozygosity confirmation in validated five loci. Predicted large sets of SSRs and SNPs throughout the genome are key to rapidly implementing genome-based breeding approaches, for identifying genes underlying key traits, and for genome-wide association studies. Detailed knowledge of genetic relationships among breeding material can also be useful for breeders in planning crosses or for plant variety protection. Single-marker assays are useful for diagnostic applications.