Total white blood cell (WBC) and neutrophil counts are lower among individuals of African descent due to the common African-derived “null” variant of the Duffy Antigen Receptor for Chemokines (DARC) gene. Additional common genetic polymorphisms were recently associated with total WBC and WBC sub-type levels in European and Japanese populations. No additional loci that account for WBC variability have been identified in African Americans. In order to address this, we performed a large genome-wide association study (GWAS) of total WBC and cell subtype counts in 16,388 African-American participants from 7 population-based cohorts available in the Continental Origins and Genetic Epidemiology Network. In addition to the DARC locus on chromosome 1q23, we identified two other regions (chromosomes 4q13 and 16q22) associated with WBC in African Americans (P

In species with large and complex genomes such as conifers, dense linkage maps are a useful for supporting genome assembly and laying the genomic groundwork at the structural, populational and functional levels. However, most of the 600+ extant conifer species still lack extensive genotyping resources, which hampers the development of high-density linkage maps. In this study, we developed a linkage map relying on 21,570 SNP makers in Sitka spruce (Picea sitchensis [Bong.] Carr.), a long-lived conifer from western North America that is widely planted for productive forestry in the British Isles. We used a single-step mapping approach to efficiently combine RAD-Seq and genotyping array SNP data for 528 individuals from two full-sib families. As expected for spruce taxa, the saturated map contained 12 linkages groups with a total length of 2,142 cM. The positioning of 5,414 unique gene coding sequences allowed us to compare our map with that of other Pinaceae species, which provided eviden..., The data included in this dataset is genotypic data for two full-sib families of Sitka spruce (Picea sitchensis) in the United Kingdom and resulting linkage maps for the species. Samples for DNA extraction and genotyping were collected from two full-sib genetic field trials as described in the accompanying publication. A SNP Chip array was developed for this work using exome capture. A subset of the samples had been genotyped using RAD Seq from a previous project (Fuentes-Utrilla et al 2017). The dataset includes information on the SNP array developed for the project and genotype data that has been filtered for missingness and minor allele frequency. Final results are in the form of linkage maps stored in csv files. Further information on collection methods and processing are detailed in the accompanying manuscript and scripts for data processing are available on GitHub (https://github.com/HayleyTumas/SitkaLinkageMap)., All files should be able to be opened using open access, freely available software. All tabular data are CSV or text files for the larger genotype data files. Code files are stored as bash script and can be opened using any text editor or in .R files that can be opened using the freely available R software., File generated 01-17-2024 by Hayley Tumas

#####GENERAL INFORMATION#####

Title: High-density genetic linkage mapping in Sitka spruce advances the integration of genomic resources in conifers

This is data and code accompanying the publication "High-density genetic linkage mapping in Sitka spruce advances the integration of genomic resources in conifers" in G3 (Tumas et al. 2024, Accepted, DOI pending).

PROJECT: The project developed a high-density genetic linkage map for Sitka spruce using genotype data for two full sib families from the UK Sitka spruce breeding population. Samples were genotyped using both a SNP array developed for the project and RAD-Seq. These two genotype datasets were used separately to generate genetic maps and together in a single combined map using the software LepMap-3. This combined genetic map (RADChip map) was used along with a genetic map for white spruce (Pavy et al 2017) to create an integrated species map. The data includes information on the SNP arra...

Analysis of genomic variation among related populations can sometimes reveal distinct species that were previously undescribed due to similar morphological appearances, and close examination of such cases can provide much insight regarding speciation. Genomic data can also reveal the role of reticulated evolution in differentiation and speciation. White-breasted nuthatches (Sitta carolinensis) are widely distributed North American songbirds that are currently classified as a single species but have been suspected to represent a case of cryptic speciation. Previous genetic analyses suggested four divergent groups, but it was unclear whether these represented multiple reproductively isolated species. Using extensive genomic sampling of over 350 white-breasted nuthatches from across North America and a new chromosome-level reference genome, we asked if white-breasted nuthatches are comprised of multiple species and whether introgression has occurred between divergent populations. Genomic variation of over 300,000 loci revealed four highly differentiated populations (Pacific, n = 45; Eastern, n = 23; Rocky Mountains North, n = 138; and Rocky Mountains South, n = 150) with geographic ranges that are adjacent. We observed a moderate degree of admixture between Rocky Mountain populations but only a small number of hybrids between the Rockies and the Eastern population. The rarity of hybrids together with high levels of differentiation between populations is supportive of populations having some level of reproductive isolation. Between populations, we show evidence for introgression from a divergent ghost lineage of white-breasted nuthatches into the Rocky Mountains South population, which is otherwise closely related to Rocky Mountains North. We conclude that white-breasted nuthatches are best considered at least 3 species and that ghost lineage introgression has contributed to differentiation between the two Rocky Mountain populations. White-breasted nuthatches provide a dramatic case of morphological similarity despite high genomic differentiation, and the varying levels of reproductive isolation among the four groups provide an example of the speciation continuum.

