Maximum-likelihood models for mapping genetic markers showing segregation distortion. 2. F2 populations

In F₂ populations, gametic and zygotic selection may affect the analysis of linkage in different ways. Therefore, specific likelihood equations have to be developed for each case, including dominant and codominant markers. The asymptotic bias of the classical estimates are derived for each case, in order to compare them with the standard errors of the suggested estimates. We discuss the utility and the efficiency of a previous model developed for dominant markers. We show that dominant markers provide very poor information in the case of segregation distortion and, therefore, should be used with circumspection. On the other hand, the estimation of recombination fractions between codominant markers is less affected by selection than is that for dominant markers. We also discuss the analysis of linkage between dominant and codominant markers.     

On the formation of rho - petites in yeast. III. Effects of temperature on transmission and recombination of mitochondrial markers and on rho - cell formation in temperature sensitive mutants of Saccharomyces cerevisiae.

Summary The -factor stability is shown to be affected by four conditional mutations, tsm-8 (mitochondrial), tsp-20, tsp-25 and tsp-30 (nuclear). Growth of mutant cells at high temperature (35°C) results in the rapid production of ^– cells and concomittantly in the decrease of the ability to transmit mitochondrial genetic information to the ⁺ progeny of crosses. Kinetics of ^– cell formation during growth at 35°C have been compared with variations in transmission and recombination of mitochondrial markers in crosses. In all cases the transmission of mitochondrial markers of the ts-parent decreases as the number of cell generations increases. The frequencies of recombinants between mitochondrial markers either increase or decrease depending on the markers considered and the alleles of the -locus involved in the crosses.The results of all crosses performed have been compared with the predictions of the model for recombination and segregation of mitochondrial genes proposed by Dujon et al. (1974). This comparison indicates that the main result of high temperature treatment is a diminution of the input of mitochondrial information from the ts-parent into zygotes. Consequences of the induced variations of input follow the predictions of the model. The correlation found in ts-strains between the reduction of input in crosses and the formation of ^– cells is discussed in terms of molecular events occurring in mitDNA molecules during high temperature induction of ⁺ to ^– mutation.This paper is dedicated to Professor Dr. A. Butenandt on the occasion of his 75th birthday     

Frequent recombination in the human T-cell receptor beta gene complex

Although individual TCRVBV gene segments exhibit limited polymorphism, human T-cell receptor beta (TCRB) haplotypes are characterized by multiple different combinations of allelic markers. This observation suggests that genetic recombination may have played a role in the generation of these haplotypes. Meiotic recombination in a region spanning 250 kilobases (kb) at the 3 end of the TCRB gene complex was investigated by extended family studies and by analysis of single sperm. Segregation patterns of polymorphic TCRB markers in families allowed the assignment of TCRB alleles to parental haplotypes and detection of recombinants among the offspring. Among the 178 informative paternal meioses, four (2%) were recombinant, whereas no recombinants were found in the 199 maternal meioses. In addition, segregation of two allelic markers was examined in a total of 1101 individual sperm from two heterozygous donors to detect exchange events in this region. The results revealed a similar rate of recombination, 1.3%, which, along with the family data, suggests that at, least in males, meiotic recombination in this 250 kb region may be six times higher than the average rate of 1% per 10⁶ bases that has been estimated for the human genome.     

Generation of heteroplastidic Nicotiana cybrids by protoplast fusion: analysis for plastid recombinant types

Summary Protoplasts of a mutant line of Nicotiana tabacum having a maternally-transmitted chlorophyll deficiency were fused with protoplasts of two alloplasmic-male-sterile Nicotiana lines by the donor-recipient technique. In both fusion experiments variegated plantlets were regenerated which were shown to contain cytoplasms of mixed chloroplast nature. This confirms that with the donor-recipient method one can obtain mixed cytoplasms of genetically different chloroplasts. We present a convenient system to assay for genetic recombination between chloroplasts by combining use of several cytoplasmic markers: vis. chlorophyll pigmentation, chloroplast DNA restriction patterns, tentoxin resistance and male sterility. Within the limits of the experiment no recombinant types were recovered.     

