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1.
Mol Plant Microbe Interact ; 32(12): 1581-1597, 2019 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-31657672

RESUMO

Vascular wilt bacteria such as Pantoea stewartii, the causal agent of Stewart's bacterial wilt of maize (SW), are destructive pathogens that are difficult to control. These bacteria colonize the xylem, where they form biofilms that block sap flow leading to characteristic wilting symptoms. Heritable forms of SW resistance exist and are used in maize breeding programs but the underlying genes and mechanisms are mostly unknown. Here, we show that seedlings of maize inbred lines with pan1 mutations are highly resistant to SW. However, current evidence suggests that other genes introgressed along with pan1 are responsible for resistance. Genomic analyses of pan1 lines were used to identify candidate resistance genes. In-depth comparison of P. stewartii interaction with susceptible and resistant maize lines revealed an enhanced vascular defense response in pan1 lines characterized by accumulation of electron-dense materials in xylem conduits visible by electron microscopy. We propose that this vascular defense response restricts P. stewartii spread through the vasculature, reducing both systemic bacterial colonization of the xylem network and consequent wilting. Though apparently unrelated to the resistance phenotype of pan1 lines, we also demonstrate that the effector WtsE is essential for P. stewartii xylem dissemination, show evidence for a nutritional immunity response to P. stewartii that alters xylem sap composition, and present the first analysis of maize transcriptional responses to P. stewartii infection.


Assuntos
Resistência à Doença , Pantoea , Zea mays , Resistência à Doença/genética , Genoma de Planta/genética , Pantoea/fisiologia , Plântula/microbiologia , Xilema/microbiologia , Zea mays/genética , Zea mays/microbiologia
2.
Nucleic Acids Res ; 47(18): 9842-9856, 2019 10 10.
Artigo em Inglês | MEDLINE | ID: mdl-31392988

RESUMO

To elucidate the molecular nature of evolutionary changes of telomeres in the plant order Asparagales, we aimed to characterize telomerase RNA subunits (TRs) in these plants. The unusually long telomere repeat unit in Allium plants (12 nt) allowed us to identify TRs in transcriptomic data of representative species of the Allium genus. Orthologous TRs were then identified in Asparagales plants harbouring telomere DNA composed of TTAGGG (human type) or TTTAGGG (Arabidopsis-type) repeats. Further, we identified TRs across the land plant phylogeny, including common model plants, crop plants, and plants with unusual telomeres. Several lines of functional testing demonstrate the templating telomerase function of the identified TRs and disprove a functionality of the only previously reported plant telomerase RNA in Arabidopsis thaliana. Importantly, our results change the existing paradigm in plant telomere biology which has been based on the existence of a relatively conserved telomerase reverse transcriptase subunit (TERT) associating with highly divergent TRs even between closely related plant taxa. The finding of a monophyletic origin of genuine TRs across land plants opens the possibility to identify TRs directly in transcriptomic or genomic data and/or predict telomere sequences synthesized according to the respective TR template region.


Assuntos
Evolução Molecular , Filogenia , RNA/genética , Telomerase/genética , Telômero/genética , Allium/genética , Arabidopsis/genética , Asparagales/genética , Embriófitas/genética , Genoma de Planta/genética , Humanos
3.
Physiol Plant ; 166(4): 892-893, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31294874

RESUMO

Drought is an increasingly common climatic event that can devastate ecosystems, as well as surrounding agricultural and forestry industries. Few places face this challenge more than Australia, where millennia of droughts linked to geography and climatic drivers, such as El Niño, have shaped the flora and fauna into forms predicated on resilience and economy. How an organism responds to these cyclic challenges is a combination of the inherent tolerance mechanisms encoded in their genome and outside influences, such as the effect of nutrients and symbiotic interactions. In this issue of Physiologia Plantarum, Tariq et al. (2019) describes how the presence of the element phosphorus can bolster the physiological and biochemical response of eucalypt seedlings to severe drought conditions.


