Heritability of racing performance in the Australian Thoroughbred racing population

Performance data for 164 046 Thoroughbreds entered in a race or official barrier trial in Australia were provided by Racing Information Services Australia. Analyses estimating the heritability for a range of racing performance traits using a single‐trait animal model were performed using asreml ‐r . Log of cumulative earnings (LCE; 0.19 ± 0.01), log of earnings per race start (0.23 ± 0.02) and best race distance (0.61 ± 0.03) were all significantly heritable. Fixed effects for sex were significant (P < 0.001) for all performance traits aside from LCE (P = 0.382). With the exception of annual earnings, trainer was also significant for all performance traits. As the application of modern genetic selection methodologies continues to gain popularity in the racing industry, contemporary heritability estimates from the current population of Thoroughbreds will play a vital role in identifying which traits are better suited to selection and in the development of more accurate genomic evaluations for racing performance.     

The quantitative genetics of sexually selected traits,preferred traits and preference: a review and analysis of the data

The maintenance of variation in sexually selected traits is a puzzle that has received increasing attention in the past several decades. Traits that are related to fitness, such as life‐history or sexually selected traits, are expected to have low additive genetic variance (and hence, heritability) due to the rapid fixation of advantageous alleles. However, previous analyses have suggested that the heritabilities of sexually selected traits are on average higher than nonsexually selected traits. We show that the heritabilities of sexually selected traits are not significantly different from those of nonsexually selected traits overall or when separated into the three trait categories: behavioural, morphological and physiological. In contrast with previous findings, the heritability of preference is quite low (h² = 0.25 ± 0.06) and is in the same range as life‐history traits. We distinguish preferred traits as a category of sexually selected traits and find that the heritability of the former is not significantly different than sexually selected traits overall (0.48 ± 0.04 vs. 0.46 ± 0.03). We test the hypothesis that the heritability of sexually selected traits is negatively correlated with the strength of sexual selection. As predicted, there is a significant negative correlation between the heritabilities of sexually selected traits and the strength of selection. This suggests that heritabilities do indeed decrease as sexual selection increases but sexual selection is not strong enough to cause heritabilities of sexually selected traits to deviate from the same type of nonsexually selected traits.     

Association analysis between feed efficiency studies and expression of hypothalamic neuropeptide genes in laying ducks

Residual feed intake (RFI) is now considered a more reasonable metric to evaluate animal feed efficiency. In this study, the correlation between RFI and other feed efficiency traits was investigated and gene expression within the hypothalamus was determined in low RFI (LRFI) and high RFI (HRFI) ducks. Further, several hypothalamic neuropeptide genes were measured using quantitative real‐time PCR. The mean feed intake value was 160 g/day, whereas the egg mass laid (EML) and body weight were approximately 62.4 g/day and 1.46 kg respectively. Estimates for heritability of RFI, feed conversion ratio (FCR) and feed intake were 0.26, 0.18 and 0.23 respectively. RFI is phenotypically positively correlated with feed intake and FCR (P < 0.01). The expression of neuropeptide Y (NPY) and neuropeptide Y receptor Y5 (NPY5R) mRNA was higher in HRFI ducks compared with LRFI ducks (P < 0.05), whereas that of proopiomelanocortin (POMC), melanocortin 4 receptor (MC4R) and cholecystokinin (CCK) was lower (P < 0.05). The mRNA expression of gonadotropin‐releasing hormone 1 (luteinizing‐releasing hormone) (GNRH1) and prolactin receptor (PRLR) was unchanged between LRFI and HRFI ducks. The results indicate that selection for LRFI could reduce feed intake without significant changes in EML, whereas selection on FCR will increase EML.     

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.     

Identification of quantitative trait loci affecting gastrointestinal parasite resistance in an experimental Angus population

DNA markers associated with quantitative trait loci (QTL) affecting host tolerance to gastrointestinal (GI) parasite infection are ideal targets for marker‐assisted selection. However, few studies in cattle have attempted to identify this type of QTL due to the difficulty of generating accurate phenotypic data from a resource population with adequate statistical power for detection. For this effort, we amassed fecal egg count (FEC) measures from annual natural field challenges with GI nematodes that spanned 12 different contemporary groups of Angus calves (1992–2000) derived from a closed breeding population. FEC and blood pepsinogen measures were taken weekly over a 26‐week period post‐weaning, and the FEC data were Box‐Cox transformed to normalize the distribution of phenotypes. These 305 test animals and more than 100 founding animals from the extended pedigree were genotyped across 190 microsatellites markers. The genome‐wide analyses identified a suggestive genome‐wide QTL on bovine chromosome (Chr) 8 (P < 0.002) and nominal QTL on Chr 4, 12 and 17 (P < 0.05). These findings were unique for cattle, and some corresponded to previously identified QTL locations for parasite‐related traits in sheep to provide genome locations for further fine mapping of parasite resistance/susceptibility in Angus cattle.     

