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PubMed1980

Recombination and chromosome segregation during the single division meiosis in SPO12-1 and SPO13-1 diploids.

This paper reports a study of chromosome segregation and recombination during sporulation of spo12-1 and spo13-1 diploid strains of S. cerevisiae. These strains undergo a single division to form asci containing two diploid or near-diploid spores. The segregation of centromere-linked markers in the two-spored (dyad) products indicates that the division is generally equational. However, in a small percentage of the spo12-1 and spo13-1 cells, it appears that a meiosis I-like division occurs. Aberrant segregation of the MAT locus on chromosome III, yielding a monosomic and a trisomic spores pair, occurs in 12% of all dyads. The segregation patterns of markers at various distances from their centromeres and several pairs of markers on the same chromosome indicate that recombination takes place in both strains at nearly standard meiotic levels.

Chromosomes↗

PubMed2026

Integrating genomic additive relationship matrices improves the efficiency in diploid banana breeding.

Partitioning of genetic variance into additive and non-additive components using the pedigree-based best linear unbiased prediction (P-BLUP) model is possible because of the family structure and replicated clones in clonally propagated crops, but this model may overestimate these components. However, the genomic best linear unbiased prediction (G-BLUP) method, which integrates the genetic relationship through molecular marker information reduces the overestimation. Alternatively, a combination of the P-BLUP and G-BLUP, sourcing to create a hybrid matrix that estimates hybrid best linear unbiased prediction (H-BLUP), is proposed. We investigated if integrating molecular information into the clonal model could improve the partitioning of the variance components leading to more accurate estimates of genetic parameters and prediction accuracy of breeding values of 14 key traits in diploid banana. In this study, we used clones of 14 full-sib families from a factorial mating design of four female and five diploid male banana (Musa acuminata) parents, generated at the International Institute of Tropical Agriculture in Arusha. The genomic-based relationship matrices were constructed using a set of 2792 filtered single-nucleotide polymorphism markers. Additive variance and heritability derived from G-BLUP and H-BLUP models reduced bias compared to the P-BLUP model. The H-BLUP estimated the highest prediction accuracies for yield-related and cycling traits, while the P-BLUP model had the highest prediction accuracy estimates for agronomic traits. The use of marker-based models enhances the accuracy of predicting breeding values, contributing to accurate estimates of genetic gain while paving a way for further genomic exploration in diploid banana breeding programs.

Journal Article↗

PubMed2003

Postzygotic diploidization of triploids as a source of unusual cases of mosaicism, chimerism and twinning.

Triploidy is one of the most frequent chromosomal errors responsible for reproduction failure. This paper encompasses, in one conceptual frame, four recent findings in reproduction biology: predominant dispermic origin of triploids, paternal centrosome inheritance, eccentric cleavage divisions of dispermic triploid zygotes and certain intricate cases of mosaicism/chimerism. It is argued that dispermic zygotes, in contrast to digynic ones, are characterized by cytogenetic phenomenon described here as postzygotic diploidization of triploids (PDT). PDT embraces three main developmental scenarios: (i) the maintenance of the triploid state accompanied by regular segregation of 2n cells and the 2n/3n mixoploid populations; (ii) immediate diploidization with elimination of an odd haploid set of chromosomes and regular appearance of 1n/2n, 2n/3n and other mixoploids and (iii) tripolar spindle formation leading to gross aneuploidy, cell death with occasional survival of 2n+1 or 2n+1+1 trisomics and uniparental disomics. According to the PDT concept, a trisomy and disomy might occur due to generalized karyotype instability of dispermic triploids. PDT may provide a natural explanation for the regular appearance of 2n homozygous androgenic moles, various 2n/3n, 2n/2n molar/twin complexes without necessitating the concept of the 'empty' oocyte fertilization. Convincing evidence for a reservoir of anuclear oocytes does not exist. Peculiar implications are expected in the case of two rounds of diploidizations or involvement of triploid cell derivatives in the twinning process. Cryptic mosaic/chimeras and unusual twins intermediate between monozygotic (MZ) and dizygotic (DZ) are expected. Thus, PDT could have an explanation for the broad spectrum of odd reproductive cytogenetic events and might provide additional alternatives and definite predictions.

