Investigations on Genetic Architecture of Hairy Loci in Dairy Cattle by Using Single and Whole Genome Regression Approaches

Development of body hair is an important physiological and cellular process that leads to better adaption in tropical environments for dairy cattle. Various studies suggested a major gene and, more recently, associated genes for hairy locus in dairy cattle. Main aim of this study was to i) employ a variant of the discordant sib pair model, in which half sibs from the same sires are randomly sampled using their affection statues, ii) use various single marker regression approaches, and iii) use whole genome regression approaches to dissect genetic architecture of the hairy gene in the cattle. Whole and single genome regression approaches detected strong genomic signals from Chromosome 23. Although there is a major gene effect on hairy phenotype sourced from chromosome 23: whole genome regression approach also suggested polygenic component related with other parts of the genome. Such a result could not be obtained by any of the single marker approaches

Multiple hypothesis testing in a genome wide association study of bovine tuberculosis

Genome-wide association studies (GWAS) have been used to detect single nucleotide polymorphisms (SNPs) related to various animal traits. The outcome of GWAS is based on quality of the both phenotypic and genotypic datasets. False positive (or negative) associations can be obtained due to multiple hypothesis testing procedures, quality control measures, or an undetected population structure. The objectives of this study were to 1) investigate different multiple hypothesis testing procedures with different quality measures and 2) to detect and correct ancestral stratification using different single SNPs models of the bovine tuberculosis GWA data set. Based on a regression model, SNPs from chromosomes 2, 7, 8 and 13 were detected at a significance level of P<0.001 without correction for multiple hypothesis testing. However, after Bonferroni correction, Hochberg"s method and permutation test for multiple hypothesis correction genomic signals, it became non-significant. Only a false discovery rate approach detected weak signals (at level of 0.54) from chromosomes 2, 8, and 13. We used a model that took into account the effect of linkage disequilibrium to the multiple hypothesis testing procedures by combining adjacent SNPs test statistics with windows sizes of 2, 4 and 6. We detected strong genomic signals from chromosomes 13, 8, 6 and 2 at windows size 6. The results of this study showed that multiple hypothesis testing procedures are related to false positive genomic signals. It is difficult to suggest universally acceptable multiple hypothesis testing and QC measures and their thresholds due to sources of variations between species and within populations. However, additional analytical approaches and studies are needed to evaluate the effects of linkage disequilibrium on the multiple hypothesis testing procedures and QC measures (especially for minor allele frequencies) to GWAS under various scenarios including, but not limited to, level of heritability, linkage disequilibrium, population structure, and population size

The trend of breeding value research in animal science: bibliometric analysis

This study aims to identify trends and hot topics in breeding value to support researchers in finding new directions for future research in that area. The data of this study consist of 7072 academic studies on breeding value in the Web of Science database. Network visualizations and in-depth bibliometric analysis were performed on cited references, authors, countries, institutions, journals, and keywords through CiteSpace. VanRaden (2008) is the most cited work and has an essential place in the field. The most prolific writer is Ignacy Misztal. While the most productive country in breeding value studies is the United States, the People's Republic of China is an influential country that has experienced a strong citation burst in the last 3 years. The National Institute for Agricultural Research and Wageningen University are important institutions that play a critical role in connecting other institutions. Also, these two institutions have the highest centrality values. “Genomic prediction” is the outstanding sub-study field in the active clusters appearing in the analysis results. We have summarized the literature on breeding value, including publication information, country, institution, author, and journal. We can say that hot topics today are “genome-wide association”, “feed efficiency”, and “genomic prediction”. While the studies conducted in the past years have focused on economic value and accuracy, the studies conducted in recent years have started to be studies that consider technological developments and changing world conditions such as global warming and carbon emission.</p

