Journal articles on the topic 'Parental genome'
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Cattanach, B. M. "Parental origin effects in mice." Development 97, Supplement (October 1, 1986): 137–50. http://dx.doi.org/10.1242/dev.97.supplement.137.
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Nuclear transplantation experiments in mice, reviewed elsewhere in this Symposium, have clearly demonstrated that the maternal and paternal genomes from which the embryo is formed are not functionally equivalent. The paternal genome appears to be essential for the normal development of extraembryonic tissues and the maternal genome for some stage of embryonic development. These findings provide some explanation for the observations that in mammals diploid parthenotes possessing two maternal genomes fail to survive (Markert, 1982) and that, in man, embryos with two paternal chromosome sets are inviable, forming hydatidiform moles (Kajii & Ohama, 1977). It has been proposed that a specific ‘imprinting’ of the paternal genomes occurs during gametogenesis so that the presence of both a female and male pronculeus is essential in an egg for full-term development (Barton, Surani & Norris, 1984; McGrath & Solter, 1984a; Surani, Barton & Norris, 1984).
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Bento, Miguel, J. Perry Gustafson, Wanda Viegas, and Manuela Silva. "Size matters in Triticeae polyploids: larger genomes have higher remodeling." Genome 54, no. 3 (March 2011): 175–83. http://dx.doi.org/10.1139/g10-107.
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Polyploidization is one of the major driving forces in plant evolution and is extremely relevant to speciation and diversity creation. Polyploidization leads to a myriad of genetic and epigenetic alterations that ultimately generate plants and species with increased genome plasticity. Polyploids are the result of the fusion of two or more genomes into the same nucleus and can be classified as allopolyploids (different genomes) or autopolyploids (same genome). Triticeae synthetic allopolyploid species are excellent models to study polyploids evolution, particularly the wheat–rye hybrid triticale, which includes various ploidy levels and genome combinations. In this review, we reanalyze data concerning genomic analysis of octoploid and hexaploid triticale and different synthetic wheat hybrids, in comparison with other polyploid species. This analysis reveals high levels of genomic restructuring events in triticale and wheat hybrids, namely major parental band disappearance and the appearance of novel bands. Furthermore, the data shows that restructuring depends on parental genomes, ploidy level, and sequence type (repetitive, low copy, and (or) coding); is markedly different after wide hybridization or genome doubling; and affects preferentially the larger parental genome. The shared role of genetic and epigenetic modifications in parental genome size homogenization, diploidization establishment, and stabilization of polyploid species is discussed.
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Pustovalova, Eleonora, Lukaš Choleva, Dmytro Shabanov, and Dmitrij Dedukh. "The high diversity of gametogenic pathways in amphispermic water frog hybrids from Eastern Ukraine." PeerJ 10 (August 23, 2022): e13957. http://dx.doi.org/10.7717/peerj.13957.
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Interspecific hybridization can disrupt canonical gametogenic pathways, leading to the emergence of clonal and hemiclonal organisms. Such gametogenic alterations usually include genome endoreplication and/or premeiotic elimination of one of the parental genomes. The hybrid frog Pelophylax esculentus exploits genome endoreplication and genome elimination to produce haploid gametes with chromosomes of only one parental species. To reproduce, hybrids coexist with one of the parental species and form specific population systems. Here, we investigated the mechanism of spermatogenesis in diploid P. esculentus from sympatric populations of P. ridibundus using fluorescent in situ hybridization. We found that the genome composition and ploidy of germ cells, meiotic cells, and spermatids vary among P. esculentus individuals. The spermatogenic patterns observed in various hybrid males suggest the occurrence of at least six diverse germ cell populations, each with a specific premeiotic genome elimination and endoreplication pathway. Besides co-occurring aberrant cells detected during meiosis and gamete aneuploidy, alterations in genome duplication and endoreplication have led to either haploid or diploid sperm production. Diploid P. esculentus males from mixed populations of P. ridibundus rarely follow classical hybridogenesis. Instead, hybrid males simultaneously produce gametes with different genome compositions and ploidy levels. The persistence of the studied mixed populations highly relies on gametes containing a genome of the other parental species, P. lessonae.
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Kotseruba, Violetta, Dorota Gernand, Armin Meister, and Andreas Houben. "Uniparental loss of ribosomal DNA in the allotetraploid grass Zingeria trichopoda (2n = 8)." Genome 46, no. 1 (February 1, 2003): 156–63. http://dx.doi.org/10.1139/g02-104.
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Analysis of the grass Zingeria trichopoda (2n = 8, 2C = 5.3 pg) revealed a dynamic evolution with the following characteristics. (i) Genomic in situ hybridization (GISH) demonstrates that Z. trichopoda evolved from an interspecific hybrid involving a species like contemporary Zingeria biebersteiniana (2n = 4) and a second species with a similar low number of chromosomes. The nucleus of Z. trichopoda is spatially organized at the genome level and the two parental genomes occupy distinct and separate domains of lateral arrangements. (ii) The copy number of the Z. biebersteiniana specific pericentromeric tandem repeat family Zbcen1 is drastically reduced in Z. trichopoda. (iii) GISH in combination with labeled rDNA sequences simultaneously discriminated the two parental genomes and the corresponding 5S and 45S rDNA sites. Hence, following allopolyploidization of Z. trichopoda the Z. biebersteiniana like parental chromosomes probably underwent drastic loss of 45S rDNA. This could have arisen either through the loss ofZ. biebersteiniana derived 45S rDNA or through Z. trichopoda genome-wide homogenization of Z. biebersteiniana type 45S rDNA and subsequent elimination of 45S rDNA loci from Z. biebersteiniana derived chromosomes. Finally, 5S rDNA loci are present in both subgenomes of Z. trichopoda and the chromosomal position of these loci is similar for both Z. biebersteiniana and the Z. biebersteiniana like parental genome of Z. trichopoda.Key words: genome evolution, polyploidy, ribosomal DNA, Poaceae.
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Dedukh, Dmitrij, Sergey Riumin, Krzysztof Kolenda, Magdalena Chmielewska, Beata Rozenblut-Kościsty, Mikołaj Kaźmierczak, Maria Ogielska, and Alla Krasikova. "Maintenance of pure hybridogenetic water frog populations: Genotypic variability in progeny of diploid and triploid parents." PLOS ONE 17, no. 7 (July 6, 2022): e0268574. http://dx.doi.org/10.1371/journal.pone.0268574.
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An intriguing outcome of hybridisation is the emergence of clonally and hemiclonally reproducing hybrids, that can sustain, reproduce, and lead to the emergence of polyploid forms. However, the maintenance of diploid and polyploid hybrid complexes in natural populations remains unresolved. We selected water frogs from the Pelophylax esculentus complex to study how diploid and triploid hybrids, which reproduce hemiclonally via hybridogenesis, are maintained in natural populations. During gametogenesis in diploid hybrids, one of the parental genomes is eliminated, and the remaining genome is endoreplicated. In triploid hybrids, the single-copy genome is typically eliminated, while genome endoreplication does not occur. To investigate how diploid and triploid hybrid frogs reproduce in populations without parental species, we crossed these hybrid animals from two separate pure hybrid populations located in Poland. Using cytogenetic analysis of tadpoles that emerged from the crosses, we established which gametes were produced by parental hybrids. The majority of hybrid females and hybrid males produced one type of gamete with the P. ridibundus genome. However, in both studied populations, approximately half of the diploid and triploid hybrids simultaneously produced gametes with different genome compositions and ploidy levels, specifically, the P. ridibundus and P. lessonae genomes, as well as diploid gametes with genomes of both parental species. Triploid hybrid males and females mostly produced haploid gametes with the P. lessonae genome; however, gametes with the P. ridibundus genome have also been observed. These results suggest that not all hybrids follow the classical hybridogenetic reproduction program and reveal a significant level of alterations in the gametogenesis pathways. In addition, we found a variable survival rate of particular progeny genotypes when we crossed hybrid females with different males suggesting the important role of postzygotic barriers on the maintenance of pure hybrid systems. We suggest that the observed variability in produced gametes and the different survival rate of the progeny with certain genotypes is crucial for the existence of pure hybrid systems.
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Adams, S., R. Vinkenoog, M. Spielman, H. G. Dickinson, and R. J. Scott. "Parent-of-origin effects on seed development in Arabidopsis thaliana require DNA methylation." Development 127, no. 11 (June 1, 2000): 2493–502. http://dx.doi.org/10.1242/dev.127.11.2493.
