Imputation of non-genotyped sheep from the genotypes of their mates and resulting progeny

Accurate genomic analyses are predicated on access to a large quantity of accurately genotyped and phenotyped animals. Because the cost of genotyping is often less than the cost of phenotyping, interest is increasing in generating genotypes for phenotyped animals. In some instances this may imply the requirement to genotype older animals with greater phenotypic information content. Biological material for these older informative animals may, however, no longer exist. The objective of the present study was to quantify the ability to impute 11 129 single nucleotide polymorphism (SNP) genotypes of non-genotyped animals (in this instance sires) from the genotypes of their progeny with or without including the genotypes of the progenys’ dams (i.e. mates of the sire to be imputed). The impact on the accuracy of genotype imputation by including more progeny (and their dams’) genotypes in the imputation reference population was also quantified. When genotypes of the dams were not available, genotypes of 41 sires with at least 15 genotyped progeny were used for the imputation; when genotypes of the dams were available, genotypes of 21 sires with at least 10 genotyped progeny were used for the imputation. Imputation was undertaken exploiting family and population level information. The mean and variability in the proportion of genotypes per individual that could not be imputed reduced as the number of progeny genotypes used per individual increased. Little improvement in the proportion of genotypes that could not be imputed was achieved once genotypes of seven progeny and their dams were used or genotypes of 11 progeny without their respective dam’s genotypes were used. Mean imputation accuracy per individual (depicted by both concordance rates and correlation between true and imputed) increased with increasing progeny group size. Moreover, the range in mean imputation accuracy per individual reduced as more progeny genotypes were used in the imputation. If the genotype of the mate of the sire was also used, high accuracy of imputation (mean genotype concordance rate per individual of 0.988), with little additional benefit thereafter, was achieved with seven genotyped progeny. In the absence of genotypes on the dam, similar imputation accuracy could not be achieved even using genotypes on up to 15 progeny. Results therefore suggest, at least for the SNP density used in the present study, that it is possible to accurately impute the genotypes of a non-genotyped parent from the genotypes of its progeny and there is a benefit of also including the genotype of the sire’s mate (i.e. dam of the progeny).     

SOCIAL CAUSES OF CORRELATIONAL SELECTION AND THE RESOLUTION OF A HERITABLE THROAT COLOR POLYMORPHISM IN A LIZARD

Abstract When selection acts on social or behavioral traits, the fitness of an individual depends on the phenotypes of its competitors. Here, we describe methods and statistical inference for measuring natural selection in small social groups. We measured selection on throat color alleles that arises from microgeographic variation in allele frequency at natal sites of side‐blotched lizards (Uta stansburiana). Previous game‐theoretic analysis indicates that two color morphs of female side‐blotched lizards are engaged in an offspring quantity‐quality game that promotes a density‐and frequency‐dependent cycle. Orange‐throated females are r‐strategists. They lay large clutches of small progeny, which have poor survival at high density, but good survival at low density. In contrast, yellow‐throated females are K‐strategists. They lay small clutches of large progeny, which have good survival at high density. We tested three predictions of the female game: (1) orange progeny should have a fitness advantage at low density; (2) correlational selection acts to couple color alleles and progeny size; and (3) this correlational selection arises from frequency‐dependent selection in which large hatchling size confers an advantage, but only when yellow alleles are rare. We also confirmed the heritability of color, and therefore its genetic basis, by producing progeny from controlled matings. A parsimonious cause of the high heritability is that three alleles (o, b, y) segregate as one genetic factor. We review the physiology of color formation to explain the possible genetic architecture of the throat color trait. Heritability of color was nearly additive in our breeding study, allowing us to compute a genotypic value for each individual and thus predict the frequency of progeny alleles released on 116 plots. Rather than study the fitness of individual progeny, we studied how the fitness of their color alleles varied with allele frequency on plots. We confirmed prediction 1: When orange alleles are present in female progeny, they have higher fitness at low density when compared to other alleles. Even though the difference in egg size of the female morphs was small (0.02 g), it led to knife‐edged survival effects for their progeny depending on local social context. Selection on hatchling survival was not only dependent on color alleles, but on a fitness interaction between color alleles and hatchling size, which confirmed prediction 2. Sire effects, which are not confounded by maternal phenotype, allowed us to resolve the frequency dependence of correlational selection on egg size and color alleles and thereby confirmed prediction 3. Selection favored large size when yellow sire alleles were rare, but small size when they were common. Correlational selection promotes the formation of a self‐reinforcing genetic correlation between the morphs and life‐history variation, which causes selection in the next density and frequency cycle to be exacerbated. We discuss general conditions for the evolution of self‐reinforcing genetic correlations that arise from social selection associated with frequency‐dependent sexual and natural selection.     