Attempt to detect recombination between B-F and B-L genes within the chicken B complex by serological typing,in vitro MLR,and RFLP analyses

In search for recombinants within the chicken major histocompatibility B complex, 1155 animals from crosses between the congenic lines CB (B¹²) and CC (B⁴) were tested with alloantibodies and monoclonal antibodies for the B-F (class I), B-L (class II), and B-G (class IV) antigens and by mixed lymphocyte reaction. The absence of detectable recombination was confirmed by restriction fragment length polymorphism analysis with B-L and B-F probes. Together with previous reports, this indicates that the distance between the B-F and B-L loci is below 0.01 centimorgan.     

RFLP mapping in barely of a dominant gene conferring resistance to scald (Rhynchosporium secalis)

A progeny consisting of 52 anther-derived doubled haploid barley lines from a F₁ between the winter cultivars Igri (susceptible) and Triton (resistant) was tested for resistance to Rhynchosporium secalis. A dominant gene was detected and tagged by a series of cosegregating RFLP markers located in the proximal portion of the long arm of chromosome 3, close to the centromere. One of the cosegregating RFLP markers, cMWG680, was converted into a codominant sequence tagged site marker. Polymerase chain reaction analysis with this marker of a series of accessions carrying known resistance genes provided evidence that scald resistance in cv Triton is due to the presence of the Rh gene.     

Malic dehydrogenase locus of Paramecium tetraurelia

A search was undertaken for naturally occurring genetic markers for use in clonal aging studies of Paramecium tetraurelia. Clonal age is defined as the number of cell divisions since the last sexual process. Autogamy (self-fertilization) is a sexual process which can occur in aging lines, resulting in homozygosity and initiation of the next generation. Such illicit autogamies must be detected and eliminated from the aged clone. With codominant alleles, heterozygous aging lines can be established which will express a phenotype distinguishable from that of either parental type and autogamy can then be monitored by the appearance of either segregant homozygous phenotype. However, very few codominant alleles are available in this species. Electrophoretic mobilities of malic dehydrogenase (MDH) were assayed in 11 stocks of Paramecium tetraurelia by polyacrylamide gel electrophoresis. Nine stocks showed a singlebanded stock 51 type, while stock 174 and stock 29 each exhibited unique mobility. Crosses between stock 51 and the deviant stocks revealed distinct three-banded patterns indicative of heterozygosity of the F₁ generation. In the autogamous F₂ generation, 1:1 segregation of the parental types were recovered. The pattern of inheritance is consistent with codominant alleles and Mendelian inheritance. These naturally occurring biochemical markers are stable with increasing clonal age and are therefore useful genetic markers for studies of cellular aging.This work was supported by NSF Grant PCM 7704315.     

Recombination behaviour and gene transfer in Petunia hybrida after pollen irradiation

Summary The genes An2, Rt and An1 are located in chromosome VI and closely linked. Pollination of the triple recessive line W127 (an2an2rtrtan1) with irradiated pollen of the triple dominant line M1 (An2An2RtRtAn1An1) led to the recovery of at least 3.3% induced an2 recessives. Karyotype analysis and genetic data showed that these mutants all contained a deletion on the short arm of chromosome VI, ranging from non-detectable (a non-transmissable mutant, showing no visible deletion) to the complete short arm. It is concluded that An2 is located distally in the short arm, Rt and An1 in the long arm of chromosome VI. Deleted chromosomes are not transmitted to the next generation, neither through the male nor through the female; transmission of the dominant markers in the long arm of chromosome VI is possible after completion of the chromosome by crossing-over. There is a relationship between the length of the deletion in the short arm and the recombination frequency between the markers (Rt and An1) in the long arm: recombination increases with increasing length of the deletion. After completion of the chromosme by crossing-over, the normal recombination frequency is restored.     

