scholarly journals Narrow-sense heritability estimation of complex traits using identity-by-descent information

2017 ◽  
Author(s):  
Luke M. Evans ◽  
Rasool Tahmasbi ◽  
Matthew Jones ◽  
Scott I. Vrieze ◽  
Gonçalo R. Abecasis ◽  
...  
Keyword(s):  
Complex Traits ◽  
Genetic Variance ◽  
Additive Genetic Variance ◽  
Fundamental Parameter ◽  
Last Common Ancestor ◽  
Narrow Sense ◽  
Narrow Sense Heritability ◽  
Heritability Estimation ◽  
Causal Variants ◽  
Heritability Estimates

ABSTRACTHeritability is a fundamental parameter in genetics. Traditional estimates based on family or twin studies can be biased due to shared environmental or non-additive genetic variance. Alternatively, those based on genotyped or imputed variants typically underestimate narrow-sense heritability contributed by rare or otherwise poorly-tagged causal variants. Identical-by-descent (IBD) segments of the genome share all variants between pairs of chromosomes except new mutations that have arisen since the last common ancestor. Therefore, relating phenotypic similarity to degree of IBD sharing among classically unrelated individuals is an appealing approach to estimating the near full additive genetic variance while avoiding biases that can occur when modeling close relatives. We applied an IBD-based approach (GREML-IBD) to estimate heritability in unrelated individuals using phenotypic simulation with thousands of whole genome sequences across a range of stratification, polygenicity levels, and the minor allele frequencies of causal variants (CVs). IBD-based heritability estimates were unbiased when using unrelated individuals, even for traits with extremely rare CVs, but stratification led to strong biases in IBD-based heritability estimates with poor precision. We used data on two traits in ~120,000 people from the UK Biobank to demonstrate that, depending on the trait and possible confounding environmental effects, GREML-IBD can be applied successfully to very large genetic datasets to infer the contribution of very rare variants lost using other methods. However, we observed apparent biases in this real data that were not predicted from our simulation, suggesting that more work may be required to understand factors that influence IBD-based estimates.

scholarly journals Efficiencies of Clonally Replicated and Seedling Testing for Spruce Breeding and Deployment Strategies

2009 ◽  
Vol 58 (1-6) ◽  
pp. 292-300
Author(s):  
Y. H. Weng ◽  
Y. S. Park ◽  
D. Simpson ◽  
T. J. Mullin
Keyword(s):  
Genetic Variance ◽  
Gene Diversity ◽  
Additive Genetic Variance ◽  
Seed Orchard ◽  
Narrow Sense ◽  
Family Selection ◽  
Narrow Sense Heritability ◽  
Additive Variance ◽  
Clonal Seed Orchard ◽  
Seedling Test

AbstractGenetic gains based on a genetic test using clonal replicates were compared to those based on a test using seedlings at the same gene diversity and testing effort levels using POPSIM™ Simulator. Three testing and deployment strategies targeting for white spruce (P. glauca [Moench] Voss) and black spruce (P. mariana (Mill.) B.S.P.) in New Brunswick were compared: seedling test with clonal seed orchard deployed as seedlings (CSO_ST), clonally replicated test with clonal seed orchard deployed as seedlings (CSO_CRT), and clonally replicated test deployed as a clone mix (MVF). The breeding populations (BP) were formed by balanced within-family selection and the production populations (PP) were selected by strong restriction on relatedness, i.e., no parent in common. Compared to the seedling test, the clonally replicated test resulted in faster accumulation of additive effects but quicker loss of additive variance in the BP, and this is particular true in the case of lower narrow-sense heritability or less non-additive genetic variance. The quicker loss in BP additive variance was overcompensated for by its faster accumulation in BP additive effect, resulting in higher gain in the clonally replicated test based PPs. Compared to the CSO_ST, the gain superiority of the CSO_CRT increased with generations, decreasing narrow-sense heritability or reducing the amount of non-additive variance. Implementing MVF was the most effective in terms of gain in most simulated cases and its superiority over the CSO_ST increased with generations, decreasing narrowsense heritability, or increasing non-additive genetic variance. Overall results demonstrated significant advantages of using clonally replicated test both for BP advancement and PP selection in most of the scenarios, suggesting that clonally replicated test should be incorporated into current spruce breeding strategies.

