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In sexually dimorphic and polygynous mammals, sexual selection often favours large males with well-developed weaponry, as these secondary sexual characters confer advantages in intrasexual competition and are often preferred by females. Little is known, however, about the effects of sexually selected paternal traits on offspring phenotype in wild mammals, especially when considering that shared phenotypic traits and selection can also differ greatly between genders. Here, we conducted molecular parentage analyses in a long-term study population of mountain goats (Oreamnos americanus), an ungulate exhibiting high sexual dimorphism in mass, to first assess the determinants of yearly reproductive success (YRS) in males. We then examined the effects of paternal characteristics on offspring mass at 1 year of age. Paternity was highly skewed, with 9 per cent of 57 males siring 51 per cent of 96 offspring assigned over 12 years. Male YRS increased with age until apparent reproductive senescence at 9 years, but mass was a stronger determinant of siring success than age, horn length or social rank. Mass of sons increased with paternal mass, but the mass of daughters was negatively related to that of their father, a finding consistent with recent theory on intralocus sexual conflict. Because early differences in mass persisted to early adulthood, sex-specific effects of paternal mass can have important fitness consequences, as adult mass is positively linked with reproduction in both sexes. Divergent father-offspring phenotypic correlations may partly explain the maintenance of sexual dimorphism in mountain goats and the large variance observed for this homologous trait within each gender in polygynous mammals.

We studied phenotypic and genetic adaptation of the visual system of three-spined sticklebacks, Gasterosteus aculeatus , from North Uist, Scotland. We quantified differences in opsin gene expression of the four cone opsin genes among wild-caught fish from three lakes with clear and from three with tea-stained water and their offspring that were raised in clear water. In addition, visual sensitivity of wild-caught fish was modelled from opsin expression levels. Wild-caught fish from tea-stained waters had a lower SWS1 proportional expression than fish from clear waters, a difference that tended to be maintained in lab-bred fish. Compared to lab-bred fish, wild-caught fish had a higher SWS1 but lower SWS2 proportional expression independent of water clarity. For RH2 and LWS there were significant interactions between generation and water clarity. Reproductively mature fish had a higher LWS but lower proportional expression of RH2 than non-reproductive fish. Sex did not have a significant effect on expression. There was a significant positive association and, depending on chromophore ratio, a distinct match between the centre wavelengths, used as a proxy for spectral distribution, of ambient habitat light and spectral sensitivity indicating that the visual system of sticklebacks is tuned to their local light environment, suggesting adaptation.

The aim of pumpkin breeding programs is to develop cultivars that meet the production, commercial quality, and nutritional value, considering several attributes. Therefore, the objective of this study was to select pumpkin genotypes with high fruit quality for future use in genetic breeding programs. Two production cycles were carried out. The evaluations included the determination of genetic parameters (the additive genetic variance, environmental variance between residual variances and individual phenotypic variance, accuracy of progeny selection, restricted heritability, coefficient of individual additive genetic variation, coefficient of genotypic variation between progenies, coefficient of residual variation, coefficient of relative variation, variance of the prediction error of the genotypic values of the progeny), the prediction of genetic gains, and the selection of genotypes with fruits of better physical and chemical quality attributes. The carotenoid and β-carotene contents of the pulp were distinguished by high values of additive genetic variance, residual variance and individual variance. Additionally, genetic gains were achieved for the main carotenoid compounds, as xanthophyll (68%), lycopene (58%) and β-carotene (49%). In the second production cycle, using the technique of Mulamba and Mock, a new ranking method was used to select the best genotypes. These genetic parameters, especially restricted heritability, indicate the potential for advancing new selection stages to develop pumpkin cultivars with superior qualities, including fruit length (0.976), skin thickness (0.951) and orange pigments, particularly β-carotene (0.894). Additionally, firmer fruits with high ascorbic acid content and a pulp hue angle representing an orange color were ranked among the best genotypes.

