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1.
Int J Mol Sci ; 22(5)2021 Mar 05.
Artigo em Inglês | MEDLINE | ID: mdl-33807984

RESUMO

Black root rot (BRR) is an economically important disease of cotton and other crops, especially in cooler regions with short growing seasons. Symptoms include black discoloration of the roots, reduced number of lateral roots and stunted or slow plant growth. The cultivated tetraploid Gossypium species are susceptible to BRR. Resistance to BRR was identified in G. arboreum accession BM13H and is associated with reduced and restricted hyphal growth and less sporulation. Transcriptome analysis indicates that BM13H responds to infection at early time points 2- and 3-days post-inoculation, but by day 5, few differentially expressed genes are observed between infected and uninfected roots. Inheritance of BM13H resistance to BRR was evaluated in an F6 recombinant inbred population and shows a single semi-dominant locus conferring resistance that was fine mapped to a region on chromosome 1, containing ten genes including five putative resistance-like genes.


Assuntos
Ascomicetos/metabolismo , Mapeamento Cromossômico , Resistência à Doença/genética , Gossypium , Doenças das Plantas , Raízes de Plantas , Regulação da Expressão Gênica de Plantas , Gossypium/genética , Gossypium/metabolismo , Gossypium/microbiologia , Doenças das Plantas/genética , Doenças das Plantas/microbiologia , Raízes de Plantas/genética , Raízes de Plantas/metabolismo , Raízes de Plantas/microbiologia , Tetraploidia
2.
Nat Genet ; 53(4): 467-476, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33731941

RESUMO

Gene regulatory divergence is thought to play a central role in determining human-specific traits. However, our ability to link divergent regulation to divergent phenotypes is limited. Here, we utilized human-chimpanzee hybrid induced pluripotent stem cells to study gene expression separating these species. The tetraploid hybrid cells allowed us to separate cis- from trans-regulatory effects, and to control for nongenetic confounding factors. We differentiated these cells into cranial neural crest cells, the primary cell type giving rise to the face. We discovered evidence of lineage-specific selection on the hedgehog signaling pathway, including a human-specific sixfold down-regulation of EVC2 (LIMBIN), a key hedgehog gene. Inducing a similar down-regulation of EVC2 substantially reduced hedgehog signaling output. Mice and humans lacking functional EVC2 show striking phenotypic parallels to human-chimpanzee craniofacial differences, suggesting that the regulatory divergence of hedgehog signaling may have contributed to the unique craniofacial morphology of humans.


Assuntos
Quimera/genética , Síndrome de Ellis-Van Creveld/genética , Peptídeos e Proteínas de Sinalização Intercelular/genética , Crista Neural/metabolismo , Pan troglodytes/genética , Crânio/metabolismo , Animais , Evolução Biológica , Diferenciação Celular , Quimera/metabolismo , Síndrome de Ellis-Van Creveld/metabolismo , Síndrome de Ellis-Van Creveld/patologia , Feminino , Expressão Gênica , Genótipo , Humanos , Células-Tronco Pluripotentes Induzidas/citologia , Células-Tronco Pluripotentes Induzidas/metabolismo , Peptídeos e Proteínas de Sinalização Intercelular/deficiência , Masculino , Camundongos , Camundongos Knockout , Crista Neural/patologia , Pan troglodytes/anatomia & histologia , Pan troglodytes/metabolismo , Fenótipo , Transdução de Sinais , Crânio/anatomia & histologia , Especificidade da Espécie , Tetraploidia
3.
DNA Cell Biol ; 40(3): 441-456, 2021 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-33600242

RESUMO

IGT family genes function critically to regulate lateral organ orientation in plants. However, little information is available about this family of genes in Brassica napus. In this study, 27 BnIGT genes were identified on 16 chromosomes and divided into seven clades, namely LAZY1∼LAZY6 and TAC1 (Tiller Angle Control 1), based on their phylogenetic relationships. Duplication analysis revealed that 91.1% of the gene pairs were derived from whole-genome duplication. Most BnIGT genes had a similar structural pattern with one or two very short exons followed by a long and a shorter exon. Common and specific motifs were identified among the seven clades, and motif 1, containing the family-specific GφL(A/T)IGT sequence, was observed in all clades except LAZY5. Three types of cis-elements pertinent to transcription factor binding, light responses, and hormone signaling were detected in the BnIGT promoters. Intriguingly, more than half of the BnIGT genes exhibited no or very low expression in various tissues, and the LAZY1 and TAC1 clade members showed distinct tissue expression preferences. Coexpression analysis revealed that the LAZY1 members had strong associations with cell wall biosynthesis genes. This analysis provides a deeper understanding of the BnIGT gene family and will facilitate further deduction of their role in regulating plant architecture in B. napus.


