Isolation and characterization of polymorphic microsatellite DNA markers in the brown sole,Pleuronectes herzensteini

New microsatellite DNA markers from brown sole were developed and characterized. Fourteen primer sets were designed from 40 microsatellite regions. Eight of 14 loci exhibited variations comprising 8–31 alleles. Observed and expected heterozygosities ranged from 0.611 to 0.833 and from 0.647 to 0.968 among 36 individuals, respectively. Phz3, Phz8 and Phz12 significantly deviated from Hardy–Weinberg equilibrium, and there was a significant linkage disequilibrium between Phz2 and Phz12. Seven of eight loci conformed to the Mendelian manner of inheritance in a full‐sib family. Seven to four loci of three related species were cross‐amplified by primers for brown sole.     

Evaluation of designs for reference families for livestock linkage mapping experiments

Abstract

The development of dense linkage maps consisting of highly polymorphic loci for livestock species is technically feasible. However, linkage mapping experiments are expensive as they involve many animals and marker typings per animal. To minimize costs of developing linkage maps for livestock species, optimizing designs for mapping studies is necessary. This study provides a general framework for evaluating the efficiency of designs for reference families consisting of two‐ or three‐ generation full‐sib or half‐sib families selected from a segregating population. The influence of number of families, number of offspring per family, family structure (either half‐sib or full‐sib) and marker polymorphism is determined. Evaluation is done for two markers with a recombination rate of .20 and for a marker and a dominant single gene with a recombination rate of .20. Two evaluation criteria are used: expected maximum lod score for detection of linkage and accuracy of an estimated recombination rate defined as probability that the true recombination rate is in an interval around the estimated recombination rate. First, for several designs the contribution of reference families to expected maximum lod score and accuracy is given. Second, the required number of families in a design to obtain a certain value for the evaluation criteria is calculated when number of offspring per family, family structure and marker polymorphism are specified. The required numbers increase when designs are optimized not only for expected maximum lod score but also for accuracy. The required number of animals to map a dominant single gene is very large. Therefore, a set of reference families should be designed for strictly mapping marker loci. Examples illustrate how tabulated results can be generalized to determine the values for a wide range of designs containing two‐ or three‐generation full‐sib or half‐sib families.     

Effects of genetic sex and genomic background on epistasis in rainbow trout (Oncorhynchus mykiss)

Epistasis among quantitative trait loci (QTL) for survival (upper thermal tolerance, UTT) and morphological (fork length, FL and condition factor, K) traits was detected in purestrain and interstrain rainbow trout (Oncorhynchus mykiss) families. One sex-linked (OmyFGT19TUF) and three autosomal (Omy325UoG, Ssa14DU and Ssa20.19NUIG; linkage groups B, D and S, respectively) microsatellite loci linked to UTT QTL in this species were used. Within half sib families, significant effects of full sib family on epistasis involving Omy325UoG and OmyFGT19TUF were detected at a rate significantly higher than expected for UTT (p < 0.001*) and FL (p < 0.01*), using results significant at comparisonwise significance thresholds derived from permutational analysis. Measured across half sib families, the phenotype of female genotypic classes was more divergent from the family trait mean than that of males where epistasis involved the sex-linked locus OmyFGT19TUF (p = 0.0176*), and also for means over all families (p = 0.0355*). Female genotypic classes were also more divergent (p = 0.0011**) from the full sib trait mean where three-way interaction between OmyFGT19TUF, one of the autosomal loci and full sib family was significant, and marginally more divergent for trait means of genotypic classes across all full sib families (p = 0.0856). There was no evidence that these effects were more pronounced in hybrid F₁ families than purestrains.     

Separation of common environment and dominance effects with classic kinship correlation models

Abstract

Common family environmental effect (γ²) and dominance effect (d² ) are usually confounded; either or both may make the sib‐sib correlation larger than the parent‐child correlation. The classic three kinship correlations (parent‐parent, parent‐offspring, sib‐sib) can accommodate either dominance (Model D) or common family environment effects (Model C), but not both. The relationship between the various components of the three correlations of Models D and C are given. In order to include both dominance and common family environment effects, a fourth correlation, that between half‐sibs, is added to the system which enables us to separate the dominance effects from the common family environments effects. Half‐sibs may constitute a potentially new source material for study of quantitative inheritance. The principle of the constant heredity/environment ratio is discussed.     

