High-density Genotyping Research Articles

Identification of novel 3D-genome altering and complex structural variants underlying retinitis pigmentosa type 17 through a multistep and high-throughput approach

IntroductionAutosomal dominant retinitis pigmentosa type 17 (adRP, type RP17) is caused by complex structural variants (SVs) affecting a locus on chromosome 17 (chr17q22). The SVs disrupt the 3D regulatory landscape by altering the topologically associating domain (TAD) structure of the locus, creating novel TAD structures (neo-TADs) and ectopic enhancer-gene contacts. Currently, screening for RP17-associated SVs is not included in routine diagnostics given the complexity of the variants and a lack of cost-effective detection methods. The aim of this study was to accurately detect novel RP17-SVs by establishing a systematic and efficient workflow.MethodsGenetically unexplained probands diagnosed with adRP (n = 509) from an international cohort were screened using a smMIPs or genomic qPCR-based approach tailored for the RP17 locus. Suspected copy number changes were validated using high-density SNP-array genotyping, and SV breakpoint characterization was performed by mutation-specific breakpoint PCR, genome sequencing and, if required, optical genome mapping. In silico modeling of novel SVs was performed to predict the formation of neo-TADs and whether ectopic contacts between the retinal enhancers and the GDPD1-promoter could be formed.ResultsUsing this workflow, potential RP17-SVs were detected in eight probands of which seven were confirmed. Two novel SVs were identified that are predicted to cause TAD rearrangement and retinal enhancer-GDPD1 contact, one from Germany (DE-SV9) and three with the same SV from the United States (US-SV10). Previously reported RP17-SVs were also identified in three Australian probands, one with UK-SV2 and two with SA-SV3.DiscussionIn summary, we describe a validated multi-step pipeline for reliable and efficient RP17-SV discovery and expand the range of disease-associated SVs. Based on these data, RP17-SVs can be considered a frequent cause of adRP which warrants the inclusion of RP17-screening as a standard diagnostic test for this disease.

Assessment of DNA quality for whole genome library preparation

In recent years, more sophisticated DNA technologies for genotyping have enabled considerable progress in various fields such as clinical genetics, archaeogenetics and forensic genetics. DNA samples previously rejected as too challenging to analyze due to low amounts of degraded DNA can now provide useful information. To increase the chances of success with the new methodologies, it is crucial to know the fragment size of the template DNA molecules, and whether the DNA in a sample is mostly single or double stranded. With this knowledge, an appropriate library preparation method can be chosen, and the DNA shearing parameters of the protocol can be adjusted to the DNA fragment size in the sample. In this study, we first developed and evaluated a user-friendly fluorometry-based protocol for estimation of DNA strandedness. We also evaluated different capillary electrophoresis methods for estimation of DNA fragmentation levels. Next, we applied the developed methodologies to a broad variety of DNA samples processed with different DNA extraction protocols. Our findings show that both the applied DNA extraction method and the sample type affect the DNA strandedness and fragmentation. The established protocols and the gained knowledge will be applicable for future sequencing-based high-density SNP genotyping in various fields.

Generation of genome-wide SNP markers from minimally invasive sampling in endangered animals and applications in species ecology and conservation.

High-density genotyping methods have revolutionized the field of population and conservation genetics in the past decade. To exploit the technological and analytical advances in the field, access to high-quality genetic material is a key component. However, access to such samples in endangered and rare animals is often challenging or even impossible. Here, we used a minimally invasive sampling method (MIS) in the endangered cave salamander Proteus anguinus, the olm, to generate thousands of genetic markers using ddRADseq for population and conservation genomic analyses. Using tail clips and MIS skin swabs taken from the same individual, we investigated genotyping data properties of the two different sampling types. We found that sufficient DNA can be extracted from swab samples to generate up to 200,000 polymorphic SNPs in divergent Proteus lineages. Swab and tissue samples were highly reproducible exhibiting low SNP genotyping error rates. We found that SNPs were most frequently (~50%) located within genic regions, while the rest mapped to mostly flanking regions of repetitive DNA. The vast majority of DNA recovered from swabbing was host DNA. However, a fraction of DNA recovered from swabs contained additional ecological information on the species, including eDNA from the surrounding environment and bacterial skin fauna. Most exogenous DNA recovered from swabs were bacteria (~80%), followed by vertebrates (~20%). Our results demonstrate that MIS can be used to (i) generate tens of thousands of ddRADseq markers for conservation and population genomic analyses and (ii) inform on the species health status and ecology from exogenous DNA.

