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  1. Article ; Online: Hitchhiking Mapping of Candidate Regions Associated with Fat Deposition in Iranian Thin and Fat Tail Sheep Breeds Suggests New Insights into Molecular Aspects of Fat Tail Selection

    Mohammad Hossein Moradi / Ardeshir Nejati-Javaremi / Mohammad Moradi-Shahrbabak / Ken G. Dodds / Rudiger Brauning / John C. McEwan

    Animals, Vol 12, Iss 1423, p

    2022  Volume 1423

    Abstract: The fat tail is a phenotype that divides indigenous Iranian sheep genetic resources into two major groups. The objective of the present study is to refine the map location of candidate regions associated with fat deposition, obtained via two separate ... ...

    Abstract The fat tail is a phenotype that divides indigenous Iranian sheep genetic resources into two major groups. The objective of the present study is to refine the map location of candidate regions associated with fat deposition, obtained via two separate whole genome scans contrasting thin and fat tail breeds, and to determine the nature of the selection occurring in these regions using a hitchhiking approach. Zel (thin tail) and Lori-Bakhtiari (fat tail) breed samples that had previously been run on the Illumina Ovine 50 k BeadChip, were genotyped with a denser set of SNPs in the three candidate regions using a Sequenom Mass ARRAY platform. Statistical tests were then performed using different and complementary methods based on either site frequency (F ST and Median homozygosity) or haplotype (iHS and XP-EHH). The results from candidate regions on chromosome 5 and X revealed clear evidence of selection with the derived haplotypes that was consistent with selection to near fixation for the haplotypes affecting fat tail size in the fat tail breed. An analysis of the candidate region on chromosome 7 indicated that selection differentiated the beneficial alleles between breeds and homozygosity has increased in the thin tail breed which also had the ancestral haplotype. These results enabled us to confirm the signature of selection in these regions and refine the critical intervals from 113 kb, 201 kb, and 2831 kb to 28 kb, 142 kb, and 1006 kb on chromosome 5, 7, and X respectively. These regions contain several genes associated with fat metabolism or developmental processes consisting of TCF7 and PPP2CA (OAR5), PTGDR and NID2 (OAR7), AR , EBP , CACNA1F , HSD17B10, SLC35A2 , BMP15 , WDR13 , and RBM3 (OAR X), and each of which could potentially be the actual target of selection. The study of core haplotypes alleles in our regions of interest also supported the hypothesis that the first domesticated sheep were thin tailed, and that fat tail animals were developed later. Overall, our results provide a comprehensive ...
    Keywords genomic scan ; selection signature ; lipid metabolisms ; candidate genes ; fat tail sheep ; Veterinary medicine ; SF600-1100 ; Zoology ; QL1-991
    Subject code 630
    Language English
    Publishing date 2022-05-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Low-cost sample preservation methods for high-throughput processing of rumen microbiomes

    Juliana C. C. Budel / Melanie K. Hess / Timothy P. Bilton / Hannah Henry / Ken G. Dodds / Peter H. Janssen / John C. McEwan / Suzanne J. Rowe

    Animal Microbiome, Vol 4, Iss 1, Pp 1-

    2022  Volume 17

    Abstract: Abstract Background The use of rumen microbial community (RMC) profiles to predict methane emissions has driven interest in ruminal DNA preservation and extraction protocols that can be processed cheaply while also maintaining or improving DNA quality ... ...

