The value of a new crop species is usually judged by the overall performance of multiple traits. Therefore, in most quantitative trait locus (QTL) mapping experiments, researchers tend to collect phenotypic records for multiple traits. Some traits may vary continuously and others may vary in a discrete fashion. Although mapping QTLs jointly for multiple traits is more efficient than mapping QTLs separately for individual traits, the latter is still commonly practised in QTL mapping. This is primarily due to the lack of efficient statistical methods and computer software packages to implement the methods. Mapping multiple QTLs simultaneously in a single multivariate model has not been available, especially when categorical traits are involved. In the present study, we developed a Bayesian method to map QTLs of the entire genome for multiple traits with continuous, discrete or both types of phenotypic distribution. Instead of using the reversible jump Markov chain Monte Carlo (MCMC) for model selection, we adopt a parameter shrinkage approach to estimate the genetic effects of all marker intervals. We demonstrate the method by analysing a set of simulated data with both continuous and discrete traits. We also apply the method to mapping QTLs responsible for multiple disease resistances to the blast fungus of rice. A computer program written in SAS/IML that implements the method is freely available, on request, to academic researchers.

A triosephosphate isomerase (TPI) mutant, Tpi1a-m6Neu, with approximately 57% residual enzyme activity in blood compared with wild-type was detected among offspring of triethylenemelamine-treated male mice. Homozygous mutants with about 13% residual enzyme activity were recovered in progeny of inter se matings of heterozygotes. The loss of TPI activity was evident both in blood and in other tissue extracts. Values for haematocrit, haemoglobin, number of red blood cells (RBC), mean corpuscular volume of RBC, mean corpuscular haemoglobin concentration and spleen weight show significant differences between wild-type animals and homozygous mutants. Sequence analysis revealed a substitution (c.A149G) in the Tpi1 gene. This mutation results in an Asp to Gly substitution at codon 49 in exon 2 at a highly conserved position located in the functional domain of the TPI protein which is responsible for the correct dimerization of the subunits. As a potential animal model, Tpi1a-m6Neu represents the only available TPI-deficient homozygous viable mouse mutation.

Dense marker genotypes allow the construction of the realized relationship matrix between individuals, with elements the realized proportion of the genome that is identical by descent (IBD) between pairs of individuals. In this paper, we demonstrate that by replacing the average relationship matrix derived from pedigree with the realized relationship matrix in best linear unbiased prediction (BLUP) of breeding values, the accuracy of the breeding values can be substantially increased, especially for individuals with no phenotype of their own. We further demonstrate that this method of predicting breeding values is exactly equivalent to the genomic selection methodology where the effects of quantitative trait loci (QTLs) contributing to variation in the trait are assumed to be normally distributed. The accuracy of breeding values predicted using the realized relationship matrix in the BLUP equations can be deterministically predicted for known family relationships, for example half sibs. The deterministic method uses the effective number of independently segregating loci controlling the phenotype that depends on the type of family relationship and the length of the genome. The accuracy of predicted breeding values depends on this number of effective loci, the family relationship and the number of phenotypic records. The deterministic prediction demonstrates that the accuracy of breeding values can approach unity if enough relatives are genotyped and phenotyped. For example, when 1000 full sibs per family were genotyped and phenotyped, and the heritability of the trait was 0·5, the reliability of predicted genomic breeding values (GEBVs) for individuals in the same full sib family without phenotypes was 0·82. These results were verified by simulation. A deterministic prediction was also derived for random mating populations, where the effective population size is the key parameter determining the effective number of independently segregating loci. If the effective population size is large, a very large number of individuals must be genotyped and phenotyped in order to accurately predict breeding values for unphenotyped individuals from the same population. If the heritability of the trait is 0·3, and Ne=1000, approximately 5750 individuals with genotypes and phenotypes are required in order to predict GEBVs of un-phenotyped individuals in the same population with an accuracy of 0·7.

