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1.
Plant Cell Rep ; 38(12): 1515-1525, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31473791

RESUMO

KEY MESSAGE: A single division meiosis mechanism of meiotic restitution is incompletely penetrant but significantly associated with restored fertility in triticale haploids (n = 21, genome formula ABR). Meiotic restitution, or failure of meiosis to produce gametes with a reduced chromosome number, can lead to the restoration of fertility in allohaploids. Meiotic restitution is of major interest for producing doubled haploids, as haploid plants undergoing meiotic restitution can often form seeds without the need to apply mitosis inhibitors to double chromosome number. We aimed to characterize meiotic restitution in a population of 183 haploids (n = 21, genome formula ABR) derived from an F1 wheat-rye hybrid where one parent was known to carry factors responsible for restoration of fertility in wide-cross haploids. Based on cytological analysis, approximately half of the plants analyzed were characterized by normal meiosis, while half showed at least some cytological evidence of meiotic restitution. However, this mechanism was incompletely penetrant in the population, with no individual plant showing 100% unreduced gamete formation: restitution occurred sectorially within each anther and was not observed in all the anthers of a given plant. Hence, the absence of meiotic restitution could not be confirmed conclusively for any individual plant, confounding this analysis. However, cytological observation of meiotic restitution was significantly associated with seed set, further confirming the role of meiotic restitution in fertility restoration. Our results provide insight into this mechanism of unreduced gamete formation, and provide a basis for future work identifying the genetic factors responsible for this trait.


Assuntos
Cromossomos de Plantas/genética , Meiose/fisiologia , Triticale/genética , Haploidia , Hibridização Genética/genética , Hibridização Genética/fisiologia , Meiose/genética , Poliploidia
2.
Zool Res ; 40(4): 293-304, 2019 Jul 18.
Artigo em Inglês | MEDLINE | ID: mdl-31271004

RESUMO

Divergence of gene expression and alternative splicing is a crucial driving force in the evolution of species; to date, however the molecular mechanism remains unclear. Hybrids of closely related species provide a suitable model to analyze allele-specific expression (ASE) and allele-specific alternative splicing (ASS). Analysis of ASE and ASS can uncover the differences in cis-regulatory elements between closely related species, while eliminating interference of trans-regulatory elements. Here, we provide a detailed characterization of ASE and ASS from 19 and 10 transcriptome datasets across five tissues from reciprocal-cross hybrids of horse×donkey (mule/hinny) and cattle×yak (dzo), respectively. Results showed that 4.8%-8.7% and 10.8%-16.7% of genes exhibited ASE and ASS, respectively. Notably, lncRNAs and pseudogenes were more likely to show ASE than protein-coding genes. In addition, genes showing ASE and ASS in mule/hinny were found to be involved in the regulation of muscle strength, whereas those of dzo were involved in high-altitude adaptation. In conclusion, our study demonstrated that exploration of genes showing ASE and ASS in hybrids of closely related species is feasible for species evolution research.


Assuntos
Alelos , Processamento Alternativo , Bovinos/genética , Equidae/genética , Hibridização Genética/genética , Animais , Sequência de Bases , Regulação da Expressão Gênica , RNA/genética , RNA/metabolismo
3.
Plant Dis ; 103(9): 2295-2304, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31355734

RESUMO

Phytophthora species hybrids have been repeatedly reported as causing damaging diseases to cultivated and wild plants. Two known hybrids, P. andina and P. × pelgrandis, are pathogens of Solanaceae and ornamentals, respectively, although the extent of their host ranges are unknown. P. andina emerged from hybridization of P. infestans and an unidentified related species, whereas P. × pelgrandis emerged from P. nicotianae and P. cactorum. Considering that hybrids and parental species can coexist in the same regions and to distinguish them usually requires cloning or whole genome sequencing, we aimed to develop a rapid tool to distinguish them. Specifically, we used high-resolution melting (HRM) assays to differentiate genotypes based on their amplicon melting profiles. We designed primers for P. × pelgrandis and parental species based on available sequences of P. nicotianae and P. cactorum nuclear genes containing polymorphisms between species. For P. andina, heterozygous sites from Illumina short reads were used for the same purpose. We identified multiple amplicons exhibiting differences in melting curves between parental species and hybrids. We propose HRM as a rapid method for differentiation of P. andina and P. × pelgrandis hybrids from parental species that could be employed to advance research on these pathogens.


