High-density SNP Array Research Articles

Different Shades of Kale—Approaches to Analyze Kale Variety Interrelations

Brassica oleracea is a vegetable crop with an amazing morphological diversity. Among the various crops derived from B. oleracea, kale has been in the spotlight globally due to its various health-benefitting compounds and many different varieties. Knowledge of the existing genetic diversity is essential for the improved breeding of kale. Here, we analyze the interrelationships, population structures, and genetic diversity of 72 kale and cabbage varieties by extending our previous diversity analysis and evaluating the use of summed potential lengths of shared haplotypes (SPLoSH) as a new method for such analyses. To this end, we made use of the high-density Brassica 60K SNP array, analyzed SNPs included in an available Brassica genetic map, and used these resources to generate and evaluate the information from SPLoSH data. With our results we could consistently differentiate four groups of kale across all analyses: the curly kale varieties, Italian, American, and Russian varieties, as well as wild and cultivated types. The best results were achieved by using SPLoSH information, thus validating the use of this information in improving analyses of interrelations in kale. In conclusion, our definition of kale includes the curly varieties as the kales in a strict sense, regardless of their origin. These results contribute to a better understanding of the huge diversity of kale and its interrelations.

Association Mapping of Agronomic traits in Bread Wheat using a high Density 90k SNP Array

A genome-wide association study (GWAS) was performed using a high-density infinium 90K SNP array. We identified a total markers traits associations (MTAs) (p ?0.000) for the following plant traits; days taken to 50% heading(DH), days to 50% maturity (DM), plant height (Ph) cm, flag leaf area cm2 (FLA), tillers number per plant, spike length (SL) cm and grain yield per plant (GP) g. Most of the SNPs were identified in the A and B genome as compared to the D genome. The significant associated SNPs were mainly distributed on the chromosome 2B, 3B, 5A, and 5B. Nine SNPs on chromosome 5A, 2B and 2D were identified having pleiotropic effects The correlation analysis showed a significant positive association among SL, NT, GP. Which depicted that these traits are promising for breeding high yielding wheat cultivars. This study provided useful information of the valuable genetic loci for marker-assisted breeding.

Improving genomic prediction accuracy for harvest traits in Asian seabass (Lates calcarifer, Bloch 1790) via marker selection

Genomic selection provides an efficient strategy to improve growth performance and processing traits in aquaculture. However, the high cost of genotyping animals using high-density SNP arrays may prevent its application in small-sized breeding programs. The aim of this study was to evaluate the utility of low-density SNPs for genomic prediction of harvest traits in Asian seabass. A total of 1047 fish were genotyped for 29,521 single nucleotide polymorphisms. Genome-wide association studies (GWAS) using the weighted genomic best linear unbiased prediction (wGBLUP) procedure revealed polygenic nature of harvest traits. GBLUP and BayesB were implemented using five sets of informative SNPs specific to each trait (ranging from 500 to 12,000) and five sets of evenly-spaced markers at the same density. Prediction accuracies were evaluated using five-fold cross-validation with five replications. Using trait-specific panels with the largest effects of 500 to 2000 SNPs under GBLUP, prediction accuracies increased substantially for all traits relative to those from full SNPs, i.e., by ~70% for body weight (BW), by ~100% for standard length (SL), by ~97% for fillet weight (FW) and by ~660% for fillet yield (FY). A similar trend in prediction accuracy was observed from BayesB. Improvement in accuracy was marginal for evenly-spaced markers compared to full SNPs, i.e., by ~25% for BW, SL, FW and by ~30% for FY. Close relationship between training and validation fish appeared to be a major contributing factor to the favorable performance of prediction models for the within-family selection scheme of Asian seabass.

Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array.