Adaptive social and maternal induction of antipredator dorsal patterns in a lizard with alternative social strategies

Maternal effects facilitate adaptation to changing environments because they alter individual offspring traits to match current conditions. We show that maternal effects can also resolve context-dependent, correlational selection on multiple offspring traits, promoting adaptation to more complex environments. In side-blotched lizards ( Uta stansburiana ), two alternative pathways of dorsal pattern induction involve maternal oestradiol and alleles for throat colouration (∼social strategy). In one pathway, females increased yolk oestradiol when mated to yellow-throated sires; oestradiol induced dorsal barring in yellow-throated progeny of both sexes. In another pathway, females elevated yolk oestradiol in response to a high frequency of orange alleles in experimental social neighbourhoods. When the sire lacked yellow alleles, this secondary pathway resulted in striped, orange sons and striped, non-orange daughters. All maternally induced types had high fitness in the wild. These results illustrate a (previously undescribed) mechanism for females to simultaneously resolve differing correlational selection pressures on different progeny.     

MATERNAL ADJUSTMENT OF EGG SIZE ORGANIZES ALTERNATIVE ESCAPE BEHAVIORS,PROMOTING ADAPTIVE PHENOTYPIC INTEGRATION

Numerous integrated traits contribute to any aspect of organismal performance, but favorable trait combinations are difficult to maintain in the face of genetic recombination. We investigated the role of maternal effects in promoting integration of alternative reproductive strategies (～throat colors) with antipredator traits (escape behaviors and dorsal patterns) in the side‐blotched lizard (Uta stansburiana). Previously, we reported that maternally derived estradiol adaptively pairs dorsal patterns with progeny throat colors. Here we show adaptive maternal effects on escape behaviors within each throat color morph. Specifically, yellow‐throated females and all females mated to yellow‐throated sires lay larger eggs. Larger eggs produce stockier offspring, who remain stockier throughout life. Stockiness promotes evasive escape behaviors (e.g., reversals), which are adaptive in barred, yellow‐throated offspring. Orange‐throated females lay smaller eggs, producing leaner hatchlings who perform vertical escape behaviors (e.g., jumping). Vertical behaviors enhance survival in striped, orange‐throated progeny. Escape behavior was not heritable, but was organized by natural or experimental egg size variation. Maternal effects on adaptive phenotypic integration are likely common in polymorphic species, because recombination otherwise breaks apart beneficial trait combinations. Furthermore, our results provide insight into the role of body shape in organizing (and constraining) evolution of integrated reproductive and antipredator strategies.     

Within-clutch variation in offspring sex determined by differences in sire body size: cryptic mate choice in the wild

Sexual selection theory predicts that paternal quality should drive female investment in progeny. We tested whether polyandrous female side-blotched lizards, Uta stansburiana, would adjust within-clutch progeny investment according to sire phenotypes. In two different years, polyandrous females selectively used sperm from larger sires to produce sons and used sperm from smaller sires to produce daughters. This cryptic sperm choice had significant effects on progeny survival to maturity that were consistent with sexually antagonistic effects associated with sire body size. Large sires produced sons with high viability and small sires produced daughters with high viability. These results are consistent with our previous findings that alleles for male body size have different fitness effects in male and female progeny. Breeding experiments in the laboratory indicate that results from the wild are more likely due to female choice than biased sperm production by males. Our results demonstrate highly refined gender-specific female choice for sperm and indicate that sire body size may signal the quality of sons or daughters that a sire will produce.     