    Abstract Abstract Background The use of rumen microbial community (RMC) profiles to predict methane emissions has driven interest in ruminal DNA preservation and extraction protocols that can be processed cheaply while also maintaining or improving DNA quality for RMC profiling. Our standard approach for preserving rumen samples, as defined in the Global Rumen Census (GRC), requires time-consuming pre-processing steps of freeze drying and grinding prior to international transportation and DNA extraction. This impedes researchers unable to access sufficient funding or infrastructure. To circumvent these pre-processing steps, we investigated three methods of preserving rumen samples for subsequent DNA extraction, based on existing lysis buffers Tris-NaCl-EDTA-SDS (TNx2) and guanidine hydrochloride (GHx2), or 100% ethanol. Results Rumen samples were collected via stomach intubation from 151 sheep at two time-points 2 weeks apart. Each sample was separated into four subsamples and preserved using the three preservation methods and the GRC method (n = 4 × 302). DNA was extracted and sequenced using Restriction Enzyme-Reduced Representation Sequencing to generate RMC profiles. Differences in DNA yield, quality and integrity, and sequencing metrics were observed across the methods (p < 0.0001). Ethanol exhibited poorer quality DNA (A260/A230 < 2) and more failed samples compared to the other methods. Samples preserved using the GRC method had smaller relative abundances in gram-negative genera Anaerovibrio, Bacteroides, Prevotella, Selenomonas, and Succiniclasticum, but larger relative abundances in the majority of 56 additional genera compared to TNx2 and GHx2. However, log10 relative abundances across all genera and time-points for TNx2 and GHx2 were on average consistent (R2 > 0.99) but slightly more variable compared to the GRC method. Relative abundances were moderately to highly correlated (0.68 ± 0.13) between methods for samples collected within a time-point, which was greater than the average correlation (0.17 ...
    Keywords Genotyping-by-sequencing ; Rumen microbial profiles ; PstI ; RE-RRS ; Rumen microbiology ; Superorganism ; Veterinary medicine ; SF600-1100 ; Microbiology ; QR1-502
    Language English
    Publishing date 2022-06-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article: Factors affecting differences between birth weight of littermates (BWTD) and the effects of BWTD on lamb performance

    Juengel, Jennifer L / George H. Davis / Ken G. Dodds / Peter D. Johnstone / Roger Wheeler

    Animal reproduction science. 2018 Apr., v. 191

    2018  

    Abstract: The objectives of this study were to determine factors affecting lamb birth weight (BWT) and differences between BWT of the largest and smallest littermates (BWTD) and to assess the relative importance of BWT and BWTD on lamb survival and growth to ... ...

    Abstract The objectives of this study were to determine factors affecting lamb birth weight (BWT) and differences between BWT of the largest and smallest littermates (BWTD) and to assess the relative importance of BWT and BWTD on lamb survival and growth to weaning. Records from twin (n = 5369) or triplet (n = 1664) litters born on pasture were utilised. Breeds included Coopworth, Romney, Perendale, composite and Texel. Ewe and sire breed, age and weight of the dam, sex, and number of lambs born (NLB) affected BWT. Neither embryo loss nor ovulation pattern (i.e. all ova released from one ovary or some from each) were associated with BWT. Dam weight and NLB affected BWTD but dam age, sire or dam breed did not. Loss of an embryo reduced BWTD, and BWTD was lower when the ewe ovulated from both ovaries versus only one ovary for twins, but not triplets. Whereas BWT was moderately heritable (h2 = 0.20), BWTD was not heritable (h2 = 0.003). Lamb survival was positively associated with BWT. Lambs with BWTD > 1.3 kg were less likely to survive (73.3%) than those from litters of smaller BWTD (range 82.8–85.7% survival). Growth rate of twin and triplet lambs was positively associated with BWT. Surprisingly, lambs from litters with moderately high BWTD had slightly greater (approximately 3%) growth rate than those from lambs of low to intermediate BWTD. Thus, while large BWTD were negatively associated with survival, BWT itself, which was moderately heritable, appeared to be a stronger driver of lamb survival and average daily gain.
    Keywords age ; animal ovaries ; average daily gain ; birth weight ; Coopworth ; dams (mothers) ; embryonic mortality ; ewes ; lambs ; ova ; ovulation ; pastures ; Romney ; sires ; Texel ; twins ; weaning
    Language English
    Dates of publication 2018-04
    Size p. 34-43.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 429674-6
    ISSN 1873-2232 ; 0378-4320
    ISSN (online) 1873-2232
    ISSN 0378-4320
    DOI 10.1016/j.anireprosci.2018.02.002
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: The Use of “Genotyping-by-Sequencing” to Recover Shared Genealogy in Genetically Diverse Eucalyptus Populations

