Single Marker Analysis Research Articles

Locating QTLs controlling overwintering trait in Chinese perennial Dongxiang wild rice.

Overwintering (OW) is the process by which rice passes through the winter season and germinates in the following spring. OW is also a typical quantitative inheritance trait. Currently, the molecular genetic basis of OW trait in Chinese perennial Dongxiang wild rice (DXWR) still remains to be known. In this study, a linkage map consisting of 139 simple sequence repeat (SSR) markers was constructed using an F2 population derived from a cross between DXWR and 93-11. This map covered the rice genome by approximately 1778.72cM with approximately 12.80cM average interval. The phenotype data of OW trait were investigated for QTL analysis in the following spring of 2017. The gene ontology (GO) annotation of the M-QTL was performed through the rice genome annotation project system. A major QTL-qOW6 was flanked by RM20069 (16,542,428bp) and RM3498 (20,982,059bp) on chromosome 6 and detected repeatedly by both inclusive composite interval and single-marker analysis mapping with an LOD score of 9.45 and explained 22.22% of phenotypic variance. In addition, two small QTLs (qOW2 and qOW3) controlling OW trait were detected on the second and third chromosomes, respectively. No epistatic interaction was detected between these QTLs, suggesting their unique genetic model. A total of 183 candidate genes at qOW6 locus were involved in 887 GO terms. Among them, 52 candidate genes were involved in response to stress. The other 28 candidate genes were related to cell membrane, which might affect the OW trait in perennial DXWR. These results may establish the foundation for understanding the genetic mechanism about OW trait and provide a novel gene resource for OW rice variety improvement.

Mapping of QTLs for Seed Phorbol Esters, a Toxic Chemical in Jatropha curcas (L.).

Jatropha (Jatropha curcas L.) is an oil-bearing plant that has potential to be cultivated as a biodiesel crop. The seed cake after oil extraction has 40–50% protein that can be used in animal feeds. A major limitation in utilizing the cake is the presence of phorbol esters (PE), a heat-tolerant toxic chemical. To identify the quantitative trait loci (QTLs) for PE, we constructed a genetic linkage map from an F2 population of 95 individuals from a cross “Chai Nat” × “M10” using 143 simple sequence repeat (SSR) markers. M10 is low in seed PE while Chai Nat is high. Seeds from each F2 individual were quantified for PE content by high performance liquid chromatography. A single marker analysis revealed five markers from linkage group 3 (LG3) and nine markers from LG8 associated with seed PE. Inclusive composite interval mapping identified two QTLs, each on LG3 (qPE3.1) and LG8 (qPE8.1) responsible for the PE. qPE3.1 and qPE8.1 accounted for 14.10%, and 15.49% of total variation in seed PE, respectively. Alelle(s) from M10 at qPE3.1 increased seed PE, while at qPE8.1 decreased seed PE. qPE3.1 is a new loci for PE, while qPE8.1 is the same locus with that reported recently for PE.

SSR markers associated to early leaf spot disease resistance through selective genotyping and single marker analysis in groundnut (Arachis hypogaea L.)

Groundnut (Arachis hypogaea L.) is an important oilseed and food crop of the world. Breeding for disease resistance is one of major objectives in groundnut breeding. Early leaf spot (ELS) is one of the major destructive diseases worldwide and in West Africa, particularly in Burkina Faso causing significant yield losses. Conventional breeding approaches have been employed to develop improved varieties resistant to ELS. Molecular dissection of resistance traits using QTL analysis can improve the efficiency of resistance breeding. In the present study, an ELS susceptible genotype QH243C and an ELS resistant genotype NAMA were crossed and the F2 population genotypic and F3 progenies phenotypic data were used for marker-trait association analysis. Parents were surveyed with 179 simple sequence repeat (SSR) markers out of which 103 SSR markers were found to be polymorphic between the parents. These polymorphic markers were utilized to genotype the F2 population followed by marker-trait analysis through single marker analysis (SMA) and selective genotyping of the population using 23 resistant and 23 susceptible genotypes. The SMA revealed 13 markers while the selective genotyping method identified 8 markers associated with ELS resistance. Four markers (GM1911, GM1883, GM1000 and Seq13E09) were found common between the two trait mapping methods. These four markers could be employed in genomics-assisted breeding for selection of ELS resistant genotypes in groundnut breeding.