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Some genes in mammals and flowering plants are subject to parental imprinting, a process by which differential epigenetic marks are imposed on male and female gametes so that one set of alleles is silenced on chromosomes contributed by the mother while another is silenced on paternal chromosomes. Therefore, each genome contributes a different set of active alleles to the offspring, which develop abnormally if the parental genome balance is disturbed. In Arabidopsis, seeds inheriting extra maternal genomes show distinctive phenotypes such as low weight and inhibition of mitosis in the endosperm, while extra paternal genomes result in reciprocal phenotypes such as high weight and endosperm overproliferation. DNA methylation is known to be an essential component of the parental imprinting mechanism in mammals, but there is less evidence for this in plants. For the present study, seed development was examined in crosses using a transgenic Arabidopsis line with reduced DNA methylation. Crosses between hypomethylated and wild-type diploid plants produced similar seed phenotypes to crosses between plants with normal methylation but different ploidies. This is consistent with a model in which hypomethylation of one parental genome prevents silencing of alleles that would normally be active only when inherited from the other parent - thus phenocopying the effects of extra genomes. These results suggest an important role for methylation in parent-of-origin effects, and by inference parental imprinting, in plants. The phenotype of biparentally hypomethylated seeds is less extreme than the reciprocal phenotypes of uniparentally hypomethylated seeds. The observation that development is less severely affected if gametes of both sexes (rather than just one) are ‘neutralized’ with respect to parent-of-origin effects supports the hypothesis that parental imprinting is not necessary to regulate development.
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Lukhtanov, Vladimir A., Nazar A. Shapoval, Boris A. Anokhin, Alsu F. Saifitdinova, and Valentina G. Kuznetsova. "Homoploid hybrid speciation and genome evolution via chromosome sorting." Proceedings of the Royal Society B: Biological Sciences 282, no. 1807 (May 22, 2015): 20150157. http://dx.doi.org/10.1098/rspb.2015.0157.
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Genomes of numerous diploid plant and animal species possess traces of interspecific crosses, and many researches consider them as support for homoploid hybrid speciation (HHS), a process by which a new reproductively isolated species arises through hybridization and combination of parts of the parental genomes, but without an increase in ploidy. However, convincing evidence for a creative role of hybridization in the origin of reproductive isolation between hybrid and parental forms is extremely limited. Here, through studying Agrodiaetus butterflies, we provide proof of a previously unknown mode of HHS based on the formation of post-zygotic reproductive isolation via hybridization of chromosomally divergent parental species and subsequent fixation of a novel combination of chromosome fusions/fissions in hybrid descendants. We show that meiotic segregation, operating in the hybrid lineage, resulted in the formation of a new diploid genome, drastically rearranged in terms of chromosome number. We also demonstrate that during the heterozygous stage of the hybrid species formation, recombination was limited between rearranged chromosomes of different parental origin, representing evidence that the reproductive isolation was a direct consequence of hybridization.
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Mandáková, Terezie, Judita Zozomová-Lihová, Hiroshi Kudoh, Yunpeng Zhao, Martin A. Lysak, and Karol Marhold. "The story of promiscuous crucifers: origin and genome evolution of an invasive species, Cardamine occulta (Brassicaceae), and its relatives." Annals of Botany 124, no. 2 (March 14, 2019): 209–20. http://dx.doi.org/10.1093/aob/mcz019.
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Abstract Background and Aims Cardamine occulta (Brassicaceae) is an octoploid weedy species (2n = 8x = 64) originated in Eastern Asia. It has been introduced to other continents including Europe and considered to be an invasive species. Despite its wide distribution, the polyploid origin of C. occulta remained unexplored. The feasibility of comparative chromosome painting (CCP) in crucifers allowed us to elucidate the origin and genome evolution in Cardamine species. We aimed to investigate the genome structure of C. occulta in comparison with its tetraploid (2n = 4x = 32, C. kokaiensis and C. scutata) and octoploid (2n = 8x = 64, C. dentipetala) relatives. Methods Genomic in situ hybridization (GISH) and large-scale CCP were applied to uncover the parental genomes and chromosome composition of the investigated Cardamine species. Key Results All investigated species descended from a common ancestral Cardamine genome (n = 8), structurally resembling the Ancestral Crucifer Karyotype (n = 8), but differentiated by a translocation between chromosomes AK6 and AK8. Allotetraploid C. scutata originated by hybridization between two diploid species, C. parviflora and C. amara (2n = 2x = 16). By contrast, C. kokaiensis has an autotetraploid origin from a parental genome related to C. parviflora. Interestingly, octoploid C. occulta probably originated through hybridization between the tetraploids C. scutata and C. kokaiensis. The octoploid genome of C. dentipetala probably originated from C. scutata via autopolyploidization. Except for five species-specific centromere repositionings and one pericentric inversion post-dating the polyploidization events, the parental subgenomes remained stable in the tetra- and octoploids. Conclusions Comparative genome structure, origin and evolutionary history was reconstructed in C. occulta and related species. For the first time, whole-genome cytogenomic maps were established for octoploid plants. Post-polyploid evolution in Asian Cardamine polyploids has not been associated with descending dysploidy and intergenomic rearrangements. The combination of different parental (sub)genomes adapted to distinct habitats provides an evolutionary advantage to newly formed polyploids by occupying new ecological niches.
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Reik, Wolf, and Jörn Walter. "Genomic imprinting: parental influence on the genome." Nature Reviews Genetics 2, no. 1 (January 2001): 21–32. http://dx.doi.org/10.1038/35047554.
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Ma, Xue-Feng, and J. Perry Gustafson. "Timing and rate of genome variation in triticale following allopolyploidization." Genome 49, no. 8 (August 1, 2006): 950–58. http://dx.doi.org/10.1139/g06-078.
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The timing and rate of genomic variation induced by allopolyploidization in the intergeneric wheat-rye (Triticum spp. – Secale cereale L.) hybrid triticale (× Triticosecale Wittmack) was studied using amplified fragment length polymorphism (AFLP) analyses with 2 sets of primers, EcoRI–MseI (E–M) and PstI–MseI (P–M), which primarily amplify repetitive and low-copy sequences, respectively. The results showed that allopolyploidization induced genome sequence variation in triticale and that a great degree of the genome variation occurred immediately following wide hybridization. Specifically, about 46.3% and 36.2% of the wheat parental band loss and 74.5% and 68.4% of the rye parental band loss occurred in the F1 hybrids (before chromosome doubling) for E–M and P–M primers, respectively. The sequence variation events that followed chromosome doubling consisted of continuous modifications that occurred at a very small rate compared with the rate of variation before chromosome doubling. However, the rate of sequence variation involving the rye parental genome was much higher in the first 5 generations following chromosome doubling than in any subsequent generation. Surprisingly, the highest rate of rye genomic variation occurring after chromosome doubling was in C3 or later, but not in C1. The data suggested that the cytoplasm and the degree of the relationship between the parental genomes were the key factors in determining the direction, amount, timing, and rate of genomic sequence variation occurring during intergeneric allopolyploidization.Key words: genome evolution, sequence variation, allopolyploid, triticale, AFLP.
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Jang, Tae-Soo, and Hanna Weiss-Schneeweiss. "Formamide-Free Genomic in situ Hybridization Allows Unambiguous Discrimination of Highly Similar Parental Genomes in Diploid Hybrids and Allopolyploids." Cytogenetic and Genome Research 146, no. 4 (2015): 325–31. http://dx.doi.org/10.1159/000441210.
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Polyploidy and hybridization play an important role in plant diversification and speciation. The application of genomic in situ hybridization (GISH) allows the identification of parental genomes in hybrids, thus elucidating their origins and allowing for analysis of their genomic evolution. The performance of GISH depends on the similarity of the parental genomes and on the age of hybrids. Here, we present the formamide-free GISH (ff-GISH) protocol applied to diploid and polyploid hybrids of monocots (Prospero, Hyacinthaceae) and dicots (Melampodium, Asteraceae) differing in similarity of the parental genomes and in chromosome and genome sizes. The efficiency of the new protocol is compared to the standard GISH protocol. As a result, ff-GISH allowed efficient labeling and discrimination of the parental chromosome sets in diploid and allopolyploid hybrids in Prospero autumnale species complex. In contrast, the standard GISH protocol failed to differentiate the parental genomes due to high levels of similar repetitive DNA. Likewise, an unambiguous identification of parental genomes in allotetraploid Melampodium nayaritense (Asteraceae) was possible after ff-GISH, whereas the standard GISH hybridization performance was suboptimal. The modified method is simple and non-toxic and allows the discrimination of very similar parental genomes in hybrids. This method lends itself to modifications and improvements and can also be used for FISH.
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Coustau, Christine, François Renaud, Claude Maillard, Nicole Pasteur, and Bernard Delay. "Differential susceptibility to a trematode parasite among genotypes of the Mytilus edulis/galloprovincialis complex." Genetical Research 57, no. 3 (June 1991): 207–12. http://dx.doi.org/10.1017/s0016672300029359.