Selection on structural allelic variation biases plasticity estimates

Wang and Althoff (2019) explored the capacity of Drosophila melanogaster to exhibit adaptive plasticity in a novel environment. In a full‐sib, half‐sib design, they scored the activity of the enzyme alcohol dehydrogenase (ADH) and plastic responses, measured as changes in ADH activity across ethanol concentrations in the range of 0–10% (natural variation) and 16% (the novel environment). ADH activity increased with alcohol concentration, and there was a positive association between larval viability and ADH activity in the novel environment. They also reported that families exhibiting greater plasticity had higher larval survival in the novel environment, concluding that ADH plasticity is adaptive. However, the four authors now concur that, since the study estimated plasticity from phenotypic differences across environments using full‐sib families, it is not possible to disentangle the contributions of allele frequency changes at the Adh locus from regulatory control at loci known to influence ADH activity. Selective changes in allele frequencies may thus conflate estimates of plasticity; any type of “plasticity” (adaptive, neutral, or maladaptive) could be inferred depending on allele frequencies. The problem of scoring sib‐groups after selection should be considered in any plasticity study that cannot use replicated genotypes. Researchers should monitor changes in allele frequencies as one mechanism to deal with this issue.     

Can microsatellite markers replace PIT tags in rohu (Labeo rohita Hamilton, 1822) selective breeding programmes?

This study was undertaken to assess the feasibility of microsatellite markers for resolving parentage in Labeo rohita (rohu) selective breeding programmes in lieu of conventional PIT tag marking. Ten microsatellite markers were used to assign offspring parentage. A total of 160 individuals were tested from eight full‐sibling families. Eight highly polymorphic loci with allele numbers ranging from 2 to 8 and polymorphism information content (PIC) values in the 0.47–0.82 range were utilized. With the use of a real data set from a breeding programme, all but 12 individuals out of 160 could be assigned exclusively to their correct parental pairs. The matching rate was 92.5%, which was lower than in a simulated study (98.44%, Excl‐2). Discrepancies between simulations and real data sets may be due to several factors such as genetic relatedness among candidate parents (half‐sib and full‐sib), presence of null alleles, and sampling variance of the parents. The results of this study suggest that a marker panel probably with a wider genome coverage may be necessary for near‐100% accuracy in assigning parentage in rohu selective breeding programmes.     

Quantitative trait loci affecting morphology traits in gilthead seabream (Sparus aurata L.)

We report a quantitative trait loci (QTL) mapping study on 18 morphometric characters in gilthead seabream based on a total of 74 informative microsatellite markers genotyped in 409 offspring coming from 10 paternal half‐sib families. Statistical analysis was carried out using a linear regression approach, and various suggestive and significant morphology QTL were detected in three (9, 21 and 25) of nine linkage groups examined. Fitting body weight as a covariate reduced the significance of some QTL but revealed three new QTL in other linkage groups (LG6 and LG10). Current results combined with those obtained from previous studies underline highly significant loci affecting overall growth and morphology in S. aurata.     

Population Genetics of Indigenous Quercus robur L. Populations and of Derived Half‐Sib Families has Implications for the Reproductive Management of the Species

Abstract: In the Netherlands indigenous Quercus robur L. populations are rare and have been maintained as patches in ancient woodland. For adequate conservation of these populations, information about genetic variation and population structure is necessary. In order to assess the genetic variation and structure of these populations, microsatellite polymorphisms were studied in two autochthonous populations. These two populations differed slightly for their gene diversity, which was as high as was observed for Q. robur populations in France and Germany. For reforestation purposes there is an interest in the genetic variation of a half‐sib family harvested from one tree. The gene diversity of the two studied half‐sib families ‐ obtained from a forest and an urban area ‐ was similar, but relatively low. This indicates that, for reforestation purposes, seeds should be harvested from many different trees in order to obtain a population with a genetic variation as high as was observed for an autochthonous population.     

Consequences of genetic incompatibility on fitness and mate choice: the male point of view

Hymenopterans under single‐locus complementary sex determination (sl‐CSD) face inbreeding costs due to this sex determination mode. Under sl‐CSD, homozygote eggs at the sl‐CSD locus usually develop into unviable or sterile diploid males. Production of such costly males increases when sib‐mating happens because related individuals share half of their genome. In the hymenopteran Venturia canescens (a solitary parasitoid wasp), diploid males are sterile, leading to fitness costs through genetic incompatibility between parents. Whereas the costs of producing diploid males and behavioural strategies that would reduce such costs have been studied in females, the potential fitness costs faced by males have not. Here, we aimed to investigate fitness costs that males endure after a single sib‐mating and tested whether they have the ability to avoid sib‐mating through kin recognition. Our results show that males have a reduced fitness (i.e. they produce fewer daughters) when mating with their sibs. We also show that males have the ability to distinguish between non‐sib and sib females (i.e. kin). They use chemical marks emitted by the females to discriminate kin from non‐kin. We discuss the evolution of kin recognition in males in the context of mate choice for genetic compatibility. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 279–286.     