Locus Mapping, Molecular Cloning, and Expression Analysis of rps6kb2, a Novel Metamorphosis-Related Gene in Chinese Tongue Sole (Cynoglossus semilaevis).

Flatfish metamorphosis denotes the extraordinary transformation of a symmetric pelagic larva into an asymmetric benthic juvenile. This unique process involves eye migration, a 90° rotation in posture, and asymmetrical pigmentation for adaptation to a benthic lifestyle. In the present study, we used genetics to map a metamorphosis-related locus (q-10M) in the male linkage group (LG10M), a small interval of 0.9cM corresponding to a 1.8M-bp physical area in chromosome 9 in the Chinese tongue sole (Cynoglossus semilaevis). Combined with single-marker analysis, ribosomal protein S6 kinase 2 (rps6kb2) a member of the family of AGC kinases was identified as a novel metamorphosis-related candidate gene. Its expression pattern during metamorphosis was determined by quantitative RT-PCR and whole-mount in situ hybridization analysis. rps6kb2 gene was significantly expressed in metamorphic climax stage larvae and distributed in all the tissues transforming during metamorphosis, including tail, jaw, eye and skin of larvae. The results suggest that rps6kb2 has a general role in tissue transformations during flatfish metamorphosis including tail changes, skull remodeling, eye migration, and asymmetrical pigmentation.

Detection of paternal uniparental disomy 9 in a neonate with prenatally detected mosaicism for a small supernumerary marker chromosome 9 and a supernumerary ring chromosome 9

ObjectiveWe present the association of paternal uniparental disomy (UPD) 9 with mosaicism for a small supernumerary marker chromosome 9 [sSMC(9)] and a supernumerary ring chromosome 9 [r(9)]. Materials and methodsA 38-year-old woman underwent amniocentesis at 17 weeks of gestation because of advanced maternal age. Amniocentesis revealed a karyotype of 47,XY,+mar [25]/48,XY,+mar,+r(9) [4]/47,XY,+r(9) [1]/46,XY [6]. The parental karyotypes were normal. Array comparative genomic hybridization (aCGH) of cultured amniocytes revealed a result of de novo 9p13.1q21.11 (38,792,472–71,026,063) × 2.64. The marker chromosome was determined to be an sSMC(9) by spectral karyotyping and aCGH. A phenotypically normal baby was delivered at 38 weeks of gestation. During pediatric follow-ups at age two years, the neonate manifested normal psychomotor and growth development. Cytogenetic analysis, metaphase fluorescence in situ hybridization (FISH), single nucleotide polymorphism (SNP) aCGH and polymorphic DNA marker analysis were performed on the peripheral blood of the neonate. ResultsThe neonate's blood had the following results. Metaphase FISH confirmed coexistence of the sSMC(9) and the supernumerary r(9). The karyotype was 47,XY,+sSMC(9) [14]/48,XY, +sSMC(9),+r(9) [10]/47,XY,+r(9) [6]/46,XY [10]. SNP aCGH revealed arr 9p22.3q21.11 (14,234,165–71,035,608) × 2–3, arr 9p24.3p22.3 (216,123–14,629,321)hmz, arr 9p21.3p13.2 (24,769,722–36,732,597)hmz and arr 9q21.11q34.3 (71,013,799–141,011,581)hmz. Polymorphic DNA marker analysis showed paternal isodisomy 9. ConclusionIndividuals with mosaicism for sSMC(9) and supernumerary r(9) may be associated with paternal UPD 9.

Validation of SSR markers linked to oil content in groundnut (Arachis hypogaea L.)

A set of 14 SSR markers that are specific for six QTLs for oil content reported by various authors was selected for validation in the present study. The F4:5 mapping population of the cross ICGV 00440 x ICGV 03128 was used to validate the markers as well as QTLs specific for oil content. Among the selected markers, six markers were polymorphic for the parents ICGV 00440 and ICGV 03128. Among the six polymorphic SSR markers, two markers IPAHM103 and PGS16F10 revealed a strong association for oil content with a PVE of 15.3 and 19.6 respectively in single marker analysis. Validation of QTLs was also performed through composite interval mapping analysis. A QTL with flanking markers IPAHM103 and PM36 could be considered as a potential tool for marker assisted selection of the trait oil content in groundnut.

Genetic Contribution to Alcohol Dependence: Investigation of a Heterogeneous German Sample of Individuals with Alcohol Dependence, Chronic Alcoholic Pancreatitis, and Alcohol-Related Cirrhosis.

