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1.
BMC Plant Biol ; 19(1): 348, 2019 Aug 09.
Artigo em Inglês | MEDLINE | ID: mdl-31399046

RESUMO

BACKGROUND: Resistance to pre-harvest sprouting (PHS) is one of the major objectives in wheat breeding programs. However, the complex quantitative nature of this trait presents challenges when breeding for PHS resistance. Characterization of PHS using near-isogenic lines (NILs) targeting major quantitative trait locus/loci (QTL/QTLs) can be an effective strategy for the identification of responsible genes and underlying mechanisms. RESULTS: In this study, multiple pairs of NILs were developed and confirmed for a major QTL located on the 4BL chromosome arm that contributes to PHS resistance in wheat, using a combined heterogeneous inbred family method and a fast generation cycling system. Phenotypic characterization of these confirmed NILs revealed significant differences in PHS resistance between the isolines, where the presence of the resistant allele increased the resistance to sprouting on spikes by 54.0-81.9% (average 70.8%) and reduced seed germination by 59.4-70.5% (average 66.2%). The 90 K SNP genotyping assay on the confirmed NIL pairs identified eight SNPs on 4BL, associated with five candidate genes; two of the candidate genes were related to seed dormancy. Agronomic traits in the NIL pairs were investigated; both plant height and grain number per spike were positively correlated with PHS susceptibility. CONCLUSIONS: This study confirmed multiple pairs of NILs and identified SNPs between PHS isolines, which are valuable resources for further fine-mapping of this locus to clone the major genes for PHS resistance and investigate the possible functional regulation of these genes on important agronomic traits, such as plant height and grain number per spike.


Assuntos
Triticum/genética , Cromossomos de Plantas , Genótipo , Fenótipo , Melhoramento Vegetal , Desenvolvimento Vegetal/genética , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Triticum/crescimento & desenvolvimento , Triticum/metabolismo
2.
BMC Plant Biol ; 19(1): 332, 2019 Jul 29.
Artigo em Inglês | MEDLINE | ID: mdl-31357930

RESUMO

BACKGROUND: Good establishment is important for rapid leaf area development in wheat crops. Poor establishment results in fewer, later-emerging plants, reduced leaf area and tiller number. In addition, poorly established crops suffer from increased soil moisture loss through evaporation and greater competition from weeds while fewer spikes are produced which can reduce grain yield. By protecting the emerging first leaf, the coleoptile is critical for achieving good establishment, and its length and interaction with soil physical properties determine the ability of a cultivar to emerge from depth. RESULTS: Here we characterise a locus on chromosome 1AS, that increases coleoptile length in wheat, which we designate as Lcol-A1. We identified Lcol-A1 by bulked-segregant analysis and used a Halberd-derived population to fine map the gene to a 2 cM region, equivalent to 7 Mb on the IWGSC genome reference sequence of Chinese Spring (RefSeqv1.0). By sowing recently released cultivars and near-isogenic lines in the field at both conventional and deep sowing depths, we confirmed that Locl-A1 was associated with increased emergence from depth in the presence and absence of conventional dwarfing genes. Flanking markers IWB58229 and IWA710 were developed to assist breeders to select for long coleoptile wheats. CONCLUSIONS: Increased coleoptile length is sought in many global wheat production areas to improve crop emergence. The identification of the gene Lcol-A1, together with tools to allow wheat breeders to track the gene, will enable improvements to be made for this important trait.


Assuntos
Cotilédone/crescimento & desenvolvimento , Genes de Plantas/fisiologia , Triticum/genética , Mapeamento Cromossômico , Cromossomos de Plantas/genética , Genes de Plantas/genética , Estudos de Associação Genética , Loci Gênicos , Folhas de Planta/crescimento & desenvolvimento , Polimorfismo de Nucleotídeo Único/genética , Característica Quantitativa Herdável , Triticum/crescimento & desenvolvimento
3.
BMC Plant Biol ; 19(1): 330, 2019 Jul 23.
Artigo em Inglês | MEDLINE | ID: mdl-31337343

