A SNP-based genetic dissection of versatile traits in bread wheat (Triticum aestivum L.)

The continuous increase in global population prompts increased wheat production. Future wheat (Triticum aestivum L.) breeding will heavily rely on dissecting molecular and genetic bases of wheat yield and related traits which is possible through the discovery of quantitative trait loci (QTLs) in constructed populations, such as recombinant inbred lines (RILs). Here, we present an evaluation of 92 RILs in a bi-parental RIL mapping population (the International Triticeae Mapping Initiative Mapping Population [ITMI/MP]) using newly generated phenotypic data in 3-year experiments (2015), older phenotypic data (1997–2009), and newly created single nucleotide polymorphism (SNP) marker data based on 92 of the original RILs to search for novel and stable QTLs. Our analyses of more than 15 unique traits observed in multiple experiments included analyses of 46 traits in three environments in the USA, 69 traits in eight environments in Germany, 149 traits in 10 environments in Russia, and 28 traits in four environments in India (292 traits in 25 environments) with 7584 SNPs (292 × 7584 = 2 214 528 data points). A total of 874 QTLs were detected with limit of detection (LOD) scores of 2.01–3.0 and 432 QTLs were detected with LOD > 3.0. Moreover, 769 QTLs could be assigned to 183 clusters based on the common markers and relative proximity of related QTLs, indicating gene-rich regions throughout the A, B, and D genomes of common wheat. This upgraded genotype–phenotype information of ITMI/MP can assist breeders and geneticists who can make crosses with suitable RILs to improve or investigate traits of interest.     

Bibenzyls and dihydroisocoumarins from white salsify (Tragopogon porrifolius subsp. porrifolius)

A phytochemical investigation of three accessions of Tragopogon porrifolius L. subsp. porrifolius (Asteraceae, Lactuceae) yielded three new bibenzyl derivatives, 5,4'-dihydroxy-3-alpha-l-rhamnopyranosyl-(1-->3)-beta-d-xylopyranosyloxybibenzyl, 2-carboxyl-3,4'-dihydroxy-5-beta-d-xylopyranosyloxybibenzyl, tragopogonic acid (2'carboxyl-3',5',4'-trihydroxyphenylethanone) and three dihydroisocoumarin derivatives, including the new natural product 6-O-methylscorzocreticoside I. One of the isolated bibenzyl derivatives is considered to be a precursor to the biosynthesis of dihydroisocoumarins. Structures of new compounds were established by HR mass spectrometry, extensive 1D and 2D NMR spectroscopy, and CD spectroscopy. Moreover, radical scavenging activities of the polyphenolic compounds were measured using the 2,2-diphenyl-1-picrylhydrazyl assay; two of the bibenzyls showed moderate and two of the dihydroisocoumarins showed weak radical scavenging activities. The chemosystematic impact of bibenzyls and dihydroisocoumarins is discussed briefly.     

Molecular markers in management of ex situ PGR – A case study

Worldwide germplasm collections contain about 7.4 million accessions of plant genetic resources for food and agriculture. One of the 10 largest ex situ genebanks of our globe is located at the Leibniz Institute of Plant Genetics and Crop Plant Research in Gatersleben, Germany. Molecular tools have been used for various gene bank management practices including characterization and utilization of the germplasm. The results on genetic integrity of long-term-stored gene bank accessions of wheat (self-pollinating) and rye (open-pollinating) cereal crops revealed a high degree of identity for wheat. In contrast, the out-pollinating accessions of rye exhibited shifts in allele frequencies. The genetic diversity of wheat and barley germplasm collected at intervals of 40 to 50?years in comparable geographical regions showed qualitative rather than a quantitative change in diversity. The inter- and intraspecific variation of seed longevity was analysed and differences were detected. Genetic studies in barley, wheat and oilseed rape revealed numerous QTL, indicating the complex and quantitative nature of seed longevity. Some of the loci identified were in genomic regions that co-localize with genes determining agronomic traits such as spike architecture or biotic and abiotic stress response. Finally, a genome-wide association mapping analysis of a core collection of wheat for flowering time was performed using diversity array technology (DArT) markers. Maker trait associations were detected in genomic regions where major genes or QTL have been described earlier. In addition, new loci were also detected, providing opportunities to monitor genetic variation for crop improvement.     