Chimera↗

PubMed2000

Uptake and retranslocation of leaf-applied cadmium (109Cd) in diploid, tetraploid and hexaploid wheats.

Uptake and retranslocation of leaf-applied radiolabeled cadmium (109Cd) was studied in three diploid (Triticum monococcum, AA), four tetraploid (Triticum turgidum, BBAA) and two hexaploid (Triticum aestivum, BBAADD) wheat genotypes grown for 9 d under controlled environmental conditions in nutrient solution. Among the tetraploid wheats, two genotypes were primitive (ssp. dicoccum) and two genotypes modern wheats (ssp. durum). Radiolabelled Cd was applied by immersing the tips (3 cm) of mature leaf into a 109Cd radiolabelled solution. There was a substantial variation in the uptake and export of 109Cd among and within wheat species. On average, diploid wheats (AA) absorbed and translocated more 109Cd than other wheats. The largest variation in 109Cd uptake was found within tetraploid wheats (BBAA). Primitive tetraploid wheats (ssp. dicoccum) had a greater uptake capacity for 109Cd than modern tetraploid wheats (ssp. durum). In all wheats studied, the amount of the 109Cd exported from the treated leaf into the roots and the remainder of the shoots was poorly related to the total absorption. For example, bread wheat cultivars were more or less similar in total absorption, but differed greatly in the amount of 109Cd retranslocated. The diploid wheat genotype 'FAL-43' absorbed the lowest amount of 109Cd, but retranslocated the greatest amount of 109Cd in roots and remainder of shoots. The results indicate the existence of substantial genotypic variation in the uptake and retranslocation of leaf-applied 109Cd. This variation is discussed in terms of potential genotypic differences in binding of Cd to cell walls and the composition of phloem sap ligands possibly affecting Cd transport into sink organs.

Biological Transport↗

PubMedDate not supplied

Genetics of gamma-irradiation-induced mutations in Arabidopsis thaliana: large chromosomal deletions can be rescued through the fertilization of diploid eggs.

Despite the demonstrated value of chromosomal deletions and deficiencies as tools in plant and animal genome research, in the genetic model plant species Arabidopsis thaliana, such mutations have not been extensively studied. For example, it is not known whether large deletions in different regions of the genome can be tolerated in diploid plants that are heterozygous for such mutations. Similarly the viability or inviability of monosomics has not been examined in detail. To investigate these questions, we have used gamma-irradiated haploid wild-type pollen to pollinate diploid and tetraploid multimarker lines of Arabidopsis. Examination of M1 progenies revealed that chromosome loss mutations and large deletions were induced in the irradiated pollen. Such mutations were eliminated in diploid M1 plants due to dominant lethality but could be rescued in triploid M1 progeny. The use of irradiated pollen and tetraploid marker lines of Arabidopsis is a convenient way of generating deletions and modified chromosomes and provides a genetic tool for deletion mapping and for analysis of chromosomal regions essential for chromosome maintenance.

Arabidopsis↗

PubMed2002

Comparison of gene expression during preimplantation development between diploid and haploid mouse embryos.

Haploid development is a normal part of the life cycle for some animals, but it has not been observed in mammals. Studies in mice have revealed that the preimplantation developmental potential of haploid embryos is significantly impaired relative to diploid embryos. The reasons for the severely limited developmental potential of haploid embryos in mammals have not been discerned. To examine the effects of haploid development on gene expression, and in particular on X-linked gene expression, and to evaluate to what degree newer techniques of producing and culturing such embryos might affect developmental potential, haploid and diploid parthenogenetic and androgenetic embryos were produced and reevaluated for developmental potential, genomic integrity, and relative expression levels of specific autosomal and X-linked gene transcripts. Our data confirm the previously observed restriction in haploid developmental potential, eliminate chromosomal abnormalities as a major factor in this restriction, and reveal subtle alterations in gene expression. Haploid parthenogenones display only very subtle alterations in the expression of most mRNAs but a consistent elevation in X-linked Bex1 mRNA expression. Haploid androgenones seem to lack repression of the Pgk1 gene that is seen in diploid androgenones, but this may reflect ongoing loss of those haploid androgenones that experience X chromosome inactivation. The significance and possible explanations for these differences are discussed.