The present study investigated the genetic contribution to alcohol dependence (AD) using genome-wide association data from three German samples. These comprised patients with: (i) AD; (ii) chronic alcoholic pancreatitis (ACP); and (iii) alcohol-related liver cirrhosis (ALC). Single marker, gene-based, and pathway analyses were conducted. A significant association was detected for the ADH1B locus in a gene-based approach (puncorrected = 1.2 × 10−6; pcorrected = 0.020). This was driven by the AD subsample. No association with ADH1B was found in the combined ACP + ALC sample. On first inspection, this seems surprising, since ADH1B is a robustly replicated risk gene for AD and may therefore be expected to be associated also with subgroups of AD patients. The negative finding in the ACP + ALC sample, however, may reflect genetic stratification as well as random fluctuation of allele frequencies in the cases and controls, demonstrating the importance of large samples in which the phenotype is well assessed.

ESTABLISHING THE EFFECT OF CODING VARIANTS ON ALZHEIMER’S DISEASE RELATED ENDOPHENOTYPES

To discover novel genetic factors contributing to AD pathogenesis, we focused on the genetics of AD-relevant endophenotypes. This strategy assumes that measurable biological properties are more strongly related to the underlying AD pathogenesis than the diagnostic classification, and therefore will have stronger effect sizes, allowing to perform genetic analyses with lower sample sizes. By using an AD cohort with detailed endophenotypic data on CSF biomarkers, MRI images and neuropsychological tests, we aim to establish novel genetic factors that contribute to AD. The Amsterdam Dementia cohort harbors a collection of individuals diagnosed with AD, mild cognitive impairment (MCI) or subjective cognitive decline. A total of 1281 patients were genotyped using the Illumina neuroX exome array, which is enriched for rare coding variants as it consists of ∼240,000 variants of the Illumina HumanExome array v1.1. Additionally, a custom content of ∼25,000 neurodegenerative specific variants were included. To perform single-marker and gene-based association analyses we used PLINK [1] and MAGMA [2], respectively. As anticipated, a strong genetic influence was observed for the well-established APOE locus on amyloid beta and (phosphorylated) tau CSF protein levels. We furthermore observed a close to significant association to the MRI-phenotype posterior cortical atrophy for SNCA (coding for alpha-synuclein), a GWAS locus highly associated to Parkinson's disease. The gene-based association analysis to Ab42/Tau ratio revealed, besides the genes within the APOE locus, a strong and novel association for FZD1, a gene coding for a receptor of Wnt signalling proteins which has been suggested to regulate adult hippocampal neurogenesis [3]. Multiple independent variants and genes show a significant association to AD-related endophenotypes. After replication of these genetic factors in a second independent genetic dataset, future functional follow up experiments will further elucidate their specific role in AD pathogenesis.

Joint genotype- and ancestry-based genome-wide association studies in admixed populations.

In genome-wide association studies (GWAS) genetic loci that influence complex traits are localized by inspecting associations between genotypes of genetic markers and the values of the trait of interest. On the other hand, admixture mapping, which is performed in case of populations consisting of a recent mix of two ancestral groups, relies on the ancestry information at each locus (locus-specific ancestry). Recently it has been proposed to jointly model genotype and locus-specific ancestry within the framework of single marker tests. Here, we extend this approach for population-based GWAS in the direction of multimarker models. A modified version of the Bayesian information criterion is developed for building a multilocus model that accounts for the differential correlation structure due to linkage disequilibrium (LD) and admixture LD. Simulation studies and a real data example illustrate the advantages of this new approach compared to single-marker analysis or modern model selection strategies based on separately analyzing genotype and ancestry data, as well as to single-marker analysis combining genotypic and ancestry information. Depending on the signal strength, our procedure automatically chooses whether genotypic or locus-specific ancestry markers are added to the model. This results in a good compromise between the power to detect causal mutations and the precision of their localization. The proposed method has been implemented in R and is available at http://www.math.uni.wroc.pl/~mbogdan/admixtures/.