Genomic Reference Resource for African Cattle: Genome Sequences and High-Density Array Variants

The diversity in genome resources is fundamental to designing genomic strategies for local breed improvement and utilisation. These resources also support gene discovery and enhance our understanding of the mechanisms of resilience with applications beyond local breeds. Here, we report the genome sequences of 555 cattle (208 of which comprise new data) and high-density (HD) array genotyping of 1,082 samples (537 new samples) from indigenous African cattle populations. The new sequences have an average genome coverage of ~30X, three times higher than the average (~10X) of the over 300 sequences already in the public domain. Following variant quality checks, we identified approximately 32.3 million sequence variants and 661,943 HD autosomal variants mapped to the Bos taurus reference genome (ARS-UCD1.2). The new datasets were generated as part of the Centre for Tropical Livestock Genetics and Health (CTLGH) Genomic Reference Resource for African Cattle (GRRFAC) initiative, which aspires to facilitate the generation of this livestock resource and hopes for its utilisation for complete indigenous breed characterisation and sustainable global livestock improvement.

Using high-density SNP data to unravel the origin of the Franches-Montagnes horse breed

BackgroundThe Franches-Montagnes (FM) is the last native horse breed of Switzerland, established at the end of the 19th century by cross-breeding local mares with Anglo-Norman stallions. We collected high-density SNP genotype data (Axiom™ 670 K Equine genotyping array) from 522 FM horses, including 44 old-type horses (OF), 514 European Warmblood horses (WB) from Sweden and Switzerland (including a stallion used for cross-breeding in 1990), 136 purebred Arabians (AR), 32 Shagya Arabians (SA), and 64 Thoroughbred (TB) horses, as introgressed WB stallions showed TB origin in their pedigrees. The aim of the study was to ascertain fine-scale population structures of the FM breed, including estimation of individual admixture levels and genomic inbreeding (FROH) by means of Runs of Homozygosity.ResultsTo assess fine-scale population structures within the FM breed, we applied a three-step approach, which combined admixture, genetic contribution, and FROH of individuals into a high-resolution network visualization. Based on this approach, we were able to demonstrate that population substructures, as detected by model-based clustering, can be either associated with a different genetic origin or with the progeny of most influential sires. Within the FM breed, admixed horses explained most of the genetic variance of the current breeding population, while OF horses only accounted for a small proportion of the variance. Furthermore, we illustrated that FM horses showed high TB admixture levels and we identified inconsistencies in the origin of FM horses descending from the Arabian stallion Doktryner. With the exception of WB, FM horses were less inbred compared to the other breeds. However, the relatively few but long ROH segments suggested diversity loss in both FM subpopulations. Genes located in FM- and OF-specific ROH islands had known functions involved in conformation and behaviour, two traits that are highly valued by breeders.ConclusionsThe FM remains the last native Swiss breed, clearly distinguishable from other historically introgressed breeds, but it suffered bottlenecks due to intensive selection of stallions, restrictive mating choices based on arbitrary definitions of pure breeding, and selection of rare coat colours. To preserve the genetic diversity of FM horses, future conservation managements strategies should involve a well-balanced selection of stallions (e.g., by integrating OF stallions in the FM breeding population) and avoid selection for rare coat colours.

Identification of genes associated with color characteristics of meat and fat tissue of aberdeen-angus cattle

Currently, full genome association studies and identification of candidate genes for economically useful traits in farm animals are topical, scientifically sound and practice-oriented, and fulfill one of the objectives of the Strategy for Scientific and Technical Development of the Russian Federation. This article presents the results of GWAS on color spectral values of meat and fat tissue of Aberdeen-Angus cattle, known for its meat characteristics of high grade. The animals were genotyped on high-density BovineHD Genotyping BeadChip chips containing ≈53,000 SNPs. After quality control, 39,928 remained. By analysis and structural annotation, 25 and 26 candidate genes for meat and fat color were identified, respectively. According to functional annotation, the genes were categorized into 6 groups: nervous system functions, organ development, vascular, joints, metabolic processes and biosynthesis, cellular processes, muscle, tissue and bone, reproduction and embryonic development. The obtained genes were checked through the Animal QTL database, as a result of which 13 genes were confirmed, of which 3 were localized SNPs, in connection with which the LRP2, SCIN and ANTXR1 genes have advantages for their further application in the molecular diagnostics of cattle not only meat, but also dairy productivity.