Assuntos
Brassica napus , Regulação da Expressão Gênica de Plantas/fisiologia , Família Multigênica , Proteínas de Plantas , Tetraploidia , Brassica napus/genética , Brassica napus/metabolismo , Estudo de Associação Genômica Ampla , Proteínas de Plantas/biossíntese , Proteínas de Plantas/genética
4.
BMC Plant Biol ; 21(1): 115, 2021 Feb 25.
Artigo em Inglês | MEDLINE | ID: mdl-33632125

RESUMO

BACKGROUND: Cotton stem trichomes and seed fibers are each single celled structures formed by protrusions of epidermal cells, and were found sharing the overlapping molecular mechanism. Compared with fibers, cotton stem trichomes are more easily observed, but the molecular mechanisms underlying their development are still poorly understood. RESULTS: In this study, Gossypium hirsutum (Gh) and G. barbadense (Gb) were found to differ greatly in percentages of varieties/accessions with glabrous stems and in trichome density, length, and number per trichopore. Gh varieties normally had long singular and clustered trichomes, while Gb varieties had short clustered trichomes. Genetic mapping using five F2 populations from crosses between glabrous varieties and those with different types of stem trichomes revealed that much variation among stem trichome phenotypes could be accounted for by different combinations of genes/alleles on Chr. 06 and Chr. 24. The twenty- six F1 generations from crosses between varieties with different types of trichomes had varied phenotypes, further suggesting that the trichomes of tetraploid cotton were controlled by different genes/alleles. Compared to modern varieties, a greater proportion of Gh wild accessions were glabrous or had shorter and denser trichomes; whereas a smaller proportion of Gb primitive accessions had glabrous stems. A close correlation between fuzz fiber number and stem trichome density was observed in both Gh and Gb primitive accessions and modern varieties. CONCLUSION: Based on these findings, we hypothesize that stem trichomes evolved in parallel with seed fibers during the domestication of cultivated tetraploid cotton. In addition, the current results illustrated that stem trichome can be used as a morphological index of fiber quality in cotton conventional breeding.


Assuntos
Gossypium/crescimento & desenvolvimento , Tricomas/crescimento & desenvolvimento , Evolução Biológica , Fibra de Algodão , Produtos Agrícolas/genética , Produtos Agrícolas/crescimento & desenvolvimento , Cruzamentos Genéticos , Especiação Genética , Gossypium/genética , Caules de Planta/citologia , Caules de Planta/genética , Caules de Planta/crescimento & desenvolvimento , Especificidade da Espécie , Tetraploidia , Tricomas/genética
5.
BMC Plant Biol ; 21(1): 89, 2021 Feb 10.
Artigo em Inglês | MEDLINE | ID: mdl-33568051

RESUMO

BACKGROUND: Dirigent (DIR) proteins mediate regioselectivity and stereoselectivity during lignan biosynthesis and are also involved in lignin, gossypol and pterocarpan biosynthesis. This gene family plays a vital role in enhancing stress resistance and in secondary cell-wall development, but systematical understanding is lacking in cotton. RESULTS: In this study, 107 GbDIRs and 107 GhDIRs were identified in Gossypium barbadense and Gossypium hirsutum, respectively. Most of these genes have a classical gene structure without intron and encode proteins containing a signal peptide. Phylogenetic analysis showed that cotton DIR genes were classified into four distinct subfamilies (a, b/d, e, and f). Of these groups, DIR-a and DIR-e were evolutionarily conserved, and segmental and tandem duplications contributed equally to their formation. In contrast, DIR-b/d mainly expanded by recent tandem duplications, accompanying with a number of gene clusters. With the rapid evolution, DIR-b/d-III was a Gossypium-specific clade involved in atropselective synthesis of gossypol. RNA-seq data highlighted GhDIRs in response to Verticillium dahliae infection and suggested that DIR gene family could confer Verticillium wilt resistance. We also identified candidate DIR genes related to fiber development in G. barbadense and G. hirsutum and revealed their differential expression. To further determine the involvement of DIR genes in fiber development, we overexpressed a fiber length-related gene GbDIR78 in Arabidopsis and validated its function in trichomes and hypocotyls. CONCLUSIONS: These findings contribute novel insights towards the evolution of DIR gene family and provide valuable information for further understanding the roles of DIR genes in cotton fiber development as well as in stress responses.