Animals↗

PubMed2004

Use of diploid male frequency data as an indicator of pollinator decline.

Pollination deficits in agricultural and natural systems are suggestive of large reductions in pollinator populations. However, actual declines are difficult to demonstrate using census data. Here, we show census data to be misleading because many abundant pollinators exhibit high levels of production of sterile diploid males usually found only in small inbred hymenopteran populations; Euglossa imperialis exhibits high levels of diploid male production induced by low effective population sizes (Ne approximately 15), despite being the most abundant orchid bee in lowland tropical forests in Panama. We caution that although some pollinators appear abundant on the basis of census data, their long-term persistence may be highly tenuous based on genetic evidence. We propose the use of diploid male frequency data as a metric for assessing the sustainability of bee populations.

Alleles↗

PubMed2006

Sexual conflict and the alternation of haploid and diploid generations.

Land plants possess a multicellular diploid stage (sporophyte) that begins development while attached to a multicellular haploid progenitor (gametophyte). Although the closest algal relatives of land plants lack a multicellular sporophyte, they do produce a zygote that grows while attached to the maternal gametophyte. The diploid offspring shares one haploid set of genes with the haploid mother that supplies it with resources and a paternal haploid complement that is not shared with the mother. Sexual conflict can arise within the diploid offspring because the offspring's maternal genome will be transmitted in its entirety to all other sexual and asexual offspring that the mother may produce, but the offspring's paternally derived genes may be absent from these other offspring. Thus, the selective forces favouring the evolution of genomic imprinting may have been present from the origin of modern land plants. In bryophytes, where gametophytes are long-lived and capable of multiple bouts of asexual and sexual reproduction, we predict strong sexual conflict over allocation to sporophytes. Female gametophytes of pteridophytes produce a single sporophyte and often lack means of asexual reproduction. Therefore, sexual conflict is predicted to be attenuated. Finally, we explore similarities among models of mate choice, offspring choice and segregation distortion.

Bryophyta↗

PubMed2025

A complete diploid human genome benchmark for personalized genomics.

Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and structurally polymorphic regions of the genome unmapped. Consequently, existing variant benchmarks, generated by the same methods, fail to assess these complex regions. To address this limitation, we present a telomere-to-telomere genome benchmark that achieves near-perfect accuracy (i.e. no detectable errors) across 99.4% of the complete, diploid HG002 genome. This benchmark adds 701.4 Mb of autosomal sequence and both sex chromosomes (216.8 Mb), totaling 15.3% of the genome that was absent from prior benchmarks. We also provide a diploid annotation of genes, transposable elements, segmental duplications, and satellite repeats, including 39,144 protein-coding genes across both haplotypes. To facilitate application of the benchmark, we developed tools for measuring the accuracy of sequencing reads, phased variant call sets, and genome assemblies against a diploid reference. Genome-wide analyses show that state-of-the-art de novo assembly methods resolve 2-7% more sequence and outperform variant calling accuracy by an order of magnitude, yielding just one error per 100 kb across 99.9% of the benchmark regions. Adoption of genome-based benchmarking is expected to accelerate the development of cost-effective methods for complete genome sequencing, expanding the reach of genomic medicine to the entire genome and enabling a new era of personalized genomics.

Journal Article↗

PubMed2005

High-resolution ROMA CGH and FISH analysis of aneuploid and diploid breast tumors.

Combining representational oligonucleotide microarray analysis (ROMA) of tumor DNA with fluorescence in situ hybridization (FISH) of individual tumor cells provides the opportunity to detect and validate a wide range of amplifications, deletions, and rearrangements directly in frozen tumor samples. We have used these combined techniques to examine 101 aneuploid and diploid breast tumors for which long-term follow-up and detailed clinical information were available. We have determined that ROMA provides accurate and sensitive detection of duplications, amplifications, and deletions and yields defined boundaries for these events with a resolution of <50 kbp in most cases. We find that diploid tumors exhibit fewer rearrangements on average than aneuploids, but rearrangements occur at the same locations in both types. Diploid tumors reflect at least three consistent patterns of rearrangement. The reproducibility and frequency of these events, especially in very early stage tumors, provide insight into the earliest chromosomal events in breast cancer. We have also identified correlations between certain sets of rearrangement events and clinically relevant parameters such as long-term survival. These correlations may enable novel prognostic indicators for breast and other cancers as more samples are analyzed.

