Haplotype-based Association Study Research Articles

Identification of transcription factor BnHDG4-A08 as a novel candidate associated with the accumulation of oleic, linoleic, linolenic, and erucic acid in Brassica napus.

We screened 47 significantly associated haplotype blocks for oleic, linoleic, linolenic, and erucic acid, with 17 blocks influencing multiple traits. A novel candidate of transcription factor BnHDG4 A08 influencing oleic, linoleic, linolenic, and erucic acid was identified, by a joint strategy of haplotype-based genome-wide association study, genomic resequencing, gene cloning, and co-expression network Fatty acid (FA) composition determines the quality and economic value of rapeseed oil (Brassica napus). However, the molecular network of FAs is unclear. In the current study, multi-strategies of haplotype-based genome-wide association study (GWAS), genomic resequencing, gene cloning, and co-expression network were joint to reveal novel genetic factors influencing FA accumulation in rapeseed. We identified 47 significantly associated haplotype blocks for oleic, linoleic, linolenic, and erucic acid, with 17 blocks influencing multiple traits, using a haplotype-based GWAS with phenotype data from 203 Chinese semi-winter accessions. A total of 61 rapeseed orthologs involved in acyl-lipid metabolism, carbohydrate metabolism, or photosynthesis were identified in these 17 blocks. Among these genes, BnHDG4-A08, encoding a class IV homeodomain leucine-zipper transcription factor, exhibited two single-nucleotide polymorphisms (SNPs) in the exon and intron, with significant associations with oleic, linoleic, linolenic, and erucic acid. Gene cloning further validated two SNPs in the exon of BnHDG4-A08 in a population with 75 accessions, leading to two amino acid changes (T372A and P366L) and significant variation of oleic, linoleic, linolenic, and erucic acid. A competitive allele-specific PCR (KASP) marker based on the SNPs was successfully developed and validated. Moreover, 98 genes exhibiting direct interconnections and high weight values with BnHDG4-A08 were identified through co-expression network analysis using transcriptome data from 13 accessions. Our study identified a novel FA candidate of transcription factor BnHDG4-A08 influencing oleic, linoleic, linolenic, and erucic acid. This gene provides a potential promising gene resource for the novel mechanistic understanding of transcription factors regulating FA accumulation.

Haplotype-based association study of TCF7L2 gene variants with the development of diabetic retinopathy in an Iranian population

ABSTRACT Background Diabetic retinopathy (DR) is recognized as one of the most prevalent complications of diabetes and a major cause of morbidity. Transcription factor 7-like 2 (TCF7L2), a pivotal component in the Wnt-signaling pathway, plays a significant role in β-cell development, blood-glucose homeostasis, cell survival, cell migration, and cell proliferation. Thus, this study aimed to assess the association between TCF7L2 variants (rs7903146, rs11196205, and rs12255372) with DR in a population-based association study. Materials and Methods DNA was extracted from whole blood of all subjects by salting-out procedure. Total 524 T2DM patients including 234 T2DM individuals without DR and 290 T2DM individuals with DR were genotyped by TaqMan assay technology. Clinical characteristics of subjects were conducted to evaluate the plausible association between TCF7L2 variants and DR with univariate linear regression analysis. Results Demographic analysis between case and control groups revealed significant differences in FBS, HbA1c, lipidemia, heart disease, and family history of T2DM (p < 0.05). No significant difference was observed in either genotypes distribution or allele frequency (p > 0.05) between T2DM individuals with and without DR in any models of inheritance. Genotype-phenotype association showed no significant association. Result of analysis indicated that HbAlc with adjusted OR of 1.8 (p < 0.0001) and first-degree relatives of family history with adjusted OR of 3.04 (p < 0.0001) were significantly associated with DR. Finally, haplotype analysis showed no noticeable association. Conclusion In conclusion, there was no significant genetic association between rs7903146, rs11196205, and rs12255372 with DR among T2DM Iranians; however, these variants may play unknown roles in other populations.

Haplotype-Based Genome-Wide Association Analysis Using Exome Capture Assay and Digital Phenotyping Identifies Genetic Loci Underlying Salt Tolerance Mechanisms in Wheat.