Comparison of analyses of the QTLMAS XIV common dataset. II: QTL analysis

Background - A quantitative and a binary trait for the 14th QTLMAS 2010 workshop were simulated under a model which combined additive inheritance, epistasis and imprinting. This paper aimed to compare results submitted by the participants of the workshop.Methods - The results were compared according to three criteria: the success rate (ratio of mapped QTL to the total number of simulated QTL), and the error rate (ratio of false positives to the number of reported positions), and mean distance between a true mapped QTL and the nearest submitted position. Results - Seven groups submitted results for the quantitative trait and five for the binary trait. Among the 37 simulated QTL 17 remained undetected. Success rate ranged from 0.05 to 0.43, error rate was between 0.00 and 0.92, and the mean distance ranged from 0.26 to 0.77 Mb. Conclusions - Our comparison shows that differences among methods used by the participants increases with the complexity of genetic architecture. It was particularly visible for the quantitative trait which was determined partly by non-additive QTL. Furthermore, an imprinted QTL with a large effect may remain undetected if the applied model tests only for Mendelian genes

Association analyses of the MAS-QTL data set using grammar, principal components and Bayesian network methodologies

<p>Abstract</p> <p>Background</p> <p>It has been shown that if genetic relationships among individuals are not taken into account for genome wide association studies, this may lead to false positives. To address this problem, we used Genome-wide Rapid Association using Mixed Model and Regression and principal component stratification analyses. To account for linkage disequilibrium among the significant markers, principal components loadings obtained from top markers can be included as covariates. Estimation of Bayesian networks may also be useful to investigate linkage disequilibrium among SNPs and their relation with environmental variables.</p> <p>For the quantitative trait we first estimated residuals while taking polygenic effects into account. We then used a single SNP approach to detect the most significant SNPs based on the residuals and applied principal component regression to take linkage disequilibrium among these SNPs into account. For the categorical trait we used principal component stratification methodology to account for background effects. For correction of linkage disequilibrium we used principal component logit regression. Bayesian networks were estimated to investigate relationship among SNPs.</p> <p>Results</p> <p>Using the Genome-wide Rapid Association using Mixed Model and Regression and principal component stratification approach we detected around 100 significant SNPs for the quantitative trait (p<0.05 with 1000 permutations) and 109 significant (p<0.0006 with local FDR correction) SNPs for the categorical trait. With additional principal component regression we reduced the list to 16 and 50 SNPs for the quantitative and categorical trait, respectively.</p> <p>Conclusions</p> <p>GRAMMAR could efficiently incorporate the information regarding random genetic effects. Principal component stratification should be cautiously used with stringent multiple hypothesis testing correction to correct for ancestral stratification and association analyses for binary traits when there are systematic genetic effects such as half sib family structures. Bayesian networks are useful to investigate relationships among SNPs and environmental variables.</p

Analysis of the genetics of boar taint reveals both single SNPs and regional effects

BACKGROUND: Boar taint is an offensive urine or faecal-like odour, affecting the smell and taste of cooked pork from some mature non-castrated male pigs. Androstenone and skatole in fat are the molecules responsible. In most pig production systems, males, which are not required for breeding, are castrated shortly after birth to reduce the risk of boar taint. There is evidence for genetic variation in the predisposition to boar taint. A genome-wide association study (GWAS) was performed to identify loci with effects on boar taint. Five hundred Danish Landrace boars with high levels of skatole in fat (>0.3 μg/g), were each matched with a litter mate with low levels of skatole and measured for androstenone. DNA from these 1,000 non-castrated boars was genotyped using the Illumina PorcineSNP60 Beadchip. After quality control, tests for SNPs associated with boar taint were performed on 938 phenotyped individuals and 44,648 SNPs. Empirical significance thresholds were set by permutation (100,000). For androstenone, a ‘regional heritability approach’ combining information from multiple SNPs was used to estimate the genetic variation attributable to individual autosomes. RESULTS: A highly significant association was found between variation in skatole levels and SNPs within the CYP2E1 gene on chromosome 14 (SSC14), which encodes an enzyme involved in degradation of skatole. Nominal significance was found for effects on skatole associated with 4 other SNPs including a region of SSC6 reported previously. Genome-wide significance was found for an association between SNPs on SSC5 and androstenone levels and nominal significance for associations with SNPs on SSC13 and SSC17. The regional analyses confirmed large effects on SSC5 for androstenone and suggest that SSC5 explains 23% of the genetic variation in androstenone. The autosomal heritability analyses also suggest that there is a large effect associated with androstenone on SSC2, not detected using GWAS. CONCLUSIONS: Significant SNP associations were found for skatole on SSC14 and for androstenone on SSC5 in Landrace pigs. The study agrees with evidence that the CYP2E1 gene has effects on skatole breakdown in the liver. Autosomal heritability estimates can uncover clusters of smaller genetic effects that individually do not exceed the threshold for GWAS significance. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-424) contains supplementary material, which is available to authorized users