Family-based association analysis of NAV2 gene with the risk and age at onset of Alzheimer's disease

The neuron navigator 2 (NAV2) gene is highly expressed in brain and involved in the nervous system development and may play a role in Alzheimer's disease (AD). We aimed to investigate the associations of 317 single-nucleotide polymorphisms (SNPs) in the NAV2 gene with the risk and age at onset (AAO) of AD using a family-based sample (1266 AD cases and 1279 healthy relatives). Association with the risk of AD was assessed using family-based association test -generalized estimating equations (FBAT- GEE) statistics while the association with AAO as a quantitative trait was evaluated using the FBAT-Wilcoxon statistic. Single marker analysis showed that 20 SNPs were significantly associated with the risk of AD (top SNP rs7112354 with p=8.46×10−4) and 11 SNPs were associated with AAO (top SNP rs1354269 with p=2.87×10−3). Interestingly, two SNPs rs17614100 and rs12364788 were associated with both the risk (p=1.7×10−2 and 2.71×10−2; respectively) and AAO (p=1.85×10−3 and 6.06×10−3; respectively). Haplotype analyses further supported the results of single marker analyses. In addition, functional analysis showed that NAV2 mRNA had significant expression across ten human brain regions examined and significantly correlated with APOE expression in four of ten regions. The present study is the first study providing evidence of several genetic variants within the NAV2 gene influencing the risk and AAO of AD.

Genetic analysis and molecular resistance to race 2 of Fusarium wilt in pigeonpea [Cajanus cajan (L.) Millsp.

The long-stagnated productivity of pigeonpea may be attributed to its vulnerability to several diseases of which vascular wilt caused by Fusarium udum Butler is of paramount significance. Disease management approaches that rely on chemicals are not very appropriate especially in view of rising environmental concerns and resource poor nature of marginal farmers. Therefore, deploying host plant resistance in genetic improvement schemes through molecular tagging of underlying resistance genes is central to resistance breeding. To this end, here we offer SSR markers for resistance to race 2 of Fusarium wilt (FW) in KPL 43 (resistant) through bulked segregant analysis (BSA). The analysis of disease incidence data on 271 F2 individuals derived from Bahar (susceptible) × KPL 43 (resistant) revealed the involvement of two or more recessive genes (1:15) with duplicate dominant epistasis. Marker polymorphism survey using 270 hypervariable pigeonpea-specific SSR markers (HASSRs) yielded 115 polymorphic markers (42.6%) between the parents. SSR markers HASSR8190, HASSR58180 and HASSR121170 differentiated resistant and susceptible bulks. A joint segregation analysis between the each marker with FW resistance in F2 population supported the linkage between FW and the SSRs. Recessive class analysis (RCA) based on genotypic data of ten resistant F2 individual also confirmed linkage between SSRs and FW resistance gene. The independent assortments was observed between the pair of associated SSR markers, and this corroborated with the alignment of these three SSR markers on three different chromosomes in the pigeonpea genome. The association of SSR markers HASSR8190 and HASSR58180 with FW resistance was further validated in a panel of 89 pigeonpea genotypes through single marker analysis (SMA) and Kruskal Wallis test. Given the recessive nature of the genes conferring FW resistance, these SSR markers have tremendous implications for breeding FW resistant pigeonpea genotypes.

Involvement of Interferon Regulatory Factor 5 (IRF5) Gene Polymorphisms and Haplotype in Endometriosis-related Infertility

Introduction The IRF5 gene belongs to a family of transcription factors involved in modulating cell growth, differentiation, apoptosis, and immune system activity. A growing body of evidence indicates that immunological alterations are involved in the pathogenesis of endometriosis, and as a result, polymorphisms in autoimmune-related genes have emerged as possible candidates linked to disease development. Here, we aimed to evaluate a possible association between IRF5 polymorphisms (rs2004640/T>G, rs3807306/G>T, rs10488631/T>C and rs2280714/T>C) and the pathogenesis of endometriosis. Methods A case-control study was performed comprising an experimental group of 236 infertile women with endometriosis and a control group of 232 fertile women. IRF5 polymorphisms were identified by real-time PCR using the TaqMan method. Genotype distribution and allele frequency were calculated, and haplotype analysis was performed. Results Single-marker analysis revealed that the IRF5 rs10488631 (polymorphic C allele) polymorphism was significantly associated with moderate/severe endometriosis (p = 0.028; OR = 1.79, 95% IC = 1.09–2.94). No association was found with respect to rs2004640, rs3807306 and rs2280714 polymorphisms and the endometriosis group. The combined genotypes of four IRF5 polymorphisms identified the haplotype “GGTT”, which was associated with protection against minimal/mild endometriosis-related infertility (p = 0.003), while the haplotype “GTCT” was associated with a risk of developing moderate/severe endometriosis-related infertility (p = 0.047). Conclusions This is the first study to report an association between IRF5 polymorphisms and endometriosis, and the findings suggest that the IRF5 rs10488631 polymorphism and haplotype “GTCT” were involved in the risk of moderate/severe endometriosis development. The haplotype “GGTT” was associated with protection against minimal/mild endometriosis.

