Detecting Pedigree Relationship Errors

2017 ◽  
pp. 25-44 ◽  
Author(s):  
Lei Sun
Keyword(s):  
Pedigree Relationship

scholarly journals A multivariate analysis of subline divergence in the shape of the mandible in C57BL/Gr mice

1973 ◽  
Vol 21 (2) ◽  
pp. 121-132 ◽  
Author(s):  
Michael Festing
Keyword(s):  
Multivariate Analysis ◽  
Distance Function ◽  
Canonical Variate ◽  
Multivariate Techniques ◽  
Graphical Display ◽  
Classification Analysis ◽  
Variate Analysis ◽  
Pedigree Relationship ◽  
Highly Correlated ◽  
Generalized Distance

SUMMARYThe shape of the mandible in. nine sublines of C57BL/Gr, seven other strains of ‘C57 ancestry’ and four unrelated strains was studied by multivariate techniques. The generalized distance function was used to classify individuals in the groups which they most closely resembled. The degree of misclassification depended on the pedigree relationship between strains and sublines. The generalized distance between pairs of subline centeroids was also highly correlated (r = 0·60) with the number of generations between them. A canonical variate analysis was used to reduce the dimensionality so that a graphical display of the relationships between strains and sublines could be made. The results agreed closely with the classification analysis. It was concluded that the shape of the mandible could be used for subline identification though the accuracy of this technique depends on how closely the sublines are related.

scholarly journals Identification of Pedigree Relationship from Genome Sharing

2013 ◽  
Vol 3 (9) ◽  
pp. 1553-1571 ◽  
Author(s):  
William G. Hill ◽  
Ian M. S. White
Keyword(s):  
Pedigree Relationship ◽  
Genome Sharing

scholarly journals Effect of Heterogeneity in Recombination Rate on Variation in Realised Relationship

2018 ◽  
Author(s):  
Ian M.S. White ◽  
William G. Hill
Keyword(s):  
Recombination Rate ◽  
Genetic Information ◽  
Fine Scale ◽  
Recombination Rates ◽  
Recombination Hotspots ◽  
Identical By Descent ◽  
Small Influence ◽  
Scale Levels ◽  
Pedigree Relationship ◽  
Actual Relationship

ABSTRACTIndividuals of specified pedigree relationship vary in the proportion of the genome they share identical by descent, i.e. in their realised or actual relationship. Basing predictions of the variance in realised relationship solely on the proportion of the map length shared implicitly assumes that both recombination rate and genetic information are uniformly distributed along the genome, ignoring the possible existence of recombination hotspots, and failing to distinguish between coding and non-coding sequences. In this paper we quantify the effects of heterogeneity in recombination rate at broad and fine scale levels on the variation in realised relationship. A chromosome with variable recombination rate usually shows more variance in realised relationship than does one having the same map length with constant recombination rate, especially if recombination rates are higher towards chromosome ends. Reductions in variance can also be found, and the overall pattern of change is quite complex. In general, local (fine-scale) variation in recombination rate, e.g. hotspots, has a small influence on the variance in realised relationship. Differences in rates across longer regions and between chromosome ends can increase or decrease the variance in realised relationship, depending on the genomic architecture.

scholarly journals Genomic Evidences Support an Independent History of Grapevine Domestication in the Levant

2020 ◽  
Author(s):  
Aviad Sivan ◽  
Oshrit Rahimi ◽  
Mail Salmon-Divon ◽  
Ehud Weiss ◽  
Elyashiv Drori ◽  
...  
Keyword(s):  
Sequence Data ◽  
Genetic Load ◽  
Whole Genome Sequence ◽  
Local Varieties ◽  
Caucasus Region ◽  
Demographic Models ◽  
Comprehensive Survey ◽  
History Of ◽  
Distinct Lineage ◽  
Pedigree Relationship

AbstractThe ancient grapevines of the Levant have inspired beliefs and rituals in human societies which are still practiced today in religious and traditional ceremonies around the world. Despite their importance, the original Levantine wine-grapes varieties were lost due to cultural turnovers commencing in the 7th century CE, which lead to the collapse of a flourishing winemaking industry in this region. Recently, a comprehensive survey of feral grapevines was conducted in Israel in an attempt to identify local varieties, yet the origin of these domesticated accessions is unclear. Here we study the origin of Levantine grapevines using whole-genome sequence data generated for a diversity panel of wild and cultivated accessions. Comparison between Levantine and Eurasian grapevines indicated that the Levantine varieties represent a distinct lineage from the Eurasian varieties. Demographic models further supported this observation designating that domestication in the Caucasus region predated the emergence of the Levantine samples in circa 5000 years and that authentic descendants of ancient varieties are represented among the Levantine samples. We further explore the pedigree relationship among cultivated grapevines, identify footprints of selective sweeps, and estimate the extent of genetic load in each group. We conclude that the Levantine varieties are distinct from the Eurasian varieties and that resistance to disease and abiotic stress are key traits in the development of both Eurasian and Levantine varieties.

kingroup: a program for pedigree relationship reconstruction and kin group assignments using genetic markers

2004 ◽  
Vol 4 (4) ◽  
pp. 779-782 ◽  
Author(s):  
DMITRY A. KONOVALOV ◽  
CLINT MANNING ◽  
MICHAEL T. HENSHAW
Keyword(s):  
Genetic Markers ◽  
Pedigree Relationship