Imputation of ungenotyped parental genotypes in dairy and beef cattle from progeny genotypes

The objective of this study was to quantify the accuracy of imputing the genotype of parents using information on the genotype of their progeny and a family-based and population-based imputation algorithm. Two separate data sets were used, one containing both dairy and beef animals (n=3122) with high-density genotypes (735 151 single nucleotide polymorphisms (SNPs)) and the other containing just dairy animals (n=5489) with medium-density genotypes (51 602 SNPs). Imputation accuracy of three different genotype density panels were evaluated representing low (i.e. 6501 SNPs), medium and high density. The full genotypes of sires with genotyped half-sib progeny were masked and subsequently imputed. Genotyped half-sib progeny group sizes were altered from 4 up to 12 and the impact on imputation accuracy was quantified. Up to 157 and 258 sires were used to test the accuracy of imputation in the dairy plus beef data set and the dairy-only data set, respectively. The efficiency and accuracy of imputation was quantified as the proportion of genotypes that could not be imputed, and as both the genotype concordance rate and allele concordance rate. The median proportion of genotypes per animal that could not be imputed in the imputation process decreased as the number of genotyped half-sib progeny increased; values for the medium-density panel ranged from a median of 0.015 with a half-sib progeny group size of 4 to a median of 0.0014 to 0.0015 with a half-sib progeny group size of 8. The accuracy of imputation across different paternal half-sib progeny group sizes was similar in both data sets. Concordance rates increased considerably as the number of genotyped half-sib progeny increased from four (mean animal allele concordance rate of 0.94 in both data sets for the medium-density genotype panel) to five (mean animal allele concordance rate of 0.96 in both data sets for the medium-density genotype panel) after which it was relatively stable up to a half-sib progeny group size of eight. In the data set with dairy-only animals, sufficient sires with paternal half-sib progeny groups up to 12 were available and the within-animal mean genotype concordance rates continued to increase up to this group size. The accuracy of imputation was worst for the low-density genotypes, especially with smaller half-sib progeny group sizes but the difference in imputation accuracy between density panels diminished as progeny group size increased; the difference between high and medium-density genotype panels was relatively small across all half-sib progeny group sizes. Where biological material or genotypes are not available on individual animals, at least five progeny can be genotyped (on either a medium or high-density genotyping platform) and the parental alleles imputed with, on average, ⩾96% accuracy.     

Detection of recombination events,haplotype reconstruction and imputation of sires using half-sib SNP genotypes

Background

Identifying recombination events and the chromosomal segments that constitute a gamete is useful for a number of applications in genomic analyses. In livestock, genotypic data are commonly available for half-sib families. We propose a straightforward but computationally efficient method to use single nucleotide polymorphism marker genotypes on half-sibs to reconstruct the recombination and segregation events that occurred during meiosis in a sire to form the haplotypes observed in its offspring. These meiosis events determine a block structure in paternal haplotypes of the progeny and this can be used to phase the genotypes of individuals in single half-sib families, to impute haplotypes of the sire if they are not genotyped or to impute the paternal strand of the offspring’s sequence based on sequence data of the sire.

Methods

The hsphase algorithm exploits information from opposing homozygotes among half-sibs to identify recombination events, and the chromosomal regions from the paternal and maternal strands of the sire (blocks) that were inherited by its progeny. This information is then used to impute the sire’s genotype, which, in turn, is used to phase the half-sib family. Accuracy (defined as R²) and performance of this approach were evaluated by using simulated and real datasets. Phasing results for the half-sibs were benchmarked to other commonly used phasing programs – AlphaPhase, BEAGLE and PedPhase 3.

Results

Using a simulated dataset with 20 markers per cM, and for a half-sib family size of 4 and 40, the accuracy of block detection, was 0.58 and 0.96, respectively. The accuracy of inferring sire genotypes was 0.75 and 1.00 and the accuracy of phasing was around 0.97, respectively. hsphase was more robust to genotyping errors than PedPhase 3, AlphaPhase and BEAGLE. Computationally, hsphase was much faster than AlphaPhase and BEAGLE.

Conclusions

In half-sib families of size 8 and above, hsphase can accurately detect block structure of paternal haplotypes, impute genotypes of ungenotyped sires and reconstruct haplotypes in progeny. The method is much faster and more accurate than other widely used population-based phasing programs. A program implementing the method is freely available as an R package (hsphase).     