Assuntos
Produtos Agrícolas/genética , Evolução Molecular , Genes de Plantas , Gossypium/genética , Proteínas de Plantas/genética , Tetraploidia , Regulação da Expressão Gênica de Plantas , Variação Genética , Genótipo , Filogenia
6.
J Plant Res ; 134(2): 195-208, 2021 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-33559786

RESUMO

Phegopteris decursivepinnata includes diploids, tetraploids, and triploid hybrids based on x = 30. We obtained polyploid progeny from triploid hybrids through selfing and crossing experiments. Triploids occasionally formed well-filled spores. The mean occurrence frequencies of well-filled and germinated spores were 2.8% and 0.8%, respectively. Viable spores that succeeded in germinating were regarded as unreduced, triploid spores, because the resulting gametophytes yielded triploid (2n = 86-92) and hexaploid (2n = 170-184) progeny in both isolated and mixed cultures of gametophytes. The triploid and hexaploid progeny likely arose apogamously and sexually, respectively. One of the hexaploid progeny yielded hexaploid sporophytes (2n = 169-180) in the mixed culture of its gametophytes. Artificial crossing between triploid and diploid sporophytes produced tetraploid (2n = 116, 120) and pentaploid (2n = 145-150) progeny that likely arose through the mating of 3x gametes from the triploid with both 1x and 2x gametes from the diploid, respectively. Unreduced spore formation was confirmed in diploid sporophytes. The tetraploid progeny formed viable spores at a frequency of 63-75%. Triploid hybrids of this species are thus expected to produce new triploids, tetraploids, and hexaploids in nature. The wide range of variation in chromosome numbers of hexaploid progeny suggests that viable spores from parental triploid hybrids had unreduced chromosomes, whose numbers, however, deviated considerably from those of the hybrids. This chromosome deviation of viable spores may result from errant movements of chromatids of univalents when unreduced dyads form in meiosis. Downward chromosome deviation from the chromosome number of the parental hybrids may affect the developmental progress of viable spores more tolerantly than upward chromosome deviation.


Assuntos
Poliploidia , Triploidia , Diploide , Células Germinativas Vegetais , Humanos , Hibridização Genética , Esporos/genética , Tetraploidia
7.
Am J Bot ; 108(2): 297-308, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-33580499

RESUMO

PREMISE: Whole-genome duplication (polyploidy) is an important force shaping flowering-plant evolution. Ploidy-specific plant-pollinator interactions represent important community-level biotic interactions that can lead to nonrandom mating and the persistence of mixed-ploidy populations. METHODS: At a naturally occurring diploid-tetraploid contact zone of the autopolyploid desert shrub Larrea tridentata, we combined flower phenology analyses, collections of bees on plants of known cytotype, and flow cytometry analyses of bee-collected pollen loads to investigate whether (1) diploid and tetraploid plants have unique bee pollinator assemblages, (2) bee taxa exhibit ploidy-specific visitation and pollen collection biases, and (3) specialist and generalist bee taxa have ploidy-specific visitation and pollen collection biases. RESULTS: Although bee assemblages overlapped, we found significant differences in bee visitation to co-occurring diploids and tetraploids, with the introduced honeybee (Apis mellifera) and one native species (Andrena species 12) more frequently visiting tetraploids. Consistent with bee assemblage differences, we found that diploid pollen was overrepresented among pollen loads on native bees, while pollen loads on A. mellifera did not deviate from the random expectation. However, mismatches between the ploidy of pollen loads and plants were common, consistent with ongoing intercytotype gene flow. CONCLUSIONS: Our data are consistent with cytotype-specific bee visitation and suggest that pollinator behavior contributes to reduced diploid-tetraploid mating. Differences in bee visitation and pollen movement potentially contribute to an easing of minority cytotype exclusion and the facilitation of cytotype co-occurrence.