scholarly journals Estimation of non-additive genetic variance in human complex traits from a large sample of unrelated individuals

2020 ◽  
Author(s):  
Valentin Hivert ◽  
Julia Sidorenko ◽  
Florian Rohart ◽  
Michael E Goddard ◽  
Jian Yang ◽  
...  
Keyword(s):  
Complex Traits ◽  
Genetic Variance ◽  
Additive Genetic Variance ◽  
Sampling Variance ◽  
Analysis Model ◽  
Additive Variance ◽  
Snp Data ◽  
Causal Variants ◽  
The Uk ◽  
Epistatic Variance

AbstractNon-additive genetic variance for complex traits is traditionally estimated from data on relatives. It is notoriously difficult to estimate without bias in non-laboratory species, including humans, because of possible confounding with environmental covariance among relatives. In principle, non-additive variance attributable to common DNA variants can be estimated from a random sample of unrelated individuals with genome-wide SNP data. Here, we jointly estimate the proportion of variance explained by additive , dominance and additive-by-additive genetic variance in a single analysis model. We first show by simulations that our model leads to unbiased estimates and provide new theory to predict standard errors estimated using either least squares or maximum likelihood. We then apply the model to 70 complex traits using 254,679 unrelated individuals from the UK Biobank and 1.1M genotyped and imputed SNPs. We found strong evidence for additive variance (average across traits . In contrast, the average estimate of across traits was 0.001, implying negligible dominance variance at causal variants tagged by common SNPs. The average epistatic variance across the traits was 0.058, not significantly different from zero because of the large sampling variance. Our results provide new evidence that genetic variance for complex traits is predominantly additive, and that sample sizes of many millions of unrelated individuals are needed to estimate epistatic variance with sufficient precision.

scholarly journals Genetic variance and heritability estimation of hybridized pepper plants (Capsicum annuum L.) F2 progeny for begomovirus resistance in growth stage

2022 ◽  
Vol 951 (1) ◽  
pp. 012103
Author(s):  
E Kesumawati ◽  
Sabaruddin ◽  
E Hayati ◽  
N Hadisah ◽  
R Hayati ◽  
...  
Keyword(s):  
Growth Stage ◽  
Genetic Variance ◽  
Broad Sense ◽  
Phenotypic Variance ◽  
Broad Sense Heritability ◽  
Narrow Sense ◽  
Narrow Sense Heritability ◽  
Training Centre ◽  
Tertiary Branch ◽  
Heritability Estimation

Abstract Pepper is widely cultivated as a condiment and cash crop in Indonesia. However, Pepper yellow leaf curl disease (PepYLCD) caused by begomovirus is currently seriously affect the domestic pepper production. Breeding for begomovirus resistance material by crossing is currently necessary to overcome the constraint. The present study is aimed to determine the resistance of pepper (C. annuum) plants F2 progenies to begomovirus infection in the growth stage. Two local C. annuum accessions, BaPep-5 as a resistance donor for pepy-1 begomovirus resistance gene (locally called Perintis) and BaPep-4 as a susceptible parent (locally called Kencana) were crossed to generate F2 progenies. The research was conducted in Agricultural Extension Training Centre (BLPP) Saree and Horticulture Laboratory of Syiah Kuala University from February to July 2020. 500 F2 progenies were transplanted to the field along with 15 plants of each parent as control. The result suggested that plant height and crown width had the highest broad sense heritability value, whereas the dichotomous height, stem diameter, secondary branch, and tertiary branch had the lowest broad sense heritability value. Coefficient of genetic variance and coefficient of phenotypic variance from overall characteristics were relatively low which suggest the narrow sense to slightly narrow sense heritability.

