Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches

被引:141
|
作者
Berenos, Camillo [1 ]
Ellis, Philip A. [1 ]
Pilkington, Jill G. [1 ]
Pemberton, Josephine M. [1 ]
机构
[1] Univ Edinburgh, Inst Evolutionary Biol, Sch Biol Sci, Edinburgh EH9 3JT, Midlothian, Scotland
基金
欧洲研究理事会; 英国自然环境研究理事会;
关键词
body size; genetic architecture; genomic relatedness; heritability; maternal genetic effect; SNP genotyping; BODY-SIZE; NATURAL-POPULATIONS; SOAY SHEEP; SPATIAL AUTOCORRELATION; SIRE MISIDENTIFICATION; VARIANCE-COMPONENTS; RELATIONSHIP MATRIX; WEANING WEIGHT; COMPLEX TRAITS; ANIMAL-MODEL;
D O I
10.1111/mec.12827
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The estimation of quantitative genetic parameters in wild populations is generally limited by the accuracy and completeness of the available pedigree information. Using relatedness at genomewide markers can potentially remove this limitation and lead to less biased and more precise estimates. We estimated heritability, maternal genetic effects and genetic correlations for body size traits in an unmanaged long-term study population of Soay sheep on St Kilda using three increasingly complete and accurate estimates of relatedness: (i) Pedigree 1, using observation-derived maternal links and microsatellite-derived paternal links; (ii) Pedigree 2, using SNP-derived assignment of both maternity and paternity; and (iii) whole-genome relatedness at 37 037 autosomal SNPs. In initial analyses, heritability estimates were strikingly similar for all three methods, while standard errors were systematically lower in analyses based on Pedigree 2 and genomic relatedness. Genetic correlations were generally strong, differed little between the three estimates of relatedness and the standard errors declined only very slightly with improved relatedness information. When partitioning maternal effects into separate genetic and environmental components, maternal genetic effects found in juvenile traits increased substantially across the three relatedness estimates. Heritability declined compared to parallel models where only a maternal environment effect was fitted, suggesting that maternal genetic effects are confounded with direct genetic effects and that more accurate estimates of relatedness were better able to separate maternal genetic effects from direct genetic effects. We found that the heritability captured by SNP markers asymptoted at about half the SNPs available, suggesting that denser marker panels are not necessarily required for precise and unbiased heritability estimates. Finally, we present guidelines for the use of genomic relatedness in future quantitative genetics studies in natural populations.
引用
收藏
页码:3434 / 3451
页数:18
相关论文
共 50 条
  • [1] Genomic estimation of quantitative genetic parameters in wild admixed populations
    Aase, Kenneth
    Jensen, Henrik
    Muff, Stefanie
    [J]. METHODS IN ECOLOGY AND EVOLUTION, 2022, 13 (05): : 1014 - 1026
  • [2] Genomic Relationship Matrix for Correcting Pedigree Errors in Breeding Populations: Impact on Genetic Parameters and Genomic Selection Accuracy
    Munoz, Patricio R.
    Resende, Marcio F. R., Jr.
    Huber, Dudley A.
    Quesada, Tania
    Resende, Marcos D. V.
    Neale, David B.
    Wegrzyn, Jill L.
    Kirst, Matias
    Peter, Gary F.
    [J]. CROP SCIENCE, 2014, 54 (03) : 1115 - 1123
  • [3] THE COMPARISON OF QUANTITATIVE GENETIC-PARAMETERS BETWEEN POPULATIONS
    SHAW, RG
    [J]. EVOLUTION, 1991, 45 (01) : 143 - 151
  • [4] Comparison of experimental designs for estimating quantitative genetic parameters in fish
    Blanc, JM
    [J]. AQUACULTURE RESEARCH, 2003, 34 (12) : 1099 - 1105
  • [5] ESTIMATING GENETIC PARAMETERS IN BEEF POPULATIONS
    BROWN, DT
    MCLAREN, JB
    JAMISON, HM
    RICHARDSON, DO
    [J]. JOURNAL OF ANIMAL SCIENCE, 1976, 42 (01) : 249 - 249
  • [6] Genetic approaches for estimating the effective size of populations
    Leberg, P
    [J]. JOURNAL OF WILDLIFE MANAGEMENT, 2005, 69 (04): : 1385 - 1399
  • [7] Genomic and Fitness Consequences of Genetic Rescue in Wild Populations
    Fitzpatrick, Sarah W.
    Bradburd, Gideon S.
    Kremer, Colin T.
    Salerno, Patricia E.
    Angeloni, Lisa M.
    Funk, W. Chris
    [J]. CURRENT BIOLOGY, 2020, 30 (03) : 517 - +
  • [8] Estimating quantitative genetic parameters in haplodiploid organisms
    Fu-Hua Liu
    Sandy M Smith
    [J]. Heredity, 2000, 85 : 373 - 382
  • [9] Estimating quantitative genetic parameters in haplodiploid organisms
    Liu, FH
    Smith, SM
    [J]. HEREDITY, 2000, 85 (04) : 373 - 382
  • [10] A comparison of methods to estimate genomic relationships using pedigree and markers in livestock populations
    Forneris, N. S.
    Steibel, J. P.
    Legarra, A.
    Vitezica, Z. G.
    Bates, R. O.
    Ernst, C. W.
    Basso, A. L.
    Cantet, R. J. C.
    [J]. JOURNAL OF ANIMAL BREEDING AND GENETICS, 2016, 133 (06) : 452 - 462