QTL Identification and Mapping in Soft Spring Wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.) under Controlled Agroecological and Biological Testing Area Conditions with and without Nitrogen Fertilizer

Quantitative trait loci (QTL) of agriculturally valuable traits of soft spring wheat (Triticum aestivum L.) were mapped in two simultaneous and independent experiments that were carried out in different agronomical backgrounds with respect to nitrogen availability (i.e., with and without introduction of a mineral nitrogen fertilizer) in order to reveal the effects of physiological and genetic interaction between the genotype and the environment. In total, 94 QTLs, which determine 31 physiologically and agriculturally important traits, have been identified. The connection between the loci identified and polymorphism by certain traits has been proven. The connection between the trait expression and introduction of the fertilizer has been confirmed by both correlation analysis and the single-factor analysis of variance. The analyses of QTL and correlation, as well as the single-factor analysis of variance, showed that 15 of 31 traits varied confidently. This shows that the expression of these traits depends on the presence of nitrogen nutrition. The data obtained are important for further study of physiological and genetic regulatory mechanisms of expression of the traits that were evaluated in the system of interaction between the genotype and the environment as well as for the marker-assisted selection of wheat.     

Regulation of NKT cells by Ly49: analysis of primary NKT cells and generation of NKT cell line

TCRalphabeta(+)NK1.1(+) (NKT) cells are known to express various NK cell-associated molecules including the Ly49 family of receptors for MHC class I, but its functional significance has been unclear. Here, we examined the expression of Ly49A, C/I and G2 on various NKT cell populations from normal and MHC class I-deficient C57BL/6 mice as well as their responsiveness to alpha-galactosylceramide (alpha-GalCer), a potent stimulator of CD1d-restricted NKT cells. The frequency and the level of Ly49 expression varied among NKT cells from different tissues, and were regulated by the expression of MHC class I and CD1d in the host. Stimulation of various NKT cells with alpha-GalCer suggested that Ly49 expression inversely correlates with the responsiveness of NKT cells to alpha-GalCer. Moreover, alpha-GalCer presented by normal dendritic cells stimulated purified Ly49(-), but not Ly49(+), splenic NKT cells, whereas MHC class I-deficient dendritic cells presented alpha-GalCer to both Ly49(+) and Ly49(-) NKT cells equally well. Therefore, MHC class I on APCs seems to inhibit activation of NKT cells expressing Ly49. To further characterize CD1d-restricted NKT cells, we generated an alpha-GalCer-responsive NKT cell line from thymocytes. The line could only be generated from Ly49(-)NK1.1(+)CD4(+) thymocytes but not from other NKT cell subsets, and it lost expression of NK1.1 and CD4 during culture. Together, these results indicate the functional significance of Ly49 expression on NKT cells.     

Discovery of loci determining pre-harvest sprouting and dormancy in wheat and barley applying segregation and association mapping

Three wheat and two barley populations were studied in order to find loci responsible for dormancy and pre-harvest sprouting. A classical quantitative trait loci analysis was combined with an association mapping approach. Many quantitative trait loci and marker trait associations could be detected on all seven chromosome groups of wheat and on the chromosomes 2H, 3H, 5H, 6H, and 7H of barley. Especially, the known regions on chromosomes 3A and 4A for wheat and 5H for barley were confirmed. Putative functions could be found via a candidate homologues search and via expressed sequence tag annotation. On chromosome 3A, the viviparous1 gene is located which is associated to preharvest sprouting and dormancy. On chromosome 4A, a protein is detected which belongs to the aquaporin family. In barley, an association with the aleurain gene on chromosome 5H was found. The expression of aleurain is regulated by abscisic acid and gibberelic acid. An influence of both hormones on dormancy and pre-harvest sprouting is known. It can be concluded that dormancy and pre-harvest sprouting are very complex traits regulated by multigenes and/or quantitative trait loci.     

Mapping of quantitative trait loci (QTL) associated with activity of disulfide reductase and lipoxygenase in grain of bread wheat <Emphasis Type="Italic">Triticum aestivum</Emphasis> L.