Assuntos
Diploide , Larrea , Animais , Abelhas/genética , Pólen , Simpatria , Tetraploidia
8.
J Agric Food Chem ; 69(4): 1300-1307, 2021 Feb 03.
Artigo em Inglês | MEDLINE | ID: mdl-33494603

RESUMO

We profiled and quantified primary (amine, organic acids, tricarboxylic acid cycle intermediates, amino acids, and carbohydrates) and secondary metabolites (triterpenoids, phenolic acids, carotenoids, flavonoids, and anthocyanins) in the edible parts (leaves and fruits) of the diploid and tetraploid cultivar Morus alba L. 'Cheongil.' Through comprehensive metabolic profiling, the tetraploid mulberry cultivar was able to produce diverse metabolites supported by higher accumulation patterns of primary and secondary metabolites in their edible parts. In particular, the edible parts of the tetraploid showed higher accumulation patterns of most metabolites (amino acids, carbohydrates, carotenoids, and anthocyanins) than the diploid, which was supported by the results of principal component analyses (PCAs) showing a clear separation between the diploid and tetraploid groups. Additionally, this metabolome study comprehensively described the correlation between primary and secondary metabolites in the edible parts of diploid and tetraploid mulberry cultivars and provided information useful for plant breeding strategies to improve metabolite biosynthesis using polyploidy.


Assuntos
Frutas/química , Frutas/metabolismo , Morus/genética , Antocianinas/análise , Antocianinas/metabolismo , Carotenoides/análise , Carotenoides/metabolismo , Diploide , Frutas/genética , Metabolômica , Morus/química , Morus/metabolismo , Extratos Vegetais , Metabolismo Secundário , Tetraploidia
9.
Int J Mol Sci ; 22(2)2021 Jan 07.
Artigo em Inglês | MEDLINE | ID: mdl-33430246

RESUMO

Among the fungal diseases of apple trees, serious yield losses are due to an apple scab caused by Venturia inaequalis. Protection against this disease is based mainly on chemical treatments, which are currently very limited. Therefore, it is extremely important to introduce cultivars with reduced susceptibility to this pathogen. One of the important sources of variability for breeding is the process of polyploidization. Newly obtained polyploids may acquire new features, including increased resistance to diseases. In our earlier studies, numerous tetraploids have been obtained for several apple cultivars with 'Free Redstar' tetraploids manifesting enhanced resistance to apple scab. In the present study, tetraploids of 'Free Redstar' were assessed in terms of phenotype and genotype with particular emphasis on the genetic background of their increased resistance to apple scab. Compared to diploid plants, tetraploids (own-rooted plants) were characterized with poor growth, especially during first growing season. They had considerably shorter shoots, fewer branches, smaller stem diameter, and reshaped leaves. In contrast to own-rooted plants, in M9-grafted three-year old trees, no significant differences between diplo- and tetraploids were observed, either in morphological or physiological parameters, with the exceptions of the increased leaf thickness and chlorophyll content recorded in tetraploids. Significant differences between sibling tetraploid clones were recorded, particularly in leaf shape and some physiological parameters. The amplified fragment length polymorphism (AFLP) analysis confirmed genetic polymorphism of tetraploid clones. Methylation-sensitive amplification polymorphism (MSAP) analysis showed that the level of DNA methylation was twice as high in young tetraploid plants as in a diploid donor tree, which may explain the weaker vigour of neotetraploids in the early period of their growth in the juvenile phase. Molecular analysis showed that 'Free Redstar' cultivar and their tetraploids bear six Rvi genes (Rvi5, Rvi6, Rvi8, Rvi11, Rvi14 and Rvi17). Transcriptome analysis confirmed enhanced resistance to apple scab of 'Free Redstar' tetraploids since the expression levels of genes related to resistance were strongly enhanced in tetraploids compared to their diploid counterparts.


