Wheat streak mosaic (WSM), a viral disease affecting cereals and grasses, causes substantial losses in crop yields. Wheat streak mosaic virus (WSMV) is the main causal agent of the complex, but mixed infections with Triticum mosaic virus (TriMV) and High plains wheat mosaic emaravirus (HPWMoV) were reported as well. Although resistant varieties are effective for the disease control, a WSMV resistance-breaking isolate and several potential resistance-breaking isolates have been reported, suggesting that viral populations are genetically diverse. Previous phylogenetic studies of WSMV were conducted by focusing only on the virus coat protein (CP) sequence, while there is no such study for either TriMV or HPWMoV. Here, we studied the genetic variation and evolutionary mechanisms of natural populations of WSM-associated viruses mainly in Kansas fields and fields in some other parts of the Great Plains using high-throughput RNA sequencing. In total, 28 historic and field samples were used for total RNA sequencing to obtain full genome sequences of WSM-associated viruses. Field survey results showed WSMV as the predominant virus followed by mixed infections of WSMV + TriMV. Phylogenetic analyses of the full genome sequences demonstrated that WSMV Kansas isolates are widely distributed in sub-clades. In contrast, phylogenetic analyses for TriMV isolates showed no significant diversity. Recombination was identified as the major evolutionary force of WSMV and TriMV variation in KS fields, and positive selection was detected in some encoding genomic regions in the genome of both viruses. Furthermore, the full genome sequence of a second Kansas HPWMoV isolate was reported. Here, we also identified previously unknown WSMV isolates in the Great Plains sharing clades and high nucleotide sequence similarities with Central Europe isolates. The findings of this study will provide more insights into the genetic structure of WSM-associated viruses and, in turn, help in improving strategies for disease management.
In areas of the Pacific Northwest (PNW), snow mold, a fungal disease with multiple causal agents, can have severe impacts on winter wheat (Triticum aestivum L. subsp. aestivum) yields. Growing tolerant varieties is the best option to manage the disease; however, genetic diversity for the trait is limited in local varieties. The winter wheat
A doubled haploid mapping population was developed from a cross between the hard red winter wheat (Triticum aestivum L. subsp. aestivum) landrace PI 173438 and WA 8137, a soft white winter wheat breeding line developed by the Washington State University winter wheat breeding program in Pullman, WA. The PI 173438/WA 8137 (Reg. no. MP‐16, NSL 543858 MAP) population consists of 437 individuals, with 358 of these individuals used to identify quantitative trait loci associated with snow mold (Typhula spp.) tolerance in PI 173438. Genotypic information was gathered on these individuals using genotype‐by‐sequencing and processed using a pipeline developed by the USDA Eastern Regional Small Grains Genotyping Laboratory. Twenty‐three linkage groups covering the whole genome with groups for the long and short arms of chromosomes 3D and 7D were constructed using 4,029 single nucleotide polymorphisms from the sequenced individuals. Quantitative trait loci associated with snow mold tolerance and snow mold recovery attributed to PI 173438 were successfully identified in this population. PI 173438 has also been used to identify other traits associated with snow mold tolerance, such as freezing tolerance and carbohydrate reserves, and has been important in research investigating dwarf and common bunt. This population may continue to expand current knowledge in these areas, and, given the landrace status of PI 173438, the population may be useful in identifying other novel traits of interest.
A mapping population (Reg. no. MP-15, NSL 540708 MAP) composed of a cross between the soft white common winter wheat (Triticum aestivum L. subsp. aestivum) 'Brundage' (PI 599193) and the soft white club winter wheat (T. aestivum L. subsp. compactum) 'Coda' (PI 594372) was developed to maximize diversity within the soft white market class. The population comprises 268 F 6:7 lines developed through single seed descent. The genetic linkage map consists of 2,144 DNA markers and is assigned to 32 linkage groups covering all chromosomes except 1D. This population was initially developed to determine additional markers linked to the Pch1 gene in wheat. It has further been used to identify quantitative trait loci (QTL) associated with resistance to other diseases such as Cephalosporium stripe (caused by Cephalosporium gramineum) and stripe rust (caused by Puccinia striiformis Westend. f. sp. tritici Erikss). The mapping population has also been used for identification of DNA markers associated with freezing tolerance, end-use quality, and the compactum locus.From the differences in traits between the parental lines, the Coda/Brundage population provides the opportunity for further inquiry into the genes behind the identified QTL. The parents have only been phenotypically screened for a limited number of traits, and further screening may identify more polymorphic traits which the population can be used to map. It can also serve as a validation population for marker-trait associations identified in other populations or other genetic studies such as recombination frequency.
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