| Title |
Compression distance can discriminate animals by genetic profile, build relationship matrices and estimate breeding values
|
|---|---|
| Published in |
Genetics Selection Evolution, October 2015
|
| DOI | 10.1186/s12711-015-0158-9 |
| Pubmed ID | |
| Authors |
Nicholas J. Hudson, Laercio Porto-Neto, James W. Kijas, Antonio Reverter |
| Abstract |
Genetic relatedness is currently estimated by a combination of traditional pedigree-based approaches (i.e. numerator relationship matrices, NRM) and, given the recent availability of molecular information, using marker genotypes (via genomic relationship matrices, GRM). To date, GRM are computed by genome-wide pair-wise SNP (single nucleotide polymorphism) correlations. We describe a new estimate of genetic relatedness using the concept of normalised compression distance (NCD) that is borrowed from Information Theory. Analogous to GRM, the resultant compression relationship matrix (CRM) exploits numerical patterns in genome-wide allele order and proportion, which are known to vary systematically with relatedness. We explored properties of the CRM in two industry cattle datasets by analysing the genetic basis of yearling weight, a phenotype of moderate heritability. In both Brahman (Bos indicus) and Tropical Composite (Bos taurus by Bos indicus) populations, the clustering inferred by NCD was comparable to that based on SNP correlations using standard principal component analysis approaches. One of the versions of the CRM modestly increased the amount of explained genetic variance, slightly reduced the 'missing heritability' and tended to improve the prediction accuracy of breeding values in both populations when compared to both NRM and GRM. Finally, a sliding window-based application of the compression approach on these populations identified genomic regions influenced by introgression of taurine haplotypes. For these two bovine populations, CRM reduced the missing heritability and increased the amount of explained genetic variation for a moderately heritable complex trait. Given that NCD can sensitively discriminate closely related individuals, we foresee CRM having possible value for estimating breeding values in highly inbred populations. |
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Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Denmark | 1 | 50% |
| Australia | 1 | 50% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 1 | 50% |
| Scientists | 1 | 50% |
Mendeley readers
The data shown below were compiled from readership statistics for 26 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| New Zealand | 1 | 4% |
| United States | 1 | 4% |
| Denmark | 1 | 4% |
| France | 1 | 4% |
| Unknown | 22 | 85% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Researcher | 8 | 31% |
| Other | 6 | 23% |
| Student > Ph. D. Student | 3 | 12% |
| Student > Master | 2 | 8% |
| Student > Doctoral Student | 1 | 4% |
| Other | 2 | 8% |
| Unknown | 4 | 15% |
| Readers by discipline | Count | As % |
|---|---|---|
| Agricultural and Biological Sciences | 12 | 46% |
| Biochemistry, Genetics and Molecular Biology | 3 | 12% |
| Mathematics | 2 | 8% |
| Pharmacology, Toxicology and Pharmaceutical Science | 1 | 4% |
| Computer Science | 1 | 4% |
| Other | 3 | 12% |
| Unknown | 4 | 15% |
Attention Score in Context
This research output has an Altmetric Attention Score of 5. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 19 September 2018.
All research outputs
#7,047,954
of 25,374,917 outputs
Outputs from Genetics Selection Evolution
#222
of 822 outputs
Outputs of similar age
#79,897
of 291,306 outputs
Outputs of similar age from Genetics Selection Evolution
#3
of 19 outputs
Altmetric has tracked 25,374,917 research outputs across all sources so far. This one has received more attention than most of these and is in the 71st percentile.
So far Altmetric has tracked 822 research outputs from this source. They receive a mean Attention Score of 4.1. This one has gotten more attention than average, scoring higher than 72% of its peers.
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We're also able to compare this research output to 19 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 84% of its contemporaries.