Genome‐wide prediction of age at puberty and reproductive longevity in sows

Traditional selection for sow reproductive longevity is ineffective due to low heritability and late expression of the trait. Incorporation of DNA markers into selection programs is potentially a more practical approach for improving sow lifetime productivity. Using a resource population of crossbred gilts, we explored pleiotropic sources of variation that influence age at puberty and reproductive longevity. Of the traits recorded before breeding, only age at puberty significantly affected the probability that females would produce a first parity litter. The genetic variance explained by 1‐Mb windows of the sow genome, compared across traits, uncovered regions that influence both age at puberty and lifetime number of parities. Allelic variants of SNPs located on SSC5 (27–28 Mb), SSC8 (36–37 Mb) and SSC12 (1.2–2 Mb) exhibited additive effects and were associated with both early expression of puberty and a greater than average number of lifetime parities. Combined analysis of these SNPs showed that an increase in the number of favorable alleles had positive impact on reproductive longevity, increasing number of parities by up to 1.36. The region located on SSC5 harbors non‐synonymous alleles in the arginine vasopressin receptor 1A (AVPR1A) gene, a G‐protein‐coupled receptor associated with social and reproductive behaviors in voles and humans and a candidate for the observed effects. This region is characterized by high levels of linkage disequilibrium in different lines and could be exploited in marker‐assisted selection programs across populations to increase sow reproductive longevity.     

Egg color variation,but not egg rejection behavior,changes in a cuckoo host breeding in the absence of brood parasitism

Interactions between parasitic cuckoos and their songbird hosts form a classical reciprocal “arms race,” and are an excellent model for understanding the process of coevolution. Changes in host egg coloration via the evolution of interclutch variation in egg color or intraclutch consistency in egg color are hypothesized counter adaptations that facilitate egg recognition and thus limit brood parasitism. Whether these antiparasitism strategies are maintained when the selective pressure of parasitism is relaxed remains debated. However, introduced species provide unique opportunities for testing the direction and extent of natural selection on phenotypic trait maintenance and variation. Here, we investigated egg rejection behavior and egg color polymorphism in the red‐billed leiothrix (Leiothrix lutea), a common cuckoo (Cuculus canorus) host, in a population introduced to Hawaii 100 years ago (breeding without cuckoos) and a native population in China (breeding with cuckoos). We found that egg rejection ability was equally strong in both the native and the introduced populations, but levels of interclutch variation and intraclutch consistency in egg color in the native population were higher than in the introduced population. This suggests that egg rejection behavior in hosts can be maintained in the absence of brood parasitism and that egg appearance is maintained by natural selection as a counter adaptation to brood parasitism. This study provides rare evidence that host antiparasitism strategies can change under parasite‐relaxed conditions and reduced selection pressure.     

Embryogenesis of Heliconius erato (Lepidoptera,Nymphalidae): A contribution to the anatomical development of an evo‐devo model organism

This study reports on the embryogenesis of Heliconius erato phyllis between blastoderm formation and the prehatching larval stage. Syncytial blastoderm formation occurred approximately 2 h after egg laying (AEL) and at about 4 h, the cellular blastoderm was formed. The germ band arose from the entire length of the blastoderm, and rapidly became compacted occupying approximately two‐thirds of the egg length. At about 7 h AEL, protocephalon and protocorm differentiation occurred. Continued proliferation of the germ band was followed by penetration into the yolk mass, forming a C‐shaped embryo at about 10 h. Approximately 12 h AEL, the gnathal, thoracic and abdominal segments became visible. The primordium of the mouthparts and thoracic legs formed as paired evaginations, while the prolegs formed as paired lobes. At about 30 h, the embryo reversed dorsoventrally. Approximately 32 h AEL, the protocephalon and gnathal segments fused, shifting the relative position of the rudimentary appendages in this region. At about 52 h, the embryo was U‐shaped in lateral view and at approximately 56 h, the bristles began evagination from the larval cuticle. Larvae hatched at about 72 h. We found that H. erato phyllis followed an embryonic pattern consistent with long‐germ embryogenesis. Thus, we believe that H. erato phyllis should be classified as a long‐germ lepidopteran. The study of H. erato phyllis embryogenesis provided a structural glimpse into the morphogenetic events that occur in the Heliconius egg period. This study could help future molecular approaches to understanding the evolution of Heliconius development.     

