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1.
DNA Cell Biol ; 39(10): 1850-1861, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32790504

RESUMO

Strigolactones (SLs) are the major plant hormones that play important roles in regulating organ development and environmental stress tolerance in plants. Even though the SL-related genes have been identified and well characterized in some plants, the information of SL-related genes in soybean is not fully established yet, especially in response to salt and alkaline stresses. In this study, we identified nine SL biosynthetic genes that include two D27, two CCD7, two CCD8, and three MAX1, as well as seven SL signaling genes that comprised two D14, two MAX2, and three D53 in the soybean genome. We found that SL biosynthetic and signaling genes are evolutionary conserved among different species. Syntenic analysis of these genes revealed their location on nine chromosomes as well as the presence of 10 pairs of duplication genes. Moreover, plant hormone and stress-responsive elements were identified in the promoter regions of SL biosynthetic and signaling genes. By using reverse transcription quantitative real-time PCR, we confirmed that SL genes have different tissue expressions in roots, stems, and leaves. The expression profile of SL biosynthetic and signaling genes under salt and alkaline stresses further confirmed the regulatory roles of SL biosynthetic and signaling genes under stress. In conclusion, we identified and provided valuable information on the soybean SL biosynthetic and signaling genes, and established a foundation for further functional analysis of soybean SL-related genes in response to salt and alkaline stresses.


Assuntos
Compostos Heterocíclicos com 3 Anéis/metabolismo , Lactonas/metabolismo , Proteínas de Plantas/genética , Estresse Salino , Soja/genética , Cromossomos de Plantas/genética , Duplicação Gênica , Proteínas de Plantas/metabolismo , Transdução de Sinais , Soja/metabolismo , Sintenia
2.
PLoS One ; 15(8): e0237774, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32797075

RESUMO

The source-sink relationship determines the ultimate grain yield of rice. In this study, we used a set of reciprocal introgression lines (ILs) derived from Xuishui09 × IR2061 to map quantitative trait loci (QTLs) that were associated with sink-, source-, and grain yield-related traits. A total of 95 QTLs influencing eight measured traits were identified using 6181 high-quality single nucleotide polymorphism markers. Nine background-independent QTLs were consistently detected in seven chromosomal regions in different genetic backgrounds. Seven QTLs clusters simultaneously affected sink-, source-, and grain yield-related traits, probably due to the genetic basis of significant correlations of grain yield with source and sink traits. We selected 15 candidate genes in the four QTLs consistently identified in the two populations by performing gene-based association and haplotype analyses using 2288 accessions from the 3K project. Among these, LOC_Os03g48970 for qTSN3b, LOC_Os06g04710 for qFLL6a, and LOC_Os07g32510 for qTGW7 were considered as the most likely candidate genes based on functional annotations. These results provide a basis for further study of candidate genes and for the development of high-yield rice varieties by balancing source-sink relationships using marker-assisted selection.


Assuntos
Grão Comestível/genética , Oryza/genética , Locos de Características Quantitativas , Cromossomos de Plantas/genética , Grão Comestível/crescimento & desenvolvimento , Genes de Plantas , Oryza/crescimento & desenvolvimento , Polimorfismo de Nucleotídeo Único
3.
PLoS Genet ; 16(7): e1008900, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32667955

RESUMO

In this study we performed a genotype-phenotype association analysis of meiotic stability in 10 autotetraploid Arabidopsis lyrata and A. lyrata/A. arenosa hybrid populations collected from the Wachau region and East Austrian Forealps. The aim was to determine the effect of eight meiosis genes under extreme selection upon adaptation to whole genome duplication. Individual plants were genotyped by high-throughput sequencing of the eight meiosis genes (ASY1, ASY3, PDS5b, PRD3, REC8, SMC3, ZYP1a/b) implicated in synaptonemal complex formation and phenotyped by assessing meiotic metaphase I chromosome configurations. Our results reveal that meiotic stability varied greatly (20-100%) between individual tetraploid plants and associated with segregation of a novel ASYNAPSIS3 (ASY3) allele derived from A. lyrata. The ASY3 allele that associates with meiotic stability possesses a putative in-frame tandem duplication (TD) of a serine-rich region upstream of the coiled-coil domain that appears to have arisen at sites of DNA microhomology. The frequency of multivalents observed in plants homozygous for the ASY3 TD haplotype was significantly lower than in plants heterozygous for ASY3 TD/ND (non-duplicated) haplotypes. The chiasma distribution was significantly altered in the stable plants compared to the unstable plants with a shift from proximal and interstitial to predominantly distal locations. The number of HEI10 foci at pachytene that mark class I crossovers was significantly reduced in a plant homozygous for ASY3 TD compared to a plant heterozygous for ASY3 ND/TD. Fifty-eight alleles of the 8 meiosis genes were identified from the 10 populations analysed, demonstrating dynamic population variability at these loci. Widespread chimerism between alleles originating from A. lyrata/A. arenosa and diploid/tetraploids indicates that this group of rapidly evolving genes may provide precise adaptive control over meiotic recombination in the tetraploids, the very process that gave rise to them.