Soil salinity can impose substantial stress on plant growth and cause significant yield losses. Crop varieties tolerant to salinity stress are needed to sustain yields in saline soils. This requires effective genotyping and phenotyping of germplasm pools to identify novel genes and QTL conferring salt tolerance that can be utilised in crop breeding schemes. We investigated a globally diverse collection of 580 wheat accessions for their growth response to salinity using automated digital phenotyping performed under controlled environmental conditions. The results show that digitally collected plant traits, including digital shoot growth rate and digital senescence rate, can be used as proxy traits for selecting salinity-tolerant accessions. A haplotype-based genome-wide association study was conducted using 58,502 linkage disequilibrium-based haplotype blocks derived from 883,300 genome-wide SNPs and identified 95 QTL for salinity tolerance component traits, of which 54 were novel and 41 overlapped with previously reported QTL. Gene ontology analysis identified a suite of candidate genes for salinity tolerance, some of which are already known to play a role in stress tolerance in other plant species. This study identified wheat accessions that utilise different tolerance mechanisms and which can be used in future studies to investigate the genetic and genic basis of salinity tolerance. Our results suggest salinity tolerance has not arisen from or been bred into accessions from specific regions or groups. Rather, they suggest salinity tolerance is widespread, with small-effect genetic variants contributing to different levels of tolerance in diverse, locally adapted germplasm.

Haplotype-based association study of production and reproduction traits in multigenerational Vrindavani population

Haplotype-based association analysis promises to reveal important information regarding the effect of genetic variants on economic traits of interest. The present study aimed to evaluate the haplotype structure of Vrindavani cattle and explore the association of haplotypes with (re)production traits of economic interest. Genotyping array data of medium density (Bovine50KSNP BeadChip) on 96 randomly selected Vrindavani cows was used in the present study. Genotypes were called in GenomeStudio program while quality control was undertaken in PLINK using standard thresholds. The phenotypic traits used in the present study included age at first calving, dry days, lactation length, peak yield, total lactation milk yield, inter-calving period and service period. The haplotype structure of Vrindavani population was assessed, using a sliding window of 20 SNP with a shift of 5 SNPs at a time, in terms of the size of haplotype blocks regarding their length (in Kb) and frequency in chromosome-wise fashion. Haplotype blocks were assessed for possible association with important production and reproduction traits across three lactation cycles in Vrindavani cattle population. The first ten principal components were included in the model for haplotype-based association analysis to correct for stratification effects of assessed individuals. Multiple haplotypes were found to be associated with age at first calving, total lactation milk yield, peak yield, dry days, inter-calving period and service period. Various candidate genes were found to overlap haplotypes that were significantly associated with age at first calving (CDH18, MARCHF11, MYO10, FBXL7), total lactation milk yield (TGF, PDE1A, and COL8A1), peak yield (PPARGC1A, RCAN1, KCNE1, SMIM34 and MRPS6), dry days (CPNE4, ACAD11 and MRAS), inter-calving period (ABCG5, ABCG8 and COX7A2L) and service period (FOXL2 and PIK3CB). The putative candidate genes overlapping the significantly associated haplotypes revealed important pathways affecting the production and reproduction performance of animals. The identified genes and pathways may serve as good candidate markers to select animals for improved production and reproduction performance in future generations.

Evaluation of Fusarium Head Blight Resistance Effects by Haplotype-Based Genome-Wide Association Study in Winter Wheat Lines Derived by Marker Backcrossing Approach.

