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1.
Nat Commun ; 11(1): 495, 2020 01 24.
Artigo em Inglês | MEDLINE | ID: mdl-31980630

RESUMO

Maize rough dwarf disease (MRDD), caused by various species of the genus Fijivirus, threatens maize production worldwide. We previously identified a quantitative locus qMrdd1 conferring recessive resistance to one causal species, rice black-streaked dwarf virus (RBSDV). Here, we show that Rab GDP dissociation inhibitor alpha (RabGDIα) is the host susceptibility factor for RBSDV. The viral P7-1 protein binds tightly to the exon-10 and C-terminal regions of RabGDIα to recruit it for viral infection. Insertion of a helitron transposon into RabGDIα intron 10 creates alternative splicing to replace the wild-type exon 10 with a helitron-derived exon 10. The resultant splicing variant RabGDIα-hel has difficulty being recruited by P7-1, thus leading to quantitative recessive resistance to MRDD. All naturally occurring resistance alleles may have arisen from a recent single helitron insertion event. These resistance alleles are valuable to improve maize resistance to MRDD and potentially to engineer RBSDV resistance in other crops.


Assuntos
Resistência à Doença , Inibidores de Dissociação do Nucleotídeo Guanina/metabolismo , Doenças das Plantas/virologia , Proteínas de Plantas/metabolismo , Vírus de Plantas/fisiologia , Zea mays/virologia , Alelos , Resistência à Doença/genética , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Inibidores de Dissociação do Nucleotídeo Guanina/genética , Modelos Biológicos , Mapeamento Físico do Cromossomo , Doenças das Plantas/genética , Proteínas de Plantas/genética , Plantas Geneticamente Modificadas , Ligação Proteica , Locos de Características Quantitativas/genética , RNA Mensageiro/genética , RNA Mensageiro/metabolismo , Reprodutibilidade dos Testes , Proteínas Virais/metabolismo , Zea mays/genética , Zea mays/ultraestrutura
2.
Nat Commun ; 10(1): 4097, 2019 09 10.
Artigo em Inglês | MEDLINE | ID: mdl-31506438

RESUMO

Phenotypic variation of quantitative traits is orchestrated by a complex interplay between the environment (e.g. diet) and genetics. However, the impact of gene-environment interactions on phenotypic traits mostly remains elusive. To address this, we feed 1154 mice of an autoimmunity-prone intercross line (AIL) three different diets. We find that diet substantially contributes to the variability of complex traits and unmasks additional genetic susceptibility quantitative trait loci (QTL). By performing whole-genome sequencing of the AIL founder strains, we resolve these QTLs to few or single candidate genes. To address whether diet can also modulate genetic predisposition towards a given trait, we set NZM2410/J mice on similar dietary regimens as AIL mice. Our data suggest that diet modifies genetic susceptibility to lupus and shifts intestinal bacterial and fungal community composition, which precedes clinical disease manifestation. Collectively, our study underlines the importance of including environmental factors in genetic association studies.


Assuntos
Cruzamentos Genéticos , Dieta , Genes , Estudos de Associação Genética , Característica Quantitativa Herdável , Animais , Animais não Endogâmicos , Anticorpos Antinucleares/genética , Bactérias/crescimento & desenvolvimento , Biodiversidade , Feminino , Fungos/crescimento & desenvolvimento , Predisposição Genética para Doença , Nefrite Lúpica/genética , Nefrite Lúpica/imunologia , Masculino , Camundongos , Microbiota , Mapeamento Físico do Cromossomo , Locos de Características Quantitativas/genética , Baço/metabolismo , Transcriptoma/genética , Sequenciamento Completo do Genoma
3.
J Genet ; 982019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-31544776

