Comparison of linkage maps of mouse chromosome 12 derived from laboratory strain intraspecific and Mus spretus interspecific backcrosses

Progeny from an interspecific backcross between laboratory mice and Mus spretus were typed for inheritance of eight genetic markers on chromosome 12. Marker order determined by segregation analyses of 115 meiotic events was in good agreement with that determined previously using intraspecific laboratory strain backcrosses. Two additional markers, D12Nyu5 and Lamb-1, previously not ordered, were located in the middle of the interval between D12Nyu12 and D12Nyu1. Marker spacing was reduced in the interspecific cross relative to that observed in intraspecific crosses. Furthermore, the interspecific cross was characterized by marked deviation from 1:1 segregation in the recombinant chromosomes and very strong positive interference. These data suggest that comparisons of different mouse crosses may facilitate the understanding of underlying mechanisms that govern recombination events in complex genomes.     

Sex, strain, and species differences affect recombination across an evolutionarily conserved segment of mouse chromosome 16

A region of substantial genetic homology exists between human chromosome 21 (HSA21) and mouse chromosome 16 (MMU16). Analysis of 520 backcross animals has been used to establish gene order in the homologous segment. D21S16h and Mx are shown to represent the known proximal and distal limits of homology between the chromosomes, while Gap43, whose human homolog is on HSA3, is the next proximal marker on MMU16 that has been mapped in the human genome. Recombination frequencies (RFs) in four intervals defined by five loci in the HSA21-homologous region of MMU16 were analyzed in up to 895 progeny of eight different backcrosses. Two of the eight crosses were made with F1 males and six with F1 females. The average RF of 0.249 in 265 backcross progeny of F1 males was significantly higher than the 0.106 average recombination in 320 progeny of F1 females in the interval from D21S16h to Ets-2. This is in contrast to HSA21, which shows higher RFs in female meiosis in the corresponding region. Considerable variation in RF was observed between crosses involving different strains, both in absolute and in relative sizes of the intervals measured. The highest RFs occurred in a cross between the laboratory strain C57BL/6 and MOLD/Rk, an inbred strain derived from Mus musculus molossinus. RFs on this cross were nearly fivefold higher than those reported previously for an interspecific cross between C57BL/6 and Mus spretus.     

Using lod scores to detect sex differences in male-female recombination fractions

Human recombination fraction (RF) can differ between males and females, but investigators do not always know which disease genes are located in genomic areas of large RF sex differences. Knowledge of RF sex differences contributes to our understanding of basic biology and can increase the power of a linkage study, improve gene localization, and provide clues to possible imprinting. One way to detect these differences is to use lod scores. In this study we focused on detecting RF sex differences and answered the following questions, in both phase-known and phase-unknown matings: (1) How large a sample size is needed to detect a RF sex difference? (2) What are "optimal" proportions of paternally vs. maternally informative matings? (3) Does ascertaining nonoptimal proportions of paternally or maternally informative matings lead to ascertainment bias? Our results were as follows: (1) We calculated expected lod scores (ELODs) under two different conditions: "unconstrained," allowing sex-specific RF parameters (theta(female), theta(male)); and "constrained," requiring theta(female) = theta(male). We then examined the DeltaELOD (identical with difference between maximized constrained and unconstrained ELODs) and calculated minimum sample sizes required to achieve statistically significant DeltaELODs. For large RF sex differences, samples as small as 10 to 20 fully informative matings can achieve statistical significance. We give general sample size guidelines for detecting RF differences in informative phase-known and phase-unknown matings. (2) We defined p as the proportion of paternally informative matings in the dataset; and the optimal proportion p(circ) as that value of p that maximizes DeltaELOD. We determined that, surprisingly, p(circ) does not necessarily equal (1/2), although it does fall between approximately 0.4 and 0.6 in most situations. (3) We showed that if p in a sample deviates from its optimal value, no bias is introduced (asymptotically) to the maximum likelihood estimates of theta(female) and theta(male), even though ELOD is reduced (see point 2). This fact is important because often investigators cannot control the proportions of paternally and maternally informative families. In conclusion, it is possible to reliably detect sex differences in recombination fraction.     