Assuntos
Secas , Genoma de Planta/genética , Fósforo/metabolismo , Plântula/genética , Plântula/metabolismo , Austrália
4.
Planta ; 250(3): 971-977, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31256257

RESUMO

MAIN CONCLUSION: In spite of the limited investment in orphan crops, access to new technologies such as bioinformatics and low-cost genotyping opens new doors to modernise their breeding effectively. Innovation in plant breeding is imperative to meet the world's growing demand for staple food and feed crops, and orphan crops can play a significant role in increasing productivity and quality, especially in developing countries. The short breeding history of most orphan crops implies that genetic gain should be achievable through easy-to-implement approaches such as forward breeding for simple traits or introgression of elite alleles at key target trait loci. However, limited financial support and access to sufficient, relevant and reliable phenotypic data continue to pose major challenges in terms of resources and capabilities. Digitalisation of orphan-crop breeding programmes can help not only to improve data quality and management, but also to mitigate data scarcity by allowing data to be accumulated and analysed over time and across teams. Bioinformatics tools and access to technologies such as molecular markers, some of them provided as services via specific platforms, allow breeders to implement modern strategies to improve breeding efficiency. In orphan crops, more marker-trait associations relevant to breeding germplasm are generally needed, but implementing digitalization, marker-based quality control or simple trait screening and introgression will help modernising breeding. Finally, the development of local capacities-of both people and infrastructure-remains a necessity to ensure the sustainable adoption of modern breeding approaches.


Assuntos
Produção Agrícola/métodos , Produtos Agrícolas , Melhoramento Vegetal/métodos , Biologia Computacional , Produtos Agrícolas/genética , Genoma de Planta/genética
5.
Nat Commun ; 10(1): 2989, 2019 07 05.
Artigo em Inglês | MEDLINE | ID: mdl-31278252

RESUMO

Multiple cotton genomes (diploid and tetraploid) have been assembled. However, genomic variations between cultivars of allotetraploid upland cotton (Gossypium hirsutum L.), the most widely planted cotton species in the world, remain unexplored. Here, we use single-molecule long read and Hi-C sequencing technologies to assemble genomes of the two upland cotton cultivars TM-1 and zhongmiansuo24 (ZM24). Comparisons among TM-1 and ZM24 assemblies and the genomes of the diploid ancestors reveal a large amount of genetic variations. Among them, the top three longest structural variations are located on chromosome A08 of the tetraploid upland cotton, which account for ~30% total length of this chromosome. Haplotype analyses of the mapping population derived from these two cultivars and the germplasm panel show suppressed recombination rates in this region. This study provides additional genomic resources for the community, and the identified genetic variations, especially the reduced meiotic recombination on chromosome A08, will help future breeding.


Assuntos
Ordem dos Genes/genética , Gossypium/genética , Haplótipos/genética , Melhoramento Vegetal , Poliploidia , Mapeamento Cromossômico , Cromossomos de Plantas/genética , Variação Genética , Genoma de Planta/genética , Sequenciamento de Nucleotídeos em Larga Escala
6.
PLoS Genet ; 15(6): e1008209, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31199791

RESUMO

Plants with facultative crassulacean acid metabolism (CAM) maximize performance through utilizing C3 or C4 photosynthesis under ideal conditions while temporally switching to CAM under water stress (drought). While genome-scale analyses of constitutive CAM plants suggest that time of day networks are shifted, or phased to the evening compared to C3, little is known for how the shift from C3 to CAM networks is modulated in drought induced CAM. Here we generate a draft genome for the drought-induced CAM-cycling species Sedum album. Through parallel sampling in well-watered (C3) and drought (CAM) conditions, we uncover a massive rewiring of time of day expression and a CAM and stress-specific network. The core circadian genes are expanded in S. album and under CAM induction, core clock genes either change phase or amplitude. While the core clock cis-elements are conserved in S. album, we uncover a set of novel CAM and stress specific cis-elements consistent with our finding of rewired co-expression networks. We identified shared elements between constitutive CAM and CAM-cycling species and expression patterns unique to CAM-cycling S. album. Together these results demonstrate that drought induced CAM-cycling photosynthesis evolved through the mobilization of a stress-specific, time of day network, and not solely the phasing of existing C3 networks. These results will inform efforts to engineer water use efficiency into crop plants for growth on marginal land.


Assuntos
Adaptação Fisiológica/genética , Fotossíntese/genética , Proteínas de Plantas/genética , Sedum/genética , Carbono/metabolismo , Ciclo do Carbono/genética , Dióxido de Carbono/metabolismo , Secas , Regulação da Expressão Gênica de Plantas , Genoma de Planta/genética , Proteínas de Plantas/metabolismo , Sedum/metabolismo , Água/química
7.
Mol Genet Genomics ; 294(5): 1327-1341, 2019 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-31187273

