The effectiveness of using co-dominant polymorphic allelic series for (1) checking pedigrees and (2) distinguishing full-sib pair members

Improvement of sperm traits related to the high level of extra-pair fertilization in tree sparrow population under long-term environmental heavy metal pollution

Environmental stress can affect sperm traits whose changes have been reported to be associated with extra-pair fertilization (EPF) level in natural animal populations. However, little is known regarding how exposure to environmental heavy metals influences sperm traits and EPF level in free-living bird populations. In a previous study, we found that a tree sparrow (Passer montanus) population that has been exposed to heavy metal pollution over 60 years (Baiyin, BY) exhibits increased sperm quality compared with a population from a relatively unpolluted area (Liujiaxia, LJX). The high sperm quality could be related to extra-pair mating rates. Therefore, the present study investigated EPF level (the ratio of extra-pair offspring) in tree sparrow populations from BY and LJX, and analyzed the relationship between sperm traits (morphology, velocity and quantity) and EPF success. EPF success of tree sparrows was significantly correlated with their sperm velocity (p = 0.048) and total sperm length (p = 0.045), indicating that these sperm traits were important for EPF success. Tree sparrows from the BY population produced longer sperm with lower head/flagellum ratio and faster swimming sperm and showed a significantly higher EPF level than conspecifics from LJX. Thus, adaptive variation of sperm characteristics was related to the high EPF level in tree sparrows under long-term environmental heavy metal pollution. The findings are of scientific significance for exploring the evolution of mating tactics in wild bird populations under environmental stress.

Evolutionary history of a Scottish harbour seal population

Efforts to conserve marine mammals are often constrained by uncertainty over their population history. Here, we examine the evolutionary history of a harbour seal (Phoca vitulina) population in the Moray Firth, northeast Scotland using genetic tools and microsatellite markers to explore population change. Previous fine-scale analysis of UK harbour seal populations revealed three clusters in the UK, with a northeastern cluster that included our Moray Firth study population. Our analysis revealed that the Moray Firth cluster is an independent genetic group, with similar levels of genetic diversity across each of the localities sampled. These samples were used to assess historic abundance and demographic events in the Moray Firth population. Estimates of current genetic diversity and effective population size were low, but the results indicated that this population has remained at broadly similar levels following the population bottleneck that occurred after post-glacial recolonization of the area.

Discovery of Genome-Wide Microsatellite Markers in Scombridae: A Pilot Study on Albacore Tuna

Recent developments in sequencing technologies and bioinformatics analysis provide a greater amount of DNA sequencing reads at a low cost. Microsatellites are the markers of choice for a variety of population genetic studies, and high quality markers can be discovered in non-model organisms, such as tuna, with these recent developments. Here, we use a high-throughput method to isolate microsatellite markers in albacore tuna, Thunnus alalunga, based on coupling multiplex enrichment and next-generation sequencing on 454 GS-FLX Titanium pyrosequencing. The crucial minimum number of polymorphic markers to infer evolutionary and ecological processes for this species has been described for the first time. We provide 1670 microsatellite design primer pairs, and technical and molecular genetics selection resulting in 43 polymorphic microsatellite markers. On this panel, we characterized 34 random and selectively neutral markers («neutral») and 9 «non-neutral» markers. The variability of «neutral» markers was screened with 136 individuals of albacore tuna from southwest Indian Ocean (42), northwest Indian Ocean (31), South Africa (31), and southeast Atlantic Ocean (32). Power analysis demonstrated that the panel of genetic markers can be applied in diversity and population genetics studies. Global genetic diversity for albacore was high with a mean number of alleles at 16.94; observed heterozygosity 66% and expected heterozygosity 77%. The number of individuals was insufficient to provide accurate results on differentiation. Of the 9 «non-neutral» markers, 3 were linked to a sequence of known function. The one is located to a sequence having an immunity function (ThuAla-Tcell-01) and the other to a sequence having energy allocation function (ThuAla-Hki-01). These two markers were genotyped on the 136 individuals and presented different diversity levels. ThuAla-Tcell-01 has a high number of alleles (20), heterozygosity (87–90%), and assignment index. ThuAla-Hki-01 has a lower number of alleles (9), low heterozygosity (24–27%), low assignment index and significant inbreeding. Finally, the 34 «neutral» and 3 «non-neutral» microsatellites markers were tested on four economically important Scombridae species—Thunnus albacares, Thunnus thynnus, Thunnus obesus, and Acanthocybium solandri.