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SummaryWe show that parasitism by the trematode Prosorhynchus squamatus in parental and introgressed Mytilus edulis/galloprovincialis (Bivalvia) mussels occurs in individuals with a predominantly M. edulis genome. This result suggests that the restricted specificity of P. squamatus is dependent on genetic factor(s) present in M. edulis. Because of its strong pathogenic effects (i.e. total castration and possible death), this parasite may be a source of intense selection against M. edulis genomes when they are present in a site. As a consequence, it may favour the geographic extension of the M. galloprovincialis genome. Previous studies have indicated that, in hybrid zones, recombinant genotypes are more susceptible to parasitic infections than either parental genotype. We demonstrate that this is not the case for the M. edulis/M. galloprovincialis system, and that the parental genotype alone determines susceptibility.
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Miura, Ikuo, Vladimir Vershinin, Svetlana Vershinina, Andrei Lebedinskii, Alexander Trofimov, Ivan Sitnikov, and Michihiko Ito. "Hybridogenesis in the Water Frogs from Western Russian Territory: Intrapopulation Variation in Genome Elimination." Genes 12, no. 2 (February 8, 2021): 244. http://dx.doi.org/10.3390/genes12020244.
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Hybridogenesis in an interspecific hybrid frog is a coupling mechanism in the gametogenic cell line that eliminates the genome of one parental species with endoduplication of the remaining genome of the other parental species. It has been intensively investigated in the edible frog Pelophylax kl. esculentus (RL), a natural hybrid between the marsh frog P. ridibundus (RR) and the pool frog P. lessonae (LL). However, the genetic mechanisms involved remain unclear. Here, we investigated the water frogs in the western Russian territory. In three of the four populations, we genetically identified 16 RL frogs living sympatrically with the parental LL species, or with both parental species. In addition, two populations contained genome introgression with another species, P. bedriagae (BB) (a close relative of RR). In the gonads of 13 RL frogs, the L genome was eliminated, producing gametes of R (or R combined with the B genome). In sharp contrast, one RL male eliminated the L or R genome, producing both R and L sperm. We detected a variation in genome elimination within a population. Based on the genetic backgrounds of RL frogs, we hypothesize that the introgression of the B genome resulted in the change in choosing a genome to be eliminated.
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Hardie, David C., and Paul DN Hebert. "Genome-size evolution in fishes." Canadian Journal of Fisheries and Aquatic Sciences 61, no. 9 (September 1, 2004): 1636–46. http://dx.doi.org/10.1139/f04-106.
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Fishes possess both the largest and smallest vertebrate genomes, but the evolutionary significance of this variation is unresolved. The present study provides new genome-size estimates for more than 500 species, with a focus on the cartilaginous and ray-finned fishes. These results confirm that genomes are smaller in ray-finned than in cartilaginous fishes, with the exception of polyploids, which account for much genome-size variation in both groups. Genome-size diversity in ray-finned fishes is not related to metabolic rate, but is positively correlated with egg diameter, suggesting linkages to the evolution of parental care. Freshwater and other eurybiotic fishes have larger genomes than their marine and stenobiotic counterparts. Although genome-size diversity among the fishes appears less clearly linked to any single biological correlate than in the birds, mammals, or amphibians, this study highlights several particularly variable taxa that are suitable for further study.
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Koroma, Alie Patrick, Raymond Jones, and Pawel Michalak. "Snapshot of DNA methylation changes associated with hybridization in Xenopus." Physiological Genomics 43, no. 22 (November 2011): 1276–80. http://dx.doi.org/10.1152/physiolgenomics.00110.2011.
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Hybridization often results in dramatic genome reconfigurations including epigenetic changes that control gene expression. Here we survey methylation patterns of interspecific Xenopus F1 hybrids relative to parental species X. laevis and X. muelleri, using methyl-sensitive amplification polymorphisms (MSAPs). Out of a total of 546 MSAP markers, 364 were effective in elucidating the difference in methylation patterns between the hybrids and the parental species. Principal coordinate analysis of methylated fragments revealed four distinct clusters with the two parental species separate from hybrid males and females. On average, hybrids were characterized by a higher proportion (70.6%) of methylated fragments compared with the parental species (64.5%), and this difference was consistent with previously observed disruptions of hybrid transcriptomes. The proportion of methylated fragments did not correlate with variation in genome size, as measured with flow cytometry. The levels of methylation in sterile hybrid males (73.8%) were higher than in fertile hybrid females (68.6%), but this difference was not statistically significant. A total of 76 methylated fragments (20.9%) were hybrid-unique, presumably originating from methylation alterations in hybrid genomes.
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Renard, J. P., P. Baldacci, V. Richoux-Duranthon, S. Pournin, and C. Babinet. "A maternal factor affecting mouse blastocyst formation." Development 120, no. 4 (April 1, 1994): 797–802. http://dx.doi.org/10.1242/dev.120.4.797.
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Normal development of the mouse embryo requires the presence of both paternal and maternal genomes. This is due to functional differences having their origin in a differential imprinting of parental genomes. Furthermore, several lines of evidence show that the very early interactions between egg cytoplasm and pronuclei may influence the programming of the embryonic genome and modulate the functional inequality of the parental contribution even during preimplantation stages. In this paper, we show that a factor present in ovulated oocytes of the mouse mutant strain DDK and therefore of maternal origin prevents the formation of the blastocyst. This factor, which acts via an interaction with the paternal genome, is present in oocytes as an RNA and is still active in preimplantation embryos. This is the first direct evidence of such a maternal control in the mouse.
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Tartakoff, Alan Michael, and Purnima Jaiswal. "Nuclear Fusion and Genome Encounter during Yeast Zygote Formation." Molecular Biology of the Cell 20, no. 12 (June 15, 2009): 2932–42. http://dx.doi.org/10.1091/mbc.e08-12-1193.
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When haploid cells of Saccharomyces cerevisiae are crossed, parental nuclei congress and fuse with each other. To investigate underlying mechanisms, we have developed assays that evaluate the impact of drugs and mutations. Nuclear congression is inhibited by drugs that perturb the actin and tubulin cytoskeletons. Nuclear envelope (NE) fusion consists of at least five steps in which preliminary modifications are followed by controlled flux of first outer and then inner membrane proteins, all before visible dilation of the waist of the nucleus or coalescence of the parental spindle pole bodies. Flux of nuclear pore complexes occurs after dilation. Karyogamy requires both the Sec18p/NSF ATPase and ER/NE luminal homeostasis. After fusion, chromosome tethering keeps tagged parental genomes separate from each other. The process of NE fusion and evidence of genome independence in yeast provide a prototype for understanding related events in higher eukaryotes.
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RAGGHIANTI, MATILDE, STEFANIA BUCCI, SILVIA MARRACCI, CLAUDIO CASOLA, GIORGIO MANCINO, HANSJÜRG HOTZ, GASTON-DENIS GUEX, JÖRG PLÖTNER, and THOMAS UZZELL. "Gametogenesis of intergroup hybrids of hemiclonal frogs." Genetical Research 89, no. 1 (February 2007): 39–45. http://dx.doi.org/10.1017/s0016672307008610.
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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.
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Buteler, Mario I., Don R. LaBonte, and Robert L. Jarret. "Sweetpotato Genome Fingerprinting and Parental Analysis Using Microsatellites." HortScience 31, no. 4 (August 1996): 612a—612. http://dx.doi.org/10.21273/hortsci.31.4.612a.
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Microsatellites or simple sequence repeats (SSRs) were used to characterize 20 sweetpotato genotypes and to assign paternity for offspring from crosses among them. The PCR amplifications were performed with each of the sweetpotato genotypes and primers flanking a SSR loci previously characterized with the varieties Beauregard and Excel and 20 offspring from a cross among them. The PCR reaction products were separated in nondenaturing 12% acrylamide gels run at 25 V·cm–1 for 5 hours, and DNA fragments were visualized with silver staining. Gels were scanned on a flat bed scanner and analyzed using the Pro-RFLP software package. Three primer pairs were sufficient to produce an allelic profile capable of differentiating the 20 genotypes from each other. More than seven alleles/loci were found using each of the three primer pairs assayed. Occasionally primers produced allelic products clearly localized in two or three regions of the gel. These multiple loci segregated independently in a diploid fashion. This evidence suggests that there is not total homology among the three sweetpotato genomes.
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Jullien, Pauline E., and Frédéric Berger. "Parental Genome Dosage Imbalance Deregulates Imprinting in Arabidopsis." PLoS Genetics 6, no. 3 (March 19, 2010): e1000885. http://dx.doi.org/10.1371/journal.pgen.1000885.