Simple SummaryEvaluating population genetic background and genomic selection signatures can provide important insights into the uniqueness and the genetic relationship among breeds. In this study, we analyzed the genetic diversity, population structure, and phylogenetic relationships between Huaxi cattle and its ancestors. The results showed that Huaxi cattle has formed its own unique genetic structure features, which could be clearly distinguished from its ancestors and similar populations. Moreover, some genes associated with important economic traits, including growth and development, reproduction, milk quality, and immune response, were identified by scanning potentially selected genomic regions, which may play an essential role in the excellent environmental adaptability and growth performance of Huaxi cattle. Our study will contribute to the genetic evaluation and rational breeding strategy, and give an extensive reference for understanding the genetic basis of economically important traits in Huaxi cattle.Huaxi cattle, a specialized beef cattle breed in China, has the characteristics of fast growth, high slaughter rate, and net meat rate, good reproductive performance, strong stress resistance, and wide adaptability. In this study, we evaluated the genetic diversity, population structure, and genetic relationships of Huaxi cattle and its ancestor populations at the genome-wide level, as well as detecting the selection signatures of Huaxi cattle. Principal component analysis (PCA) and phylogenetic analysis revealed that Huaxi cattle were obviously separated from other cattle populations. The admixture analysis showed that Huaxi cattle has distinct genetic structures among all populations at K = 4. It can be concluded that Huaxi cattle has formed its own unique genetic features. Using integrated haplotype score (iHS) and composite likelihood ratio (CLR) methods, we identified 143 and 199 potentially selected genes in Huaxi cattle, respectively, among which nine selected genes (KCNK1, PDLIM5, CPXM2, CAPN14, MIR2285D, MYOF, PKDCC, FOXN3, and EHD3) related to ion binding, muscle growth and differentiation, and immunity were detected by both methods. Our study sheds light on the unique genetic feature and phylogenetic relationship of Huaxi cattle, provides a basis for the genetic mechanism analysis of important economic traits, and guides further intensive breeding improvement of Huaxi cattle.

New insights into genetics underlying of plumage color

Plumage color can be considered as a social signal in chickens and a breeding identification tool among breeders. The relationship between plumage color and trait groups of immunity, growth and fertility is still a controversial issue. This research aimed to determine the genome-wide additive and epistatic variants affecting plumage color variation in chickens using the chicken Illumina 60k high-density SNP array. Two scenarios of genome-wide additive association studies using all SNPs and independent SNPs were carried out. To perform epistatic association analysis, the LD pruning approach was used to reduce the complexity of the analysis. We detected seven novel significant loci using all of the SNPs in the model and 14 SNPs using the LD pruning approach associated with plumage color. Moreover, 89 significantly associated SNP-SNP interactions (P-value <10-6 ) distributed in 25 chromosomes were identified, indicating that all of the signals together putatively influence the quantitative variation of plumage color. By annotating genes relevant to top SNPs, we have distinguished 18 potential candidate genes comprising HNF4beta, CKMT1B, TBC1D22A, RPL8, CACNA2D1, FZD4, SGMS1, IRF8, OPTN, LOC420362, TRABD, OvoDA1, DAD1, USP6, RBM12B, MIR1772, MIR1709 and MIR6696 and also 89 putative gene-gene combinations responsible for plumage color variation in chickens. Furthermore, several KEGG pathways including metabolic pathway, cytokine-cytokine receptor interaction, focal adhesion, melanogenesis, glycosaminoglycan biosynthesis-keratan sulfate and sphingolipid metabolism were enriched in the gene-set analysis. The results indicated that plumage color is a highly polygenic trait which, in turn, can be affected by multiple coding genes, regulatory genes and gene-gene epistasis interactions. In addition to genes with additive effects, epistatic genes with tiny individual effect sizes but significant effects in a pair have the potential to control plumage coloration in chickens.

Genome analyses revealed genetic admixture and selection signatures in Bos indicus

The genomic diversity and relationship among seven diverse cattle breeds viz. Sahiwal, Tharparkar, Gir, Vechur, Ongole, Kangayam and Hariana were investigated in 132 random samples based on high density SNP array comprising > 777 K SNPs. A total of 1993 SNPs (0.25% of the total) having greater power (FST ≥ 0.20) to differentiate these cattle populations were identified, and utilized to partition genome of each animal into a predefined number of clusters. The structure of these cattle indicated shared ancestry of dairy breeds viz. Gir, Tharparkar and Sahiwal. Most of the animals (> 76%) of different populations under study except Vechur clustered into their own group of animals called breed. Vechur population retained highest rate of admixture, consistent with its crossing with other breeds. Ongole, Kangayam and Hariana shared comparatively less of their genome (≤ 15%) with other breeds. The study indicated that all seven breeds evolved from their independent ancestry but there was intermixing of these breeds in the recent past. The selection signatures identified between draft (Kangayam) and dairy breeds included several genes like FAM19A2, RAB31P, BEST3, DGKA, AHCY, PIGU and PFKP which are involved in immune response, metabolic pathway, transportation of glucose and sugars, signaling pathways, cellular processes, cell division and glycolysis regulation, respectively. Moreover, these genomic regions also harbour QTLs affecting milk performance traits. The signatures were also identified even between the dairy breeds. In comparison to large-sized cattle, there were significant differences in the number of QTLs affecting production (body weight, growth rate etc.) and morphological traits (height) in short-statured Vechur breed. The presence of HMGA2 gene in the selection signature on chromosome 5 may explain the variations in stature between these cattle.