A Beta-mixture model for assessing genetic population structure

Summary An important fraction of recently generated molecular data is dominant markers. They contain substantial information about genetic variation but dominance makes it impossible to apply standard techniques to calculate measures of genetic differentiation, such as F‐statistics. In this article, we propose a new Bayesian beta‐mixture model that more accurately describes the genetic structure from dominant markers and estimates multiple F_ST s from the sample. The model also has important application for codominant markers and single‐nucleotide polymorphism (SNP) data. The number of F_ST is assumed unknown beforehand and follows a random distribution. The reversible jump algorithm is used to estimate the unknown number of multiple F_ST s. We evaluate the performance of three split proposals and the overall performance of the proposed model based on simulated dominant marker data. The model could reliably identify and estimate a spectrum of degrees of genetic differentiation present in multiple loci. The estimates of F_ST s also incorporate uncertainty about the magnitude of within‐population inbreeding coefficient. We illustrate the method with two examples, one using dominant marker data from a rare orchid and the other using codominant marker data from human populations.     

The chromosomal locations and linkage relationships of the structural genes for the prolamin storage proteins (secalins) of rye

Summary Rye secalins are a polymorphic mixture of polypeptides which are classified into four major groups. Previous studies have shown that the structural genes for two of the groups (the -secalins and 40K -secalins) are located on the short arm of chromosome 1R and those for a third group (the high molecular weight secalins) on the long arm of the same chromosome. Analysis of F₂ grain from crosses between inbred lines of S. cereale shows that the structural genes for the -secalins (designated Sec 1) and the high molecular weight secalins (designated Sec 3) are loosely linked (40.8 ±3.76% recombination, 57.4 ± 11.30 cM). Analysis of wheat rye addition lines shows that the structural genes for the 75K -secalins are present on chromosome 2R. This locus is provisionally designated Sec 2. These genes are probably derived from those for the 40K -secalins by duplication, divergence and translocation. Analysis of secalin fractions from wild species of rye shows that all contain 75K -secalins, indicating that the duplication and divergence, if not the translocation, occurred before speciation of the genus.     

Polymorphism and Inheritance of Seed Storage Protein in Sunflower

The data on polymorphism and inheritance of the seed storage protein helianthinin are presented. The results of hybrid analysis indicate that in the annual sunflower Helianthus annuus, helianthinin synthesis is controlled by at least three loci: HelA, HelB, and HelC. Codominant alleles controlling different electrophoretic variants of polypeptides were identified at each of the loci. The HelA locus was inherited independently of HelB and HelC in a series of dihybrid crosses. The frequencies of recombination between loci HelB and HelC estimated in F₂ and BC of two crossing combinations were respectively 21.8 and 19.0%. Segregation of the HelC-controlled variants in the progenies from the crosses of cultured sunflower with annual wild species and forms corresponded to that theoretically expected for Mendelian inheritance. The maternal type of helianthinin inheritance was observed in the progenies from the crosses of inbred H. annuus L. lines with perennial diploid and polyploid HelianthusL. species. Altered expression of the HelClocus was detected in some hybrid combinations. These alterations appeared in early (F₁, F₂) hybrid generations and were similar in different hybrid combinations. They did not depend on the perennial paternal species being more influenced by the maternal genotype and by the mode of obtaining hybrids (in an embryo culture or in the field). These results are explained by genomic shock generated by hybridization of genetically incompatible species.     

Nonsense mutants of Serratia phage Kappa

Summary Auxotrophs of Serr. marcescens HY, which behaved like nonsense mutants when tested according to Whitfield et al. (1966), were induced to revert to anauxotrophy. Some of the revertants (called su ⁺), together with the parental auxotrophs (called su ^-), allowed to isolate conditional-lethal (sus) mutants of phage Kappa, which produce infectious progeny only in su ⁺ bacteria. All su ⁺ mutants of Serr. marcescens HY were identified as nonsense suppressors using su ⁺ _amber, su ⁺ _ochre, and su ^- strains of Salm. typhimurium as references and the flagella-specific phage Chi as the main tool to connect the Salmonella system with that of Serratia.After treatment of Kappa with three different mutagens 128 sus mutants were isolated which comprise at least 19 complementation groups. 18 sus mutants, representing different cistrons, and the unselective markers c1, c2, and c49 were mapped mainly by two-factor crosses. Reciprocal three-factor crosses of the general type a x bz and az x b (i.e. with outside markers) revealed a circular linkage map of an estimated maximum length of 90 RU (recombination units). Joined rescue of outside markers, e.g. sus ⁺ A94 and e49, from UV-irradiated phage supported the assumption of circular gene linkage. Some data indicate that certain regions of the phage genome might have a higher chance to recombine than others.Abbreviations moi multiplicity of infection - eop efficiency of plating - RU recombination units - MR marker rescue     

