scholarly journals Genomic evaluation using SNP- and haplotype-based genomic relationship matrices in a closed line of Duroc pigs

2017 ◽  
Vol 88 (10) ◽  
pp. 1465-1474 ◽  
Author(s):  
Yoshinobu Uemoto ◽  
Shuji Sato ◽  
Takashi Kikuchi ◽  
Sachiko Egawa ◽  
Kimiko Kohira ◽  
...  
Keyword(s):  
Genomic Relationship ◽  
Genomic Evaluation ◽  
Closed Line

scholarly journals 353 ASAS-EAAP Talk: Low-coverage whole-genome sequencing in local livestock breeds

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 81-82
Author(s):  
Joaquim Casellas ◽  
Melani Martín de Hijas-Villalba ◽  
Marta Vázquez-Gómez ◽  
Samir Id Lahoucine
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Error Rate ◽  
Allele Frequencies ◽  
Paternity Testing ◽  
Sequencing Error ◽  
Whole Genome ◽  
Genomic Evaluation ◽  
Sequencing Error Rate ◽  
Low Coverage

Abstract Current European regulations for autochthonous livestock breeds put a special emphasis on pedigree completeness, which requires laboratory paternity testing by genetic markers in most cases. This entails significant economic expenditure for breed societies and precludes other investments in breeding programs, such as genomic evaluation. Within this context, we developed paternity testing through low-coverage whole-genome data in order to reuse these data for genomic evaluation at no cost. Simulations relied on diploid genomes composed by 30 chromosomes (100 cM each) with 3,000,000 SNP per chromosome. Each population evolved during 1,000 non-overlapping generations with effective size 100, mutation rate 10–4, and recombination by Kosambi’s function. Only those populations with 1,000,000 ± 10% polymorphic SNP per chromosome in generation 1,000 were retained for further analyses, and expanded to the required number of parents and offspring. Individuals were sequenced at 0.01, 0.05, 0.1, 0.5 and 1X depth, with 100, 500, 1,000 or 10,000 base-pair reads and by assuming a random sequencing error rate per SNP between 10–2 and 10–5. Assuming known allele frequencies in the population and sequencing error rate, 0.05X depth sufficed to corroborate the true father (85,0%) and to discard other candidates (96,3%). Those percentages increased up to 99,6% and 99,9% with 0,1X depth, respectively (read length = 10,000 bp; smaller read lengths slightly improved the results because they increase the number of sequenced SNP). Results were highly sensitive to biases in allele frequencies and robust to inaccuracies regarding sequencing error rate. Low-coverage whole-genome sequencing data could be subsequently integrated into genomic BLUP equations by appropriately constructing the genomic relationship matrix. This approach increased the correlation between simulated and predicted breeding values by 1.21% (h2 = 0.25; 100 parents and 900 offspring; 0.1X depth by 10,000 bp reads). Although small, this increase opens the door to genomic evaluation in local livestock breeds.

scholarly journals Actionable clinical decisions based on comprehensive genomic evaluation in asymptomatic adults

2015 ◽  
Vol 3 (5) ◽  
pp. 433-439 ◽  
Author(s):  
Nir Pillar ◽  
Ofer Isakov ◽  
Daphna Weissglas‐Volkov ◽  
Shay Botchan ◽  
Eitan Friedman ◽  
...  
Keyword(s):  
Clinical Decisions ◽  
Genomic Evaluation

scholarly journals Genomic selection in French dairy cattle

2012 ◽  
Vol 52 (3) ◽  
pp. 115 ◽  
Author(s):  
D. Boichard ◽  
F. Guillaume ◽  
A. Baur ◽  
P. Croiseau ◽  
M. N. Rossignol ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Genomic Selection ◽  
Reference Population ◽  
Specific Reference ◽  
Nucleotide Polymorphisms ◽  
Genomic Evaluation ◽  
Linear Unbiased Prediction ◽  
Best Linear Unbiased ◽  
Estimated Breeding Values ◽  
Restricted Use

Genomic selection is implemented in French Holstein, Montbéliarde, and Normande breeds (70%, 16% and 12% of French dairy cows). A characteristic of the model for genomic evaluation is the use of haplotypes instead of single-nucleotide polymorphisms (SNPs), so as to maximise linkage disequilibrium between markers and quantitative trait loci (QTLs). For each trait, a QTL-BLUP model (i.e. a best linear unbiased prediction model including QTL random effects) includes 300–700 trait-dependent chromosomal regions selected either by linkage disequilibrium and linkage analysis or by elastic net. This model requires an important effort to phase genotypes, detect QTLs, select SNPs, but was found to be the most efficient one among all tested ones. QTLs are defined within breed and many of them were found to be breed specific. Reference populations include 1800 and 1400 bulls in Montbéliarde and Normande breeds. In Holstein, the very large reference population of 18 300 bulls originates from the EuroGenomics consortium. Since 2008, ~65 000 animals have been genotyped for selection by Labogena with the 50k chip. Bulls genomic estimated breeding values (GEBVs) were made official in June 2009. In 2010, the market share of the young bulls reached 30% and is expected to increase rapidly. Advertising actions have been undertaken to recommend a time-restricted use of young bulls with a limited number of doses. In January 2011, genomic selection was opened to all farmers for females. Current developments focus on the extension of the method to a multi-breed context, to use all reference populations simultaneously in genomic evaluation.

scholarly journals Multiple-breed genomic evaluation by principal component analysis in small size populations

animal ◽  
2015 ◽  
Vol 9 (5) ◽  
pp. 738-749 ◽  
Author(s):  
G. Gaspa ◽  
H. Jorjani ◽  
C. Dimauro ◽  
M. Cellesi ◽  
P. Ajmone-Marsan ◽  
...  
Keyword(s):  
Principal Component Analysis ◽  
Principal Component ◽  
Component Analysis ◽  
Genomic Evaluation

Genomic evaluation of dairy heifer livability

2021 ◽  
Author(s):  
M. Neupane ◽  
J.L. Hutchison ◽  
C.P. Van Tassell ◽  
P.M. VanRaden
Keyword(s):  
Genomic Evaluation ◽  
Dairy Heifer

Technical note: Updating the inverse of the genomic relationship matrix1

2013 ◽  
Vol 91 (6) ◽  
pp. 2583-2586 ◽  
Author(s):  
K. Meyer ◽  
B. Tier ◽  
H.-U. Graser
Keyword(s):  
Technical Note ◽  
Genomic Relationship
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