Assuntos
/genética , Genoma/genética , Malus/genética , Doenças das Plantas/genética , /patogenicidade , Duplicação Gênica/genética , Genótipo , Fenótipo , Melhoramento Vegetal , Doenças das Plantas/microbiologia , Tetraploidia
10.
Nature ; 590(7846): 492-497, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-33505027

RESUMO

Whole-genome doubling (WGD) is common in human cancers, occurring early in tumorigenesis and generating genetically unstable tetraploid cells that fuel tumour development1,2. Cells that undergo WGD (WGD+ cells) must adapt to accommodate their abnormal tetraploid state; however, the nature of these adaptations, and whether they confer vulnerabilities that can be exploited therapeutically, is unclear. Here, using sequencing data from roughly 10,000 primary human cancer samples and essentiality data from approximately 600 cancer cell lines, we show that WGD gives rise to common genetic traits that are accompanied by unique vulnerabilities. We reveal that WGD+ cells are more dependent than WGD- cells on signalling from the spindle-assembly checkpoint, DNA-replication factors and proteasome function. We also identify KIF18A, which encodes a mitotic kinesin protein, as being specifically required for the viability of WGD+ cells. Although KIF18A is largely dispensable for accurate chromosome segregation during mitosis in WGD- cells, its loss induces notable mitotic errors in WGD+ cells, ultimately impairing cell viability. Collectively, our results suggest new strategies for specifically targeting WGD+ cancer cells while sparing the normal, non-transformed WGD- cells that comprise human tissue.


Assuntos
Genoma Humano/genética , Mitose/efeitos dos fármacos , Neoplasias/genética , Neoplasias/patologia , Tetraploidia , Cariótipo Anormal/efeitos dos fármacos , Neoplasias da Mama/genética , Neoplasias da Mama/patologia , Linhagem Celular Tumoral , Feminino , Genes Letais/genética , Humanos , Cinesina/deficiência , Cinesina/genética , Cinesina/metabolismo , Pontos de Checagem da Fase M do Ciclo Celular/efeitos dos fármacos , Masculino , Mitose/genética , Complexo de Endopeptidases do Proteassoma/metabolismo , Reprodutibilidade dos Testes , Fuso Acromático/efeitos dos fármacos
11.
Plant Physiol Biochem ; 160: 94-105, 2021 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-33485151

RESUMO

The Hylocereus species that are grown as exotic fruit crops are very often farmed under marginal agronomic conditions, which may include exposure to high temperatures. Here we present a pioneering investigation of grafting as an agro-technique to improve heat tolerance in Hylocereus. To this end, we studied the diploid species H. undatus, the tetraploid H. megalanthus and its di-haploid gamete-derived line 2719, and the interspecific-interploid tetraploid Z-10, all grafted onto H. undatus as the rootstock. Self-grafted, grafted and non-grafted plants were acclimated for one week (to obtain baseline values) and then exposed to heat stress (45/35 °C day/night) for three days, followed by a one-week recovery period under optimal temperatures (30/22 °C). A comparison of the physiological, biochemical and molecular performances of the grafted and self-grafted plants under heat stress and during the recovery period vs those of non-stressed plants (control; 30/22 °C) showed that the grafted and self-grafted plants performed better in most of the assessments: grafted and self-grafted plants recovered more rapidly from the heat stress and suffered far less stem damage. An unexpected - but important - finding that may have implications for other crop was that the self-grafted plants showed better performance than non-grafted plants throughout the trial. Our findings provide support for grafting as a strategy for coping with the stress induced by extremely high temperatures. This study thus paves the way for further investigations of grafting in Hylocereus as a valuable technique that will maintain crop productivity in the face of increasing worldwide temperatures.