Live animal measurements, carcass composition and plasma hormone and metabolite concentrations in male progeny of sires differing in genetic merit for beef production

In genetic improvement programmes for beef cattle, the effect of selecting for a given trait or index on other economically important traits, or their predictors, must be quantified to ensure no deleterious consequential effects go unnoticed. The objective was to compare live animal measurements, carcass composition and plasma hormone and metabolite concentrations of male progeny of sires selected on an economic index in Ireland. This beef carcass index (BCI) is expressed in euros and based on weaning weight, feed intake, carcass weight and carcass conformation and fat scores. The index is used to aid in the genetic comparison of animals for the expected profitability of their progeny at slaughter. A total of 107 progeny from beef sires of high (n = 11) or low (n = 11) genetic merit for the BCI were compared in either a bull (slaughtered at 16 months of age) or steer (slaughtered at 24 months of age) production system, following purchase after weaning (8 months of age) from commercial beef herds. Data were analysed as a 2 × 2 factorial design (two levels of genetic merit by two production systems). Progeny of high BCI sires had heavier carcasses, greater (P < 0.01) muscularity scores after weaning, greater (P < 0.05) skeletal scores and scanned muscle depth pre-slaughter, higher (P < 0.05) plasma insulin concentrations and greater (P < 0.01) animal value (obtained by multiplying carcass weight by carcass value, which was based on the weight of meat in each cut by its commercial value) than progeny of low BCI sires. Regression of progeny performance on sire genetic merit was also undertaken across the entire data set. In steers, the effect of BCI on carcass meat proportion, calculated carcass value (c/kg) and animal value was positive (P < 0.01), while a negative association was observed for scanned fat depth pre-slaughter and carcass fat proportion (P < 0.01), but there was no effect in bulls. The effect of sire expected progeny difference (EPD) for carcass weight followed the same trends as BCI. Muscularity scores, carcass meat proportion and calculated carcass value increased, whereas scanned fat depth, carcass fat and bone proportions decreased with increasing sire EPD for conformation score. The opposite association was observed for sire EPD for fat score. Results from this study show that selection using the BCI had positive effects on live animal muscularity, carcass meat proportion, proportions of high-value cuts and carcass value in steer progeny, which are desirable traits in beef production.     

Biparental inheritance of chloroplast DNA and the existence of heteroplasmic cells in alfalfa

Summary Mapping of chloroplast DNA (ctDNA) restriction fragment patterns from a chlorophyll deficient mutant and two phenotypically normal alfalfa genotypes (Medicago sativa L.) has demonstrated the existence of a distinct ctDNA genotype from each source. These unique restriction fragment patterns were utilized to identify maternal or paternal origin of ctDNA in hybrid plants from crosses involving the normal alfalfa genotypes as females and the yellow-green chlorophyll deficient sectors as males. Progeny from these crosses expressing the yellow-green sectored phenotypes contained paternal ctDNA in the chlorophyll deficient sectors and maternal ctDNA in the normal sectors, confirming biparental plastid inheritance. The existence of mixed cells containing both mutant and normal plastids at various stages of sorting-out was observed by transmission electron microscopy of mesophyll cells in mosaic tissue from hybrid plants. This observation verified the biparental transmission of plastids in alfalfa.     

Carotenoid status signaling in captive and wild red-collared widowbirds: independent effects of badge size and color

Carotenoid-based plumage ornaments are typically consideredto be sexually selected traits, functioning as honest condition-dependentsignals of phenotypic quality, but few studies have addressedthe function of carotenoid color variation in male contestcompetition. Using two experiments, we investigated the statussignaling function of the variable (ranging from yellow tored) carotenoid throat patch (collar) in the polygynous, sexually dimorphic red-collared widowbird (Euplectes ardens). First,we tested if the red collar functions as a dominance signalby painting spectrometrically controlled collar patches ontothe brown plumage of nonbreeding males and staging dyadic malecontests over food resources. Red-collared males dominatedorange males, which in turn dominated the control brown andnovel blue collars. Red dominance persisted when the collar manipulations were reversed within dyads and also when testedagainst testosterone implanted males. In the second experimentthe collar size and color of breeding males were manipulatedin the field before and after territories were established.All males with enlarged red and most with enlarged orange orreduced red collars obtained territories, whereas most maleswith reduced orange and all with blackened (removed) collarsfailed to establish or retain territories. In addition, amongthe territorial males, those with reduced signals defendedsmaller territories, received more intrusions, and spent moretime in aggressive interactions. Redness and, to a lesser extent,size of the carotenoid ornament both seem to independently indicate male dominance status or fighting ability in male contest competition.     