RESUMO

Genetic information of polymerase chain reaction (PCR)-based markers, one of the main tools of genetics and genomics research in wheat, have been well documented in wheat. However, the physical position in relation to these markers has not yet been systematically characterized. Aim of this study was to characterize the physical information of thousands of widely used molecular markers.We first assigned 2705 molecular markers to wheat physical map, of which 86.1% and 84.7% were the best hits to chromosome survey sequencing (CSS) project (CSS-contigs) and International Wheat Genome Sequencing Consortium Reference Sequence v1.0 (IWGSC RefSeq v1.0), respectively. Physical position of 96.2% markers were predicated based on BLAST analysis, were in accordance with that of the previous nullisomic/aneuploidy/linkage analysis. A suggestive high-density physical map with 4643 loci was constructed, spanning 14.01 Gb (82.4%) of the wheat genome, with 3.02 Mb between adjacent markers. Both forward and reverse primer sequences of 1166 markers had consistent best hits to IWGSC RefSeq v1.0 based on BLAST analysis, and the corresponding allele sizes were characterized. A detailed physical map with 1532 loci was released, spanning 13.93 Gb (81.9%) of the wheat genome, with 9.09 Mb between adjacent markers. Characteristic of recombination rates in different chromosomal regions was discussed. In addition, markers with multiple sites were aligned to homoeologous sites with a consistent order, confirming that a collinearity existed among A, B and D subgenomes. This study facilitates the integration of physical and genetical information of molecular markers, which could be of value for use in genetics and genomics research such as gene/QTL map-based cloning and marker-assisted selection.


Assuntos
Mapeamento Físico do Cromossomo , Triticum/genética , Ligação Genética , Marcadores Genéticos , Genoma de Planta , Reação em Cadeia da Polimerase , Recombinação Genética/genética
4.
BMC Genomics ; 20(1): 479, 2019 Jun 11.
Artigo em Inglês | MEDLINE | ID: mdl-31185912

RESUMO

BACKGROUND: The mammalian major histocompatibility complex (MHC) harbours clusters of genes associated with the immunological defence of animals against infectious pathogens. At present, no complete MHC physical map is available for any of the wild ruminant species in the world. RESULTS: The high-density physical map is composed of two contigs of 47 overlapping bacterial artificial chromosome (BAC) clones, with an average of 115 Kb for each BAC, covering the entire addax MHC genome. The first contig has 40 overlapping BAC clones covering an approximately 2.9 Mb region of MHC class I, class III, and class IIa, and the second contig has 7 BAC clones covering an approximately 500 Kb genomic region that harbours MHC class IIb. The relative position of each BAC corresponding to the MHC sequence was determined by comparative mapping using PCR screening of the BAC library of 192,000 clones, and the order of BACs was determined by DNA fingerprinting. The overlaps of neighboring BACs were cross-verified by both BAC-end sequencing and co-amplification of identical PCR fragments within the overlapped region, with their identities further confirmed by DNA sequencing. CONCLUSIONS: We report here the successful construction of a high-quality physical map for the addax MHC region using BACs and comparative mapping. The addax MHC physical map we constructed showed one gap of approximately 18 Mb formed by an ancient autosomal inversion that divided the MHC class II into IIa and IIb. The autosomal inversion provides compelling evidence that the MHC organizations in all of the ruminant species are relatively conserved.


Assuntos
Antílopes/genética , Cromossomos Artificiais Bacterianos/genética , Genômica , Antígenos de Histocompatibilidade Classe II/genética , Antígenos de Histocompatibilidade Classe I/genética , Mapeamento Físico do Cromossomo/métodos , Animais , Bovinos , Evolução Molecular , Masculino , Reação em Cadeia da Polimerase
5.
BMC Bioinformatics ; 20(1): 348, 2019 Jun 18.
Artigo em Inglês | MEDLINE | ID: mdl-31215408

RESUMO

BACKGROUND: In computational biology, the physical mapping of DNA is a key problem. We know that the double digest problem (DDP) is NP-complete. Many algorithms have been proposed for solving the DDP, although it is still far from being resolved. RESULTS: We present DDmap, an open-source MATLAB package for solving the DDP, based on a newly designed genetic algorithm that combines six genetic operators in searching for optimal solutions. We test the performance of DDmap by using a typical DDP dataset, and we depict exact solutions to these DDP instances in an explicit manner. In addition, we propose an approximate method for solving some hard DDP scenarios via a scaling-rounding-adjusting process. CONCLUSIONS: For typical DDP test instances, DDmap finds exact solutions within approximately 1 s. Based on our simulations on 1000 random DDP instances by using DDmap, we find that the maximum length of the combining fragments has observable effects towards genetic algorithms for solving the DDP problem. In addition, a Maple source code for illustrating DDP solutions as nested pie charts is also included.