Activity of two enzymes of thiol-disulfide cell metabolism, lipoxygenase (LOX, EC 1.13.11.12) and disulfide-reductase (TPDO, EC 1.8.4.2) was studied in recombinant inbred lines of bread wheat ITMI. Their activity in the caryopsis may be connected with the gluten quality, one of the most important traits significant for breeding. The activity of lipoxygenase under favorable and droughty environmental conditions was shown to be associated with the quantitative trait locus (QTL) located on chromosome 4BS near the structural gene of a subunit of this enzyme. However, no QTL common to this enzyme and any characteristic of gluten quality have been found. Four loci responsible for the activity of disulfide reductase were identified on chromosomes 4A, 5D, 6A, and 7D. Previously, indicators of grain and flour properties, such as elasticity, flour strenght, and grain hardiness were mapped at the same loci. This indicates that the given enzyme participates in the formation of the protein complex upon maturation of wheat grain. The detected QTL can be involved in further genetic studies designed to establish the regularities of gluten formation.     

QTL mapping of bread wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.) grown under controlled conditions of an agroecobiological testing ground

To determine the effects of physiological and genetic interaction between the genotype and environment, QTL (quantitative trait loci) mapping of valuable traits of bread wheat (Triticum aestivum L.) manifesting under controlled conditions of an agroecobiological testing ground has been first carried out. In the course of two experiments, differing from each other only by temperature and illumination regimes and providing the strict control and invariability of other growing parameters, 99 QTLs determining 30 different agronomically important traits have been identified. According to the results of the QTL mapping and a single-factor ANOVA, changes in the temperature and illumination regimes did not influence 21 of 30 studied traits, which remained stable in their manifestation; only nine traits varied under these conditions, which indicates that their manifestation is dependent on changes in these environmental factors. Both statistical approaches used in this study demonstrated complementary results; for each of them, the maximum likelihood criterion was used, statistical significance was determined, and significance of results was evaluated. The significance of a correlation between the identified QTLs and the polymorphism of individual traits studied was assessed using the threshold value of LOD (logarithm of odds) score. In addition, QTL analysis allowed a block structure of the T. aestivum genome to be revealed, the percentage of a phenotypic variability determined by each of the identified QTLs to be calculated, and the determination of which of the parents donated individual QTL alleles. The obtained results can be used for the further study of the physiological and genetic mechanisms of realization of traits evaluated within the framework of the “genotype–environment” interaction and also for the marker-assisted breeding of wheat.     

Molecular mapping of genomic regions associated with wheat seedling growth under osmotic stress

A quantitative trait loci (QTL) approach was applied to dissect the genetic control of the common wheat seedling response to osmotic stress. A set of 114 recombinant inbred lines was subjected to osmotic stress from the onset of germination to the 8^th day of seedling development, induced by the presence of 12 % polyethylene glycol. Root, coleoptile and shoot length, and root/shoot length ratio were compared under stress and control conditions. In all, 35 QTL mapping to ten chromosomes, were identified. Sixteen QTL were detected in controls, 17 under stressed conditions, and two tolerance index QTL were determined. The majority of the QTL were not stress-specific. In regions on five chromosome arms (1AS, 1BL, 2DS, 5BL and 6BL) the QTL identified under stress co-mapped with QTL affecting the same trait in controls, and these were classified as seedling vigour QTL, in addition to those expressed in controls. Tolerance-related QTL were detected on four chromosome arms. A broad region on chromosome 1AL, including five QTL, with a major impact of the gene Glu-A1 (LOD 3.93) and marker locus Xksuh9d (LOD 2.91), positively affected root length under stress and tolerance index for root length, respectively. A major QTL (LOD 3.60), associated with marker locus Xcdo456a (distal part of chromosome arm 2BS) determined a tolerance index for shoot length. Three minor QTL (LOD < 3.0) for root length and root/shoot length ratio under osmotic stress were identified in the distal parts of chromosome arms 6DL (marker locus Xksud27a) and 7DL (marker locus Xksue3b). Selecting for the favourable alleles at marker loci associated with the detected QTL for growth traits may represent an efficient approach to enhance the plants’ ability to maintain the growth of roots, coleoptile and shoots in drought-prone soils at the critical early developmental stages.