Background The purpose of a selection index is that its use to select animals for breeding maximizes the profit of a breed in future generations. The profit of a breed is in general a quantity that predicts the satisfaction of future owners with their breed, and the satisfaction of the consumers with the products that are produced by the breed. Many traits, such as conformation traits and product quality traits have intermediate optima. Traditional selection index theory applies only to directional selection and cannot achieve any further improvement once the trait means have reached their optima. A well-founded theory is needed that extends the established selection index theory to cover directional as well as stabilizing selection as limiting cases, and that can be applied to maximize the profit of a breed in both situations. Results The optimum selection index shifts the trait means towards the optima and, in the case of stabilizing selection, decreases the phenotypic variance, which causes the phenotypes to be closer to the optimum. The optimum index depends not only on the breeding values, but also on the squared breeding values, the allele contents of major quantitative trait loci (QTL), the QTL heterozygosities, the inbreeding coefficient of the animal, and the kinship of the animal with the population. Conclusion The optimum selection index drives the alleles of major QTL to fixation when the trait mean approaches the optimum because decreasing the phenotypic variance shifts the trait values closer to the optimum, which increases the profit of the breed. The index weight on the kinship coefficient balances the increased genetic gain that can be achieved in future generations by outcrossing, and the increased genetic gain that can be achieved under stabilizing selection by reducing the phenotypic variance. In a model with dominance variance, it can also account for the effect of inbreeding depression. The combining ability between potential mating partners, which predicts the total merit of their offspring, could become an important parameter for mate allocation that could be used to further shift the phenotypes towards their optimum values.

A major goal in marine ecology is to understand patterns of larval dispersal and population connectivity. Dispersal plasticity allows for adaptive variation in dispersal phenotypes in response to variation in environmental conditions and may help to explain intraspecific variation in dispersal distances. However, this phenomenon has only been hypothesized for marine fishes. Here, we test the hypothesis that parents produce larvae with different dispersal‐related traits in response to variation in environmental quality using the orange anemonefish, Amphiprion percula. By manipulating food rations in a crossover experimental design, we show that parents produce larger offspring on low‐food rations than on high‐food rations. However, there was no effect of parental diet on larval critical swimming speed. We also show that parents produce larvae with smaller otolith cores while on low‐food rations, which, in combination with parentage analyses, may provide a way to test the dispersal plasticity hypothesis in the field. This study shows that parents can produce different larval phenotypes in response to variation in environmental conditions, demonstrating plasticity in a dispersal‐related larval trait that may help to explain observed variation in A. percula larval dispersal distances. Incorporating dispersal plasticity into our understanding of marine dispersal patterns may enhance our understanding of marine metapopulation ecology, fisheries management, and conservation. In this study, we investigate whether dispersal‐related larval traits are plastic in response to parental habitat quality in a marine fish: the clown anemonefish, Amphiprion percula. Results from this study show that parents can produce different larval dispersal‐related phenotypes in response to variation in food rations, which may explain some of the observed variation in A. percula larval dispersal distances.

