Population Genomics Related to Adaptation in Elite Oat Germplasm

Six hundred thirty five oat ( L.) lines and 4561 single-nucleotide polymorphism (SNP) loci were used to evaluate population structure, linkage disequilibrium (LD), and genotype–phenotype association with heading date. The first five principal components (PCs) accounted for 25.3% of genetic variation. Neither the eigenvalues of the first 25 PCs nor the cross-validation errors from = 1 to 20 model-based analyses suggested a structured population. However, the PC and = 2 model-based analyses supported clustering of lines on spring oat vs. southern United States origin, accounting for 16% of genetic variation ( < 0.0001). Single-locus -statistic () in the highest 1% of the distribution suggested linkage groups that may be differentiated between the two population subgroups. Population structure and kinship-corrected LD of = 0.10 was observed at an average pairwise distance of 0.44 cM (0.71 and 2.64 cM within spring and southern oat, respectively). On most linkage groups LD decay was slower within southern lines than within the spring lines. A notable exception was found on linkage group Mrg28, where LD decay was substantially slower in the spring subpopulation. It is speculated that this may be caused by a heterogeneous translocation event on this chromosome. Association with heading date was most consistent across location-years on linkage groups Mrg02, Mrg12, Mrg13, and Mrg24

A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement

Hexaploid oat ( L., 2 = 6 = 42) is a member of the Poaceae family and has a large genome (∼12.5 Gb) containing 21 chromosome pairs from three ancestral genomes. Physical rearrangements among parental genomes have hindered the development of linkage maps in this species. The objective of this work was to develop a single high-density consensus linkage map that is representative of the majority of commonly grown oat varieties. Data from a cDNA-derived single-nucleotide polymorphism (SNP) array and genotyping-by-sequencing (GBS) were collected from the progeny of 12 biparental recombinant inbred line populations derived from 19 parents representing oat germplasm cultivated primarily in North America. Linkage groups from all mapping populations were compared to identify 21 clusters of conserved collinearity. Linkage groups within each cluster were then merged into 21 consensus chromosomes, generating a framework consensus map of 7202 markers spanning 2843 cM. An additional 9678 markers were placed on this map with a lower degree of certainty. Assignment to physical chromosomes with high confidence was made for nine chromosomes. Comparison of homeologous regions among oat chromosomes and matches to orthologous regions of rice ( L.) reveal that the hexaploid oat genome has been highly rearranged relative to its ancestral diploid genomes as a result of frequent translocations among chromosomes. Heterogeneous chromosome rearrangements among populations were also evident, probably accounting for the failure of some linkage groups to match the consensus. This work contributes to a further understanding of the organization and evolution of hexaploid grass genomes

SNP Discovery and Chromosome Anchoring Provide the First Physically-Anchored Hexaploid Oat Map and Reveal Synteny with Model Species

A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources

Changing Trends in the Referral and Timing of Treatment for Congenital Cryptorchidism: A Single-Center Experience from Bosnia and Herzegovina.

Cryptorchidism is the most common male urogenital tract disorder identified at birth. Treatment delays of cryptorchidism may be associated with significant complications such as subfertility and testicular cancer. The currently recommended age for performing orchidopexy is between 6 and 12 months of age and no later than 18 months. The aim of this study was to investigate the trends in the pattern of referral and age of boys at the time of operative treatment of congenital cryptorchidism at the largest tertiary care center in Bosnia and Herzegovina. The study included all boys who underwent orchidopexy for congenital cryptorchidism during two equivalents periods: 2008-2010 and 2015-2017. We assessed the referral age of patients, the age of patients at the time of orchidopexy, laterality of cryptorchidism, position of cryptorchidic testes palpated before surgery, the intraoperative position of cryptorchidic testis, a clinical position of the testis at follow up, and risk factors for late orchidopexy. In total, 324 patients with 386 testes underwent orchidopexy for congenital cryptorchidism during the study periods. Of these patients, 62 received a bilateral orchidopexy (19.1%). Total referral age of patients with congenital cryptorchidism was 23 months (range, 4-74.5 months). Total median age at surgery was 24 months (range, 6-74 months). One hundred and eleven patients (28.8%) underwent surgery at less than the age of 12 months, 136 (35.2%) at less than the age of 18 months, and 250 (64.8%) patients underwent surgery after the age of 18 months. The analysis of the observed two periods (2008-2010 and 2015-2017) showed a statistically significant decrease in the mean referral age and the mean age at surgery over the last 5 years (2015-2017) (p = 0.007 and p = 0.003, respectively). Current guidelines for timely operative treatment for congenital cryptorchidism have not been fully implemented in Bosnia and Herzegovina but a gradual improvement is evident. The main factor contributing to delays in orchidopexy was delayed or neglected referral by referring physicians. Optimizing the time of orchidopexy will require an improved coordination at all levels of pediatric health care to diminish the long-term consequences of cryptorchidism. Retrospective. III

Silencing efficiency of dsRNA fragments targeting Fusarium graminearum TRI6 and patterns of small interfering RNA associated with reduced virulence and mycotoxin production.