RESUMO

BACKGROUND: Dioecy is an important sexual system wherein, male and female flowers are borne on separate unisexual plants. Knowledge of sex-related differences can enhance our understanding in molecular and developmental processes leading to unisexual flower development. Coccinia grandis is a dioecious species belonging to Cucurbitaceae, a family well-known for diverse sexual forms. Male and female plants have 22A + XY and 22A + XX chromosomes, respectively. Previously, we have reported a gynomonoecious form (22A + XX) of C. grandis bearing morphologically hermaphrodite flowers (GyM-H) and female flowers (GyM-F). Also, we have showed that foliar spray of AgNO3 on female plant induces morphologically hermaphrodite bud development (Ag-H) despite the absence of Y-chromosome. RESULTS: To identify sex-related differences, total proteomes from male, female, GyM-H and Ag-H flower buds at early and middle stages of development were analysed by label-free proteomics. Protein search against the cucumber protein sequences (Phytozome) as well as in silico translated C. grandis flower bud transcriptome database, resulted in the identification of 2426 and 3385 proteins (FDR ≤ 1%), respectively. The latter database was chosen for further analysis as it led to the detection of higher number of proteins. Identified proteins were annotated using BLAST2GO pipeline. SWATH-MS-based comparative abundance analysis between Female_Early_vs_Male_Early, Ag_Early_vs_Female_Early, GyM-H_Middle_vs_Male_Middle and Ag_Middle_vs_ Male_Middle led to the identification of 650, 1108, 905 and 805 differentially expressed proteins, respectively, at fold change ≥1.5 and P ≤ 0.05. Ethylene biosynthesis-related candidates as highlighted in protein interaction network were upregulated in female buds compared to male buds. AgNO3 treatment on female plant induced proteins related to pollen development in Ag-H buds. Additionally, a few proteins governing pollen germination and tube growth were highly enriched in male buds compared to Ag-H and GyM-H buds. CONCLUSION: Overall, current proteomic analysis provides insights in the identification of key proteins governing dioecy and unisexual flower development in cucurbitaceae, the second largest horticultural family in terms of economic importance. Also, our results suggest that the ethylene-mediated stamen inhibition might be conserved in dioecious C. grandis similar to its monoecious cucurbit relatives. Further, male-biased proteins associated with pollen germination and tube growth identified here can help in understanding pollen fertility.


Assuntos
Cucurbitaceae/crescimento & desenvolvimento , Flores/crescimento & desenvolvimento , Diferenciação Sexual , Cromossomos de Plantas/fisiologia , Regulação da Expressão Gênica de Plantas , Proteínas de Plantas/fisiologia , Proteoma/fisiologia
4.
J Agric Food Chem ; 67(32): 8766-8772, 2019 Aug 14.
Artigo em Inglês | MEDLINE | ID: mdl-31313921

RESUMO

In decades of hybrid rice breeding, the combining ability has been successfully used to evaluate excellent parental lines and predict heterosis. However, previous studies for the combining ability mainly focused on cultivated rice and rarely involved wild rice. In this study, for the first time, we identified 20 new quantitative trait loci (QTLs) for the combining ability in wild rice using a North Carolina II mating design. Among them, qGCA1, one of the major QTLs that can significantly improve the general combining ability of the plant height, spikelet number, and yield per plant, was delimited to an interval of about 72 kb on chromosome 1. qSCA8, another major QTL, which can significantly improve the specific combining ability of the seed-setting rate and yield per plant, was located in an interval of about 90 kb on chromosome 8. These QTLs discovered from wild rice will provide new ideas to explain the genetic mechanism of the combining ability and establish the basis for breeding of high-combining-ability rice.


Assuntos
Cromossomos de Plantas/genética , Oryza/genética , Locos de Características Quantitativas , Mapeamento Cromossômico , Oryza/crescimento & desenvolvimento , Oryza/metabolismo , Fenótipo , Melhoramento Vegetal , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo
5.
BMC Plant Biol ; 19(1): 312, 2019 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-31307379

RESUMO

BACKGROUND: The WOX (WUSCHEL-RELATED HOMEOBOX) gene family encodes a class of transcription factors that are unique to green plants, where they are involved in regulating the development of plant tissues and organs by determining cell fate. Although the importance of the WOX gene is well known, there are few studies describing their functions in cotton. RESULTS: In this study, 32 WOX genes were found in Gossypium hirsutum. Phylogenetic analysis showed that WOX proteins of cotton can be divided into three clades: the ancient, intermediate, and WUS clades. The number of WOX proteins in the WUS clade was greater than the sum of the proteins in the other two clades. Our analysis revealed that 20 GhWOX genes are distributed on 16 cotton chromosomes and that duplication events are likely to have contributed to the expansion of the GhWOX family. All GhWOX genes have introns, and each GhWOX protein contains multiple motifs. RNA-seq data and real-time PCR showed that GhWOX13 gene subfamily is specifically expressed at a high level in cotton fibers. We also identified putative GA, NAA, and BR response elements in the promoter regions of the GhWOX13 genes and GhWOX13 transcripts were significantly induced by GA, NAA, and BR. CONCLUSIONS: Our data provides a useful resource for future studies on the functional roles of cotton WOX genes and shows that the GhWOX13 genes may influence cotton fiber development. Our results also provide an approach for identifying and characterizing WOX protein genes in other species.