The data release details the samples, methods, and raw data used to generate high-quality genome assemblies for greater sage-grouse (Centrocercus urophasianus), white-tailed ptarmigan (Lagopus leucura), and trumpeter swan (Cygnus buccinator). The raw data have been deposited in the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI), the authoritative repository for public biological sequence data, and are not included in this data release. Instead, the accessions that link to those data via the NCBI portal (www.ncbi.nlm.nih.gov) are provided herein. The release consists of a single file, sample.metadata.txt, which maps NCBI accessions to the samples sequenced and the different types of sequencing performed to generate the assemblies and annotate their gene features.

The geographic expansion of chronic wasting disease (CWD) in U.S. white-tailed deer (Odocoileus virginianus) has been largely unabated by best management practices, diagnostic surveillance, and depopulation of positive herds. Using a custom Affymetrix Axiom® single nucleotide polymorphism (SNP) array, we demonstrate that both differential susceptibility to CWD, and natural variation in disease progression, are moderately to highly heritable ( among farmed U.S. white-tailed deer, and that loci other than PRNP are involved. Genome-wide association analyses using 123,987 quality filtered SNPs for a geographically diverse cohort of 807 farmed U.S. white-tailed deer (n = 284 CWD positive; n = 523 CWD non-detect) confirmed the prion gene (PRNP; G96S) as a large-effect risk locus (P-value < 6.3E-11), as evidenced by the estimated proportion of phenotypic variance explained (PVE ≥ 0.05), but also demonstrated that more phenotypic variance was collectively explained by loci other than PRNP. Genomic best linear unbiased prediction (GBLUP; n = 123,987 SNPs) with k-fold cross validation (k = 3; k = 5) and random sampling (n = 50 iterations) for the same cohort of 807 farmed U.S. white-tailed deer produced mean genomic prediction accuracies ≥ 0.81; thereby providing the necessary foundation for exploring a genomically-estimated CWD eradication program.

Gene-level analysis of ImmunoChip or genome-wide association studies (GWAS) data has not been previously reported for systemic sclerosis (SSc, scleroderma). The objective of this study was to analyze genetic susceptibility loci in SSc at the gene level and to determine if the detected associations were shared in African-American and White populations, using data from ImmunoChip and GWAS genotyping studies. The White sample included 1833 cases and 3466 controls (956 cases and 2741 controls from the US and 877 cases and 725 controls from Spain) and the African American sample, 291 cases and 260 controls. In both Whites and African Americans, we performed a gene-level analysis that integrates association statistics in a gene possibly harboring multiple SNPs with weak effect on disease risk, using Versatile Gene-based Association Study (VEGAS) software. The SNP-level analysis was performed using PLINK v.1.07. We identified 4 novel candidate genes (STAT1, FCGR2C, NIPSNAP3B, and SCT) significantly associated and 4 genes (SERBP1, PINX1, TMEM175 and EXOC2) suggestively associated with SSc in the gene level analysis in White patients. As an exploratory analysis we compared the results on Whites with those from African Americans. Of previously established susceptibility genes identified in Whites, only TNFAIP3 was significant at the nominal level (p = 6.13x10-3) in African Americans in the gene-level analysis of the ImmunoChip data. Among the top suggestive novel genes identified in Whites based on the ImmunoChip data, FCGR2C and PINX1 were only nominally significant in African Americans (p = 0.016 and p = 0.028, respectively), while among the top novel genes identified in the gene-level analysis in African Americans, UNC5C (p = 5.57x10-4) and CLEC16A (p = 0.0463) were also nominally significant in Whites. We also present the gene-level analysis of SSc clinical and autoantibody phenotypes among Whites. Our findings need to be validated by independent studies, particularly due to the limited sample size of African Americans.

