Association Analysis of MBL1 Gene SNPs, Genotype and Haplotypes with Clinical Mastitis in Murrah Buffaloes

Mannose-binding lectins (MBL1) gene a most important constituent of immune response system of an organism, the primary role of this gene in the classical and lectin-activation pathways is to provide protection against various dieases or bacterial pathogens. In this study, eight novel SNPs identified in the promoter region of MBL1 gene were 154C>T, 235G>A, 252A>T, 265C>A, 268T>C, 282G>A, 431G>A and 551C>G, when compared to reference sequence of Bubalus bubalis (NCBI accession number KC415281). Genomic DNA isolated from 200 lactating Murrah buffaloes was amplified for the targeted sequence of MBL1. PCR products were custom sequenced, edited and used for further analysis. The results indicated that only 551C>G polymorphism locus met Hardy–Weinberg equilibrium (c2 (2df) = 4.4: P=0.11). Pair linkage disequilibrium analysis and haplotype construction of MBL1 gene were performed using SHEsis software. Pair linkage disequilibrium analysis revealed moderate to strong linkage disequilibrium between the eight SNPs loci A total of 17 haplotypes were generated from eight SNPs in promoter region of MBL1 gene. Association between eight SNPs of MBL1 gene in Murrah buffalo has been analyzed and relative risks of the alleles for clinical mastitis were estimated with an odds ratio. Allelic association analysis showed that T allele of 154C>T, A allele of 235G>A, A allele of 252A>T, A allele of 265C>A , T allele of 268T>C, A allele of 282G>A , A allele of 431G>A and G allele of 551C>G had significant association with increased risk of clinical mastitis (P< 0.01). Haplotype analysis showed that Hap15 (CAAATAAG) and Hap16 (TAAATAAG) i.e. the haplotypes containing all 8 “at-risk” alleles, were significantly associated with clinical mastitis (P< 0.01). Hap6 (CGAATAAC) and Hap8 (CGTCCGGC) were significantly associated with a lower risk of clinical mastitis in Murrah buffaloes (P< 0.01).On the other hand, the Hap6 (CGAATAAC) and Hap8 (CGTCCGGC) which are unrepresented in affected group and without “at-risk” alleles were significantly associated with a lower risk for clinical mastitis (P<0.01).These findings indicated a MBL1 gene polymorphism could be used as genetic marker for mastitis resistance in Murrah buffaloes.

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Association Analysis (Linkage Disequilibrium Analysis)

Dictionary of Bioinformatics and Computational Biology ◽

10.1002/0471650129.dob0039 ◽

2004 ◽

Author(s):

Mark McCarthy ◽

Steven Wiltshire

Keyword(s):

Linkage Disequilibrium ◽

Association Analysis ◽

Linkage Disequilibrium Analysis

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Refined mapping of a QTL for somatic cell score on BTA27 in the German Holstein using combined linkage and linkage disequilibrium analysis

Canadian Journal of Animal Science ◽

10.4141/cjas09069 ◽

2010 ◽

Vol 90 (2) ◽

pp. 169-178 ◽

Cited By ~ 2

Author(s):

C. Baes ◽

M. Mayer ◽

J. Tetens ◽

Z. Liu ◽

F. Reinhardt ◽

...

Keyword(s):

Linkage Disequilibrium ◽

Somatic Cell ◽

Fine Mapping ◽

Bos Taurus ◽

Genetic Selection ◽

Region Of Interest ◽

Clinical Mastitis ◽

Somatic Cell Score ◽

Linkage Disequilibrium Analysis ◽

Trait Locus

Genetic selection for udder health is often based on the indicator trait somatic cell score (SCS), which is correlated with clinical mastitis and has a moderate heritability. We used combined linkage and linkage disequilibrium analysis to refine mapping of a previously reported quantitative trait locus (QTL) affecting SCS on Bos taurus autosome 27 (BTA27) in the German Holstein population. A granddaughter design of six grandsire families with 492 sons progeny tested for an average of 190 daughters per son was investigated. Nineteen microsatellite markers were genotyped along a segment of 26.2 cM proximally on BTA27. A chromosome-wide significant QTL was identified between DIK2879 and KIBS272 using combined analysis. The region of interest for future fine mapping experiments was narrowed to the marker interval KIBS272-DIK2191 with a confidence interval of 3.27 cM. The QTL was estimated to be responsible for 18% of the genetic variation in SCS. Application of a 2-QTL model did not result in higher test statistics. Animals likely to be heterozygous or homozygous at the QTL were identified. This study provides a basis for the selection of further markers in linkage disequilibrium with the QTL affecting SCS on BTA27. Key words: Fine-mapping, mastitis, BTA27, somatic cell score, Holstein