Assuntos
Proteínas de Arabidopsis/genética , Arabidopsis/genética , Proteínas Cromossômicas não Histona/genética , Meiose/genética , Alelos , Arabidopsis/crescimento & desenvolvimento , Pareamento Cromossômico/genética , Segregação de Cromossomos , Cromossomos de Plantas/genética , Proteínas de Ligação a DNA/genética , Diploide , Tetraploidia
4.
BMC Evol Biol ; 20(1): 91, 2020 07 29.
Artigo em Inglês | MEDLINE | ID: mdl-32727363

RESUMO

BACKGROUND: The SIAMESE (SIM) locus is a cell-cycle kinase inhibitor (CKI) gene that has to date been identified only in plants; it encodes a protein that promotes transformation from mitosis to endoreplication. Members of the SIAMESE-RELATED (SMR) family have similar functions, and some are related to cell-cycle responses and abiotic stresses. However, the functions of SMRs are poorly understood in maize (Zea mays L.). RESULTS: In the present study, 12 putative SMRs were identified throughout the entire genome of maize, and these were clustered into six groups together with the SMRs from seven other plant species. Members of the ZmSMR family were divided into four groups according to their protein sequences. Various cis-acting elements in the upstream sequences of ZmSMRs responded to abiotic stresses. Expression analyses revealed that all ZmSMRs were upregulated at 5, 20, 25, and 35 days after pollination. In addition, we found that ZmSMR9/11/12 may have regulated the initiation of endoreplication in endosperm central cells. Additionally, ZmSMR2/10 may have been primarily responsible for the endoreplication regulation of outer endosperm or aleurone cells. The relatively high expression levels of almost all ZmSMRs in the ears and tassels also implied that these genes may function in seed development. The effects of treatments with ABA, heat, cold, salt, and drought on maize seedlings and expression of ZmSMR genes suggested that ZmSMRs were strongly associated with response to abiotic stresses. CONCLUSION: The present study is the first to conduct a genome-wide analysis of members of the ZmSMR family by investigating their locations in chromosomes, identifying regulatory elements in their promoter regions, and examining motifs in their protein sequences. Expression analysis of different endosperm developmental periods, tissues, abiotic stresses, and hormonal treatments suggests that ZmSMR genes may function in endoreplication and regulate the development of reproductive organs. These results may provide valuable information for future studies of the functions of the SMR family in maize.


Assuntos
Evolução Molecular , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Família Multigênica , Zea mays/genética , Sequência de Aminoácidos , Sequência de Bases , Cromossomos de Plantas/genética , Sequência Conservada/genética , Endosperma/genética , Duplicação Gênica , Genes de Plantas , Filogenia , Proteínas de Plantas/química , Proteínas de Plantas/genética , Regiões Promotoras Genéticas/genética , Análise de Regressão , Especificidade da Espécie , Estresse Fisiológico/efeitos dos fármacos , Sintenia/genética
5.
Plant Mol Biol ; 104(1-2): 81-95, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32621166

RESUMO

KEY MESSAGE: Genome-wide identification of WD40-like genes reveals a duplication of COP1-like genes, one of the key players involved in regulation of flowering time and photomorphogenesis, with strong functional diversification in Rosaceae. WD40 proteins play crucial roles in a broad spectrum of developmental and physiological processes. Here, we conducted a systematic characterization of this family of genes in Rosa chinensis 'Old Blush' (OB), a founder genotype for modern rose domestication. We identified 187 rose WD40 genes and classified them into 5 clusters and 15 subfamilies with 11 of RcWD40s presumably generated via tandem duplication. We found RcWD40 genes were expressed differentially following stages of vegetative and reproductive development. We detected a duplication of CONSTITUTIVE PHOTOMORPHOGENIC1-like genes in rose (RcCOP1 and RcCOP1L) and other Rosaceae plants. Featuring a distinct expression pattern and a different profile of cis-regulatory-elements in the transcriptional regulatory regions, RcCOP1 seemed being evolutionarily conserved while RcCOP1L did not dimerize with RcHY5 and RcSPA4. Our data thus reveals a functional diversification of COP1-like genes in Rosacaeae plants, and provides a valuable resource to explore the potential function and evolution of WD40-like genes in Rosaceae plants.