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Martinez, German, Philip Wolff, Zhenxing Wang, Jordi Moreno-Romero, Juan Santos-González, Lei Liu Conze, Christopher DeFraia, R. Keith Slotkin, and Claudia Köhler. "Paternal easiRNAs regulate parental genome dosage in Arabidopsis." Nature Genetics 50, no. 2 (January 15, 2018): 193–98. http://dx.doi.org/10.1038/s41588-017-0033-4.
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Nishijima, Ryo, Kentaro Yoshida, Kohei Sakaguchi, Shin-ichi Yoshimura, Kazuhiro Sato, and Shigeo Takumi. "RNA Sequencing-Based Bulked Segregant Analysis Facilitates Efficient D-genome Marker Development for a Specific Chromosomal Region of Synthetic Hexaploid Wheat." International Journal of Molecular Sciences 19, no. 12 (November 26, 2018): 3749. http://dx.doi.org/10.3390/ijms19123749.
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Common wheat originated from interspecific hybridization between cultivated tetraploid wheat and its wild diploid relative Aegilops tauschii followed by amphidiploidization. This evolutionary process can be reproduced artificially, resulting in synthetic hexaploid wheat lines. Here we performed RNA sequencing (RNA-seq)-based bulked segregant analysis (BSA) using a bi-parental mapping population of two synthetic hexaploid wheat lines that shared identical A and B genomes but included with D-genomes of distinct origins. This analysis permitted identification of D-genome-specific polymorphisms around the Net2 gene, a causative locus to hybrid necrosis. The resulting single nucleotide polymorphisms (SNPs) were classified into homoeologous polymorphisms and D-genome allelic variations, based on the RNA-seq results of a parental tetraploid and two Ae. tauschii accessions. The difference in allele frequency at the D-genome-specific SNP sites between the contrasting bulks (ΔSNP-index) was higher on the target chromosome than on the other chromosomes. Several SNPs with the highest ΔSNP-indices were converted into molecular markers and assigned to the Net2 chromosomal region. These results indicated that RNA-seq-based BSA can be applied efficiently to a synthetic hexaploid wheat population to permit molecular marker development in a specific chromosomal region of the D genome.
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Ma, Xue-Feng, Peng Fang, and J. Perry Gustafson. "Polyploidization-induced genome variation in triticale." Genome 47, no. 5 (October 1, 2004): 839–48. http://dx.doi.org/10.1139/g04-051.
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Polyploidization-induced genome variation in triticale (× Triticosecale Wittmack) was investigated using both AFLP and RFLP analyses. The AFLP analyses were implemented with both EcoRI–MseI (E–M) and PstI–MseI (P–M) primer combinations, which, because of their relative differences in sensitivity to cytosine methylation, primarily amplify repetitive and low-copy sequences, respectively. The results showed that the genomic sequences in triticale involved a great degree of variation including both repetitive and low-copy sequences. The frequency of losing parental bands was much higher than the frequency of gaining novel bands, suggesting that sequence elimination might be a major force causing genome variation in triticale. In all cases, variation in E–M primer-amplified parental bands was more frequent in triticale than that using P–M primers, suggesting that repetitive sequences were more involved in variation than low-copy sequences. The data also showed that the wheat (Triticum spp.) genomes were relatively highly conserved in triticales, especially in octoploid triticales, whereas the rye (Secale cereale L.) genome consistently demonstrated a very high level of genomic sequence variation (68%–72%) regardless of the triticale ploidy levels or primers used. In addition, when a parental AFLP band was present in both wheat and rye, the tendency of the AFLP band to be present in triticale was much higher than when it was present in only one of the progenitors. Furthermore, the cDNA-probed RFLP analyses showed that over 97% of the wheat coding sequences were maintained in triticale, whereas only about 61.6% of the rye coding sequences were maintained, suggesting that the rye genome variation in triticale also involved a high degree of rye coding sequence changes. The data also suggested that concerted evolution might occur in the genomic sequences of triticale. In addition, the observed genome variation in wheat–rye addition lines was similar to that in triticale, suggesting that wheat–rye addition lines can be used to thoroughly study the genome evolution of polyploid triticale.Key words: wheat, rye, polyploid, genome evolution, sequence elimination.
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Kopecký, David, Denisa Šimoníková, Marc Ghesquière, and Jaroslav Doležel. "Stability of Genome Composition and Recombination between Homoeologous Chromosomes in Festulolium (Festuca × Lolium) Cultivars." Cytogenetic and Genome Research 151, no. 2 (2017): 106–14. http://dx.doi.org/10.1159/000458746.
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Festulolium are hybrids between fescue (Festuca) and ryegrass (Lolium) species and combine high seed yield of ryegrasses with abiotic stress tolerance of fescues. Chromosomes of Festuca and Lolium present in Festulolium freely pair and recombine, which results in highly variable progeny where every single plant has a unique chromosome constitution. Thus, the stability of the genomic composition in Festulolium cultivars is an important issue. In this work, we used in situ hybridization to examine the genomic composition (understood as the proportion of parental genomes present) over 3 consecutive generations of propagation via outcrossing (the first one being the generation used for cultivar registration) of 3 Festulolium cultivars. Our analysis revealed that the genome composition largely differs among the plants from individual cultivars but appears to be relatively stable over the generations. A gradual shift in the genome composition towards Lolium observed in the early generations of hybrids appears to reach a plateau where the proportions of parental genomes become stabilized. Nevertheless, the proportion remains unbalanced to a certain extent (always in favor of the Lolium genome) in each cultivar. Our observations indicate a possibility to modulate genomic composition in hybrids by breeders' selection without a compromise on stability.
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Heslop-Harrison, J. S. "Gene expression and parental dominance in hybrid plants." Development 108, Supplement (April 1, 1990): 21–28. http://dx.doi.org/10.1242/dev.108.supplement.21.
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Genomic imprinting, where the genes from one parent have different expression properties to those of the other parent, occurs in plants. It has potentially significant consequences because of the importance of hybrids in plant evolution and plant breeding, and provides a mechanism that can hide genetic variation for many generations. The study of nuclear organization shows that chromosome and genome position relates to imprinting in F1 hybrids, with peripheral genomes tending to be expressed preferentially. In some inbred, polyploid hybrids, such as Triticale (a wheat × rye hybrid), treatment with the demethylation agent azacytidine releases hidden variation, which was perhaps lost because of imprinting phenomena.
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Camillo, Julceia, André P. Leão, Alexandre A. Alves, Eduardo F. Formighieri, Ana L. s. Azevedo, Juliana D. Nunes, Guy de Capdeville, Jean K. A. de Mattos, and Manoel T. Souza. "Reassessment of the Genome Size in Elaeis guineensis and Elaeis oleifera, and Its Interspecific Hybrid." Genomics Insights 7 (January 2014): GEI.S15522. http://dx.doi.org/10.4137/gei.s15522.
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Aiming at generating a comprehensive genomic database on Elaeis spp., our group is leading several R&D initiatives with Elaeis guineensis (African oil palm) and Elaeis oleifera (American oil palm), including the whole-genome sequencing of the last. Genome size estimates currently available for this genus are controversial, as they indicate that American oil palm genome is about half the size of the African oil palm genome and that the genome of the interspecific hybrid is bigger than both the parental species genomes. We estimated the genome size of three E. guineensis genotypes, five E. oleifera genotypes, and two interspecific hybrids genotypes. On average, the genome size of E. guineensis is 4.32 ± 0.173 pg, while that of E. oleifera is 4.43 ± 0.018 pg. This indicates that both genomes are similar in size, even though E. oleifera is in fact bigger. As expected, the hybrid genome size is around the average of the two genomes, 4.40 ± 0.016 pg. Additionally, we demonstrate that both species present around 38% of GC content. As our results contradict the currently available data on Elaeis spp. genome sizes, we propose that the actual genome size of the Elaeis species is around 4 pg and that American oil palm possesses a larger genome than African oil palm.
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Pedersen, C. B., D. Demontis, M. S. Pedersen, E. Agerbo, P. B. Mortensen, A. D. Børglum, D. M. Hougaard, M. V. Hollegaard, O. Mors, and E. Cantor-Graae. "Risk of schizophrenia in relation to parental origin and genome-wide divergence." Psychological Medicine 42, no. 7 (November 9, 2011): 1515–21. http://dx.doi.org/10.1017/s0033291711002376.