In this study, we attempted a molecular characterization of the 5S rDNA in two closely related species of carcharhiniform sharks, Rhizoprionodon lalandii and Rhizoprionodon porosus, as well as a further comparative analysis of available data on lampreys, several fish groups and other vertebrates. Our data show that Rhizoprionodon sharks carry two 5S rDNA classes in their genomes: a short repeat class (termed class I) composed of ~185 bp repeats, and a large repeat class (termed class II) arrayed in ~465 bp units. These classes were differentiated by several base substitutions in the 5S coding region and by completely distinct non-transcribed spacers (NTS). In class II, both species showed a similar composition for both the gene coding region and the NTS region. In contrast, class I varied extensively both within and between the two shark species. A comparative analysis of 5S rRNA gene sequences of elasmobranchs and other vertebrates showed that class I is closely related to the bony fishes, whereas the class II gene formed a separate cartilaginous clade. The presence of two variant classes of 5S rDNA in sharks likely maintains the tendency for dual ribosomal classes observed in other fish species. The present data regarding the 5S rDNA organization provide insights into the dynamics and evolution of this multigene family in the fish genome, and they may also be useful in clarifying aspects of vertebrate genome evolution.

This paper calls attention to an overlooked logical difficulty that has impeded the directed mutation debate for over half a century. It further suggests that the random mutation hypothesis be regarded at present as a null hypothesis in evolutionary biology.

The EU ban on in-feed antibiotics has stimulated research on weaning diets as a way of reducing post-weaning gut disorders and growth check in pigs. Many bioactive components have been investigated but only few have shown to be effective. Amongst these, organic acids (OA) have been shown to exert a bactericidal action mediated by non-dissociated OA, by lowering gastric pH, increasing gut and pancreas enzyme secretion and improving gut wall morphology. It has been postulated that they may also enhance non-specific immune responses and improve disease resistance. In contrast, relatively little attention has been paid to the impact of OA on the stomach but recent data show they can differently affect gastric histology, acid secretion and gastric emptying. Butyrate and precursors of butyric acid have received special attention and although promising results have been obtained, their effects are dependent upon the dose, treatment duration, initial age of piglets, gastrointestinal site and other factors. The amino acids (AA) like glutamine, tryptophan and arginine are supportive in improving digestion, absorption and retention of nutrients by affecting tissue anabolism, stress and (or) immunity. Glutamine, cysteine and threonine are important for maintaining mucin and permeability of intestinal barrier function. Spray-dried plasma (SDP) positively affects gut morphology, inflammation and reduces acquired specific immune responses via specific and a-specific influences of immunoglobulins and other bioactive components. Effects are more pronounced in early-weaned piglets and under poorer health conditions. Little interaction between plasma protein and antibiotics has been found, suggesting distinct modes of action and additive effects. Bovine colostrum may act more or less similarly to SDP. The composition of essential oils is highly variable, depending on environmental and climatic conditions and distillation methods. These oils differ widely in their antimicrobial activity in vitro and some components of weaning diets may decrease their activity. Results in young pigs are highly variable depending upon the product and doses used. These studies suggest that relatively high concentrations of essential oils are needed for beneficial effects to be observed and it has been assumed that these plant extracts mimic most of the effects of antibiotics active on gut physiology, microbiology and immunology. Often, bioactive substances protective to the gut also stimulate feed intake and growth performance. New insights on the effects of selected OA and AA, protein sources (especially SDP, bovine colostrum) and plant extracts with anti-bacterial activities on the gut are reported in this review.

The accumulation of seed mass in soybean is affected by both genotype and environment. The aim of the present study was to measure additive, epistatic and quantitative trait locus (QTL)×environment (QE) interaction effects of QTLs on the development of 100-seed weight in a population of 143 F5 derived recombinant inbred lines (RILs) developed from the cross between the soybean cultivars ‘Charleston’ and ‘Dong Nong 594’. Broad-sense heritability of 100-seed weight from 30 days (30D) to 80D stages was 0·58, 0·52, 0·62, 0·60, 0·66 and 0·57, respectively. A total of 17 QTLs with conditional additive (a) effect and/or conditional additive×environment interaction (ae) effect at specific stages were identified in ten linkage groups by conditional mapping. Of them, only 4 QTLs had significant a effect or ae effect at different stages of seed development. Among QTLs with significant a effect, five acted positively and six acted negatively on seed development. A total of 35 epistatic pairwise QTLs of 100-seed weight were identified by conditional mapping at different developmental stages. Five pairs of QTL showed the additive×additive epistatic (aa) effect and 16 QTLs showed the aa×environment interaction (aae) effect at the different developmental stages. QTLs with aa effect as well with their environmental interaction effect appeared to vary at different developmental stages. Overall, the results indicated that 100-seed weight in soybean is under developmental, genetic and environmental control.