Genetic and environmental effects on the morphological asymmetry in the scale‐eating cichlid fish,Perissodus microlepis

The scale‐eating cichlid fish, Perissodus microlepis, from Lake Tanganyika are a well‐known example of an asymmetry dimorphism because the mouth/head is either left‐bending or right‐bending. However, how strongly its pronounced morphological laterality is affected by genetic and environmental factors remains unclear. Using quantitative assessments of mouth asymmetry, we investigated its origin by estimating narrow‐sense heritability (h²) using midparent–offspring regression. The heritability estimates [field estimate: h² = 0.22 ± 0.06, P = 0.013; laboratory estimate: h² = 0.18 ± 0.05, P = 0.004] suggest that although variation in laterality has some additive genetic component, it is strongly environmentally influenced. Family‐level association analyses of a putative microsatellite marker that was claimed to be linked to gene(s) for laterality revealed no association of this locus with laterality. Moreover, the observed phenotype frequencies in offspring from parents of different phenotype combinations were not consistent with a previously suggested single‐locus two‐allele model, but they neither were able to reject with confidence a random asymmetry model. These results reconcile the disputed mechanisms for this textbook case of mouth asymmetry where both genetic and environmental factors contribute to this remarkable case of morphological asymmetry.     

Genotypic characterization of Brochothrix spp. isolated from meat,poultry and fish

Aim: To study genotypic diversity of isolates of Brochothrix thermosphacta recovered from meat, poultry and fish. Methods and Results: A total of 27 bacteria isolated from 19 samples of meat, poultry and fish were identified phenotypically and genotypically using PCR amplification of 16S‐23S rDNA intergenic transcribed spacer (ITS‐PCR), repetitive sequence‐based PCR (rep‐PCR) and 16S rDNA sequencing. Using ITS‐PCR, all bacteria showed the same DNA profile as the reference strains of Br. thermosphacta, allowing typing of the isolates at species level. Using 16S rDNA sequencing, all isolates were identified, at genus and species level, as Br. thermosphacta. Identification as Br. campestris was observed with a lower, but very close, level of similarity. Rep‐PCR was more discriminatory than ITS‐PCR and allowed differentiation of four subgroups among the isolates. Conclusion: Minor genotypic differences among Br. thermosphacta strains from meat, poultry and fish were observed. Significance and Impact of the Study: A rudimentary exploration of genotypic differences of Br. thermosphacta from meat, poultry and fish resulted in preliminary confirmation of the suitability of ITS‐PCR for typing Br. thermosphacta and confirmed the value of rep‐PCR fingerprinting to discriminate between Br. thermosphacta strains.     

Validated quantitative trait loci for eggshell quality in experimental and commercial laying hens

Compromised eggshell quality causes considerable economic losses for the egg industry. Breeding for improved eggshell quality has been very challenging. Eggshell quality is a trait that would greatly benefit from marker‐assisted selection, which would allow the selection of sires for their direct contribution to the trait and would also allow implementation of measurements integrating a number of shell parameters that are difficult to measure. In this study, we selected the most promising autosomal quantitative trait loci (QTL) affecting eggshell quality on chromosomes 2, 3, 6 and 14 from earlier experiments and we extended the F₂ population to include 1599 F₂ females. The study was repeated on two commercial populations: Lohmann Tierzucht Rhode Island Red line (n = 692 females) and a Hy‐Line White Plymouth Rock line (n = 290 progeny tested males). We analyzed the selected autosomal QTL regions on the three populations with SNP markers at 4–13 SNPs/Mb density. QTL for eggshell quality were replicated on all studied regions in the F₂ population. New QTL were detected for eggshell color on chromosomes 3 and 6. Marker associations with eggshell quality traits were validated in the tested commercial lines on chromosomes 2, 3 and 6, thus paving the way for marker‐assisted selection for improved eggshell quality.     