Assuntos
Genes de Plantas , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Rosaceae/genética , Rosaceae/metabolismo , Ubiquitina-Proteína Ligases/genética , Sequência de Aminoácidos , Arabidopsis/genética , Arabidopsis/metabolismo , Cromossomos de Plantas/genética , Domesticação , Duplicação Gênica , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Filogenia , Plantas Geneticamente Modificadas , Rosa/genética , Rosa/metabolismo , Ubiquitina-Proteína Ligases/metabolismo
6.
Nat Commun ; 11(1): 3670, 2020 07 29.
Artigo em Inglês | MEDLINE | ID: mdl-32728126

RESUMO

Our understanding of polyploid genome evolution is constrained because we cannot know the exact founders of a particular polyploid. To differentiate between founder effects and post polyploidization evolution, we use a pan-genomic approach to study the allotetraploid Brachypodium hybridum and its diploid progenitors. Comparative analysis suggests that most B. hybridum whole gene presence/absence variation is part of the standing variation in its diploid progenitors. Analysis of nuclear single nucleotide variants, plastomes and k-mers associated with retrotransposons reveals two independent origins for B. hybridum, ~1.4 and ~0.14 million years ago. Examination of gene expression in the younger B. hybridum lineage reveals no bias in overall subgenome expression. Our results are consistent with a gradual accumulation of genomic changes after polyploidization and a lack of subgenome expression dominance. Significantly, if we did not use a pan-genomic approach, we would grossly overestimate the number of genomic changes attributable to post polyploidization evolution.


Assuntos
Brachypodium/genética , Diploide , Evolução Molecular , Genoma de Planta , Poliploidia , Cromossomos de Plantas/genética , Genoma de Cloroplastos , Genômica , Hibridização Genética , Filogenia , Polimorfismo de Nucleotídeo Único , Retroelementos/genética , Especificidade da Espécie
7.
Nat Commun ; 11(1): 2764, 2020 06 02.
Artigo em Inglês | MEDLINE | ID: mdl-32488019

RESUMO

Not necessarily all cells of an organism contain the same genome. Some eukaryotes exhibit dramatic differences between cells of different organs, resulting from programmed elimination of chromosomes or their fragments. Here, we present a detailed analysis of programmed B chromosome elimination in plants. Using goatgrass Aegilops speltoides as a model, we demonstrate that the elimination of B chromosomes is a strictly controlled and highly efficient root-specific process. At the onset of embryo differentiation B chromosomes undergo elimination in proto-root cells. Independent of centromere activity, B chromosomes demonstrate nondisjunction of chromatids and lagging in anaphase, leading to micronucleation. Chromatin structure and DNA replication differ between micronuclei and primary nuclei and degradation of micronucleated DNA is the final step of B chromosome elimination. This process might allow root tissues to survive the detrimental expression, or overexpression of B chromosome-located root-specific genes with paralogs located on standard chromosomes.


Assuntos
Aegilops/embriologia , Aegilops/genética , Cromossomos de Plantas , Proteínas de Plantas/metabolismo , Raízes de Plantas/embriologia , Raízes de Plantas/crescimento & desenvolvimento , Anáfase , Centrômero , Cromatina , Cromossomos de Plantas/genética , Replicação do DNA , Desenvolvimento Embrionário , Genes de Plantas/genética , Genoma de Planta/genética , Histonas , Proteínas de Plantas/genética , Raízes de Plantas/citologia , Sequenciamento Completo do Genoma
8.
Cytogenet Genome Res ; 160(5): 272-282, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32516773

RESUMO

Saccharum spontaneum is a wild germplasm resource of the genus Saccharum that has many valuable traits. Ty1-copia retrotransposons constitute a large proportion of plant genomes and affect genome sequence organization and evolution. This study aims to analyze the sequence heterogeneity, phylogenetic diversity, copy number, and chromosomal dispersion patterns of Ty1-copia retrotransposons in S. spontaneum. A total of 44 Ty1-copia reverse transcriptase subclones isolated from S. spontaneum showed a range of heterogeneity, and all sequences were A-T rich, averaging approximately 54.59%. Phylogenetic analysis divided the 44 reverse transcriptase sequences into 5 distinct lineages (Retrofit/Ale, Sire/Maximus, Bianca, Tork/TAR, and Ty1-copia like). Dot-blot hybridization revealed that Ty1-copia retrotransposons consisted of a significant component of approximately 38,900 copies and 16,300 copies per genome in the accessions YN82-114 (2n = 10x = 80) and AP85-441 (2n = 4x = 32), respectively. The results of a local blast analysis showed that there are 15,069 Ty1-copia retrotransposon copies in the genome of AP85-441, of which the Retrofit/Ale lineage had the highest copy number, followed by the Tork/TAR, Sire/Maximus, and Bianca lineages. Furthermore, both FISH and the local blast analysis with AP85-441 genomic data demonstrated that the Ty1-copia retrotransposons were unevenly distributed throughout the chromosomes. Taken together, this study provides insights into the role of Ty1-copia retrotransposons in the evolution and organization of the S. spontaneum genome.


