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

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.

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

10.1101/164848 ◽

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.

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

Silvae Genetica ◽

10.1515/sg-2009-0038 ◽

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.

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Genetic variance for body size in a natural population of Drosophila buzzatii.

Genetics ◽

10.1093/genetics/128.4.739 ◽

1991 ◽

Vol 128 (4) ◽

pp. 739-750

Author(s):

A Ruiz ◽

M Santos ◽

A Barbadilla ◽

J E Quezada-Díaz ◽

E Hasson ◽

...

Keyword(s):

Genetic Variance ◽

Genetic Model ◽

Phenotypic Variance ◽

Total Phenotypic Variance ◽

Fourth Chromosome ◽

Narrow Sense Heritability ◽

Additive Variance ◽

Thorax Length ◽

Drosophila Buzzatii ◽

F2 Generation

Abstract Previous work has shown thorax length to be under directional selection in the Drosophila buzzatii population of Carboneras. In order to predict the genetic consequences of natural selection, genetic variation for this trait was investigated in two ways. First, narrow sense heritability was estimated in the laboratory F2 generation of a sample of wild flies by means of the offspring-parent regression. A relatively high value, 0.59, was obtained. Because the phenotypic variance of wild flies was 7-9 times that of the flies raised in the laboratory, "natural" heritability may be estimated as one-seventh to one-ninth that value. Second, the contribution of the second and fourth chromosomes, which are polymorphic for paracentric inversions, to the genetic variance of thorax length was estimated in the field and in the laboratory. This was done with the assistance of a simple genetic model which shows that the variance among chromosome arrangements and the variance among karyotypes provide minimum estimates of the chromosome's contribution to the additive and genetic variances of the trait, respectively. In males raised under optimal conditions in the laboratory, the variance among second-chromosome karyotypes accounted for 11.43% of the total phenotypic variance and most of this variance was additive; by contrast, the contribution of the fourth chromosome was nonsignificant. The variance among second-chromosome karyotypes accounted for 1.56-1.78% of the total phenotypic variance in wild males and was nonsignificant in wild females. The variance among fourth chromosome karyotypes accounted for 0.14-3.48% of the total phenotypic variance in wild flies. At both chromosomes, the proportion of additive variance was higher in mating flies than in nonmating flies.

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Ancestral Contributions to Roasted Peanut Attribute1

Peanut Science ◽

10.3146/pnut.22.1.0009 ◽

1995 ◽

Vol 22 (1) ◽

pp. 42-48 ◽

Cited By ~ 2

Author(s):

T. G. Isleib ◽

H. E. Pattee ◽

F. G. Giesbrecht

Keyword(s):

Phenotypic Variation ◽

Model Building ◽

Additive Genetic Variance ◽

Genotypic Variation ◽

Multiple Regression Model ◽

Pedigree Information ◽

Narrow Sense ◽

Narrow Sense Heritability ◽

Breeding Lines ◽

Total Phenotypic Variation

Abstract Estimates of broad-sense heritability for roasted flavor attribute of peanut (Arachis hypogaea L.) range from 9 to 24% on a single-plot basis. Response to selection is determined by the narrow-sense heritability, calculated from estimates of additive genetic variance which are not available for this trait. One way to assess the additive component of genetic variation is to determine how much of the total phenotypic variation can be predicted from genetic contributions of ancestors of the individuals measured. From 1986 to 1991, samples of 128 peanut cultivars and breeding lines were obtained from peanut research programs representing the three major production areas in the U.S. Samples were roasted to a nearly common color, ground into paste, and assessed for roasted flavor and fruity attribute by a trained sensory panel. CIELAB L* color was also measured for use as a covariate in statistical analysis to adjust for small differences in color. The sum of squares associated with the 128 genotypes accounted for 11% of the total phenotypic variation. Ancestry of the lines was traced back to 47 progenitors for which no further pedigree information was available. Eight progenitors made ancestral contributions that were linearly dependent on the other 39. Ancestral effects accounted for 53% of the genotypic variation, i.e., 6% of the phenotypic variation. Despite shortcomings of this 6% figure as an estimate of narrow-sense heritability for roasted flavor, no other estimates are extant. The residual (nonadditive) variation among genotypes after accounting for ancestral (additive) effects was highly significant. Multiple regression model-building techniques were used to identify 13 ancestors exerting significant effects on roasted flavor. Jenkins Jumbo, F231 (a cross of Dixie Giant with Small White Spanish 3x-2), and Improved Spanish 2B were the only ancestors among the 13 that were common to 40 or more of the 128 lines tested. Jenkins Jumbo was the single most important ancestor, exerting a negative effect on flavor (b = −1.25±0.19). Its progeny would be expected to have roast flavor scores reduced by |b|/2 = 0.62 units and grandprogeny by |b|/4 = 0.31 units. All but four of the 13 ancestors deemed important had deleterious effects on flavor.