Fusarium head blight (FHB) of wheat caused by Fusarium species is a destructive disease, causing grain yield and quality losses. Developing FHB-resistant cultivars is crucial to minimize the extent of the disease. The first objective of this study was incorporation of Fhb1 from a resistant donor into five Polish wheat breeding lines with good agronomical traits and different origins. We also performed a haplotype-based GWAS to identify chromosome regions in derived wheat families associated with Fusarium head blight resistance. As a result of marker-assisted backcrossing (MABC), five wheat combinations were obtained. Fungal inoculation and disease assessment were conducted for two years, 2019 and 2020. In 2019 the average phenotypic response of type II resistance was 2.2, whereas in 2020 it was 2.1. A haploblock-based GWAS performed on 10 phenotypic traits (related to type of resistance, year of experiment and FHB index) revealed nine marker-trait associations (MTA), among which six belong to chromosome 2D, two to 3B and one to 7D. Phenotypic variation (R2) explained by the identified haplotypes in haploblocks ranged from 6% to 49%. Additionally, an association weight matrix (AWM) was created, giving the partial correlation-information theory (PCIT) pipeline of 171 edges and 19 nodes. The resultant data and high level of explained phenotypic variance of MTA create the opportunity for data utilization in MAS.

Failing the four-gamete test enables exact phasing: the Corners’ Algorithm

BackgroundFailing the four-gamete test for two polymorphic DNA markers is an indication that two or three rather than four haplotypes segregate in the population. The objective of this paper is to show that when just three haplotypes are segregating, all three haplotypes can be fully and unambiguously phase-resolved.Theory and methodsThe Corners’ Algorithm tests the four corners in a 3 × 3 table of two-locus genotypes. If one of the four corners is filled with zeroes, then the missing haplotype is identified and the phases of all three haplotypes can be unambiguously resolved for all individuals. Three applications of this method are proposed when the four-gamete test fails: (1) direct estimation of linkage disequilibrium (LD), (2) haplotype-based genome-wide association studies (GWAS) of three haplotypes (single-marker GWAS tests for two out of three haplotypes only), and (3) haplotyping of chromosomal regions that are comprised of pairs of single nucleotide polymorphisms (SNPs) that consist of just three haplotypes. An example based on 435 sows with performance records for total number of piglets born is used to illustrate the methods.ResultsOf 20,339 SNPs, approximately 50% of the pairs of flanking SNPs failed the four-gamete test. For those, the expectation maximization (EM) algorithm gave the same results. The average of the absolute value of the difference in r2 between flanking SNPs across the genome between the two methods was 0.00082. Single-marker GWAS (using two of three haplotypes) detected significant associations for total number of piglets born on chromosomes 1, 2, 6, 9, 10, 12, 13, 14, 15, and 18. Haplotype-based GWAS using the third haplotype resolved with the Corners’ Algorithm detected additional significant associations for total number of piglets born on chromosomes 2, 5, 10, 13, 14, 15, and 18. Estimated substitution effects ranged from 0.40 to 1.35 piglets. Haplotyping of chromosomal regions that failed the four-gamete test for any pair of SNPs covered 961 Mb out of the 2249 Mb by the SNP array.ConclusionsThe Corner’s Algorithm allows to fully phase haplotypes when the four-gamete test fails. Longer haplotypes in chromosomal regions in which the four-gamete test fails for any pair of SNPs can be used as a multi-allelic marker with increased polymorphism information content.

High male specific contribution of the X-chromosome to individual global recombination rate in dairy cattle

BackgroundMeiotic recombination plays an important role in reproduction and evolution. The individual global recombination rate (GRR), measured as the number of crossovers (CO) per gametes, is a complex trait that has been shown to be heritable. The sex chromosomes play an important role in reproduction and fertility related traits. Therefore, variants present on the X-chromosome might have a high contribution to the genetic variation of GRR that is related to meiosis and to reproduction.ResultsWe herein used genotyping data from 58,474 New Zealand dairy cattle to estimate the contribution of the X-chromosome to male and female GRR levels. Based on the pedigree-based relationships, we first estimated that the X-chromosome accounted for 30% of the total additive genetic variance for male GRR. This percentage was equal to 19.9% when the estimation relied on a SNP-BLUP approach assuming each SNP has a small contribution. We then carried out a haplotype-based association study to map X-linked QTL, and subsequently fine-mapped the identified QTL with imputed sequence variants. With this approach we identified three QTL with large effect accounting for 7.7% of the additive genetic variance of male GRR. The associated effects were equal to + 0.79, − 1.16 and + 1.18 CO for the alternate alleles. In females, the estimated contribution of the X-chromosome to GRR was null and no significant association with X-linked loci was found. Interestingly, two of the male GRR QTL were associated with candidate genes preferentially expressed in testis, in agreement with a male-specific effect. Finally, the most significant QTL was associated with PPP4R3C, further supporting the important role of protein phosphatase in double-strand break repair by homologous recombination.ConclusionsOur study illustrates the important role the X-chromosome can have on traits such as individual recombination rate, associated with testis in males. We also show that contribution of the X-chromosome to such a trait might be sex dependent.