Predicting heterosis for egg production traits in crossbred offspring of individual White Leghorn sires using genome-wide SNP data

Background

The development of a reliable method to predict heterosis would greatly improve the efficiency of commercial crossbreeding schemes. Extending heterosis prediction from the line level to the individual sire level would take advantage of variation between sires from the same pure line, and further increase the use of heterosis in crossbreeding schemes. We aimed at deriving the theoretical expectation for heterosis due to dominance in the crossbred offspring of individual sires, and investigating how much extra variance in heterosis can be explained by predicting heterosis at the individual sire level rather than at the line level. We used 53 421 SNP (single nucleotide polymorphism) genotypes of 3427 White Leghorn sires, allele frequencies of six White Leghorn dam-lines and cage-based records on egg number and egg weight of ~210 000 crossbred hens.

Results

We derived the expected heterosis for the offspring of individual sires as the between- and within-line genome-wide heterozygosity excess in the offspring of a sire relative to the mean heterozygosity of the pure lines. Next, we predicted heterosis by regressing offspring performance on the heterozygosity excess. Predicted heterosis ranged from 7.6 to 16.7 for egg number, and from 1.1 to 2.3 grams for egg weight. Between-line differences accounted for 99.0% of the total variance in predicted heterosis, while within-line differences among sires accounted for 0.7%.

Conclusions

We show that it is possible to predict heterosis at the sire level, thus to distinguish between sires within the same pure line with offspring that show different levels of heterosis. However, based on our data, variation in genome-wide predicted heterosis between sires from the same pure line was small; most differences were observed between lines. We hypothesise that this method may work better if predictions are based on SNPs with identified dominance effects.     

Inheritance of flower color and spininess in safflower (Carthamus tinctorius L.)

Safflower (Carthamus tinctorius L.) flowers are used for coloring and flavoring food and also as fresh-cut and dried flowers. The most important characteristics which contribute to the ornamental value of safflower are flower color and spinelessness. The objective of this study was to determine the inheritance mode and the number of genes controlling spininess and flower color in some Iranian genotypes of safflower. The results indicated that the existence of spines on the leaves and bracts of safflower is controlled by a single dominant gene in which the spiny phenotype was completely dominant to spineless. In some crosses, flower color was controlled by two epistatic loci each with two alleles, resulting in a ratio of 13:3 in the segregating F2 population for plants with orange and yellow flowers. Also, other mechanisms of genetic control, such as duplicate dominance and duplicate recessive types of epistasis, were observed for flower color in other crosses that led to ratios of 7:9 and 15:1 for plants with orange and yellow flowers, respectively. The results suggest that for ornamental use or in the food dying industry, genotypes with orange or yellow flowers and without spines on the leaves and bracts can be produced.     

The effect of selection of both sire and dam on the response of F1 generation lambs to vaccination with irradiated Trichostrongylus colubriformis larvae

Windon R. G. and Dineen J. K. (1981). The effect of selection of both sire and dam on the response of F₁ generation lambs to vaccination with irradiated Trichostrongylus colubriformis larvae. International Journal for Parasitology11: 11–18. Rams and ewes, tested for responsiveness to vaccination with irradiated T. colubriformis larvae at an early age, were mated on the basis of responder × responder and non-responder × non-responder. Progeny were vaccinated at 8 and 12 weeks of age with 20,000 irradiated larvae, treated with anthelmintic at 16 weeks and challenged with 20,000 normal larvae at 17 weeks. Faecal egg counts of progeny from responder matings were significantly lower than progeny from non-responders, and within each mating type, ewe lambs had markedly lower egg counts than ram lambs. The level of circulating complement-fixing antibodies to T. colubriformis larval extract were inversely related to egg counts. Thus, ewe progeny from responder matings had the highest serum antibody levels, non-responder ram progeny had the lowest levels and responder rams and non-responder ewes had similar intermediate levels. In vitro responses of cells stimulated with T. colubriformis L₃ antigen were greater in progeny from responder matings, whereas responses to bacterial lipopolysaccharide were higher in progeny from non-responder matings. The results confirm that the response to vaccination at an early age is genetically determined, and show that the response of progeny is most vigorously expressed when both sires and dams have been selected.     