Assuntos
Cromossomos de Plantas/genética , Evolução Molecular , Genoma de Planta/genética , Retroelementos/genética , Saccharum/genética , Filogenia
9.
PLoS One ; 15(6): e0233800, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32497070

RESUMO

Several studies suggest the relation of DNA methylation to diseases in humans and important phenotypes in plants drawing attention to this epigenetic mark as an important source of variability. In the last decades, several methodologies were developed to assess the methylation state of a genome. However, there is still a lack of affordable and precise methods for genome wide analysis in large sample size studies. Methyl sensitive double digestion MS-DArT sequencing method emerges as a promising alternative for methylation profiling. We developed a computational pipeline for the identification of DNA methylation using MS-DArT-seq data and carried out a pilot study using the Eucalyptus grandis tree sequenced for the species reference genome. Using a statistic framework as in differential expression analysis, 72,515 genomic sites were investigated and 5,846 methylated sites identified, several tissue specific, distributed along the species 11 chromosomes. We highlight a bias towards identification of DNA methylation in genic regions and the identification of 2,783 genes and 842 transposons containing methylated sites. Comparison with WGBS, DNA sequencing after treatment with bisulfite, data demonstrated a precision rate higher than 95% for our approach. The availability of a reference genome is useful for determining the genomic context of methylated sites but not imperative, making this approach suitable for any species. Our approach provides a cost effective, broad and reliable examination of DNA methylation profile on MspI/HpaII restriction sites, is fully reproducible and the source code is available on GitHub (https://github.com/wendelljpereira/ms-dart-seq).


Assuntos
Análise Custo-Benefício , Metilação de DNA/genética , Eucalyptus/genética , Técnicas de Genotipagem/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Folhas de Planta/genética , Análise de Sequência de DNA/métodos , Árvores/genética , Cromossomos de Plantas/genética , Enzimas de Restrição do DNA/genética , Elementos de DNA Transponíveis/genética , Genes de Plantas/genética , Técnicas de Genotipagem/economia , Sequenciamento de Nucleotídeos em Larga Escala/economia , Projetos Piloto , Reprodutibilidade dos Testes , Mapeamento por Restrição , Análise de Sequência de DNA/economia , Sulfitos/farmacologia
10.
PLoS Genet ; 16(6): e1008894, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32598340

RESUMO

Meiotic crossovers (COs) are important for reshuffling genetic information between homologous chromosomes and they are essential for their correct segregation. COs are unevenly distributed along chromosomes and the underlying mechanisms controlling CO localization are not well understood. We previously showed that meiotic COs are mis-localized in the absence of AXR1, an enzyme involved in the neddylation/rubylation protein modification pathway in Arabidopsis thaliana. Here, we report that in axr1-/-, male meiocytes show a strong defect in chromosome pairing whereas the formation of the telomere bouquet is not affected. COs are also redistributed towards subtelomeric chromosomal ends where they frequently form clusters, in contrast to large central regions depleted in recombination. The CO suppressed regions correlate with DNA hypermethylation of transposable elements (TEs) in the CHH context in axr1-/- meiocytes. Through examining somatic methylomes, we found axr1-/- affects DNA methylation in a plant, causing hypermethylation in all sequence contexts (CG, CHG and CHH) in TEs. Impairment of the main pathways involved in DNA methylation is epistatic over axr1-/- for DNA methylation in somatic cells but does not restore regular chromosome segregation during meiosis. Collectively, our findings reveal that the neddylation pathway not only regulates hormonal perception and CO distribution but is also, directly or indirectly, a major limiting pathway of TE DNA methylation in somatic cells.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/genética , Cromossomos de Plantas/genética , Metilação de DNA , Meiose/genética , Proteínas de Arabidopsis/genética , Pareamento Cromossômico , Segregação de Cromossomos , Troca Genética , Quebras de DNA de Cadeia Dupla , Elementos de DNA Transponíveis/genética , Técnicas de Inativação de Genes , Plantas Geneticamente Modificadas
11.
Proc Natl Acad Sci U S A ; 117(25): 14561-14571, 2020 06 23.
Artigo em Inglês | MEDLINE | ID: mdl-32518116