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BackgroundSecond-generation immigrants have an increased risk of schizophrenia, a finding that still lacks a satisfactory explanation. Various operational definitions of second-generation immigrants have been used, including foreign parental country of birth. However, with increasing global migration, it is not clear that parental country of birth necessarily is informative with regard to ethnicity. We compare two independently collected measures of parental foreign ethnicity, parental foreign country of birth versus genetic divergence, based on genome-wide genotypic data, to access which measure most efficiently captures the increased risk of schizophrenia among second-generation immigrants residing in Denmark.MethodA case–control study covering all children born in Denmark since 1981 included 892 cases of schizophrenia and 883 matched controls. Genetic divergence was assessed using principal component analyses of the genotypic data. Independently, parental foreign country of birth was assessed using information recorded prospectively in the Danish Civil Registration System. We compared incidence rate ratios of schizophrenia associated with these two independently collected measures of parental foreign ethnicity.ResultsPeople with foreign-born parents had a significantly increased risk of schizophrenia [relative risk (RR) 1.94 (95% confidence intervals (CI) 1.41–2.65)]. Genetically divergent persons also had a significant increased risk [RR 2.43 (95% CI 1.55–3.82)]. Mutual adjustment of parental foreign country of birth and genetic divergence showed no difference between these measures with regard to their potential impact on the results.ConclusionsIn terms of RR of schizophrenia, genetic divergence and parental foreign country of birth are interchangeable entities, and both entities have validity with regard to identifying second-generation immigrants.
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Cui, Litao, Tai Chen, Xin Zhao, Shunli Wang, Xiuxia Ren, Jingqi Xue, and Xiuxin Zhang. "Karyotype Analysis, Genomic and Fluorescence In Situ Hybridization (GISH and FISH) Reveal the Ploidy and Parental Origin of Chromosomes in Paeonia Itoh Hybrids." International Journal of Molecular Sciences 23, no. 19 (September 27, 2022): 11406. http://dx.doi.org/10.3390/ijms231911406.
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Itoh hybrids are intersectional hybrids in Paeonia L. with sect. Moutan and sect. Paeonia as paternal and maternal parents, respectively. Therefore, these hybrids have herbaceous stems with improved ornamental value introduced by the paternal parent. Although both of their parents are diploids, Itoh hybrids are triploids. Moreover, the parental origin of their chromosomes has not been extensively studied. This study systematically analyzed the genome size, ploidy, and karyotype of Itoh hybrids and compared them with their parental taxa. Although the monoploid genome size of Itoh hybrids was different, it was not significantly different from that of the parents. However, the size of varieties in the two parental taxa was significantly different from the wild species, probably due to genome rearrangements caused by artificial selection. Further karyotype analysis, correlation analysis, and hierarchical clustering could not identify the parental origin of chromosomes in Itoh hybrids. Verification through genomic and fluorescence in situ hybridization (GISH and FISH) suggested that for the three sets of chromosomes in Itoh hybrids, two were from the paternal parent, and one was from the maternal parent. One of the first two sets was from wild species, and the other from a cultivated variety. GISH could not label the chromosomes of cultivated peonies from the sect. Moutan, probably due to the huge and complex genomes compared with the wild species. Meanwhile, 5S rDNA-based FISH was first applied in Paeonia, which may be used for ploidy assessment. This work may give insights into the utilization of Itoh hybrid resources.
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Takasaka, Tomokazu, Nobuyuki Goya, Hideki Ishida, Kazunari Tanabe, Hiroshi Toma, Tomoaki Fujioka, So Omori, et al. "Stability of the BK polyomavirus genome in renal-transplant patients without nephropathy." Journal of General Virology 87, no. 2 (February 1, 2006): 303–6. http://dx.doi.org/10.1099/vir.0.81368-0.
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To clarify the stability of the BK polyomavirus (BKPyV) genome in renal transplant (RT) recipients, three to five complete BKPyV genomes from each of six RT recipients with surviving renal allografts were molecularly cloned. The complete sequences of these clones were determined and compared in each patient. No nucleotide difference was detected among clones in two patients, and a few nucleotide variations were found among those in four patients. In each of these patients a parental sequence (usually the major sequence), from which variant sequences (usually minor sequences) with nucleotide substitutions would have been generated, were identified. A comparison between the parental and variant sequences in each patient identified a single nucleotide substitution in each variant sequence. From these findings, it was concluded that the genome of BKPyV is stable in RT recipients without nephropathy, with only minor nucleotide substitutions in the coding region.
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Monjane, Adérito L., Darren P. Martin, Francisco Lakay, Brejnev M. Muhire, Daniel Pande, Arvind Varsani, Gordon Harkins, Dionne N. Shepherd, and Edward P. Rybicki. "Extensive Recombination-Induced Disruption of Genetic Interactions Is Highly Deleterious but Can Be Partially Reversed by Small Numbers of Secondary Recombination Events." Journal of Virology 88, no. 14 (April 30, 2014): 7843–51. http://dx.doi.org/10.1128/jvi.00709-14.
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ABSTRACTAlthough homologous recombination can potentially provide viruses with vastly more evolutionary options than are available through mutation alone, there are considerable limits on the adaptive potential of this important evolutionary process. Primary among these is the disruption of favorable coevolved genetic interactions that can occur following the transfer of foreign genetic material into a genome. Although the fitness costs of such disruptions can be severe, in some cases they can be rapidly recouped by either compensatory mutations or secondary recombination events. Here, we used a maize streak virus (MSV) experimental model to explore both the extremes of recombination-induced genetic disruption and the capacity of secondary recombination to adaptively reverse almost lethal recombination events. Starting with two naturally occurring parental viruses, we synthesized two of the most extreme conceivable MSV chimeras, each effectively carrying 182 recombination breakpoints and containing thorough reciprocal mixtures of parental polymorphisms. Although both chimeras were severely defective and apparently noninfectious, neither had individual movement-, encapsidation-, or replication-associated genome regions that were on their own “lethally recombinant.” Surprisingly, mixed inoculations of the chimeras yielded symptomatic infections with viruses with secondary recombination events. These recombinants had only 2 to 6 breakpoints, had predominantly inherited the least defective of the chimeric parental genome fragments, and were obviously far more fit than their synthetic parents. It is clearly evident, therefore, that even when recombinationally disrupted virus genomes have extremely low fitness and there are no easily accessible routes to full recovery, small numbers of secondary recombination events can still yield tremendous fitness gains.IMPORTANCERecombination between viruses can generate strains with enhanced pathological properties but also runs the risk of producing hybrid genomes with decreased fitness due to the disruption of favorable genetic interactions. Using two synthetic maize streak virus genome chimeras containing alternating genome segments derived from two natural viral strains, we examined both the fitness costs of extreme degrees of recombination (both chimeras had 182 recombination breakpoints) and the capacity of secondary recombination events to recoup these costs. After the severely defective chimeras were introduced together into a suitable host, viruses with between 1 and 3 secondary recombination events arose, which had greatly increased replication and infective capacities. This indicates that even in extreme cases where recombination-induced genetic disruptions are almost lethal, and 91 consecutive secondary recombination events would be required to reconstitute either one of the parental viruses, moderate degrees of fitness recovery can be achieved through relatively small numbers of secondary recombination events.
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Mayer, Wolfgang, Avril Smith, Reinald Fundele, and Thomas Haaf. "Spatial Separation of Parental Genomes in Preimplantation Mouse Embryos." Journal of Cell Biology 148, no. 4 (February 21, 2000): 629–34. http://dx.doi.org/10.1083/jcb.148.4.629.
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We have used two different experimental approaches to demonstrate topological separation of parental genomes in preimplantation mouse embryos: mouse eggs fertilized with 5-bromodeoxyuridine (BrdU)-labeled sperm followed by detection of BrdU in early diploid embryos, and differential heterochromatin staining in mouse interspecific hybrid embryos. Separation of chromatin according to parental origin was preserved up to the four-cell embryo stage and then gradually disappeared. In F1 hybrid animals, genome separation was also observed in a proportion of somatic cells. Separate nuclear compartments during preimplantation development, when extreme chromatin remodelling occurs, and possibly in some differentiated cell types, may be associated with epigenetic reprogramming.
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Martin, Olivier C., and Frédéric Hospital. "Distribution of Parental Genome Blocks in Recombinant Inbred Lines." Genetics 189, no. 2 (August 11, 2011): 645–54. http://dx.doi.org/10.1534/genetics.111.129700.
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Pignatta, Daniela, and Luca Comai. "Parental squabbles and genome expression: lessons from the polyploids." Journal of Biology 8, no. 4 (2009): 43. http://dx.doi.org/10.1186/jbiol140.
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Picolo, Floriane, Anna Grandchamp, Benoît Piégu, Antoine D. Rolland, Reiner A. Veitia, and Philippe Monget. "Genes Encoding Teleost Orthologs of Human Haploinsufficient and Monoallelically Expressed Genes Remain in Duplicate More Frequently Than the Whole Genome." International Journal of Genomics 2021 (July 29, 2021): 1–6. http://dx.doi.org/10.1155/2021/9028667.