DNA markers and crossbreeding scheme as means to select sires for heterosis in egg production of chickens

Genotypes for 24 microsatellite markers, dispersed across the chicken genome, were used to predict progeny performance and heterosis for egg production (number and mass) in 'layers' (egg-type chickens). These markers were used to evaluate genetic distance between each of 39 sires sampled from two-layer male-lines; Rhode Island Red (RIR) and White egg Leghorn (Leghorn), and a DNA pool of 30 randomly sampled females from a Brown-egg female line (Silver). Each sire was analysed for egg production across months in the laying period and cumulatively in each of three subperiods; onset (2 month), mid (9 month) and late (1 month). The average Reynolds' genetic distance between Leghorn sires and the Silver female line (theta;=0.6) was significantly higher than that between RIR sires and the Silver female line (theta;=0.5). Neither performance nor heterosis values in the RIR sire's daughters were associated with genetic distance values between sires and the Silver female line. On the other hand, performance as well as heterosis values of Leghorn's daughters were positively associated with genetic distance. This association was particularly evident in the mid-subperiod. If 25% of the most genetically distant Leghorn sires from the Silver female line had been selected in a single generation on the basis of DNA markers information only, average egg production of the crossbred daughters would have been improved by about nine eggs (3%). In principle, further improvement is possible if selection to increase genetic distance between the parental lines is carried on.     

CONDITION, GENOTYPE-BY-ENVIRONMENT INTERACTION, AND CORRELATIONAL SELECTION IN LIZARD LIFE-HISTORY MORPHS

Abstract We compared reproductive allocation and variation in condition and survivorship of two heritable female throat color morphs (orange and yellow) in a free‐living population of side‐blotched lizards (Uta stansburiana). Using path analysis and structural equation modeling, we investigated how variation in the social environment affected clutch size and egg mass and two condition traits (postlaying mass, immunological condition) and how these traits in turn affected female field survival. In the presence of many neighbors, both morphs increased their clutch sizes, although these effects were only significant in yellow females. In addition, yellow females increased their egg mass in the presence of many orange neighbors. Orange females surrounded by many orange neighbors showed sign of stress in the form of immunosuppression, whereas this effect was less pronounced in yellow females. The morphs also differed in the impact of variation in clutch size and egg mass on both condition traits. Finally, female morphotype and immune responsiveness affected fitness interactively, and hence these two traits showed signs of fitness epistasis: Selection gradients on this trait were opposite in sign in the two morphs. The correlational selection gradient (_{γthroatxantibody response}) between female throat color and antibody responsiveness was ‐0.365. Our data thus reveal important interactive effects such as genotype‐by‐environment interaction toward the social environment and morph‐specific trade‐offs as well as the occurrence of correlational selection. We discuss the use of naturally occurring and conspicuous genetic polymorphisms in field studies of selection and life‐history allocation.     

Prediction of informativeness for microsatellite markers among progeny of sires used for detection of economic trait loci in dairy cattle

Individual loci affecting economic traits can be located using genetic linkage. Application of either daughter or granddaughter designs requires determination of allele origin in the progeny. If only the sires and their progeny are genotyped, the paternal allele origin of progeny having the same genotype as the sire cannot be determined. The expected frequency of informative sons can be predicted for each sire and genetic marker from the allele frequencies in the population. The accuracy of a predictor of the frequency of informative progeny was tested on 103 grandsire x microsatellite combinations. Number of sons per grandsire varied from 24 to 129. Allele frequencies in the population were estimated by genotyping seven sires. The regression of the frequency of informative sons on the predicted frequency was 1.04 with a zero intercept model. Thus, considering the large number of genetic markers available for analysis, predicted informative frequency is a useful criterion for selection of genetic markers.     

Inheritance of resistance to clopyralid and picloram in yellow starthistle (Centaurea solstitialis L.) is controlled by a single nuclear recessive gene

The noxious weed yellow starthistle (Centaurea solstitialis L.) can be controlled effectively at the seedling stage with foliar application of the auxinic herbicides picloram or clopyralid. Although resistance to these herbicides is rare, a yellow starthistle biotype resistant to picloram and cross-resistant to clopyralid was observed in 1989 near Dayton, WA, in a pasture that had been subjected to intensive picloram selective pressure. Our objective was to determine the mode of inheritance for this resistance trait. Transmission of the resistant phenotype was monitored in reciprocal F(1) crosses between susceptible (SCI) and resistant (RDW) plants, their testcross and pseudo-F(2) progeny. Progeny from all crosses, as well as RDW and SCI seedlings of original populations, were sprayed with picloram or clopyralid to distinguish between susceptible and resistant individuals. All F(1) progeny were susceptible to both herbicides, indicating that the resistance trait was of nuclear origin and recessive in nature. Segregation of the resistant phenotype among pseudo-F(2) and testcross progeny of F(1) genotypes demonstrated monofactorial inheritance (P >.25) for resistance to both herbicides. The conclusion that resistance is conferred by a single recessive allele is consistent with the observation that no other picloram-resistant yellow starthistle populations have been identified in the area since picloram selection pressure was abated.     