Biological introductions are unintended “natural experiments” that provide unique insights into evolutionary processes. Invasive phytophagous insects are of particular interest to evolutionary biologists studying adaptation, as introductions often require rapid adaptation to novel host plants. However, adaptive potential of invasive populations may be limited by reduced genetic diversity—a problem known as the “genetic paradox of invasions”. One potential solution to this paradox is if there are multiple invasive waves that bolster genetic variation in invasive populations. Evaluating this hypothesis requires characterizing genetic variation and population structure in the invaded range. To this end, we assemble a reference genome and describe patterns of genetic variation in the introduced white pine sawfly, Diprion similis. This species was introduced to North America in 1914, where it has rapidly colonized the thin-needled eastern white pine (Pinus strobus), making it an ideal invasion system for studying adaptation to novel environments. To evaluate evidence of multiple introductions, we generated whole-genome resequencing data for 64 D. similis females sampled across the North American range. Both model-based and model-free clustering analyses supported a single population for North American D. similis. Within this population, we found evidence of isolation-by-distance and a pattern of declining heterozygosity with distance from the hypothesized introduction site. Together, these results support a single-introduction event. We consider implications of these findings for the genetic paradox of invasion and discuss priorities for future research in D. similis, a promising model system for invasion biology. Methods Full methods on how this data was prepared and processed can be found at the linked publication. In brief: Raw genetic material was collected from larval tissue from insects and extracted using Qiagen kits. DNA libraries were prepared using KAPA HyperPrep kits and was then sequenced on NovaSeq 6000 S4 flowcell. vcftools and ANGSD programs were used to prepare the sam and beagle files respectively. See the paper methods for more details.

Results of the gene-level analyses for known genes associated with risk of SSc in Whites and African Americans, based on ImmunoChip.

Genes most significant (at p

Comparison of novel candidate genes (at p

As plate tectonics pushed Antarctica into a polar position, by ~34 million years ago, the continent and its surrounding Southern Ocean (SO) became geographically and thermally isolated by the Antarctic Circumpolar Current. Terrestrial and marine glaciation followed, resulting in extinctions as well as the survival and radiation of unique flora and fauna. The notothenioid fish survived and arose from a common ancestral stock into tax with 120 species that dominates today's SO fish fauna. The Notothenioids evolved adaptive traits including novel antifreeze proteins for survival in extreme cold, but also suffered seemingly adverse trait loss including red blood cells in the icefish family, and the ability to mount cellular responses to mitigate heat stress ? otherwise ubiquitous across all life. This project aims to understand how the notothenoid genomes have changed and contributed to their evolution in the cold. The project will sequence, analyze and compare the genomes of two strategic pairs of notothenioid fishes representing both red-blooded and white-blooded species. Each pair will consist of one Antarctic species and one that has readapted to the temperate waters of S. America or New Zealand. The project will also compare the Antarctic species genomes to a genome of the closet non-Antarctic relative representing the temperate notothenioid ancestor. The work aims to uncover the mechanisms that enabled the adaptive evolution of this ecologically vital group of fish in the freezing Southern Ocean, and shed light on their adaptability to a warming world. The finished genomes will be made available to promote and advance Antarctic research and the project will host a symposium of Polar researchers to discuss the cutting edge developments regarding of genomic adaptations in the polar region.

Despite subzero, icy conditions that are perilous to teleost fish, the fish fauna of the isolated Southern Ocean (SO) surrounding Antarctica is remarkably bountiful. A single teleost group - the notothenioid fishes - dominate the fauna, comprising over 120 species that arose from a common ancestor. When Antarctica became isolated and SO temperatures began to plunge in early Oligocene, the prior temperate fishes became extinct. The ancestor of Antarctic notothenioids overcame forbidding polar conditions and, absent niche competition, it diversified and filled the SO. How did notothenioids adapt to freezing environmental selection pressures and achieve such extraordinary success? And having specialized to life in chronic cold for 30 myr, can they evolve in pace with today's warming climate to stay viable? Past studies of Antarctic notothenioid evolutionary adaptation have discovered various remarkable traits including the key, life-saving antifreeze proteins. But life specialized to cold also led to paradoxical trait changes such as the loss of the otherwise universal heat shock response, and of the O2-transporting hemoglobin and red blood cells in the icefish family. A few species interestingly regained abilities to live in temperate waters following the escape of their ancestor out of the freezing SO.

This proposed project is the first major effort to advance the field from single trait studies to understanding the full spectrum of genomic and genetic responses to climatic and environmental change during notothenioid evolution, and to evaluate their adaptability to continuing climate change. To this end, the project will sequence the genomes of four key species that embody genomic responses to different thermal selection regimes during notothenioids' evolutionary history, and by comparative analyses of genomic structure, architecture and content, deduce the responding changes. Specifically, the project will (i) obtain whole genome assemblies of the red-blooded T. borchgrevinki and the S. American icefish C. esox; (ii) using the finished genomes from (i) as template, obtain assemblies of the New Zealand notothenioid N. angustata, and the white-blooded icefish C. gunnari, representing a long (11 myr) and recent (1 myr) secondarily temperate evolutionary history respectively. Genes that are under selection in the temperate environment but not in the Antarctic environment can be inferred to be directly necessary for that environment and the reverse is also true for genes under selection in the Antarctic but not in the temperate environment. Further, genes important for survival in temperate waters will show parallel selection between N. angustata and C. esox despite the fact that the two fish left the Antarctic at far separated time points. Finally, gene families that expanded due to strong selection within the cold Antarctic should show a degradation of duplicates in the temperate environment. The project will test these hypotheses using a number of techniques to compare the content and form of genes, the structure of the chromosomes containing those genes, and through the identification of key characters, such as selfish genetic elements, introns, and structural variants.