Assuntos
Cactaceae/fisiologia , Horticultura/métodos , Temperatura Alta , Estresse Fisiológico , Cactaceae/classificação , Tetraploidia
12.
PLoS One ; 16(1): e0240703, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33417607

RESUMO

The tetraploid Avena species in the section Pachycarpa Baum, including A. insularis, A. maroccana, and A. murphyi, are thought to be involved in the evolution of hexaploid oats; however, their genome designations are still being debated. Repetitive DNA sequences play an important role in genome structuring and evolution, so understanding the chromosomal organization and distribution of these sequences in Avena species could provide valuable information concerning genome evolution in this genus. In this study, the chromosomal organizations and distributions of six repetitive DNA sequences (including three SSR motifs (TTC, AAC, CAG), one 5S rRNA gene fragment, and two oat A and C genome specific repeats) were investigated using non-denaturing fluorescence in situ hybridization (ND-FISH) in the three tetraploid species mentioned above and in two hexaploid oat species. Preferential distribution of the SSRs in centromeric regions was seen in the A and D genomes, whereas few signals were detected in the C genomes. Some intergenomic translocations were observed in the tetraploids; such translocations were also detected between the C and D genomes in the hexaploids. These results provide robust evidence for the presence of the D genome in all three tetraploids, strongly suggesting that the genomic constitution of these species is DC and not AC, as had been thought previously.


Assuntos
Avena/genética , Cromossomos de Plantas/genética , Genoma de Planta , Tetraploidia
13.
Int J Mol Sci ; 22(2)2021 Jan 15.
Artigo em Inglês | MEDLINE | ID: mdl-33467721

RESUMO

Neo-tetraploid rice with high fertility is a useful germplasm for polyploid rice breeding, which was developed from the crossing of different autotetraploid rice lines. However, little information is available on the molecular mechanism underlying the fertility of neo-tetraploid rice. Here, two contrasting populations of tetraploid rice, including one with high fertility (hereafter referred to as JG) and another with low fertility (hereafter referred to as JD), were generated by crossing Huaduo 3 (H3), a high fertility neo-tetraploid rice that was developed by crossing Jackson-4x with 96025-4x, and Huajingxian74-4x (T452), a low fertility autotetraploid rice parent. Cytological, global genome sequencing-based bulked-segregant (BSA-seq) and CRISPR/Cas9 technology were employed to study the genes associated with pollen fertility in neo-tetraploid rice. The embryo sacs of JG and JD lines were normal; however, pollen fertility was low in JD, which led to scarce fertilization and low seed setting. Cytological observations displayed low pollen fertility (25.1%) and approximately 31.3 and 27.2% chromosome lagging at metaphase I and II, and 28.8 and 24.8% chromosome straggling at anaphase I and II in JD, respectively. BSA-seq of F2-3 generations and RNA-seq of F4 generation detected a common fragment, i.e., 18,915,234-19,500,000, at chromosome 7, which was comprised of 78 genes associated with fertility. Among 78 genes, 9 genes had been known to be involved in meiosis and pollen development. Two mutants ny1 (LOC_Os07g32406) and ny2 (LOC_Os07g32040) were generated by CRISPR/Cas9 knockout in neo-tetraploid rice, and which exhibited low pollen fertility and abnormal chromosome behavior. Our study revealed that two unknown genes, LOC_Os07g32406 (NY1) and LOC_Os07g32040 (NY2) play an important role in pollen development of neo-tetraploid rice and provides a new perspective about the genetic mechanisms of fertility in polyploid rice.


Assuntos
Regulação da Expressão Gênica de Plantas , Genoma de Planta , Oryza/genética , Pólen/genética , Tetraploidia , Sistemas CRISPR-Cas , Mapeamento Cromossômico , Cromossomos de Plantas/genética , Perfilação da Expressão Gênica , Meiose , Mutação , Oryza/fisiologia , Melhoramento Vegetal , Infertilidade das Plantas/genética , RNA-Seq
14.
Methods Mol Biol ; 2264: 177-186, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33263910

RESUMO

The cultivated potato is tetraploid with four probably equivalent loci for each gene. A potato variety is furthermore commonly genetically heterogeneous and selected based on a beneficial genetic context which is maintained by clonal propagation. When introducing genetic changes by genome editing it is then desirable to achieve edits in all four loci for a certain gene target. This is in order to avoid crosses to achieve homozygosity for edited gene loci and at the same time reduce risk of inbreeding depression. In such a context transient transfection of protoplasts for the introduction of mutations, avoiding stable insertion of foreign DNA, would be very attractive. The protocol of this chapter has been shown to be applicable for the introduction of mutations by DNA vectors containing expression cassettes of TALEN, Cas9, and Cas9 deaminase fusions together with sgRNA expression cassettes on either single or separate vectors. Furthermore, the protoplast-based system has been shown to work very efficiently for mutations introduced by in vitro-produced and transfected RNP (ribonucleoprotein) complexes.