Further evidence for genetic variation at the serotonin transporter gene SLC6A4 contributing toward anxiety.

Social anxiety disorder (SAD) is a common and heritable psychiatric disorder. However, genetic studies in SAD are rare and only a few candidate genes have been implicated so far. In the present study, we investigated whether single-nucleotide polymorphisms (SNPs) associated with other psychiatric disorders also contribute toward the development of SAD and followed up variants associated with SAD on the phenotypic level. We genotyped a total of 24 SNPs in a German sample of 321 SAD patients and 804 controls. We carried out single-marker analyses as well as quantitative association analyses of SAD severity and harm avoidance. None of the variants investigated showed an association with SAD in our case-control sample after Bonferroni correction. Two SNPs reached nominal significance (rs818702, P=0.032; rs140701, P=0.048). Of these, only rs140701 showed an association in the same allelic direction as reported previously. This SNP is located within the serotonin transporter gene SLC6A4, which is the primary target of selective-serotonin reuptake inhibitors used for the treatment of depressive and anxiety disorders. The quantitative association analysis of all cases with available data on symptom severity showed four SNPs with a nominal significant association. Among these SNPs, rs10994359 showed the strongest association (P=0.001) and was located near the ANK3 gene. In addition, rs10994359 was nominally associated with harm avoidance scores (P=0.001). Our results provide further evidence for an involvement of the serotonin transporter gene SLC6A4 in the etiology of anxiety-related traits. Furthermore, our study implicates that genetic variation at the genome-wide associated bipolar disorder locus ANK3 might influence anxiety-related personality traits.

Genome-wide association study of borderline personality disorder reveals genetic overlap with bipolar disorder, major depression and schizophrenia

Borderline personality disorder (BOR) is determined by environmental and genetic factors, and characterized by affective instability and impulsivity, diagnostic symptoms also observed in manic phases of bipolar disorder (BIP). Up to 20% of BIP patients show comorbidity with BOR. This report describes the first case–control genome-wide association study (GWAS) of BOR, performed in one of the largest BOR patient samples worldwide. The focus of our analysis was (i) to detect genes and gene sets involved in BOR and (ii) to investigate the genetic overlap with BIP. As there is considerable genetic overlap between BIP, major depression (MDD) and schizophrenia (SCZ) and a high comorbidity of BOR and MDD, we also analyzed the genetic overlap of BOR with SCZ and MDD. GWAS, gene-based tests and gene-set analyses were performed in 998 BOR patients and 1545 controls. Linkage disequilibrium score regression was used to detect the genetic overlap between BOR and these disorders. Single marker analysis revealed no significant association after correction for multiple testing. Gene-based analysis yielded two significant genes: DPYD (P=4.42 × 10−7) and PKP4 (P=8.67 × 10−7); and gene-set analysis yielded a significant finding for exocytosis (GO:0006887, PFDR=0.019; FDR, false discovery rate). Prior studies have implicated DPYD, PKP4 and exocytosis in BIP and SCZ. The most notable finding of the present study was the genetic overlap of BOR with BIP (rg=0.28 [P=2.99 × 10−3]), SCZ (rg=0.34 [P=4.37 × 10−5]) and MDD (rg=0.57 [P=1.04 × 10−3]). We believe our study is the first to demonstrate that BOR overlaps with BIP, MDD and SCZ on the genetic level. Whether this is confined to transdiagnostic clinical symptoms should be examined in future studies.

Identifying markers associated with yield traits in Nagina22 rice mutants grown in low phosphorus field or in alternate wet/dry conditions

Mutants are powerful genetic resources in plant breeding and functional genomics studies. Sixty seven stable ethyl methane sulphonate (EMS) induced rice mutants and the wild type parent Nagina 22 (N22) were characterized for plant height, tiller number, panicle number and grain yield under normal, low P field and alternate wet and dry (AWD) conditions in the same season. They were also genotyped with 44 SSR markers and four Pup1 (Phosphorus uptake1) gene specific markers. Genetic diversity was analysed by combining phenotype and marker data using Ward- MLM method. Single marker analysis showed significant association of four markers RM19696, RM263, RM3688 and RM1942 with grain yield in all three conditions. K-1, a Pup1 gene specific marker was significantly associated with tiller number only under low P conditions. The average dissimilarity between mutants was 0.86 and cophenetic correlation coefficient was 0.74. Six mutants were selected as gain-of-function mutants as they showed significantly higher grain yield in all three conditions, compared with N22. The selected mutants are an important resource for gene discovery for enhanced tolerance to low P and water stress conditions and associated markers can be useful in marker assisted selection.