Exploiting single-marker and haplotype-based genome-wide association studies to identify QTL for the number of teats in Italian Duroc pigs

The number of teats is a morphological trait of high economic relevance for the pig industry. Here, to dissect the genomic architecture of this trait in the Italian Duroc pig population, we present the results of genome-wide association studies in this Italian heavy pig breed. A total of 1,162 pigs, for which the number of teats was recorded, was genotyped with two high-throughput single nucleotide polymorphism (SNP) genotyping platforms (60 K and 70 K). Genome-wide association analyses were based on a single-marker approach and on a haplotype-based approach. Two quantitative trait loci (QTL) affecting the number of teats were identified. The most significant QTL, identified by the single-marker analysis and confirmed by the haplotype-based method, was located on Sus scrofa chromosome (SSC) 7, in the region of the vertnin (VRTN) gene. Suggestively associated markers (SNPs and haplotypes) were located on SSC10, in the region of the FERM domain containing 4A (FRMD4A) gene, the second identified QTL. These findings confirm previous results obtained in a few other Duroc populations. Overall, this study further supported the important role of variability in the VRTN gene region in affecting the number of teats in pigs. Moreover, the results also indicated that this trait in the Italian Duroc breed, as in many other pig breeds, is affected by few QTL, with the contribution of many other genetic factors with small effects, following the classical theory of quantitative traits.

Further host-genomic characterization of total antibody response to PRRSV vaccination and its relationship with reproductive performance in commercial sows: genome-wide haplotype and zygosity analyses

BackgroundThe possibility of using antibody response (S/P ratio) to PRRSV vaccination measured in crossbred commercial gilts as a genetic indicator for reproductive performance in vaccinated crossbred sows has motivated further studies of the genomic basis of this trait. In this study, we investigated the association of haplotypes and runs of homozygosity (ROH) and heterozygosity (ROHet) with S/P ratio and their impact on reproductive performance.ResultsThere was no association (P-value ≥ 0.18) of S/P ratio with the percentage of ROH or ROHet, or with the percentage of heterozygosity across the whole genome or in the major histocompatibility complex (MHC) region. However, specific ROH and ROHet regions were significantly associated (P-value ≤ 0.01) with S/P ratio on chromosomes 1, 4, 5, 7, 10, 11, 13, and 17 but not (P-value ≥ 0.10) with reproductive performance. With the haplotype-based genome-wide association study (GWAS), additional genomic regions associated with S/P ratio were identified on chromosomes 4, 7, and 9. These regions harbor immune-related genes, such as SLA-DOB, TAP2, TAPBP, TMIGD3, and ADORA. Four haplotypes at the identified region on chromosome 7 were also associated with multiple reproductive traits. A haplotype significantly associated with S/P ratio that is located in the MHC region may be in stronger linkage disequilibrium (LD) with the quantitative trait loci (QTL) than the previously identified single nucleotide polymorphism (SNP) (H3GA0020505) given the larger estimate of genetic variance explained by the haplotype than by the SNP.ConclusionsSpecific ROH and ROHet regions were significantly associated with S/P ratio. The haplotype-based GWAS identified novel QTL for S/P ratio on chromosomes 4, 7, and 9 and confirmed the presence of at least one QTL in the MHC region. The chromosome 7 region was also associated with reproductive performance. These results narrow the search for causal genes in this region and suggest SLA-DOB and TAP2 as potential candidate genes associated with S/P ratio on chromosome 7. These results provide additional opportunities for marker-assisted selection and genomic selection for S/P ratio as genetic indicator for litter size in commercial pig populations.

