Medicago laciniata is restricted to south of the Mediterranean basin and it extends in Tunisia from the inferior semi-arid to Saharan stages, whereas M. truncatula is a widespread species in such areas. The genetic variability in four Tunisian sympatric populations of M. laciniata and M. truncatula was analysed using 19 quantitative traits and 20 microsatellites. We investigated the amplification transferability of 52 microsatellites developed in M. truncatula to M. laciniata. Results indicate that about 78·85% of used markers are valuable genetic markers for M. laciniata. M. laciniata displayed significantly lower quantitative differentiation among populations (QST=0·12) than did M. truncatula (QST=0·45). However, high molecular differentiations, with no significant difference, were observed in M. laciniata (FST=0·48) and M. truncatula (FST=0·47). Several quantitative traits exhibited significantly smaller QST than FST for M. laciniata, consistent with constraining selection. For M. truncatula, the majority of traits displayed no statistical difference in the level of QST and FST. Furthermore, these traits are significantly associated with eco-geographical factors, consistent with selection for local adaptation rather than genetic drift. In both species, there was no significant correlation between genetic variation at quantitative traits and molecular markers. The site-of-origin explains about 5·85% and 11·27% of total quantitative genetic variability among populations of M. laciniata and M. truncatula, respectively. Established correlations between quantitative traits and eco-geographical factors were generally more moderate for M. laciniata than for M. truncatula, suggesting that the two species exhibit different genetic bases of local adaptation to varying environmental conditions. Nevertheless, no consistent patterns of associations were found between gene diversity (He) and environmental factors in either species.

Semi-dwarfism is an important agronomic trait in rice breeding programmes. sd-1, termed the ‘Green Revolution gene’, confers semi-dwarf stature, increases harvest index, improves lodging resistance, and is associated with increased responsiveness to nitrogen fertilizer. It has contributed substantially to the significant increase in rice production. In this paper, a novel semi-dwarf mutant in rice is reported. Genetic analysis revealed that only a single dominant gene locus non-allelic to sd-1, temporarily designated Sdt97, is involved in the control of semi-dwarfism of the mutant. The semi-dwarfism of the mutant could be partly restored to the tall wild-type by application of exogenous GA3, suggesting that the mutant gene Sdt97 may be involved in the gibberellin (GA) synthesis pathway and not the GA response pathway in rice. A residual heterozygous line (RHL) population derived from a recombinant inbred line (RIL) was developed. Simple sequence repeat (SSR) and bulked segregation analysis (BSA) combined with recessive class analysis (RCA) techniques were used to map Sdt97 to the long arm of chromosome 6 at the interval between two STS markers, N6 and TX5, with a genetic distance of 0·2 cM and 0·8 cM, respectively. A contig map was constructed based on the reference sequence aligned by the Sdt97 linked markers. The physical map of the Sdt97 locus was defined to a 118 kb interval, and 19 candidate genes were detected in the target region. This is the first time that a dominant semi-dwarf gene has been reported in rice. Cloning and functional analysis of gene Sdt97 will help us to learn more about molecular mechanism of rice semi-dwarfism.

European water frog hybrids Rana esculenta (R. ridibunda×R. lessonae) reproduce hemiclonally, by hybridogenesis: in the germ line they exclude the genome of one parental species and produce haploid gametes with an unrecombined genome of the other parental species. In the widespread L-E population system, both sexes of hybrids (E) coexist with R. lessonae (L). They exclude the lessonae genome and produce ridibunda gametes. In the R-E system, hybrid males coexist with R. ridibunda (R); they exclude either their ridibunda or their lessonae genome and produce sperm with a lessonae or with a ridibunda genome or a mixture of both kinds of sperm. We examined 13 male offspring, 12 of which were from crosses between L-E system and R-E system frogs. All were somatically hybrid. With one exception, they excluded the lessonae genome in the germ line and subsequently endoreduplicated the ridibunda genome. Spermatogonial metaphases contained a haploid or a diploid number of ridibunda chromosomes, identified through in situ hybridization to a satellite DNA marker, and by spermatocyte I metaphases containing a haploid number of ridibunda bivalents. The exception, an F1 hybrid between L-E system R. lessonae and R-E system R. ridibunda, was not hybridogenetic, showed no genome exclusion, and evidenced a disturbed gametogenesis resulting from the combination of two heterospecific genomes. None of the hybridogenetic hybrids showed any cell lines excluding the ridibunda genome, the pattern most frequent in hybrids of the R-E system, unique to that system, and essential for its persistence. A particular combination of R-E system lessonae and R-E system ridibunda genomes seems necessary to induce the R-E system type of hemiclonal gametogenesis.