Fine mapping of QYrsv.swust-1BL for resistance to stripe rust in durum wheat Svevo.

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a serious disease that affects wheat worldwide. There is a great need to develop cultivars with combinations of all-stage resistance (ASR) and adult-plant resistance (APR) genes for sustainable control of the disease. QYrsv.swust-1BL in the Italian durum wheat (Triticum turgidum ssp. durum) cultivar Svevo is effective against Pst races in China and Israel, and the gene has been previously mapped to the long arm of chromosome 1B. The gene is flanked by SNP (single nucleotide polymorphism) markers IWB5732 and IWB4839 (0.75 cM). In the present study, we used high-density 660K SNP array genotyping and the phenotypes of 137 recombinant inbred lines (RILs) to fine map the QYrsv.swust-1BL locus within a 1.066 Mb region in durum wheat Svevo (RefSeq Rel. 1.0) on chromosome arm 1BL. The identified 1.066 Mb region overlaps with a previously described map of Yr29/QYr.ucw-1BL, a stripe rust APR gene. Twenty-five candidate genes for QYrsv.swut-1BL were identified through comparing polymorphic genes within the 1.066 Mb region in the resistant cultivar. SNP markers were selected and converted to Kompetitive allele-specific polymerase chain reaction (KASP) markers. Five KASP markers based on SNP were validated in a F2 and F2:3 breeding population, providing further compelling evidence for the significant effects of QYrsv.swut-1BL. These markers should be useful in marker-assisted selection for incorporating Yr29/QYrsv.swust-1BL into new durum and common wheat cultivars for resistance to stripe rust.

Genome-wide association study identifies novel loci and candidate genes for rust resistance in wheat (Triticum aestivum L.)

BackgroundWheat rusts are important biotic stresses, development of rust resistant cultivars through molecular approaches is both economical and sustainable. Extensive phenotyping of large mapping populations under diverse production conditions and high-density genotyping would be the ideal strategy to identify major genomic regions for rust resistance in wheat. The genome-wide association study (GWAS) population of 280 genotypes was genotyped using a 35 K Axiom single nucleotide polymorphism (SNP) array and phenotyped at eight, 10, and, 10 environments, respectively for stem/black rust (SR), stripe/yellow rust (YR), and leaf/brown rust (LR).ResultsForty-one Bonferroni corrected marker-trait associations (MTAs) were identified, including 17 for SR and 24 for YR. Ten stable MTAs and their best combinations were also identified. For YR, AX-94990952 on 1A + AX-95203560 on 4A + AX-94723806 on 3D + AX-95172478 on 1A showed the best combination with an average co-efficient of infection (ACI) score of 1.36. Similarly, for SR, AX-94883961 on 7B + AX-94843704 on 1B and AX-94883961 on 7B + AX-94580041 on 3D + AX-94843704 on 1B showed the best combination with an ACI score of around 9.0. The genotype PBW827 have the best MTA combinations for both YR and SR resistance. In silico study identifies key prospective candidate genes that are located within MTA regions. Further, the expression analysis revealed that 18 transcripts were upregulated to the tune of more than 1.5 folds including 19.36 folds (TraesCS3D02G519600) and 7.23 folds (TraesCS2D02G038900) under stress conditions compared to the control conditions. Furthermore, highly expressed genes in silico under stress conditions were analyzed to find out the potential links to the rust phenotype, and all four genes were found to be associated with the rust phenotype.ConclusionThe identified novel MTAs, particularly stable and highly expressed MTAs are valuable for further validation and subsequent application in wheat rust resistance breeding. The genotypes with favorable MTA combinations can be used as prospective donors to develop elite cultivars with YR and SR resistance.

Genetic determinants of serum bilirubin using inferred native American gene variants in Chilean adolescents.