RESUMO

A survey of genome-wide polymorphisms between closely related species is required to understand the molecular basis of the evolutionary differentiation of their genomes. Two wild diploid wheat species, namely Triticum monococcum ssp. aegilopoides and T. urartu, are closely related and harbour the Am and A genomes, respectively. The A-genome donor of tetraploid and common wheat is T. urartu, and T. monococcum ssp. monococcum is the cultivated form derived from the wild einkorn wheat subspecies aegilopoides. Although subspecies aegilopoides has been a useful genetic resource in wheat breeding, genome-wide molecular markers for this subspecies have not been sufficiently developed. Here, we describe the detection of genome-wide polymorphisms such as single-nucleotide polymorphisms (SNPs) and insertions/deletions (indels) from RNA sequencing (RNA-seq) data of leaf transcripts in 15 accessions of the two diploid wheat species. The SNPs and indels, detected using the A genome of common wheat as the reference genome, covered the entire chromosomes of these species. The polymorphism information facilitated a comparison of the genetic diversity of einkorn wheat with that of two related diploid Aegilops species, namely, Ae. tauschii and Ae. umbellulata. Cleaved amplified polymorphic sequence (CAPS) markers converted from the SNP data were efficiently developed to confirm the addition of aegilopoides subspecies chromosomes to tetraploid wheat in nascent allohexaploid lines with AABBAmAm genomes. In addition, the CAPS markers permitted linkage map construction in mapping populations of aegilopoides subspecies accessions. Therefore, these RNA-seq data provide information for further breeding of closely related species with no reference genome sequence data.


Assuntos
Marcadores Genéticos/genética , Folhas de Planta/genética , Polimorfismo de Nucleotídeo Único/genética , Triticum/genética , Mapeamento Cromossômico/métodos , Cromossomos de Plantas/genética , Diploide , Ligação Genética/genética , Genoma de Planta/genética , Estudo de Associação Genômica Ampla/métodos , Filogenia , Análise de Sequência de RNA/métodos , Tetraploidia
8.
Nat Commun ; 10(1): 2632, 2019 06 14.
Artigo em Inglês | MEDLINE | ID: mdl-31201335

RESUMO

Chromatin loops connect regulatory elements to their target genes. They serve as bridges between transcriptional regulation and phenotypic variation in mammals. However, spatial organization of regulatory elements and its impact on gene expression in plants remain unclear. Here, we characterize epigenetic features of active promoter proximal regions and candidate distal regulatory elements to construct high-resolution chromatin interaction maps for maize via long-read chromatin interaction analysis by paired-end tag sequencing (ChIA-PET). The maps indicate that chromatin loops are formed between regulatory elements, and that gene pairs between promoter proximal regions tend to be co-expressed. The maps also demonstrated the topological basis of quantitative trait loci which influence gene expression and phenotype. Many promoter proximal regions are involved in chromatin loops with distal regulatory elements, which regulate important agronomic traits. Collectively, these maps provide a high-resolution view of 3D maize genome architecture, and its role in gene expression and phenotypic variation.


Assuntos
Cromatina/genética , Regulação da Expressão Gênica de Plantas , Redes Reguladoras de Genes/genética , Locos de Características Quantitativas/genética , Zea mays/genética , Cromatina/metabolismo , Imunoprecipitação da Cromatina , Mapeamento Cromossômico , Produção Agrícola , Elementos Facilitadores Genéticos/genética , Epigênese Genética , Epigenômica/métodos , Genoma de Planta/genética , Estudo de Associação Genômica Ampla , Mutação , Fenótipo , Regiões Promotoras Genéticas/genética
9.
BMC Plant Biol ; 19(1): 226, 2019 May 30.
Artigo em Inglês | MEDLINE | ID: mdl-31146681