RESUMO

Recombination between homeologous chromosomes, also known as homeologous exchange (HE), plays a significant role in shaping genome structure and gene expression in interspecific hybrids and allopolyploids of several plant species. However, the molecular mechanisms that govern HEs are not well understood. Here, we studied HE events in the progeny of a nascent allotetraploid (genome AADD) derived from two diploid progenitors of hexaploid bread wheat using cytological and whole-genome sequence analyses. In total, 37 HEs were identified and HE junctions were mapped precisely. HEs exhibit typical patterns of homologous recombination hotspots, being biased toward low-copy, subtelomeric regions of chromosome arms and showing association with known recombination hotspot motifs. But, strikingly, while homologous recombination preferentially takes place upstream and downstream of coding regions, HEs are highly enriched within gene bodies, giving rise to novel recombinant transcripts, which in turn are predicted to generate new protein fusion variants. To test whether this is a widespread phenomenon, a dataset of high-resolution HE junctions was analyzed for allopolyploid Brassica, rice, Arabidopsis suecica, banana, and peanut. Intragenic recombination and formation of chimeric genes was detected in HEs of all species and was prominent in most of them. HE thus provides a mechanism for evolutionary novelty in transcript and protein sequences in nascent allopolyploids.


Assuntos
Cromossomos de Plantas/genética , Genes de Plantas/genética , Proteínas de Plantas/genética , Poliploidia , Recombinação Genética , Arabidopsis/genética , Arachis/genética , Brassica/genética , Biologia Computacional , Evolução Molecular , Fusão Gênica , Cariotipagem , Musa/genética , Oryza/genética , Transcrição Genética , Triticum/genética
12.
PLoS One ; 15(6): e0235317, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32598401

RESUMO

The Dof (DNA-binding one zinc finger) transcription factor family is a representative of plant-specific classes of transcription factors. In this study, we performed a genome-wide screening and characterization of the Dof gene family within two tetraploid species Gossypium barbadense, Gossypium hirsutum, and two diploid species Gossypium arboreum, Gossypium raimondii. 115, 116, 55 and 56 Dof genes were identified respectively and all of the genes contain a sequence encoding the Dof DNA-binding domain. Those genes were unevenly distributed across 13/26 chromosomes of the cotton. Genome comparison revealed that segmental duplication may have played crucial roles in the expansion of the cotton Dof gene family, and tandem duplication also played a minor role. Analysis of RNA-Seq data indicated that cotton Dof gene expression levels varied across different tissues and in response to different abiotic stress. Overall, our results could provide valuable information for better understanding the evolution of cotton Dof genes, and lays a foundation for future investigation in cotton.


Assuntos
Proteínas de Ligação a DNA/genética , Diploide , Genoma de Planta , Gossypium/genética , Proteínas de Plantas/genética , Tetraploidia , Dedos de Zinco/genética , Cromossomos de Plantas/genética , Proteínas de Ligação a DNA/metabolismo , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Gossypium/crescimento & desenvolvimento , Gossypium/metabolismo , Família Multigênica , Filogenia , Proteínas de Plantas/metabolismo
13.
Proc Natl Acad Sci U S A ; 117(24): 13800-13809, 2020 06 16.
Artigo em Inglês | MEDLINE | ID: mdl-32493747

RESUMO

While colocalization within a bacterial operon enables coexpression of the constituent genes, the mechanistic logic of clustering of nonhomologous monocistronic genes in eukaryotes is not immediately obvious. Biosynthetic gene clusters that encode pathways for specialized metabolites are an exception to the classical eukaryote rule of random gene location and provide paradigmatic exemplars with which to understand eukaryotic cluster dynamics and regulation. Here, using 3C, Hi-C, and Capture Hi-C (CHi-C) organ-specific chromosome conformation capture techniques along with high-resolution microscopy, we investigate how chromosome topology relates to transcriptional activity of clustered biosynthetic pathway genes in Arabidopsis thaliana Our analyses reveal that biosynthetic gene clusters are embedded in local hot spots of 3D contacts that segregate cluster regions from the surrounding chromosome environment. The spatial conformation of these cluster-associated domains differs between transcriptionally active and silenced clusters. We further show that silenced clusters associate with heterochromatic chromosomal domains toward the periphery of the nucleus, while transcriptionally active clusters relocate away from the nuclear periphery. Examination of chromosome structure at unrelated clusters in maize, rice, and tomato indicates that integration of clustered pathway genes into distinct topological domains is a common feature in plant genomes. Our results shed light on the potential mechanisms that constrain coexpression within clusters of nonhomologous eukaryotic genes and suggest that gene clustering in the one-dimensional chromosome is accompanied by compartmentalization of the 3D chromosome.


