• Title/Summary/Keyword: Linkage and Association

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Further Evidence of Linkage at the tva and tvc Loci in the Layer Lines and a Possibility of Polyallelism at the tvc Locus

  • Ghosh, A.K.;Pani, P.K.
    • Asian-Australasian Journal of Animal Sciences
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    • v.18 no.5
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    • pp.601-605
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    • 2005
  • Three lines of White Leghorn (WL) chickens (IWJ, IWG and IWC) maintained at Central Avian Research Institute, Izatnagar (UP), were used for chorioallantoic membrane (CAM) and liver tumour (LT) assay. Eleven-day-old embryos of each line were partitioned into three groups and inoculated with 0.2 ml of subgroup A, subgroup C and an equal mixture of subgroup A and C Rous sarcoma virus (RSV). Subgroup virus receptor on the cell surface membrane for subgroup A is coded for by tumour virus a (tva) locus and for subgroup C by tumour virus c (tvc) locus. The random association of the genes at the tva and tvc loci in IWJ and IWC line was assessed and the $x^2$-values for phenotypic classes were found to be significant, indicating the linkage between the tva and tvc loci. The linkage value was estimated to be 0.09 on pooled sex and pooled line basis. On the basis of four subclass tumour phenotypes a 4-allele model was proposed for tva locus having $a^{s1}$, $a^{s2}$, $a^{r1}$ and $a^{r2}$ alleles and the frequencies were calculated as 0.47, 0.13, 0.13 and 0.27 for IWJ line, 0.31, 0.33, 0.14 and 0.22 for IWG line and 0.44, 0.11, 0.21 and 0.24 for IWC line, respectively. Similarly, for tvc locus the frequencies of four alleles i.e. $c^{s1}$, $c^{s2}$, $c^{r1}$ and $c^{r2}$ were calculated as 0.42, 0.20, 0.21 and 0.17 for IWJ line, 0.42, 0.17, 0.27 and 0.14 for IWG line and 0.30, 0.21, 0.16 and 0.33 for IWC line, respectively. The $x^2$-values for all classes of observations were not significant (p>0.05), indicating a good fit to the 4-allele model for the occurrence of 4-subclass tumour phenotypes for tva and tvc loci. On the basis of the 2-allele model both tva and tvc locus carries three genotypes each. But, on the basis of the 4-allele model tva and tvc locus carries 10 genotypes each. The interaction between A-resistance and C-resistance (both CAM and LT death) was ascertained by taking the 10 genotypes of tva locus and 3 genotypes of tvc locus by pooling the lines and partitioning the observations into 3 classes. The $x^2$-values for the genotypic classes of CAM (-) LT (+) and CAM (-) LT (-) phenotypes to mixed virus (A+C) infection were found to be highly significant (p<0.01), indicating increased resistance, which indicates the joint segregation of $a^r$ and $c^r$ genes, suggesting the existence of close linkage between the tva and tvc loci. Therefore, an indirect selection approach using subgroup C viruses can be employed to generate stocks resistant to subgroup A LLV, obviating contamination with the most common agent causing LL in field condition.

Highly Polymorphic Bovine Leptin Gene

  • Yoon, D.H.;Cho, B.H.;Park, B.L.;Choi, Y.H.;Cheong, H.S.;Lee, H.K.;Chung, E.R.;Cheong, I.C.;Shin, H.D.
    • Asian-Australasian Journal of Animal Sciences
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    • v.18 no.11
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    • pp.1548-1551
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    • 2005
  • The leptin, an anti-obesity protein, is a hormone protein expressed and secreted mainly from adipocyte tissue, and involved in regulation of body weight, food intake and energy metabolism. In an effort to discover polymorphism(s) in genes whose variant(s) might be implicated in phenotypic traits of growth, we have sequenced exons and their boundaries of leptin gene including 1,000 bp upstream of promoter region with twenty-four unrelated Korean cattle. Fifty-seven sequence variants were identified: fourteen in 5' flanking region, twenty-seven in introns, eight in exons, and eight in 3' flanking region. By pair-wise linkage analysis among polymorphisms, ten sets of SNPs were in absolute linkage disequilibrium (LD) (|D'| = 1 and $r^2$ = 1). Among variants identified, thirty-six SNPs were newly identified, and twenty-one SNPs, which were reported in other breeds, were also confirmed in Korean cattle. The allele frequencies of variants were quite different among breeds. The information from SNPs of bovine leptin gene could be useful for further genetic studies of this gene.