    Jaroslav Klápště / Rachael L. Ashby / Emily J. Telfer / Natalie J. Graham / Heidi S. Dungey / Rudiger Brauning / Shannon M. Clarke / Ken G. Dodds

    Forests, Vol 12, Iss 904, p

    2021  Volume 904

    Abstract: The recovery of genealogy in both natural and captive populations is critical for any decision in the management of genetic resources. It allows for the estimation of genetic parameters such as heritability and genetic correlations, as well as defining ... ...

    Abstract The recovery of genealogy in both natural and captive populations is critical for any decision in the management of genetic resources. It allows for the estimation of genetic parameters such as heritability and genetic correlations, as well as defining an optimal mating design that maintains a large effective population size. We utilised “genotyping-by-sequencing” (GBS) in combination with bioinformatics tools developed specifically for GBS data to recover genetic relatedness, with a focus on parent-offspring relationships in a Eucalyptus nitens breeding population as well as recognition of individuals representing other Eucalyptus species and putative hybrids. We found a clear advantage on using tools specifically designed for data of highly variable sequencing quality when recovering genetic relatedness. The parent-offspring relatedness showed a significant response to data filtering from 0.05 to 0.3 when the standard approach ( G1 ) was used, while it oscillated around 0.4 when the specifically designed method ( G5 ) was implemented. Additionally, comparisons with commonly used tools demonstrated vulnerability of the relatedness estimates to incorrect imputation of missing data when shallow sequencing information and genetically distant individuals are present in the population. In turn, these biased imputed genotypes negatively affected the estimation of genetic relatedness between parents and offspring. Careful filtering for both genetic outliers and shallowly sequenced markers led to improvements in estimations of genetic relatedness. Alternatively, a method that avoided missing data imputation and took sequence depth into consideration improved the accuracy of parent-offspring relationship coefficients where sequencing data quality was highly variable.
    Keywords genotyping-by-sequencing ; Eucalyptus ; genetic relatedness ; genotyping errors ; Plant ecology ; QK900-989
    Subject code 310
    Language English
    Publishing date 2021-07-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article: Estimation of genetic connectedness diagnostics based on prediction errors without the prediction error variance–covariance matrix

    Holmes, JohnB / Ken G. Dodds / Michael A. Lee

    Genetics, selection, evolution. 2017 Dec., v. 49, no. 1

    2017  

    Abstract: BACKGROUND: An important issue in genetic evaluation is the comparability of random effects (breeding values), particularly between pairs of animals in different contemporary groups. This is usually referred to as genetic connectedness. While various ... ...

    Abstract BACKGROUND: An important issue in genetic evaluation is the comparability of random effects (breeding values), particularly between pairs of animals in different contemporary groups. This is usually referred to as genetic connectedness. While various measures of connectedness have been proposed in the literature, there is general agreement that the most appropriate measure is some function of the prediction error variance–covariance matrix. However, obtaining the prediction error variance–covariance matrix is computationally demanding for large-scale genetic evaluations. Many alternative statistics have been proposed that avoid the computational cost of obtaining the prediction error variance–covariance matrix, such as counts of genetic links between contemporary groups, gene flow matrices, and functions of the variance–covariance matrix of estimated contemporary group fixed effects. RESULTS: In this paper, we show that a correction to the variance–covariance matrix of estimated contemporary group fixed effects will produce the exact prediction error variance–covariance matrix averaged by contemporary group for univariate models in the presence of single or multiple fixed effects and one random effect. We demonstrate the correction for a series of models and show that approximations to the prediction error matrix based solely on the variance–covariance matrix of estimated contemporary group fixed effects are inappropriate in certain circumstances. CONCLUSIONS: Our method allows for the calculation of a connectedness measure based on the prediction error variance–covariance matrix by calculating only the variance–covariance matrix of estimated fixed effects. Since the number of fixed effects in genetic evaluation is usually orders of magnitudes smaller than the number of random effect levels, the computational requirements for our method should be reduced.
    Keywords animals ; breeding value ; diagnostic techniques ; gene flow ; models ; prediction ; statistics
    Language English
    Dates of publication 2017-12
    Size p. 29.
    Publishing place BioMed Central
    Document type Article
    ZDB-ID 1005838-2
    ISSN 1297-9686 ; 0754-0264 ; 0999-193X
    ISSN (online) 1297-9686
    ISSN 0754-0264 ; 0999-193X
    DOI 10.1186/s12711-017-0302-9
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    Z 2610: Show issues