Identification of Teosinte Alleles for Resistance to Southern Leaf Blight in Near Isogenic Maize Lines

Southern leaf blight ([SLB], causal agent Cochliobolus heterostrophus) is an important fungal disease of maize (Zea mays L.). Teosinte (Z. mays ssp. parviglumis), the wild progenitor of maize, offers a novel source of resistance alleles that may have been lost during domestication. The aims of this study were to identify teosinte alleles that, when present in a temperate maize background, confer a significant level of resistance to SLB. Ten populations of BC4S2 near isogenic lines (NILs), developed by crossing 10 different teosinte accessions to the maize inbred B73, comprising 774 lines in total, were screened for SLB resistance. Quantitative trait locus (QTL) analysis identified four significant QTL associated with SLB in bins 2.04, 3.04, 3.05, and 8.05. Sixteen individual NILs which were significantly different to the susceptible recurrent parent, B73 and which were carrying at least one of the teosinte‐derived resistance alleles were used to develop F2:3 populations by crossing each to B73 followed by two rounds of self‐pollination. These F2:3 populations were evaluated for SLB resistance and genotyped at the loci of interest. In 13 of 19 cases single marker analysis validated allelic substitution effects predicted from the original NIL population analysis, while in five cases we were not able to validate the effects and in one case a significant effect was detected in the opposite to the predicted direction. An allele at the QTL in bin 2.04 was shown to confer resistance to both SLB and a second maize foliar disease, gray leaf spot (GLS).

Identifikasi Penanda SSR yang Berasosiasi dengan Bobot Tandan Buah Kelapa Sawit (Elaeis guineensis Jacq.)

Oil palm is a perennial oil crop that contribute the most important source of vegetable oil in the world. Oil palm breeding cycle take a long period, therefore molecular marker-assisted selection (MAS) is required to shorten the selection time. This MAS require the associated marker to desired trait, particularly for yield and the component that as a complex trait and depend on genetic background. The aim of this study was to obtain SSR marker that associated with average of bunch weight (ABW). Plant material was used in this study is Tenera population derived from Deli Dura x AVROS Pisifera. Seven SSR markers from public database were associated to ABW trait. Molecular data analysed for SSR markers profile which consisted of allelic diversity, heterozygosity level, and polymorphism information content (PIC). Association between SSR markers to ABW traits was performed with single marker analysis using one way analysis of variance. The results showed that SSR markers were able to amplify DNA with two to three number of alleles with the average of 2.3 alleles per locus. ABW trait for this population was significantly associated with mEgCIR3428 marker. This marker may be used in the selection of Deli Dura and AVROS Pisifera palm on the next selection cycle.Keywords: Average of bunch weight, AVROS Pisifera, Deli Dura, single marker analysis

Breast Cancer Clinical Trial of Chemotherapy and Trastuzumab: Potential Tool to Identify Cardiac Modifying Variants of Dilated Cardiomyopathy.

Doxorubicin and the ERBB2 targeted therapy, trastuzumab, are routinely used in the treatment of HER2+ breast cancer. In mouse models, doxorubicin is known to cause cardiomyopathy and conditional cardiac knock out of Erbb2 results in dilated cardiomyopathy and increased sensitivity to doxorubicin-induced cell death. In humans, these drugs also result in cardiac phenotypes, but severity and reversibility is highly variable. We examined the association of decline in left ventricular ejection fraction (LVEF) at 15,204 single nucleotide polymorphisms (SNPs) spanning 72 cardiomyopathy genes, in 800 breast cancer patients who received doxorubicin and trastuzumab. For 7033 common SNPs (minor allele frequency (MAF) > 0.01) we performed single marker linear regression. For all SNPs, we performed gene-based testing with SNP-set (Sequence) Kernel Association Tests: SKAT, SKAT-O and SKAT-common/rare under rare variant non-burden; rare variant optimized burden and non-burden tests; and a combination of rare and common variants respectively. Single marker analyses identified seven missense variants in OBSCN (p = 0.0045–0.0009, MAF = 0.18–0.50) and two in TTN (both p = 0.04, MAF = 0.22). Gene-based rare variant analyses, SKAT and SKAT-O, performed very similarly (ILK, TCAP, DSC2, VCL, FXN, DSP and KCNQ1, p = 0.042–0.006). Gene-based tests of rare/common variants were significant at the nominal 5% level for OBSCN as well as TCAP, DSC2, VCL, NEXN, KCNJ2 and DMD (p = 0.044–0.008). Our results suggest that rare and common variants in OBSCN, as well as in other genes, could have modifying effects in cardiomyopathy.