Gene variants in the UGT1A1 gene are strongly associated with circulating bilirubin levels in several populations, as well as other variants of modest effect across the genome. However, the effects of such variants are unknown regarding the Native American ancestry of the admixed Latino population. Our objective was to assess the Native American genetic determinants of serum bilirubin in Chilean admixed adolescents using the local ancestry deconvolution approach. We measured total serum bilirubin levels in 707 adolescents of the Chilean Growth and Obesity Cohort Study (GOCS) and performed high-density genotyping using the Illumina-MEGA array (>1.7 million genotypes). We constructed a local ancestry reference panel with participants from the 1000 Genomes Project, the Human Genome Diversity Project, and our GOCS cohort. Then, we inferred and isolated haplotype tracts of Native American, European, or African origin to perform genome-wide association studies. In the whole cohort, the rs887829 variant and others near UGT1A1 were the unique signals achieving genome-wide statistical significance (b = 0.30; p = 3.34 × 10-57). After applying deconvolution methods, we found that significance is also maintained in Native American (b = 0.35; p = 3.29 × 10-17) and European (b = 0.28; p = 1.14 × 10-23) ancestry components. The rs887829 variant explained a higher percentage of the variance of bilirubin in the Native American (37.6%) compared to European ancestry (28.4%). In Native American ancestry, carriers of the TT genotype of this variant averaged 4-fold higher bilirubinemia compared to the CC genotype (p = 2.82 × 10-12). We showed for the first time that UGT1A1 variants are the primary determinant of bilirubin levels in Native American ancestry, confirming its pan-ethnic relevance. Our study illustrates the general value of the local ancestry deconvolution approach to assessing isolated ancestry effects in admixed populations.

Population structure and genomic diversity of the Einsiedler horse.

The breeding history of the Einsiedler horse is closely connected with the Benedictine cloister Einsiedeln. In the mid-nineteenth century, it was decided to use European Warmblood stallions for cross-breeding and to abandon the selection of stallions. Since that time, it has only been possible to trace back the origin of Einsiedler horses using maternal ancestry information. Here, we collected high-density genotype data for European Warmblood horses (Selle Français, Swiss Warmblood and Einsiedler) and Franches-Montagnes horses, the last native Swiss horse breed, to unravel the current population structure of the Einsiedler horse. Using commonly applied methods to ascertain fine-scale population structures, it was not possible to clearly differentiate the Einsiedler from other European Warmblood horses. However, by means of runs of homozygosity (ROH) we were able to detect breed-specific ROH islands for the Einsiedler horse, including genes involved in domestication and adaptation to high altitude. Therefore, future breeding activities should involve the screening of these breed-specific ROH segments, the revival of cryopreserved sperm and the selection of Einsiedler stallions.

Abstract 3430: Mosaic loss of the Y chromosome is associated with prostate cancer risk