GENETIC VARIANCES IN AN EIGHT PARENT HALF DIALLEL OF OATS

1976 ◽  
Vol 18 (3) ◽  
pp. 419-427 ◽  
Author(s):  
D. R. Sampson ◽  
I. Tarumoto
Keyword(s):  
Grain Yield ◽  
Genetic Variance ◽  
Additive Genetic Variance ◽  
Heading Date ◽  
Phenotypic Variance ◽  
Narrow Sense ◽  
Narrow Sense Heritability ◽  
Additive Component ◽  
Tests Of Fit ◽  
Half Diallel

Twenty-eight progenies with their eight parent cultivars of Avena saliva L. (2n = 6x = 42) were grown in F1, F2 and F3 in separate years; the F1 as spaced plants, the F2 and F3 as dense seeded populations. Additive genetic variance constituted most of the phenotypic variance of eight traits (heading date, plant height, stem diameter, grain yield and four components of yield) according to a Griffing Method 4, Model II analysis. Similarly, additive × year interactions were more important than nonadditive × year interactions. A Hayman-Jinks analysis of the same material but with the parents included showed that the additive component was 2 to 16 times larger than the dominance components in the F1 However in the F2 and F3 the dominance components became larger than the additive components for most traits instead of declining in importance as expected. Further, tests of fit to the hypotheses underlying the Hayman-Jinks analysis were negative in 8 of 24 cases. It is postulated that these discrepancies result from epistatic variance which caused an upward bias in the dominance estimates. The calculation and uses of two estimates of narrow-sense heritability are discussed.

scholarly journals Narrow-Sense Heritability of Selected Sensory Descriptors in Virginia-Type Peanut (Arachis hypogaea L.)1

2003 ◽  
Vol 30 (1) ◽  
pp. 64-66 ◽  
Author(s):  
T. G. Isleib ◽  
H. E. Pattee ◽  
F. G. Giesbrecht
Keyword(s):  
Arachis Hypogaea ◽  
Genetic Variance ◽  
Genetic Model ◽  
Additive Genetic Variance ◽  
Narrow Sense ◽  
Roasted Peanut ◽  
Narrow Sense Heritability ◽  
Breeding Lines ◽  
Arachis Hypogaea L ◽  
F2 Generation

Abstract The sweet, bitter and roasted peanut attributes of roasted peanut (Arachis hypogaea L.) flavor have been shown to be heritable traits. Previous research has estimated broad-sense heritability (H) and breeding values of numerous peanut cultivars and breeding lines for these attributes, but no study has estimated narrow-sense heritability (h2) in a specific population derived through hybridization and inbreeding. A population of 120 F3-derived families was developed without selection from the cross of NC 7/NC Ac 18431, a virginia-type line identified in 1990 as having a good flavor profile. The parents and F3:5 families were grown at two locations in North Carolina in 1995. SMK samples from each plot were roasted, ground to paste, tasted by a sensory panel, and scored for roasted peanut, sweet, bitter and astringent attributes. Additive and nonadditive genetic variances were estimated by equating variances among F2-derived families and among F3-derived families within F2-derived families to genetic covariances among inbred relatives. Regardless of whether the genetic model included dominance or additive-by-additive epistasis, the estimates of additive genetic variance for flavor attributes were small compared to those for nonadditive genetic variance. Narrow-sense heritability in the F2 generation was estimated at 0 for roasted peanut and astringent, 0.02 to 0.04 for sweet, and 0.01 to 0.03 for bitter, depending on the model used. Because of the low values of h2, which are specific to this population, gain from selection in early generations is expected to be limited within this population. Selection in this population should be practiced in late generations. Other parents have been identified whose crosses should produce greater improvement in sensory quality than can be expected from the NC 7 / NC Ac 18431 population.

scholarly journals Narrow-sense heritability estimation of complex traits using identity-by-descent information

Heredity ◽  
2018 ◽  
Vol 121 (6) ◽  
pp. 616-630 ◽  
Author(s):  
Luke M. Evans ◽  
◽  
Rasool Tahmasbi ◽  
Matt Jones ◽  
Scott I. Vrieze ◽  
...  
Keyword(s):  
Complex Traits ◽  
Narrow Sense ◽  
Identity By Descent ◽  
Narrow Sense Heritability ◽  
Heritability Estimation