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GENETIC VARIANCES IN AN EIGHT PARENT HALF DIALLEL OF OATS

Canadian Journal of Genetics and Cytology ◽

10.1139/g76-051 ◽

1976 ◽

Vol 18 (3) ◽

pp. 419-427 ◽

Cited By ~ 2

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.

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

Canadian Journal of Genetics and Cytology ◽

10.1139/g71-120 ◽

1971 ◽

Vol 13 (4) ◽

pp. 864-872 ◽

Cited By ~ 13

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.

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Selection strategies of segregant soybean populations for resistance to Asian rust

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2009001100012 ◽

2009 ◽

Vol 44 (11) ◽

pp. 1452-1459 ◽

Cited By ~ 8

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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Reaction of Select Peanut (Arachis hypogaea L.) Lines to Southern Stem Rot and Pythium Pod Rot Under Varied Disease Pressure

Peanut Science ◽

10.3146/i0095-3679-16-1-3 ◽

1989 ◽

Vol 16 (1) ◽

pp. 9-14 ◽

Cited By ~ 9

Author(s):

O. D. Smith ◽

T. E. Boswell ◽

W. J. Grichar ◽

C. E. Simpson

Keyword(s):

Arachis Hypogaea ◽

Disease Incidence ◽

Sclerotium Rolfsii ◽

Stem Rot ◽

Resistant Parent ◽

Breeding Lines ◽

Arachis Hypogaea L ◽

Significant Yield ◽

Considerable Resistance ◽

Disease Pressure

Abstract Eight breeding lines, three parents, and the cultivar Florunner were compared under two levels of disease pressure induced by Sclerotium rolfsii Sacc., or Pythium myriotylum Drechs. at each of two locations for three years to ascertain the effectiveness of the host plant resistance to each pathogen. Varied disease pressures were created by application of fungicides and supplement of fungal inoculum. Mean Florunner pod yields varied more than 1000 kg/ha as a result of the S. rolfsii treatments but the yields of the resistant TxAG-3 were not affected. Disease incidence, as measured by frequency of S. rolfsii infection sites and diseased pods, was much higher for Florunner than TxAG-3. Breeding lines for which TxAG-3 was a parent sustained significant yield reductions. The disease incidence in these lines was higher than the resistant parent, equal or less than Tamnut 74, their other parent, and less than Florunner. The grades of TxAG-3 and its derivatives were lower than Florunner. Pod rot incidence differed for the P. myriotylum treatments but pod yields were not different. TxAG-3 and Toalson sustained less pod disease than Florunner and Tamnut 74. The percent of diseased pod tissue for one derivative of Toalson was lower than Toalson and TxAG-3, and that of one TxAG-3 derivative was equal to its best parent. The breeding lines varied in reaction to the two diseases and some lines showed considerable resistance to both organisms.

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Peanut Peg Strength and Associated Pod Yield and Loss by Cultivar

Peanut Science ◽

10.3146/ps17-1.1 ◽

2017 ◽

Vol 44 (2) ◽

pp. 77-82 ◽

Cited By ~ 1

Author(s):

R. B. Sorensen ◽

R.C. Nuti ◽

C.C. Holbrook ◽

C.Y. Chen

Keyword(s):

Arachis Hypogaea ◽

Breeding Lines ◽

Late Season ◽

Pod Yield ◽

Harvest Dates ◽

Arachis Hypogaea L ◽

Peanut Cultivars ◽

Stems And Leaves

ABSTRACT Peanut (Arachis hypogaea L.) peg strength and associated pod yield and digging loss were documented for nine cultivars and two breeding genotypes across three harvest dates (early, mid, and late season) at two Southwest Georgia locations during 2010 and 2011. Cultivars selected were Georgia Green, Georgia Greener, Georgia-02C, Georgia-06G, Georgia-07W, Georgia-09B, Georgia-10T, Florida-07, Tifguard, and advanced breeding lines EXP27-1516 and TifGP-2. Prior to digging, a minimum of three peanut plants from each plot were selected and excess stems and leaves were removed with scissors leaving individual peanut pegs and pods with about 5-cm of stem. Each peanut pod was placed in a “U” shaped metal bracket attached to an electronic force gauge and the stem was pulled manually until the pod detached. After digging and combining, a tractor-mounted scavenger machine was used to collect pods remaining in the soil. Peg strength was greater at Dawson (6.14 N) compared to Tifton (5.28 N) in 2010 but were similar in 2011 (4.51 and 4.39 N, respectively). Dawson had consistently higher yields (5326 kg/ha) and lower pod loss (562 kg/ha) compared with Tifton (3803 kg/ha and 936 kg/ha, respectively). Peanut cultivars with greater peg strength across locations were Georgia-06G, Florida-07, and Georiga-02C. Cultivar Georiga-06G showed the greatest yield across locations and years. Other cultivars may have had stronger peg strength, greater pod yield, or lower pod loss but none were more consistent than these three cultivars across years, locations, and harvest dates.

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