Diversification, spread, and admixture of octoploid strawberry in the Western Hemisphere.

PremisePolyploid species often have complex evolutionary histories that have, until recently, been intractable due to limitations of genomic resources. While recent work has further uncovered the evolutionary history of the octoploid strawberry (Fragaria L.), there are still open questions. Much is unknown about the evolutionary relationship of the wild octoploid species, Fragaria virginiana and Fragaria chiloensis, and gene flow within and among species after the formation of the octoploid genome.MethodsWe leveraged a collection of wild octoploid ecotypes of strawberry representing the recognized subspecies and ranging from Alaska to southern Chile, and a high‐density SNP array to investigate wild octoploid strawberry evolution. Evolutionary relationships were interrogated with phylogenetic analysis and genetic clustering algorithms. Additionally, admixture among and within species is assessed with model‐based and tree‐based approaches.ResultsPhylogenetic analysis revealed that the two octoploid strawberry species are monophyletic sister lineages. The genetic clustering results show substructure between North and South American F. chiloensis populations. Additionally, model‐based and tree‐based methods support gene flow within and among the two octoploid species, including newly identified admixture in the Hawaiian F. chiloensis subsp. sandwicensis population.Conclusions F. virginiana and F. chiloensis are supported as monophyletic and sister lineages. All but one of the subspecies show extensive paraphyly. Furthermore, phylogenetic relationships among F. chiloensis populations supports a single population range expansion southward from North America. The inter‐ and intraspecific relationships of octoploid strawberry are complex and suggest substantial gene flow between sympatric populations among and within species.

GWAS Hits for Bilateral Convergent Strabismus with Exophthalmos in Holstein Cattle Using Imputed Sequence Level Genotypes.

Bilateral convergent strabismus with exophthalmos (BCSE) is a malformation of the eyes and is recognized as a mild but progressive disorder that affects cattle in the first two years of life. This most likely inherited disorder is rarely described in cattle resembling autosomal dominantly inherited forms of human progressive external ophthalmoplegia (PEO). In German Braunvieh cattle, two linked genome regions were found that could be responsible for the development and/or progression of BCSE. The goal of this study was to phenotypically characterize BCSE in Holstein cattle from Germany and Switzerland as well as to identify associated genome regions by GWAS. The clinicopathological phenotype of 52 BCSE-affected Holstein cattle was in accordance with the phenotype described in German Braunvieh cattle, but in addition, signs of degeneration and cellular infiltration in the eye muscles were found. By using imputed sequence level genotype data, three genome-wide significant GWAS hits were revealed on different chromosomes that were not detected by initial GWAS based on high density SNP array data highlighting the usefulness of this approach for mapping studies. The associated genome regions include the ABCC4 gene as well as markers adjacent to the NCOR2 and DNAJC3 genes all illustrating possible functional candidate genes. Our results challenge a monogenic mode of inheritance and indicate a more complex inheritance of BCSE in Holstein cattle. Furthermore, in comparison to previous results from German Braunvieh cattle, it illustrates an obvious genetic heterogeneity causing BSCE in cattle. Subsequent whole genome sequencing (WGS)-based analyses might elucidate pathogenic variants in the future.

Limited Therapeutical Impact of Extensive Genomic Profiling in Relapsed Pediatric B-Cell Precursor Acute Lymphoblastic Leukemia: Population-Based Four-Year Consecutive Cohort