Assuntos
Hibridização Genética , Tipagem Molecular , Phytophthora , Primers do DNA , Hibridização Genética/genética , Tipagem Molecular/métodos , Tipagem Molecular/normas , Phytophthora/classificação , Phytophthora/genética , Solanaceae/parasitologia , Temperatura de Transição
4.
BMC Res Notes ; 12(1): 311, 2019 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-31151479

RESUMO

OBJECTIVES: The objective of this study was to establish transcriptome assemblies of Festulolium hybrids under salt stress, and identify genes regulated across the hybrids in response to salt stress. The development of transcriptome assemblies for Festulolium hybrids and cataloguing of genes regulated under salt stress will facilitate further downstream studies. RESULTS: Plants were grown at three salt concentrations (0.5%, 1% and 1.5%) and phenotypic and transcriptomic data was collected. Salt stress was confirmed by progressive loss of green leaves as salt concentration increased from 0 to 1.5%. We generated de-novo transcriptome assemblies for two Festulolium pabulare festucoid genotypes, for a single Festulolium braunii genotype, and a single F. pabulare loloid genotype. We also identified 1555 transcripts that were up regulated and 1264 transcripts that were down regulated in response to salt stress in the Festulolium hybrids. Some of the identified transcripts showed significant sequence similarity with genes known to be regulated during salt and other abiotic stresses.


Assuntos
Festuca/genética , Regulação da Expressão Gênica de Plantas , Hibridização Genética/genética , Lolium/genética , Estresse Salino/genética , Transcriptoma , Festuca/crescimento & desenvolvimento , Perfilação da Expressão Gênica , Genes de Plantas/genética , Sequenciamento de Nucleotídeos em Larga Escala , Lolium/crescimento & desenvolvimento , Folhas de Planta/genética , Folhas de Planta/crescimento & desenvolvimento , Transcrição Genética
5.
Plant Sci ; 285: 122-131, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31203876

RESUMO

Domestication and subsequent breeding have eroded genetic diversity in the modern chickpea crop by ˜100-fold. Corresponding reductions to trait variation create the need, and an opportunity, to identify and harness the genetic capacity of wild species for crop improvement. Here we analyze trait segregation in a series of wild x cultivated hybrid populations to delineate the genetic underpinnings of domestication traits. Two species of wild chickpea, C. reticulatum and C. echinospermum, were crossed with the elite, early flowering C. arietinum cultivar ICCV96029. KASP genotyping of F2 parents with an FT-linked molecular marker enabled selection of 284 F3 families with reduced phenological variation: 255 F3 families of C. arietinum x reticulatum (AR) derived from 17 diverse wild parents and 29 F3 families of C. arietinum x echinospermum (AE) from 3 wild parents. The combined 284 lineages were genotyped using a genotyping-by-sequencing strategy and phenotyped for agronomic traits. 50 QTLs in 11 traits were detected from AR and 35 QTLs in 10 traits from the combined data. Using hierarchical clustering to assign traits to six correlated groups and mixed model based multi-trait mapping, four pleiotropic loci were identified. Bayesian analysis further identified four inter-trait relationships controlling the duration of vegetative growth and seed maturation, for which the underlying pleiotropic genes were mapped. A random forest approach was used to explore the most extreme trait differences between AR and AE progenies, identifying traits most characteristic of wild species origin. Knowledge of the genomic basis of traits that segregate in wild-cultivated hybrid populations will facilitate chickpea improvement by linking genetic and phenotypic variation in a quantitative genetic framework.