Assuntos
Sistemas CRISPR-Cas , Edição de Genes , Genoma de Planta , Proteínas de Plantas/antagonistas & inibidores , Protoplastos/fisiologia , Solanum tuberosum/genética , Tetraploidia , Mutação , Proteínas de Plantas/genética , Solanum tuberosum/crescimento & desenvolvimento
15.
BMC Evol Biol ; 20(1): 148, 2020 11 09.
Artigo em Inglês | MEDLINE | ID: mdl-33167862

RESUMO

BACKGROUND: Gene flow and polyploidy have been found to be important in Juniperus evolution. However, little evidence has been published elucidating the association of both phenomena in juniper taxa in the wild. Two main areas were studied in Spain (Eastern Iberian Range and Sierra de Baza) with both diploid and tetraploid taxa present in sympatry. Gene flow and ploidy level were assessed for these taxa and the resulted offspring. RESULTS: Twenty-two allo-triploid hybrids between J. sabina var. sabina and J. thurifera were found in the Eastern Iberian Range population. However, in the Sierra de Baza population no triploids were found. Instead, 18 allo-tetraploid hybrids between two tetraploid taxa: J. sabina var. balkanensis and J. thurifera were discovered. High genetic diversity was exhibited among the tetraploid hybrids at Sierra de Baza, in contrast to the genetically identical triploid hybrids at the Eastern Iberian Range; this suggests meiotic difficulties within the triploid hybrids. In addition, unidirectional gene flow was observed in both studied areas. CONCLUSION: Polyploidy and hybridization can be complementary partners in the evolution of Juniperus taxa in sympatric occurrences. Juniperus was shown to be an ideal coniferous model to study these two phenomena, independently or in concert.


Assuntos
Diploide , Fluxo Gênico , Juniperus , Hibridização Genética , Juniperus/genética , Espanha , Tetraploidia
17.
Nat Genet ; 52(10): 1018-1023, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-32989320

RESUMO

Potato (Solanum tuberosum L.) is the most important tuber crop worldwide. Efforts are underway to transform the crop from a clonally propagated tetraploid into a seed-propagated, inbred-line-based hybrid, but this process requires a better understanding of potato genome. Here, we report the 1.67-Gb haplotype-resolved assembly of a diploid potato, RH89-039-16, using a combination of multiple sequencing strategies, including circular consensus sequencing. Comparison of the two haplotypes revealed ~2.1% intragenomic diversity, including 22,134 predicted deleterious mutations in 10,642 annotated genes. In 20,583 pairs of allelic genes, 16.6% and 30.8% exhibited differential expression and methylation between alleles, respectively. Deleterious mutations and differentially expressed alleles were dispersed throughout both haplotypes, complicating strategies to eradicate deleterious alleles or stack beneficial alleles via meiotic recombination. This study offers a holistic view of the genome organization of a clonally propagated diploid species and provides insights into technological evolution in resolving complex genomes.


Assuntos
Genoma de Planta/genética , Haplótipos/genética , Anotação de Sequência Molecular , Solanum tuberosum/genética , Alelos , Diploide , Heterozigoto , Tetraploidia
18.
PLoS One ; 15(9): e0239377, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32986735