High throughput genomic technologies, such as high-density SNP arrays and whole exome and transcriptome sequencing (WES, RNAseq), significantly deepened our insight into the genomic background and biology of acute lymphoblastic leukemia (ALL) during the past decade. Novel genetic aberrations and genomic and gene expression patterns have been described which led to the definition of several novel ALL subtypes and risk-predictive factors and to the identification of novel druggable and/or resistance-associated lesions potentially impacting therapy tailoring. Anecdotal evidence of therapeutical interventions based on the up-to-date genetic data has resulted into a great demand for these investigations. However, it is unclear what proportion of pediatric ALL patients, especially the cases of therapy-resistant leukemia, would really benefit from extensive genomic profiling.Between V/2013 and VIII/2017, relapse of Ph-negative B-cell precursor (BCP) ALL was diagnosed in 20 children (1-18 years) within the Czech Republic. In addition to the routine genetics, 18/20 cases were profiled by high density SNP array (18/18), WES (18/18) and RNAseq (17/18). The examined cohort comprised 10 B-other, 4 hyperdiploid, 3 ETV6-RUNX1 -positive and 1 KMT2A -rearranged ALL. At primary leukemia manifestation, all children were treated according to the ALL-BFM protocols [BFM 95 (n=1), BFM 2000 (n=1) and BFM 2009 (n=16)] and suffered very early (n=1), early (n=4) or late relapses (n=13). Upon disease relapse, 5, 11 and 2 cases were treated according to ALL-REZ BFM 2002 and IntReALL 2010 SR and HR protocols, respectively.Bulk bone marrow (BM) samples or sorted leukemic blasts were analyzed in isolated BM (n=15) and combined BM+CNS (n=2) relapses, while tissue from uterus infiltrated with blasts was analyzed in a single case of isolated extramedullary relapse. In addition to leukemic blasts, remission samples were analyzed by WES in all and by SNP array in selected cases to distinguish germline genetic variants. Somatic copy number aberrations and regions of uniparental disomy were called from SNP array data using commercial softwares. WES and RNAseq data were processed and somatic single nucleotide variants, indels and fusion transcripts were called using in-house pipeline based on publicly available software tools. Targeted analysis was performed to identify DUX4 gene rearrangements (r.). Hierarchical clustering based on gene expression profiles (unsupervised clustering and clustering with gene sets defining DUX4 -r., Ph-like and ETV6-RUNX1 -like ALL) was performed using RNAseq data. To facilitate this analysis, gene expression data from relapse cohort were combined with primary diagnosis data from >50 B-other ALL cases. Clinically important findings were reported to national study centre.Two B-other cases were classified as DUX4 -r. and 2 other cases as Ph-like ALL. Of note, 2 cases (both treated as standard risk in primary diagnosis) had iAMP21. Apart from 3 CRLF2 -rearrangements (1 present in Ph-like case), 6 KRAS and 2 NRAS genes mutations, no potentially druggable lesions were found. While the frequency of CRLF2 -rearrangements and RAS mutations found in relapse was comparable to that seen in primary disease, relapse cohort was enriched for lesions associated with unfavorable prognosis and therapy resistance. Three and four cases harbored deletion of TP53 gene and IKZF1 plus deletion pattern; however, in 1/2 cases with available data from primary diagnosis the IKZF1 plus pattern was identified only in relapse. Deletion of CREBBP and TBL1XR1 genes, potentially associated with resistance to glucocorticoids, were found in 2 cases and 1 case, respectively. Mutations of NT5C2 gene resulting in resistance to mercaptopurine were found in 2 cases. Three out of 18 analyzed cases did not harbor any of the above mentioned lesions. None of the genetic findings directly impacted patients' treatment.To conclude, we successfully implemented advanced genomics into centralized diagnostics of resistant ALL at the national level. Although it improved our understanding of disease relapse (yet, not in 100% of cases) the results were not translated to therapy tailoring in patients treated according to the large international protocols, thus, questioning the cost/benefit ratio of such extensive genetic diagnostics.Support: AZV 15-30626A and 16-30186A, GACR 15-06049Y, Primus/MED/28 DisclosuresNo relevant conflicts of interest to declare.

Dissecting Childhood B-Other Acute Lymphoblastic Leukemia: Lower Frequency of Druggable Gene Fusions in European Population?

