Linkage mapping bovine EST-based SNP

Snelling, W. M.; Casas, Eduardo; Stone, R. T.; Keele, J. W.; Harhay, Gregory P; Bennett, G. L.; Smith, Timothy P. L.

doi:10.1186/1471-2164-6-74

Cited by 59 publications

(38 citation statements)

References 28 publications

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“…Single nucleotide polymorphisms (SNP) are the most abundant form of DNA variation in the genome and are becoming preferred over other genetic markers because of their relatively low mutation rate as well as the ease and low cost of genotyping (Hinds et al 2005;Snelling et al 2005). SNP have been used for the detection and localization of QTL for complex traits in many species (Daw et al 2005).…”

Section: Discussionmentioning

confidence: 99%

A whole genome scan to map QTL for milk production traits and somatic cell score in Canadian Holstein bulls

Kolbehdari

Wang

Grant

et al. 2009

J Animal Breeding Genetics

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The detection and mapping of genetic markers linked to quantitative trait loci (QTL) can be utilized to enhance genetic improvement of livestock populations. With the completion of the bovine genome sequence assembly, single nucleotide polymorphisms (SNP) assays spanning the whole bovine genome and research work on large scale identification, validation and analysis of genotypic variation in cattle has become possible. The objective of the present study was to perform a whole genome scan to identify and map QTL affecting milk production traits and somatic cell scores using linkage disequilibrium (LD) regression and 1536 SNP markers. Three and 18 SNP were found to be associated with only milk yield (MY) at a genome and chromosome wise significance (p < 0.05) level respectively. Among the 21 significant SNP, 16 were in a region reported to have QTL for MY in other dairy cattle populations and while the rest five were new QTL finding. Four SNP out of 21 are significant for the milk production traits (MY, fat yield, protein yield (PY), and milk contents) in the present study. Six and nine SNP were associated with PY at a genome and chromosome wise significant (p < 0.05) level respectively. Three and 17 SNP were found to be associated with FY at a genome and chromosome wise significant (p < 0.05) level. Five and seven SNP were mapped with somatic cell score at a genome and chromosome wise significant (p < 0.05) level respectively. The results of this study have revealed QTL for MY, PY, protein percentage, FY, fat percentage, somatic cell score and persistency of milk in the Canadian dairy cattle population. The chromosome regions identified in this study should be further investigated to potentially identify the causative mutations underlying the QTL.

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Section: Discussionmentioning

confidence: 99%

A whole genome scan to map QTL for milk production traits and somatic cell score in Canadian Holstein bulls

Kolbehdari

Wang

Grant

et al. 2009

J Animal Breeding Genetics

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“…Alleles designated as T 9 and T 10 describe 9 or 10 consecutive thymidine bases on the sense strand of SPP1, respectively. Microsatellite genotyping procedures were previously described by Kappes et al (2000), and map positions were used directly from the USMARC linkage map (Snelling et al, 2005). Previously, Kappes et al (2000) had genotyped 181 progeny-tested sires from this population for 12 microsatellites on BTA6.…”

Section: Genotypingmentioning

confidence: 99%

Association of a single nucleotide polymorphism in SPP1 with growth traits and twinning in a cattle population selected for twinning rate1,2

Allan

Thallman

Cushman

et al. 2007

Journal of Animal Science

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Continued validation of genetic markers for economically important traits is crucial to establishing marker-assisted selection as a tool in the cattle industry. The objective of the current study was to evaluate the association of a SNP (T(9)/T(10)) in the osteopontin gene (SPP1) with growth rate in a large cattle population spanning multiple generations and representing alleles from 12 founding breeds. This population has been maintained at the US Meat Animal Research Center since 1981 and subjected to selection for twinning rate. Phenotypic records for this population included twinning rate and ovulation rate, providing an opportunity to examine the potential effects of SPP1 genotype on reproductive traits. A set of 2,701 animals was geno-typed for the T(9)/T(10) polymorphism at SPP1. The geno-typic data, including previously genotyped markers on chromosome 6 (BTA6), were used in conjunction with pedigree information to estimate genotypic probabilities for all 14,714 animals with phenotypic records. The genotypic probabilities for females were used to calculate independent variables for regressions of additive, dominance, and imprinting effects. Genotypic regressions were fit as fixed effects in a mixed model analysis, in which each trait was analyzed in a 2-trait model where single births were treated as a separate trait from twin births. The association of the SPP1 marker with birth weight (P < 0.006), weaning weight (P < 0.007), and yearling weight (P < 0.003) was consistent with the previously reported effects of SPP1 genotype on yearling weight. Our data supports the conclusion that the SNP successfully tracks functional alleles affecting growth in cattle. The previously undetected effect of the SNP on birth and weaning weight suggests this particular SPP1 marker may explain a portion of the phenotypic variance explained by QTL for birth and HCW on BTA6.

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“…Many groups of closely linked SNPs have been discovered in recent years through analysis of expressed sequence tags (e.g. Snelling et al. 2005) and potential candidate genes (e.g.…”

Section: Resultsmentioning

confidence: 99%

Use of linked loci as individuals or haplotypes for marker‐assisted breed assignment

et al. 2008

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The objective of this study was to use simulation to evaluate the benefits of considering haplotypes of loci when linked single nucleotide polymorphisms are used for breed assignment. Three breeds of 10,000 females each were simulated under eight scenarios that differed according to the number of generations separating the breeds, size of breed founder populations and recombination rate between linked loci. Molecular genotypes consisted of 20 groups of three linked loci each. Breed assignment was performed in the final generation and was based on the frequency method. Haplotypes were reconstructed using the expectation-maximization algorithm. Accuracy of breed assignment was based on the frequency of correct breed assignment. Assignment accuracy increased as more genotypes (loci or haplotypes) were considered and more animals were used to estimate genotypic frequencies within breed. For most scenarios, use of haplotypes yielded equal or greater accuracies than when loci were considered independent. The advantage of haplotypes tended to increase as linkage disequilibrium between adjacent loci increased. The greatest advantage for using haplotypes was observed when recombination rate was low (0.001), breeds were separated by few generations (100), and a relatively large number of founder animals (110) was used to form new breeds. In this situation, 90% accuracy of breed assignment was achieved using nine to 14 haplotypes (i.e. 27-42 loci) depending on breed, vs. 39-57 individual loci.

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Linkage mapping bovine EST-based SNP

Cited by 59 publications

References 28 publications

A whole genome scan to map QTL for milk production traits and somatic cell score in Canadian Holstein bulls

A whole genome scan to map QTL for milk production traits and somatic cell score in Canadian Holstein bulls

Association of a single nucleotide polymorphism in SPP1 with growth traits and twinning in a cattle population selected for twinning rate1,2

Use of linked loci as individuals or haplotypes for marker‐assisted breed assignment

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