Assuntos
Fibra de Algodão , Genes de Plantas , Gossypium/genética , Mapeamento Cromossômico , Cromossomos de Plantas , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Gossypium/crescimento & desenvolvimento , Proteínas de Homeodomínio/genética , Filogenia , Reguladores de Crescimento de Planta/fisiologia , Proteínas de Plantas/genética
6.
BMC Plant Biol ; 19(1): 310, 2019 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-31307401

RESUMO

BACKGROUND: The hypersensitive defense response (HR) in plants is a fast, localized necrotic response around the point of pathogen ingress. HR is usually triggered by a pathogen recognition event mediated by a nucleotide-binding site, leucine-rich repeat (NLR) protein. The autoactive maize NLR gene Rp1-D21 confers a spontaneous HR response in the absence of pathogen recognition. Previous work identified a set of loci associated with variation in the strength of Rp1-D21-induced HR. A polygalacturonase gene homolog, here termed ZmPGH1, was identified as a possible causal gene at one of these loci on chromosome 7. RESULTS: Expression of ZmPGH1 inhibited the HR-inducing activity of both Rp1-D21 and that of another autoactive NLR, RPM1(D505V), in a Nicotiana benthamiana transient expression assay system. Overexpression of ZmPGH1 in a transposon insertion line of maize was associated with suppression of chemically-induced programmed cell death and with suppression of HR induced by Rp1-D21 in maize plants grown in the field. CONCLUSIONS: ZmPGH1 functions as a suppressor of programmed cell death induced by at least two autoactive NLR proteins and by two chemical inducers. These findings deepen our understanding of the control of the HR in plants.


Assuntos
Apoptose/fisiologia , Proteínas de Plantas/fisiologia , Poligalacturonase/fisiologia , Zea mays/fisiologia , Apoptose/genética , Mapeamento Cromossômico , Cromossomos de Plantas , Genes de Plantas , Leucina , Proteínas de Plantas/química , Proteínas de Plantas/genética , Poligalacturonase/química , Poligalacturonase/genética , Recombinação Genética , Sequências Repetitivas de Aminoácidos , Tabaco/genética , Zea mays/enzimologia , Zea mays/genética , Zea mays/imunologia
7.
BMC Plant Biol ; 19(1): 318, 2019 Jul 16.
Artigo em Inglês | MEDLINE | ID: mdl-31311506

RESUMO

BACKGROUND: Single Nucleotide Polymorphism (SNP) array and re-sequencing technologies have different properties (e.g. calling rate, minor allele frequency profile) and drawbacks (e.g. ascertainment bias). This lead us to study their complementarity and the consequences of using them separately or combined in diversity analyses and Genome-Wide Association Studies (GWAS). We performed GWAS on three traits (grain yield, plant height and male flowering time) measured in 22 environments on a panel of 247 F1 hybrids obtained by crossing 247 diverse dent maize inbred lines with a same flint line. The 247 lines were genotyped using three genotyping technologies (Genotyping-By-Sequencing, Illumina Infinium 50 K and Affymetrix Axiom 600 K arrays). RESULTS: The effects of ascertainment bias of the 50 K and 600 K arrays were negligible for deciphering global genetic trends of diversity and for estimating relatedness in this panel. We developed an original approach based on linkage disequilibrium (LD) extent in order to determine whether SNPs significantly associated with a trait and that are physically linked should be considered as a single Quantitative Trait Locus (QTL) or several independent QTLs. Using this approach, we showed that the combination of the three technologies, which have different SNP distributions and densities, allowed us to detect more QTLs (gain in power) and potentially refine the localization of the causal polymorphisms (gain in resolution). CONCLUSIONS: Conceptually different technologies are complementary for detecting QTLs by tagging different haplotypes in association studies. Considering LD, marker density and the combination of different technologies (SNP-arrays and re-sequencing), the genotypic data available were most likely enough to well represent polymorphisms in the centromeric regions, whereas using more markers would be beneficial for telomeric regions.


Assuntos
Estudo de Associação Genômica Ampla/métodos , Técnicas de Genotipagem , Haplótipos , Análise de Sequência com Séries de Oligonucleotídeos , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Zea mays/genética , Alelos , Biodiversidade , Cromossomos de Plantas , Marcadores Genéticos , Genoma de Planta , Desequilíbrio de Ligação , Zea mays/crescimento & desenvolvimento
8.
BMC Plant Biol ; 19(1): 319, 2019 Jul 16.
Artigo em Inglês | MEDLINE | ID: mdl-31311507