Adaptive plasticity and epigenetic variation in response to warming in an Alpine plant

Environmentally induced phenotypic plasticity may be a critical component of response to changing environments. We examined local differentiation and adaptive phenotypic plasticity in response to elevated temperature in half‐sib lines collected across an elevation gradient for the alpine herb, Wahlenbergia ceracea. Using Amplified Fragment Length Polymorphism (AFLP), we found low but significant genetic differentiation between low‐ and high‐elevation seedlings, and seedlings originating from low elevations grew faster and showed stronger temperature responses (more plasticity) than those from medium and high elevations. Furthermore, plasticity was more often adaptive for plants of low‐elevation origin and maladaptive for plants of high elevation. With methylation sensitive‐AFLP (MS‐AFLP), we revealed an increase in epigenetic variation in response to temperature in low‐elevation seedlings. Although we did not find significant direct correlations between MS‐AFLP loci and phenotypes, our results demonstrate that adaptive plasticity in temperature response to warming varies over fine spatial scales and suggest the involvement of epigenetic mechanisms in this response.     

A genome‐wide association study to detect genetic variation for postpartum dysgalactia syndrome in five commercial pig breeding lines

Postpartum dysgalactia syndrome (PDS) in sows is an important disease after parturition with a relevant economic impact, affecting the health and welfare of both sows and piglets. The genetic background of this disease has been discussed and its heritability estimated, but further genetic analyses are lacking in detail. The aim of the current study was to detect loci affecting the susceptibility to PDS through a genome‐wide association approach. The study was designed as a family‐based association study with matched sampling of affected sows and healthy half‐ or full‐sib control sows on six farms. For the study, 597 sows (322 affected vs. 275 healthy control sows) were genotyped on 62 163 single nucleotide polymorphisms (SNPs) using the Illumina PorcineSNP60 BeadChip. After quality control, 585 sows (314 affected vs. 271 healthy control sows) and 49 740 SNPs remained for further analysis. Statistics were performed mainly with the r package genabel and included a principal component analysis. A statistically significant genome‐wide associated SNP was identified on porcine chromosome (SSC) 17. Further promising results with moderate significance were detected on SSC 13 and on an unplaced scaffold with an older annotation on SSC 15. The PRICKLE2 and NRP2 genes were identified as candidate genes near associated SNPs. Several quantitative trait loci (QTL) have been previously described in these genomic regions, including QTL for mammary gland condition, as teat number and non‐functional nipples QTL, as well as QTL for body temperature and gestation length.     

Quantitative trait loci for resistance to fish pasteurellosis in gilthead sea bream (Sparus aurata)

Fish pasteurellosis is a bacterial disease causing important losses in farmed fish, including gilthead sea bream, a teleost fish of great relevance in marine aquaculture. We report in this study a QTL analysis for resistance to fish pasteurellosis in this species. An experimental population of 500 offspring originating from eight sires and six dams in a single mass‐spawning event was subjected to a disease challenge with Photobacterium damselae subsp. piscicida (Phdp), the causative agent of fish pasteurellosis. A total of 151 microsatellite loci were genotyped in the experimental population, and half‐sib regression QTL analysis was carried out on two continuous traits, body length at time of death and survival, and for two binary traits, survival at day 7 and survival at day 15, when the highest peaks of mortality were observed. Two significant QTLs were detected for disease resistance. The first one was located on linkage group LG3 affecting late survival (survival at day 15). The second one, for overall survival, was located on LG21, which allowed us to highlight a potential marker (Id13) linked to disease resistance. A significant QTL was also found for body length at death on LG6 explaining 5–8% of the phenotypic variation.     

Improved genetic markers for monitoring recruitment dynamics in the endangered Mary River cod (Maccullochella mariensis)

The Mary River cod (Maccullochella mariensis) is a large predatory freshwater fish identified as a potential flagship for freshwater ecosystem conservation in Australia. The species is endemic to the Mary River catchment in eastern Australia, and is listed as Endangered. Previous conservation genetic assessment of Mary River cod was based on a small set of microsatellite loci developed for congeneric Maccullochella species. Here we develop a novel set of 15 microsatellite loci specific to M. mariensis, and demonstrate that these markers exhibit higher variability than those used previously. Mean number of alleles per locus was 4 and mean expected heterozygosity was 0.57. We genotyped 35 Mary River cod larvae belonging to a single cohort using the 15 novel loci and eight previously used loci, and found 10 full‐sib family groups along with clear genetic differentiation between individuals collected from the two sub‐catchments – Tinana Creek and Mary River. Microsatellites presented here will be useful for cost‐effective monitoring of genetic diversity and recruitment dynamics in this endangered fish species.     