RESUMO

Double pollen fertility neutral genes, San and Sbn, can control pollen sterility in intersubspecific (indica × japonica) rice hybrids, which has excellent potential to increase rice yield. Previous studies showed that polyploidy could increase the interaction of three pollen sterility loci, i.e. Sa, Sb and Sc, which cause pollen sterility in autotetraploid rice hybrids, and hybrid fertility could be improved by double neutral genes, San and Sbn, in autotetraploid rice hybrids. We compared cytological and transcriptome data between autotetraploid and diploid rice hybrid during meiosis and single microspore stages to understand the molecular mechanism of neutral genes for overcoming pollen sterility in autotetraploid rice hybrids, which harbored double neutral genes. Cytological results revealed that the double neutral genes resulted in higher pollen fertility (76.74%) and lower chromosomal abnormalities in autotetraploid hybrid than in parents during metaphase I, metaphase II, anaphase I and anaphase II. Moreover, autotetraploid rice hybrid displayed stronger heterosis than a diploid hybrid. Compared with diploid rice hybrid, a total of 904 and 68 differently expressed genes (DEGs) were identified explicitly in autotetraploid hybrid at meiosis and single microspore stages, respectively. Of these, 133 and 41 genes were detected in higher-parent dominance and transgressive up-regulation dominance, respectively, which were considered autotetraploid potential heterosis genes, including a meiosis-related gene (Os01g0917500, MSP1) and two meiosis specific-genes (Os07g0624900 and Os04g0208600). Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genomes pathway (KEGG) analysis revealed that DEGs significantly enriched in amino acid metabolism and photosynthesis metabolism. These results indicated that meiosis-specific and meiosis-related genes, and amino acids and photosynthesis metabolism-related genes contribute to higher yield and pollen fertility in autotetraploid rice hybrid. This study provides a theoretical basis for molecular mechanisms of heterosis in autotetraploid rice harboring double neutral genes for pollen fertility.


Assuntos
Análise Citogenética , Diploide , Perfilação da Expressão Gênica , Genes de Plantas/genética , Oryza/genética , Tetraploidia , Cromossomos de Plantas/genética , Fenótipo , Infertilidade das Plantas/genética , Pólen/genética , Pólen/fisiologia
19.
Nat Commun ; 11(1): 4572, 2020 09 11.
Artigo em Inglês | MEDLINE | ID: mdl-32917907

RESUMO

Undomesticated wild species, crop wild relatives, and landraces represent sources of variation for wheat improvement to address challenges from climate change and the growing human population. Here, we study 56,342 domesticated hexaploid, 18,946 domesticated tetraploid and 3,903 crop wild relatives in a massive-scale genotyping and diversity analysis. Using DArTseqTM technology, we identify more than 300,000 high-quality SNPs and SilicoDArT markers and align them to three reference maps: the IWGSC RefSeq v1.0 genome assembly, the durum wheat genome assembly (cv. Svevo), and the DArT genetic map. On average, 72% of the markers are uniquely placed on these maps and 50% are linked to genes. The analysis reveals landraces with unexplored diversity and genetic footprints defined by regions under selection. This provides fertile ground to develop wheat varieties of the future by exploring specific gene or chromosome regions and identifying germplasm conserving allelic diversity missing in current breeding programs.


Assuntos
Variação Genética , Genoma de Planta , Triticum/genética , Alelos , Domesticação , Genótipo , Modelos Genéticos , Polimorfismo de Nucleotídeo Único , Alinhamento de Sequência , Tetraploidia
20.
PLoS One ; 15(6): e0235475, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32603381

RESUMO

Sea barley Hordeum marinum is an important germplasm resource. However, the origin of this tetraploid H. marinum subsp. gussoneanum is still unclear, which has caused great perplexity to the exploration and utilization of germplasm resources. We used two single-copy nuclear genes, thioredoxin-like gene (TRX) and waxy1 gene encoding granule-bound starch synthase (WAXY1) to analyze 41 accessions of Hordeum marinum. The phylogenies of different genes told different story of evolution of tetraploids of H. marinum subsp. gussoneanum. The phylogenetic trees showed that two distinct copies of sequences from both genes were detected for some accessions of the tetraploids of H. marinum subsp. gussoneanum, and diploid marinum might also contribute to the origin and evolution of the tetraploid gussoneanum. Our findings suggested that tetraploid more likely originated from the diploids of H. marinum subsp. gussoneanum and another ancestor that might be an extinct unknown diploid species. Homogenization of gene in tetraploids also occurred after polyploidization as both TRX and WAXY1 sequences in some accessions of tetraploid H. marinum subsp. gussoneanum cannot be distinguished, indicating the complicated evolution of this tetraploid.


Assuntos
Hordeum/genética , Filogenia , Evolução Biológica , Genes de Plantas , Genoma de Planta , Poliploidia , Sintase do Amido/genética , Tetraploidia , Tiorredoxinas/genética
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