Validation of microsatellite molecular markers linked with resistance toBipolaris sorokinianain wheat (Triticum aestivumL.)

SUMMARYSpot blotch disease caused byBipolaris sorokiniana(Sacc.) Shoem causes yield losses and reduces grain quality in wheat. Molecular markers reported to be linked with resistance toB. sorokinianacould accelerate the identification of resistant genotypes as they are independent of the environmental effect. However, before they can be utilized for marker assisted selection (MAS), validation in an independent population is required. The objective of the present study was therefore to validate three simple sequence repeat (SSR) molecular markers (Xwgm570, Xgwm544andXgwm437) linked with resistance toB. sorokiniana.The markers were validated using 66 wheat genotypes comprising 11 parental genotypes and 55 F2progenies. Single marker analysis was performed using simple linear regression to ascertain the relationship between the marker and the trait. All the markers were confirmed to be associated with resistance. They all gave significant association with resistance toB. sorokiniana.The markers amplified DNA fragments in the resistant parental genotypes that were similar to those observed in resistant F2progenies, but absent in the susceptible ones. Hence, these markers could be useful in increasing the efficiency of selection for resistance toB. sorokinianain wheat breeding. Since theR2values are low, a combination of two or three SSR markers can be employed during MAS. This was evident by the multiple linear equation which gave a combinedR2value of 18·0%, obtained from the inclusion of all three markers.

Abstract P112: Genes in Genome-wide Association Study-identified Loci and Risk of Atherosclerosis in Adolescents and Young Adults

Background: Genome-wide association studies (GWASs) have identified multiple genomic loci associated with atherosclerotic diseases. However, specific genes underlying the observed associations are largely unknown. Objectives: We aimed to examine the associations between genes that harbor variants in high LD with index variants in GWAS-identified loci and pathologically determined atherosclerosis in major arteries from the Pathobiological Determinants of Atherosclerosis in Youth (PDAY) study. Methods and Results: Data for 1,938 single nucleotide polymorphisms (SNPs) from 28 genes were retrieved from whole exome sequence data. Atherosclerosis was confirmed by postmortem examination of major arteries from 1,005 young persons (aged 15-34 years) who died from non-cardiovascular causes. Logistic regression was used to evaluate associations between common SNPs and atherosclerosis controlling for age and sex. Gene-based analysis was conducted using Sequence Kernel Association Test (SKAT) method to test the combined effect of rare and common variants on atherosclerosis controlling for age and gender. All analyses were performed separately in blacks and whites. Statistical significance was determined by false positive discovery rate (FDR) method. In gene-based analyses, BUD13 ( P =1.11х10 -2 ) and COL4A1 ( P =3.58х10 -2 ) were associated with atherosclerosis among young blacks; none of the 28 genes was associated with atherosclerosis in whites. In single marker analysis of common SNPs, LRP1 missense variant rs7397167 ( P =8.50х10 -3 ), COL4A1 variant rs16975492 ( P =4.60х10 -3 ), STK32B variant rs168985 ( P =4.00х10 -3 ), and SMARCA4 variant rs8104480 ( P =1.20х10 -3 ) were associated with atherosclerosis in blacks; MIA3 variant rs17465637 ( P =8.00х10 -3 ), DUS4L missense variant rs6957510 ( P =6.4х10 -3 ), BOLL variant rs771018 ( P =6.2х10 -3 ), BUD3 missense variant rs11820589 ( P =2.1х10 -3 ), and COL4A1 variant rs1133219 ( P =1.8х10 -3 ) were associated with atherosclerosis in whites. Conclusion: Genes in GWAS-identified loci may play a role in the development of atherosclerosis at a young age.