High-resolution mapping and recombination interval analysis of mouse Chromosome 17

Analysis of homologous recombination in eukaryotes has shown that some meiotic crossing-over occurs preferentially at specific genomic sites of limited physical distance called recombinational hotspots. In the mouse, recombinational hotspots have only been defined in the major histocompatibility complex (MHC) on chromosome (Chr) 17. In an attempt to examine whether hotspots are unique to the MHC or are present throughout the genome, high-resolution linkage maps of Chr 17 based on five backcrosses involving different inbred strains have been generated. These maps separate many markers that were previously shown at the same map position and allow a detailed analysis of recombination patterns across Chr 17. Corresponding recombination intervals in these maps have been compared for the identification of intervals with very little or no recombination in certain genetic crosses and considerable recombination in other genetic crosses. This approach has been termed Recombination Interval Analysis. Possible haplotype-dependent non-MHC hotspots, as well as previously identified MHC hotspots, have been detected by interval analysis. Received: 1 December 1997/ Accepted: 27 February 1998     

The effect of genome and sex on recombination rates in Pennisetum species

The effects of homoeology and sex on recombination frequency were studied in crosses between cultivated pearl millet, Pennisetum glaucum, and two wild subspecies, P. violaceum and P. mollissimum. For the two wild x cultivated crosses, reciprocal three-way crosses were made between the F₁ hybrid and an inbred line (Tift 23DB₁). The three-way cross populations were mapped to produce a female map of each wide cross (where the F₁ was the female) and a male map (where the F₁ was the male). Total genetic map lengths of the two inter-subspecies crosses were broadly similar and around 85 % of a comparable intervarietal map. In the P. glaucumxP. mollissimum crosses, the map was further shortened by a large (40 cM) inversion in linkage group 1. Comparison of the recovered recombinants from male and female meiocytes showed an overall trend for the genetic maps to be longer in the male (10%) in both inter-subspecific crosses; however, analysis of individual linkage intervals showed no significant differences. Gametophytic selection was prevalent, and sometimes extreme, for example 121 in favour of wild alleles in the P. glaucumxP. mollissimum male recombinant population. One of the loci which determines panicle type in cultivated pearl millet and wild relatives, H, was mapped 9 cM from Xpsm812 on linkage group 7 in the P. violaceum cross.     

A catalog of nonsynonymous polymorphism on mouse Chromosome 16

Numerous phenotypic traits differ among inbred mice, and the genetic diversity of inbred strains has been exploited in studies of quantitative trait loci (QTL). Sequencing the mouse genome has resulted in improved tools for the study of QTL, but a comprehensive catalog of sequence variants between strains would be of great value in identifying and testing potentially causative alleles. A/J DNA was included in the Celera shotgun sequence of the mouse genome and C57BL/6 DNA was sequenced by an international consortium. We have resequenced A/J and B6 DNA to cover nearly all of the protein-coding portions of mouse Chromosome 16, revealing that there are 106 nonsynonymous substitutions in 74 of the 779 genes on the chromosome. The pattern of substitution is more similar to the spectrum of benign polymorphism in the human population than it is to human disease-causing mutations. In mouse, polymorphic variants tend to be associated with one another on large haplotypes; this pattern also holds true for nonsynonymous polymorphism. However, sufficient fragmentation of haplotypes is present to suggest that only a very-high-resolution haplotype map will enable effective inference of alleles in additional strains. SNP data have been submitted to dbSNP with ssid No. 46531525-46532013.     

How important are species richness,species evenness and interspecific differences to productivity? A mathematical model

We present a theoretical model to quantify the influence of diversity on productivity and nutrient acquisition in plant communities during exponential growth. The model fractionates diversity into three components, namely species richness ( S ), species evenness ( E ) and the degree of difference between species ( D ). The influence of each of these components is assessed individually: S is varied by changing the number of species, E by changing their population size, and D by changing the range of species traits critical to productivity (specific nutrient uptake rate, Σ _r , or nutrient use efficiency, NUE ). D was quantified as the coefficient of variation of Σ _r or NUE . All three components of diversity enhance the biomass and nutrient stocks in the community, but the response patterns are different. Species richness has a saturating influence, whereas effects of E and D are linear and exponential, respectively. In all cases the non-linear dependence of productivity and nutrient acquisition on Σ _r and NUE during exponential growth was the single mechanism underlying these effects. This causes the presence of plants with extreme traits to promote productivity, and S , E and D all affect the abundance and/or intensity of these extremes. The model offers a framework to explain differences between experimental observations, and suggests a concept of diversity where S and E are structural components and D a qualitative or functional component, which modulates the influence of the two others. We propose to explicitly recognise D as an integral constituent of plant diversity in future studies.     