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  6. Article ; Online: Characterization of the Ruminal Microbiome of Water Buffaloes (Bubalus bubalis) Kept in Different Ecosystems in the Eastern Amazon

    Gerlane Nunes Noronha / Melanie K. Hess / Ken G. Dodds / André Guimarães Maciel e Silva / Shirley Motta de Souza / Jamile Andréa Rodrigues da Silva / Diego Assis das Graças / Thomaz Cyro Guimarães de Carvalho Rodrigues / Welligton Conceição da Silva / Éder Bruno Rebelo da Silva / Peter H. Janssen / Hannah M. Henry / Suzanne J. Rowe / Vinicius Costa Gomes de Castro / José de Brito Lourenço-Júnior

    Animals, Vol 13, Iss 24, p

    2023  Volume 3858

    Abstract: Increasing the efficiency of rumen fermentation is one of the main ways to maximize the production of ruminants. It is therefore important to understand the ruminal microbiome, as well as environmental influences on that community. However, there are no ... ...

    Abstract Increasing the efficiency of rumen fermentation is one of the main ways to maximize the production of ruminants. It is therefore important to understand the ruminal microbiome, as well as environmental influences on that community. However, there are no studies that describe the ruminal microbiota in buffaloes in the Amazon. The objective of this study was to characterize the rumen microbiome of the water buffalo ( Bubalus bubalis ) in the eastern Amazon in the dry and rainy seasons in three grazing ecosystems: Baixo Amazonas (BA), Continente do Pará (CP), Ilha do Marajó (IM), and in a confinement system: Tomé-Açu (TA). Seventy-one crossbred male buffaloes (Murrah × Mediterranean) were used, aged between 24 and 36 months, with an average weight of 432 kg in the rainy season and 409 kg in the dry season, and fed on native or cultivated pastures. In the confinement system, the feed consisted of sorghum silage, soybean meal, wet sorghum premix, and commercial feed. Samples of the diet from each ecosystem were collected for bromatological analysis. The collections of ruminal content were carried out in slaughterhouses, with the rumen completely emptied and homogenized, the solid and liquid fractions separated, and the ruminal pH measured. DNA was extracted from the rumen samples, then sequenced using Restriction Enzyme Reduced Representation Sequencing. The taxonomic composition was largely similar between ecosystems. All 61 genera in the reference database were recognized, including members of the domains Bacteria and Archaea. The abundance of 23 bacterial genera differed significantly ( p < 0.01) between the Tomé-Açu confinement and other ecosystems. Bacillus , Ruminococcus , and Bacteroides had lower abundance in samples from the Tomé-Açu system. Among the Archaea, the genus Methanomicrobium was less abundant in Tomé-Açu, while Methanosarcina was more abundant. There was a difference caused by all evaluated factors, but the diet (available or offered) was what most influenced the ruminal microbiota.
    Keywords Amazonia ; ruminal microorganisms ; restriction enzyme-reduced representation sequencing ; Veterinary medicine ; SF600-1100 ; Zoology ; QL1-991
    Subject code 590
    Language English
    Publishing date 2023-12-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article: Incidence and heritability of ovine pneumonia, and the relationship with production traits in New Zealand sheep

    McRae, Kathryn M / Hayley J. Baird / Ken G. Dodds / Matthew J. Bixley / Shannon M. Clarke

    Small ruminant research. 2016 Dec., v. 145

    2016  

    Abstract: The cost of ovine pneumonia and pleurisy to the New Zealand economy is high, with the majority of loss through slower growth and reduced carcass value at slaughter. Farm management practices and vaccine development have traditionally been the main focus ... ...