SNP- and Haplotype-Based GWAS of Flowering-Related Traits in Brassica napus.

Traits related to flowering time are the most promising agronomic traits that directly impact the seed yield and oil quality of rapeseed (Brassica napus L.). Developing early flowering and maturity rapeseed varieties is an important breeding objective in B. napus. Many studies have reported on days to flowering, but few have reported on budding, bolting, and the interval between bolting and DTF. Therefore, elucidating the genetic architecture of QTLs and genes regulating flowering time, we presented an integrated investigation on SNP and haplotype-based genome-wide association study of 373 diverse B. napus germplasm, which were genotyped by the 60K SNP array and were phenotyped in the four environments. The results showed that a total of 15 and 37 QTLs were detected from SNP and haplotype-based GWAS, respectively. Among them, seven QTL clusters were identified by haplotype-based GWAS. Moreover, three and eight environmentally stable QTLs were detected by SNP-GWAS and haplotype-based GWAS, respectively. By integrating the above two approaches and by co-localizing the four traits, ten (10) genomic regions were under selection on chromosomes A03, A07, A08, A10, C06, C07, and C08. Interestingly, the genomic regions FT.A07.1, FT.A08, FT.C06, and FT.C07 were identified as novel. In these ten regions, a total of 197 genes controlling FT were detected, of which 14 highly expressed DEGs were orthologous to 13 Arabidopsis thaliana genes after integration with transcriptome results. In a nutshell, the above results uncovered the genetic architecture of important agronomic traits related to flowering time and provided a basis for multiple molecular marker-trait associations in B. napus.

27 Machine Learning Algorithms Based on Haplotype Libraries for Classification of Stillbirth Susceptibility in Holstein Cows

Abstract Reduced fertility is one of the main causes of economic losses in dairy farms. The cost of a stillbirth is estimated in US$ 938 per case in Holstein herds. Machine learning (ML) is gaining popularity in the livestock sector as a mean to identify hidden patterns and due to its potential to address dimensionality problems. Here we investigate the application of ML algorithms for the prediction of cows with higher stillbirth susceptibility in two scenarios: cows with &amp;gt;25% and &amp;gt;33.33% of stillbirths among birth records. These thresholds correspond to percentiles 75 (still_75) and 90 (still_90), respectively. A total of 10,570 cows and 50,541 birth records were collected to perform a haplotype-based genome-wide association study. Five-hundred significant pseudo single nucleotide polymorphisms (pseudo-SNPs) (False-Discovery Rate&amp;lt; 0.05) were used as input features of ML-based predictions to determine if the cow is in the top-75 and top-90 percentiles. Table 1 shows the classification performance of the investigated ML and linear models. The ML models outperformed linear models for both thresholds. In general, still_75 showed higher F1 values compared to still_90, suggesting a lower misclassification ratio when a less stringent threshold is used. We observe that accuracy of the models in our study is higher when compared to ML-based prediction accuracies in other breeds, e.g. compared to the accuracies of 0.46 and 0.67 that were achieved using SNPs for body weight in Brahman and fertility traits in Nellore, respectively. Xgboost algorithm shows the highest balanced accuracy (BA; 0.625), F1-score (0.588) and area under the curve (AUC; 0.688), suggesting that xgboost can achieve the highest predictive performance and the lowest difference in misclassification ratio between classes. The ML applied over haplotype libraries is an interesting approach for the detection of animals with higher susceptibility to stillbirths due to highest predictive accuracy and relatively lower misclassification ratio.