RESUMO

BACKGROUND: Repetitive DNA motifs - not coding genetic information and repeated millions to hundreds of times - make up the majority of many genomes. Here, we identify the nature, abundance and organization of all the repetitive DNA families in oats (Avena sativa, 2n = 6x = 42, AACCDD), a recognized health-food, and its wild relatives. RESULTS: Whole-genome sequencing followed by k-mer and RepeatExplorer graph-based clustering analyses enabled assessment of repetitive DNA composition in common oat and its wild relatives' genomes. Fluorescence in situ hybridization (FISH)-based karyotypes are developed to understand chromosome and repetitive sequence evolution of common oat. We show that some 200 repeated DNA motifs make up 70% of the Avena genome, with less than 20 families making up 20% of the total. Retroelements represent the major component, with Ty3/Gypsy elements representing more than 40% of all the DNA, nearly three times more abundant than Ty1/Copia elements. DNA transposons are about 5% of the total, while tandemly repeated, satellite DNA sequences fit into 55 families and represent about 2% of the genome. The Avena species are monophyletic, but both bioinformatic comparisons of repeats in the different genomes, and in situ hybridization to metaphase chromosomes from the hexaploid species, shows that some repeat families are specific to individual genomes, or the A and D genomes together. Notably, there are terminal regions of many chromosomes showing different repeat families from the rest of the chromosome, suggesting presence of translocations between the genomes. CONCLUSIONS: The relatively small number of repeat families shows there are evolutionary constraints on their nature and amplification, with mechanisms leading to homogenization, while repeat characterization is useful in providing genome markers and to assist with future assemblies of this large genome (c. 4100 Mb in the diploid). The frequency of inter-genomic translocations suggests optimum strategies to exploit genetic variation from diploid oats for improvement of the hexaploid may differ from those used widely in bread wheat.


Assuntos
Avena/genética , DNA de Plantas , Evolução Molecular , Sequências Repetitivas de Ácido Nucleico , Cromossomos de Plantas/genética , Diploide , Genoma de Planta/genética , Hibridização in Situ Fluorescente , Cariotipagem , Poliploidia , Sequenciamento Completo do Genoma
10.
Nat Commun ; 10(1): 2449, 2019 06 04.
Artigo em Inglês | MEDLINE | ID: mdl-31164644

RESUMO

DNA base modifications, such as C5-methylcytosine (5mC) and N6-methyldeoxyadenosine (6mA), are important types of epigenetic regulations. Short-read bisulfite sequencing and long-read PacBio sequencing have inherent limitations to detect DNA modifications. Here, using raw electric signals of Oxford Nanopore long-read sequencing data, we design DeepMod, a bidirectional recurrent neural network (RNN) with long short-term memory (LSTM) to detect DNA modifications. We sequence a human genome HX1 and a Chlamydomonas reinhardtii genome using Nanopore sequencing, and then evaluate DeepMod on three types of genomes (Escherichia coli, Chlamydomonas reinhardtii and human genomes). For 5mC detection, DeepMod achieves average precision up to 0.99 for both synthetically introduced and naturally occurring modifications. For 6mA detection, DeepMod achieves ~0.9 average precision on Escherichia coli data, and have improved performance than existing methods on Chlamydomonas reinhardtii data. In conclusion, DeepMod performs well for genome-scale detection of DNA modifications and will facilitate epigenetic analysis on diverse species.


Assuntos
Chlamydomonas reinhardtii/genética , Metilação de DNA , Escherichia coli/genética , Genoma Bacteriano/genética , Genoma Humano/genética , Genoma de Planta/genética , Redes Neurais (Computação) , Bases de Dados de Ácidos Nucleicos , Epigênese Genética , Humanos , Nanoporos
11.
BMC Genomics ; 20(1): 476, 2019 Jun 11.
Artigo em Inglês | MEDLINE | ID: mdl-31185891

RESUMO

BACKGROUND: The redundancy of genomic resources, including transcript and molecular markers, and their uncertain position in the genome have dramatically hindered the study of traits in ramie, an important natural fiber crop. RESULTS: We obtained a high-quality transcriptome consisting of 30,591 non-redundant transcripts using single-molecule long-read sequencing and proposed it as a universal ramie transcriptome. Additionally, 55,882 single nucleotide polymorphisms (SNPs) were identified and a high-density genetic map was developed. Based on this genetic map, 181.7 Mb ramie genome sequences were assembled into 14 chromosomes. For the convenient use of these resources, 29,286 (~ 95.7%) of the transcripts and all 55,882 SNPs, along with 1827 previously reported sequence repeat markers (SSRs), were mapped into the ramie genome, and 22,343 (~ 73.0%) transcripts, 50,154 (~ 89.7%) SNPs, and 1466 (~ 80.3%) SSRs were assigned to a specific location in the corresponding chromosome. CONCLUSION: This is the first study to characterize the ramie transcriptome by long-read sequencing, and the substantial number of transcripts of significant length obtained will accelerate our understanding of ramie growth and development. This integration of genome sequences, expressed transcripts, and genetic markers will provide an extremely useful resource for genetic, molecular, and breeding studies of ramie.