    Abstract The cost of ovine pneumonia and pleurisy to the New Zealand economy is high, with the majority of loss through slower growth and reduced carcass value at slaughter. Farm management practices and vaccine development have traditionally been the main focus for prevention of pneumonia. The objective of this study was to estimate the heritability of pneumonia in New Zealand lambs, and investigate the genetic relationship with key production traits.The lungs of 11,437 lambs from pedigree-recorded flocks were scored for the presence and severity of pneumonic lesions at slaughter. On average 28% of lambs had pneumonic lesions at slaughter, with 7% showing severe lesions. The incidence of pleurisy in these animals was 6%. Heritability estimates for pneumonic lesions and pleurisy were 0.07±0.02 and 0.02±0.01, respectively. There was a significant positive genetic correlation between pneumonic lesions and faecal egg count (0.30±0.13). Animals with pneumonic lesions had grown faster from birth to weaning, and slower from weaning to slaughter than animals without lesions.This study has shown that there is a heritable component to pneumonia in sheep. Including more data from pedigree-recorded flocks with severe pneumonia and a high incidence of pleurisy will enable more accurate estimates of genetic parameters, and subsequent correlations with production and disease traits. This would be aided by routine recording of pneumonia in lungs at slaughter by processing plants.
    Keywords farm management ; fecal egg count ; flocks ; genetic correlation ; genetic relationships ; heritability ; lambs ; lungs ; pleurisy ; pneumonia ; slaughter ; vaccine development ; weaning ; New Zealand
    Language English
    Dates of publication 2016-12
    Size p. 136-141.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 286928-7
    ISSN 0921-4488
    ISSN 0921-4488
    DOI 10.1016/j.smallrumres.2016.11.003
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    Z 4801: Show issues

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  8. Article: Estimation of linkage disequilibrium and effective population size in New Zealand sheep using three different methods to create genetic maps

    Prieur, Vincent / Shannon M. Clarke / Luiz F. Brito / John C. McEwan / Michael A. Lee / Rudiger Brauning / Ken G. Dodds / Benoît Auvray

    BMC genetics. 2017 Dec., v. 18, no. 1

    2017  

    Abstract: BACKGROUND: Investments in genetic selection have played a major role in the New Zealand sheep industry competitiveness. Selection may erode genetic diversity, which is a crucial factor for the success of breeding programs. Better understanding of ... ...