Assuntos
Regiões Operadoras Genéticas , Mapeamento Físico do Cromossomo/métodos , Software , Algoritmos , DNA/genética
6.
BMC Plant Biol ; 19(1): 179, 2019 May 03.
Artigo em Inglês | MEDLINE | ID: mdl-31053089

RESUMO

BACKGROUND: Fusarium head blight resistance genes, Fhb1 (for Type-II resistance), Fhb2 (Type-II), and Fhb5 (Type-I plus some Type-II), which originate from Sumai 3, are among the most important that confer resistance in hexaploid wheat. Near-isogenic lines (NILs), in the CDC Alsask (susceptible; n = 32) and CDC Go (moderately susceptible; n = 38) backgrounds, carrying these genes in all possible combinations were developed using flanking microsatellite markers and evaluated for their response to FHB and deoxynivalenol (DON) accumulation in eight environments. NILs were haplotyped with wheat 90 K iSelect assay to elucidate the genomic composition and confirm alleles' presence. Other than evaluating the effects of three major genes in common genetic background, the study elucidated the epistatic gene interactions as they influence FHB measurements; identified loci other than Fhb1, Fhb2, and Fhb5, in both recurrent and donor parents and examined annotated proteins in gene intervals. RESULTS: Genotyping using 81,857 single nucleotide polymorphism (SNP) markers revealed polymorphism on all chromosomes and that the NILs carried < 3% of alleles from the resistant donor. Significant improvement in field resistance (Type-I + Type-II) resulted only among the CDC Alsask NILs, not the CDC Go NILs. The phenotypic response of NILs carrying combinations of Sumai 3 derived genes suggested non-additive responses and Fhb5 was as good as Fhb1 in conferring field resistance in both populations. In addition to Fhb1, Fhb2, and Fhb5, four to five resistance improving alleles in both populations were identified and three of five in CDC Go were contributed by the susceptible parent. The introgressed chromosome regions carried genes encoding disease resistance proteins, protein kinases, nucleotide-binding and leucine rich repeats' domains. Complex epistatic gene-gene interactions among marker loci (including Fhb1, Fhb2, Fhb5) explained > 20% of the phenotypic variation in FHB measurements. CONCLUSIONS: Immediate Sumai 3 derivatives carry a number of resistance improving minor effect alleles, other than Fhb1, Fhb2, Fhb5. Results verified that marker-assisted selection is possible for the introgression of exotic FHB resistance genes, however, the genetic background of the recipient line and epistatic interactions can have a strong influence on expression and penetrance of any given gene.


Assuntos
Fusarium/fisiologia , Triticum/genética , Triticum/microbiologia , Alelos , Cromossomos de Plantas , Resistência à Doença/genética , Epistasia Genética , Genes de Plantas , Marcadores Genéticos , Genótipo , Padrões de Herança , Fenótipo , Mapeamento Físico do Cromossomo , Doenças das Plantas/genética , Doenças das Plantas/microbiologia
7.
Theor Appl Genet ; 132(8): 2353-2365, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-31079164

RESUMO

KEY MESSAGE: Wild emmer allele of GNI-A1 ease competition among developing grains through the suppression of floret fertility and increase grain weight in tetraploid wheat. Grain yield is a highly polygenic trait determined by the number of grains per unit area, as well as by grain weight. In wheat, grain number and grain weight are usually negatively correlated. Yet, the genetic basis underlying trade-off between the two is mostly unknown. Here, we fine-mapped a grain weight QTL using wild emmer introgressions in a durum wheat background and showed that grain weight is associated with the GNI-A1 gene, a regulator of floret fertility. In-depth characterization of grain number and grain weight indicated that suppression of distal florets by the wild emmer GNI-A1 allele increases weight of proximal grains in basal and central spikelets due to alteration in assimilate distribution. Re-sequencing of GNI-A1 in tetraploid wheat demonstrated the rich allelic repertoire of the wild emmer gene pool, including a rare allele which was present in two gene copies and contained a nonsynonymous mutation in the C-terminus of the protein. Using an F2 population generated from a cross between wild emmer accessions Zavitan, which carries the rare allele, and TTD140, we demonstrated that this unique polymorphism is associated with grain weight, independent of grain number. Moreover, we showed, for the first time, that GNI-A1 proteins are transcriptional activators and that selection targeted compromised activity of the protein. Our findings expand the knowledge of the genetic basis underlying trade-off between key yield components and may contribute to breeding efforts for enhanced grain yield.


