Fine Mapping of Milk Production QTL on BTA6 by Combined Linkage and Linkage Disequilibrium Analysis

Olsen, Harald; Lien, Sigbjørn; Svendsen, Mathias Tiedemann; Nilsen, Heidi; Røseth, Arne; Opsal, M.A.; Meuwissen, Theo H. E.

doi:10.3168/jds.s0022-0302(04)73212-9

Cited by 58 publications

(53 citation statements)

References 20 publications

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“…For this reason, and its relative ease of use, the IBD method of Meuwissen and Goddard (2000) and its extension to include linkage information (Meuwissen et al 2002) have become the basis for many QTL fine-mapping studies conducted in livestock (e.g., Blott et al 2003;Olsen et al 2004). However, it has been shown here that additional mapping precision could be obtained with the IBD method if marker information is used in a selective manner to estimate IBD probabilities at any given position.…”

Section: Discussionmentioning

confidence: 99%

“…Recently, Olsen et al (2004) utilized the combined linkage and LD mapping method of Meuwissen et al (2002) to fine map QTL for milk production traits in dairy cattle. Thus, the IBD method is becoming widely used for fine mapping QTL in livestock, especially in combination with linkage information, because it fits with the established framework in animal breeding of performing genetic analysis of outbred populations using mixed linear models.…”

Section: W Ith the Identification Of Numerous Quantitativementioning

confidence: 99%

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Optimal Haplotype Structure for Linkage Disequilibrium-Based Fine Mapping of Quantitative Trait Loci Using Identity by Descent

et al. 2006

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A linkage disequilibrium-based method for fine mapping quantitative trait loci (QTL) has been described that uses similarity between individuals' marker haplotypes to determine if QTL alleles are identical by descent (IBD) to model covariances among individuals' QTL alleles for a mixed linear model. Mapping accuracy with this method was found to be sensitive to the number of linked markers that was included in the haplotype when fitting the model at a putative position of the QTL. The objective of this study was to determine the optimal haplotype structure for this IBD-based method for fine mapping a QTL in a previously identified QTL region. Haplotypes consisting of 1, 2, 4, 6, or all 10 available markers were fit as a ''sliding window'' across the QTL region under ideal and nonideal simulated population conditions. It was found that using haplotypes of 4 or 6 markers as a sliding ''window'' resulted in the greatest mapping accuracy under nearly all conditions, although the true IBD state at a putative QTL position was most accurately predicted by IBD probabilities obtained using all markers. Using 4 or 6 markers resulted in greater discrimination of IBD probabilities between positions while maintaining sufficient accuracy of IBD probabilities to detect the QTL. Fitting IBD probabilities on the basis of a single marker resulted in the worst mapping accuracy under all conditions because it resulted in poor accuracy of IBD probabilities. In conclusion, for fine mapping using IBD methods, marker information must be used in a manner that results in sensitivity of IBD probabilities to the putative position of the QTL while maintaining sufficient accuracy of IBD probabilities to detect the QTL. Contrary to expectation, use of haplotypes of 4-6 markers to derive IBD probabilities, rather than all available markers, best fits these criteria. Thus for populations similar to those simulated here, optimal mapping accuracy for this IBD-based fine-mapping method is obtained with a haplotype structure including a subset of all available markers. W ITH the identification of numerous quantitative trait loci (QTL) regions in economically important livestock species, the focus has now shifted to fine mapping these QTL as the next step toward identifying genes underlying complex traits. Methods that utilize historical recombination information on the basis of linkage disequilibrium (LD) allow fine mapping using existing outbred populations instead of experimental mapping populations. These methods are becoming popular for QTL fine mapping in livestock, where the creation of mapping populations such as advanced intercrossed lines (Darvasi and Soller 1995) is expensive and time consuming.Meuwissen and Goddard (2000) proposed a haplotype-based method to fine map QTL, using a mixed linear model that models covariances between individuals at a putative QTL on the basis of similarity of their marker haplotypes. Individuals with similar marker haplotypes are likely to share QTL alleles that are identical by descent (IBD) and so...

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Section: Discussionmentioning

confidence: 99%

Section: W Ith the Identification Of Numerous Quantitativementioning

confidence: 99%

Optimal Haplotype Structure for Linkage Disequilibrium-Based Fine Mapping of Quantitative Trait Loci Using Identity by Descent

et al. 2006

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“…Several whole-genome scans in cattle have identified QTL affecting milk production traits on BTA 6 close to OPN gene location (Zhang et al, 1998;Nadesalingam et al, 2001;Ron et al, 2001;Ashwell et al, 2004;Olsen et al, 2004). Schnabel et al (2005) reported OPN as a strong candidate gene underlying the QTL region of BTA 6 that harbors the largest number of milk-related QTLs.…”

Section: Introductionmentioning

confidence: 99%

Characterization of Osteopontin gene of Bubalus bubalis

Tantia

Kumar

Mishra

et al. 2008

Animal

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Osteopontin, a glycoprotein, is expressed in several tissues including the mammary gland. The gene has been reported to be associated with milk and its constituents in various livestock species. This gene was sequenced in buffalo and it coded for the protein of 280 amino acids with the conserved GRGDS domain. The sequence was confirmed from the cDNA sequence derived from the mammary gland of buffalo. The earlier-reported 9T/10T variation in the upstream region of the gene was investigated for its effect on milk in buffalo and it was found to be non-significant.

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“…Moreover, OPN is highly expressed in bone, macrophages, endothelial, smooth muscle and epithelial cells (13). OPN is involved in diverse biological, physiological and pathological processes including recruiting and stimulating macrophages in response to infection (13), interactions with ions (13), inflammation (17), biomineralization, leukocyte recruitment and cell survival (17). Cow milk was reported to have 8 mg.L -1 OPN (18).…”

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confidence: 99%

The Association of Bovine Osteopontin (OPN) Gene with Milk Production Traits in Iranian Holstein Bulls

et al. 2015

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Fine Mapping of Milk Production QTL on BTA6 by Combined Linkage and Linkage Disequilibrium Analysis

Cited by 58 publications

References 20 publications

Optimal Haplotype Structure for Linkage Disequilibrium-Based Fine Mapping of Quantitative Trait Loci Using Identity by Descent

Optimal Haplotype Structure for Linkage Disequilibrium-Based Fine Mapping of Quantitative Trait Loci Using Identity by Descent

Characterization of Osteopontin gene of Bubalus bubalis

The Association of Bovine Osteopontin (OPN) Gene with Milk Production Traits in Iranian Holstein Bulls

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