    Abstract BACKGROUND: Investments in genetic selection have played a major role in the New Zealand sheep industry competitiveness. Selection may erode genetic diversity, which is a crucial factor for the success of breeding programs. Better understanding of linkage disequilibrium (LD) and ancestral effective population size (Nₑ) through quantifying this diversity and comparison between populations allows for more informed decisions with regards to selective breeding taking population genetic diversity into account. The estimation of N ₑ can be determined via genetic markers and requires knowledge of genetic distances between these markers. Single nucleotide polymorphisms (SNP) data from a sample of 12,597 New Zealand crossbred and purebred sheep genotyped with the Illumina Ovine SNP50 BeadChip was used to perform a genome-wide scan of LD and N ₑ . Three methods to estimate genetic distances were investigated: 1) M1: a ratio fixed across the whole genome of one Megabase per centiMorgan; 2) M2: the ratios of genetic distance (using M3, below) over physical distance fixed for each chromosome; and, 3) M3: a genetic map of inter-SNP distances estimated using CRIMAP software (v2.503). RESULTS: The estimates obtained with M2 and M3 showed much less variability between autosomes than those with M1, which tended to give lower N ₑ results and higher LD decay. The results suggest that N ₑ has decreased since the development of sheep breeds in Europe and this reduction in Nₑ has been accelerated in the last three decades. The N ₑ estimated for five generations in the past ranged from 71 to 237 for Texel and Romney breeds, respectively. A low level of genetic kinship and inbreeding was estimated in those breeds suggesting avoidance of mating close relatives. CONCLUSIONS: M3 was considered the most accurate method to create genetic maps for the estimation of LD and Nₑ. The findings of this study highlight the history of genetic selection in New Zealand crossbred and purebred sheep and these results will be very useful to understand genetic diversity of the population with respect to genetic selection. In addition, it will help geneticists to identify genomic regions which have been preferentially selected within a variety of breeds and populations.
    Keywords Romney ; Texel ; autosomes ; breeding programs ; computer software ; effective population size ; genetic distance ; genetic markers ; genetic variation ; geneticists ; genome ; genotyping ; inbreeding ; kinship ; linkage disequilibrium ; natural selection ; purebreds ; selection methods ; sheep ; sheep industry ; single nucleotide polymorphism ; Europe ; New Zealand
    Language English
    Dates of publication 2017-12
    Size p. 68.
    Publishing place BioMed Central
    Document type Article
    ISSN 1471-2156
    DOI 10.1186/s12863-017-0534-2
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  9. Article: Genetic diversity of a New Zealand multi-breed sheep population and composite breeds’ history revealed by a high-density SNP chip

    Brito, LuizF / John C. McEwan / Stephen P. Miller / Natalie K. Pickering / Wendy E. Bain / Ken G. Dodds / Flávio S. Schenkel / Shannon M. Clarke

    BMC genetics. 2017 Dec., v. 18, no. 1

    2017  

    Abstract: BACKGROUND: Knowledge about the genetic diversity of a population is a crucial parameter for the implementation of successful genomic selection and conservation of genetic resources. The aim of this research was to establish the scientific basis for the ... ...

    Abstract BACKGROUND: Knowledge about the genetic diversity of a population is a crucial parameter for the implementation of successful genomic selection and conservation of genetic resources. The aim of this research was to establish the scientific basis for the implementation of genomic selection in a composite Terminal sheep breeding scheme by providing consolidated linkage disequilibrium (LD) measures across SNP markers, estimating consistency of gametic phase between breed-groups, and assessing genetic diversity measures, such as effective population size (Nₑ), and population structure parameters, using a large number of animals (n = 14,845) genotyped with a high density SNP chip (606,006 markers). Information generated in this research will be useful for optimizing molecular breeding values predictions and managing the available genetic resources. RESULTS: Overall, as expected, levels of pairwise LD decreased with increasing distance between SNP pairs. The mean LD r² between adjacent SNP was 0.26 ± 0.10. The most recent effective population size for all animals (687) and separately per breed-groups: Primera (974), Lamb Supreme (380), Texel (227) and Dual-Purpose (125) was quite variable. The genotyped animals were outbred or had an average low level of inbreeding. Consistency of gametic phase was higher than 0.94 for all breed pairs at the average distance between SNP on the chip (~4.74 kb). Moreover, there was not a clear separation between the breed-groups based on principal component analysis, suggesting that a mixed-breed training population for calculation of molecular breeding values would be beneficial. CONCLUSIONS: This study reports, for the first time, estimates of linkage disequilibrium, genetic diversity and population structure parameters from a genome-wide perspective in New Zealand Terminal Sire composite sheep breeds. The levels of linkage disequilibrium indicate that genomic selection could be implemented with the high density SNP panel. The moderate to high consistency of gametic phase between breed-groups and overlapping population structure support the pooling of the animals in a mixed training population for genomic predictions. In addition, the moderate to high Nₑ highlights the need to genotype and phenotype a large training population in order to capture most of the haplotype diversity and increase accuracies of genomic predictions. The results reported herein are a first step toward understanding the genomic architecture of a Terminal Sire composite sheep population and for the optimal implementation of genomic selection and genome-wide association studies in this sheep population.
    Keywords Texel ; breeding value ; composite breeds ; effective population size ; genetic variation ; genome-wide association study ; genotyping ; haplotypes ; inbreeding ; linkage disequilibrium ; marker-assisted selection ; mixed breeds ; phenotype ; population structure ; prediction ; principal component analysis ; reports ; sheep ; single nucleotide polymorphism ; sires ; New Zealand
    Language English
    Dates of publication 2017-12
    Size p. 25.
    Publishing place BioMed Central
    Document type Article
    ISSN 1471-2156
    DOI 10.1186/s12863-017-0492-8
    Database NAL-Catalogue (AGRICOLA)