a) The total number of somatic genome changes in the samples along with the cell type, and the sex and race of the donors. b) The median values and P-values for Mann-Whitney tests for pairwise comparisons of the somatic genome changes between the sets of clones obtained from White and African American donors. (XLSX)

Many well-powered genome-wide association studies have identified genetic determinants of self-reported smoking behaviors and measures of nicotine dependence, but most have not considered the role of structural variants, such as copy number variation (CNVs), influencing these phenotypes. Here, we included 2,889 African American and 6,187 non-Hispanic White subjects from the COPDGene cohort (http://www.copdgene.org) to carefully investigate the role of polymorphic CNVs across the genome on various measures of smoking behavior. We identified a CNV component (a hemizygous deletion) on chromosome 3p26.1 associated with two quantitative phenotypes related to smoking behavior among African Americans. This polymorphic hemizygous deletion is significantly associated with pack-years and cigarettes smoked per day among African American subjects in the COPDGene study. We sought evidence of replication in African Americans from the population based Atherosclerosis Risk in Communities (ARIC) study. While we observed similar CNV counts, the extent of exposure to cigarette smoking among ARIC subjects was quite different and the smaller sample size of heavy smokers in ARIC severely limited statistical power, so we were unable to replicate our findings from the COPDGene cohort. But meta-analyses of COPDGene and ARIC study subjects strengthened our association signal. However, a few linkage studies have reported suggestive linkage to the 3p26.1 region, and a few genome-wide association studies (GWAS) have reported markers in the gene (GRM7) nearest to this 3p26.1 area of polymorphic deletions are associated with measures of nicotine dependence among subjects of European ancestry.

Demographic characteristics and smoking behavior distributions among African-American and Non Hispanic White study subjects from COPDGene.

Candidate genes selected based on annotation of the top 22 markers found to be within genes and fitting the pattern of the alternate allele being present at a higher frequency in the NAA samples.

Phenotypes for NAA selected for whole-genome resequencing.

Atena Oladzad, PhD. Department of Plant Sciences, North Dakota State University, Fargo, ND, USA, 58102. Email: Atena.oladzad@ndsu.eduTimothy Porch, PhD. USDA-ARS, Tropical Agricultural Research Station Mayaguez Puerto Rico. Email: Timothy.Porch@ars.usda.govJuan Carlos Rosas, Ph.D. Department of Agricultural Engineering, Zamorano University, Zamorano, Honduras. Email: jcrosas@zamorano.eduSamira Mafi Moghaddam, PhD. Plant Resilience Institute, Department of Plant Biology, Michigan State University, East Lansing, MI, USA, 48824. Email: smafi@msu.eduJames Beaver, PhD. Department of Agronomy and Soils, University of Puerto Rico, Mayaguez, Puerto Rico 00680. Email: j_beaver@hotmail.comSteve E. Beebe, PhD. International Center for Tropical Agriculture (CIAT), Cali, Colombia. Email: s.beebe@cgiar.orgJames Burridge, PhD. Department of Plant Science, Pennsylvania State University, State Collage, PA, 16801, USA. Email: jdb450@psu.eduCelestina Nhagupana Jochua, PhD. South Zonal Center, Maputo, Mozambique. Email: celestina_jochua@hotmail.comMagalhaes Amade Miguel, PhD. Mozambic Institute of Agricultural Research, Chimoio, Mozambic. Email: magalhaes_amade@hotmail.com Phillip N Miklas, PhD. USDA-ARS, Grain Legume Genetics Physiology Research , Prosser, WA, USA. Email: phil.miklas@ars.usda.gov Bodo Ratz, PhD. International Center for Tropical Agriculture (CIAT), Cali, Colombia. Email: b.raatz@cgiar.orgJeffery W. White, PhD. USDA-ARS, Plant Physiology and Genetics Research Maricopa, AZ, USA. Email: jeffrey.white@ars.usda.govJonathan Lynch, PhD. Department of Plant Science, Pennsylvania State University, State Collage, PA, 16801, USA. Email: jpl4@psu.eduPhillip E. McClean, PhD. Department of Plant Science, North Dakota State University, Fargo, ND, 58102, USA. Email: phillip.mcclean@ndsu.edu

All tufted birds are characterized by an 8.3kb heterozygous deletion on chromosome 15.

Results from genotyping of wildtype, tailed, partial and rumpless NAA chicken breeds for SNP variants SV1 and SV2 from wing vein blood.

This table contains the median value of Log2 ratios comparing WL to NAA, KA and KD in the first intron of SOX5.