Abstract Mosaic loss of the Y chromosome (mLOY), a type of clonal hematopoiesis, is the most frequent chromosomal alteration observed in leukocytes of aging men. mLOY is a putative biomarker of genomic instability with evidence of associations with risk of some solid tumors, but more studies are needed to refine associations and identify potential mechanisms for cancer risk. Prostate cancer (PCa), the most common non-cutaneous cancer in males, is also associated with aging. To further investigate potential relationships between mLOY and PCa, we examined DNA derived from leukocytes of male participants in two large biobanks: the UK Biobank (UKBB; N = 210,103) and the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO, N = 26,795). Of the 236,898 male participants without previous cancer diagnosis, 14,253 (6.0%) were diagnosed with incident PCa after DNA collection. High-density genotyping array data collected during the studies were used to create virtual karyotypes for detecting mLOY in whole blood samples utilizing a phase-based detection method in MoChA software. Analyses were restricted to men without cancer at genotyping and multivariable regression models were adjusted for age, smoking status, and genetic similarity. Men with detectable mLOY were older (mean = 62 vs 56 years) and more likely to be smokers (14.8% vs 9.7%) than men without mLOY. A total of 3,848 (27.0%) men with PCa and 42,835 (19.2%) men free of PCa had detectable mLOY. mLOY clonal fraction ranged from 0.01% to 72.1% of total leukocytes. 18.7% of PCa cases and 13.6% of men free of PCa had high clonal fraction mLOY, defined as greater than 10% of leukocytes with mLOY. Fixed effect meta-analysis of multivariable models from UKBB and PLCO produced evidence for a positive association between mLOY in leukocytes and incident PCa; (Odds Ratio (OR) = 1.062, 95% Confidence Interval (CI) [1.020, 1.107], P-Value (p) = 0.004). The effect estimate was the same in men with low clonal fraction of mLOY (OR = 1.062, 95% CI [1.012, 1.113], p = 0.014) and men with high clonal fraction of mLOY (OR = 1.065, 95% CI [0.998, 1.137], p = 0.057). Age at PCa diagnosis was not associated with mLOY or the clonal fraction of mLOY. A sub-analysis of separate participants from PLCO with mLOY detected in buccal cells (n = 18,011) also showed a small positive effect between mLOY and PCa risk, but the relationship did not reach statistical significance (OR = 1.036, 95% CI [0.877, 1.224], p = 0.673)). Our investigation of the relationship between mLOY and PCa in two large prospective studies provides additional evidence for an association between mLOY detected in the blood and increased PCa risk, meriting additional studies of potential biologic mechanisms underlying the relationship. Citation Format: Rebecca L. Kelly, Weiyin Zhou, Kara M. Barnao, Corey D. Young, Aubrey K. Hubbard, Sairah M. Khan, Wen-Yi Huang, Stephen J. Chanock, Mitchell J. Machiela. Mosaic loss of the Y chromosome is associated with prostate cancer risk [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3430.

Abstract 921: The value of cancer genomic data sharing

Abstract Our understanding of and ability to combat cancer relies on the generation, analysis, and sharing of data. The Epidemiology and Genomics Research Program in the National Cancer Institute’s Division of Cancer Control and Population Sciences (DCCPS) has supported generation of large genomic data sets and advocated for and/or required broad sharing of this data. One of DCCPS’s scientific priorities is focused on data strategies namely, “the use, enhancement, expansion, and accessibility of new and existing DCCPS-supported data resources to accelerate cancer control research” (https://cancercontrol.cancer.gov/overview-highlights/2022/future_directions.html).EGRP funded the Genetic Associations and Mechanisms in Oncology (GAME-ON) Initiative, a multidisciplinary collaboration of researchers focused on understanding the genetic architecture, biology, and clinical and epidemiologic utility of common cancer risk variants. This program focused on 5 common cancer types - breast, colorectal, lung, ovarian, and prostate - and required research that incorporated multiple research domains and sharing of any data generated. A major accomplishment of this program was development of the OncoArray genotyping chip, which used information from genetic epidemiology studies, biological/functional analyses, and clinical and epidemiologic insights to create a comprehensive, high-density genotyping array for pan-cancer studies that has led to the discovery of hundreds of new cancer predisposition variants. This chip was used in a massive, coordinated genotyping effort that culminated in the generation of 7 datasets comprising genotyping data for nearly 500,000 individuals. All the data were deposited in dbGaP between 2014 and 2021 and are available (via controlled access) to any investigators. To understand the secondary use of these data, we determined the number of times the data had been downloaded, who downloaded the data, and types of research for which it was used. We also identified publications using OncoArray data and characterized the publications by research type, cancer type, and other details. Through this analysis, we explore how well the GAME-ON initiative and the OncoArray projects promote the DCCPS scientific priority of optimizing secondary research by making the data findable, accessible, interoperable, and reusable (FAIR). Citation Format: Stefanie Nelson, Charlisse Caga Anan, Elizabeth Gillanders. The value of cancer genomic data sharing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 921.