Reproductive traits that mediate differential fitness associated with mate acquisition and fertilisation success are often strongly linked to the overall condition. We investigated the effects of resource quality and parental provisioning in the phenotypic expression of sexual and non‐sexual traits in a rainforest dung beetle, Onthophagus c.f. babirussa (Eschscholtz, 1822) from Singapore. F1 individuals were reared from wild‐caught beetles and paired up to produce offspring (F2), and F2 larvae from the same F1 parents were reared on two dung substrates (herbivore and omnivore) in a full‐sib design. Sexual traits displayed greater phenotypic variation in response to dung resource quality, with the precopulatory trait (horn length) responding more than the postcopulatory trait (testes weight). Notably, genotype‐by‐environment interactions between parental lines (genotype) and dung type (environment) affected male body size and horn length only, suggesting sex‐specific variance in plasticity associated with sexually selected precopulatory traits. Dung type had significant effects on all measured traits. Offspring that were provisioned higher quality resource (omnivore dung) had larger absolute and relative trait values. Parental lines only significantly affected female body size but none of the male traits, suggesting an important role of environment and resource partitioning in determining precopulatory success of male offspring. Parental provisioning of larval resource varied with resource quality and brood sequence. Parents provisioned more dung when herbivore dung was presented than when they were given omnivore dung and provisioned more dung for their earlier broods when using herbivore dung but not omnivore dung. This suggests a trade‐off between early offspring fitness and resource quality. We tested directly for genotype‐by‐environment (G × E) interactions in the expression of several morphological traits relevant to dung beetle fitness and documented that offspring with similar phenotypes may result from completely different parental resource allocation strategies. We discuss the importance of studying parental investment on trait variation and its implications on dung beetle ecology. We investigated the effects of resource quality and parental provisioning in the phenotypic expression of sexual and non‐sexual traits in a rainforest dung beetle, Onthophagus babirussa (Eschscholtz, 1822) from Singapore. ‘Higher quality’ dung resulted in offspring exhibiting greater phenotypic fitness, and mother beetles compensated dung quality with the dung amount when using ‘lower quality’ dung. Genotype‐by‐environment interactions between parental lines (genotype) and dung type (environment) affected male body size and horn length only, suggesting sex‐specific variance in plasticity associated with sexually selected precopulatory traits.

Background First flower node (FFN) is an important trait for evaluating fruit earliness in pepper ( Capsicum annuum L.). The trait is controlled by quantitative trait loci (QTL); however, studies have been limited on QTL mapping and genes contributing to the trait. Results In this study, we developed a high density genetic map using specific-locus amplified fragment sequencing (SLAF-seq), a high-throughput strategy for de novo single nucleotide polymorphism discovery, based on 146 recombinant inbred lines (RILs) derived from an intraspecific cross between PM702 and FS871. The map contained 9328 SLAF markers on 12 linkage groups (LGs), and spanned a total genetic distance of 2009.69 centimorgan (cM) with an average distance of 0.22 cM. The sequencing depth for the map was 72.39-fold in the male parent, 57.04-fold in the female parent, and 15.65-fold in offspring. Using the genetic map, two major QTLs, named Ffn2.1 and Ffn2.2 , identified on LG02 were strongly associated with FFN, with a phenotypic variance explanation of 28.62 and 19.56%, respectively. On the basis of the current annotation of C. annuum cv. Criollo de Morelos (CM334), 59 candidate genes were found within the Ffn2.1 and Ffn2.2 region, but only 3 of 59 genes were differentially expressed according to the RNA-seq results. Eventually we identified one gene associated with the FFN based on the function through GO, KEGG, and Swiss-prot analysis. Conclusions Our research showed that the construction of high-density genetic map using SLAF-seq is a valuable tool for fine QTL mapping. The map we constructed is by far the most saturated complete genetic map of pepper, and using it we conducted fine QTL mapping for the important trait, FFN. QTLs and candidate genes obtained in this study lay a good foundation for the further research on FFN-related genes and other genetic applications in pepper.

When provisioning offspring, mothers balance the benefits of producing a few large, fitter offspring with the costs of decreased fecundity. The optimal balance between offspring size and fecundity depends on the environment. Theory predicts that larger offspring have advantages in adverse conditions, but in favorable conditions size is less important. Thus, if environmental quality varies, selection should favor mothers that adaptively allocate resources in response to local conditions to maximize maternal fitness. In the bryozoanBugula neritina, we show that the intensity of intraspecific competition dramatically changes the offspring size/performance relationship in the field. In benign or extremely competitive environments, offspring size is less important, but at intermediate levels of competition, colonies from larger larvae have higher performance than colonies from smaller larvae. We predicted mothers should produce larger offspring when intermediate competition is likely and tested these expectations in the field by manipulating the density of brood colonies. Our findings matched expectations: mothers produced larger larvae at high densities and smaller larvae at low densities. In addition, mothers from high‐density environments produced larvae that have higher dispersal potential, which may enable offspring to escape crowded environments. It appears mothers can adaptively adjust offspring size to maximize maternal fitness, altering the offspring phenotype across multiple life‐history stages.