Meiotic studies ofElymus nutans andE. jacquemontii (Poaceae,Triticeae) and their hybrids withPseudoroegneria spicata and seventeenElymus species

Hybridizations ofElymus nutans andE. jacquemontii were carried out with one species ofPseudoroegneria (S genome), and 20Elymus species, each containing either of the SH, SY, SYH, or SYW genomes. Chromosome configurations were analysed at metaphase I of the two target taxa and their interspecific hybrids. It is concluded that (i)E. nutans is an allohexaploid containing the SYH genomes, andE. jacquemontii is an allotetraploid having the SY genomes; (ii) the genomic affinity is associated with the geographic distance between the species studied; (iii) minor genomic structural rearrangements have occurred within the hexaploid taxon ofE. nutans.     

Establishment of molecular markers and linkage groups in two F2 populations of Upland cotton

Two F₂ populations of cotton (Gossypium hirsutum L.) from the crosses of HS46 x MARCABUCAG8US-1-88 (MAR) and HS46 x Pee Dee 5363 (PD5363) were characterized for restriction fragment length polymorphisms (RFLPs) using DNA probes. Seventy-three probe/enzyme combinations were used in the HS46 x MAR population analysis, which resulted in 42 informative polymorphic fragments. These 42 moleclar markers represented 26 polymorphic loci, which consisted of 15 codominant and 11 dominant (+/-) genotypes. Chi-square analyses of these loci fit expected genotypic ratios of 121 and 31, respectively An analysis of these loci with the MAPMAKER program resulted in the establishment of four linkage groups A, B, C, and D with 4,2,2, and 2 loci, respectively, as well as 16 unlinked loci. Six probe-enzyme combinations were assayed on the HS46 x PD5363 population, which resulted in 11 informative polymorphic fragments. These 11 fragments represented 6 polymorphic loci, 1 dominant (+/-) and 5 codominant genotypes. The MAPMAKER analysis of these loci yielded 2 linked loci. Thus, a total of 53 polymorphic fragments and 32 polymorphic loci, representing five linkage groups, were identified among the two families.Contribution of the USDA-ARS in cooperation with the Miss Agric For Exp Stn.     

Transmission and recombination of extranuclear genes during sexual crosses in Aspergillus nidulans

Summary Three extranuclear mitochondrial mutations in Aspergillus nidulans, (oliA1), (camA1) and (cs67), were used as markers in sexual crosses to provide information on the frequencies of transmission and recombination of the mitochondrial genome. Any individual perithecium contained ascospores of only one extranuclear genotype.Using mono-, bi- and trifactorial crosses it was found that all three markers could be recovered from the progeny, although the transmission frequencies were different for each marker. This bias was present irrespective of the nuclear background or the presence of selective agents in the medium on which the cross was established. These findings enable a series of transmission strength to be established, as shown below:- (cs67,{\text{ }}camA1) > ( + ) = (cs67) > (oliA1,cs67) \hfill \\ {\text{ }} > (oliA1) > (oliA1,{\text{ }}camA1) \hfill \\ \end{gathered} $$ " align="middle" border="0"> However, the numbers of recombinants isolated were so variable as to make this form of analysis unsuitable for mapping the mitochondrial genome.     