Goat casein genotypes are associated with milk production traits in the Sarda breed

The aim of the current work was to analyze, in the Sarda breed goat, genetic polymorphism within the casein genes and to assess their influence on milk traits. Genetic variants at the CSN1S1, CSN2, CSN1S2 and CSN3 gene loci were investigated using PCR‐based methods, cloning and sequencing. Strong alleles prevailed at the CSN1S1 gene locus and defective alleles also were revealed. Null alleles were evidenced at each calcium‐sensitive gene locus. At the CSN3 gene locus, we observed a prevalence of the CSN3 A and B alleles; the occurrence of rare alleles such as CSN3 B'', C, C', D, E and M; and the CSN3 S allele (GenBank KF644565 ) described here for the first time in Capra hircus. Statistical analysis showed that all genes, except CSN3, significantly influenced milk traits. The CSN1S1 BB and AB genotypes were associated with the highest percentages of protein (4.41 and 4.40 respectively) and fat (5.26 and 5.34 respectively) (P < 0.001). A relevant finding was that CSN2 and CSN1S2 genotypes affected milk protein content and yield. The polymorphism of the CSN2 gene affected milk protein percentage with the highest values recorded in the CSN2 AA goats (4.35, at P < 0.001). The CSN1S2 AC goats provided the highest fat (51.02 g/day) and protein (41.42 g/day) (P < 0.01) production. This information can be incorporated into selection schemes for the Sarda breed goat.     

Identifying chromosomal selection‐sweep regions in facial eczema selection‐line animals using an ovine 50K‐SNP array

Facial eczema (FE) is a hepato‐mycotoxicosis found mainly in New Zealand sheep and cattle. When genetics was found to be a factor in FE susceptibility, resistant and susceptible selection lines of Romney sheep were established to enable further investigations of this disease trait. Using the Illumina OvineSNP50 BeadChip, we conducted a selection‐sweep experiment on these FE genetic lines. Two analytical methods were used to detect selection signals, namely the Peddrift test (Dodds & McEwan, 1997) and fixation index F_ST (Weir & Hill, 2002). Of 50 975 single nucleotide polymorphism (SNP) markers tested, there were three that showed highly significant allele frequency differences between the resistant and susceptible animals (Peddrift nominal P < 0.000001). These SNP loci are located on chromosomes OAR1, OAR11 and OAR12 that coincide precisely with the three highest genomic F_ST peaks. In addition, there are nine less significant Peddrift SNPs (nominal P ≤ 0.000009) on OAR6 (n = 2), OAR9 (n = 2), OAR12, OAR19 (n = 2), OAR24 and OAR26. In smoothed F_ST (five‐SNP moving average) plots, the five most prominent peaks are on OAR1, OAR6, OAR7, OAR13 and OAR19. Although these smoothed F_ST peaks do not coincide with the three most significant Peddrift SNP loci, two (on OAR6 and OAR19) overlap with the set of less significant Peddrift SNPs above. Of these 12 Peddrift SNPs and five smoothed F_ST regions, none is close to the FE candidate genes catalase and ABCG2; however, two on OAR1 and one on OAR13 fall within suggestive quantitative trait locus regions identified in a previous genome screen experiment. The present studies indicated that there are at least eight genomic regions that underwent a selection sweep in the FE lines.     

Heritable variation in circulating glucocorticoids and endocrine flexibility in a free‐living songbird

Phenotypic flexibility is a central way that organisms cope with challenging and changing environments. As endocrine signals mediate many phenotypic traits, heritable variation in hormone levels, or their context‐dependent flexibility, could present an important target for selection. Several studies have estimated the heritability of circulating glucocorticoid levels under acute stress conditions, but little is known about the potential for either baseline hormone levels or rapid endocrine flexibility to evolve. Here, we assessed the potential for selection to operate on the elevation (circulating hormone levels) and flexibility of glucocorticoid reaction norms to acute restraint stress. Multivariate animal models revealed low but significant heritability in baseline (h² = 0.13–0.14) and stress‐induced glucocorticoids (h² = 0.18), and moderate heritability in glucocorticoid flexibility in response to acute stress (h² = 0.38) in free‐living juvenile tree swallows (Tachycineta bicolor; n = 408). Baseline glucocorticoids were not genetically correlated with either stress‐induced glucocorticoids or glucocorticoid flexibility. These findings indicate that baseline glucocorticoids and the acute stress response are distinct traits that can be independently shaped by selection. Microevolutionary changes that influence the expression or flexibility of these endocrine mediators of phenotype may be an important way that populations adapt to changing environments and novel threats.     