Assuntos
Boehmeria/genética , Perfilação da Expressão Gênica , Marcadores Genéticos/genética , Genômica/métodos , Genoma de Planta/genética , Anotação de Sequência Molecular , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Análise de Sequência de RNA
12.
BMC Genomics ; 20(1): 483, 2019 Jun 11.
Artigo em Inglês | MEDLINE | ID: mdl-31185893

RESUMO

BACKGROUND: In reported plants, the bZIP family is one of the largest transcription factor families. bZIP genes play roles in the light signal, seed maturation, flower development, cell elongation, seed accumulation protein, abiotic and biological stress and other biological processes. While, no detailed identification and genome-wide analysis of bZIP family genes in Fagopyum talaricum (tartary buckwheat) has previously been published. The recently reported genome sequence of tartary buckwheat provides theoretical basis for us to study and discuss the characteristics and expression of bZIP genes in tartary buckwheat based on the whole genome. RESULTS: In this study, 96 FtbZIP genes named from FtbZIP1 to FtbZIP96 were identified and divided into 11 subfamilies according to their genetic relationship with 70 bZIPs of A. thaliana. FtbZIP genes are not evenly distributed on the chromosomes, and we found tandem and segmental duplication events of FtbZIP genes on 8 tartary buckwheat chromosomes. According to the results of gene and motif composition, FtbZIP located in the same group contained analogous intron/exon organizations and motif composition. By qRT-PCR, we quantified the expression of FtbZIP members in stem, root, leaf, fruit, and flower and during fruit development. Exogenous ABA treatment increased the weight of tartary buckwheat fruit and changed the expressions of FtbZIP genes in group A. CONCLUSIONS: Through our study, we identified 96 FtbZIP genes in tartary buckwheat and synthetically further analyzed the structure composition, evolution analysis and expression pattern of FtbZIP proteins. The expression pattern indicates that FtbZIP is important in the course of plant growth and development of tartary buckwheat. Through comprehensively analyzing fruit weight and FtbZIP genes expression after ABA treatment and endogenous ABA content of tartary buckwheat fruit, ABA may regulate downstream gene expression by regulating the expression of FtPinG0003523300.01 and FtPinG0003196200.01, thus indirectly affecting the fruit development of tartary buckwheat. This will help us to further study the function of FtbZIP genes in the tartary buckwheat growth and improve the fruit of tartary buckwheat.


Assuntos
Fatores de Transcrição de Zíper de Leucina Básica/genética , Evolução Molecular , Fagopyrum/genética , Perfilação da Expressão Gênica , Genômica , Filogenia , Cromossomos de Plantas/genética , Sequência Conservada , Fagopyrum/crescimento & desenvolvimento , Frutas/crescimento & desenvolvimento , Duplicação Gênica , Genoma de Planta/genética , Motivos de Nucleotídeos , Especificidade de Órgãos
13.
Planta ; 250(2): 589-601, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31134341

RESUMO

MAIN CONCLUSION: The absence of state transitions in a Nt(Hn) cybrid is due to a cleavage of the threonine residue from the misprocessed N-terminus of the LHCII polypeptides. The cooperation between the nucleus and chloroplast genomes is essential for plant photosynthetic fitness. The rapid and specific interactions between nucleus-encoded and chloroplast-encoded proteins are under intense investigation with potential for applications in agriculture and renewable energy technology. Here, we present a novel model for photosynthesis research in which alien henbane (Hyoscyamus niger) chloroplasts function on the nuclear background of a tobacco (Nicotiana tabacum). The result of this coupling is a cytoplasmic hybrid (cybrid) with inhibited state transitions-a mechanism responsible for balancing energy absorption between photosystems. Protein analysis showed differences in the LHCII composition of the cybrid plants. SDS-PAGE analysis revealed a novel banding pattern in the cybrids with at least one additional 'LHCII' band compared to the wild-type parental species. Proteomic work suggested that the N-terminus of at least some of the cybrid Lhcb proteins was missing. These findings provide a mechanistic explanation for the lack of state transitions-the N-terminal truncation of the Lhcb proteins in the cybrid included the threonine residue that is phosphorylated/dephosphorylated in order to trigger state transitions and therefore crucial energy balancing mechanism in plants.