Assuntos
Cicer/genética , Genes de Plantas/genética , Melhoramento Vegetal/métodos , Teorema de Bayes , Cicer/crescimento & desenvolvimento , DNA de Plantas/genética , Domesticação , Estudos de Associação Genética , Ligação Genética/genética , Hibridização Genética/genética , Locos de Características Quantitativas/genética , Característica Quantitativa Herdável , Sementes/crescimento & desenvolvimento
6.
Evol Anthropol ; 28(4): 189-209, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31222847

RESUMO

During the late Pleistocene, isolated lineages of hominins exchanged genes thus influencing genomic variation in humans in both the past and present. However, the dynamics of this genetic exchange and associated phenotypic consequences through time remain poorly understood. Gene exchange across divergent lineages can result in myriad outcomes arising from these dynamics and the environmental conditions under which it occurs. Here we draw from our collective research across various organisms, illustrating some of the ways in which gene exchange can structure genomic/phenotypic diversity within/among species. We present a range of examples relevant to questions about the evolution of hominins. These examples are not meant to be exhaustive, but rather illustrative of the diverse evolutionary causes/consequences of hybridization, highlighting potential drivers of human evolution in the context of hybridization including: influences on adaptive evolution, climate change, developmental systems, sex-differences in behavior, Haldane's rule and the large X-effect, and transgressive phenotypic variation.


Assuntos
Evolução Biológica , Hominidae , Hibridização Genética/genética , Animais , Antropologia Física , Feminino , Genoma Humano/genética , Hominidae/anatomia & histologia , Hominidae/genética , Humanos , Masculino , Camundongos , Homem de Neandertal/anatomia & histologia , Homem de Neandertal/genética , Fenótipo , Crânio/anatomia & histologia
7.
J Dairy Sci ; 102(7): 6263-6275, 2019 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-31103297

RESUMO

Domestic yaks (Bos grunniens) and domestic Taurus cattle (Bos taurus) are closely related. An interesting phenomenon in interspecific crossings is male sterility in the F1 hybrid (yattle) and F2 backcross, with no late meiotic cells or spermatids in the seminiferous tubules. The mammalian Y chromosome is crucial for spermatogenesis and male fertility. This study investigated the copy number variations and mRNA of Y-transitional region genes TSPY2 (testis specific protein, Y-linked 2 and testis-specific Y-encoded protein 3-like) and PRAMEY (preferentially expressed antigen in melanoma, Y-linked), and Y-ampliconic region genes TSPY (testis-specific Y-encoded protein 1-like), ZNF280BY (zinc finger protein 280B, Y-linked) and HSFY (heat-shock transcription factor, Y-linked) in mature testes from Taurus cattle, yaks, and yattle. Phylogenetic trees divided 33 copies of TSPY into major 2 types (TSPY-T1 and TSPY-T2), 19 copies of TSPY2 into 2 types (TSPY2-T1 and T2), and 8 copies of PRAMEY into 4 types (PRAMEY-T1 to T4). Searching by the Basic Local Alignment Search Tool of the TSPY2 coding sequences in GenBank revealed that TSPY2 was conserved in Bovidae. The TSPY2-T2 sequences were absent, whereas PRAMEY-T2 and PRAMEY-T4 were amplified on the yak Y chromosome. The average copy numbers of TSPY-T2 and ZNF280BY were significantly different between cattle and yaks. The TSPY-T2, TSPY2, PRAMEY, ZNF280BY, and HSFY genes were uniquely or predominantly expressed in testes. Reverse-transcription quantitative PCR showed that the TSPY-T2, PRAMEY-T2, HSFY, ZNF280BY, protamine 1 (PRM1), and protamine 2 (PRM2) genes were almost not expressed in yattle. The PRM1 and PRM2 genes are used as positive markers for spermatozoa. Thus, our results showed that the genomic structure of the Y-transitional and Y-ampliconic region differed between Taurus cattle and yaks. Dysregulated expression of Y-ampliconic region genes TSPY-T2, HSPY, ZNF280BY, and Y-transitional region gene PRAMEY-T2 may be associated with hybrid male sterility in yattle.


Assuntos
Antígenos de Neoplasias/genética , Bovinos/genética , Proteínas de Ciclo Celular/genética , Ligação Genética/genética , Hibridização Genética/genética , Cromossomo Y/genética , Animais , Cruzamentos Genéticos , Variações do Número de Cópias de DNA , Expressão Gênica , Regulação da Expressão Gênica , Variação Genética/genética , Infertilidade Masculina/genética , Masculino , Filogenia , RNA Mensageiro/análise , Espermatogênese/genética , Testículo/metabolismo
8.
PLoS Comput Biol ; 15(4): e1006949, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30986215