Genetic exchanges caused by ultraviolet photoproducts in phage λ DNA molecules: The role of DNA replication

Summary Genetic recombination induced by structural damage in DNA molecules was investigated in E. coli K12 () lysogens infected with genetically marked phage . Photoproducts were induced in the phage DNA before infection by exposing them either to 313 nm light in the presence of acetophenone or to 254 nm light. To test the role of the replication of the damaged phage DNA on the frequency of the induced recombination, both heteroimmune and homoimmune crosses were performed.First, samples of a heteroimmune phage imm434 P80 exposed to these treatments were allowed to infect cells lysogenic for prophage cI857 P3. Phage DNA replication and maturation took place, and the resulting progeny phages were assayed for the frequency of P ⁺ recombinants. Recombination was less frequent in infected cells exposed to visible light and in wild type cells able to perform excision repair than in excision-defective lysogens. Therefore, much of the induced recombination can be atributed to the pyrimidine dimers in the phage DNA, the only photoproducts known to be dissociated by photoreactivating enzyme.Second, in homoimmune crosses, samples of similarly treated homoimmune P3 phages were allowed to infect lysogens carrying cI857 P80. Replication of the phage DNA containing ultraviolet photoproducts was repressed by immunity, and was futher blocked by the lack of the P gene product needed for replication. The lysogens were purified and scored for both colony forming ability and for P ⁺ recombinant prophages. The 254 nm photoproducts increased the frequency of recombination in these homimmune crosses, even though phage DNA replication was blocked. Irradiation with 313 nm light and acetophenone M, which produces dimers and unknown photoproducts, was not as effective per dimer as the 254 nm light.It is concluded from these results that certain unidentified 254 nm photoproducts can cause recombination even in the absence of DNA replication. They are not pyrimidine dimers, as they are not susceptible to excision repair or photoreactivation. In contrast, pyrimidine dimers appear to cause recombination only when the DNA containing them undergoes replication.     

Recombination between kappa chain genetic markers in the mouse

In this study we report the first instance of recombination between kappa chain genetic markers in the mouse. The recombination frequency, 0.45% (95% limits, 0.12–1.61), is similar to that previously found for recombination between the kappa chain locus and the Lyt-2, 3 locus (0.3%, 95% limits, 0.05–1.6), but is relatively low in comparison with that found at the heavy chain locus (0.41–5.4%). Lyt-2, 3-typing of the recombinants permits a partial ordering of the kappa chain and Lyt-2, 3 loci as (Lyt-2, 3, Igk-Ef1) - Igk-Ef2. Light chains controlled by the two kappa markers include the V_k-(ser) subgroup (controlled by Igk-Ef1) and V_k–1 (controlled by Igk-Ef2). One of the recombinants has been recovered in a homozygous state (NAK) and should be suitable for V _k gene mapping studies.Abbreviations C complement - C_H constant region of the Ig heavy chain - CI cytotoxicity index - DNP dinitrophenyl - FMF flow microfluorimetry - IEF isoelectric focusing - IF immunofluorescence - Ig immunoglobulin - KLH keyhole limpet hemocyanin - V_H variable region of the Ig heavy chain - V_k variable region of the Ig kappa chain - V-region variable region     

Genetic mapping of QTLs controlling horticultural traits in diploid roses

A segregating progeny set of 96 F₁ diploid hybrids (2n=2x=14) between Blush Noisette (D10), one of the first seedlings from the original Champneys Pink Cluster, and Rosa wichurana (E15), was used to construct a genetic linkage map of the rose genome following a pseudo-testcross mapping strategy. A total of 133 markers (130 RAPD, one morphological and two microsatellites) were located on the 14 linkage groups (LGs) of the D10 and E15 maps, covering total map lengths of 388 and 260 cM, respectively. Due to the presence of common biparental markers the homology of four LGs between parental maps (D10-1/E15-1 to D10-4/E15-4) could be inferred. Four horticulturally interesting quantitative traits, flower size (FS), days to flowering (DF), leaf size (LS), and resistance to powdery mildew (PM) were analysed in the progeny in order to map quantitative trait loci (QTLs) controlling these traits. A total of 13 putative QTLs (LOD>3.0) were identified, four for FS, two for flowering time, five for LS, and two for resistance to PM. Possible homologies between QTLs detected in the D10 and E15 maps could be established between Fs1 and Fs3, Fs2 and Fs4, and Ls1 and Ls3. Screening for pairwise epistatic interactions between loci revealed additional, epistatic QTLs (EQTLs) for DF and LS that were not detected in the original QTL analysis. The genetic maps developed in this study will be useful to add new markers and locate genes for important traits in the genus providing a practical resource for marker-assisted selection programs in roses.