Genome-wide association studies for production, respiratory disease, and immune-related traits in Landrace pigs

Identification of a quantitative trait locus (QTL) related to a chronic respiratory disease such as Mycoplasmal pneumonia of swine (MPS) and immune-related traits is important for the genetic improvement of disease resistance in pigs. The objective of this study was to detect a novel QTL for a total of 22 production, respiratory disease, and immune-related traits in Landrace pigs. A total of 874 Landrace purebred pigs, which were selected based on MPS resistance, were genotyped using the Illumina PorcineSNP60 BeadChip. We performed single nucleotide polymorphism (SNP)-based and haplotype-based genome-wide association studies (GWAS) to detect a novel QTL and to evaluate the possibility of a pleiotropic QTL for these traits. SNP-based GWAS detected a total of six significant regions in backfat thickness, ratio of granular leucocytes to lymphatic cells, plasma concentration of cortisol at different ages, and complement alternative pathway activity in serum. The significant region detected by haplotype-based GWAS was overlapped across the region detected by SNP-based GWAS. Most of these detected QTL regions were novel regions with some candidate genes located in them. With regard to a pleiotropic QTL among traits, only three of these detected QTL regions overlapped among traits, and many detected regions independently affected the traits.

40 Novel Genomic Regions Associated with Igg Antibody Response to PRRSV Vaccination Revealed by Haplotype-based GWAS

Abstract Previous studies on genomics of antibody response, measured as sample-to-positive (S/P) ratio, to Porcine Reproductive and Respiratory Syndrome virus (PRRSV) have reported a major quantitative trait locus (QTL) on the major histocompatibility complex (MHC) on chromosome 7, explaining ~25% of the genetic variance of this trait. S/P ratio following modified live PRRSV vaccination in crossbred commercial gilts has been proposed as genetic indicator for reproductive performance in non-infected purebred sows and PRRSV-vaccinated crossbred sows. This motivated further genomic study for this trait by performing haplotype-based genome-wide association study (GWAS). 906 naïve F1 (Landrace x Large White) had blood samples taken at ~50d after vaccination for measuring PRRSV ELISA S/P ratio and genotyping. Haplotype-based GWAS identified 8 genomic regions on chromosomes 4 (108 Mb), 7 (15, 21, and 24–27 Mb), and 9 (33 Mb) that were associated (q-value &amp;lt; 0.07) with S/P ratio. From those, only the MHC region (chromosome 7; 24 – 26 Mb) had been identified in the SNP based GWAS. The main SNP identified in the SNP based GWAS (H3GA0020505) was not in LD with the haplotype; thus, we added this SNP to the haplotype model. We observed that the haplotype explained more of the genetic variance compared to the H3GA0020505 SNP, indicating that the MHC haplotype is in stronger LD with the QTL than the H3GA0020505 SNP. All the significant regions associated with S/P ratio included immune-related candidate genes, such as SLA-DOB, TAP2, TAPBP, TMIGD3, and ADORA. This study validated the QTL identified on the MHC region, narrowing the search for causal genes in this region, and identified new genomic regions, along with candidate genes associated with S/P ratio. Identifying novel genomic regions provides more resources for marker-assisted selection and genomic prediction of S/P ratio in purebred and commercial pig populations.

Functional variants in the chromosome 4q21 locus contribute to allergic rhinitis risk by modulating the expression of N-acylethanolamine acid amidase.

Previous haplotype-based association studies identified chromosome 4q21 as an allergic rhinitis (AR) susceptibility locus; however, the functional role of 4q21 single nucleotide polymorphisms (SNPs) on AR risk remains unclear. To investigate the functional effect of 4q21 SNPs on AR risk by conducting cohort-based functional genomics and genetic association analyses. The associations between 4q21 SNPs and mRNA expression levels of three 4q21-associated genes (SDAD1, NAAA and CXCL9) in peripheral blood mononuclear cells (PBMCs) were assessed in a Singapore/Malaysia Chinese cohort (n=291). Exon expression levels of these genes in PBMCs were tested against the tag-SNP genotypes in a Singapore Chinese cohort (n=30). Serum protein levels of these genes were assessed with tag-SNP genotypes in a Singapore Chinese cohort (n=193). SNP functions were characterized through luciferase assay. In a Singapore Chinese cohort (n=1794), we confirmed the associations between functional SNPs and AR. Forty SNPs in 4q21 showed significant associations with NAAA (but not SDAD1 or CXCL9) mRNA expression in PBMCs, of which were tagged by two tag-SNPs, rs17001237 and rs2242470. Both tag-SNPs rs2242470 and rs12648687 (a proxy for rs17001237) were also significantly associated with the expression level of NAAA exon 1. Tag-SNP rs12648687 was correlated with serum NAAA level. A four promoter SNPs-haplotype tagged by rs17001237 influenced the NAAA promoter activity in HEK293T cells. Lastly, individuals carrying the risk allele A of rs12648687 exhibited significantly higher AR risk in the Singapore Chinese population. The rs17001237 linkage set SNPs in the 4q21 locus are associated with NAAA expression at both gene and protein levels ex vivo, have functional consequences in vitro and contribute to AR susceptibility in our study population. Our findings provided a better understanding of the genetic mechanism that contributes to AR pathogenesis.

