Grain yield and semolina quality traits are essential selection criteria in durum wheat breeding. However, high phenotypic screening costs limit selection to relatively few breeding lines in late generations. This selection paradigm confers relatively low selection efficiency due to the advancement of undesirable lines into expensive yield trials for grain yield and quality trait testing. Marker-aided selection can enhance selection efficiency, especially for traits that are difficult or costly to phenotype. The aim of this study was to identify major quality trait quantitative trait loci (QTL) for marker-assisted selection (MAS) and to explore potential application of genomic selection (GS) in a durum wheat breeding program. In this study, genome-wide association mapping was conducted for five quality traits using 1184 lines from the North Dakota State University (NDSU) durum wheat breeding program. Several QTL associated with test weight, semolina color, and gluten strength were identified. Genomic selection models were developed and forward prediction accuracies of 0.27 to 0.66 were obtained for the five quality traits. Our results show the potential for grain and semolina quality traits to be selected more efficiently through MAS and GS with further refinement. Considerable opportunity exists to extend these techniques to other traits such as grain yield and agronomic characteristics, further improving breeding efficiency in durum cultivar development. Durum wheat (Triticum turgidum var. durum, 2n = 4x = 28, AABB), one of the first domesticated crops, is a staple food crop with an annual global production of

An induced mutation of the common wheat (2n = 6x = 42, AABBDD genomes) cultivar ‘Fidel’ has been shown to provide resistance to the imidazolinone class of herbicides. This class of herbicide gives broad-spectrum weed control including the weedy relative of wheat, jointed goatgrass (2n = 4x = 28, CCDD genomes). Because wheat and jointed goatgrass share a common genome, genes present on the D genome may transfer between the two species as a result of natural hybridization and selective pressures. Our objectives were to determine which genome of common wheat contained the herbicide resistance gene in the mutated Fidel and to genetically map its position. We investigated the chromosomal location of this gene using both durum (2n = 4x = 28, AABB genomes) and common wheat (6x) backgrounds. From crosses of durum wheat genotypes as the recurrent parent with mutated Fidel (cv. 9804, resistant), only BC1plants containing chromosome 6D (inherited from cv. 9804) were resistant to applications of labeled rates of imazamox, an imidazolinone herbicide. No other D-genome chromosome was absolutely associated with herbicide resistance. To confirm this chromosomal location and genetically map the position of this gene, two populations of F3families from the cross of cv. 9804 to the common wheat cultivars ‘Cashup’ and ‘Madsen’ were screened for reaction to imazamox, followed by genetic mapping with microsatellite markers. Two linked microsatellite markers were associated with the resistance trait, and one of them,Xgdm127, was located to chromosome 6D using aneuploid stocks, confirming the location of this gene on 6D. These results indicate that this resistance gene is in the genome that common wheat shares with jointed goatgrass. Therefore, imidazolinone-resistant wheat will need to be carefully managed to minimize the occurrence and spread of resistant jointed goatgrass, whether such plants arise because of hybridization with resistant common wheat or by independent mutation, a frequent occurrence with this herbicide class.

Mutation of the gene coding for the granule bound starch synthase (waxy protein) leads to reduced amylose content in cereal endosperm. Durum wheat (Triticum turgidum L. var. durum) has one waxy locus in each of its two genomes. Full waxy durum wheat is produced when both genomes carry the waxy null alleles. When only one locus is mutated, partial waxy durum wheat is obtained. Partial and full waxy near‐isogenic lines of durum wheat developed by a breeding program were analyzed as to their quality characteristics. Amylose was largely eliminated in full waxy lines; however, no reduction in amylose content was detected in partial waxy lines. The waxy mutation did not affect grain yield, kernel size, or kernel hardness. Full waxy durum lines had higher kernel ash content, α‐amylase activity, and a unique nonvitreous kernel appearance. Protein quality, as evaluated by SDS microsedimentation value, gluten index, and wet gluten was slightly lower in the full waxy lines than in the other genotypes. However, comparisons with current cultivars indicated that protein quality of all derived lines remained in the range of strong gluten cultivars. Semolina yield was lowered by the waxy mutations due to lower friability that resulted in less complete separation of the endosperm from the bran. Waxy semolina was more sensitive to mechanical damage during milling, but modified tempering and milling conditions may limit the damage. Overall, quality characteristics of waxy durum grain were satisfactory and suitable for application testing.

Interspecific hybridization can be considered an accelerator of evolution, otherwise a slow process, solely dependent on mutation and recombination. Upon interspecific hybridization, several novel interactions between nuclear and cytoplasmic genomes emerge which provide additional sources of diversity. The magnitude and essence of intergenomic interactions between nuclear and cytoplasmic genomes remain unknown due to the direction of many crosses. This study was conducted to address the role of nuclear-cytoplasmic interactions as a source of variation upon hybridization. Wheat (Triticum aestivum) alloplasmic lines carrying the cytoplasm of Aegilops mutica along with an integrated approach utilizing comparative quantitative trait locus (QTL) and epigenome analysis were used to dissect this interaction. The results indicate that cytoplasmic genomes can modify the magnitude of QTL controlling certain physiological traits such as dry matter weight. Furthermore, methylation profiling analysis detected eight polymorphic regions affected by the cytoplasm type. In general, these results indicate that novel nuclear-cytoplasmic interactions can potentially trigger an epigenetic modification cascade in nuclear genes which eventually change the genetic network controlling physiological traits. These modified genetic networks can serve as new sources of variation to accelerate the evolutionary process. Furthermore, this variation can synthetically be produced by breeders in their programs to develop epigenomic-segregating lines.