RESUMO

BACKGROUND: Non-host resistance (NHR) presents a compelling long-term plant protection strategy for global food security, yet the genetic basis of NHR remains poorly understood. For many diseases, including stem rust of wheat [causal organism Puccinia graminis (Pg)], NHR is largely unexplored due to the inherent challenge of developing a genetically tractable system within which the resistance segregates. The present study turns to the pathogen's alternate host, barberry (Berberis spp.), to overcome this challenge. RESULTS: In this study, an interspecific mapping population derived from a cross between Pg-resistant Berberis thunbergii (Bt) and Pg-susceptible B. vulgaris was developed to investigate the Pg-NHR exhibited by Bt. To facilitate QTL analysis and subsequent trait dissection, the first genetic linkage maps for the two parental species were constructed and a chromosome-scale reference genome for Bt was assembled (PacBio + Hi-C). QTL analysis resulted in the identification of a single 13 cM region (~ 5.1 Mbp spanning 13 physical contigs) on the short arm of Bt chromosome 3. Differential gene expression analysis, combined with sequence variation analysis between the two parental species, led to the prioritization of several candidate genes within the QTL region, some of which belong to gene families previously implicated in disease resistance. CONCLUSIONS: Foundational genetic and genomic resources developed for Berberis spp. enabled the identification and annotation of a QTL associated with Pg-NHR. Although subsequent validation and fine mapping studies are needed, this study demonstrates the feasibility of and lays the groundwork for dissecting Pg-NHR in the alternate host of one of agriculture's most devastating pathogens.


Assuntos
Basidiomycota/fisiologia , Berberis/genética , Berberis/microbiologia , Doenças das Plantas/genética , Mapeamento Cromossômico , Cromossomos de Plantas , Resistência à Doença/genética , Perfilação da Expressão Gênica , Genoma de Planta , Hibridização Genética , Padrões de Herança , Fenótipo , Doenças das Plantas/microbiologia , Caules de Planta/microbiologia , Locos de Características Quantitativas
9.
Genome Biol ; 20(1): 136, 2019 07 12.
Artigo em Inglês | MEDLINE | ID: mdl-31300020

RESUMO

BACKGROUND: Bread wheat is one of the most important and broadly studied crops. However, due to the complexity of its genome and incomplete genome collection of wild populations, the bread wheat genome landscape and domestication history remain elusive. RESULTS: By investigating the whole-genome resequencing data of 93 accessions from worldwide populations of bread wheat and its diploid and tetraploid progenitors, together with 90 published exome-capture data, we find that the B subgenome has more variations than A and D subgenomes, including SNPs and deletions. Population genetics analyses support a monophyletic origin of domesticated wheat from wild emmer in northern Levant, with substantial introgressed genomic fragments from southern Levant. Southern Levant contributes more than 676 Mb in AB subgenomes and enriched in the pericentromeric regions. The AB subgenome introgression happens at the early stage of wheat speciation and partially contributes to their greater genetic diversity. Furthermore, we detect massive alien introgressions that originated from distant species through natural and artificial hybridizations, resulting in the reintroduction of ~ 709 Mb and ~ 1577 Mb sequences into bread wheat landraces and varieties, respectively. A large fraction of these intra- and inter-introgression fragments are associated with quantitative trait loci of important traits, and selection events are also identified. CONCLUSION: We reveal the significance of multiple introgressions from distant wild populations and alien species in shaping the genetic components of bread wheat, and provide important resources and new perspectives for future wheat breeding.


Assuntos
Evolução Biológica , Variação Genética , Genoma de Planta , Hibridização Genética , Triticum/genética , Cromossomos de Plantas , Domesticação , Sequenciamento Completo do Genoma
10.
Nat Plants ; 5(6): 575-580, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31182848

RESUMO

Doubled haploid (DH) breeding based on in vivo haploid induction has led to a new approach for maize breeding1. All modern haploid inducers used in DH breeding are derived from the haploid inducer line Stock6. Two key quantitative trait loci, qhir1 and qhir8, lead to high-frequency haploid induction2. Mutation of the gene MTL/ZmPLA1/NLD in qhir1 could generate a ~2% haploid induction rate (HIR)3-5; nevertheless, this mutation is insufficient for modern haploid inducers whose average HIR is ~10%6. Therefore, cloning of the gene underlying qhir8 is important for illuminating the genetic basis of haploid induction. Here, we present the discovery that mutation of a non-Stock6-originating gene in qhir8, namely, ZmDMP, enhances and triggers haploid induction. ZmDMP was identified by map-based cloning and further verified by CRISPR-Cas9-mediated knockout experiments. A single-nucleotide change in ZmDMP leads to a 2-3-fold increase in the HIR. ZmDMP knockout triggered haploid induction with a HIR of 0.1-0.3% and exhibited a greater ability to increase the HIR by 5-6-fold in the presence of mtl/zmpla1/nld. ZmDMP was highly expressed during the late stage of pollen development and localized to the plasma membrane. These findings provide important approaches for studying the molecular mechanism of haploid induction and improving DH breeding efficiency in maize.