Molecular marker development from transcript sequences and germplasm evaluation for cultivated peanut (Arachis hypogaea L.)

Molecular markers are important tools for genotyping in genetic studies and molecular breeding. The SSR and SNP are two commonly used marker systems developed from genomic or transcript sequences. The objectives of this study were to: (1) assemble and annotate the publicly available ESTs in Arachis and the in-house short reads, (2) develop and validate SSR and SNP markers, and (3) investigate the genetic diversity and population structure of the peanut breeding lines and the U.S. peanut mini core collection using developed SSR markers. An NCBI EST dataset with 252,951 sequences and an in-house 454 RNAseq dataset with 288,701 sequences were assembled separately after trimming. Transcript sequence comparison and phylogenetic analysis suggested that peanut is closer to cowpea and scarlet bean than to soybean, common bean and Medicago. From these two datasets, 6455 novel SSRs and 11,902 SNPs were identified. Of the discovered SSRs, 380 representing various SSR types were selected for PCR validation. The amplification rate was 89.2 %. Twenty-two (6.5 %) SSRs were polymorphic between at least one pair of four genotypes. Sanger sequencing of PCR products targeting 110 SNPs revealed 13 true SNPs between tetraploid genotypes and 193 homoeologous SNPs within genotypes. Eight out of the 22 polymorphic SSR markers were selected to evaluate the genetic diversity of Florida peanut breeding lines and the U.S. peanut mini core collection. This marker set demonstrated high discrimination power by displaying an average polymorphism information content value of 0.783, a combined probability of identity of 10(-11), and a combined power of exclusion of 0.99991. The structure analysis revealed four sub-populations among the peanut accessions and lines evaluated. The results of this study enriched the peanut genomic resources, provided over 6000 novel SSR markers and the credentials for true peanut SNP marker development, and demonstrated the power of newly developed SSR markers in genotyping peanut germplasm and breeding materials.

Parentage Reconstruction in Eucalyptus nitens Using SNPs and Microsatellite Markers: A Comparative Analysis of Marker Data Power and Robustness

Pedigree reconstruction using molecular markers enables efficient management of inbreeding in open-pollinated breeding strategies, replacing expensive and time-consuming controlled pollination. This is particularly useful in preferentially outcrossed, insect pollinated Eucalypts known to suffer considerable inbreeding depression from related matings. A single nucleotide polymorphism (SNP) marker panel consisting of 106 markers was selected for pedigree reconstruction from the recently developed high-density Eucalyptus Infinium SNP chip (EuCHIP60K). The performance of this SNP panel for pedigree reconstruction in open-pollinated progenies of two Eucalyptus nitens seed orchards was compared with that of two microsatellite panels with 13 and 16 markers respectively. The SNP marker panel out-performed one of the microsatellite panels in the resolution power to reconstruct pedigrees and out-performed both panels with respect to data quality. Parentage of all but one offspring in each clonal seed orchard was correctly matched to the expected seed parent using the SNP marker panel, whereas parentage assignment to less than a third of the expected seed parents were supported using the 13-microsatellite panel. The 16-microsatellite panel supported all but one of the recorded seed parents, one better than the SNP panel, although there was still a considerable level of missing and inconsistent data. SNP marker data was considerably superior to microsatellite data in accuracy, reproducibility and robustness. Although microsatellites and SNPs data provide equivalent resolution for pedigree reconstruction, microsatellite analysis requires more time and experience to deal with the uncertainties of allele calling and faces challenges for data transferability across labs and over time. While microsatellite analysis will continue to be useful for some breeding tasks due to the high information content, existing infrastructure and low operating costs, the multi-species SNP resource available with the EuCHIP60k, opens a whole new array of opportunities for high-throughput, genome-wide or targeted genotyping in species of Eucalyptus.