Assuntos
Grão Comestível/genética , Proteínas de Plantas/genética , Locos de Características Quantitativas/genética , Tetraploidia , Triticum/genética , Alelos , Sequência de Aminoácidos , Biomassa , Grão Comestível/anatomia & histologia , Dosagem de Genes , Haplótipos/genética , Mapeamento Físico do Cromossomo , Proteínas de Plantas/química
8.
Theor Appl Genet ; 132(8): 2169-2179, 2019 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-30941465

RESUMO

KEY MESSAGE: The fuzzless gene GaFzl was fine mapped to a 70-kb region containing a GIR1 gene, Cotton_A_11941, responsible for the fuzzless trait in Gossypium arboreum DPL972. Cotton fiber is the most important natural textile resource. The fuzzless mutant DPL972 (Gossypium arboreum) provides a useful germplasm resource to explore the molecular mechanism underlying fiber and fuzz initiation and development. In our previous research, the fuzzless gene in DPL972 was identified as a single dominant gene and named GaFzl. In the present study, we fine mapped this gene using F2 and BC1 populations. By combining traditional map-based cloning and next-generation sequencing, we mapped GaFzl to a 70-kb region containing seven annotated genes. RNA-Sequencing and re-sequencing analysis narrowed these candidates to two differentially expressed genes, Cotton_A_11941 and Cotton_A_11942. Sequence alignment uncovered no variation in coding or promoter regions of Cotton_A_11942 between DPL971 and DPL972, whereas two single-base mutations in the promoter region and a TTG insertion in the coding region were detected in Cotton_A_11941 in DPL972. Cotton_A_11941 encoding a homologous gene of GIR1 (GLABRA2-interacting repressor) in Arabidopsis thaliana is thus the candidate gene most likely responsible for the fuzzless trait in DPL972. Our findings should lead to a better understanding of cotton fuzz formation, thereby accelerating marker-assisted selection during cotton breeding.


Assuntos
Genes de Plantas , Gossypium/genética , Mapeamento Físico do Cromossomo , Segregação de Cromossomos/genética , Cromossomos de Plantas/genética , Fibra de Algodão , Regulação da Expressão Gênica de Plantas , Estudos de Associação Genética , Mutação INDEL/genética , Repetições de Microssatélites/genética , Mutação/genética , Fases de Leitura Aberta/genética , Fenótipo , Polimorfismo de Nucleotídeo Único/genética , Sementes/genética
9.
BMC Plant Biol ; 19(1): 149, 2019 Apr 17.
Artigo em Inglês | MEDLINE | ID: mdl-31003597

RESUMO

BACKGROUND: Wheat is a cool seasoned crop requiring low temperature during grain filling duration and therefore increased temperature causes significant yield reduction. A set of 125 spring wheat genotypes from International Maize and Wheat Improvement Centre (CIMMYT-Mexico) was evaluated for phenological and yield related traits at three locations in Pakistan under normal sowing time and late sowing time for expose to prolonged high temperature. With the help of genome-wide association study using genotyping-by-sequencing, marker trait associations (MTAs) were observed separately for the traits under normal and late sown conditions. RESULTS: Significant reduction ranging from 9 to 74% was observed in all traits under high temperature. Especially 30, 25, 41 and 66% reduction was observed for days to heading (DH), plant height (PH), spikes per plant (SPP) and yield respectively. We identified 55,954 single nucleotide polymorphisms (SNPs) using genotyping by sequencing of these 125 hexaploid spring wheat genotypes and conducted genome-wide association studies (GWAS) for days to heading (DH), grain filled duration (GFD), plant height (PH), spikes per plant (SPP), grain number per spike (GNS), thousand kernel weight (TKW) and grain yield per plot (GY). Genomic regions identified through GWAS explained up to 13% of the phenotypic variance, on average. A total of 139 marker-trait associations (MTAs) across three wheat genomes (56 on genome A, 55 on B and 28 on D) were identified for all the seven traits studied. For days to heading, 20; grain filled duration, 21; plant height, 23; spikes per plant, 13; grain numbers per spike, 8; thousand kernel weight, 21 and for grain yield, 33 MTAs were detected under normal and late sown conditions. CONCLUSIONS: This study identifies the essential resource of genetics research and underpins the chromosomal regions of seven agronomic traits under normal and high temperature. Significant relationship was observed between the number of favored alleles and trait observations. Fourteen protein coding genes with their respective annotations have been searched with the sequence of seven MTAs which were identified in this study. These findings will be helpful in the development of a breeder friendly platform for the selection of high yielding wheat lines at high temperature areas.