Novel biological subtypes within B-other (B-o) acute lymphoblastic leukemia (ALL) have been described recently, based on the presence of genomic rearrangements (r.) of specific genes (DUX4 , ZNF384 and MEF2D ) or gene expression signatures (Ph-like and ETV6-RUNX1 -like ALL). Genomic profiling not only helped to dissect heterogeneity of B-o phenotype and outcome, but it also identified novel druggable aberrations such as kinase and cytokine receptor gene fusions, that were shown to occur mainly in Ph-like ALL. Unfortunately, only very limited population-based data are available to estimate an unbiased frequency of these novel genetic aberrations and subtypes, especially in European countries.We have analyzed a consecutive cohort of pediatric B-o ALL (negative for ETV6-RUNX1 , TCF3-PBX1 , BCR-ABL1 and KMT2A -involving fusions, hyper- and hypo-diploidy) diagnosed in the Czech Republic between 11/2012 and 5/2017. Transcriptome sequencing (RNAseq) was performed in 69/75 cases. High-density SNP array and whole exome sequencing were performed in 65 and 48 of those, respectively. Fusion transcripts, SNVs and indels were called from sequencing data using in-house pipeline based on publicly available software tools. Targeted analysis was performed to identify DUX4- r. Hierarchical clustering based on published gene sets defining DUX4 -r., Ph-like and ETV6-RUNX1 -like ALL was performed using RNAseq data. Somatic copy number aberrations and regions of uniparental disomy were called from SNP array data.Seventy five B-o cases represented 24% of all pediatric ALL (1-18 years) diagnosed within this period. According to hierarchical clustering, 23/69 cases were classified as DUX4 -r. ALL; all harbored DUX4 -r. They accounted for 33% of B-o ALL, representing a larger proportion than reported by others (Liu et al., EBioMedicine 2016; Lilljebjörn et al., Nat Commun 2016). Three cases (4%) and one case (1%) were positive for ZNF384-r. and MEF2D-r., respectively. Eleven cases (16%) were classified as Ph-like ALL; this subgroup included 7/9 cases with CRLF2 -r. and a single case with ETV6-ABL1 fusion. No other kinase/cytokine receptor gene fusion was detected. Four patients (6%) were classified as ETV6-RUNX1 -like ALL; all harbored aberrations of ETV6 . Strikingly, all 4 ETV6-RUNX1 -like cases displayed concurrently also Ph-like signature. The remaining 27 cases (39%) were not assigned to any novel subtype. Other lesions activating kinase signaling [mutations of NRAS (n=14), KRAS (n=7), FLT3 (n=4), PTPN11 (n=3), JAK2 (n=3), JAK1 (n=1), NF1 (n=1) and BRAF (n=1)] were found in 36 cases and were not enriched in Ph-like or other subtype. Of note, 9/27 of “unassigned” (but 0/42 of “assigned”) B-o harbored in-frame “non-kinase” PAX5 gene-involving fusions, both already described and novel, with largely unknown biological and clinical significance.Our data show that frequency of ZNF384 -r., MEF2D -r. and, importantly, also of kinase/cytokine receptor gene fusions (apart from CRLF2 -r.) might be lower in European population than estimated from data based on non-consecutive non-European cohorts (Liu et al.; Gu et al., Nat Commun 2016). To that extent our findings correspond with the recently published Swedish study (Lilljebjörn et al.); however, higher frequency of DUX4-r. ALL in our cohort indicates that differences in genetic composition of pediatric ALL may still occur even within Europe. Our findings highlight one of the flaws of Ph-like testing - non-specificity of Ph-like signature. Of note, the overlap of Ph-like and ETV6-RUNX1 -like signatures is also evidenced by positivity of Ph-like signature in ETV6-RUNX1 + ALL in study by Reshmi et al. (Blood 2017). Very low frequency of “kinase fusions” (apart from CRLF2 -r. which can be indirectly, yet reliably, diagnosed by flow cytometry) questions the use of Ph-like testing as a tool to pre-select ALL with high probability of having these lesions. Despite the use of complex genomics techniques a significant proportion of B-o ALL remains unclassified; interestingly, PAX5 fusions seem to be present in a significant proportion of them.To conclude, our population-based data confirm and specify novel genetic subtypes of pediatric B-o ALL; however, the low incidence of druggable kinase-activating fusions questions the extent of applicability of recently promoted individually “tailored” treatment.Support: AZV 15-30626A; AZV 16-30186A; GACR 15-06049Y; Primus/MED/28 DisclosuresNo relevant conflicts of interest to declare.

Frequency and origin of the c.2090T>G p.(Leu697Trp) MYO3A variant associated with autosomal dominant hearing loss.