Large scale genome-wide association and LDLA mapping study identifies QTLs for boar taint and related sex steroids

<p>Abstract</p> <p>Background</p> <p>Boar taint is observed in a high proportion of uncastrated male pigs and is characterized by an unpleasant odor/flavor in cooked meat, primarily caused by elevated levels of androstenone and skatole. Androstenone is a steroid produced in the testis in parallel with biosynthesis of other sex steroids like testosterone and estrogens. This represents a challenge when performing selection against androstenone in breeding programs, without simultaneously decreasing levels of other steroids. The aim of this study was to use high-density genome wide association (GWA) in combination with linkage disequilibrium-linkage analysis (LDLA) to identify quantitative trait loci (QTL) associated with boar taint compounds and related sex steroids in commercial Landrace (n = 1,251) and Duroc (n = 918) breeds.</p> <p>Results</p> <p>Altogether, 14 genome wide significant (GWS) QTL regions for androstenone in subcutaneous fat were obtained from the LDLA study in Landrace and 14 GWS QTL regions in Duroc. LDLA analysis revealed that 7 of these QTL regions, located on SSC 1, 2, 3, 7 and 15, were obtained in both breeds. All 14 GWS androstenone QTLs in Landrace are also affecting the estrogens at chromosome wise significance (CWS) or GWS levels, while in Duroc, 3 of the 14 QTLs affect androstenone without affecting any of the estrogens. For skatole, 10 and 4 QTLs were GWS in the LDLA analysis for Landrace and Duroc respectively, with 4 of these detected in both breeds. The GWS QTLs for skatole obtained by LDLA are located at SSC 1, 5, 6, 7, 10, 11, 13 and 14.</p> <p>Conclusion</p> <p>This is the first report applying the Porcine 60 K SNP array for simultaneous analysis of boar taint compounds and related sex hormones, using both GWA and LDLA approaches. Several QTLs are involved in regulation of androstenone and skatole, and most of the QTLs for androstenone are also affecting the levels of estrogens. Seven QTLs for androstenone were detected in one breed and confirmed in the other, i.e. in an independent sample, although the majority of QTLs are breed specific. Most QTLs for skatole do not negatively affect other sex hormones and should be easier to implement into the breeding scheme.</p

Adölesanlarda duygu değişiklikleri ile yeme eğilimi ilişkisinin değerlendirilmesi