Assuntos
Agricultura , Genoma de Planta , Estudo de Associação Genômica Ampla , Característica Quantitativa Herdável , Triticum/genética , Alelos , Pão , Genes de Plantas , Marcadores Genéticos , Genótipo , Desequilíbrio de Ligação/genética , Fenótipo , Mapeamento Físico do Cromossomo , Análise de Componente Principal
10.
Int J Mol Sci ; 20(5)2019 Feb 26.
Artigo em Inglês | MEDLINE | ID: mdl-30813619

RESUMO

Shewanella sp. O23S is a dissimilatory arsenate reducing bacterial strain involved in arsenic transformations within the abandoned gold mine in Zloty Stok (SW Poland). Previous physiological studies revealed that O23S may not only release arsenic from minerals, but also facilitate its immobilization through co-precipitation with reduced sulfur species. Given these uncommon, complementary characteristics and the application potential of the strain in arsenic-removal technologies, its genome (~5.3 Mbp), consisting of a single chromosome, two large plasmids (pSheA and pSheB) and three small plasmid-like phages (pSheC-E) was sequenced and annotated. Genes encoding putative proteins involved in heavy metal transformations, antibiotic resistance and other phenotypic traits were identified. An in-depth comparative analysis of arsenic respiration (arr) and resistance (ars) genes and their genetic context was also performed, revealing that pSheB carries the only copy of the arr genes, and a complete ars operon. The plasmid pSheB is therefore a unique natural vector of these genes, providing the host cells arsenic respiration and resistance abilities. The functionality of the identified genes was determined based on the results of the previous and additional physiological studies, including: the assessment of heavy metal and antibiotic resistance under various conditions, adhesion-biofilm formation assay and BiologTM metabolic preferences test. This combined genetic and physiological approach shed a new light on the capabilities of O23S and their molecular basis, and helped to confirm the biosafety of the strain in relation to its application in bioremediation technologies.


Assuntos
Arseniatos/metabolismo , Genes Bacterianos , Genômica , Plasmídeos/genética , Shewanella/genética , Shewanella/metabolismo , Antibacterianos/farmacologia , Aderência Bacteriana/efeitos dos fármacos , Biofilmes/efeitos dos fármacos , Cromossomos Bacterianos/genética , Elementos de DNA Transponíveis/genética , Resistência Microbiana a Medicamentos/efeitos dos fármacos , Resistência Microbiana a Medicamentos/genética , Oxirredução , Filogenia , Mapeamento Físico do Cromossomo , Shewanella/crescimento & desenvolvimento
11.
Int J Mol Sci ; 20(5)2019 Feb 27.
Artigo em Inglês | MEDLINE | ID: mdl-30818833

RESUMO

It is clear that the incompatibility system in Fragaria is gametophytic, however, the genetic mechanism behind this remains elusive. Eleven second-generation lines of Fragaria viridis with different compatibility were obtained by manual self-pollination, which can be displayed directly by the level of fruit-set rate. We sequenced two second-generation selfing lines with large differences in fruit-set rate: Ls-S2-53 as a self-incompatible sequencing sample, and Ls-S2-76 as a strong self-compatible sequencing sample. Fragaria vesca was used as a completely self-compatible reference sample, and the genome-wide variations were identified and subsequently annotated. The distribution of polymorphisms is similar on each chromosome between the two sequencing samples, however, the distribution regions and the number of homozygous variations are inconsistent. Expression pattern analysis showed that six candidate genes were significantly associated with self-incompatibility. Using F. vesca as a reference, we focused our attention on the gene FIP2-like (FH protein interacting protein), associated with actin cytoskeleton formation, as the resulting proteins in Ls-S2-53 and Ls-S2-76 have each lost a number of different amino acids. Suppression of FIP2-like to some extent inhibits germination of pollen grains and growth of pollen tubes by reducing F-actin of the pollen tube tips. Our results suggest that the differential distribution of homozygous variations affects F. viridis fruit-set rate and that the fully encoded FIP2-like can function normally to promote F-actin formation, while the new FIP2-like proteins with shortened amino acid sequences have influenced the (in)compatibility of two selfing lines of F. viridis.