RESUMO

Understanding genomic structural variation such as inversions and translocations is a key challenge in evolutionary genetics. We develop a novel statistical approach to comparative genetic mapping to detect large-scale structural mutations from low-level sequencing data. The procedure, called Genome Order Optimization by Genetic Algorithm (GOOGA), couples a Hidden Markov Model with a Genetic Algorithm to analyze data from genetic mapping populations. We demonstrate the method using both simulated data (calibrated from experiments on Drosophila melanogaster) and real data from five distinct crosses within the flowering plant genus Mimulus. Application of GOOGA to the Mimulus data corrects numerous errors (misplaced sequences) in the M. guttatus reference genome and confirms or detects eight large inversions polymorphic within the species complex. Finally, we show how this method can be applied in genomic scans to improve the accuracy and resolution of Quantitative Trait Locus (QTL) mapping.


Assuntos
Mapeamento Cromossômico/métodos , Biologia Computacional/métodos , Variação Genética/genética , Algoritmos , Animais , Evolução Biológica , Drosophila/genética , Genética Populacional/métodos , Genoma/fisiologia , Genômica , Hibridização Genética/genética , Cadeias de Markov , Mimulus/genética , Fenótipo , Locos de Características Quantitativas/genética
9.
BMC Bioinformatics ; 20(1): 207, 2019 Apr 23.
Artigo em Inglês | MEDLINE | ID: mdl-31014244

RESUMO

BACKGROUND: Research over the last 10 years highlights the increasing importance of hybridization between species as a major force structuring the evolution of genomes and potentially providing raw material for adaptation by natural and/or sexual selection. Fueled by research in a few model systems where phenotypic hybrids are easily identified, research into hybridization and introgression (the flow of genes between species) has exploded with the advent of whole-genome sequencing and emerging methods to detect the signature of hybridization at the whole-genome or chromosome level. Amongst these are a general class of methods that utilize patterns of single-nucleotide polymorphisms (SNPs) across a tree as markers of hybridization. These methods have been applied to a variety of genomic systems ranging from butterflies to Neanderthals to detect introgression, however, when employed at a fine genomic scale these methods do not perform well to quantify introgression in small sample windows. RESULTS: We introduce a novel method to detect introgression by combining two widely used statistics: pairwise nucleotide diversity dxy and Patterson's D. The resulting statistic, the distance fraction (df), accounts for genetic distance across possible topologies and is designed to simultaneously detect and quantify introgression. We also relate our new method to the recently published fd and incorporate these statistics into the powerful genomics R-package PopGenome, freely available on GitHub (pievos101/PopGenome) and the Comprehensive R Archive Network (CRAN). The supplemental material contains a wide range of simulation studies and a detailed manual how to perform the statistics within the PopGenome framework. CONCLUSION: We present a new distance based statistic df that avoids the pitfalls of Patterson's D when applied to small genomic regions and accurately quantifies the fraction of introgression (f) for a wide range of simulation scenarios.


Assuntos
Genômica/métodos , Hibridização Genética/genética , Modelos Genéticos , Sequenciamento Completo do Genoma/métodos , Bases de Dados Genéticas , Fluxo Gênico , Modelos Estatísticos , Polimorfismo de Nucleotídeo Único
10.
Nat Plants ; 5(4): 369-379, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30962527

RESUMO

The evolution of domesticated cereals was a complex interaction of shifting selection pressures and repeated episodes of introgression. Genomes of archaeological crops have the potential to reveal these dynamics without being obscured by recent breeding or introgression. We report a temporal series of archaeogenomes of the crop sorghum (Sorghum bicolor) from a single locality in Egyptian Nubia. These data indicate no evidence for the effects of a domestication bottleneck, but instead reveal a steady decline in genetic diversity over time coupled with an accumulating mutation load. Dynamic selection pressures acted sequentially to shape architectural and nutritional domestication traits and to facilitate adaptation to the local environment. Later introgression between sorghum races allowed the exchange of adaptive traits and achieved mutual genomic rescue through an ameliorated mutation load. These results reveal a model of domestication in which genomic adaptation and deterioration were not focused on the initial stages of domestication but occurred throughout the history of cultivation.