Application of Linkage Disequilibrium Mapping Methods to Detect QTL for Carcass Quality on Chromosome 6 Using a High Density SNP Map in Hanwoo

  • Lia, Y.;Lee, J.H.;Lee, Y.M.;Kim, J.J.
    • Asian-Australasian Journal of Animal Sciences
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    • v.24 no.4
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    • pp.457-462
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    • 2011
  • The purpose of this study was to detect QTL for carcass quality on bovine chromosome (BTA) 6 using a high density SNP map in a Hanwoo population. The data set comprised 45 sires and their 427 Hanwoo steers that were born between spring of 2005 and fall of 2007. The steers that were used for progeny testing in the Hanwoo Improvement Center in Seosan, Korea, were genotyped with the 2,535SNPs on BTA6 that were embedded in the Illumina bovine SNP 50K chip. Four different linkage disequilibrium (LD) mapping models were applied to detect significant SNPs for carcass quality traits; the fixed model with a single marker, the random model with a single marker, the random model with haplotype effects using two adjacent markers, and the random model at hidden state. A total of twelve QTL were detected, for which four, one, three and four SNPs were detected on BTA6 under the respective models (p<0.001). Among the detected QTL, four, two, five and one QTL were associated with carcass weight, backfat thickness, longissimus dorsi muscle area, and marbling score, respectively (p<0.001). Our results suggest that the use of multiple LD mapping approaches may be beneficial in increasing power to detect QTL given a limited sample size and magnitude of QTL effect.

Evaluation of a Fine-mapping Method Exploiting Linkage Disequilibrium in Livestock Populations: Simulation Study

  • Kim, JongJoo;Farnir, Frederic
    • Asian-Australasian Journal of Animal Sciences
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    • v.19 no.12
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    • pp.1702-1705
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    • 2006
  • A simulation study was conducted to evaluate a fine-mapping method exploiting population-wide linkage disequilibrium. Data were simulated according to the pedigree structure based on a large paternal half-sib family population with a total of 1,034 or 2,068 progeny. Twenty autosomes of 100 cM were generated with 5 cM or 1 cM marker intervals for all founder individuals in the pedigree, and marker alleles and a number of quantitative trait loci (QTL) explaining a total of 70% phenotypic variance were generated and randomly assigned across the whole chromosomes, assuming linkage equilibrium between the markers. The founder chromosomes were then descended through the pedigree to the current offspring generation, including recombinants that were generated by recombination between adjacent markers. Power to detect QTL was high for the QTL with at least moderate size, which was more pronounced with larger sample size and denser marker map. However, sample size contributed much more significantly to power to detect QTL than map density to the precise estimate of QTL position. No QTL was detected on the test chromosomes in which QTL was not assigned, which did not allow detection of false positive QTL. For the multiple QTL that were closely located, the estimates of the QTL positions were biased, except when the QTL were located on the right marker positions. Our fine mapping simulation results indicate that construction of dense maps and large sample size is needed to increase power to detect QTL and mapping precision for QTL position.

QTL Identification Using Combined Linkage and Linkage Disequilibrium Mapping for Milk Production Traits on BTA6 in Chinese Holstein Population

  • Hu, F.;Liu, J.F.;Zeng, Z.B.;Ding, X.D.;Yin, C.C.;Gong, Y.Z.;Zhang, Q.
    • Asian-Australasian Journal of Animal Sciences
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    • v.23 no.10
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    • pp.1261-1267
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    • 2010
  • Milk production traits are important economic traits for dairy cattle. The aim of the present study was to refine the position of previously detected quantitative trait loci (QTL) on bovine chromosome 6 affecting milk production traits in Chinese Holstein dairy cattle. A daughter design with 918 daughters from 8 elite sire families and 14 markers spanning the previously identified QTL region were used in the analysis. We employed a combined linkage and linkage disequilibrium analysis (LDLA) approach with two options for calculating the IBD probabilities, one was based on haplotypes of all 14 markers (named Method 1) and the other based on haplotypes with sliding windows of 5 markers (named Method 2). For milk fat yield, the two methods revealed a highly significant QTL located within a 6.5 cM interval (Method 1) and a 4.0 cM interval (Method 2), respectively. For milk protein yield, a highly significant QTL was detected within a 3.0 cM interval (Method 1) or a 2.5 cM interval (Method 2). These results confirmed the findings of our previous study and other studies, and greatly narrowed down the QTL positions.