Assuntos
Arabidopsis/genética , Cromossomos de Plantas/genética , Lycopersicon esculentum/genética , Família Multigênica , Proteínas de Plantas/genética , Zea mays/genética , Arabidopsis/metabolismo , Cromossomos de Plantas/metabolismo , Genoma de Planta , Lycopersicon esculentum/metabolismo , Oryza/genética , Oryza/metabolismo , Proteínas de Plantas/metabolismo , Zea mays/metabolismo
14.
Mol Genet Genomics ; 295(5): 1187-1195, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32476049

RESUMO

Cowpea (Vigna unguiculate (L.) Walp.) is a worldwide important multifunctional legume crop for food grain, vegetable, fodder, and cover crop. Nevertheless, only limited research has been conducted on agronomic traits. Here, we report quantitative trait locus (QTL) analysis of the days to flowering (DTF) and plant height (PH) using a dense SNP linkage map recently developed from a recombinant inbred line (RIL) population derived from a cross between Golden Eye Cream and IT98K-476-8. The population was phenotyped for DTF and PH through field and greenhouse trials under two environments. The QTLs controlling these traits were mapped using multiple-environment combined and individual trial phenotypic data. The combined data analysis identified one major QTL (qDTF9.1) for DTF, and one major QTL (qPH9.1) and a minor QTL (qPH4.1) for PH. qDTF9.1 and qPH9.1 were adjacent to each other on Chromosome 9 and each explained 29.3% and 29.5% of the phenotypic variation (PVE), respectively. The individual trial data analysis identified a minor QTL (qDTF2.1) on Chromosome 2 for DTF and two minor QTLs (qPH4.1 and qPH4.2) on Chromosome 4 for PH, while the major QTLs, qDTF9.1 and qPH9.1, were consistently identified in all trials conducted. Epistasis analysis revealed that qDTF9.1 interacted with one locus on Chromosome 4, contributed 50% of the PVE, and qPH9.1 interacted with one locus on each of Chromosomes 4 and 6, contributing 30% and 23% of the PVE, respectively, suggesting that epistasis plays an important role in the trait performance. These results, therefore, provide a deeper understanding of the genetic architecture of plant DTF and PH, and molecular tools necessary for cloning the genes and for enhanced cowpea breeding.


Assuntos
Mapeamento Cromossômico/métodos , Locos de Características Quantitativas , Vigna/fisiologia , Cromossomos de Plantas/genética , Cruzamentos Genéticos , Epistasia Genética , Flores/genética , Flores/crescimento & desenvolvimento , Fenótipo , Polimorfismo de Nucleotídeo Único , Vigna/anatomia & histologia , Vigna/genética
15.
Nat Commun ; 11(1): 2494, 2020 05 19.
Artigo em Inglês | MEDLINE | ID: mdl-32427850

RESUMO

Artificially improving traits of cultivated alfalfa (Medicago sativa L.), one of the most important forage crops, is challenging due to the lack of a reference genome and an efficient genome editing protocol, which mainly result from its autotetraploidy and self-incompatibility. Here, we generate an allele-aware chromosome-level genome assembly for the cultivated alfalfa consisting of 32 allelic chromosomes by integrating high-fidelity single-molecule sequencing and Hi-C data. We further establish an efficient CRISPR/Cas9-based genome editing protocol on the basis of this genome assembly and precisely introduce tetra-allelic mutations into null mutants that display obvious phenotype changes. The mutated alleles and phenotypes of null mutants can be stably inherited in generations in a transgene-free manner by cross pollination, which may help in bypassing the debate about transgenic plants. The presented genome and CRISPR/Cas9-based transgene-free genome editing protocol provide key foundations for accelerating research and molecular breeding of this important forage crop.