Background Inbreeding, resulting from mating between relatives, leads to inbreeding depression, which can be traced back to hidden ancestral inbreeding loads. These loads exhibit variability and act as additive genetic effects that are only expressed in the inbred offspring. The objective of this study was to quantify the variance of the inbreeding loads and its correlation with additive genetic effects for seven traits in the Rubia Gallega population: birth weight, weaning weight, cold carcass weight, carcass conformation, carcass fatness, calving interval, and age at first parity. A single-step GBLUP Bayesian analysis was used by a Gibbs sampler. Additionally, the equivalence between GBLUP and SNP-BLUP was used for locating the genomic regions associated with the highest variances. Results The pedigree included 522,885 animals, of which 4984 were genotyped with the Axiom_BovMDv3 chip. A total of 246,393 individuals were inbred, with an average inbreeding coefficient of 0.044 ± 0.059, attributed to 4712 ancestors through 9.8 million partial inbreeding contributions. The estimated proportion of phenotypic variance explained by inbreeding loads for an inbreeding coefficient of 0.10 ranged from 0.012 (Birth weight) to 0.101 (Weaning weight), consistently below the heritabilities of the traits. Genetic correlations between inbreeding load and additive effects were always negative. The average prediction accuracy for inbreeding-load effects in young selection candidates was low and exceeded 0.7 only in older animals. The genomic distribution of additive and inbreeding load variances was uneven, with some regions overlapping and others being specific to inbreeding load. Conclusions This study demonstrates that the inbreeding load variance is low compared to the additive genetic variance across a range of growth, carcass, and reproductive traits. The results were also consistent with a previous study that theoretically demonstrated a negative correlation between additive effects and inbreeding load. The potential to purge deleterious alleles appears limited, largely due to the low prediction accuracy observed in young individuals. Nevertheless, the higher accuracy of inbreeding-load estimates in ancestral animals could still be exploited to guide the unavoidable inbreeding in small populations through informed mating strategies, thereby minimizing undesirable inbreeding-depression effects. The heterogeneous genomic distribution of the inbreeding load suggests new opportunities for identifying genes in which deleterious or semideleterious alleles may be located.

Background In egg-laying animals, mothers can influence the developmental environment and thus the phenotype of their offspring by secreting various substances into the egg yolk. In birds, recent studies have demonstrated that different yolk substances can interactively affect offspring phenotype, but the implications of such effects for offspring fitness and phenotype in natural populations have remained unclear. We measured natural variation in the content of 31 yolk components known to shape offspring phenotypes including steroid hormones, antioxidants and fatty acids in eggs of free-living great tits ( Parus major ) during two breeding seasons. We tested for relationships between yolk component groupings and offspring fitness and phenotypes. Results Variation in hatchling and fledgling numbers was primarily explained by yolk fatty acids (including saturated, mono- and polyunsaturated fatty acids) - but not by androgen hormones and carotenoids, components previously considered to be major determinants of offspring phenotype. Fatty acids were also better predictors of variation in nestling oxidative status and size than androgens and carotenoids. Conclusions Our results suggest that fatty acids are important yolk substances that contribute to shaping offspring fitness and phenotype in free-living populations. Since polyunsaturated fatty acids cannot be produced de novo by the mother, but have to be obtained from the diet, these findings highlight potential mechanisms (e.g., weather, habitat quality, foraging ability) through which environmental variation may shape maternal effects and consequences for offspring. Our study represents an important first step towards unraveling interactive effects of multiple yolk substances on offspring fitness and phenotypes in free-living populations. It provides the basis for future experiments that will establish the pathways by which yolk components, singly and/or interactively, mediate maternal effects in natural populations.