Microhaplotypes generate higher breeding value accuracy compared to SNPs for imputation-based breeding strategies

The cost of genotyping remains a persistent barrier to the adoption of genomic selection for many breeding programs. This is particularly prominent in the aquaculture industry because the high number and diversity of cultured species impedes the reduction of genotyping costs through a shared genetic panel (e.g., a high-density SNP array). One solution is to reserve high-density genotyping for key individuals and apply a low-density SNP panel along with pedigree-informed imputation to the remaining individuals. We examined the possibility of further lowering the cost of this strategy by targeting microhaplotypes instead of SNPs in the low-density panel, which could allow smaller panels to be used. We simulated Pacific oyster, eastern oyster, and Atlantic salmon breeding programs for three generations and compared imputation and GEBV accuracy using low-density panels targeting SNPs or microhaplotypes. Panels targeting microhaplotypes yielded higher imputation and GEBV accuracy than that of equally sized panels targeting SNPs. In the Pacific and eastern oyster simulations, close to the maximum imputation and GEBV accuracy was reached when the low-density panel contained 150–250 microhaplotypes or 350–450 SNPs. In the Atlantic salmon simulations, this level of accuracy was reached with low-density panels of 350–450 microhaplotypes or 650–750 SNPs. Using low-density panels targeting microhaplotypes instead of SNPs can reduce the cost of genotyping and thereby make genomic selection feasible for a wider range of programs.

Genetic sex validation for sample tracking in next-generation sequencing clinical testing

ObjectiveData from DNA genotyping via a 96-SNP panel in a study of 25,015 clinical samples were utilized for quality control and tracking of sample identity in a clinical sequencing network. The study aimed to demonstrate the value of both the precise SNP tracking and the utility of the panel for predicting the sex-by-genotype of the participants, to identify possible sample mix-ups.ResultsPrecise SNP tracking showed no sample swap errors within the clinical testing laboratories. In contrast, when comparing predicted sex-by-genotype to the provided sex on the test requisition, we identified 110 inconsistencies from 25,015 clinical samples (0.44%), that had occurred during sample collection or accessioning. The genetic sex predictions were confirmed using additional SNP sites in the sequencing data or high-density genotyping arrays. It was determined that discrepancies resulted from clerical errors (49.09%), samples from transgender participants (3.64%) and stem cell or bone marrow transplant patients (7.27%) along with undetermined sample mix-ups (40%) for which sample swaps occurred prior to arrival at genome centers, however the exact cause of the events at the sampling sites resulting in the mix-ups were not able to be determined.

GWABLUP: genome-wide association assisted best linear unbiased prediction of genetic values

BackgroundSince the very beginning of genomic selection, researchers investigated methods that improved upon SNP-BLUP (single nucleotide polymorphism best linear unbiased prediction). SNP-BLUP gives equal weight to all SNPs, whereas it is expected that many SNPs are not near causal variants and thus do not have substantial effects. A recent approach to remedy this is to use genome-wide association study (GWAS) findings and increase the weights of GWAS-top-SNPs in genomic predictions. Here, we employ a genome-wide approach to integrate GWAS results into genomic prediction, called GWABLUP.ResultsGWABLUP consists of the following steps: (1) performing a GWAS in the training data which results in likelihood ratios; (2) smoothing the likelihood ratios over the SNPs; (3) combining the smoothed likelihood ratio with the prior probability of SNPs having non-zero effects, which yields the posterior probability of the SNPs; (4) calculating a weighted genomic relationship matrix using the posterior probabilities as weights; and (5) performing genomic prediction using the weighted genomic relationship matrix. Using high-density genotypes and milk, fat, protein and somatic cell count phenotypes on dairy cows, GWABLUP was compared to GBLUP, GBLUP (topSNPs) with extra weights for GWAS top-SNPs, and BayesGC, i.e. a Bayesian variable selection model. The GWAS resulted in six, five, four, and three genome-wide significant peaks for milk, fat and protein yield and somatic cell count, respectively. GWABLUP genomic predictions were 10, 6, 7 and 1% more reliable than those of GBLUP for milk, fat and protein yield and somatic cell count, respectively. It was also more reliable than GBLUP (topSNPs) for all four traits, and more reliable than BayesGC for three of the traits. Although GWABLUP showed a tendency towards inflation bias for three of the traits, this was not statistically significant. In a multitrait analysis, GWABLUP yielded the highest accuracy for two of the traits. However, for SCC, which was relatively unrelated to the yield traits, including yield trait GWAS-results reduced the reliability compared to a single trait analysis.ConclusionsGWABLUP uses GWAS results to differentially weigh all the SNPs in a weighted GBLUP genomic prediction analysis. GWABLUP yielded up to 10% and 13% more reliable genomic predictions than GBLUP for single and multitrait analyses, respectively. Extension of GWABLUP to single-step analyses is straightforward.