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Gene dosage is an important issue both in cell and evolutionary biology. Most genes are present in two copies or alleles in diploid eukariotic cells. The most outstanding exception is monoallelic gene expression (MA) that concerns genes localized on the X chromosome or in regions undergoing parental imprinting in eutherians, and many other genes scattered throughout the genome. In diploids, haploinsufficiency (HI) implies that a single functional copy of a gene in a diploid organism is insufficient to ensure a normal biological function. One of the most important mechanisms ensuring functional innovation during evolution is whole genome duplication (WGD). In addition to the two WGDs that have occurred in vertebrate genomes, the teleost genomes underwent an additional WGD, after their divergence from tetrapods. In the present work, we have studied on 57 teleost species whether the orthologs of human MA or HI genes remain more frequently in duplicates or returned more frequently in singleton than the rest of the genome. Our results show that the teleost orthologs of HI human genes remained more frequently in duplicate than the rest of the genome in all of the teleost species studied. No signal was observed for the orthologs of genes mapping to the human X chromosome or subjected to parental imprinting. Surprisingly, the teleost orthologs of the other human MA genes remained in duplicate more frequently than the rest of the genome for most teleost species. These results suggest that the teleost orthologs of MA and HI human genes also undergo selective pressures either related to absolute protein amounts and/or of dosage balance issues. However, these constraints seem to be different for MA genes in teleost in comparison with human genomes.
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Yin, Tongming, Xinye Zhang, Minren Huang, Minxiu Wang, Qiang Zhuge, Shengming Tu, Li-Huang Zhu, and Rongling Wu. "Molecular linkage maps of the Populus genome." Genome 45, no. 3 (June 1, 2002): 541–55. http://dx.doi.org/10.1139/g02-013.
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We report molecular genetic linkage maps for an interspecific hybrid population of Populus, a model system in forest-tree biology. The hybrids were produced by crosses between P. deltoides (mother) and P. euramericana (father), which is a natural hybrid of P. deltoides (grandmother) and P. nigra (grandfather). Linkage analysis from 93 of the 450 backcross progeny grown in the field for 15 years was performed using random amplified polymorphic DNAs (RAPDs), amplified fragment length polymorphisms (AFLPs), and inter-simple sequence repeats (ISSRs). Of a total of 839 polymorphic markers identified, 560 (67%) were testcross markers heterozygous in one parent but null in the other (segregating 1:1), 206 (25%) were intercross dominant markers heterozygous in both parents (segregating 3:1), and the remaining 73 (9%) were 19 non-parental RAPD markers (segregating 1:1) and 54 codominant AFLP markers (segregating 1:1:1:1). A mixed set of the testcross markers, non-parental RAPD markers, and codominant AFLP markers was used to construct two linkage maps, one based on the P. deltoides (D) genome and the other based on P. euramericana (E). The two maps showed nearly complete coverage of the genome, spanning 3801 and 3452 cM, respectively. The availability of non-parental RAPD and codominant AFLP markers as orthologous genes allowed for a direct comparison of the rate of meiotic recombination between the two different parental species. Generally, the rate of meiotic recombination was greater for males than females in our interspecific poplar hybrids. The confounded effect of sexes and species causes the mean recombination distance of orthologous markers to be 11% longer for the father (P. euramericana; interspecific hybrid) than for the mother (P. deltoides; pure species). The linkage maps constructed and the interspecific poplar hybrid population in which clonal replicates for individual genotypes are available present a comprehensive foundation for future genomic studies and quantitative trait locus (QTL) identification.Key words: AFLP, Genetic map, poplar, RAPD, SSR.
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Tunner, Heinz. "Evidence for genomic imprinting in unisexual triploid hybrid frogs." Amphibia-Reptilia 21, no. 2 (2000): 135–41. http://dx.doi.org/10.1163/156853800507327.
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AbstractThe hybridogenetic hybrid R. esculenta arose through hybridization between R. ridibunda and R. lessonae. Usually hybrids are diploid. In some populations, however, they are triploid, with one genome from R. ridibunda and two genomes from R. lessonae (LLR-genotype). These triploids live with and mate with R. ridibunda. Thus, hybrids and R. ridibunda are sexual competitors. I studied the influence of the additional lessonae genome (dosage effect) on the morphology, biology and the electrophoretic pattern of two polymorphic proteins of triploid hybrids. The two lessonae genomes are not expressed according to a simple dose effect. Genetic information of the lessonae genome is obviously switched off because it would increase the dissimilarity between triploids and R. ridibunda, the parental species upon which reproduction of hybrids depends. Imprinting can account for the observed unusual pattern of inheritance.
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Hosaka, K., S. F. Kianian, J. M. McGrath, and C. F. Quiros. "Development and chromosomal localization of genome-specific DNA markers of Brassica and the evolution of amphidiploids and n = 9 diploid species." Genome 33, no. 1 (February 1, 1990): 131–42. http://dx.doi.org/10.1139/g90-021.
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Ten genome-specific probes were developed from Brassica napus and B. oleracea genomic DNA libraries. Selection was based on polymorphism between and limited variation within genomes, permitting their localization on six individual C-genome chromosomes. Chromosome assignment was accomplished by using two sets of B. campestris – oleracea alien addition lines derived from (i) B. napus and (ii) the artificially synthesized B. napus 'Hakuran'. The presence of shared fragments between A, B, and C genomes indicates partial homology of the three genomes. However, several genome-specific markers could separate these three genomes. Genome-specific clones developed in this study served to confirm the parental diploid species originating the three amphidiploids, B. napus, B. carinata, and B. juncea. At least one clone suggests that B. napus has a polyphyletic origin. These clones were also useful to confirm the close evolutionary proximity among wild species in the B. oleracea cytodeme; however, no clear trends were found to suggest specific wild ancestors for the different B. oleracea horticultural types. Brassica oxyrrhina was distinct from other n = 9 species with most clones tested.Key words: restriction fragment length polymorphism, DNA marker, chromosome addition lines, Brassica oleracea cytodeme, amphidiploids, genome-specific markers.
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Hwang, Liang-Dar, Justin D. Tubbs, Justin Luong, Mischa Lundberg, Gunn-Helen Moen, Geng Wang, Nicole M. Warrington, Pak C. Sham, Gabriel Cuellar-Partida, and David M. Evans. "Estimating indirect parental genetic effects on offspring phenotypes using virtual parental genotypes derived from sibling and half sibling pairs." PLOS Genetics 16, no. 10 (October 26, 2020): e1009154. http://dx.doi.org/10.1371/journal.pgen.1009154.
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Indirect parental genetic effects may be defined as the influence of parental genotypes on offspring phenotypes over and above that which results from the transmission of genes from parents to their children. However, given the relative paucity of large-scale family-based cohorts around the world, it is difficult to demonstrate parental genetic effects on human traits, particularly at individual loci. In this manuscript, we illustrate how parental genetic effects on offspring phenotypes, including late onset conditions, can be estimated at individual loci in principle using large-scale genome-wide association study (GWAS) data, even in the absence of parental genotypes. Our strategy involves creating “virtual” mothers and fathers by estimating the genotypic dosages of parental genotypes using physically genotyped data from relative pairs. We then utilize the expected dosages of the parents, and the actual genotypes of the offspring relative pairs, to perform conditional genetic association analyses to obtain asymptotically unbiased estimates of maternal, paternal and offspring genetic effects. We apply our approach to 19066 sibling pairs from the UK Biobank and show that a polygenic score consisting of imputed parental educational attainment SNP dosages is strongly related to offspring educational attainment even after correcting for offspring genotype at the same loci. We develop a freely available web application that quantifies the power of our approach using closed form asymptotic solutions. We implement our methods in a user-friendly software package IMPISH (IMputing Parental genotypes In Siblings and Half Siblings) which allows users to quickly and efficiently impute parental genotypes across the genome in large genome-wide datasets, and then use these estimated dosages in downstream linear mixed model association analyses. We conclude that imputing parental genotypes from relative pairs may provide a useful adjunct to existing large-scale genetic studies of parents and their offspring.
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Evtushenko, Elena V., Yulia A. Lipikhina, Petr I. Stepochkin, and Alexander V. Vershinin. "Cytogenetic and molecular characteristics of rye genome in octoploid triticale (× Triticosecale Wittmack)." Comparative Cytogenetics 13, no. 4 (December 16, 2019): 423–34. http://dx.doi.org/10.3897/compcytogen.v13i4.39576.
