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.

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.

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.

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.

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.

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.

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.