Genome-wide detection of positive and balancing signatures of selection shared by four domesticated rainbow trout populations (Oncorhynchus mykiss).

Evolutionary processes leave footprints along the genome over time. Highly homozygous regions may correspond to positive selection of favorable alleles, while maintenance of heterozygous regions may be due to balancing selection phenomena. We analyzed data from 176 fish from four disconnected domestic rainbow trout populations that were genotyped using a high-density Axiom Trout genotyping 665K single nucleotide polymorphism array, including 20 from the US and 156 from three French lines. Using methods based on runs of homozygosity and extended haplotype homozygosity, we detected signatures of selection in these four populations. Nine genomic regions that included 253 genes were identified as being under positive selection in all four populations Most were located on chromosome 2 but also on chromosomes 12, 15, 16, and 20. In addition, four heterozygous regions that contain 29 genes that are putatively under balancing selection were also shared by the four populations. These were located on chromosomes 10, 13, and 19. Regardless of the homozygous or heterozygous nature of the regions, in each region, we detected several genes that are highly conserved among vertebrates due to their critical roles in cellular and nuclear organization, embryonic development, or immunity. We identified new candidate genes involved in rainbow trout fitness, as well as 17 genes that were previously identified to be under positive selection, 10 of which in other fishes (auts2, atp1b3, zp4, znf135, igf-1α, brd2, col9a2, mrap2, pbx1, and emilin-3). Using material from disconnected populations of different origins allowed us to draw a genome-wide map of signatures of positive selection that are shared between these rainbow trout populations, and to identify several regions that are putatively under balancing selection. These results provide a valuable resource for future investigations of the dynamics of genetic diversity and genome evolution during domestication.

Identification of Candidate Genes Controlling Red Seed Coat Color in Cowpea (Vigna unguiculata [L.] Walp)

Seed coat color is an important consumer-related trait of the cowpea (Vigna unguiculata [L.] Walp.) and has been a subject of study for over a century. Utilizing newly available resources, including mapping populations, a high-density genotyping platform, and several genome assemblies, the red seed coat color has been mapped to two loci, Red-1 (R-1) and Red-2 (R-2), on Vu03 and Vu07, respectively. A gene model (Vigun03g118700) encoding a dihydroflavonol 4-reductase, a homolog of anthocyanidin reductase 1, which catalyzes the biosynthesis of epicatechin from cyanidin, has been identified as a candidate gene for R-1. Possible causative variants have also been identified for Vigun03g118700. A gene model on Vu07 (Vigun07g118500), with predicted nucleolar function and high relative expression in the developing seed, has been identified as a candidate for R-2. The observed red color is believed to be the result of a buildup of cyanidins in the seed coat.

Risk of Sperm Disorders and Impaired Fertility in Frozen-Thawed Bull Semen: A Genome-Wide Association Study.

Cryopreservation is a widely used method of semen conservation in animal breeding programs. This process, however, can have a detrimental effect on sperm quality, especially in terms of its morphology. The resultant sperm disorders raise the risk of reduced sperm fertilizing ability, which poses a serious threat to the long-term efficacy of livestock reproduction and breeding. Understanding the genetic factors underlying these effects is critical for maintaining sperm quality during cryopreservation, and for animal fertility in general. In this regard, we performed a genome-wide association study to identify genomic regions associated with various cryopreservation sperm abnormalities in Holstein cattle, using single nucleotide polymorphism (SNP) markers via a high-density genotyping assay. Our analysis revealed a significant association of specific SNPs and candidate genes with absence of acrosomes, damaged cell necks and tails, as well as wrinkled acrosomes and decreased motility of cryopreserved sperm. As a result, we identified candidate genes such as POU6F2, LPCAT4, DPYD, SLC39A12 and CACNB2, as well as microRNAs (bta-mir-137 and bta-mir-2420) that may play a critical role in sperm morphology and disorders. These findings provide crucial information on the molecular mechanisms underlying acrosome integrity, motility, head abnormalities and damaged cell necks and tails of sperm after cryopreservation. Further studies with larger sample sizes, genome-wide coverage and functional validation are needed to explore causal variants in more detail, thereby elucidating the mechanisms mediating these effects. Overall, our results contribute to the understanding of genetic architecture in cryopreserved semen quality and disorders in bulls, laying the foundation for improved animal reproduction and breeding.

