https://aipl.arsusda.gov/publish/jds/2009/92_16.pdf

Invited review: reliability of genomic predictions for North American Holstein bulls.

When a genetic marker and a quantitative trait locus (QTL) are in linkage disequilibrium (LD) in one population, they may not be in LD in another population or their LD phase may be reversed. The objectives of this study were to compare the extent of LD and the persistence of LD phase across multiple cattle populations. LD measures r and r(2) were calculated for syntenic marker pairs using genomewide single-nucleotide polymorphisms (SNP) that were genotyped in Dutch and Australian Holstein-Friesian (HF) bulls, Australian Angus cattle, and New Zealand Friesian and Jersey cows. Average r(2) was approximately 0.35, 0.25, 0.22, 0.14, and 0.06 at marker distances 10, 20, 40, 100, and 1000 kb, respectively, which indicates that genomic selection within cattle breeds with r(2) >or= 0.20 between adjacent markers would require approximately 50,000 SNPs. The correlation of r values between populations for the same marker pairs was close to 1 for pairs of very close markers (<10 kb) and decreased with increasing marker distance and the extent of divergence between the populations. To find markers that are in LD with QTL across diverged breeds, such as HF, Jersey, and Angus, would require approximately 300,000 markers.

https://www.genetics.org/content/genetics/179/3/1503.full.pdf

Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle

The widespread use of elite sires by means of artificial insemination in livestock breeding leads to the frequent emergence of recessive genetic defects, which cause significant economic and animal welfare concerns. Here we show that the availability of genome-wide, high-density SNP panels, combined with the typical structure of livestock populations, markedly accelerates the positional identification of genes and mutations that cause inherited defects. We report the fine-scale mapping of five recessive disorders in cattle and the molecular basis for three of these: congenital muscular dystony (CMD) types 1 and 2 in Belgian Blue cattle and ichthyosis fetalis in Italian Chianina cattle. Identification of these causative mutations has an immediate translation into breeding practice, allowing marker assisted selection against the defects through avoidance of at-risk matings.

/pdf/highly-effective-snp-based-association-mapping-and-k60oxseytg.pdf

Highly effective SNP-based association mapping and management of recessive defects in livestock

Consequences of selection for milk yield from a geneticist's viewpoint.

The Effects of Inbreeding on the Lifetime Performance of Dairy Cattle

The estimate of inbreeding for registered Holstein females born during 1990 was 5.1 f 0.4% for a random sample of 600 two-line pedigrees. Previously published estimates were 4.7% for 1970, 3.8% for 1976, and 4.3% for 1982 from similar samples of pedigrees. These estimates were calculated using a base of approximately 1884, or the initiation of herdbook registration in the US. The estimate of relationship between randomly paired females born during 1990 was 10.2 f 0.8%; relationships were 5.2% for 1970, 7.3% for 1976, and 9.8% for 1982. Average relationship within the breed increased significantly without a corresponding increase in inbreeding. Inbreeding was also estimated for alternative base years with 10-yr increments to determine the effect of base year on estimates of inbreeding. Using 1950 as the base year, inbreeding was estimated at 0.5% for 1970, 0.3% for 1976, 1.6% for 1982, and 2.1% for 1990. Estimates using 1920 as the base year were 2.0% for 1970, 1.9% for 1976, 2.3% for 1982, and 3.2% for 1990. More recent base years gave lower estimates of inbreeding, as expected, but showed an exaggerated percentage of increase in inbreeding from 1970 to 1990. However, the annual amount of increase of inbreeding from 1976 to 1990 was not significantly affected by time of base year and ranged from 0.08 to 0.12/yr. The five most influential bulls of the breed were Pawnee Farm Arlinda Chief 1427381, Round Oak Rag Apple Elevation 1491007, S-W-D Valiant 1650414, Osborndale Ivanhoe 1189870, and Sir Pietertje Ormsby Mercedes 4493 1; estimated direct relationships to the breed were 0.123, 0.122, 0.096, 0.083, and 0.074, respectively.

OUR INDUSTRY TODAY Estimates of Inbreeding and Relationship Among Registered Holstein Females in the United States

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OUR INDUSTRY TODAY Estimates of Inbreeding and Relationship Among Registered Holstein Females in the United States