Assuntos
Domesticação , Sorghum/genética , Adaptação Fisiológica/genética , Produtos Agrícolas/genética , Produtos Agrícolas/história , História Antiga , Hibridização Genética/genética , Característica Quantitativa Herdável
11.
PLoS Genet ; 15(3): e1008055, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30875370

RESUMO

Lethal recessive alleles cause pre- or postnatal death in homozygous affected individuals, reducing fertility. Especially in small size domestic and wild populations, those alleles might be exposed by inbreeding, caused by matings between related parents that inherited the same recessive lethal allele from a common ancestor. In this study we report five relatively common (up to 13.4% carrier frequency) recessive lethal haplotypes in two commercial pig populations. The lethal haplotypes have a large effect on carrier-by-carrier matings, decreasing litter sizes by 15.1 to 21.6%. The causal mutations are of different type including two splice-site variants (affecting POLR1B and TADA2A genes), one frameshift (URB1), and one missense (PNKP) variant, resulting in a complete loss-of-function of these essential genes. The recessive lethal alleles affect up to 2.9% of the litters within a single population and are responsible for the death of 0.52% of the total population of embryos. Moreover, we provide compelling evidence that the identified embryonic lethal alleles contribute to the observed heterosis effect for fertility (i.e. larger litters in crossbred offspring). Together, this work marks specific recessive lethal variation describing its functional consequences at the molecular, phenotypic, and population level, providing a unique model to better understand fertility and heterosis in livestock.


Assuntos
Genes Letais , Mutação com Perda de Função , Sus scrofa/embriologia , Sus scrofa/genética , Sequência de Aminoácidos , Animais , Feminino , Fertilidade/genética , Genes Recessivos , Deriva Genética , Genética Populacional , Haplótipos , Vigor Híbrido/genética , Hibridização Genética/genética , Tamanho da Ninhada de Vivíparos/genética , Masculino , Gravidez , RNA Polimerase I/genética , Análise de Sequência de RNA , Sequenciamento Completo do Genoma
12.
Nat Genet ; 51(3): 541-547, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30804557

RESUMO

Cultivated strawberry emerged from the hybridization of two wild octoploid species, both descendants from the merger of four diploid progenitor species into a single nucleus more than 1 million years ago. Here we report a near-complete chromosome-scale assembly for cultivated octoploid strawberry (Fragaria × ananassa) and uncovered the origin and evolutionary processes that shaped this complex allopolyploid. We identified the extant relatives of each diploid progenitor species and provide support for the North American origin of octoploid strawberry. We examined the dynamics among the four subgenomes in octoploid strawberry and uncovered the presence of a single dominant subgenome with significantly greater gene content, gene expression abundance, and biased exchanges between homoeologous chromosomes, as compared with the other subgenomes. Pathway analysis showed that certain metabolomic and disease-resistance traits are largely controlled by the dominant subgenome. These findings and the reference genome should serve as a powerful platform for future evolutionary studies and enable molecular breeding in strawberry.


Assuntos
Fragaria/genética , Genoma de Planta/genética , Cromossomos de Plantas/genética , Diploide , Evolução Molecular , Expressão Gênica/genética , Hibridização Genética/genética , Melhoramento Vegetal/métodos , Poliploidia
13.
PLoS Pathog ; 15(1): e1007513, 2019 01.
Artigo em Inglês | MEDLINE | ID: mdl-30673782

RESUMO

Mesenteric infection by the parasitic blood fluke Schistosoma bovis is a common veterinary problem in Africa and the Middle East and occasionally in the Mediterranean Region. The species also has the ability to form interspecific hybrids with the human parasite S. haematobium with natural hybridisation observed in West Africa, presenting possible zoonotic transmission. Additionally, this exchange of alleles between species may dramatically influence disease dynamics and parasite evolution. We have generated a 374 Mb assembly of the S. bovis genome using Illumina and PacBio-based technologies. Despite infecting different hosts and organs, the genome sequences of S. bovis and S. haematobium appeared strikingly similar with 97% sequence identity. The two species share 98% of protein-coding genes, with an average sequence identity of 97.3% at the amino acid level. Genome comparison identified large continuous parts of the genome (up to several 100 kb) showing almost 100% sequence identity between S. bovis and S. haematobium. It is unlikely that this is a result of genome conservation and provides further evidence of natural interspecific hybridization between S. bovis and S. haematobium. Our results suggest that foreign DNA obtained by interspecific hybridization was maintained in the population through multiple meiosis cycles and that hybrids were sexually reproductive, producing viable offspring. The S. bovis genome assembly forms a highly valuable resource for studying schistosome evolution and exploring genetic regions that are associated with species-specific phenotypic traits.