Genotyping of SNPs in bread wheat at reduced cost from pooled experiments and imputation

Key messagePooling and imputation are computational methods that can be combined for achieving cost-effective and accurate high-density genotyping of both common and rare variants, as demonstrated in a MAGIC wheat population.The plant breeding industry has shown growing interest in using the genotype data of relevant markers for performing selection of new competitive varieties. The selection usually benefits from large amounts of marker data, and it is therefore crucial to dispose of data collection methods that are both cost-effective and reliable. Computational methods such as genotype imputation have been proposed earlier in several plant science studies for addressing the cost challenge. Genotype imputation methods have though been used more frequently and investigated more extensively in human genetics research. The various algorithms that exist have shown lower accuracy at inferring the genotype of genetic variants occurring at low frequency, while these rare variants can have great significance and impact in the genetic studies that underlie selection. In contrast, pooling is a technique that can efficiently identify low-frequency items in a population, and it has been successfully used for detecting the samples that carry rare variants in a population. In this study, we propose to combine pooling and imputation and demonstrate this by simulating a hypothetical microarray for genotyping a population of recombinant inbred lines in a cost-effective and accurate manner, even for rare variants. We show that with an adequate imputation model, it is feasible to accurately predict the individual genotypes at lower cost than sample-wise genotyping and time-effectively. Moreover, we provide code resources for reproducing the results presented in this study in the form of a containerized workflow.

Genomic inbreeding measures applied to a population of mice divergently selected for birth weight environmental variance.

This study aimed to compare different inbreeding measures estimated from pedigree and molecular data from two divergent mouse lines selected for environmental birth weight during 26 generations. Furthermore, the performance of different approaches and both molecular and pedigree data sources for estimating Ne were tested in this population. A total of 1,699 individuals were genotyped using a high-density genotyping array. Genomic relationship matrices were used to calculate molecular inbreeding: Nejati-Javaremi (F NEJ), Li and Horvitz (F L&H), Van Raden method 1 (F VR1) and method 2 (F VR2), and Yang (F YAN). Inbreeding based on runs of homozygosity (F ROH) and pedigree inbreeding (F PED) were also computed. F ROH, F NEJ, and F L&H were also adjusted for their average values in the first generation of selection and named F ROH0, F NEJ0, and F L&H0. ∆F was calculated from pedigrees as the individual inbreeding rate between the individual and his parents (∆F PEDt) and individual increases in inbreeding (∆F PEDi). Moreover, individual ∆F was calculated from the different molecular inbreeding coefficients (∆F NEJ0, ∆F L&H, ∆F L&H0, ∆F VR1, ∆F VR2, ∆F YAN, and ∆F ROH0). The Ne was obtained from different ∆F, such as Ne PEDt, Ne PEDi, Ne NEJ0, Ne L&H, Ne L&H0, Ne VR1, Ne VR2, Ne YAN, and Ne ROH0. Comparing with F PED , F ROH , F NEJ and F VR2 overestimated inbreeding while F NEJ0 , F L&H , F L&H0 , F VR1 and F YAN underestimated inbreeding. Correlations between inbreeding coefficients and ∆F were calculated. F ROH had the highest correlation with F PED (0.89); F YAN had correlations >0.95 with all the other molecular inbreeding coefficients. Ne PEDi was more reliable than Ne PEDt and presented similar behaviour to Ne L&H0 and Ne NEJ0. Stable trends in Ne were not observed until the 10th generation. In the 10th generation Ne PEDi was 42.20, Ne L&H0 was 45.04 and Ne NEJ0 was 45.05 and in the last generation these Ne were 35.65, 35.94 and 35.93, respectively F ROH presented the highest correlation with F PED, which addresses the identity by descent probability (IBD). The evolution of Ne L&H0 and Ne NEJ0 was the most similar to that of Ne PEDi. Data from several generations was necessary to reach a stable trend for Ne, both with pedigree and molecular data. This population was useful to test different approaches to computing inbreeding coefficients and Ne using molecular and pedigree data.