Assuntos
Haploidia , Proteínas de Membrana/genética , Proteínas de Plantas/genética , Zea mays/genética , Mapeamento Cromossômico , Cromossomos de Plantas , Técnicas de Inativação de Genes , Mutação
11.
BMC Plant Biol ; 19(1): 265, 2019 Jun 20.
Artigo em Inglês | MEDLINE | ID: mdl-31221088

RESUMO

BACKGROUND: Chloroplast biogenesis, a complex process in higher plants, is the key to photoautotrophic growth in plants. White virescent (wv) mutants have been used to unfold the molecular mechanisms underlying the regulation of chloroplast development and chloroplast gene expression in plants. However, most of genes controlling white virescent phenotype still remain unknown. RESULTS: In this study, we identified a temperature- and light intensity-sensitive mutant, named as wv. The content of chlorophyll was dramatically decreased in the immature leaves of wv mutant under the conditions of low temperature and high-light intensity. TEM observation showed that the chloroplasts in the young leaves of wv mutant lacked an organized thylakoid membrane, whereas crescent-shaped chloroplasts with well-developed stromal and stacked grana thylakoids in the mature leaves were developed. Immunoblot analyses suggested that proteins of photosynthetic complexes were decreased substantially in wv mutants. Based on map-based cloning and transgenic analysis, we determined that the wv phenotype was caused by single base mutation in the first intron of WV gene, which encoded a thioredoxin protein with 365 amino acids. qRT-PCR analysis revealed that the expression of WV gene was significantly down-regulated in wv mutant. In addition, knockdown of WV gene through RNAi also resulted in white virescent young leaves, suggesting that the mutation possibly blocks the differentiation of chloroplasts through inhibiting the expression of WV gene. Furthermore, the expression of WV peaked in apical buds and gradually decreased along with the developmental stage, which was consistent with the wv mutant phenotype. Expression analysis of chloroplast-encoded genes by qRT-PCR showed that the wv mutation affected the expression pattern of chloroplast-encoded PEP dependent genes. CONCLUSION: Our results suggested that wv mutant was sensitive to low temperature and light intensity. WV gene was essential for chloroplast differentiation. A single base mutation in the first intron resulted in down-regulation of WV gene expression, which inhibited the expression of chloroplast-encoded genes, thereby blocking chloroplast formation and chlorophyll synthesis.


Assuntos
Cloroplastos/genética , Lycopersicon esculentum/genética , Tiorredoxinas/genética , Mapeamento Cromossômico , Cromossomos de Plantas , Temperatura Baixa , Genes de Plantas , Luz , Lycopersicon esculentum/crescimento & desenvolvimento , Lycopersicon esculentum/efeitos da radiação , Mutação , Fenótipo , Fotossíntese/genética , Alinhamento de Sequência , Tiorredoxinas/fisiologia
12.
BMC Plant Biol ; 19(1): 269, 2019 Jun 21.
Artigo em Inglês | MEDLINE | ID: mdl-31226949

RESUMO

BACKGROUND: The Growth-regulating factor (GRF) family encodes plant-specific transcription factors which contain two conserved domains, QLQ and WRC. Members of this family play vital roles in plant development and stress response processes. Although GRFs have been identified in various plant species, we still know little about the GRF family in soybean (Glycine max). RESULTS: In the present study, 22 GmGRFs distributed on 14 chromosomes and one scaffold were identified by searching soybean genome database and were clustered into five subgroups according to their phylogenetic relationships. GmGRFs belonging to the same subgroup shared a similar motif composition and gene structure. Synteny analysis revealed that large-scale duplications played key roles in the expansion of the GmGRF family. Tissue-specific expression data showed that GmGRFs were strongly expressed in growing tissues, including the shoot apical meristems, developing seeds and flowers, indicating that GmGRFs play critical roles in plant growth and development. On the basis of expression analysis of GmGRFs under shade conditions, we found that all GmGRFs responded to shade stress. Most GmGRFs were down-regulated in soybean leaves after shade treatment. CONCLUSIONS: Taken together, this research systematically analyzed the characterization of the GmGRF family and its primary roles in soybean development and shade stress response. Further studies of the function of the GmGRFs in the growth, development and stress tolerance of soybean, especially under shade stress, will be valuable.


Assuntos
Proteínas de Plantas/genética , Soja/genética , Fatores de Transcrição/genética , Cromossomos de Plantas , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Luz , Proteínas de Plantas/metabolismo , Soja/metabolismo , Estresse Fisiológico , Sintenia , Fatores de Transcrição/metabolismo , Transcriptoma
13.
BMC Plant Biol ; 19(1): 242, 2019 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-31174465