Parentage verification in field progeny testing program of Mehsana buffalo

The present study was undertaken to construct a multiplex microsatellite panel for parentage testing in Mehsana buffalo (Bubalus bubalis). The study was based on a total of 212 Mehsana buffalos (100 dams, 100 daughters, and 12 sires). Genomic DNA was extracted from blood and semen samples. A panel of 10 microsatellite markers (CSSM61, ILSTS29, ILSTS17, ILSTS28, CSSM57, CSSM22, ILSTS61, CSSM8, ETH152, and ILSTS11) was amplified in a single multiplex reaction and analyzed by capillary electrophoresis on an automated DNA sequencer. The expected heterozygosity ranged from 0.642 to 0.833 (mean 0.762). The total exclusion probability using 10 microsatellite loci with 1 known parent was 0.993. Seven out of 10 microsatellite loci revealed relatively high polymorphic information content (>0.7). Eighty-one daughters out of 100 daughters qualified by compatibility according to Mendelism. The results suggest that multiplex microsatellite panel is a fast, robust, reliable, and economic tool to verify the parentage as well as to assign the putative sire to daughters under progeny testing with very high accuracy and hence can be used in routine parentage testing.

Age before beauty? Relationships between fertilization success and age-dependent ornaments in barn swallows

When males become more ornamented and reproduce more successfully as they grow older, phenotypic correlations between ornament exaggeration and reproductive success can be confounded with age effects in cross-sectional studies, and thus say relatively little about sexual selection on these traits. This is exemplified here in a correlative study of male fertilization success in a large colony of American barn swallows (Hirundo rustica erythrogaster). Previous studies of this species have indicated that two sexually dimorphic traits, tail length and ventral plumage coloration, are positively correlated with male fertilization success, and a mechanism of sexual selection by female choice has been invoked. However, these studies did not control for potential age-related variation in trait expression. Here, we show that male fertilization success was positively correlated with male tail length but not with plumage coloration. We also show that 1-year-old males had shorter tails and lower fertilization success than older males. This age effect accounted for much of the covariance between tail length and fertilization success. Still, there was a positive relationship between tail length and fertilization success among older males. But as this group consisted of males from different age classes, an age effect may be hidden in this relationship as well. Our data also revealed a longitudinal increase in both tail length and fertilization success for individual males. We argue that age-dependent ornament expression and reproductive performance in males complicate inferences about female preferences and sexual selection.

The value of DNA paternity identification in beef cattle: Examples from Nevada's free-range ranches1

The feasibility and economic value of DNA paternity identification were investigated and illustrated using Nevada beef cattle operations. A panel of 15 microsatellites was genotyped in 2,196 animals from 8 ranches with a total of 31,571 genotypes. Probabilities of exclusion for each marker within ranch and across ranches were computed. Joint probabilities of exclusion for the 15 microsatellites were also determined, resulting in values over 0.99 for any individual ranch and across ranches. Dropping 1 or 2 microsatellites with the lowest probabilities of exclusion resulted in joint probabilities greater than 0.99 and with marginal reduction compared with the probabilities with 15 microsatellites. Formulas for benefit-cost analysis for a DNA paternity identification program in beef cattle were derived. Genotyping 15 microsatellites with 20 calves per sire resulted in benefits of $1.71 and $2.44 per dollar invested at bull culling rates of 0.20 and 0.30, respectively. The breakpoints for the program to be profitable occurred when the ratio of the price of 1 kg of calf liveweight over the cost of genotyping 1 microsatellite was greater than 1.1 for a bull culling rate of 0.30. Benefit-cost analysis was also derived under incomplete DNA paternity identification using a lower number of DNA markers than necessary to achieve joint probabilities of exclusion of 0.99. Approximately a 20% increase in the benefit-cost ratio was achieved using 10 vs. 12 microsatellites with incomplete paternity identification. The greater the number of bulls in the operation, the lower the benefit-cost ratio of the paternity testing program. Low probabilities of exclusion and a high number of bulls in the beef operation reduced the benefit-cost ratio dramatically. The DNA paternity identification programs are feasible and may be profitable for free-range beef cattle operations.