Aneuploidy↗

PubMed2004

A distinct endogenous pararetrovirus family in Nicotiana tomentosiformis, a diploid progenitor of polyploid tobacco.

A distinct endogenous pararetrovirus (EPRV) family corresponding to a previously unknown virus has been identified in the genome of Nicotiana tomentosiformis, a diploid ancestor of allotetraploid tobacco (Nicotiana tabacum). The putative virus giving rise to N. tomentosiformis EPRVs (NtoEPRVs) is most similar to tobacco vein clearing virus, an episomal form of a normally silent EPRV family in Nicotiana glutinosa; it is also related to a putative virus giving rise to the NsEPRV family in Nicotiana sylvestris (the second diploid progenitor of tobacco) and in the N. sylvestris fraction of the tobacco genome. The copy number of NtoEPRVs is significantly higher in N. tomentosiformis than in tobacco. This suggests that after the polyploidization event, many copies were lost from the polyploid genome or were accumulated specifically in the diploid genome. By contrast, the copy number of NsEPRVs has remained constant in N. sylvestris and tobacco, indicating that changes have occurred preferentially in the NtoEPRV family during evolution of the three Nicotiana species. NtoEPRVs are often flanked by Gypsy retrotransposon-containing plant DNA. Although the mechanisms of NtoEPRV integration, accumulation, and/or elimination are unknown, these processes are possibly linked to retrotransposon activity.

Base Sequence↗

PubMed1981

Similarity of Ribulose-1,5-bisphosphate Carboxylases of Isogenic Diploid and Tetraploid Ryegrass (Lolium perenne L.) Cultivars.

Partially purified ribulose-1,5-bisphosphate carboxylase (EC 4.1.1.39) was isolated from diploid and tetraploid cultivars of ryegrass (Lolium perenne L.) using two separate methods. The apparent K(m) (CO(2)) values for the enzymes prepared by either method did not differ significantly between diploid and tetraploid when assayed by two separate techniques. The unpurified enzymes from freshly lysed (and fully functional) protoplasts of both diploid and tetraploid cultivars gave virtually identical apparent K(m) (CO(2)) values. There was no indication of large differences in affinity for CO(2) of illuminated intact protoplasts from the two cultivars.

Journal Article↗

PubMed2005

Similarity coefficients for molecular markers in studies of genetic relationships between individuals for haploid, diploid, and polyploid species.

Determining true genetic dissimilarity between individuals is an important and decisive point for clustering and analysing diversity within and among populations, because different dissimilarity indices may yield conflicting outcomes. We show that there are no acceptable universal approaches to assessing the dissimilarity between individuals with molecular markers. Different measures are relevant to dominant and codominant DNA markers depending on the ploidy of organisms. The Dice coefficient is the suitable measure for haploids with codominant markers and it can be applied directly to (0,1)-vectors representing banding profiles of individuals. None of the common measures, Dice, Jaccard, simple mismatch coefficient (or the squared Euclidean distance), is appropriate for diploids with codominant markers. By transforming multiallelic banding patterns at each locus into the corresponding homozygous or heterozygous states, a new measure of dissimilarity within locus was developed and expanded to assess dissimilarity between multilocus states of two individuals by averaging across all codominant loci tested. There is no rigorous well-founded solution in the case of dominant markers. The simple mismatch coefficient is the most suitable measure of dissimilarity between banding patterns of closely related haploid forms. For distantly related haploid individuals, the Jaccard dissimilarity is recommended. In general, no suitable method for measuring genetic dissimilarity between diploids with dominant markers can be proposed. Banding patterns of diploids with dominant markers and polyploids with codominant markers represent individuals' phenotypes rather than genotypes. All dissimilarity measures proposed and developed herein are metrics.

Genetic Markers↗

PubMed1987

Lymphotoxin-induced growth stimulation of diploid human fibroblasts in the presence and absence of gamma interferon.