RESUMO

BACKGROUND: Recurrent drought associated with climate change is a major constraint to wheat (Triticum aestivum L.) productivity. This study aimed to (i) quantify the effects of addition/substitution/translocation of chromosome segments from wild relatives of wheat on the root, physiological and yield traits of hexaploid wheat under drought, and (ii) understand the mechanism(s) associated with drought tolerance or susceptibility in wheat-alien chromosome lines. METHODS: A set of 48 wheat-alien chromosome lines (addition/substitution/translocation lines) with Chinese Spring background were used. Seedling root traits were studied on solid agar medium. To understand the influence of drought on the root system of adult plants, these 48 lines were grown in 150-cm columns for 65 d under full irrigation or withholding water for 58 d. To quantify the effect of drought on physiological and yield traits, the 48 lines were grown in pots under full irrigation until anthesis; after that, half of the plants were drought stressed by withholding water for 16 d before recording physiological and yield-associated traits. RESULTS: The alien chromosome lines exhibited altered root architecture and decreased photochemical efficiency and seed yield and its components under drought. The wheat-alien chromosome lines T5DS·5S#3L (TA5088) with a chromosome segment from Aegilops speltoides (5S) and T5DL.5 V#3S (TA5638) with a chromosome segment from Dasypyrum villosum (5 V) were identified as drought tolerant, and the drought tolerance mechanism was associated with a deep, thin and profuse root system. CONCLUSIONS: The two germplasm lines (TA5088 and TA5638) could be used in wheat breeding programs to improve drought tolerance in wheat and understand the underlying molecular genetic mechanisms of root architecture and drought tolerance.


Assuntos
Cromossomos de Plantas/genética , Secas , Genes de Plantas/genética , Melhoramento Vegetal , Triticum/genética , Aegilops/genética , Raízes de Plantas/anatomia & histologia , Raízes de Plantas/genética , Raízes de Plantas/crescimento & desenvolvimento , Poaceae/genética , Triticum/anatomia & histologia , Triticum/crescimento & desenvolvimento
14.
BMC Plant Biol ; 19(1): 259, 2019 Jun 17.
Artigo em Inglês | MEDLINE | ID: mdl-31208337

RESUMO

BACKGROUND: Cultivated rice (Oryza sativa L.) is one of the staple food for over half of the world's population. Thus, improvement of cultivated rice is important for the development of the world. It has been shown that abundant elite genes exist in rice landraces in previous studies. RESULTS: A genome-wide association study (GWAS) performed with EMMAX for 12 agronomic traits measured in both Guangzhou and Hangzhou was carried out using 150 accessions of Ting's core collection selected based on 48 phenotypic traits from 2262 accessions of Ting's collection, the GWAS included more than 3.8 million SNPs. Within Ting's core collection, which has a simple population structure, low relatedness, and rapid linkage disequilibrium (LD) decay, we found 32 peaks located closely to previously cloned genes such as Hd1, SD1, Ghd7, GW8, and GL7 or mapped QTL, and these loci might be natural variations in the cloned genes or QTL which influence potentially agronomic traits. Furthermore, we also detected 32 regions where new genes might be located, and some peaks of these new candidate genes such as the signal on chromosome 11 for heading days were even higher than that of Hd1. Detailed annotation of these significant loci were shown in this study. Moreover, according to the estimated LD decay distance of 100 to 350 kb on the 12 chromosomes in this study, we found 13 identical significant regions in the two locations. CONCLUSIONS: This research provided important information for further mining these elite genes within Ting's core collection and using them for rice breeding.


Assuntos
Oryza/genética , Característica Quantitativa Herdável , Mapeamento Cromossômico , Cromossomos de Plantas/genética , Genes de Plantas/genética , Estudos de Associação Genética , Estudo de Associação Genômica Ampla , Desequilíbrio de Ligação/genética , Locos de Características Quantitativas/genética
15.
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
16.
Gene ; 710: 291-306, 2019 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-31185283

RESUMO

The WD40 transcription factor family is a superfamily found in all eukaryotes that plays important roles in regulating growth and development. To our knowledge, to date, WD40 superfamily genes have been identified and characterized in several plant species, but little information is available on the WD40 superfamily genes in peach. In this study, we identified 220 members of the WD40 superfamily in the peach genome, and these members were further classified into five subfamilies based on phylogenetic comparison with those in Arabidopsis. The members within each subfamily had conserved motifs and gene structures. The WD40 genes were unevenly distributed on chromosomes 1 to 8 of the peach genome. Additionally, 58 pairs of paralog WD40 members were found on eight chromosomes in peach, and 242 pairs of orthologous WD40 genes in peach and Arabidopsis were matched. The 54 selected putative WD40 genes in peach had diverse expression patterns in red-fleshed and white-fleshed peach fruits at five developmental stages. Prupe.6G211800.1 was located only on the cytomembrane, while Prupe.1G428200.1 and Prupe.I003200.1 were located on both the cytomembrane and in the nucleus; Prupe.1G558700.1 was densely localized around the nuclear rim but relatively faintly localized in the nucleoplasm; Prupe.5G116300.1 was located in the nucleus and cytomembrane with strong signals but showed weak signals in the cytoplasm; and Prupe.8G212400.1 and Prupe.1G053600.1 were located mainly in the nuclear envelope and cytomembrane but relatively faintly in the nucleoplasm. This study provides a foundation for the further functional verification of WD40 genes in peach.