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Association Analysis (Linkage Disequilibrium Analysis)

Dictionary of Bioinformatics and Computational Biology ◽

10.1002/9780471650126.dob0039.pub2 ◽

2004 ◽

Author(s):

Andrew Collins ◽

Mark McCarthy ◽

Steven Wiltshire

Keyword(s):

Linkage Disequilibrium ◽

Association Analysis ◽

Linkage Disequilibrium Analysis

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SNPAnalyzer 2.0: A web-based integrated workbench for linkage disequilibrium analysis and association analysis

BMC Bioinformatics ◽

10.1186/1471-2105-9-290 ◽

2008 ◽

Vol 9 (1) ◽

pp. 290 ◽

Cited By ~ 68

Author(s):

Jinho Yoo ◽

Youngbok Lee ◽

Yujung Kim ◽

Sun Rha ◽

Yangseok Kim

Keyword(s):

Linkage Disequilibrium ◽

Association Analysis ◽

Linkage Disequilibrium Analysis ◽

Web Based

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Linkage and linkage disequilibrium analysis of the lipoprotein lipase gene with lipid profiles in Chinese hypertensive families

Clinical Science ◽

10.1042/cs20040101 ◽

2005 ◽

Vol 108 (2) ◽

pp. 137-142 ◽

Cited By ~ 5

Author(s):

Wenjie YANG ◽

Jianfeng HUANG ◽

Cailiang YAO ◽

Shaoyong SU ◽

Donghai LIU ◽

...

Keyword(s):

Linkage Disequilibrium ◽

Lipoprotein Lipase ◽

Lipid Profiles ◽

Strong Linkage Disequilibrium ◽

Nucleotide Polymorphisms ◽

Linkage Disequilibrium Analysis ◽

Lipid Levels ◽

Lipase Gene ◽

Significant Independent Risk Factor ◽

Lpl Gene

Elevated TG [triacylglycerol (triglyceride)] is a significant independent risk factor for cardiovascular disease. LPL (lipoprotein lipase) is one of the key enzymes in the metabolism of the TG-rich lipoproteins which hydrolyses TG from the chylomicrons and very-LDL (low-density lipoprotein). To investigate the relationship between the LPL gene and lipid profiles, especially TG, in 148 hypertensive families, we have chosen seven flanking microsatellite markers and four internal markers of the LPL gene and conducted linkage analysis by SOLAR and S.A.G.E. (statistical analysis for genetic epidemiology)/SIBPAL 2 programs, and linkage disequilibrium analysis by QTDT (quantitative transmission/disequilibrium test) and GOLD (graphical overview of linkage disequilibrium). There were statistically significant differences in lipid levels between subjects without and with hypertension within families. A maximum LOD score of 1.3 with TG at the marker D8S261 was observed by SOLAR. Using S.A.G.E./SIBPAL 2, we identified a linkage with TG at the marker ‘ATTT’ located within intron 6 of the LPL gene (P=0.0095). Two SNPs (single nucleotide polymorphisms), HindIII and HinfI, were found in linkage disequilibrium with LDL-cholesterol levels (P=0.0178 and P=0.0088 respectively). A strong linkage disequilibrium was observed between the HindIII in intron 8 and HinfI in the exon 9 (P<0.00001, D′=0.895). Linkage disequilibrium was also found between the ‘ATTT’ polymorphism in intron 6 and two SNPs (P=0.0021 and D′=0.611 for HindIII; and P=0.00004, D′=0.459 for HinfI). The present study in the Chinese families with hypertension suggested that the LPL gene might influence lipid levels, especially TG metabolism. Replication studies both in Chinese and other populations are warranted to confirm these results.

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