Association of CA repeat polymorphism at intron 1 of insulin-like growth factor (IGF-I) gene with circulating IGF-I concentration, growth, and fatness in swine

Evidence is accumulating that intronic polymorphic cytosine-adenosine (CA) repeats may play a role in gene expression. In this work, we investigated whether a polymorphic CA short tandem repeat (STR) located at the first intron of the pig insulin-like growth factor I (IGF-I) gene influences plasma IGF-I concentration in pigs as well as phenotypic variation in growth and fatness traits. We measured plasma IGF-I levels at one to four time points from 35 to 215 days of age in 340 performance-tested Landrace and Duroc pigs previously genotyped for the IGF-I STR. Data were analyzed within breed with a linear mixed model with the number of CA repeats as a covariate. At least five alleles were segregating in each breed, differing in one to seven repeats. The results showed that in each breed, circulating IGF-I at 160 days of age increased with the length of the shortest allele, accounting for an average trend of 4.38 +/- 1.28 ng/ml of IGF-I per additional repeat (P = 0.001). Longer repeats were associated with early growth in Landrace boars (1.92 +/- 0.92 kg per CA at 160 days; P = 0.038) and with back fat thickness (-0.57 +/- 0.20 mm per CA; P = 0.005) and lean content (7.52 +/- 3.00 g/kg per CA at 105 kg; P = 0.013) adjusted for carcass weight in Duroc barrows, as expected from the effect of circulating IGF-I on these traits. The consistency of the results across populations supports the hypothesis that the length of the CA repeats at intron 1 of the IGF-I gene is associated with circulating IGF-I levels, and that this effect is not neutral with respect to growth and fatness.

Polyandry in coal tits Parus ater: fitness consequences of putting eggs into multiple genetic baskets

Females of many species mate with multiple males within a single reproductive cycle. One hypothesis to explain polyandry postulates that females benefit from increasing within-brood genetic diversity. Two mechanisms may render sire genetic diversity beneficial for females, genetic bet-hedging vs. non-bet-hedging. We analysed whether females of the socially monogamous coal tit (Parus ater) benefit via either of these mechanisms when engaging in extra-pair (i.e. polyandrous) mating. To obtain a measure of within-brood genetic diversity as a function of paternal genetic contributions, we calculated a sire diversity index based on the established Shannon-Wiener Index. In 246 broods from two consecutive years, sire genetic diversity had no effect on either the mean or the variance in brood fitness measured as offspring recruitment within 4 years after birth. The hypothesis that benefits of increasing sire diversity contribute to selection for female extra-pair mating behaviour in P. ater was therefore not supported.

Brood Sex Ratios are Related to Male Size but not to Attractiveness in Common Yellowthroats (Geothlypis Trichas)

When the reproductive value of sons differs from that of daughters, selection will favor broods biased toward the sex that can provide greater fitness benefits. In species where female choice is based on male ornamentation, females mated to highly ornamented males may experience a reproductive advantage by skewing the brood sex ratio toward sons. In the Common Yellowthroat (Geothlypis trichas), males with larger black facial masks are more likely to gain a social mate and sire extrapair young and, as a result, have increased seasonal reproductive success. Females mated to larger-masked males could benefit if they produced more sons. Given that larger- masked males are preferred as extrapair sires, females may also benefit by producing more extrapair sons. We tested these hypotheses during a five-year study of Common Yellowthroats in Wisconsin. Contrary to our predictions, females did not produce more sons when mated to males with larger masks, and extrapair young were not more likely to be male. However, sons were more likely to be sired by males with longer tarsi, which suggests that females may respond to male body size rather than to male ornament size.