In the present study we investigated the effect of lymphotoxin (LT) on the growth of human diploid fibroblasts, in the presence and absence of gamma interferon (IFN-gamma). Recombinant LT (rLT) had a growth stimulatory effect on diploid human FS-4 fibroblasts. This growth-stimulatory effect was reduced in the presence of recombinant IFN-gamma (rIFN-gamma). LT thus has a similar effect on diploid fibroblasts as tumour necrosis factor (TNF).

Cell Division↗

PubMed1983

The amino-acid sequence of a purothionin from Triticum monococcum, a diploid wheat.

Purothionins were extracted and purified from the diploid wheat Triticum monococcum. Two proteins were obtained, one of which was present in only very small amounts. The major purothionin of T. monococcum was sequenced and it had an amino acid sequence identical with that of the beta-purothionin of Triticum aestivum (hexaploid bread wheat). It is known that T. monococcum contains the wheat A genome, so the structural gene coding for the beta-purothionin must comprise a part of the A genome. There have been no observable (as amino acid replacements) changes in the DNA comprising either the beta-purothionin gene of T. aestivum or the purothionin gene of T. monococcum, since T. monococcum (or its wild equivalent, Triticum boeoticum) hybridized with the diploid wheat B genome progenitor and started the evolution from diploid to allohexaploid wheat. All of the investigated characteristics of the purothionin-like protein isolated in small amounts suggested that it was essentially identical in amino acid sequence with the T. monococcum purothionin. It may be a dimerized form of beta-purothionin.

Amino Acid Sequence↗

PubMed2005

Long-term genome diploidization in allopolyploid Nicotiana section Repandae (Solanaceae).

Here, we analyze long-term evolution in Nicotiana allopolyploid section Repandae (the closest living diploids are N. sylvestris, the maternal parent, and N. obtusifolia, the paternal parent). We compare data with other more recently formed Nicotiana allopolyploids. We investigated 35S and 5S nuclear ribosomal DNA (rDNA) chromosomal location and unit divergence. A molecular clock was applied to the Nicotiana phylogenetic tree to determine allopolyploid ages. N. tabacum and species of Repandae were c. 0.2 and 4.5 Myr old, respectively. In all Repandae species, the numbers of both 35S and 5S rDNA loci were less than the sum of those of the diploid progenitors. Trees based on 5S rDNA spacer sequences indicated units of only the paternal parent. In recent Nicotiana allopolyploids, the numbers of rDNA loci equal the sum of those of their progenitors. In the Repandae genomes, diploidization is associated with locus loss. Sequence analysis indicates that 35S and 5S units most closely resemble maternal and paternal progenitors, respectively. In Nicotiana, 4.5 Myr of allopolyploid evolution renders genomic in situ hybridization (GISH) unsuitable for the complete resolution of parental genomes.

Biological Evolution↗

PubMed1966

Triploid-diploid mosaic chicken embryo.

Cytological analysis of an underdeveloped chicken embryo at 6 days of incubation revealed a triploid-diploid mosaic condition. Of the 30 metaphases observed, 19 were triploid and 11 diploid. The triploid cells were 3A-ZZZ and diploid cells 2A-ZZ, as determined for the six largest pairs of chromnosomes.

Animals↗

PubMed1972

Hemoglobin concentration in normal diploid and intersex triploid chickens: genetic inactivation or canalization?

Of 19 adult intersex chickens examined, 17 were triploid animals with ZZW sex chromosomes. Triploid erythrocytes were about 1.5 times the size of diploid erythrocytes, and were present in amounts that were about two-thirds the number of diploid erythrocytes. Both diploid and triploid animals had similar hematocrits and hemoglobin concentrations. Triploidy is reflected in a relative increase in RNA, as well as in DNA, per erythrocyte. This, in addition to the trisomic mode of inheritance observed in several genetically distinct loci determining isoantigens, indicates that all three sets of chromosomes in the triploid animals are genetically active. Apparently, there is a homeostatic mechanism maintaining the concentration of hemoglobin for the species in spite of triploidy and its effect on erythrocyte size.

Animals↗