Heritability of gonad size varies across season in a wild songbird

Many organisms advance their seasonal reproduction in response to global warming. In birds, which regress their gonads to a nonfunctional state each winter, these shifts are ultimately constrained by the time required for gonadal development in spring. Gonadal development is photoperiodically controlled and shows limited phenotypic plasticity in relation to environmental factors, such as temperature. Heritable variation in the time required for full gonadal maturation to be completed, based on both onset and speed of development and resulting in seasonally different gonad sizes among individuals, is thus a crucial prerequisite for an adaptive advancement of seasonal reproduction in response to changing temperatures. We measured seasonal gonadal development in climate‐controlled aviaries for 144 great tit (Parus major) pairs, which consisted of siblings obtained as whole broods from the wild. We show that the extent of ovarian follicle development (follicle size) in early spring is highly heritable (h² = 0.73) in females, but found no heritability of the extent of testis development in males. However, heritability in females decreased as spring advanced, caused by an increase in environmental variance and a decrease in additive genetic variation. This low heritability of the variation in a physiological mechanism underlying reproductive timing at the time of selection may hamper genetic adaptation to climate change, a key insight as this great tit population is currently under directional selection for advanced egg‐laying.     

A genome‐wide scan for selection signatures in Nellore cattle

Brazilian Nellore cattle (Bos indicus) have been selected for growth traits for over more than four decades. In recent years, reproductive and meat quality traits have become more important because of increasing consumption, exports and consumer demand. The identification of genome regions altered by artificial selection can potentially permit a better understanding of the biology of specific phenotypes that are useful for the development of tools designed to increase selection efficiency. Therefore, the aims of this study were to detect evidence of recent selection signatures in Nellore cattle using extended haplotype homozygosity methodology and BovineHD marker genotypes (>777 000 single nucleotide polymorphisms) as well as to identify corresponding genes underlying these signals. Thirty‐one significant regions (P < 0.0001) of possible recent selection signatures were detected, and 19 of these overlapped quantitative trait loci related to reproductive traits, growth, feed efficiency, meat quality, fatty acid profiles and immunity. In addition, 545 genes were identified in regions harboring selection signatures. Within this group, 58 genes were associated with growth, muscle and adipose tissue metabolism, reproductive traits or the immune system. Using relative extended haplotype homozygosity to analyze high‐density single nucleotide polymorphism marker data allowed for the identification of regions potentially under artificial selection pressure in the Nellore genome, which might be used to better understand autozygosity and the effects of selection on the Nellore genome.     

Extraordinary MHC class II B diversity in a non‐passerine,wild bird: the Eurasian Coot Fulica atra (Aves: Rallidae)

The major histocompatibility complex (MHC) hosts the most polymorphic genes ever described in vertebrates. The MHC triggers the adaptive branch of the immune response, and its extraordinary variability is considered an evolutionary consequence of pathogen pressure. The last few years have witnessed the characterization of the MHC multigene family in a large diversity of bird species, unraveling important differences in its polymorphism, complexity, and evolution. Here, we characterize the first MHC class II B sequences isolated from a Rallidae species, the Eurasian Coot Fulica atra. A next‐generation sequencing approach revealed up to 265 alleles that translated into 251 different amino acid sequences (β chain, exon 2) in 902 individuals. Bayesian inference identified up to 19 codons within the presumptive peptide‐binding region showing pervasive evidence of positive, diversifying selection. Our analyses also detected a significant excess of high‐frequency segregating sites (average Tajima's D = 2.36, P < 0.05), indicative of balancing selection. We found one to six different alleles per individual, consistent with the occurrence of at least three MHC class II B gene duplicates. However, the genotypes comprised of three alleles were by far the most abundant in the population investigated (49.4%), followed by those with two (29.6%) and four (17.5%) alleles. We suggest that these proportions are in agreement with the segregation of MHC haplotypes differing in gene copy number. The most widespread segregating haplotypes, according to our findings, would contain one single gene or two genes. The MHC class II of the Eurasian Coot is a valuable system to investigate the evolutionary implications of gene copy variation and extensive variability, the greatest ever found, to the best of our knowledge, in a wild population of a non‐passerine bird.     