Assuntos
Genoma de Cloroplastos/genética , Genoma de Planta/genética , Complexos de Proteínas Captadores de Luz/metabolismo , Tabaco/genética , Núcleo Celular/metabolismo , Cloroplastos/metabolismo , Complexos de Proteínas Captadores de Luz/genética , Fosforilação , Fotossíntese , Complexo de Proteína do Fotossistema II/genética , Complexo de Proteína do Fotossistema II/metabolismo , Proteômica , Treonina/metabolismo , Tabaco/fisiologia
14.
Planta ; 250(2): 603-628, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31139927

RESUMO

MAIN CONCLUSION: Compared with its parents, Brassica hexaploid underwent significant AS changes, which may provide diversified gene expression regulation patterns and could enhance its adaptability during evolution Polyploidization is considered a significant evolution force that promotes species formation. Alternative splicing (AS) plays a crucial role in multiple biological processes during plant growth and development. To explore the effects of allopolyploidization on the AS patterns of genes, a genome-wide AS analysis was performed by RNA-seq in Brassica hexaploid and its parents. In total, we found 7913 (27540 AS events), 14447 (70179 AS events), and 13205 (60804 AS events) AS genes in Brassica rapa, Brassica carinata, and Brassica hexaploid, respectively. A total of 920 new AS genes were discovered in Brassica hexaploid. There were 56 differently spliced genes between Brassica hexaploid and its parents. In addition, most of the alternative 5' splice sites were located 4 bp upstream of the dominant 5' splice sites, and most of the alternative 3' splice sites were located 3 bp downstream of the dominant 3' splice sites in Brassica hexapliod, which was similar to B. carinata. Furthermore, we cloned and sequenced all amplicons from the RT-PCR products of GRP7/8, namely, Bol045859, Bol016025 and Bol02880. The three genes were found to produce AS transcripts in a new way. The AS patterns of genes were diverse between Brassica hexaploid and its parents, including the loss and gain of AS events. Allopolyploidization changed alternative splicing sites of pre-mRNAs in Brassica hexaploid, which brought about alterations in the sequences of transcripts. Our study provided novel insights into the AS patterns of genes in allopolyploid plants, which may provide a reference for the study of polyploidy adaptability.


Assuntos
Processamento Alternativo , Brassica/genética , Regulação da Expressão Gênica de Plantas/genética , Genoma de Planta/genética , Adaptação Fisiológica , Evolução Biológica , Brassica/fisiologia , Brassica rapa/genética , Brassica rapa/fisiologia , Poliploidia
15.
BMC Plant Biol ; 19(1): 216, 2019 May 23.
Artigo em Inglês | MEDLINE | ID: mdl-31122195

RESUMO

BACKGROUND: Adaptation to drought-prone environments requires robust root architecture. Genotypes with a more vigorous root system have the potential to better adapt to soils with limited moisture content. However, root architecture is complex at both, phenotypic and genetic level. Customized mapping panels in combination with efficient screenings methods can resolve the underlying genetic factors of root traits. RESULTS: A mapping panel of 233 spring barley genotypes was evaluated for root and shoot architecture traits under non-stress and osmotic stress. A genome-wide association study elucidated 65 involved genomic regions. Among them were 34 root-specific loci, eleven hotspots with associations to up to eight traits and twelve stress-specific loci. A list of candidate genes was established based on educated guess. Selected genes were tested for associated polymorphisms. By this, 14 genes were identified as promising candidates, ten remained suggestive and 15 were rejected. The data support the important role of flowering time genes, including HvPpd-H1, HvCry2, HvCO4 and HvPRR73. Moreover, seven root-related genes, HERK2, HvARF04, HvEXPB1, PIN5, PIN7, PME5 and WOX5 are confirmed as promising candidates. For the QTL with the highest allelic effect for root thickness and plant biomass a homologue of the Arabidopsis Trx-m3 was revealed as the most promising candidate. CONCLUSIONS: This study provides a catalogue of hotspots for seedling growth, root and stress-specific genomic regions along with candidate genes for future potential incorporation in breeding attempts for enhanced yield potential, particularly in drought-prone environments. Root architecture is under polygenic control. The co-localization of well-known major genes for barley development and flowering time with QTL hotspots highlights their importance for seedling growth. Association analysis revealed the involvement of HvPpd-H1 in the development of the root system. The co-localization of root QTL with HERK2, HvARF04, HvEXPB1, PIN5, PIN7, PME5 and WOX5 represents a starting point to explore the roles of these genes in barley. Accordingly, the genes HvHOX2, HsfA2b, HvHAK2, and Dhn9, known to be involved in abiotic stress response, were located within stress-specific QTL regions and await future validation.


