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C.P. Van Tassell

Bio: C.P. Van Tassell is an academic researcher from Agricultural Research Service. The author has contributed to research in topics: Quantitative trait locus & Population. The author has an hindex of 30, co-authored 55 publications receiving 3688 citations. Previous affiliations of C.P. Van Tassell include University of Wisconsin-Madison & University of Kiel.


Papers
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Journal ArticleDOI
TL;DR: Genotypes for 38,416 markers and August 2003 genetic evaluations for 3,576 Holstein bulls born before 1999 were used to predict January 2008 daughter deviations and genomic prediction improves reliability by tracing the inheritance of genes even with small effects.

1,166 citations

Journal ArticleDOI
01 Mar 2003-Genetics
TL;DR: The low level of LD and the limited haplotype diversity suggested that the genome of any given soybean accession is a mosaic of three or four haplotypes, thereby supporting the suggestion of relatively limited genetic variation in cultivated soybean.
Abstract: Single-nucleotide polymorphisms (SNPs) provide an abundant source of DNA polymorphisms in a number of eukaryotic species. Information on the frequency, nature, and distribution of SNPs in plant genomes is limited. Thus, our objectives were (1) to determine SNP frequency in coding and noncoding soybean (Glycine max L. Merr.) DNA sequence amplified from genomic DNA using PCR primers designed to complete genes, cDNAs, and random genomic sequence; (2) to characterize haplotype variation in these sequences; and (3) to provide initial estimates of linkage disequilibrium (LD) in soybean. Approximately 28.7 kbp of coding sequence, 37.9 kbp of noncoding perigenic DNA, and 9.7 kbp of random noncoding genomic DNA were sequenced in each of 25 diverse soybean genotypes. Over the >76 kbp, mean nucleotide diversity expressed as Watterson's theta was 0.00097. Nucleotide diversity was 0.00053 and 0.00111 in coding and in noncoding perigenic DNA, respectively, lower than estimates in the autogamous model species Arabidopsis thaliana. Haplotype analysis of SNP-containing fragments revealed a deficiency of haplotypes vs. the number that would be anticipated at linkage equilibrium. In 49 fragments with three or more SNPs, five haplotypes were present in one fragment while four or less were present in the remaining 48, thereby supporting the suggestion of relatively limited genetic variation in cultivated soybean. Squared allele-frequency correlations (r(2)) among haplotypes at 54 loci with two or more SNPs indicated low genome-wide LD. The low level of LD and the limited haplotype diversity suggested that the genome of any given soybean accession is a mosaic of three or four haplotypes. To facilitate SNP discovery and the development of a transcript map, subsets of four to six diverse genotypes, whose sequence analysis would permit the discovery of at least 75% of all SNPs present in the 25 genotypes as well as 90% of the common (frequency >0.10) SNPs, were identified.

449 citations

Journal ArticleDOI
TL;DR: Within-family analysis detected putative QTL associated with pregnancy rate on six chromosomes, with the effect on chromosome 18 being the most significant statistically.

248 citations

Journal ArticleDOI
TL;DR: A high-density scan using 38,416 single nucleotide polymorphism markers for 5,285 bulls confirmed 2 previously known major genes on Bos taurus autosomes (BTA) 6 and 14 but revealed few other large effects as discussed by the authors.

224 citations

Journal ArticleDOI
TL;DR: Thousands of SNP that were polymorphic in Holsteins were monomorphic in Jerseys or Brown Swiss, which indicated that breed-specific SNP sets are required or that all breeds need to be considered in the SNP selection process.

166 citations


Cited by
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Journal Article
Fumio Tajima1
30 Oct 1989-Genomics
TL;DR: It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.

11,521 citations

Journal ArticleDOI
TL;DR: In this article, a new technology called genomic selection is revolutionizing dairy cattle breeding, which refers to selection decisions based on genomic breeding values (GEBV) and is calculated as the sum of the effects of dense genetic markers, or haplotypes of these markers, across the entire genome, thereby capturing all the quantitative trait loci (QTL) that contribute to variation in a trait.

1,461 citations

Journal Article
TL;DR: The reliabilities of GEBV achieved were significantly greater than the reliability of parental average breeding values, the current criteria for selection of bull calves to enter progeny test teams, and the increase in reliability is sufficiently high that at least 2 dairy breeding companies are already marketing bull teams for commercial use based on their GEBv only.

1,380 citations

Journal ArticleDOI
TL;DR: Genotypes for 38,416 markers and August 2003 genetic evaluations for 3,576 Holstein bulls born before 1999 were used to predict January 2008 daughter deviations and genomic prediction improves reliability by tracing the inheritance of genes even with small effects.

1,166 citations

Journal ArticleDOI
TL;DR: A national single-step genetic evaluation with the pedigree relationship matrix augmented with genomic information provided genomic predictions with accuracy and bias comparable to multiple-step procedures and could account for any population or data structure.

1,095 citations