Toward the elucidation of cytoplasmic diversity in North American grape breeding programs

Plants have an intriguing tripartite genetic system: Nuclear genome × Mitochondria × Plastids and their interactions may impact germplasm breeding. In grapevine, the study of cytoplasmic genomes has been limited, and their role with respect to grapevine germplasm diversity has yet to be elucidated. In the present study, the results of an analysis of the cytoplasmic diversity among 6073 individuals (comprising cultivars, interspecific hybrids and segregating progenies) are presented. Genotyping by sequencing (GBS) was used to elucidate plastid and mitochondrial DNA sequences, and results were analyzed using multivariate techniques. Single nucleotide polymorphism (SNP) effects were annotated in reference to plastid and mitochondrial genome sequences. The cytoplasmic diversity identified was structured according to synthetic domestication groups (wine and raisin/table grape types) and interspecific-hybridization-driven groups with introgression from North American Vitis species, identifying five cytoplasmic groups and four major clusters. Fifty-two SNP markers were used to describe the diversity of the germplasm. Ten organelle genes showed distinct SNP annotations and effect predictions, of which six were chloroplast-derived and three were mitochondrial genes, in addition to one mitochondrial SNP affecting a nonannotated open reading frame. The results suggest that the application of GBS will aid in the study of cytoplasmic genomes in grapevine, which will enable further studies on the role of cytoplasmic genomes in grapevine germplasm, and then allow the exploitation of these sources of diversity in breeding.     

Genotyping-by-sequencing to remap QTL for type II Fusarium head blight and leaf rust resistance in a wheat–tall wheatgrass introgression recombinant inbred population

Fusarium graminearum Schwabe (Fusarium head blight, FHB) and Puccinia triticina Eriks (leaf rust) are two major fungal pathogens posing a continuous threat to the wheat crop; consequently, identifying resistance genes from various sources is always of importance to wheat breeders. We identified tightly linked single nucleotide polymorphism (SNP) markers for the FHB resistance quantitative trait locus (QTL) Qfhs.pur-7EL and the leaf rust resistance locus Lr19 using genotyping-by-sequencing (GBS) in a wheat–tall wheatgrass introgression-derived recombinant inbred line (RIL) population. One thousand and seven hundred high-confidence SNPs were used to conduct the linkage and QTL analysis. Qfhs.pur-7EL was mapped to a 2.9 cM region containing four markers within a 43.6 cM segment of wheatgrass chromosome 7el₂ that was translocated onto wheat chromosome 7DL. Lr19 from 7el₁ was mapped to a 1.21 cM region containing two markers in the same area, in repulsion. Five lines were identified with the resistance-associated SNP alleles for Qfhs.pur-7EL and Lr19 in coupling. Two SNP markers in the Qfhs.pur-7EL region were converted into PCR-based KASP markers. Investigation of the genetic characteristics of the parental lines of this RIL population indicated that they are translocation lines in two different wheat cultivar genetic backgrounds instead of 7E–7D substitution lines in Thatcher wheat background, as previously reported in the literature.     

Fine‐scale distribution modeling of avian malaria vectors in north‐central Kansas

Infectious diseases increasingly play a role in the decline of wildlife populations. Vector‐borne diseases, in particular, have been implicated in mass mortality events and localized population declines are threatening some species with extinction. Transmission patterns for vector‐borne diseases are influenced by the spatial distribution of vectors and are therefore not uniform across the landscape. Avian malaria is a globally distributed vector‐borne disease that has been shown to affect endemic bird populations of North America. We evaluated shared habitat use between avian malaria vectors, mosquitoes in the genus Culex and a native grassland bird, the Greater Prairie‐Chicken (Tympanuchus cupido), by (1) modeling the distribution of Culex spp. occurrence across the Smoky Hills of north‐central Kansas using detection data and habitat variables, (2) assessing the occurrence of these vectors at nests of female Greater Prairie‐Chickens, and (3) evaluating if shared habitat use between vectors and hosts is correlated with malarial infection status of the Greater Prairie‐Chicken. Our results indicate that Culex occurrence increased at nest locations compared to other available but unoccupied grassland habitats; however the shared habitat use between vectors and hosts did not result in an increased prevalence of malarial parasites in Greater Prairie‐Chickens that occupied habitats with high vector occurrence. We developed a predictive map to illustrate the associations between Culex occurrence and infection status with malarial parasites in an obligate grassland bird that may be used to guide management decisions to limit the spread of vector‐borne diseases.     

Effects of a nonnative, invasive lovegrass on Agave palmeri distribution, abundance, and insect pollinator communities

Nonnative Lehmann lovegrass (Eragrostis lehmanniana) has invaded large areas of the Southwestern United States, and its impact on native plants is not fully understood. Palmer’s agave (Agave palmeri), an important resource for many pollinators, is a key native plant potentially threatened by E. lehmanniana. Understanding potential impacts of E. lehmanniana on A. palmeri is critical for anticipating the future of the desert community where they coexist and for addressing management concerns about associated threatened and endangered species. Our study provides strong indications that E. lehmanniana negatively impacts A. palmeri in several ways. Areas of high E. lehmanniana abundance were associated with significantly lower densities and greater relative frequencies of small A. palmeri, suggesting that E. lehmanniana may exclude A. palmeri. There were no significant differences in species richness, abundance, or community composition when comparing flower associates associated with A. palmeri in areas of high and low E. lehmanniana abundance. However, we did find significantly lower connectedness within the pollination network associated with A. palmeri in areas with high E. lehmanniana abundance. Although E. lehmanniana forms thick stands that would presumably increase fire frequency, there was no significant association between E. lehmanniana and fire frequency. Interestingly, medium to high densities of A. palmeri were associated with areas of greater fire frequency. The complex ramifications of E. lehmanniana invasion for the long-lived A. palmeri and interlinked desert community warrant continued study, as these species are likely to continue to be found in close association due to their similar soil preferences.