Assuntos
Secas , Genes de Plantas/fisiologia , Genoma de Planta/genética , Hordeum/genética , Fenótipo , Polimorfismo de Nucleotídeo Único/genética , Locos de Características Quantitativas/genética , Mapeamento Cromossômico , Estudo de Associação Genômica Ampla , Genótipo , Hordeum/crescimento & desenvolvimento , Raízes de Plantas/genética , Raízes de Plantas/crescimento & desenvolvimento , Brotos de Planta/genética , Brotos de Planta/crescimento & desenvolvimento , Plântula/genética , Plântula/crescimento & desenvolvimento
16.
Nat Plants ; 5(5): 461-470, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-31061536

RESUMO

Angiosperms are by far the most species-rich clade of land plants, but their origin and early evolutionary history remain poorly understood. We reconstructed angiosperm phylogeny based on 80 genes from 2,881 plastid genomes representing 85% of extant families and all orders. With a well-resolved plastid tree and 62 fossil calibrations, we dated the origin of the crown angiosperms to the Upper Triassic, with major angiosperm radiations occurring in the Jurassic and Lower Cretaceous. This estimated crown age is substantially earlier than that of unequivocal angiosperm fossils, and the difference is here termed the 'Jurassic angiosperm gap'. Our time-calibrated plastid phylogenomic tree provides a highly relevant framework for future comparative studies of flowering plant evolution.


Assuntos
Evolução Biológica , Magnoliopsida , Fósseis , Genes de Plantas/genética , Genoma de Planta/genética , Magnoliopsida/genética , Filogenia
17.
Plant Sci ; 283: 135-146, 2019 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31128683

RESUMO

The genetic basis of domestication and improvement remains largely unknown in sorghum as a typical multiple-origins species. In this study, the F2 and F3 populations derived from a cross between Sorghum virgatum and domesticated sorghum were used to study the genetic architecture of domestication- and improvement-related traits. We found that human selection had greatly reshaped sorghum through the Quantitative Trait Loci (QTLs) with large genetic effects in the traits of harvest, plant architecture and grain taste including the reduction of shattering, few branches, short plant stature and the removal of polyphenols from seed. The expansion of seed width was selected to improve the yield through accumulating small-effect QTLs. Two major QTLs of plant height (QTI-ph1 and dw1) were narrowed down into 24.5-kilobase (kb) and 13.9-kb, respectively. DNA diversity analysis and association mapping of dw1 gene suggested the functional variant (A1361 T) might originate from the same event not long time ago. Our results supported that parallel phenotypic changes across different species during domestication and improvement might share the same genetic basis, QTL × QTL interactions might not play an important role in the reshaping of traits during sorghum domestication and improvement, and offered new views on transgressive segregation and segregation distortion. Our study greatly deepens our understandings of the genetic basis of sorghum domestication and improvement.


Assuntos
Domesticação , Característica Quantitativa Herdável , Sorghum/genética , Mapeamento Cromossômico , Cromossomos de Plantas/genética , Genes de Plantas/genética , Genoma de Planta/genética , Melhoramento Vegetal/métodos , Locos de Características Quantitativas/genética , Sementes , Sorghum/anatomia & histologia
18.
Plant Biol (Stuttg) ; 21(5): 796-804, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31081576

RESUMO

Thellungiella salsuginea is highly tolerant to abiotic stress, while its a close relative Arabidopsis thaliana is sensitive to stress. This characteristic makes T. salsuginea an excellent model for uncovering the mechanisms of abiotic stress tolerance. Abscisic acid (ABA) plays essential roles in plant abiotic and biotic stress tolerance. To test the changes in gene expression of T. salsuginea under ABA treatment, in this study, the transcriptomes of T. salsuginea roots and leaves were compared in response to exogenously application of ABA. The results showed that ABA treatment caused different expression of 2,200 and 3,305 genes in leaves and roots, respectively, compared with the untreated control. In particular, genes encoding transcription factors such as WRKY, MYB, NAC, GATA, ethylene-responsive factors (ERFs), heat stress transcription factors, basic helix-loop-helix, PLATZ and B3 domain-containing family members were enriched. In addition, 49 and 114 differentially expressed genes were identified as ABA-regulated genes, separately in leaves and roots, respectively, which were related to biotic and abiotic stresses. The expression levels of some genes were validated by qRT-PCR. Different responses of genes to ABA treatment were discovered in T. salsuginea and A. thaliana. This transcriptome analysis expands our understanding of the role of ABA in stress tolerance in T. salsuginea. Our study provides a wealth of information for improving stress tolerance in crop plants.