Interaction between lithification and resource availability in the microbialites of Río Mesquites,Cuatro Ciénegas,México

Lithified microbial structures (microbialites) have been present on Earth for billions of years. Lithification may impose unique constraints on microbes. For instance, when CaCO₃ forms, phosphate may be captured via coprecipitation and/or adsorption and potentially rendered unavailable for biological uptake. Therefore, the growth of microbes associated with CaCO₃ may be phosphorus‐limited. In this study, we compared the effects of resource addition on biogeochemical functions of microbial communities associated with microbialites and photoautotrophic microbial communities not associated with CaCO₃ deposition in Río Mesquites, Cuatro Ciénegas, México. We also manipulated rates of CaCO₃ deposition in microbialites to determine whether lithification reduces the bioavailability of phosphorus (P). We found that P additions significantly increased rates of gross primary production (F_2,13 = 103.9, P < 0.001), net primary production (F_2,13 = 129.6, P < 0.0001) and ecosystem respiration (F_2,13 = 6.44, P < 0.05) in the microbialites, while P addition had no effect on photoautotrophic production in the non‐CaCO₃‐associated microbial communities. Growth of the non‐CaCO₃‐associated phototrophs was only marginally stimulated when nitrogen and P were added simultaneously (F_1,36 = 3.98, P = 0.053). In the microbialites, resource additions led to some shifts in the abundance of Proteobacteria, Bacteroidetes and Cyanobacteria but mostly had little effect on bacterial community composition. Ca²⁺ uptake rates increased significantly with organic carbon additions (F_1,13 = 8.02, P < 0.05). Lowering of CaCO₃ deposition by decreasing calcium concentrations in the water led to increased microbial biomass accumulation rates in terms of both organic carbon (F_4,48 = 5.23, P < 0.01) and P (F_6,48 = 13.91, P < 0.001). These results provide strong evidence in support of a role of lithification in controlling P limitation of microbialite communities.     

Time‐specific and pleiotropic quantitative trait loci coordinately modulate stem growth in Populus

In perennial woody plants, the coordinated increase of stem height and diameter during juvenile growth improves competitiveness (i.e. access to light); however, the factors underlying variation in stem growth remain unknown in trees. Here, we used linkage‐linkage disequilibrium (linkage‐LD) mapping to decipher the genetic architecture underlying three growth traits during juvenile stem growth. We used two Populus populations: a linkage mapping population comprising a full‐sib family of 1,200 progeny and an association mapping panel comprising 435 unrelated individuals from nearly the entire natural range of Populus tomentosa. We mapped 311 quantitative trait loci (QTL) for three growth traits at 12 timepoints to 42 regions in 17 linkage groups. Of these, 28 regions encompassing 233 QTL were annotated as 27 segmental homology regions (SHRs). Using SNPs identified by whole‐genome re‐sequencing of the 435‐member association mapping panel, we identified significant SNPs (P ≤ 9.4 × 10^?7) within 27 SHRs that affect stem growth at nine timepoints with diverse additive and dominance patterns, and these SNPs exhibited complex allelic epistasis over the juvenile growth period. Nineteen genes linked to potential causative alleles that have time‐specific or pleiotropic effects, and mostly overlapped with significant signatures of selection within SHRs between climatic regions represented by the association mapping panel. Five genes with potential time‐specific effects showed species‐specific temporal expression profiles during the juvenile stages of stem growth in five representative Populus species. Our observations revealed the importance of considering temporal genetic basis of complex traits, which will facilitate the molecular design of tree ideotypes.     

Microsatellite DNA markers for parental assignment in hybrid striped bass (Morone saxatilis × Morone chrysops)

Development of nine polymorphic microsatellites from a genomic library of hybrid striped bass (female Morone chrysops × male Morone saxatilus) DNA is described. Breeding of hybrid striped bass for aquaculture is based largely on breeding wild fish. Molecular markers such as microsatellites will be useful tools for developing broodstock, estimating heritability for production traits, and selective breeding via marker‐assisted selection. The nine polymorphic microsatellites include six dinucleotide and three complex repeat motifs. The number of alleles detected among a sample of 10 individuals of each species was relatively low. All polymerase chain reaction primer pairs also amplified products in the sea bass Dicentrarchus labrax.