Assuntos
Hibridização Genética/genética , Schistosoma/genética , África , África Ocidental , Animais , Sequência de Bases/genética , Bovinos , Mapeamento Cromossômico/métodos , DNA/genética , Genoma/genética , Genoma Mitocondrial/genética , Hibridização Genética/fisiologia , Oriente Médio , Filogenia , Proteoma/genética , Especificidade da Espécie , Trematódeos/genética , Sequenciamento Completo do Genoma/métodos
14.
Proc Natl Acad Sci U S A ; 116(5): 1651-1658, 2019 01 29.
Artigo em Inglês | MEDLINE | ID: mdl-30642962

RESUMO

Date palm (Phoenix dactylifera L.) is a major fruit crop of arid regions that were domesticated ∼7,000 y ago in the Near or Middle East. This species is cultivated widely in the Middle East and North Africa, and previous population genetic studies have shown genetic differentiation between these regions. We investigated the evolutionary history of P. dactylifera and its wild relatives by resequencing the genomes of date palm varieties and five of its closest relatives. Our results indicate that the North African population has mixed ancestry with components from Middle Eastern P. dactylifera and Phoenix theophrasti, a wild relative endemic to the Eastern Mediterranean. Introgressive hybridization is supported by tests of admixture, reduced subdivision between North African date palm and P. theophrasti, sharing of haplotypes in introgressed regions, and a population model that incorporates gene flow between these populations. Analysis of ancestry proportions indicates that as much as 18% of the genome of North African varieties can be traced to P. theophrasti and a large percentage of loci in this population are segregating for single-nucleotide polymorphisms (SNPs) that are fixed in P. theophrasti and absent from date palm in the Middle East. We present a survey of Phoenix remains in the archaeobotanical record which supports a late arrival of date palm to North Africa. Our results suggest that hybridization with P. theophrasti was of central importance in the diversification history of the cultivated date palm.


Assuntos
Hibridização Genética/genética , Phoeniceae/genética , África do Norte , DNA de Plantas/genética , Domesticação , Variação Genética/genética , Genoma de Planta/genética , Hibridização de Ácido Nucleico/genética , Polimorfismo de Nucleotídeo Único/genética , Análise de Sequência de DNA/métodos
15.
Mar Biotechnol (NY) ; 21(2): 139-149, 2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-30426270

RESUMO

Autopolyploids are traditionally used to demonstrate multivalent pairing and unstable inheritance. However, the autotetraploid fish (4nRR) (RRRR, 4n = 200) derived from the distant hybridization of Carassius auratus red var. (RCC) (RR, 2n = 100) (♀) × Megalobrama amblycephala (BSB) (BB, 2n = 48) (♂) exhibits chromosome number (or ploidy) stability over consecutive generations (F1-F10). Comparative analysis based on somatic and gametic chromosomal loci [centromeric, 5S rDNA, and Ag-NORs (silver-stained nucleolar organizer regions)] revealed that a substantial loss of chromosomal loci during genome doubling increases the divergence between homologous chromosomes and that diploid-like chromosome pairing was restored during meiosis in the first generation of 4nRR lineages. In addition, a comparative analysis of genomes and transcriptomes from 4nRR (F1) and its diploid progenitor (RCC) exhibited significant genomic structure and gene expression changes. From these data, we suggest that genomes and genes diverge and that expression patterns change in the first generations following autotetraploidization, which are processes that might contribute to the stable inheritance and successful establishment of autotetraploid lineages.