Inferences about genetic values and prediction of phenotypes for a quantitative trait in the presence of complex forms of gene action, issues of importance in animal and plant breeding, and in evolutionary quantitative genetics, are discussed. Current methods for dealing with epistatic variability via variance component models are reviewed. Problems posed by cryptic, non-linear, forms of epistasis are identified and discussed. Alternative statistical procedures are suggested. Non-parametric definitions of additive effects (breeding values), with and without employing molecular information, are proposed, and it is shown how these can be inferred using reproducing kernel Hilbert spaces regression. Two stylized examples are presented to demonstrate the methods numerically. The first example falls in the domain of the infinitesimal model of quantitative genetics, with additive and dominance effects inferred both parametrically and non-parametrically. The second example tackles a non-linear genetic system with two loci, and the predictive ability of several models is evaluated.

Inbreeding is a biological phenomenon of special relevance in domestic species in which its influence has been typically associated with reductions in animal fitness. Nevertheless, recent research suggests substantial founder-specific variability in terms of inbreeding depression on some productive traits, although this centred on a very reduced number of founders. This research focuses on the modelling of founder-specific inbreeding depression (FSID) effects from a more general point of view, characterizing the expected distribution of FSID effects on sow longevity. Under a change-point Weibull proportional hazards model solved through Bayesian inference, a skew-normal a priori distribution for the FSID effects of 19 founders was assumed. In terms of the deviance information criterion, this model was clearly preferred to other prior distributions for FSID effects as well as to a standard analysis of the overall inbreeding depression effect, although all models were consistent with an overall negative genetic effect of inbreeding on sow longevity. The joint posterior distribution of FSID effects showed a skewed pattern with substantial right-tail overexpression, in which the mean (0·036), mode (0·034), S.D. (0·032) and asymmetry parameter (0·045) reported a higher incidence of positive estimates (85·2%) with an unfavourable effect on sow longevity. The founder with the worst inbreeding depression effect reduced sow longevity by 32 days for 1% or 167 days for 10% partial inbreeding. As a whole, our analyses highlighted substantial variability in FSID effects, with unfavourable, neutral and even favourable influences on sow longevity. This heterogeneity could be related to an uneven distribution of the recessive deleterious genetic load among founder genomes, and also with the different selection pressures applied to each founder line. The implementation of skew-normal priors also proved an appealing way to bypass the strict scenario imposed by the standard symmetric-Gaussian distribution, allowing right- and left-tail overexpression as well as non-zero modal estimates.

In the housefly, Musca domestica L., sex is usually determined by a dominant factor, M, located on the Y chromosome. However, there are ‘autosomal male’ (AM) populations in which the M factor is located on one or more of the five autosomes (I–V) or on X. We examined changes in the frequency of AM and YM males in North Carolina populations of houseflies after 4 years in the laboratory (NC Lab 02:06) and after 4 or 5 years in the field (NC 2006 and NC 2007). In 2002, 77·7% of the male houseflies were III/III;XYM, 20% were IIIM/III;XX, and 2·3% were IIIM/III;XYM. After 4 years in the laboratory, IIIM/III males disappeared and 17·4% of the males were XMYM. Conversely, 4 years later, the field population was relatively unchanged from 2002. Thus, there was a strong selection against IIIM/III males in the laboratory, but not in the field. Field-collected flies from 2007 indicated a slight increase in the frequency of XYM males and a slight decrease in the frequency of IIIM/III males (relative to 2002 and 2006), suggesting that the relative frequency of XYM and IIIM/III can vary slightly over time in field populations. The detection of XMYM males in 2007 offered the opportunity to evaluate the frequency of the female-determining FD factor, which was found to be present in both the laboratory and field populations, but frequencies varied greatly. The present study represents the first report of FD in houseflies from North America. The significance of these results, relative to observed clines in AM versus YM males, is discussed.