We recently described a novel missense variant [c.2090T>G:p.(Leu697Trp)] in the MYO3A gene, found in two Brazilian families with late-onset autosomal dominant nonsyndromic hearing loss (ADNSHL). Since then, with the objective of evaluating its contribution to ADNSHL in Brazil, the variant was screened in additional 101 pedigrees with probable ADNSHL without conclusive molecular diagnosis. The variant was found in three additional families, explaining 3/101 (~3%) of cases with ADNSHL in our Brazilian pedigree collection. In order to identify the origin of the variant, 21 individuals from the five families were genotyped with a high-density SNP array (~600 K SNPs- Axiom Human Origins; ThermoFisher). The identity by descent (IBD) approach revealed that many pairs of individuals from the different families have a kinship coefficient equivalent to that of second cousins, and all share a minimum haplotype of ~607 kb which includes the c.2090T>G variant suggesting it probably arose in a common ancestor. We inferred that the mutation occurred in a chromosomal segment of European ancestry and the time since the most common ancestor was estimated in 1100 years (CI = 775-1425). This variant was also reported in a Dutch family, which shares a 87,121 bp haplotype with theBrazilian samples, suggesting that Dutch colonists may have brought it to Northeastern Brazil in the 17th century. Therefore, the present study opens new avenues to investigate this variant not only in Brazilians but also in European families with ADNSHL.

28. Comparison of different SNP microarray designs and whole genome sequencing for cytogenetic testing

Since the landmark consensus statement paper published in 20101, microarray testing has become the primary tool for detection of chromosomal aberrations of various sizes. In fact, high-density SNP arrays have now become one of the most popular forms of cytogenetic testing due to their ability to detect regions of homozygosity (which is clinically useful) in addition to detection of copy number variants (CNVs). We have performed extensive analytical analysis of the designs from 10 SNP arrays offered by Thermo Fisher/Affymetrix and Illumina.

Shared genomic segment analysis in a large high-risk chronic lymphocytic leukemia pedigree implicates CXCR4 in inherited risk.

Aim:Chronic lymphocytic leukemia (CLL) has been shown to cluster in families. First-degree relatives of individuals with CLL have an ~8 fold increased risk of developing the malignancy. Strong heritability suggests pedigree studies will have good power to localize pathogenic genes. However, CLL is relatively rare and heterogeneous, complicating ascertainment and analyses. Our goal was to identify CLL risk loci using unique resources available in Utah and methods to address intra-familial heterogeneity.Methods:We identified a six-generation high-risk CLL pedigree using the Utah Population Database. This pedigree contains 24 CLL cases connected by a common ancestor. We ascertained and genotyped eight CLL cases using a high-density SNP array, and then performed shared genomic segment (SGS) analysis - a method designed for extended high-risk pedigrees that accounts for heterogeneity.Results:We identified a genome-wide significant region (P = 1.9 × 10−7, LOD-equivalent 5.6) at 2q22.1. The 0.9 Mb region was inherited through 26 meioses and shared by seven of the eight genotyped cases. It sits within a ~6.25 Mb locus identified in a previous linkage study of 206 small CLL families. Our narrow region intersects two genes, including CXCR4 which is highly expressed in CLL cells and implicated in maintenance and progression.Conclusion:SGS analysis of an extended high-risk CLL pedigree identified the most significant evidence to-date for a 0.9 Mb CLL disease locus at 2q22.1, harboring CXCR4. This discovery contributes to a growing literature implicating CXCR4 in inherited risk to CLL. Investigation of the segregating haplotype in the pedigree will be valuable for elucidating risk variant(s).

Abstract 16997: Reaffirmation of GPD1L-A280V as a Brugada Syndrome Disease-Causing Variant