Assuntos
Cromossomos de Plantas/genética , Edição de Genes/métodos , Genoma de Planta/genética , Medicago sativa/genética , Tetraploidia , Transgenes/genética , Alelos , Sistemas CRISPR-Cas , Produtos Agrícolas/genética , Mutação , Fenótipo , Melhoramento Vegetal/métodos
16.
PLoS One ; 15(5): e0232756, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32407323

RESUMO

Mitogen-activated protein kinase (MAPK) is a form of serine/threonine protein kinase that activated by extracellular stimulation acting through the MAPK cascade (MAPKKK-MAPKK-MAPK). The MAPK cascade gene family, an important family of protein kinases, plays a vital role in responding to various stresses and hormone signal transduction processes in plants. In this study, we identified 14 CmMAPKs, 6 CmMAPKKs and 64 CmMAPKKKs in melon genome. Based on structural characteristics and a comparison of phylogenetic relationships of MAPK gene families from Arabidopsis, cucumber and watermelon, CmMAPKs and CmMAPKKs were categorized into 4 groups, and CmMAPKKKs were categorized into 3 groups. Furthermore, chromosome location revealed an unevenly distribution on chromosomes of MAPK cascade genes in melon, respectively. Eventually, qRT-PCR analysis showed that all 14 CmMAPKs had different expression patterns under drought, salt, salicylic acid (SA), methyl jasmonate (MeJA), red light (RL), and Podosphaera xanthii (P. xanthii) treatments. Overall, the expression levels of CmMAPK3 and CmMAPK7 under different treatments were higher than those in control. Our study provides an important basis for future functional verification of MAPK genes in regulating responses to stress and signal substance in melon.


Assuntos
Cucumis melo/enzimologia , Cucumis melo/genética , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Estudo de Associação Genômica Ampla , Sistema de Sinalização das MAP Quinases/genética , Acetatos/farmacologia , Motivos de Aminoácidos , Sequência de Aminoácidos , Cromossomos de Plantas/genética , Cucumis melo/efeitos dos fármacos , Ciclopentanos/farmacologia , Secas , Éxons/genética , Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Genes de Plantas , Íntrons/genética , Sistema de Sinalização das MAP Quinases/efeitos dos fármacos , Proteínas Quinases Ativadas por Mitógeno/química , Proteínas Quinases Ativadas por Mitógeno/genética , Proteínas Quinases Ativadas por Mitógeno/metabolismo , Oxilipinas/farmacologia , Filogenia , Folhas de Planta/efeitos dos fármacos , Folhas de Planta/genética , Domínios Proteicos , Ácido Salicílico/farmacologia , Plântula/efeitos dos fármacos , Plântula/enzimologia , Plântula/genética , Cloreto de Sódio/farmacologia , Estresse Fisiológico/efeitos dos fármacos , Estresse Fisiológico/genética
17.
Phytopathology ; 110(10): 1713-1720, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32460689

RESUMO

Secale cereale is used as a source of genes for disease resistance in wheat cultivation. In this study, a homozygous translocation line (RT14-245) that originated from a cross between a commercial wheat cultivar (Mianyang 11) and a local Chinese variety of rye (Baili) was developed. Multicolor fluorescence in situ hybridization and PCR analysis demonstrated that the translocation chromosome was 7BS.7RL. Resistance analysis showed that RT14-245 was resistant to prevalent pathotypes of stripe rust and powdery mildew. RT14-245 also exhibited high resistance to Fusarium head blight, which was similar to the resistance exhibited by the wheat cultivar Sumai 3. The results indicated that RT14-245 simultaneously exhibited high levels of resistance against stripe rust, powdery mildew, and Fusarium head blight. These results indicate that chromosome arm 7RL in the translocation line RT14-245 is an excellent new resource for wheat breeding programs.


Assuntos
Fusarium , Secale/genética , Cromossomos de Plantas/genética , Resistência à Doença/genética , Humanos , Hibridização in Situ Fluorescente , Doenças das Plantas , Triticum/genética
18.
Nat Commun ; 11(1): 1675, 2020 04 03.
Artigo em Inglês | MEDLINE | ID: mdl-32245969

RESUMO

The laurel family within the Magnoliids has attracted attentions owing to its scents, variable inflorescences, and controversial phylogenetic position. Here, we present a chromosome-level assembly of the Litsea cubeba genome, together with low-coverage genomic and transcriptomic data for many other Lauraceae. Phylogenomic analyses show phylogenetic discordance at the position of Magnoliids, suggesting incomplete lineage sorting during the divergence of monocots, eudicots, and Magnoliids. An ancient whole-genome duplication (WGD) event occurred just before the divergence of Laurales and Magnoliales; subsequently, independent WGDs occurred almost simultaneously in the three Lauralean lineages. The phylogenetic relationships within Lauraceae correspond to the divergence of inflorescences, as evidenced by the phylogeny of FUWA, a conserved gene involved in determining panicle architecture in Lauraceae. Monoterpene synthases responsible for production of specific volatile compounds in Lauraceae are functionally verified. Our work sheds light on the evolution of the Lauraceae, the genetic basis for floral evolution and specific scents.