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Alloploidization resulting from remote (interspecific or intergeneric) hybridization is one of the main factors in plant evolution, leading to the formation of new species. Triticale (× Triticosecale Wittmack, 1889) is the first artificial species created by crossing wheat (Triticum spp.) and rye (Secale cereale Linnaeus, 1753) and has a great potential as a grain and forage crop. Remote hybridization is a stress factor that causes a rapid reorganization of the parental genomes in hybrid progeny (“genomic shock”) and is accompanied by abnormalities in the chromosome set of hybrids. The formation of the hybrid genome and its subsequent stabilization are directly related to the normalization of meiosis and the correct chromosome segregation. The aim of this work was to cytogenetically characterize triticale (× Triticosecale rimpaui Wittmack, 1899, AABBDDRR) obtained by crossing Triticum aestivum Linnaeus, 1753. Triple Dirk D × Secale cereale L. Korotkostebel’naya 69 in F3–F6 generations of hybrids, and to trace the process of genetic stabilization of hybrid genomes. Also, a comparative analysis of the nucleotide sequences of the centromeric histone CENH3 genes was performed in wheat-rye allopolyploids of various ploidy as well as their parental forms. In the hybrid genomes of octoploid triticale an increased expression of the rye CENH3 variants was detected. The octoploid triticale plants contain complete chromosome sets of the parental subgenomes maintaining the chromosome balance and meiotic stability. For three generations the percentage of aneuploids in the progeny of such plants has been gradually decreasing, and they maintain a complete set of the paternal rye chromosomes. However, the emergence of hexaploid and new aneuploid plants in F5 and F6 generations indicates that stabilization of the hybrid genome is not complete yet. This conclusion was confirmed by the analysis of morphological features in hybrid plants: the progeny of one plant having the whole chromosome sets of parental subgenomes showed significant morphological variations in awn length and spike density. Thus, we expect that the results of our karyotyping of octoploid triticales obtained by crossing hexaploid wheat to diploid rye supplemented by comparative analysis of CENH3 sequences will be applicable to targeted breeding of stable octo- and hexaploid hybrids.
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Navalikhina, A. G., M. Z. Antonyuk, and T. K. Ternovska. "The role of siRNAs in genome stability maintaining in the bread wheat introgression lines." Faktori eksperimental'noi evolucii organizmiv 26 (September 1, 2020): 108–13. http://dx.doi.org/10.7124/feeo.v26.1251.
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Aim. Deviations of the siRNAs levels from the parental ones in the plants with hybrid genomes are associated with the activation of transposable elements (TE). This, in turn, lead to the further genome rearrangements. Introgression lines Triticum aestivum / Amblyopyrum muticum are cytologically stable, however, there are visible signs of genetic and (or) epigenetic restructuring that are still going on. Molecular mechanisms of these processes are the subject of our study. Methods. The levels of siRNAs in the plant lemmas were determined by small RNA-seq. Reads of the small RNA libraries were aligned to the repeats to find siRNA sequences. Results. Introgression lines (ILs) and parental amphidiploid have variable levels of siRNAs regulating MITE and CACTA transposable elements, compared with the parental bread wheat variety. For twelve TE sequences, majority of which are CACTA elements, decrease in the levels of siRNAs in ILs and amphidiploid, compared to the wheat, is statistically significant. Decreased siRNAs levels could lead to the activation of corresponding TE classes. Conclusions. Variation of siRNA levels in ILs and amphidiploid can be the key factor that cause rearrangements in their genomes. These include activation of TEs, changes in DNA methylation patterns, and gene expression variation. Therefore, detected changes in siRNA levels can be the molecular mechanisms of the processes that occur in studied hybrid genomes.
Keywords: siRNA, transposable elements, amphidiploid, introgression lines.
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Eroukhmanoff, Fabrice, Richard I. Bailey, and Glenn-Peter Sætre. "Hybridization and genome evolution I: The role of contingency during hybrid speciation." Current Zoology 59, no. 5 (October 1, 2013): 667–74. http://dx.doi.org/10.1093/czoolo/59.5.667.
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Abstract Homoploid hybrid speciation (HHS) involves the recombination of two differentiated genomes into a novel, functional one without a change in chromosome number. Theoretically, there are numerous ways for two parental genomes to recombine. Hence, chance may play a large role in the formation of a hybrid species. If these genome combinations can evolve rapidly following hybridization and sympatric situations are numerous, recurrent homoploid hybrid speciation is a possibility. We argue that three different, but not mutually exclusive, types of contingencies could influence this process. First, many of these “hopeful monsters” of recombinant parent genotypes would likely have low fitness. Only specific combinations of parental genomic contributions may produce viable, intra-fertile hybrid species able to accommodate potential constraints arising from intragenomic conflict. Second, ecological conditions (competition, geography of the contact zones or the initial frequency of both parent species) might favor different outcomes ranging from sympatric coexistence to the formation of hybrid swarms and ultimately hybrid speciation. Finally, history may also play an important role in promoting or constraining recurrent HHS if multiple hybridization events occur sequentially and parental divergence or isolation differs along this continuum. We discuss under which conditions HHS may occur multiple times in parallel and to what extent recombination and selection may fuse the parent genomes in the same or different ways. We conclude by examining different approaches that might help to solve this intriguing evolutionary puzzle.
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Timmermans, Marja C. P., O. Prem Das, and Joachim Messing. "Characterization of a Meiotic Crossover in Maize Identified by a Restriction Fragment Length Polymorphism-Based Method." Genetics 143, no. 4 (August 1, 1996): 1771–83. http://dx.doi.org/10.1093/genetics/143.4.1771.
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Abstract Genetic map lengths do not correlate directly with genome size, suggesting that meiotic recombination is not uniform throughout the genome. Further, the abundance of repeated sequences in plant genomes requires that crossing over is restricted to particular genomic regions. We used a physical mapping approach to identify these regions without the bias introduced by phenotypic selection. This approach is based on the detection of nonparental polymorphisms formed by recombination between polymorphic alleles. In an F2 population of 48 maize plants, we identified a crossover at two of the seven restriction fragment length polymorphism loci tested. Characterization of one recombination event revealed that the crossover mapped within a 534bp region of perfect homology between the parental alleles embedded in a 2773-bp unique sequence. No transcripts from this region could be detected. Sequences immediately surrounding the crossover site were not detectably methylated, except for an SstI site probably methylated via non-CpG or CpXpG cytosine methylation. Parental methylation patterns at this SstI site and at the flanking repetitive sequences were faithfully inherited by the recombinant allele. Our observations suggest that meiotic recombination in maize occurs between perfectly homologous sequences, within unmethylated, nonrepetitive regions of the genome.
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Mochizuki, Kazufumi. "RNA-directed epigenetic regulation of DNA rearrangements." Essays in Biochemistry 48 (September 20, 2010): 89–100. http://dx.doi.org/10.1042/bse0480089.
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Ciliated protozoa undergo extensive DNA rearrangements, including DNA elimination, chromosome breakage and DNA unscrambling, when the germline micronucleus produces the new macronucleus during sexual reproduction. It has long been known that many of these events are epigenetically controlled by DNA sequences of the parental macronuclear genome. Recent studies in some model ciliates have revealed that these epigenetic regulations are mediated by non-coding RNAs. DNA elimination in Paramecium and Tetrahymena is regulated by small RNAs that are produced and operated by an RNAi (RNA interference)-related mechanism. It has been proposed that the small RNAs from the micronuclear genome can be used to identify eliminated DNAs by whole-genome comparison of the parental macronucleus and the micronucleus. In contrast, DNA unscrambling in Oxytricha is guided by long non-coding RNAs that are produced from the somatic parental macronuclear genome. These RNAs are proposed to act as templates for the direct unscrambling events that occur in the developing macronucleus. The possible evolutionary benefits of these RNA-directed epigenetic regulations of DNA rearrangement in ciliates are discussed in the present chapter.
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Iovene, Marina, Salvatore Savarese, Teodoro Cardi, Luigi Frusciante, Nunzia Scotti, Philipp W. Simon, and Domenico Carputo. "Nuclear and cytoplasmic genome composition of Solanum bulbocastanum (+) S. tuberosum somatic hybrids." Genome 50, no. 5 (May 2007): 443–50. http://dx.doi.org/10.1139/g07-024.
Full textAbstract:
Somatic hybrids between the wild incongruent species Solanum bulbocastanum (2n = 2x = 24) and S. tuberosum haploids (2n = 2x = 24) have been characterized for their nuclear and cytoplasmic genome composition. Cytologic observations revealed the recovery of 8 (near-)tetraploid and 3 hexaploid somatic hybrids. Multicolor genomic in situ hybridization (GISH) analysis was carried out to study the genomic dosage of the parental species in 5 somatic hybrids with different ploidy. The GISH procedure used was effective in discriminating parental genomes in the hybrids; most chromosomes were unambiguously colored. Two (near-)tetraploid somatic hybrids showed the expected 2:2 cultivated-to-wild genomic dosage; 2 hexaploids revealed a 4:2 cultivated-to-wild genomic dosage, and 1 hexaploid had a 2:4 cultivated-to-wild genomic dosage. Characterization of hybrid cytoplasmic genomes was performed using gene-specific primers that detected polymorphisms between the fusion parents in the intergenic regions. The analysis showed that most of the somatic hybrids inherited the plastidial and mitochondrial DNA of the cultivated parent. A few hybrids, with a rearranged mitochondrial genome (showing fragments derived from both parents), were also identified. These results confirmed the potential of somatic hybridization in producing new variability for genetic studies and breeding.