Assuntos
Cyprinidae/genética , Carpa Dourada/genética , Hibridização Genética/genética , Tetraploidia , Animais , Cromossomos/genética , Feminino , Genoma , Hibridização in Situ Fluorescente , Masculino , Transcriptoma
16.
Plant Biol (Stuttg) ; 21(2): 267-277, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30382601

RESUMO

Paspalum is a noteworthy grass genus due to the forage quality of most species, with approximately 330 species, and the high proportion of those that reproduce via apomixis. Harnessing apomictic reproduction and widening knowledge about the cytogenetic relationships among species are essential tools for plant breeding. We conducted cytogenetic analyses of inter- and intraspecific hybridisations involving a sexual, colchicine-induced autotetraploid plant of P. plicatulum Michx. and five indigenous apomictic tetraploid (2n = 40) species: P. compressifolium Swallen, P. lenticulare Kunth, two accessions of P. nicorae Parodi, P. rojasii Hack. and two accessions of P. plicatulum. Fertility of the hybrids was investigated and their reproductive system was analysed considering the relative embryo:endosperm DNA content from flow cytometry. Morphological, nomenclatural and taxonomic issues were also analysed. Cytogenetic analysis suggested that all indigenous tetraploid accessions of five apomictic species are autotetraploid or segmental allotetraploid. If segmental allotetraploids, they probably originated through autoploidy followed by diploidisation processes. Autosyndetic male chromosome pairing observed in all hybrid families supported this assertion. Allosyndetic chromosome associations were also observed in all hybrid families. In the hybrids, the proportion of male parent chromosomes involved in allosyndesis per pollen mother cell varied from 5.5% to 35.0% and the maximum was between 25% and 60%. The apomictic condition of the indigenous male parents segregated in the hybrids. These results confirm a strong association between autoploidy and apomixis in Paspalum, and the existence of cytogenetic relationships between different species of the Plicatula group. Allosyndetic chromosome pairing and seed fertility of the hybrids suggest the feasibility of gene transfer among species.


Assuntos
Hibridização Genética/genética , Paspalum/genética , Poliploidia , Tetraploidia , Cromossomos de Plantas/genética , Citogenética , Meiose , Paspalum/anatomia & histologia , Paspalum/classificação , Filogeografia , Melhoramento Vegetal
17.
Sci China Life Sci ; 62(1): 22-45, 2019 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-30554295

RESUMO

Hybridization is widely used. However, for a long time, systematic theories and technologies related to hybridization in fish have been lacking. In this study, through long-term systematic research, we investigated and obtained the main rules regarding inheritance and reproduction related to fish distant hybridization. Furthermore, we established one-step and multistep breeding technologies that were suitable for interspecific hybridization and intraspecific hybridization. Simultaneously, we used these two breeding technologies to produce a batch of diploid fish lineages and tetraploid fish lineages and improved fishes. In addition, we widely discuss the methods, technologies and results of hybridization breeding, referring to the domestic and foreign literature on fish hybridization. We hope that this paper will be beneficial for the research and application of fish hybrid breeding.


Assuntos
Cruzamento/métodos , Peixes/genética , Hibridização Genética/genética , Animais , Diploide , Feminino , Peixes/classificação , Masculino , Ploidias , Reprodução/genética , Tetraploidia
18.
Mol Ecol ; 28(5): 1056-1069, 2019 03.
Artigo em Inglês | MEDLINE | ID: mdl-30582763

RESUMO

Speciation occurs when populations diverge and become reproductively isolated from each other. Natural selection is commonly accepted to play a large role in this process, and it has been widely assumed that reproductive isolation often results as a by-product of divergence driven by adaptation in allopatry. When such populations come into secondary contact, reinforcement can act to strengthen reproductive isolation, but the frequency and importance of this process are still unknown. Here, we explored genomic signatures of selection in allopatry and sympatry for loci associated with reproductive isolation using a natural primate hybrid zone. By analysing reduced-representation sequencing data, we quantified admixture and population structure across a howler monkey hybrid zone and examined the relationship between locus-specific differentiation and introgression. We detected extensive admixture that was mostly limited to the narrow contact zone. Loci with reduced introgression into the heterospecific genomic background (the pattern expected for loci associated with reproductive isolation due to selection against hybrids) were significantly more differentiated between allopatric parental populations than loci with neutral and increased introgression, supporting the hypothesis that reproductive isolation is a by-product of divergence in allopatry. Further, loci with reduced introgression showed greater differentiation in sympatry than in allopatry, suggesting a role for reinforcement. Thus, our results reflect multiple forms of selection that have shaped reproductive isolation in this system. We conclude that reproductive isolation may have initially been driven by divergence in allopatry, but later reinforced by divergent selection in sympatry.