Assuntos
Brassicaceae/fisiologia , Ácido Abscísico/farmacologia , Brassicaceae/genética , Brassicaceae/metabolismo , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Genoma de Planta/genética , Sequenciamento de Nucleotídeos em Larga Escala , Reguladores de Crescimento de Planta/farmacologia , Folhas de Planta/metabolismo , Raízes de Plantas/metabolismo , RNA de Plantas/genética , Reação em Cadeia da Polimerase em Tempo Real , Estresse Fisiológico , Fatores de Transcrição/metabolismo
19.
Planta ; 250(3): 989-1003, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31073657

RESUMO

MAIN CONCLUSION: The African Orphan Crops Consortium (AOCC) successfully initiated the ambitious genome sequencing project of 101 African orphan crops/trees with 6 genomes sequenced, 6 near completion, and 20 currently in progress. Addressing stunting, malnutrition, and hidden hunger through nutritious, economic, and resilient agri-food system is one of the major agricultural challenges of this century. As sub-Saharan Africa harbors a large portion of the severely malnourished population, the African Orphan Crops Consortium (AOCC) was established in 2011 with an aim to reduce stunting and malnutrition by providing nutritional security through improving locally adapted nutritious, but neglected, under-researched or orphan African food crops. Foods from these indigenous or naturalized crops and trees are rich in minerals, vitamins, and antioxidant, and are an integral part of the dietary portfolio and cultural, social, and economic milieu of African farmers. Through stakeholder consultations supported by the African Union, 101 African orphan and under-researched crop species were prioritized to mainstream into African agri-food systems. The AOCC, through a network of international-regional-public-private partnerships and collaborations, is generating genomic resources of three types, i.e., reference genome sequence, transcriptome sequence, and re-sequencing 100 accessions/species, using next-generation sequencing (NGS) technology. Furthermore, the University of California Davis African Plant Breeding Academy under the AOCC banner is training 150 lead African scientists to breed high yielding, nutritious, and climate-resilient (biotic and abiotic stress tolerant) crop varieties that meet African farmer and consumer needs. To date, one or more forms of sequence data have been produced for 60 crops. Reference genome sequences for six species have already been published, 6 are almost near completion, and 19 are in progress.


Assuntos
Produção Agrícola , Produtos Agrícolas/genética , Genoma de Planta/genética , África ao Sul do Saara , Produção Agrícola/organização & administração , Produtos Agrícolas/crescimento & desenvolvimento , Agricultura Florestal , Genômica/métodos , Genômica/organização & administração , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Árvores/genética , Árvores/crescimento & desenvolvimento
20.
Planta ; 250(3): 891-909, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31115659

RESUMO

MAIN CONCLUSION: Tailoring crops to withstand rising temperature and declining precipitation may be unrewarding, therefore the potential of alternative undervalued crops such as horse gram can be explored for safeguarding food and nutritional security with health benefits in the era of climate change. Horse gram [Macrotyloma uniflorum (Lam.) Verdc] under the family Fabaceae, has been cultivated for food, folklore medicine and fodder mainly by rural and tribal communities since prehistoric times in Asian and African countries. This valuable ancient legume not only offers diversification and resilience to agro-ecosystems but it also possesses high adaptation in risk-prone traditional farming systems in marginal environments of semi-arid and arid regions. Being a nutrient dense legume with remedial health-promoting effects due to the presence of various bioactive compounds, it is suitable for the development of functional food as well as for addressing micronutrient deficiencies among poor rural communities. Despite its enormous potential and a growing awareness about the utility of this underutilized crop for future climate adaptation and human well-being, this legume continues to be seriously neglected and labelled as "food of the poors". India is the major producer of horse gram and presently, cultivation of horse gram remains confined to small-scale farming systems as an inter- or mixed crop. This crop is alienated from mainstream agriculture and relegated to a status of "underutilized" due to its limited competitiveness as compared to other commercial crops. Besides a scanty basic research on this crop, no attention has been paid to the factors like improvement of plant type, yield improvement, processing, value addition to suit consumer needs and reduction of anti-nutritional factors, which restricted the diffusion of this crop outside its niche area. The present review therefore is an attempt to compile the meagre information available on crop history, evolution, genetic enhancement, nutritional and health benefits to make the crop competitive and revitalize horse gram cultivation.


Assuntos
Produtos Agrícolas/crescimento & desenvolvimento , Fabaceae/crescimento & desenvolvimento , Ração Animal , Produção Agrícola , Produtos Agrícolas/história , Fabaceae/genética , Previsões , Genoma de Planta/genética , História Antiga , Valor Nutritivo , Melhoramento Vegetal
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