Assuntos
Mapeamento Cromossômico/métodos , Família Multigênica , Proteínas de Plantas/genética , Prunus persica/genética , Núcleo Celular/genética , Núcleo Celular/metabolismo , Cromossomos de Plantas/genética , Sequência Conservada , Citoplasma/genética , Citoplasma/metabolismo , Regulação da Expressão Gênica de Plantas , Filogenia , Proteínas de Plantas/metabolismo , Prunus persica/metabolismo , Repetições WD40
17.
BMC Plant Biol ; 19(1): 183, 2019 May 06.
Artigo em Inglês | MEDLINE | ID: mdl-31060503

RESUMO

BACKGROUND: Triticum timopheevii (2n = 4x = 28; AtAtGG), is an important source for new genetic variation for wheat improvement with genes for potential disease resistance and salt tolerance. By generating a range of interspecific hybrid lines, T. timopheevii can contribute to wheat's narrow gene-pool and be practically utilised in wheat breeding programmes. Previous studies that have generated such introgression lines between wheat and its wild relatives have been unable to use high-throughput methods to detect the presence of wild relative segments in such lines. RESULTS: A whole genome introgression approach, exploiting homoeologous recombination in the absence of the Ph1 locus, has resulted in the transfer of different chromosome segments from both the At and G genomes of T. timopheevii into wheat. These introgressions have been detected and characterised using single nucleotide polymorphism (SNP) markers present on a high-throughput Axiom® Genotyping Array. The analysis of these interspecific hybrid lines has resulted in the detection of 276 putative unique introgressions from T. timopheevii, thereby allowing the generation of a genetic map of T. timopheevii containing 1582 SNP markers, spread across 14 linkage groups representing each of the seven chromosomes of the At and G genomes of T. timopheevii. The genotyping of the hybrid lines was validated through fluorescence in situ hybridisation (FISH). Comparative analysis of the genetic map of T. timopheevii and the physical map of the hexaploid wheat genome showed that synteny between the two species is highly conserved at the macro-level and confirmed the presence of inter- and intra-genomic translocations within the At and G genomes of T. timopheevii that have been previously only detected through cytological techniques. CONCLUSIONS: In this work, we report a set of SNP markers present on a high-throughput genotyping array, able to detect the presence of T. timopheevii in a hexaploid wheat background making it a potentially valuable tool for marker assisted selection (MAS) in wheat pre-breeding programs. These valuable resources of high-density molecular markers and wheat-T. timopheevii hybrid lines will greatly enhance the work being undertaken for wheat improvement through wild relative introgressions.


Assuntos
Genoma de Planta , Hibridização Genética , Poliploidia , Triticum/genética , Mapeamento Cromossômico , Cromossomos de Plantas/genética , Cruzamentos Genéticos , Ecótipo , Ligação Genética , Loci Gênicos , Marcadores Genéticos , Genótipo , Polimorfismo de Nucleotídeo Único/genética , Recombinação Genética/genética , Sementes/genética , Especificidade da Espécie
18.
BMC Plant Biol ; 19(1): 191, 2019 May 09.
Artigo em Inglês | MEDLINE | ID: mdl-31072335

RESUMO

BACKGROUND: BRASSINAZOLE-RESISTANT (BZR) family genes encode plant-specific transcription factors (TFs) that participate in brassinosteroid signal transduction. BZR TFs have vital roles in plant growth, including cell elongation. However, little is known about BZR genes in sugar beet (Beta vulgaris L.). RESULTS: Therefore, we performed a genome-wide investigation of BvBZR genes in sugar beet. Through an analysis of the BES1_N conserved domain, six BvBZR gene family members were identified in the sugar beet genome, which clustered into three subgroups according to a phylogenetic analysis. Each clade was well defined by the conserved motifs, implying that close genetic relationships could be identified among the members of each subfamily. According to chromosomal distribution mapping, 2, 1, 1, 1, and 1 genes were located on chromosomes 1, 4, 5, 6, and 8, respectively. The cis-acting elements related to taproot growth were randomly distributed in the promoter sequences of the BvBZR genes. Tissue-specific expression analyses indicated that all BvBZR genes were expressed in all three major tissue types (roots, stems, and leaves), with significantly higher expression in leaves. Subcellular localization analysis revealed that Bv1_fxre and Bv6_nyuw are localized in the nuclei, consistent with the prediction of Wolf PSORT. CONCLUSION: These findings offer a basis to predict the functions of BZR genes in sugar beet, and lay a foundation for further research of the biological functions of BZR genes in sugar beet.