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  10. Article: Assessing accuracy of imputation using different SNP panel densities in a multi-breed sheep population

    Ventura, Ricardo V / Benoit Auvray / John C. McEwan / Ken G. Dodds / Matthew Bixley / Michael Lee / Shannon M. Clarke / Stephen P. Miller

    Genetics, selection, evolution. 2016 Dec., v. 48, no. 1

    2016  

    Abstract: BACKGROUND: Genotype imputation is a key element of the implementation of genomic selection within the New Zealand sheep industry, but many factors can influence imputation accuracy. Our objective was to provide practical directions on the implementation ...

    Abstract BACKGROUND: Genotype imputation is a key element of the implementation of genomic selection within the New Zealand sheep industry, but many factors can influence imputation accuracy. Our objective was to provide practical directions on the implementation of imputation strategies in a multi-breed sheep population genotyped with three single nucleotide polymorphism (SNP) panels: 5K, 50K and HD (600K SNPs). RESULTS: Imputation from 5K to HD was slightly better (0.6 %) than imputation from 5K to 50K. Two-step imputation from 5K to 50K and then from 50K to HD outperformed direct imputation from 5K to HD. A slight loss in imputation accuracy was observed when a large fixed reference population was used compared to a smaller within-breed reference (including all 50K genotypes on animals from different breeds excluding those in the validation set i.e. to be imputed), but only for a few animals across all imputation scenarios from 5K to 50K. However, a major gain in imputation accuracy for a large proportion of animals (purebred and crossbred), justified the use of a fixed and large reference dataset for all situations. This study also investigated the loss in imputation accuracy specifically for SNPs located at the ends of each chromosome, and showed that only chromosome 26 had an overall imputation (5K to 50K) accuracy for 100 SNPs at each end higher than 60 % (r²). Most of the chromosomes displayed reduced imputation accuracy at least at one of their ends. Prediction of imputation accuracy based on the relatedness of low-density genotypes to those of the reference dataset, before imputation (without running an imputation software) was also investigated. FIMPUTE V2.2 outperformed BEAGLE 3.3.2 across all imputation scenarios. CONCLUSIONS: Imputation accuracy in sheep breeds can be improved by following a set of recommendations on SNP panels, software, strategies of imputation (one- or two-step imputation), and choice of the animals to be genotyped using both high- and low-density SNP panels. We present a method that predicts imputation accuracy for individual animals at the low-density level, before running imputation, which can be used to restrict genomic prediction only to the animals that can be imputed with sufficient accuracy.
    Keywords chromosomes ; computer software ; data collection ; genotype ; genotyping ; marker-assisted selection ; prediction ; purebreds ; sheep ; sheep breeds ; sheep industry ; single nucleotide polymorphism ; New Zealand
    Language English
    Dates of publication 2016-12
    Size p. 71.
    Publishing place BioMed Central
    Document type Article
    ZDB-ID 1005838-2
    ISSN 1297-9686 ; 0754-0264 ; 0999-193X
    ISSN (online) 1297-9686
    ISSN 0754-0264 ; 0999-193X
    DOI 10.1186/s12711-016-0244-7
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