Assuntos
Cromossomos de Plantas/genética , Evolução Molecular , Especiação Genética , Genoma de Planta , Litsea/genética , Vias Biossintéticas/genética , DNA de Plantas/genética , DNA de Plantas/isolamento & purificação , Duplicação Gênica , Perfilação da Expressão Gênica , Genômica , Inflorescência/genética , Litsea/metabolismo , Anotação de Sequência Molecular , Odorantes , Filogenia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Análise de Sequência de DNA
19.
Gene ; 747: 144674, 2020 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-32304781

RESUMO

Very long chain fatty acids (VLCFAs) that are structural components of cell membrane lipid, cuticular waxes and seed oil, play crucial roles in plant growth, development and stress response. Fatty acid elongases (FAEs) comprising KCS and ELO, are key enzymes for VLCFA biosynthesis in plants. Although reference genomes of Brassica napus and its parental speices both have been sequenced, whole-genome analysis of FAE gene family in these Brassica speices is not reported. Here, 58, 33 and 30 KCS genes were identified in B. napus, B. rapa and B. oleracea genomes, respectively, whereas 14, 6 and 8 members were obtained for ELO genes. These KCS genes were unevenly located in 37 chromosomes and 3 scaffolds of 3 Brassica species, while these ELO genes were mapped to 19 chromosomes. The KCS and ELO proteins were divided into 8 and 4 subclasses, respectively. Gene structure and protein motifs remained highly conserved in each KCS or ELO subclass. Most promoters of KCS and ELO genes harbored various plant growth-, phytohormone-, and stress response-related cis-acting elements. 20 SSR loci existed in the KCS and ELO genes/promoters. The whole-genome duplication and segmental duplication mainly contributed to expansion of KCS and ELO genes in these genomes. Transcriptome analysis showed that KCS and ELO genes in 3 Brassica species were expressed in various tissues/organs with different levels, whereas 1 BnELO gene and 6 BnKCS genes might be pathogen-responsive genes. The qRT-PCR assay showed that BnKCS22 and BnELO04 responded to various phytohormone treatments and abiotic stresses. This work lays the foundation for further function identification of KCS and ELO genes in B. napus and its progenitors.


Assuntos
Brassica napus/enzimologia , Brassica napus/genética , Elongases de Ácidos Graxos/genética , Genes de Plantas , Estudo de Associação Genômica Ampla , Família Multigênica , Brassica napus/efeitos dos fármacos , Cromossomos de Plantas/genética , Sequência Conservada/genética , Duplicação Gênica , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Loci Gênicos , Repetições de Microssatélites/genética , Motivos de Nucleotídeos , Filogenia , Reguladores de Crescimento de Planta/farmacologia , Sequências Reguladoras de Ácido Nucleico/genética , Estresse Fisiológico/efeitos dos fármacos , Estresse Fisiológico/genética , Sintenia/genética
20.
PLoS One ; 15(3): e0224534, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32231371

RESUMO

Virus resistance genes carried by wild plant species are valuable resources for plant breeding. The Rysto gene, conferring a broad spectrum of durable resistance, originated from Solanum stoloniferum and was introgressed into several commercial potato cultivars, including 'White Lady', by classical breeding. Rysto was mapped to chromosome XII in potato, and markers used for marker-assisted selection in breeding programmes were identified. Nevertheless, there was no information on the identity of the Rysto gene. To begin to reveal the identification of Rysto, fine-scale genetic mapping was performed which, in combination with chromosome walking, narrowed down the locus of the gene to approximately 1 Mb. DNA sequence analysis of the locus identified six full-length NBS-LRR-type (short NLR-type) putative resistance genes. Two of them, designated TMV2 and TMV3, were similar to a TMV resistance gene isolated from tobacco and to Y-1, which co-segregates with Ryadg, the extreme virus resistance gene originated from Solanum andigena and localised to chromosome XI. Furthermore, TMV2 of 'White Lady' was found to be 95% identical at the genomic sequence level with the recently isolated Rysto gene of the potato cultivar 'Alicja'. In addition to the markers identified earlier, this work generated five tightly linked new markers which can serve potato breeding efforts for extreme virus resistance.


Assuntos
Mapeamento Cromossômico , Cromossomos de Plantas/genética , Resistência à Doença/genética , Doenças das Plantas/genética , Solanum tuberosum/genética , Vírus do Mosaico do Tabaco , Doenças das Plantas/virologia , Solanum tuberosum/virologia
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