Genetic Regulation of Biomarkers as Stress Proxies in Dairy Cows

Stress in livestock reduces productivity and is a welfare concern. At a physiological level, stress is associated with the activation of inflammatory responses and increased levels of harmful reactive oxygen species. Biomarkers that are indicative of stress could facilitate the identification of more stress-resilient animals. We examined twenty-one metabolic, immune response, and liver function biomarkers that have been associated with stress in 416 Italian Simmental and 436 Italian Holstein cows which were genotyped for 150K SNPs. Single-SNP and haplotype-based genome-wide association studies were carried out to assess whether the variation in the levels in these biomarkers is under genetic control and to identify the genomic loci involved. Significant associations were found for the plasma levels of ceruloplasmin (Bos taurus chromosome 1—BTA1), paraoxonase (BTA4) and γ-glutamyl transferase (BTA17) in the individual breed analysis that coincided with the position of the genes coding for these proteins, suggesting that their expression is under cis-regulation. A meta-analysis of both breeds identified additional significant associations with paraoxonase on BTA 16 and 26. Finding genetic associations with variations in the levels of these biomarkers suggests that the selection for high or low levels of expression could be achieved rapidly. Whether the level of expression of the biomarkers correlates with the response to stressful situations has yet to be determined.

Haplotype-based association study of Opioid Receptor Kappa-type 1 (OPRK1) gene polymorphisms with nicotine dependence among male smokers

The WHO estimates there are 1.3 billion smokers worldwide, 80% of whom are in low- and middle-income countries, with 8 million tobacco-related deaths and 1.2 million deaths due to second-hand smoke...

Haplotype-based genomic analysis reveals novel association of CNTNAP5 genic region with primary angle closure glaucoma

Primary angle closure glaucoma (PACG) is one of the major causes of blindness worldwide. The underlying genetic aetiology is complex in nature and molecular mechanism remains elusive. Here, we identify genomic alterations using haplotype-based genome-wide association study in 148 PACG and 92 anatomically predisposed non-glaucomatous individuals. Logistic regression was performed on each common haplotype (within blocks of 3-8 SNPs) across the genotype and a total of 59 SNPs were found below genome wide suggestive threshold (p <1e-05). We found majority of these SNPs (n = 13) are located in CNTNAP5 genic region. The prioritized rs780010 of CNTNAP5 is also significantly associated with Cup to Disc ratio, which is a clinical parameter directly correlated with glaucomatous neurodegeneration. We further validated rs780010, present in all the significant haplotype blocks with p-value = 2.131e-06 (discovery phase), in a separate replication cohort (PACG, n = 50; control, n = 39) and observed significant association (p = 0.012, per G allele OR = 2.3079; 95 % CI: 1.23-4.33). Bioinformatics analyses also suggested neuronal expression of CNTNAP5 with active chromatin structure. KEGG pathway analysis indicates towards pathways related to apoptosis and neurodegeneration. Overall, these results not only indicate a strong genetic association of CNTNAP5 locus with PACG but also suggest its potential involvement in glaucomatous neurodegeneration.

Haplotype analysis from unmanned aerial vehicle imagery of rice MAGIC population for the trait dissection of biomass and plant architecture.