Coalescent theory is commonly used to perform population genetic inference at the nucleotide level. Here, we examine the procedure that fixes the number of segregating sites (henceforth the FS procedure). In this approach a fixed number of segregating sites (S) are placed on a coalescent tree (independently of the total and internode lengths of the tree). Thus, although widely used, the FS procedure does not strictly follow the assumptions of coalescent theory and must be considered an approximation of (i) the standard procedure that uses a fixed population mutation parameter θ, and (ii) procedures that condition on the number of segregating sites. We study the differences in the false positive rate for nine statistics by comparing the FS procedure with the procedures (i) and (ii), using several evolutionary models with single-locus and multilocus data. Our results indicate that for single-locus data the FS procedure is accurate for the equilibrium neutral model, but problems arise under the alternative models studied; furthermore, for multilocus data, the FS procedure becomes inaccurate even for the standard neutral model. Therefore, we recommend a procedure that fixes the θ value (or alternatively, procedures that condition on S and take into account the uncertainty of θ) for analysing evolutionary models with multilocus data. With single-locus data, the FS procedure should not be employed for models other than the standard neutral model.

Multiple-trait analyses have been shown to improve the detection of quantitative trait loci (QTLs) with multiple effects. Here we applied a multiple-trait approach on obesity- and growth-related traits that were surveyed in 275 F2 mice generated from an intercross between the high body weight selected line NMRI8 and DBA/2 as lean control. The parental lines differed 2·5-fold in body weight at the age of 6 weeks. Within the F2 population, the correlations between body weight and weights of abdominal fat weight, muscle, liver and kidney at the age of 6 weeks were about 0·8. A least squares multiple-trait QTL analysis was performed on these data to understand more precisely the cause of the genetic correlation between body weight, body composition traits and weights of inner organs. Regions on Chr 1, 2, 7 and 14 for body weights at different early ages and regions on Chr 1, 2, 4, 7, 14, 17 and 19 for organ weights at 6 weeks were found to have significant multiple effects at the genome-wide level.

Quantitative trait loci (QTLs) may affect not only the mean of a trait but also its variability. A special aspect is the variability between multiple measured traits of genotyped animals, such as the within-litter variance of piglet birth weights. The sample variance of repeated measurements is assigned as an observation for every genotyped individual. It is shown that the conditional distribution of the non-normally distributed trait can be approximated by a gamma distribution. To detect QTL effects in the daughter design, a generalized linear model with the identity link function is applied. Suitable test statistics are constructed to test the null hypothesis H0: No QTL with effect on the within-litter variance is segregating versus HA: There is a QTL with effect on the variability of birth weight within litter. Furthermore, estimates of the QTL effect and the QTL position are introduced and discussed. The efficiency of the presented tests is compared with a test based on weighted regression. The error probability of the first type as well as the power of QTL detection are discussed and compared for the different tests.

Angiotensin converting enzyme (ACE) gene polymorphism insertion (I) or deletion (D) has been widely studied in different populations, and linked to various functional effects and associated with common diseases. The purpose of the present study was to investigate the relationship between the ACE I/D frequency in different populations and geographic location; ACE I/D allele frequency in the Lebanese population and ACE II genotype contribution to the geographic trend were also identified. Five hundred and seventy healthy volunteers were recruited from the Lebanese population. Genomic DNA was extracted from buccal cells, and amplified by polymerase chain reaction; products were then identified by gel electrophoresis. The frequencies of the different ACE I/D genotypes were determined and tested for Hardy–Weinberg equilibrium (HWE). To assess the relationship between ACE I/D frequency and geographic location, and to identify how the Lebanese population contributes to the geographic trend in ACE I/D frequencies, Eurasian population samples and Asians were incorporated in the analyses from the literature. The frequency of the I allele in the Lebanese population was 27% and the corresponding II genotype was at a frequency of 7·37% (in HWE; P=0·979). The ACE I allele and genotype frequencies show an association with longitude, with frequencies increasing eastwards and westwards from the Middle East.