Localization of Quantitative Trait Loci for Bone Mineral Density on Chromosome 13 in the Mongolian Population

  • Seo, Soo-Hyun;Lim, Hae-Jeng;Ahn, Se-Jin;Lee, Joseph;Kim, Jong-Il
    • Genomics & Informatics
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    • v.7 no.3
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    • pp.152-158
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    • 2009
  • Although the genetic basis for bone mineral density (BMD) has been studied by many groups so far, genes responsible for this complex trait has not been completely revealed. In order to localize quantitative trait loci (QTLs) for BMD variation in Asian population, the study was designed using a group of Mongolian population, a genetically closed population with a homogeneous lifestyle. BMD was measured at the left and right wrists and ankles using DEXA in 1,082 participants from 142 families. Genotyping of 13 polymorphic microsatellite markers on chromosome 13 (average spacing 8-9 cM) and two-point and multipoint linkage analysis were performed. In two-point linkage analysis, we identified two markers, D13S175 (6.03 cM) and D13S265 (68.73 cM) that had LOD scores greater than 1 for left ankle (LOD=2.09, LOD=1.49, respectively). We also found a marker D13S175 (6.03 cM) with a high LOD for left wrist (LOD=1.49) and the markers D13S265 (68.73 cM) and D13S217 (17.21 cM) for the right wrist (LOD= 1.82, LOD= 1.62, respectively). Among these significant marker regions, only two regions at 17 cM (13p11) and 65 cM (13q21) for the right wrist overlapped with major QTLs reported in following multipoint linkage analysis (LOD= 1.7549, LOD=1.4462, respectively). This study provides the possible evidence of the presence of QTLs affecting right wrist BMD in Mongolian populations on 13p11 and 13q21. Modest evidence was also found for genes affecting left ankle and left wrist BMD on 13p13.

The Linkage between Planned and Spontaneous Migration: The Roles of the Migration on Coffee Production in Dak Lak, Vietnam (계획 이주와 자발적 이주 간 연계 -베트남 닥락 성 커피 생산에서 이주의 역할-)

  • Chung, Su-Yeul
    • Journal of the Economic Geographical Society of Korea
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    • v.16 no.3
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    • pp.344-358
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    • 2013
  • Vietnam's growth as the second largest coffee producer in the world has been fueled by domestic migration into central highlands. However, the detail migration processes have not been explicitly discussed. In particular, the existing literatures tend to describe the migration flow in a framework of planned migration versus spontaneous migration, paying less attention to the linkage between them. With a case study of Dak Lak province which is the leading robusta producer in Vietnam, this research investigates the linkage between planned and spontaneous migration in a multiscalar approach. The statistic data allow the researcher to know temporal association between the two type of migration in a provine scale. The survey and interview about two coffee-producing communes - Ea H'Ding in Cu M'gar district and Doan Ket in Krung Buk district - inform us that the linkage between planned and spontaneous migration is contingent to the local contexts including ethnic composition, timing of settlements, governement's development program, and timing of a large flow of in-migration.

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Characterization of Single Nucleotide Polymorphisms in 55 Disease-Associated Genes in a Korean Population

  • Lee, Seung-Ku;Kim, Hyoun-Geun;Kang, Jason-J.;Oh, Won-Il;Oh, Berm-Seok;Kwack, Kyu-Bum
    • Genomics & Informatics
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    • v.5 no.4
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    • pp.152-160
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    • 2007
  • Most common diseases are caused by multiple genetic and environmental factors. Among the genetic factors, single nucleotide polymorphisms (SNPs) are common DNA sequence variations in individuals and can serve as important genetic markers. Recently, investigations of gene-based and whole genome-based SNPs have been applied to association studies for marker discovery. However, SNPs are so population-specific that the association needs to be verified. Fifty-five genes and 384 SNPs were selected based on association with disease. Genotypes of 337 SNPs in candidate genes were determined using Illumina Sentrix Array Matrix (SAM) chips by an allele-specific extension method in 364 unrelated Korean individuals. Allelic frequencies of SNPs were compared with those of other populations obtained from the International HapMap database. Minor allele frequencies, linkage disequilibrium blocks, tagSNPs, and haplotypes of functional candidate SNPs in 55 genetic disease-associated genes were provided. Our data may provide useful information for the selection of genetic markers for gene-based genetic disease-association studies of the Korean population.