Analysis of validated and population-specific single nucleotide polymorphism parentage panels in pedigreed and commercial beef cattle populations

Buchanan, Justin W.; Woronuk, Grant; Marquess, F. L. S.; Lang, Kevin S.; James, S. T.; Deobald, H. M.; Welly, Bryan T.; Eenennaam, Alison L. Van

doi:10.1139/cjas-2016-0143

Cited by 8 publications

(8 citation statements)

References 18 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A parent–offspring assignment was made whenever the number of opposing homozygotes was less than 1% of the number of markers in the assay. Setting such a threshold for identifying parent–offspring pairs was previously used [ 38 , 42 , 43 ] as a compromise to minimize false rejection or false assignment of parentages when the number of SNPs is small.…”

Section: Methodsmentioning

confidence: 99%

SNP panels for the estimation of dairy breed proportion and parentage assignment in African crossbred dairy cattle

et al. 2021

View full text Add to dashboard Cite

Background Understanding the relationship between genetic admixture and phenotypic performance is crucial for the optimization of crossbreeding programs. The use of small sets of informative ancestry markers can be a cost-effective option for the estimation of breed composition and for parentage assignment in situations where pedigree recording is difficult. The objectives of this study were to develop small single nucleotide polymorphism (SNP) panels that can accurately estimate the total dairy proportion and assign parentage in both West and East African crossbred dairy cows. Methods Medium- and high-density SNP genotype data (Illumina BovineSNP50 and BovineHD Beadchip) for 4231 animals sampled from African crossbreds, African Bos taurus, European Bos taurus, Bos indicus, and African indigenous populations were used. For estimating breed composition, the absolute differences in allele frequency were calculated between pure ancestral breeds to identify SNPs with the highest discriminating power, and different combinations of SNPs weighted by ancestral origin were tested against estimates based on all available SNPs. For parentage assignment, informative SNPs were selected based on the highest minor allele frequency (MAF) in African crossbred populations assuming two Scenarios: (1) parents were selected among all the animals with known genotypes, and (2) parents were selected only among the animals known to be a parent of at least one progeny. Results For the medium-density genotype data, SNPs selected for the largest differences in allele frequency between West African indigenous and European Bos taurus breeds performed best for most African crossbred populations and achieved a prediction accuracy (r2) for breed composition of 0.926 to 0.961 with 200 SNPs. For the high-density dataset, a panel with 70% of the SNPs selected on their largest difference in allele frequency between African and European Bos taurus performed best or very near best across all crossbred populations with r2 ranging from 0.978 to 0.984 with 200 SNPs. In all African crossbred populations, unambiguous parentage assignment was possible with ≥ 300 SNPs for the majority of the panels for Scenario 1 and ≥ 200 SNPs for Scenario 2. Conclusions The identified low-cost SNP assays could overcome incomplete or inaccurate pedigree records in African smallholder systems and allow effective breeding decisions to produce progeny of desired breed composition.

show abstract

Section: Methodsmentioning

confidence: 99%

SNP panels for the estimation of dairy breed proportion and parentage assignment in African crossbred dairy cattle

et al. 2021

View full text Add to dashboard Cite

show abstract

“…Fernández et al [ 23 ] suggested that 2–3 SNPs are needed to obtain an equivalent exclusion power to one microsatellite, yet Gill et al [ 24 ] estimated that 4–5 SNPs with allele frequencies range from 0.2 to 0.8 give the same power of exclusion as for one microsatellite. Albeit the continuous attention to this issue, most of the research focused on SNP-PCR, SNP-chip or other approaches which conduct sequencing by NGS and genotyping SNPs via highly multiplexed laboratory assays [ 22 , 25 , 26 , 27 , 28 , 29 ], while few related reports have genotyped and filtered SNPs directly via bioinformatic pipeline based on NGS approaches such as genotyping-by-sequencing.…”

