Sequence‐based SNP genotyping in durum wheat

Summary: Marker development for marker-assisted selection in plant breeding is increasingly based on next-generation sequencing (NGS). However, marker development in crops with highly repetitive, complex genomes is still challenging. Here we applied sequence-based genotyping (SBG), which couples AFLP®-based complexity reduction to NGS, for de novo single nucleotide polymorphisms (SNP) marker discovery in and genotyping of a biparental durum wheat population. We identified 9983 putative SNPs in 6372 contigs between the two parents and used these SNPs for genotyping 91 recombinant inbred lines (RILs). Excluding redundant information from multiple SNPs per contig, 2606 (41%) markers were used for integration in a pre-existing framework map, resulting in the integration of 2365 markers over 2607 cM. Of the 2606 markers available for mapping, 91% were integrated in the pre-existing map, containing 708 SSRs, DArT markers, and SNPs from CRoPS technology, with a map-size increase of 492 cM (23%). These results demonstrate the high quality of the discovered SNP markers. With this methodology, it was possible to saturate the map at a final marker density of 0.8 cM/marker. Looking at the binned marker distribution (Figure 2), 63 of the 268 10-cM bins contained only SBG markers, showing that these markers are filling in gaps in the framework map. As to the markers that could not be used for mapping, the main reason was the low sequencing coverage used for genotyping. We conclude that SBG is a valuable tool for efficient, high-throughput and high-quality marker discovery and genotyping for complex genomes such as that of durum wheat

Molecular markers and QTL analysis for grain quality improvement in wheat

Molecular marker technology is playing an increasingly important role in the selection of wheat lines with improved quality attributes. This is due to the identification of molecular markers tightly linked to chromosome regions involved in the control of important quality characteristics such as dough properties, grain hardness, semolina and flour colour, grain protein content and starch composition, which strongly influence wheat end use, and its nutritional and market value. Marker assisted selection (MAS) will increase the efficiency of the breeding process, particularly when phenotyping requires laborious and time-consuming analyses, performed in advanced generations because of the relatively large amount of grain required. Moreover, the implementation of MAS allows the selection of individuals carrying the favourable alleles at the target loci, and also the pyramiding of favourable QTL alleles from different sources and for different traits. This notwithstanding, the progress obtained until now in applying MAS to quality characteristics has been slow compared to other traits

Association mapping for root characteristics in durum wheat

none6noneLI S.; MACCAFERRI M.; SANGUINETI M.C.; CORNETI S.; CHIARI T.; TUBEROSA R.LI S.; MACCAFERRI M.; SANGUINETI M.C.; CORNETI S.; CHIARI T.; TUBEROSA R

Reaction of 111 cultivars of Triticum durum Desf. from some the world’s main genetic pools Soil-borne cereal mosaic virus

One-hundred and eleven cultivars of durum wheat (Triticum durum Desf.) representative of a large portion of the genetic diversity present in the world’s improved durum wheat gene pool were grown two seasons in a field with natural inoculum sources of soil-borne cereal mosaic virus (SBCMV) near Bologna (Italy). The materials were evaluated for resistance on the basis of symptom severity expression and Sbcmv concentration in leaves according to Das (double antibody sandwich) ELISA. Among the cultivars screened, two-year overall means ranged from 0.1 to 3.2 for symptom severity (on a 0 to 4 scale) and from 0.036 to 1.702 for ELISA absorbance values. Thirty-five cultivars showed relatively low ELISA values and very mild symptoms in both seasons. These relatively more resistant entries included cultivar Edmore and twelve of its derivatives, independently bred in Canada, France, Italy and the U.S. Twenty-one entries consistently gave ELISA values and symptom scores higher than that of cultivar Grazia, the susceptible control. Because of their extreme reactions to Sbcmv and wide adaptability, a number of the cultivars tested should prove useful for investigating the existence of pathotypes within SBCMV, and of diverse cultivar responses in regard to Furoviruses until recently considered as belonging to the same species, namely soil-borne wheat mosaic virus (SBWMV) and Chinese wheat mosaic virus (CWMV)