Bu çalışmanın amacı, adölesanların duygu değişiklikleri ile yeme eğilimleri arasındaki ilişkinin incelenmesi ve farklı duygular esnasında tercih edilen ve tüketilmek istenen besinlerin belirlenmesidir. Çalışma, Eylül-Ekim 2018 tarihleri arasında Ankara ili Çankaya Bilgi Temel Lisesi’nde 10-19 yaş arası 193 öğrenci (62 erkek, 131 kız) üzerinde yürütülmüştür. Adölesanlara ait genel bilgiler, kişilerin sağlık durumları, duygu değişiklikleri (üzgün/mutsuz olma, endişeli/kaygılı olma, sınav stresi, mutluluk, halsiz/hasta olma, başarısızlık hissi, yalnızlık hissi ve hayal kırıklığına uğrama) ve yeme ilişkisini içeren soruların yer aldığı anket, Hollanda Yeme Davranışı Anketi (DEBQ) uygulanmış ve duygusal yeme alt ölçeği ile değerlendirilmiştir. Katılımcıların antropometrik ölçümleri saptanmıştır. Çalışmada ki katılımcıların %32.1’i erkek %67.9’u kız ve yaş ortalaması 16.2±1.2 yıl olarak saptanmıştır. Adölesanların BKİ-z skor değerlerine göre %79.7’si normal, %12.9’u hafif şişman, %4.8’i obez ve %2.6’sı zayıf olarak tespit edilmiştir. Adölesanlar, üzgün/mutsuz, endişe/kaygı, sınav stresi, hasta/halsiz, başarısızlık, yalnızlık, hayal kırıklığı hissettikleri zaman ‘daha az yerim’, mutlu hissettikleri zaman ‘herhangi bir değişiklik olmaz’ şeklinde ifade ettikleri görülmüş ve cinsiyete göre istatistiksel olarak farklılık tespit edilmiştir (p<0.05). Besin tercih eğilimine baktığımızda çikolatanın bütün duygu durumlarda ilk tercih edilen besin olduğu görülmüştür. DEBQ-duygusal yeme alt ölçek puan ortalamaları ile katılımcıların cinsiyet, yaş, teşhis edilmiş hastalık olma durumu, fiziksel aktivite ve BKİ-z skor değeri istatistiksel olarak ilişkili bulunmamıştır (p>0.05). Katılımcıların duygusal yeme eğilimlerini tespit etmek için DEBQ-duygusal yeme alt ölçeği ile 8 farklı duygu durumunun ilişkisine bakıldığında üzgün/mutsuz, endişe/kaygı, sınav stresi, mutlu, yalnızlık, hayal kırıklığı hissedilen duygu durumlarında pozitif yönlü korelasyon saptanmıştır. Sonuç olarak adölesanların genellikle olumsuz duygu durumundayken daha az yemek yeme eğilimi gösterdikleri ve ilk tercih ettikleri besinlerin de yüksek enerjili atıştırmalık karbonhidratlar olduğu belirlenmiştir. This study was planned to investigate the relationship between emotion changes and eating tendencies in adolescents and to determine the preferred foods to be consumed during different emotions. The study was conducted on 193 students (62 males, 131 females) between the age of 10-19 studying Çankaya Bilgi Temel High School in Ankara between September and October 2018. General information about adolescents, health status of individuals, emotion changes (sad / unhappy, anxious / anxious, exam stress, happiness, weak/ sick, feeling of failure, feeling loneliness and disappointment) and questions about the eating relationship, The Dutch Eating Behavior Questionnaire (DEBQ) was administered and evaluated with the emotional eating subscale. Anthropometric measurements of the participants were determined. Of the participants in the study, 32.1% were male and 67.9% were female and the mean age was 16.2 ± 1.2 years. The BMI-z scores of the adolescents in our study were 79.7% normal, 12.9% were overweight, 4.8% were obese and 2.6% were underweight. The adolescents feel sad / unhappy, worry / anxiety, exam stress, sick / weak, failure, loneliness, disappointment when they said ‘‘eating less’’, when they feel happy when they said ‘‘no change’’ and they are determined statistically by gender. (p <0.05). When we look at the preference of food, it is seen that chocolate is the first preferred food in all emotion situations. Gender, age, diagnosed disease status, physical activity and BMI-z score were not statistically significant (p> 0.05). Participants with The Dutch Eating Behavior Questionnaire-emotional eating subscale to identify emotional eating tendencies of 8 when we look at the relationship of different mood statistically significant but not sad / unhappy, worry / anxiety, exam stress, happy, lonely, dissappointment positive correlation in felt mood. As a result, it is determined that adolescents tend to eat less often while they are in negative emotions and they prefer to eat high-energy snacks

Parçalı sabit argümanlı sinir ağlarının kararlılık analizi.

Last several decades, an immense attention has been paid to the construction and analysis of neural networks since it is related to the brain activity. One of the most important neural networks is Hopfield neural network. Since it is obtained from the direct modeling of neuron activity, the results of the research have effective consequences for the modern science. Dynamical analysis of Hopfield neural networks concerns to the method of qualitative theory of differential equations. In particular, it relates to the existence and stability of oscillatory solutions, equilibrium, periodic and almost periodic solutions. Due to the significance of the Hopfield neural networks, one must modernize the models to satisfy the present and potential applications in neuroscience and other fields of the modern research. This is why in the present thesis, we have developed the Hopfield’s model by inserting piecewise constant argument of generalized type which is started to be considered in the theory of differential equations several years ago in 2005. The new models contain piecewise constant argument and constant delays. We investigate the sufficient conditions for existence and uniqueness of solutions, global exponential stability of equilibrium points for these neural networks. By means of Lyapunov functionals, the conditions for stability and linear matrix inequality method have been obtained. Ph.D. - Doctoral Progra