Introduction: Brugada Syndrome (BrS) is an inherited arrhythmia syndrome characterized by ST-segment elevation in the right precordial leads (V1-V3) and sudden cardiac death; ~20% of cases are caused by mutations in SCN5A . Over the past two decades, over 20 genes that may cause BrS have been identified. We reported that a Glycerol-3-Phosphate Dehydrogenase 1-Like mutation (GPD1L;p.A280V, chromosome 3p22.3) was linked to BrS in a large, multigenerational family with a LOD score ~4. Recent efforts in the field have called into question the pathogenicity of non- SCN5A genetic variants in BrS. Hypothesis: We sought to confirm the role of GPD1L in this family using a high density SNP array to narrow the linkage region and whole exome sequencing (WES) of the proband to rule out other possible mutations. We also sought to test whether BrS susceptibility SNPs in SCN5A and SCN10A linked to GPD1L may play a role in this family. Methods: SNPs were identified on an Illumina Global Screening Array and used for fine mapping. The exome of the proband was captured with the Agilent V6+UTR kit. SNPs were called using GATK3. BrS susceptibility SNPs were confirmed by PCR amplification and Sanger Sequencing. Results: The linkage region in this family resolved to ~3.07 MB (hg19; 3:29,899,567-32,970,637; Figure). This region contained 14 genes including GPD1L , and lacking SCN5A , SCN10A , or any other BrS-associated gene. WES identified GPD1L;p.A280V as the only coding variant in the linkage region with an allele frequency ≤ 1%. Previously identified BrS risk alleles in SCN5A and SCN10A were linked to the GPD1L;p.A280V allele in most family members (Figure). Conclusions: Our data suggests that GPD1L;p.A280V causes BrS in this family. The pathogenicity of GPD1L;p.A280V may be increased by linkage with SCN5A and SCN10A risk SNPs. The role of GPD1L mutations in the pathogenesis of BrS should be reaffirmed.

Luzhong mutton sheep: inbreeding and selection signatures.

Intense artificial selection has been imposed to Luzhong mutton sheep population in the past years. Improvements on growth and reproductive performance are two breeding goals in the present herd. Although some progresses were phenotypically observed possibly due to inbreeding induced by strong selection in terms of these traits, the genomic evaluation was poorly understood. Therefore, a high-density SNP array was used to characterize the pattern of runs of homozygosity (ROH), estimate inbreeding and inbreeding depressions on early growth performance and litter size based upon ROH, and scan positive selection signatures of recent population. Consequently, a low inbreeding level was observed which had negative effects on litter size, but not on early growth performance. And 160 genes were under selection, of which some were reported to be linked to several traits of sheep including body weight, litter size, carcass and meat quality, milk yield and composition, fiber quality and health, and the top genes were associated with growth (growth hormone [GH]- growth hormone receptor [GHR]- Insulin-like growth factor 1 [IGF1] axis) and litter size (bone morphogenic proteins [BMPs]-associated). The effectiveness of previous breeding measures was highlighted, but purging selection was proposed to alleviate the inbreeding depression on litter size, providing some genomic insights to breeding management of Luzhong mutton sheep.

Deciphering the mode of action and position of genetic variants impacting on egg number in broiler breeders

BackgroundAim of the present study was first to identify genetic variants associated with egg number (EN) in female broilers, second to describe the mode of their gene action (additive and/or dominant) and third to provide a list with implicated candidate genes for the trait. A number of 2586 female broilers genotyped with the high density (~ 600 k) SNP array and with records on EN (mean = 132.4 eggs, SD = 29.8 eggs) were used. Data were analyzed with application of additive and dominant multi-locus mixed models.ResultsA number of 7 additive, 4 dominant and 6 additive plus dominant marker-trait significant associations were detected. A total number of 57 positional candidate genes were detected within 50 kb downstream and upstream flanking regions of the 17 significant markers. Functional enrichment analysis pinpointed two genes (BHLHE40 and CRTC1) to be involved in the ‘entrainment of circadian clock by photoperiod’ biological process. Gene prioritization analysis of the positional candidate genes identified 10 top ranked genes (GDF15, BHLHE40, JUND, GDF3, COMP, ITPR1, ELF3, ELL, CRLF1 and IFI30). Seven prioritized genes (GDF15, BHLHE40, JUND, GDF3, COMP, ELF3, CRTC1) have documented functional relevance to reproduction, while two more prioritized genes (ITPR1 and ELL) are reported to be related to egg quality in chickens.ConclusionsPresent results have shown that detailed exploration of phenotype-marker associations can disclose the mode of action of genetic variants and help in identifying causative genes associated with reproductive traits in the species.

Genome-Wide Detection of CNVs and Association With Body Weight in Sheep Based on 600K SNP Arrays.

