Estimation of quantitative genetic parameters

This paper gives a short review of the development of genetic parameter estimation over the last 40 years. The need to analyse genetic processes in both animal selection experiments and animal breeding improvement programmes motivated the majority of this work. The usage of animal model in conjunction with residual maximum likelihood (REML) techniques for mixed models has revolutionized the methods. These methods to estimate quantitative genetic parameters have recently been advocated for use in evolutionary studies of natural populations. Therefore, it is perhaps timely to discuss the development of REML methods and their application to the analysis of artificial selection experiments and breeding programmes in animals. This should give extra insight into the methods and hopefully lead to synergy between both the areas.     

The Dynamics of Genetic Draft in Rapidly Adapting Populations

The accumulation of beneficial mutations on competing genetic backgrounds in rapidly adapting populations has a striking impact on evolutionary dynamics. This effect, known as clonal interference, causes erratic fluctuations in the frequencies of observed mutations, randomizes the fixation times of successful mutations, and leaves distinct signatures on patterns of genetic variation. Here, we show how this form of “genetic draft” affects the forward-time dynamics of site frequencies in rapidly adapting asexual populations. We calculate the probability that mutations at individual sites shift in frequency over a characteristic timescale, extending Gillespie’s original model of draft to the case where many strongly selected beneficial mutations segregate simultaneously. We then derive the sojourn time of mutant alleles, the expected fixation time of successful mutants, and the site frequency spectrum of beneficial and neutral mutations. Finally, we show how this form of draft affects inferences in the McDonald–Kreitman test and how it relates to recent observations that some aspects of genetic diversity are described by the Bolthausen–Sznitman coalescent in the limit of very rapid adaptation.     

NATURAL HERITABILITIES: CAN THEY BE RELIABLY ESTIMATED IN THE LABORATORY?

The validity of the assumption, that laboratory estimates of heritabilities will tend to overestimate natural heritabilities, due to a reduction in environmental variability and thus the phenotypic variance of traits, is examined. One hundred sixty-five field estimates of narrow sense heritabilities derived from the literature are compared with 189 estimates from laboratory studies on wild, outbred animal populations derived from the data set of Mousseau and Roff. The results indicate that 84% of field heritabilities are significantly different from zero and that for morphological, behavioral, and life-history traits there are no significant differences between laboratory and field estimates of heritability. Unexpectedly, mean heritabilities for morphological and life-history traits are actually higher in the field than in the lab. Twenty-two cases were found for which both laboratory and natural heritabilities had been estimated on the same traits. For this subset of the data, laboratory heritabilities tended to be higher than field estimates, but the difference was not significant. Also, the correlation between lab and field estimates was high (r = 0.6, P < 0.001), and the regression slope did not differ significantly from one. The major implications of this study are that laboratory estimates of heritability should generally provide reasonable estimations of both the magnitude and the significance of heritabilities in nature.     

Draft Sequences of the Radish (Raphanus sativus L.) Genome

Radish (Raphanus sativus L., n = 9) is one of the major vegetables in Asia. Since the genomes of Brassica and related species including radish underwent genome rearrangement, it is quite difficult to perform functional analysis based on the reported genomic sequence of Brassica rapa. Therefore, we performed genome sequencing of radish. Short reads of genomic sequences of 191.1 Gb were obtained by next-generation sequencing (NGS) for a radish inbred line, and 76,592 scaffolds of ≥300 bp were constructed along with the bacterial artificial chromosome-end sequences. Finally, the whole draft genomic sequence of 402 Mb spanning 75.9% of the estimated genomic size and containing 61,572 predicted genes was obtained. Subsequently, 221 single nucleotide polymorphism markers and 768 PCR-RFLP markers were used together with the 746 markers produced in our previous study for the construction of a linkage map. The map was combined further with another radish linkage map constructed mainly with expressed sequence tag-simple sequence repeat markers into a high-density integrated map of 1,166 cM with 2,553 DNA markers. A total of 1,345 scaffolds were assigned to the linkage map, spanning 116.0 Mb. Bulked PCR products amplified by 2,880 primer pairs were sequenced by NGS, and SNPs in eight inbred lines were identified.     

Genetic variability in the Skyros pony and its relationship with other Greek and foreign horse breeds

In Greece, seven native horse breeds have been identified so far. Among these, the Skyros pony is outstanding through having a distinct phenotype. In the present study, the aim was to assess genetic diversity in this breed, by using different types of genetic loci and available genealogical information. Its relationships with the other Greek, as well as foreign, domestic breeds were also investigated. Through microsatellite and pedigree analysis it appeared that the Skyros presented a similar level of genetic diversity to the other European breeds. Nevertheless, comparisons between DNA-based and pedigree-based results revealed that a loss of genetic diversity had probably already occurred before the beginning of breed registration. Tests indicated the possible existence of a recent bottleneck in two of the three main herds of Skyros pony. Nonetheless, relatively high levels of heterozygosity and Polymorphism Information Content indicated sufficient residual genetic variability, probably useful in planning future strategies for breed conservation. Three other Greek breeds were also analyzed. A comparison of these with domestic breeds elsewhere, revealed the closest relationships to be with the Middle Eastern types, whereas the Skyros itself remained isolated, without any close relationship, whatsoever.     