Application of single-step GBLUP in New Zealand Romney sheep

2020 ◽  
Vol 60 (9) ◽  
pp. 1136
Author(s):  
M. A. Nilforooshan
Keyword(s):  
New Zealand ◽  
Single Step ◽  
Pedigree Information ◽  
Genomic Relationship Matrix ◽  
Relationship Matrix ◽  
Genomic Relationship ◽  
Genetic Trend ◽  
Weaning Weight ◽  
Sheep Population ◽  
Pedigree Relationship

Context In New Zealand, Romney is the most predominant breed and is reared as a dual-purpose sheep. The number of genotypes is rapidly increasing in the sheep population, and making use of both genotypes and pedigree information is of importance for genetic evaluations. Single-step genomic best linear unbiased prediction (ssGBLUP) is a method for simultaneous prediction of genetic merits for genotyped and non-genotyped animals. The combination and the compatibility of the genomic relationship matrix (G) and the pedigree relationship matrix for genotyped animals (A22) is important for unbiased ssGBLUP. Aims The aim of the present study was to find an optimum genetic relationship matrix for ssGBLUP weaning-weight evaluation of Romney sheep in New Zealand. Methods Data consisted of adjusted weaning weights for 2422011 sheep, 50K single-nucleotide polymorphism genotypes for 13304 animals and 3028688 animals in the pedigree. Blending of G and A22 was tested with weights (k) ranging from 0.2 to 0.99 (kG + (1 – k)A22), followed by none or one of the three methods of tuning G to A22. Key results The averages of G and A22 were close to each other for overall, diagonal and off-diagonal elements. Therefore, differently tuned G performed similarly. However, elements of G showed larger variation than did the elements of A22 and, on average, genotyped animals were less related in G than in A22. Correlations between genomic estimated breeding values (GEBV) for the top 500 genotyped animals, as well as the rank correlations, were almost 1 among ssGBLUP evaluations using tuned G. The corresponding correlations with BLUP evaluations were increased by blending G with a larger proportion of A22, and were further increased by tuning G, indicating improved compatibility between G and A22. Blending and tuning G suppressed the inflation of GEBV and bias and it moved the genetic trend closer to the genetic trend obtained from BLUP. Conclusions A combination of blending and tuning G to A22, with a blending rate of 0.5 at most, is recommended for weaning weight of Romney sheep in New Zealand. Failure to do that resulted in inflated GEBV that can reduce the accuracy of selection, especially for genotyped animals. Implications There is a growing interest in the single-step GBLUP method for simultaneous genetic evaluation of genotyped and non-genotyped animals, in which genomic and pedigree relationship matrices are admixed. Using data from New Zealand Romney sheep, we have shown that adjustment of the genomic relationship matrix on the basis of the pedigree relationship matrix is necessary to avoid inflated evaluations. Improving the compatibility between genomic and pedigree relationship matrices is important for obtaining accurate and unbiased single-step GBLUP evaluations.

scholarly journals  Single-step prediction of genomic breeding value in a small dairy cattle population with strong import of foreign genes

2012 ◽  
Vol 57 (No. 4) ◽  
pp. 151-159 ◽  
Author(s):  
J. Přibyl ◽  
J. Haman ◽  
T. Kott ◽  
J. Přibylová ◽  
M. Šimečková ◽  
...  
Keyword(s):  
Single Step ◽  
Allele Frequencies ◽  
Breeding Value ◽  
Progeny Testing ◽  
Data Set ◽  
Genomic Breeding ◽  
Milk Performance ◽  
Pedigree Relationship ◽  
Foreign Genes ◽  
Genomic Breeding Value

The breeding value (EBV) of Holstein cattle milk performance from the first lactation was evaluated using a regular Animal Model or by Single-Step Prediction of the genomic breeding value (GEBV). A total of 838 bulls were genotyped using the Illumina BovineSNP50 Beadchip V2. Two overlapping sets of milk performances were evaluated: calving years 1991–2004, with 729 341 lactations and 1 394 487 animals in the pedigree and calving years 1996–2009, with 808 436 lactations and 1 487 608 animals in the pedigree. The older data set included 526 genotyped bulls, in which the daughters’ milk performance was known for 210 individuals. All of the genotyped animals were included in the newer data set. Of the young genotyped bulls from the older set, 279 had more than 50 daughters with performance records in the newer set. Genomic relationship matrices (G) were constructed from the allele frequencies of the current genotyped population or by assuming a constant value of 0.5 for all loci. Using current allele frequencies, the correlation of G with the pedigree relationship (A) was 0.74, while it was 0.77 when the constant value was used. G was blended with A with weights of 80 or 99%. The average EBV of the genotyped bulls exceeded the mean EBV of the entire population by 3 SD. Although the number of reference bulls was small, genotyping resulted in an increase of approximately 0.05 in the correlation of the GEBV of young bulls with their results after progeny testing. Only small differences in correlations were found in dependency on the methods used for the determination of G and in dependency on the weight used in blending G with A. Both EBV and GEBV in the older set showed higher correlations with the GEBV of the newer set than the EBV of the newer set.  

Genetic analysis of within-litter variation in piglets' birth weight using genomic or pedigree relationship matrices1

2015 ◽  
Vol 93 (4) ◽  
pp. 1471-1480 ◽  
Author(s):  
E. Sell-Kubiak ◽  
S. Wang ◽  
E. F. Knol ◽  
H. A. Mulder
Keyword(s):  
Birth Weight ◽  
Genetic Analysis ◽  
Pedigree Relationship
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