Copy number variations (CNVs) are important genomic structural variations and can give rise to significant phenotypic diversity. Herein, we used high-density 600K SNP arrays to detect CNVs in two synthetic lines of sheep (DS and SHH) and in Hu sheep (a local Chinese breed). A total of 919 CNV regions (CNVRs) were detected with a total length of 48.17 Mb, accounting for 1.96% of the sheep genome. These CNVRs consisted of 730 gains, 102 losses, and 87 complex CNVRs. These CNVRs were significantly enriched in the segmental duplication (SD) region. A CNVR-based cluster analysis of the three breeds revealed that the DS and SHH breeds share a close genetic relationship. Functional analysis revealed that some genes in these CNVRs were also significantly enriched in the olfactory transduction pathway (oas04740), including members of the OR gene family such as OR6C76, OR4Q2, and OR4K14. Using association analyses and previous gene annotations, we determined that a subset of identified genes was likely to be associated with body weight, including FOXF2, MAPK12, MAP3K11, STRBP, and C14orf132. Together, these results offer valuable information that will guide future efforts to explore the genetic basis for body weight in sheep.

Population Structure, and Selection Signatures Underlying High-Altitude Adaptation Inferred From Genome-Wide Copy Number Variations in Chinese Indigenous Cattle.

Copy number variations (CNVs) have been demonstrated as crucial substrates for evolution, adaptation and breed formation. Chinese indigenous cattle breeds exhibit a broad geographical distribution and diverse environmental adaptability. Here, we analyzed the population structure and adaptation to high altitude of Chinese indigenous cattle based on genome-wide CNVs derived from the high-density BovineHD SNP array. We successfully detected the genome-wide CNVs of 318 individuals from 24 Chinese indigenous cattle breeds and 37 yaks as outgroups. A total of 5,818 autosomal CNV regions (683 bp–4,477,860 bp in size), covering ~14.34% of the bovine genome (UMD3.1), were identified, showing abundant CNV resources. Neighbor-joining clustering, principal component analysis (PCA), and population admixture analysis based on these CNVs support that most Chinese cattle breeds are hybrids of Bos taurus taurus (hereinafter to be referred as Bos taurus) and Bos taurus indicus (Bos indicus). The distribution patterns of the CNVs could to some extent be related to the geographical backgrounds of the habitat of the breeds, and admixture among cattle breeds from different districts. We analyzed the selective signatures of CNVs positively involved in high-altitude adaptation using pairwise Fst analysis within breeds with a strong Bos taurus background (taurine-type breeds) and within Bos taurus×Bos indicus hybrids, respectively. CNV-overlapping genes with strong selection signatures (at top 0.5% of Fst value), including LETM1 (Fst = 0.490), TXNRD2 (Fst = 0.440), and STUB1 (Fst = 0.420) within taurine-type breeds, and NOXA1 (Fst = 0.233), RUVBL1 (Fst = 0.222), and SLC4A3 (Fst=0.154) within hybrids, were potentially involved in the adaptation to hypoxia. Thus, we provide a new profile of population structure from the CNV aspects of Chinese indigenous cattle and new insights into high-altitude adaptation in cattle.

Xq28 copy number gain causing moyamoya disease and a novel moyamoya syndrome

BackgroundThe molecular anomalies causing moyamoya disease (MMD) and moyamoya syndromes (MMS) are unknown in most patients.ObjectiveThis study aimed to identify de novo candidate copy number variants (CNVs) in patients with...

229 DNA sequence assisted prediction: the uncomfortable truth

Abstract Using whole genome sequence for improving genomic prediction relative to that from high density SNP arrays has been well below expectations, despite some overoptimistic computer simulations. Why is this so? First, NGS data are massive, noisy and their computer bioinformatics analysis is expensive when applied to the scale needed in animal breeding. SNP calling is a tricky procedure that is especially sensitive to low depth sequencing. This makes it NGS data far more expensive than array genotyping. Second, rare variants are the most frequent class of variants. Population genetics theory dictates that the number of SNPs of a given frequency f is inversely proportional to f. For prediction purposes, it is clear that rare variants are not useful, because it is very likely that they do not segregate in both testing and training subpopulations. Third, sequence contains highly repetitive info, the number of new SNPs decreases quickly with adding new samples and, further, low effective population sizes in domestic animals makes it disequilibrium to be large. What can we do about it? First, high density data can be imputed up to sequence; this has a mild - and limited - effect on improving accuracy. Second, sequence at very low depth on numerous animals can be obtained. This is an extremely risky option that I discourage due to strong biases in heterozygous genotype calling. Third, predictions can be constructed using some sort of prior information (e.g., based on known causative genes or from GWAS studies) together with high density, perhaps custom designed arrays. I believe this is the most promising approach.