Phylogenetic relationships in the USDA Vigna germplasm collection are somewhat unclear and their genetic diversity has not been measured empirically. To reveal interspecific phylogenetic relationships and assess their genetic diversity, 48 accessions representing 12 Vigna species were selected, and 30 gene-derived markers from legumes were employed. Some high-quality amplicons were sequenced. Indels (insertion/deletions) were discovered from the sequence alignments that were specific identifiers for some Vigna species. With regard to revealing polymorphisms, intron-spanning markers were more effective than exon-derived markers. These gene-derived markers were more successful in revealing interspecific polymorphisms than intraspecific polymorphisms at both the DNA fragment and sequence levels. Two different dendrograms were generated from DNA fragment data and sequence data, respectively. The results from these two dendrograms supported each other and showed similar phylogenetic relationships among the Vigna species investigated. The accessions clustered into four main groups and 13 subgroups. Each subgroup represents a subgenus or a species. Phylogenetic analysis revealed that an accession might be misclassified in our collection. The putative misclassified accession was further supported by seed morphology. Limited intraspecific genetic diversity was revealed by these gene-derived markers and/or sequences. The USDA Vigna germplasm collection currently consists of multiple species with many accessions further classified into specific subspecies, but very few subspecies of the total subspecies available exist within the collection. Based on our results, more attention should be paid to the subspecies, wild forms and/or botanical varieties for future curation in order to expand the genetic diversity of Vigna germplasm in the USDA collection.

Recent studies show that the PHASE algorithm is a state-of-the-art method for population-based haplotyping from individually genotyped data. We present a modified version of PHASE for estimating population haplotype frequencies from pooled DNA data. The algorithm is compared with (i) a maximum likelihood estimation under the multinomial model and (ii) a deterministic greedy algorithm, on both simulated and real data sets (HapMap data). Our results suggest that the PHASE algorithm is a method of choice also on pooled DNA data. The main reason for improvement over the other approaches is assumed to be the same as with individually genotyped data: the biologically motivated model of PHASE takes into account correlated genealogical histories of the haplotypes by modelling mutations and recombinations. The important questions of efficiency of DNA pooling as well as influence of the pool size on the accuracy of the estimates are also considered. Our results are in line with the earlier findings in that the pool size should be relatively small, only 2–5 individuals in our examples, in order to provide reliable estimates of population haplotype frequencies.

The geographical scale of genetic structure in a continuous population is highly dependent on its breeding system and dispersion capabilities, and this knowledge is important for the study of population dynamics as well as for conservation purposes. In the present study, spatial autocorrelation statistics and intersimple sequence repeat (ISSR) markers were used to describe the genetic structure of a natural population of a prominent aromatic plant, Lippia origanoides, native to the Chicamocha Canyon in northeastern Colombia. For this purpose, individuals were sampled from two localities within the Chicamocha Canyon, where the species is abundant and continuously distributed. Cluster (principal coordinate analysis (PCO) and unweighted pair group method using arithmetic averages (UPGMA)), analysis of molecular variance (AMOVA) and Bayesian analyses revealed a low level of genetic differentiation among the two localities, suggesting that they belong to a single population. Genetic diversity levels in this population, described as the percentage of polymorphic loci (P=86·21%) and quantified using Shannon's diversity index (I=0·453) and the average panmictic heterozygosity (HB=0·484), were shown to be comparable to or higher than that in other plant species with allogamous breeding systems and to other related Verbenaceae species. Fine-scale autocorrelation analyses showed a pattern consistent with the classical model of isolation by distance with moderate but significant levels of local spatial structure. Our results suggest that sampling individuals at distances greater than ~1·2 km may result in the collection of different genotypes, which could help preserve the levels of genetic diversity in a propagation programme. The causes of this spatial pattern are currently unknown and could be influenced by many contemporary factors such as restricted seed dispersal and/or short-distance pollen movement, among others.