Genome‐scan analysis for genetic mapping of quantitative trait loci underlying birth weight and onset of puberty in doe kids (Capra hircus)

The objective of this study was to locate quantitative trait loci (QTL) causing variation in birth weight and age of puberty of doe kids in a population of Rayini cashmere goats. Four hundred and thirty kids from five half‐sib families were genotyped for 116 microsatellite markers located on the caprine autosomes. The traits recorded were birth weight of the male and female kids, body weight at puberty, average daily gain from birth to age of puberty and age at puberty of the doe kids. QTL analysis was conducted using the least squares interval mapping approach. Linkage analysis indicated significant QTL for birth weight on Capra hircus chromosomes (CHI) 4, 5, 6, 18 and 21. Five QTL located on CHI 5, 14 and 29 were associated with age at puberty. Across‐family analysis revealed evidence for overlapping QTL affecting birth weight (78 cM), body weight at puberty (72 cM), average daily gain from birth to age of puberty (72 cM) and age at puberty (76 cM) on CHI 5 and overlapping QTL controlling body weight at puberty and age at puberty on CHI 14 at 18–19 cM. The proportion of the phenotypic variance explained by the detected QTL ranged between 7.9% and 14.4%. Confirming some of the previously reported results for birth weight and growth QTL in goats, this study identified more QTL for these traits and is the first report of QTL for onset of puberty in doe kids.     

QTL for body weight,morphometric traits and stress response in European sea bass Dicentrarchus labrax

Natural mating and mass spawning in the European sea bass (Dicentrarchus labrax L., Moronidae, Teleostei) complicate genetic studies and the implementation of selective breeding schemes. We utilized a two‐step experimental design for detecting QTL in mass‐spawning species: 2122 offspring from natural mating between 57 parents (22 males, 34 females and one missing) phenotyped for body weight, eight morphometric traits and cortisol levels, had been previously assigned to parents based on genotypes of 31 DNA microsatellite markers. Five large full‐sib families (five sires and two dams) were selected from the offspring (570 animals), which were genotyped with 67 additional markers. A new genetic map was compiled, specific to our population, but based on the previously published map. QTL mapping was performed with two methods: half‐sib regression analysis (paternal and maternal) and variance component analysis accounting for all family relationships. Two significant QTL were found for body weight on linkage group 4 and 6, six significant QTL for morphometric traits on linkage groups 1B, 4, 6, 7, 15 and 23 and three suggestive QTL for stress response on linkage groups 3, 14 and 23. The QTL explained between 8% and 38% of phenotypic variance. The results are the first step towards identifying genes involved in economically important traits like body weight and stress response in European sea bass.     

Selective genotyping for QTL detection using sib pair analysis in outbred populations with hierarchical structures

A simulation study illustrates the effects of the inclusion of half-sib pairs as well as the effects of selective genotyping on the power of detection and the parameter estimates in a sib pair analysis of data from an outbred population. The power of QTL detection obtained from samples of sib pairs selected according to their within family variance or according to the mean within family variance within half sib family was compared and contrasted with the power obtained when only full sib pair analysis was used. There was an increase in power (4–16%) and decrease in the bias of parameter estimates with the use of half-sib information. These improvements in power and parameter estimates depended on the number of the half sib pairs (half sib family size). Almost the same power as that obtained using all the available sib pairs could be achieved by selecting only 50–60% the animals. The most effective method was to select both full and half sib pairs on the basis of high within full sib family variance for the trait in question. The QTL position estimates were in general slightly biased towards the center of the chromosome and the QTL variance estimates were biased upwards, there being quite large differences in bias depending on the selection method.     

Choice of microsatellite markers for identifying homozygosity of mitotic gynogenetic diploids in Japanese flounder Paralichthys olivaceus

A set of 72 microsatellite markers distributed evenly among 24 linkage groups were selected from the published genetic linkage maps of Japanese flounder Paralichthys olivaceus. In two normal diploid full‐sib families, the test for Mendelian inheritance showed that genotypic segregation deviations were not significant at all analysed loci. To estimate microsatellite‐centromere map distances, four meiotic gynogenetic diploid lines were produced by the activation of eggs using UV irradiated sperm of red seabream Pagrus major and cold‐shock treatment to block the extrusion of the second polar body. Under the assumption of complete interference, 21 markers were located in the centromeric region, 39 in the telomeric region and the rest in the intermediate region of linkage groups. A total of 192 mitotic gynogenetic diploids from one spawn were identified by these markers. Genotype analysis showed that the number of homozygous individuals decreased as microsatellite‐centromere map distance increased on each linkage group.     