Section: Introductionmentioning

confidence: 99%

Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

Weng

Yang

Wang

et al. 2021

Genes

View full text Add to dashboard Cite

Pedigree information is necessary for the maintenance of diversity for wild and captive populations. Accurate pedigree is determined by molecular marker-based parentage analysis, which may be influenced by the polymorphism and number of markers, integrity of samples, relatedness of parents, or different analysis programs. Here, we described the first development of 208 single nucleotide polymorphisms (SNPs) and 11 microsatellites for giant grouper (Epinephelus lanceolatus) taking advantage of Genotyping-by-sequencing (GBS), and compared the power of SNPs and microsatellites for parentage and relatedness analysis, based on a mixed family composed of 4 candidate females, 4 candidate males and 289 offspring. CERVUS, PAPA and COLONY were used for mutually verification. We found that SNPs had a better potential for relatedness estimation, exclusion of non-parentage and individual identification than microsatellites, and > 98% accuracy of parentage assignment could be achieved by 100 polymorphic SNPs (MAF cut-off < 0.4) or 10 polymorphic microsatellites (mean Ho = 0.821, mean PIC = 0.651). This study provides a reference for the development of molecular markers for parentage analysis taking advantage of next-generation sequencing, and contributes to the molecular breeding, fishery management and population conservation.

show abstract

“…Genotypes were also used to pair sires with their progeny from a subset of available SNP markers ( McClure et al, 2015 ; Strucken et al, 2016 ; Buchanan et al, 2016a ). For the CM calves, sires were identified using a 1,000 SNP subset of the available marker panel and the SEEKPARENTF90 software to generate CM pedigree records ( Aguilar et al, 2014 ; Buchanan et al, 2016a ). For PB animals, historical 4-generation pedigree information was available containing 9,176 records.…”

Section: Methodsmentioning

confidence: 99%

Comparison of economic returns among genetic evaluation strategies in a 2-tiered Charolais-sired beef cattle production system1,2

Buchanan

MacNeil

Raymond

et al. 2018

Journal of Animal Science

View full text Add to dashboard Cite

The objective of this study was to estimate economic returns and costs associated with 4 scenarios of genetic evaluation that combine genotypes, phenotypes, and pedigree information from a vertically integrated purebred (PB) and commercial (CM) beef cattle system. Inference was to a genetic evaluation for a production system producing Charolais terminal sires for 10,000 CM cows. The first genetic evaluation scenario, denoted PB_A, modeled a genetic evaluation in which pedigree information and phenotypes are available for PB seedstock animals. Scenario PB_H contained the same information as PB_A with the addition of 25K density (GeneSeek Genomic Profiler LD) single nucleotide polymorphism (SNP) genotypes from PB animals. Scenario PBCM_A contained pedigree records and phenotypes from PB and CM cattle. Scenario PBCM_H contained phenotypes, pedigree, and genotypes from the PB and CM animals. Estimates of prediction error variance, (co)variance, and selection index parameters were used to estimate accuracy of selection candidates (rTI) and genetic gain resulting from selection on an economic index in US dollars (ΔG). Annual costs and incomes were used to determine the 30-yr cumulative net present value (CNPV) per CM calf resulting from selection in these genetic evaluation scenarios. Adding genotypes and CM production phenotypes to genetic evaluation increased the rTI of selection candidates and ΔG across all 4 scenarios. Scenario PBCM_H produced the highest annual ΔG in the PB herd at US$11.91 per head. Including CM phenotypes and parentage testing in the genetic evaluation increased the time to breakeven from 12 yr in PB_A to 19 years in PBCM_A after accounting for the cost of that information. Adding CM phenotypes and genotypes increased the breakeven time from 12 yr in PB_H to 18 yr in PBCM_H. Scenario PB_H produced the highest 30-yr CNPV per slaughtered CM calf at US$371.16. These results using field data indicate that economically relevant rTI and ΔG can be realized by adding 25K SNP genotypes and CM phenotypes to genetic evaluation, but the additional cost of that data significantly delays the economic return to the enterprise.

show abstract

Analysis of validated and population-specific single nucleotide polymorphism parentage panels in pedigreed and commercial beef cattle populations

Cited by 8 publications

References 18 publications

SNP panels for the estimation of dairy breed proportion and parentage assignment in African crossbred dairy cattle

SNP panels for the estimation of dairy breed proportion and parentage assignment in African crossbred dairy cattle

Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

Comparison of economic returns among genetic evaluation strategies in a 2-tiered Charolais-sired beef cattle production system1,2

Contact Info

Product

Resources

About