Unmanned aerial vehicles (UAVs) are popular tools for high-throughput phenotyping of crops in the field. However, their use for evaluation of individual lines is limited in crop breeding because research on what the UAV image data represent is still developing. Here, we investigated the connection between shoot biomass of rice plants and the vegetation fraction (VF) estimated from high-resolution orthomosaic images taken by a UAV 10 m above a field during the vegetative stage. Haplotype-based genome-wide association studies of multi-parental advanced generation inter-cross (MAGIC) lines revealed four quantitative trait loci (QTLs) for VF. VF was correlated with shoot biomass, but the haplotype effect on VF was better correlated with that on shoot biomass at these QTLs. Further genetic characterization revealed the relationships between these QTLs and plant spreading habit, final shoot biomass and panicle weight. Thus, genetic analysis using high-throughput phenotyping data derived from low-altitude, high-resolution UAV images during early stages of rice growing in the field provides insights into plant growth, architecture, final biomass, and yield.

Haplotype-based association study between PRCP gene polymorphisms and essential hypertension in Hani minority group from a remote region of China.

Objective:Prolylcarboxypeptidase (PRCP) is both involved in the Kallikrein-Kinin system (KKS) and renin-angiotensin-aldosterone system (RAAS). This study aimed to determine the genetic impact of PRCP gene polymorphisms on essential hypertension (EH) in an isolated population from a remote region of China.Methods:A haplotype-based study was investigated in 346 EH patients and 346 normal subjects and all samples were Hani minority residents in Southwest China. A total of 11 tag single nucleotide polymorphisms (SNPs) in PRCP gene were tested by polymerase chain reaction-restriction fragment length polymorphism method.Results:Single site analysis found that PRCP gene 3′UTR SNP rs3750931 was associated with EH. The minor allele G of rs3750931 was more prevalent in the EH patients compared to control subjects after Bonferroni correction (p < 0.05). Moreover, the rs3750931 G allele carriers showed higher average blood pressure (BP) level among the subjects. The H2 (GAGCACTAACA) haplotype without rs3750931 G allele showed the protective effect for EH (OR = 0.68, 95 CI 0.54–0.85, p = 0.001).Conclusion:The present study indicated PRCP gene rs3750931 was associated with the risk of EH. This SNP G allele could be considered as one of risk markers for EH in Hani population.

Fine mapping genetic variants associated with age at puberty and sow fertility using SowPro90 genotyping array.

Sow fertility traits, such as litter size and the number of lifetime parities produced (reproductive longevity), are economically important. Selection for these traits is difficult because they are lowly heritable and expressed late in life. Age at puberty (AP) is an early indicator of reproductive longevity. Here, we utilized a custom Affymetrix single-nucleotide polymorphisms (SNPs) array (SowPro90) enriched with positional candidate genetic variants for AP and a haplotype-based genome-wide association study to fine map the genetic sources associated with AP and other fertility traits in research (University of Nebraska-Lincoln [UNL]) and commercial sow populations. Five major quantitative trait loci (QTL) located on four Sus scrofa chromosomes (SSC2, SSC7, SSC14, and SSC18) were discovered for AP in the UNL population. Negative correlations (r = -0.96 to -0.10; P < 0.0001) were observed at each QTL between genomic estimated breeding values for AP and reproductive longevity measured as lifetime number of parities (LTNP). Some of the SNPs discovered in the major QTL regions for AP were located in candidate genes with fertility-associated gene ontologies (e.g., P2RX3, NR2F2, OAS1, and PTPN11). These SNPs showed significant (P < 0.05) or suggestive (P < 0.15) associations with AP, reproductive longevity, and litter size traits in the UNL population and litter size traits in the commercial sows. For example, in the UNL population, when the number of favorable alleles of an SNP located in the 3' untranslated region of PTPN11 (SSC14) increased, AP decreased (P < 0.0001), while LTNP increased (P < 0.10). Additionally, a suggestive difference in the observed NR2F2 isoforms usage was hypothesized to be the source of the QTL for puberty onset mapped on SSC7. It will be beneficial to further characterize these candidate SNPs and genes to understand their impact on protein sequence and function, gene expression, splicing process, and how these changes affect the phenotypic variation of fertility traits.