INHERITANCE OF ENVIRONMENTAL VARIATION IN BODY SIZE: SUPERPARASITISM OF SEEDS AFFECTS PROGENY AND GRANDPROGENY BODY SIZE VIA A NONGENETIC MATERNAL EFFECT

Maternal effects provide the most common mechanism by which environmental variation in one generation affects the phenotype of individuals in subsequent generations. In egg-laying animals, however, we typically observe that maternal effects can have large influences on early growth (egg size and early development), but these effects gradually disappear and become undetectable by the time progeny mature due to developmental plasticity in progeny. We describe a system in which an environmentally induced reduction in body size is inherited by progeny via a nongenetic maternal effect. The seed beetle, Callosobruchus maculatus, completes development inside a discrete resource package (a seed) selected by its mother. Due to superparasitism in response to low host availability, progeny frequently develop at high densities, resulting in intense larval competition and pupation at a smaller body size. Females reared at higher density (and thus emerging smaller) lay smaller eggs than females reared at lower density. Progeny from these smaller eggs mature at a smaller size than progeny reared from the larger eggs laid by females reared at lower density. Crosses between high and low density lines demonstrated that treatment differences in body size are maternally inherited, confirming that the inheritance of body size variation in part involves an environmentally based maternal effect.     

Environmental stress linked to consumption of maternally derived carotenoids in brown trout embryos (Salmo trutta)

The yellow, orange, or red colors of salmonid eggs are due to maternally derived carotenoids whose functions are not sufficiently understood yet. Here, we studied the significance of naturally acquired carotenoids as maternal environmental effects during embryo development in brown trout (Salmo trutta). We collected eggs from wild females, quantified their egg carotenoid content, fertilized them in vitro in full‐factorial breeding blocks to separate maternal from paternal effects, and raised 3,278 embryos singly at various stress conditions until hatching. We found significant sire effects that revealed additive genetic variance for embryo survival and hatching time. Dam effects were 5.4 times larger than these sire effects, indicating that maternal environmental effects play an important role in determining embryo stress tolerance. Of the eight pigment molecules that we targeted, only astaxanthin, zeaxanthin (that both affected egg redness), and lutein were detected above our confidence thresholds. No strong link could be observed between carotenoid content in unfertilized eggs and embryo mortality or hatching timing. However, the consumption of carotenoids during our stress treatment was negatively correlated to embryo survival among sib groups and explained about 14% of the maternal environmental variance. We conclude that maternally derived carotenoids play a role in the ability of embryos to cope with environmental stress, but that the initial susceptibility to the organic pollution was mainly determined by other factors.     

The inheritance of seed color in a resynthesizedBrassica napus line No. 2127-17 including a new epistatic locus

Yellow seed is an important trait inBrassica napus. To know the genet ic basis of yellow seed color inBrassica napus, we carried out genetic studies by using conventional genetics analyses. The conventional genetics was studied in generations (F1 F2 reciprocal F2, BC1, and F23) ofB. napus derived from crosses between a yellow-seeded (No. 2127-17) and nine different black-seeded parents. The results indicated that seed color was mainly controlled by the maternal genotype but influenced by the interact ion between the maternal and endosperm and/or embryonic genotypes. In the combinations which included black-seeded lines SW0780, 94560, 94545 and 1141B, the yellow seed is partially dominant over black with two or three dominance epistasis ratio. A dominant yellow-seeded gene Y which exhibits epistatic effects on the two independent dominant black-seeded genes B and C was ident ified in DH line No. 2127-17. These observations are in agreement with our previous reports. But in the rests, including the crosses with HS No.4, HS No. 3, XY No. 15, 94570 and ZS No. 10, the black seed color was dominant over yellow seed color. The inheritance of this trait in the segregating populations fits the model of a digenic dominance epistasis or triplicate dominance epistasis. A new locus was identified and designated as D: the dominant gene D for black seed color inhibits the dominant gene Y. Therefore, in combination with the Y, B and C, we found that the seed color was influenced by at least four genes. Identifying seed color genes and defining their inheritance should further our understanding of yellow seed color trait and facilitate development of new and better yellow-seeded cult ivars ofBrassics napus.