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Kumar, P. S., and P. D. Walton. "Nature of chromosome pairing in SH-genome octaploids involving Elymus canadensis and E. trachycaulus: a genome dose dependent bivalentizing mechanism." Genome 33, no. 5 (October 1, 1990): 613–18. http://dx.doi.org/10.1139/g90-091.
Full textAbstract:
In spite of regular chromosome pairing, hybrids between Elymus canadensis (Linnaeus) and E. trachycaulus (Link) Gould ex Shinners at the tetraploid level are sterile owing to structural differences between the donor genomes. However, the hybrids between these species at the octaploid level (obtained through chromosome doubling of the tetraploid hybrid and also from a cross between the octaploids of E. canadensis and E. trachycaulus) exhibited a predominance of bivalents in meiosis in spite of the autotetraploid nature of their constituent S and H genomes. The colchicine-induced amphiploids showed varying degrees of fertility. Comparison of chromosome pairing in the hybrid octaploids with that in the parental octaploids and hexaploids revealed that random bivalent formation is promoted when the S and (or) H genomes are at the tetraploid level, but not when they are in the triploid state. A bivalentizing mechanism under polygenic control is suggested to explain the predominance of bivalents in the tetraploid S and H genomes.Key words: Elymus, S genome, H genome, octaploids, bivalents, bivalentization.
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Reik, Wolf, Sarah K. Howlett, and M. Azim Surani. "Imprinting by DNA methylation: from transgenes to endogenous gene sequences." Development 108, Supplement (April 1, 1990): 99–106. http://dx.doi.org/10.1242/dev.108.supplement.99.
Full textAbstract:
A number of transgenes in the mouse show variation in methylation and expression phenotypes dependent on parental transmission. It appears that there exist at least two types of transgene imprinting; one is retained on an essentially homozygous background, while the other requires heterozygosity at some modifying loci in the genome and is observed as differences in phenotype in reciprocal crosses. For this type of imprinting to occur, the parental origin of the modifier locus itself is important, and parental asymmetry may involve specific interactions between egg cytoplasm and the chromosomes. Based on the identification of ‘methylation polymorphism’ in the mouse genome, we also show that endogenous gene sequences can undergo imprinting by DNA methylation.
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Chen, Qin, R. L. Conner, and A. Laroche. "Identification of the parental chromosomes of the wheat–alien amphiploid Agrotana by genomic in situ hybridization." Genome 38, no. 6 (December 1, 1995): 1163–69. http://dx.doi.org/10.1139/g95-154.
Full textAbstract:
Labelled total genomic DNA from four alien species, Thinopyrum ponticum (Host) Beauv. (2n = 70, genomes J1J1J1J2J2), Th. bessarabicum (Savul. &Rayss) Love (2n = 14, genome J), Th. elongatum (Host) Beauv. (2n = 14, genome E), and Haynaldia villosa (L.) Schur. (2n = 14, genome V), were used as probes in combination with blocking wheat DNA for in situ hybridization of the chromosomes of Agrotana, a wheat–alien hybrid (2n = 56) of unknown origin. The results showed that genomic DNA probes from Th. ponticum and Th. bessarabicum both clearly revealed 16 alien and 40 wheat chromosomes in Agrotana, indicating that the J genome present in these two species has a high degree of homology with the alien chromosomes in Agrotana. Biotinylated genomic DNA probe from Th. elongatum identified 10 chromosomes from Agrotana, while some regions of six other chromosomes yielded a weak or no signal. The probe from H. villosa produced no differential labelling of the chromosomes of Agrotana. The genomic formula of Agrotana was designated as AABBDDJJ. We suggest that the alien parent donor species of Agrotana is Th. ponticum rather than Th. bessarabicum. Genomic relationships of the three Thinopyrum species are discussed in relation to the distribution of GISH signals in the chromosomes of Agrotana.Key words: Thinopyrum species, wheat–alien amphiploid, genomic DNA probing, in situ hybridization, molecular cytogenetics.
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Ren, Xiujuan, Yuanyi Liu, Yiping Zhao, Bei Li, Dongyi Bai, Gerelchimeg Bou, Xinzhuang Zhang, et al. "Analysis of the Whole-Genome Sequences from an Equus Parent-Offspring Trio Provides Insight into the Genomic Incompatibilities in the Hybrid Mule." Genes 13, no. 12 (November 23, 2022): 2188. http://dx.doi.org/10.3390/genes13122188.
Full textAbstract:
Interspecific hybridization often shows negative effects on hybrids. However, only a few multicellular species, limited to a handful of plants and animals, have shown partial genetic mechanisms by which hybridization leads to low fitness in hybrids. Here, to explore the outcome of combining the two genomes of a horse and donkey, we analyzed the whole-genome sequences from an Equus parent-offspring trio using Illumina platforms. We generated 41.39× and 46.21× coverage sequences for the horse and mule, respectively. For the donkey, a 40.38× coverage sequence was generated and stored in our laboratory. Approximately 24.86 million alleles were discovered that varied from the reference genome. Single nucleotide polymorphisms were used as polymorphic markers for assigning alleles to their parental genomic inheritance. We identified 25,703 Mendelian inheritance error single nucleotide polymorphisms in the mule genome that were not inherited from the parents through Mendelian inheritance. A total of 555 de novo single nucleotide polymorphisms were also identified. The rate of de novo single nucleotide polymorphisms was 2.21 × 10−7 in the mule from the Equus parent-offspring trio. This rate is obviously higher than the natural mutation rate for Equus, which is also consistent with the previous hypothesis that interracial crosses may have a high mutation rate. The genes associated with these single nucleotide polymorphisms are mainly involved in immune processes, DNA repair, and cancer processes. The results of the analysis of three genomes from an Equus parent-offspring trio improved our knowledge of the consequences of the integration of parental genomes in mules.
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Ramzan, Fahad, Adnan Younis, and Ki-Byung Lim. "Application of Genomic In Situ Hybridization in Horticultural Science." International Journal of Genomics 2017 (2017): 1–12. http://dx.doi.org/10.1155/2017/7561909.
Full textAbstract:
Molecular cytogenetic techniques, such as in situ hybridization methods, are admirable tools to analyze the genomic structure and function, chromosome constituents, recombination patterns, alien gene introgression, genome evolution, aneuploidy, and polyploidy and also genome constitution visualization and chromosome discrimination from different genomes in allopolyploids of various horticultural crops. Using GISH advancement as multicolor detection is a significant approach to analyze the small and numerous chromosomes in fruit species, for example,Diospyroshybrids. This analytical technique has proved to be the most exact and effective way for hybrid status confirmation and helps remarkably to distinguish donor parental genomes in hybrids such asClivia,Rhododendron, andLycorisornamental hybrids. The genome characterization facilitates in hybrid selection having potential desirable characteristics during the early hybridization breeding, as this technique expedites to detect introgressed sequence chromosomes. This review study epitomizes applications and advancements of genomic in situ hybridization (GISH) techniques in horticultural plants.
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Hangloo, Sharmishta, Gazi Muhammad Abdullah Mahdi, Romesh Kumar Salgotra, and Manmohan Sharma. "Screening microsatellite markers for establishing parental polymorphism in Indian rice (Oryza sativa L.)." Archives of Agriculture and Environmental Science 7, no. 4 (December 25, 2022): 590–94. http://dx.doi.org/10.26832/24566632.2022.0704017.
Full textAbstract:
The experiment was conducted to investigate the parental diversity along the rice genome and to understand and screen out the SSR markers-indicated polymorphism between two indica rice (Oryza sativa L.) cultivars. Namely K343, the most well-liked rice variety in the hill zone of the Jammu Region, and RML22, a rice line created at IRRI, Philippines. The study is to select polymorphic markers (Simple Sequence Repeat- SSR) associated with hill ecologies rice cultivars and additional research projects like gene pyramiding and background selection to recover the recurrent parent genome (RPG) in blast gene introgression in elite lines. 450 SSR markers, evenly distributed throughout the rice genome, were used to assess the parental polymorphism between these genotypes. Of these two cultivars, 51 markers (11.33%) showed polymorphism with bands in different spectrums throughout the genome. The study has been used to Marker Assisted Backcross (MAB) breeding to integrate rice blast resistance genes in the parental genotype. The pool of polymorphic markers has the potential to use in similar studies and work, with a high probability of polymorphism for the cultivars of hill ecologies, and thus increase the chance of selection of probability in marker selection.