ADDITIVE AND NONADDITIVE GENETIC VARIANCES AND GENOTYPIC CORRELATIONS FOR YIELD AND OTHER TRAITS IN OATS

1971 ◽  
Vol 13 (4) ◽  
pp. 864-872 ◽  
Author(s):  
D. R. Sampson
Keyword(s):  
Seed Weight ◽  
Genetic Variance ◽  
Additive Genetic Variance ◽  
Heading Date ◽  
Stem Diameter ◽  
Narrow Sense ◽  
Narrow Sense Heritability ◽  
Additive Variance ◽  
Plot Yield ◽  
Panicle Number

The oat cultivate 'Dorval', 'Kelsey', 'Stormont', 'Orbit', 'Goodfield', 'Tyler' and 'Egdolon' and two numbered lines were crossed in a 3 × 6 factorial design. F1's, F2's and bullied F2 progenies were grown in successive years at seeding rates of 2.7, 9.5 and at the commercial rare of 76 Kg/ha, respectively; the F1's in irrigated cages, the F2's and F3's in nonirrigated fields. Additive genetic variance was the most important component of the phenotypic variances among progenies. Major differences occurred between the F1's and F2's, but the F2's and F3's agreed closely. The percentages of additive variance (narrow sense heritability) for the joint F2, F3 analyses were: height (91); heading date (87); seed weight (74); yield per panicle (71); seeds per panicle (63); panicle number (58); stem diameter (55); plot yield (52). Important nonadditive variance was present in the F2, F3 data for plot yield (17%), stem diameter (15%) and seed weight (12%). All traits were positively correlated with each other in the F1's. Correlations were weaker in the F2 and F3 and reversed for panicle number. Seed weight showed the least correlation with other traits. These results are discussed from the practical viewpoint of combining strong straw with high grain yield. The usefulness of selecting for seed weight and panicle yield to improve plot yield is underlined.

scholarly journals Estimation of non-additive genetic variance in human complex traits from a large sample of unrelated individuals

2021 ◽  
Author(s):  
Valentin Hivert ◽  
Julia Sidorenko ◽  
Florian Rohart ◽  
Michael E. Goddard ◽  
Jian Yang ◽  
...  
Keyword(s):  
Complex Traits ◽  
Genetic Variance ◽  
Additive Genetic Variance ◽  
Large Sample ◽  
Human Complex

scholarly journals Selection strategies of segregant soybean populations for resistance to Asian rust

2009 ◽  
Vol 44 (11) ◽  
pp. 1452-1459 ◽  
Author(s):  
Aliny Simony Ribeiro ◽  
José Francisco Ferraz de Toledo ◽  
Magno Antonio Patto Ramalho
Keyword(s):  
Genetic Variance ◽  
Additive Genetic Variance ◽  
Infected Leaf ◽  
Good Resistance ◽  
Narrow Sense Heritability ◽  
Growing Seasons ◽  
Selection Strategies ◽  
Line Selection ◽  
Soybean Resistance ◽  
Selection Of

The objective of this work was to identify the best selection strategies for the more promising parental combinations to obtain lines with good resistance to soybean Asian rust (Phakopsora pachyrhizi). Two experiments were carried out in the field during the 2006/2007 and 2007/2008 growing seasons, to determine the percentage of infected leaf area of individual plants of five parents and their segregant F2 and F3 populations. The data obtained indicates that additive genetic variance predominates in the control of soybean resistance to Asian rust, and that the year and time of assessment do not significantly influence the estimates of the genetic parameters obtained. The narrow-sense heritability (h²r) ranged from 23.12 to 55.83%, and indicates the possibility of successful selection of resistant individuals in the early generations of the breeding program. All the procedures used to select the most promising populations to generate superior inbred lines for resistance to P. pachyrhizi presented similar results and identified the BR01-18437 x BRS 232 population as the best for inbred line selection.

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