Abstract Albinism is a large group of disorders characterized by a loss of pigment in ectoderm-derived tissues – most noticeably impacting the skin, hair, and eyes. Albinism is categorized as either syndromic or non-syndromic. Syndromic albinisms include a wide range of disorders with mutations impacting not just pigmentation but other cellular functions. These include, non-exclusively, melanogenesis disorders, endosome trafficking disorders like lysosomal storage disorders, and cell migration disorders. Mutations leading to syndromic albinisms can cause multi-organ system symptoms due to broad disruption lysosome related organelles (LROs) function. Various genetic mutations impact biogenesis, cell maturation, or trafficking at different stages which can lead to a range of severity. Syndromic albinisms also present with different combinations of symptoms depending on the impacted organelles; including oculocutaneous albinism (OCA) (melanosomes), blood diathesis (platelet dense granules), pulmonary fibrosis (lamellar bodies), or chronic inflammation (multiple cellular sources). Animal models for these multisymptomatic complex disorders are needed to understand the effects on systemic health. One such area of interest is in gut health of those with syndromic albinism. Shared inflammatory patterns of syndromic albinisms like Hermansky-Pudlak Syndromes (HPS) and Inflammatory Bowel Disease (IBD) are well studied, with animal models of HPS jointly used to study patterns of inflammation in IBD. However, the impact of this shared gastrointestinal inflammation on the gut microbiome remains unexplored. Using a spontaneously identified mutant family of threespine stickleback fish, we characterize phenotypes consistent with oculocutaneous albinism and vision impairment and demonstrate shared features of gut health to IBD extend from inflammation to the gut microbiome. We argue syndromic albinism models should be explored as models to study the gut microbiome in addition to inflammatory phenotypes in IBD, and importantly, be used to test microbial/dietary interventions for both IBD and syndromic albinisms.
Abstract Fusarium head blight (FHB), primarily caused by Fusarium graminearum in North America, is a devastating disease in bread wheat (Triticum aestivum L.). The characteristic mycotoxin production and reduced grain fill cause several million metric tons of annual crop and economic losses. Exome capture-generated single nucleotide polymorphisms (SNPs) from 269 winter wheat breeding lines and cultivars representing most U.S. wheat-growing regions, were associated with FHB resistance using a genome-wide association study (GWAS). The panel was evaluated for FHB symptoms in the Rocky Ford FHB nursery (Manhattan, KS) across three field seasons. Significant variation was observed for FHB incidence (INC, %), area under the disease progress curve (AUDPC), Fusarium-damaged kernels (FDK, %), and deoxynivalenol (DON, ppm). Data analysis revealed significant FHB disease trait correlations (r = 0.32–0.70) across years and moderate broad-sense heritability (H2) estimates (0.65–0.74). We identified 22 significant loci representing priority breeding targets combating FHB damage. Many loci reside within proximity to previously identified native quantitative trait loci (QTL). A 1BL haplotype from the soft winter wheat cultivar ‘Jamestown’ reduced AUDPC and FDK by 25% and DON by 18%, demonstrating FHB resistance in an environment different from its native environment. We developed KASP assays to identify this resistance haplotype, and five other target SNPs for future incorporation in breeding pipelines increasing FHB resistance. Our findings highlight breeding progress demonstrated by the increased frequency of many resistant alleles in adapted varieties and breeding lines and emphasizes pyramiding native FHB resistance regions as the next step to prevent FHB losses.
Abstract There has been an exponential increase in the development of technologies that have offered unprecedented opportunities to unravel the genetic underpinnings of complex traits. However, despite the progress and availability of tools, there are still several challenges to overcome, such as the development of a unified framework that facilitates downstream analysis. To address this challenge, we present IDEAL-GENOM (Integrated Downstream Evaluation And anaLysis toolkit for GENOMic data), a Python-based wrapper designed to streamline the analytical workflow commonly implemented in binary (case-control) genome-wide association studies (GWAS). IDEAL-GENOM integrates widely used tools such as PLINK, GCTA, and bcftools along with custom-developed functionalities, enabling reproducible results through parameter sharing. IDEAL-GENOM provides a simplified framework for quality control (QC), GWAS, and downstream analysis that will enable beginners and advanced users to leverage the built-in functionalities to perform GWAS analysis for complex traits with binary outcomes. IDEAL-GENOM is a customizable tool that enables users to efficiently analyze genotyping data with reproducible QC, post-imputation, and GWAS pipelines.
Abstract Apicomplexan parasites of insects represent a largely unexplored branch of the tree of life. Their small size and lack of informative phenotypic traits can obscure their diversity and many lineage-specific adaptations to different host species. To better understand how these parasites have evolved, we have sequenced and annotated the genome of a neogregarine parasite of moths in the family Noctuidae, including Helicoverpa armigera. This parasite, which we term Helicoverpa-infecting Ophryocystis, has a tiny 8 Megabase genome with only 2,500 predicted protein-coding genes. Using phylogenomic methods, we placed it as the closest currently sequenced relative to Ophryocystis elektroscirrha and its sister lineage, both of which infect milkweed butterflies (Lepidoptera: Nymphalidae). We also explored the conservation of gene families, with a specific focus on the evolution of the ATPase gene family, as this is thought to be reduced in other Ophryocystis lineages. We found that our newly sequenced lineage also lacks any sodium pump ATPases, while all other types are conserved. Our results demonstrate the utility of applying modern genomic approaches to gaining insights into the evolution of insect-infecting Apicomplexa, but also shows that much remains to be discovered.
Abstract Southern stem canker (SSC), caused by Diaporthe aspalathi, is a major soybean disease causing yield losses of up to 80%. Genetic resistance is the most effective and sustainable strategy for managing SSC. “Tracy-M” is a cultivar with broad resistance to D. aspalathi isolates; however genomic location of the resistance is unknown. To determine the genetic basis of SSC resistance in Tracy-M and its derived progeny, two Tracy-M-derived lines, D85-10404 and D85-10412, were each crossed with a common susceptible parent, G81-2057, to develop recombinant inbred line (RIL) populations. Quantitative Trait Locus (QTL) sequencing (QTL-seq) and composite interval mapping (CIM) identified a common major QTL on chromosome (Chr) 2 in both lines corresponding to Rdm1 locus defined from a previous genetic study. Additionally, second QTL located on Chr 17 (Rdm2 locus) was only detected in the D85-10412-derived RIL population. To validate Tracy-M-derived resistance, an F2:3 population from G00-3213 × Tracy-M was developed. Bulked segregant analysis (BSA) and CIM identified a major QTL on Chr 14, overlapping the previously reported Rdm3 locus in “Crockett” and PI 398469, while Rdm1 was not detected, suggesting genetic background effects. Kompetitive allele-specific PCR (KASP) markers were developed to facilitate selection of Rdm1, Rdm2, and Rdm3 resistance alleles in soybean breeding programs.