Lameness is one of the most important dairy cow welfare issues and has inspired a growing body of literature on gait assessment. Validation studies have shown that several methods of gait assessment are able to successfully distinguish cows with and without painful pathologies. While subjective methods provide an immediate, on-site assessment and require no technical equipment, they show variation in observer reliability. On the other hand, objective methods of gait assessment provide accurate and reliable data, but typically require sophisticated technology, limiting their use on farms. In this critical review, we evaluate gait assessment methods, discuss the reliability and validity of measures used to date, and point to areas where new research is needed. We show how gait can be affected by hoof and leg pathologies, treatment of these ailments and the pain associated with lameness. We also discuss how cow (e.g. conformation, size and udder fill) and environmental features (e.g. flooring) contribute to variation in the way cows walk. An understanding of all these factors is important to avoid misclassifying of cows and confounding comparisons between herds.

Fertility can be defined as the natural capability of giving life. It is an important factor both for human medicine, where ~10% of the couples call for the services of assisted reproductive technologies, and for species of economic interest. In particular, in dairy cows, the recent years have seen a kind of competition between milk production and fertility, and genes improving fertility are now considered as parameters to be selected for. The study of fertility pathways is nevertheless made difficult by the strong impact of environmental factors on this parameter, as well as by the number of genes potentially involved (as shown by systematic transcriptome analysis studies in the recent years). One additional level of complexity is given by the fact that factors modulating fertility will probably be sex specific. The usage of mouse models has been one of the solutions exploited for tackling with these difficulties. Here, we review three different approaches using mice for identifying genes modulating fertility in mammals: gene invalidation, positional cloning and in vitro mutagenesis. These three approaches exploit specific characteristics of the mouse, such as the possibility of controlling precisely the environment, an excellent genetic characterization and the existence of genomic and molecular tools equalled only in humans. Many indications suggest that at least some of the results obtained in mice could be easily transposed to the species of interest.

The study involved 120 crossbred ewes (sixty 1.5 years old animals and sixty 2.5 years old animals; initial liveweight 67.6 kg, condition score 3.7), that were mated in October. They were assigned to six treatments (two shearing treatments (shorn and unshorn) × two silage feed values (low and medium) and two extended grazed herbage allowances (1.0 and 1.8 kg dry matter (DM)/day)) designed to evaluate the effects of shearing at housing, grass silage feed value and extended-grazed herbage allowance on their performance and the performance of their progeny. Swards, which had silage harvested on 6 September, received fertiliser N (34 kg/ha) for extended (deferred) grazing between 19 December and lambing in mid-March. The herbage was allocated at DM allowances of 1.0 or 1.8 kg/ewe daily until 1 February. For the final 6 weeks of pregnancy, daily herbage DM allowances were 1.5, 1.6, 2.0, 2.0 and 2.0 kg for weeks 6, 5, 4, 3 and 2 to parturition, respectively. Two grass silages (low and medium feed value) were offered from housing on 19 December to lambing in mid-March. At housing, half the ewes were shorn whilst the remainder remained unshorn. Each ewe received 23.4 kg concentrate prior to lambing. For the extended-grazed herbage and the low and medium feed-value silages, DM concentrations were 132, 225 and 265 g/kg, and metabolisable energy (ME) concentrations were 10.0, 10.0 and 10.7 MJ/kg DM, respectively. Treatment did not alter (P > 0.05) litter size or number reared. Grass silage feed value did not significantly alter silage DM intake, or ewe and subsequent lamb performance. Increasing herbage allowance in mid-pregnancy decreased herbage utilisation (P < 0.05) and increased herbage intake (P < 0.05). Shearing increased silage intake (P < 0.05), lamb birth weight (P < 0.01) and tended to increase lamb weaning weight (P = 0.07). Relative to the housed shorn ewes, extended grazing did not alter (P > 0.05) ewe or subsequent lamb performance. It is concluded that shearing ewes at housing increased lamb birth weight due to increased silage intake probably associated with cold stress immediately post shearing and reduced heat stress in late pregnancy. Based on differences in lamb weight at weaning 0.8 kg of grass silage DM intake had the same feed value as a daily extended herbage DM allowance of 1.8 kg per ewe throughout the study. Neither silage feed value nor herbage allowance in mid-pregnancy affected lamb birth weight or subsequent growth rate.