Insects and incest: Sib‐mating tolerance in natural populations of a parasitoid wasp

Sib‐mating avoidance is a pervasive behaviour that is expected to evolve in species subject to inbreeding depression. Although laboratory studies provide elegant demonstrations, small‐scaled bioassays minimize the costs of mate finding and choice, and thus may produce spurious findings. We therefore combined laboratory experiments with field observations to examine the existence of inbreeding avoidance using the parasitoid wasp Venturia canescens. In the laboratory, our approach consisted of mate‐choice experiments to assess kin discrimination in population cages with competitive interactions. A higher mating probability after sib rejections suggested that females could discriminate their sibs; however, in contrast to previous findings, sib‐mating avoidance was not observed. To compare our laboratory results to field data, we captured 241 individuals from two populations. Females laid eggs in the lab, and 226 daughters were obtained. All individuals were genotyped at 18 microsatellite loci, which allowed inference of the genotype of each female's mate and subsequently the relatedness within each mating pair. We found that the observed rate of sib‐mating did not differ from the probability that sibs encountered one another at random in the field, which is consistent with an absence of sib‐mating avoidance. In addition, we detected a weak but significant male‐biased dispersal, which could reduce encounters between sibs. We also found weak fitness costs associated with sib‐mating. As such, the sex‐biased dispersal that we found is probably sufficient to mitigate these costs. These results imply that kin discrimination has probably evolved for purposes other than mate choice, such as superparasitism avoidance.     

Quantitative trait loci associated with chemical composition of the chicken carcass

Major objectives of the poultry industry are to increase meat production and to reduce carcass fatness, mainly abdominal fat. Information on growth performance and carcass composition are important for the selection of leaner meat chickens. To enhance our understanding of the genetic architecture underlying the chemical composition of chicken carcasses, an F₂ population developed from a broiler × layer cross was used to map quantitative trait loci (QTL) affecting protein, fat, water and ash contents in chicken carcasses. Two genetic models were applied in the QTL analysis: the line‐cross and the half‐sib models, both using the regression interval mapping method. Six significant and five suggestive QTL were mapped in the line‐cross analysis, and four significant and six suggestive QTL were mapped in the half‐sib analysis. A total of eleven QTL were mapped for fat (ether extract), five for protein, four for ash and one for water contents in the carcass using both analyses. No study to date has reported QTL for carcass chemical composition in chickens. Some QTL mapped here for carcass fat content match, as expected, QTL regions previously associated with abdominal fat in the same or in different populations, and novel QTL for protein, ash and water contents in the carcass are presented here. The results described here also reinforce the need for fine mapping and to perform multi‐trait analyses to better understand the genetic architecture of these traits.     

A genome scan for quantitative trait loci influencing carcass,post‐natal growth and reproductive traits in commercial Angus cattle

To gain insight into the number of loci of large effect that underlie variation in cattle, a quantitative trait locus (QTL) scan for 14 economically important traits was performed in two commercial Angus populations using 390 microsatellites, 11 single nucleotide polymorphisms (SNPs) and one duplication loci. The first population comprised 1769 registered Angus bulls born between 1955 and 2003, with Expected Progeny Differences computed by the American Angus Association. The second comprised 38 half‐sib families containing 1622 steers with six post‐natal growth and carcass phenotypes. Linkage analysis was performed by half‐sib least squares regression with gridqtl or Bayesian Markov chain Monte Carlo analysis of complex pedigrees with loki . Of the 673 detected QTL, only 118 have previously been reported, reflecting both the conservative approach to QTL reporting in the literature, and the more liberal approach taken in this study. From 33 to 71% of the genetic variance and 35 to 56% of the phenotypic variance in each trait was explained by the detected QTL. To analyse the effects of 11 SNPs and one duplication locus within candidate genes on each trait, a single marker analysis was performed by fitting an additive allele substitution model in both mapping populations. There were 53 associations detected between the SNP/duplication loci and traits with ?log₁₀P_nominal≥ 4.0, where each association explained 0.92% to 4.4% of the genetic variance and 0.01% to 1.86% of the phenotypic variance. Of these associations, only six SNP/duplication loci were located within 8 cM of a QTL peak for the trait, with two being located at the QTL peak: SST_DG156121:c.362A>G for ribeye muscle area and TG_X05380:c.422C>T for calving ease. Strong associations between several SNP/duplication loci and trait variation were obtained in the absence of any detected linked QTL. However, we reject the causality of several commercialized DNA tests, including an association between TG_X05380:c.422C>T and marbling in Angus cattle.