Assuntos
Especiação Genética , Primatas/genética , Isolamento Reprodutivo , Seleção Genética/genética , Animais , Genética Populacional , Genoma/genética , Genômica , Hibridização Genética/genética , Primatas/crescimento & desenvolvimento , Reprodução/genética , Simpatria/genética
19.
BMC Plant Biol ; 18(1): 371, 2018 Dec 22.
Artigo em Inglês | MEDLINE | ID: mdl-30579326

RESUMO

BACKGROUND: Roses are important plants for human beings with pivotal economical and biological traits like continuous flowering, flower architecture, color and scent. Due to frequent hybridization and high genome heterozygosity, classification of roses and their relatives remains a big challenge. RESULTS: Here, to identify potential markers for phylogenetic reconstruction and to reveal the patterns of natural selection in roses, we generated sets of high quality and comprehensive reference transcriptomes for Rosa chinensis 'Old Blush' (OB) and R. wichuriana 'Basye's Thornless' (BT), two species exhibiting contrasted traits of high economical importance. The assembled reference transcriptomes showed transcripts N50 above 2000 bp. Two roses shared about 10,073 transcripts (N50 = 2282 bp), in which a set of 5959 transcripts was conserved within genera of Rosa. Further comparison with species in Rosaceae identified 4447 transcripts being common (Rosaceae-common) in Rosa, Malus, Prunus, Rubus, and Fragaria, while a pool of 164 transcripts being specific for roses (Rosa-specific). Among the Rosaceae-common transcripts, 409 transcripts showed a signature of positive selection and a clustered expression in different tissues. Interestingly, nine of these rapidly evolving genes were related to DNA damage repair and responses to environmental stimulus, a potential associated with genome confliction post hybridization. Coincident with this fast evolution pattern in rose genes, 24 F-box and four TMV resistant proteins were significantly enriched in the Rosa-specific genes. CONCLUSIONS: We expect that these Rosaceae-common and Rosa-specific transcripts should facilitate the phylogenetic analysis of Rosaceae plants as well as investigations of Rosa-specific biology. The data reported here could provide fundamental genomic tools and knowledge critical for understanding the biology and domestication of roses and for roses breeding.


Assuntos
Rosa/genética , Seleção Genética/genética , Transcriptoma/genética , Perfilação da Expressão Gênica , Genes de Plantas/genética , Hibridização Genética/genética , Filogenia , Rosácea/genética , Análise de Sequência de DNA
20.
BMC Plant Biol ; 18(1): 317, 2018 Dec 03.
Artigo em Inglês | MEDLINE | ID: mdl-30509159

RESUMO

BACKGROUND: Hybridization of species with porous genomes can eventually lead to introgression via repeated backcrossing. The potential for introgression between species is reflected by the extent of segregation distortion in later generation hybrids. Here we studied a population of hybrids between Salix purpurea and S. helvetica that has emerged within the last 30 years on a glacier forefield in the European Alps due to secondary contact of the parental species. We used 5758 biallelic SNPs produced by RAD sequencing with the aim to ascertain the predominance of backcrosses (F1 hybrid x parent) or F2 hybrids (F1 hybrid x F1 hybrid) among hybrid offspring. Further, the SNPs were used to study segregation distortion in the second hybrid generation. RESULTS: The analyses in STRUCTURE and NewHybrids revealed that the population consisted of parents and F1 hybrids, whereas hybrid offspring consisted mainly of backcrosses to either parental species, but also some F2 hybrids. Although there was a clear genetic differentiation between S. purpurea and S. helvetica (FST = 0.24), there was no significant segregation distortion in the backcrosses or the F2 hybrids. Plant height of the backcrosses resembled the respective parental species, whereas F2 hybrids were more similar to the subalpine S. helvetica. CONCLUSIONS: The co-occurrence of the parental species and the hybrids on the glacier forefield, the high frequency of backcrossing, and the low resistance to gene flow via backcrossing make a scenario of introgression in this young hybrid population highly likely, potentially leading to the transfer of adaptive traits. We further suggest that this willow hybrid population may serve as a model for the evolutionary processes initiated by recent global warming.


Assuntos
Hibridização Genética/genética , Salix/genética , Deriva Genética , Genética Populacional , Polimorfismo de Nucleotídeo Único/genética , Análise de Sequência de DNA/métodos
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