El Cociente de Sexos en las Nidadas Está Relacionado con el Tamaño de los Machos pero no con el Atractivo en Geothlypis trichas

Immune response of nestling warblers varies with extra-pair paternity and temperature

Extra-pair mating is widespread in birds, but its adaptive function remains unclear. It is often suggested that females obtain superior genes for their offspring as a consequence of extra-pair mating, but the evidence is limited. In this study, we examined the hypothesis that extra-pair mating provides females with offspring that have superior immune responses. We found that the T-cell-mediated immune response of extra-pair young was stronger than that of within-pair young in common yellowthroats (Geothlypis trichas). This paternity effect occurred when we compared all nestlings in the population, as well as in comparisons of both paternal and maternal half-siblings. Paternal half-siblings had a stronger immune response when they were produced with extra-pair females than with the male's social mate, which suggests that the greater immune response of extra-pair young was caused by nonadditive (compatible) genetic effects. However, these patterns were only significant in the colder of 2 years. Immune response was related positively to air temperature and nestlings had a stronger immune response in the warmer year. We suggest that such environmental variation could obscure the genetic benefits of extra-pair mating.

Pollen‐mediated gene dispersal within continuous and fragmented populations of a forest understorey species,Trillium cuneatum

Pollen movement plays a critical role in the distribution of genetic variation within and among plant populations. Direct measures of pollen movement in the large, continuous populations that characterize many herbaceous plant species are often technically difficult and biologically unreliable. Here, we studied contemporary pollen movement in four large populations of Trillium cuneatum. Three populations, located in the Georgia Piedmont, are exposed to strong anthropogenic disturbances, while the fourth population, located in the Southern Appalachian Mountains, is relatively undisturbed. Using the recently developed TwoGener analysis, we extracted estimates of the effective number of pollen donors (N(ep)), effective mating neighbourhood size (A(ep)) and the average distance of pollen movement (delta) for each population. We extended the TwoGener method by developing inference on the paternal gametic contribution to the embryo in situations where offspring genotypes are inferred from seeds and elaiosomes of species with bisporic megagametogenesis. Our estimates indicate that maternal plants do not sample pollen randomly from a global pool; rather, pollen movement in all four populations is highly restricted. Although the effective number of pollen donors per maternal plant is low (1.22-1.66) and pollen movement is highly localized in all populations, N(ep) in the disturbed Piedmont populations is higher and there is more pollen movement than in the mountains. The distance pollen moves is greater in disturbed sites and fragmented populations, possibly due to edge effects in Trillium habitats.

Repeatability of extra-pair mating in tree swallows

Models of sexual selection assume that female mating preferences are heritable and, thus, repeatable for individual females across multiple mating episodes. Previous studies of the repeatability of female preference have examined individuals in captivity and focused presumably on social mate choice. However, extra-pair mating is widespread and can also influence sexual selection. We examined the repeatability of extra-pair mating in a wild population of tree swallows (Tachycineta bicolor) by experimentally inducing females to lay two clutches in rapid succession within the same season. We found that the proportion of extra-pair young and the number of extra-pair sires were highly repeatable for individual females. However, the repeatability of specific extra-pair sires was low. We suggest that this unusual pattern of mating may be due to females maximizing the heterozygosity of their offspring.

Sex-specific selective pressures on body mass in the greater white-toothed shrew, Crocidura russula

The direction, intensity and shape of viability-, sexual- and fecundity selection on body mass were investigated in a natural population of the greater white-toothed shrew (Crocidura russula), combining parentage assignment through molecular techniques and mark-recapture data over several generations. A highly significant stabilizing viability selection was found in both sexes, presumably stemming from the constraints imposed by their insectivorous habits and high metabolic costs. Sexual selection, directional in both sexes, was twice as large in males than in females. Our results suggest that body mass matters in this context by facilitating the acquisition and defense of a breeding territory. No fecundity selection could be detected. The direction of sexual size dimorphism (SSD) was in agreement with the observed pattern of selective pressures: males were heavier than females, because of stronger sexual selection. SSD intensity, however, was low compared with other mammals, because of the low level of polygyny, the active role of females in territory defense and the intensity of stabilizing viability selection.

Use of microsatellites for parentage and kinship analyses in animals

Microsatellite markers are quickly becoming the molecular marker of choice for studies of parentage and kinship in animals. In this chapter, we review methods and give protocols for screening potential microsatellite markers, as well as protocols for genotyping individuals with useful markers once they have been identified. In addition, we explain how microsatellites can be used to assess parentage and kinship, give basic analytical methods, and briefly review more sophisticated approaches that can be used to circumvent many of the problems that arise in any real empirical study.