The relationship between parental genetic or phenotypic divergence and progeny variation in the maize nested association mapping population

Appropriate selection of parents for the development of mapping populations is pivotal to maximizing the power of quantitative trait loci detection. Trait genotypic variation within a family is indicative of the family's informativeness for genetic studies. Accurate prediction of the most useful parental combinations within a species would help guide quantitative genetics studies. We tested the reliability of genotypic and phenotypic distance estimators between pairs of maize inbred lines to predict genotypic variation for quantitative traits within families derived from biparental crosses. We developed 25 families composed of ~200 random recombinant inbred lines each from crosses between a common reference parent inbred, B73, and 25 diverse maize inbreds. Parents and families were evaluated for 19 quantitative traits across up to 11 environments. Genetic distances (GDs) among parents were estimated with 44 simple sequence repeat and 2303 single-nucleotide polymorphism markers. GDs among parents had no predictive value for progeny variation, which is most likely due to the choice of neutral markers. In contrast, we observed for about half of the traits measured a positive correlation between phenotypic parental distances and within-family genetic variance estimates. Consequently, the choice of promising segregating populations can be based on selecting phenotypically diverse parents. These results are congruent with models of genetic architecture that posit numerous genes affecting quantitative traits, each segregating for allelic series, with dispersal of allelic effects across diverse genetic material. This architecture, common to many quantitative traits in maize, limits the predictive value of parental genotypic or phenotypic values on progeny variance.     

A partially deficient and atypical equine transferrin variant, TF N

A new, partially deficient and phenotypically atypical transferrin variant, TF N, was detected in sera of a number of Finnhorses belonging to one family. The variant was inherited codominantly. In polyacrylamide gel electrophoresis (pH9.0) of sera, variant N appeared as a single weak band migrating slightly faster than the main anodal band of variant M. After immunoblotting or isolation an additional, still weaker, faster band was observed as well as some trace bands. The cathodal component, which is present in other transferrin variants, could not be convincingly proved. The main component of variant N contained four sialic acid residues.     

The Visible,Sustainable Farm: A Comprehensive Energy Analysis of a Midwestern Farm

The Sunshine Farm, in central Kansas, offers a unique data set detailing all the inputs and outputs of a farming project intended to be based, as much as possible, on solar energy. Such a complete and detailed data set, encompassing more than 1.25 M data points for an 85-ha, 7-year project, has never before been compiled for any farm. The data show that important energy inputs that have thus far been left out of existing farm energy efficiency estimates, with implications for biofuels and other biomass for energy technologies. The SSF achieved energy efficiencies superior to conventional agriculture while maintaining soil health and delivering more nutritious, organic products. A first-ever analysis of the energy efficiency of horse traction shows that horses are significantly less energy efficient and much less labor efficient than tractors, although the horses in the study were clearly underutilized. An analysis of the farm removing all inputs and outputs relevant to the horses shows that without horses the Sunshine Farm would have been competitive with conventional energy efficiencies even taking into account the farm's higher labor inputs and small size.     

Does natural selection alter genetic architecture? An evaluation of quantitative genetic variation among populations of Allonemobiussocius and A. fasciatus

To make long-term predictions using present quantitative genetic theory it is necessary to assume that the genetic variance–covariance matrix ( G ) remains constant or at least changes by a constant fraction. In this paper we examine the stability of the genetic architecture of two traits known to be subject to natural selection; femur length and ovipositor length in two species of the cricket Allonemobius. Previous studies have shown that in A. fasciatus and A. socius natural selection favours an increased body size southwards but a decreased ovipositor length. Such countergradient selection should tend to favour a change in G . In the total sample of eight populations of A. socius and one of A. fasciatus we show that there is significant variation in all genetic covariance components, i.e. V_A for body size, V_A for ovipositor length, and Cov_A. This variation results entirely from an increase in the covariances of A. fasciatus. However, although larger, these components are approximately proportionally increased, thereby leading to no statistically significant change in the genetic correlation. A proportional increase in the covariance components is consistent with changes resulting from genetic drift. On the other hand, the genetic covariance components are significantly correlated with the length of the growing season suggesting that the change in the genetic architecture is the result of selection and drift.     

Lack of concordance between genetic diversity estimates at the molecular and quantitative-trait levels

In many applications of population genetics, particularly in the field of conservation biology, estimates of molecular diversity are used as surrogate indicators of less easily acquired measures of genetic variation for quantitative traits. The general validity of this approach to inferring levels of quantitative genetic variation within populations is called into question by the demonstration that estimates of molecular and quantitative-genetic variation are essentially uncorrelated in natural populations of Daphnia, one of the few organisms for which multiple estimates of both quantities are available. On the other hand, molecular measures of population subdivision seem to give conservatively low estimates of the degree of genetic subdivision at the level of quantitative traits. This suggests that although molecular markers provide little information on the level of genetic variation for quantitative traits within populations, they may be valid indicators of population subdivision for such characters.