Assuntos
Beta vulgaris/genética , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Fatores de Transcrição/genética , Motivos de Aminoácidos , Beta vulgaris/efeitos dos fármacos , Cromossomos de Plantas/genética , Sequência Conservada/genética , Regulação da Expressão Gênica de Plantas/efeitos dos fármacos , Genes de Plantas , Proteínas de Fluorescência Verde/metabolismo , Motivos de Nucleotídeos/genética , Filogenia , Reguladores de Crescimento de Planta/farmacologia , Raízes de Plantas/efeitos dos fármacos , Raízes de Plantas/genética , Raízes de Plantas/crescimento & desenvolvimento , Regiões Promotoras Genéticas , Fatores de Transcrição/metabolismo
19.
BMC Plant Biol ; 19(1): 167, 2019 Apr 29.
Artigo em Inglês | MEDLINE | ID: mdl-31035914

RESUMO

BACKGROUND: First flower node (FFN) is an important trait for evaluating fruit earliness in pepper (Capsicum annuum L.). The trait is controlled by quantitative trait loci (QTL); however, studies have been limited on QTL mapping and genes contributing to the trait. RESULTS: In this study, we developed a high density genetic map using specific-locus amplified fragment sequencing (SLAF-seq), a high-throughput strategy for de novo single nucleotide polymorphism discovery, based on 146 recombinant inbred lines (RILs) derived from an intraspecific cross between PM702 and FS871. The map contained 9328 SLAF markers on 12 linkage groups (LGs), and spanned a total genetic distance of 2009.69 centimorgan (cM) with an average distance of 0.22 cM. The sequencing depth for the map was 72.39-fold in the male parent, 57.04-fold in the female parent, and 15.65-fold in offspring. Using the genetic map, two major QTLs, named Ffn2.1 and Ffn2.2, identified on LG02 were strongly associated with FFN, with a phenotypic variance explanation of 28.62 and 19.56%, respectively. On the basis of the current annotation of C. annuum cv. Criollo de Morelos (CM334), 59 candidate genes were found within the Ffn2.1 and Ffn2.2 region, but only 3 of 59 genes were differentially expressed according to the RNA-seq results. Eventually we identified one gene associated with the FFN based on the function through GO, KEGG, and Swiss-prot analysis. CONCLUSIONS: Our research showed that the construction of high-density genetic map using SLAF-seq is a valuable tool for fine QTL mapping. The map we constructed is by far the most saturated complete genetic map of pepper, and using it we conducted fine QTL mapping for the important trait, FFN. QTLs and candidate genes obtained in this study lay a good foundation for the further research on FFN-related genes and other genetic applications in pepper.


Assuntos
Capsicum/genética , Mapeamento Cromossômico/métodos , Cromossomos de Plantas , Flores/genética , Locos de Características Quantitativas , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Ligação Genética , Genótipo , Sequenciamento de Nucleotídeos em Larga Escala , Polimorfismo de Nucleotídeo Único
20.
BMC Plant Biol ; 19(1): 172, 2019 Apr 30.
Artigo em Inglês | MEDLINE | ID: mdl-31039740

RESUMO

BACKGROUND: Angiosperm sex chromosomes, where present, are generally recently evolved. The key step in initiating the development of sex chromosomes from autosomes is the establishment of a sex-determining locus within a region of non-recombination. To better understand early sex chromosome evolution, it is important to determine the process by which recombination is suppressed around the sex determining genes. We have used the dioecious angiosperm kiwifruit Actinidia chinensis var. chinensis, which has an active-Y sex chromosome system, to study recombination rates around the sex locus, to better understand key events in the development of sex chromosomes. RESULTS: We have confirmed the sex-determining region (SDR) in A. chinensis var. chinensis, using a combination of high density genetic mapping and fluorescent in situ hybridisation (FISH) of Bacterial Artificial Chromosomes (BACs) linked to the sex markers onto pachytene chromosomes. The SDR is a subtelomeric non-recombining region adjacent to the nucleolar organiser region (NOR). A region of restricted recombination of around 6 Mbp in size in both male and female maps spans the SDR and covers around a third of chromosome 25. CONCLUSIONS: As recombination is suppressed over a similar region between X chromosomes and between and X and Y chromosomes, we propose that recombination is suppressed in this region because of the proximity of the NOR and the centromere, with both the NOR and centromere suppressing recombination, and this predates suppressed recombination due to differences between X and Y chromosomes. Such regions of suppressed recombination in the genome provide an opportunity for the evolution of sex chromosomes, if a sex-determining locus develops there or translocates into this region.


Assuntos
Actinidia/genética , Cromossomos de Plantas , Recombinação Genética , Cromossomos Sexuais , Actinidia/citologia , Mapeamento Cromossômico , Cromossomos Artificiais Bacterianos , Variação Genética , Hibridização in Situ Fluorescente , Repetições de Microssatélites
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