Chromosome pairing and recombination in mice heterozygous for different translocations in chromosomes 16 and 17

In order to clarify the relationship between meiotic pairing and recombination, and electron microscopic (EM) study of synaptonemal complexes (SC) and an analysis of chiasma frequency and distribution were made in male mice singly and doubly heterozygous for Robertsonian [Rb(16.17)7Bnr] and reciprocal [T(16:17)43H] translocations and also in tertiary trisomics for the proximal region of chromosome 17. In all these genotypes an extensive zone of asynapsis/desynapsis around the breakpoints was revealed. At the same time a high frequency of non-homologous pairing was observed in precentromeric regions of acrocentric chromosomes. The presence in the proximal region of chromosome 17 of the t haplotype did not affect the synaptic behaviour of this region. Chiasma frequency in the proximal region of chromosome 17 in the T(16:17)43H heterozygotes and trisomics was increased when compared with that in Robertsonian heterozygotes.by H.C. Macgregor     

Leucine aminopeptidase polymorphism inPhaseolus and differential elimination of the donor parent genotype in interspecific backcrosses

Starch gel electrophoretic analysis of crude seed (cotyledonary) extracts of Phaseolus vulgaris, P. coccineus,F ₁ ,F ₂ ,F ₃ ,and reciprocal F ₁ backcrosses reveals monomorphic and polymorphic forms of leucine aminopeptidase (LAP) in the genus. The polymorphic forms (LAP-II) are controlled by the codominant alleles, Lap-II^a and Lap-II^b.Reciprocal backcrosses to both species show a highly significant deviation from the expected 1:1 ratio when the donor parent allele is transmitted through male gametes. There is not a significant deviation from the expected ratio when transmission is through female gametes. Differential gametic selection, in conjunction with differential sterility, suggests that structural differences exist between the genomes of these species. This research was supported in part by U.S. Public Health Service Grants GM 11612 and GM 14941-01.     

The positions of 12 simple sequence repeat markers relative to reference loci on mouse Chromosome 16

The genetic map positions of 12 simple sequence repeat (SSR) markers spanning mouse Chromosome (Chr) 16 were determined relative to reference markers on that chromosome. Interval mapping data were obtained with a panel of DNAs from two intersubspecific backcrosses. All but one of the markers were typed by use of nonradioactive polymerase chain reaction (PCR) products analyzed on agarose gels. The marker order was determined to be Prm-1, D16Mit9, Igl-1, D16Mit29, D16Mit1/D16Mit2, Smst, D16Mit4, D16Mit11, Gap43, D16Mit14, D16Mit30, D16Mit5, Pit-1, D16Mit27, D16H21S16 (formerly D21S16h), D16Mit19, App, D16Mit7, Sod-1. Two of these markers mapped to the known human Chr 21 (HSA21)/Chr 16 conserved linkage group. Nine additional SSR markers could not be typed because they were not polymorophic (four markers), did not amplify MOLD/Rk DNA (three markers), or failed to give PCR products under a range of conditions (two markers). A subset of the most robust SSRs provide a useful marker set for the analysis of previously unmapped crosses.     

Analysis of Rhesus monkey vocalizations: maturation-related sex differences in clear-cell frequency

In the first of two studies six like-sexed pairs of rhesus macaques early in their third year of life were observed for two days, then separated for two days, and finally reunited for two days. In the second, about nine months later, the same animals were paired across sex and were separated in a similar fashion to that in the previous study. The number of distress-related clear calls uttered by females remained stable through both studies, but the males showed a decrease with age in this behavior. The results of these two studies are compared with other research in which maturation-related sex differences have become apparent. These comparisons suggested that decreases in the production of clear calls accompany the onset of puberty. Since the females which were involved in our research reached puberty shortly before the time of our first study and the males did so shortly before the second, the decreases in male clear-call rate which we observed across these two studies appears to have been linked with peri-pubertal influences.