Deoxynivalenol (DON) contamination of cereal grains caused by Fusarium head blight may be addressed by future RNA interference (RNAi)-based gene silencing approaches. However, utilizing these approaches will require a greater understanding of the principles that govern RNAi effectiveness in the pathogen Fusarium graminearum. RNAi in higher eukaryotes, including fungi, involves processing double stranded RNA (dsRNA) into small interfering RNA (siRNA) that silence gene expression based on base pair complementarity. This study examined virulence, DON production, and the small RNA (sRNA) populations in response to RNAi-based silencing of TRI6, a transcription factor that positively regulates DON synthesis via control of TRI5 expression. Silencing was accomplished via the expression of transgenes encoding inverted repeats targeting various regions of TRI6 (RNAi vectors). Transgene expression was associated with novel, TRI6-specific siRNAs. For RNAi vectors targeting the majority of TRI6 sequence (~600 bp), a discontinuous, repeatable pattern was observed in which most siRNAs mapped to specific regions of TRI6. Targeting shorter regions (250-350 bp) did not alter the siRNA populations corresponding to that region of TRI6. No phased processing was observed. The 5' base of ~83% of siRNAs was uracil, consistent with DICER processing and ARGONAUTE binding preferences for siRNA. Mutant lines showed TRI6 siRNA-associated reductions of TRI5 expression on toxin inducing media and DON in infected wheat and barley spikes. Shorter RNAi vectors resulted in variable levels of silencing that were less than for the ~600 bp RNAi vector, with a 343 bp RNAi vector targeting the 5' end of TRI6 having the best silencing efficiency. This work identifies efficient shorter region for silencing of TRI6 and describes the patterns of siRNA corresponding to those regions

Allergy Risk Assessment for Newly Expressed Proteins (NEPs) in Genetically Modified (GM) Plants

Based on experience and scientific advancements over the past two decades, a revised approach for the assessment of the allergenic potential of newly expressed proteins (NEPs) in genetically modified (GM) plants is warranted. NEPs are most often not native to the crop genome, and thus regulatory reviews of the safety of GM plants include an assessment of the allergenic potential of NEPs. International standards for the assessment of allergenicity first developed in the mid-1990s required a series of characterization studies to be conducted that are, to some extent, still applicable today to the risk assessment of GM plants, with most modern versions represented in the Codex Alimentarius. This standardized guidance on allergenicity assessments, including the required characterization studies, presented two primary challenges. First, there was (and still is) no defined and accepted model (animal or in vitro) for directly testing allergy potential. Second, bioinformatic analyses were prescribed using thresholds for hazard identification that were neither universal for all allergens nor tested prior to the implementation of requirements into guidance documents. Herein, risk assessment principles are applied to structure the assessment of the allergenic potential of NEPs. This allergy risk assessment is built on a foundation of: 1) identifying hazard by assessing similarity to known allergens, and 2) assessing exposure when a hazard is identified. Supplementary studies such as IgE binding may need to be performed in special cases. These recommended revisions to current approaches to the assessment of allergy potential are designed to ensure a realistic, case-by-case approach, and consider updated molecular biology, genomics, and bioinformatic techniques that were unavailable when earlier allergy risk assessment approaches were established. doi: 10.21423/jrs-v09i1mcclai

A new genetic linkage map of barley (\u3ci\u3eHordeum vulgare\u3c/i\u3e L.) facilitates genetic dissection of height and spike length and angle

Plant height and spike length and angle are important agronomic traits in the production of barley (Hordeum vulgare L.) due to strong correlations with lodging and disease. The objective of this study was to use QTL analysis to identify genetic regions associated with each trait in a recombinant inbred line (RIL) mapping population derived from a cross of Falcon by Azhul. Falcon is a spring six-row hulless feed barley with long spikes displaying obtuse angles, while Azhul is a spring dwarf, six-row hulless food barley with short spikes displaying acute angles. The population was genotyped using SNP, DArT and SSR markers and quantitative trait loci (QTL) were detected on chromosomes 2H (102.8 cM, spikelength), 3H (89.2 cM, plant height and 38.2, spike angle and length), 4H (19.0 cM, spike length), and 5H(106.7 cM, spike angle). In conclusion, we developed a barley genetic map, which incorporated SNP, DArT and SSR markers, for detection of height and spike length and angle QTL. Three spike angle, one spike length and one plant height QTL were novel and by using comparative genomics we identified possible candidate genes involved in gibberellic acid signaling and auxin- and ethylene-responsive pathways. This knowledge can be used to generate suitable markers for barley breeding improvement