Assuntos
Fragaria/genética , Genes de Plantas , Estudos de Associação Genética , Variação Genética , Autoincompatibilidade em Angiospermas/genética , Análise de Sequência de DNA , Sequência de Aminoácidos , Cruzamentos Genéticos , Frutas/genética , Regulação da Expressão Gênica de Plantas , Germinação , Homozigoto , Mutação INDEL/genética , Anotação de Sequência Molecular , Mapeamento Físico do Cromossomo , Proteínas de Plantas/química , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Tubo Polínico/genética , Tubo Polínico/crescimento & desenvolvimento , Polimorfismo de Nucleotídeo Único/genética
12.
New Phytol ; 222(4): 1965-1980, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-30690735

RESUMO

Saffron crocus (Crocus sativus) is the source of the most expensive spice of the world, produced from manually harvested stigmas, thus serving as a cash crop for rural communities. However, despite its economic importance, its genome and chromosomes are poorly studied. C. sativus is a sterile triploid species harboring eight chromosome triplets, and propagated only as a clonal lineage by corms. Saffron's evolutionary origin, parental species and allo- or autotriploidy has been a matter of discussion for almost a century. We performed a survey sequencing of the saffron genome and selected cytogenetic landmark sequences consisting of major tandem repeats, which we used as probes in comparative multicolor fluorescent in situ hybridization (FISH). We tagged 92 chromosomal positions and resolved the chromosomal composition of saffron triplets. By comparative FISH of six Crocus species from 11 accessions, we demonstrate that C. sativus is an autotriploid hybrid derived from heterogeneous Crocus cartwrightianus cytotypes. The FISH reference karyotype of saffron is crucial for integrating genome sequencing data with chromosomes and for investigating the relationship among Crocus species. We provide an evolutionary model of the saffron emergence; the knowledge of the parental origin offers a route towards the resynthesis of C. sativus from C. cartwrightianus to broaden saffron's gene pool.


Assuntos
Cromossomos de Plantas/genética , Crocus/genética , Hibridização Genética , Poliploidia , Sequência de Bases , Evolução Biológica , Cor , DNA de Plantas/genética , DNA Satélite/genética , Cariotipagem , Mapeamento Físico do Cromossomo , Sequências de Repetição em Tandem/genética
13.
BMC Evol Biol ; 19(1): 33, 2019 01 25.
Artigo em Inglês | MEDLINE | ID: mdl-30683070

RESUMO

BACKGROUND: For over 50 years, attempts have been made to introgress agronomically useful traits from Erianthus sect. Ripidium (Tripidium) species into sugarcane based on both genera being part of the 'Saccharum Complex', an interbreeding group of species believed to be involved in the origins of sugarcane. However, recent low copy number gene studies indicate that Tripidium and Saccharum are more divergent than previously thought. The extent of genus Tripidium has not been fully explored and many species that should be included in Tripidium are still classified as Saccharum. Moreover, Tripidium is currently defined as incertae sedis within the Andropogoneae, though it has been suggested that members of this genus are related to the Germainiinae. RESULTS: Eight newly-sequenced chloroplasts from potential Tripidium species were combined in a phylogenetic study with 46 members of the Panicoideae, including seven Saccharum accessions, two Miscanthidium and three Miscanthus species. A robust chloroplast phylogeny was generated and comparison with a gene locus phylogeny clearly places a monophyletic Tripidium clade outside the bounds of the Saccharinae. A key to the currently identified Tripidium species is presented. CONCLUSION: For the first time, we have undertaken a large-scale whole plastid study of eight newly assembled Tripidium accessions and a gene locus study of five Tripidium accessions. Our findings show that Tripidium and Saccharum are 8 million years divergent, last sharing a common ancestor 12 million years ago. We demonstrate that four species should be removed from Saccharum/Erianthus and included in genus Tripidium. In a genome context, we show that Tripidium evolved from a common ancestor with and extended Germainiinae clade formed from Germainia, Eriochrysis, Apocopis, Pogonatherum and Imperata. We re-define the 'Saccharum complex' to a group of genera that can interbreed in the wild and extend the Saccharinae to include Sarga along with Sorghastrum, Microstegium vimineum and Polytrias (but excluding Sorghum). Monophyly of genus Tripidium is confirmed and the genus is expanded to include Tripidium arundinaceum, Tripidium procerum, Tripidium kanashiroi and Tripidium rufipilum. As a consequence, these species are excluded from genus Saccharum. Moreover, we demonstrate that genus Tripidium is distinct from the Germainiinae.


Assuntos
Genoma de Cloroplastos , Filogenia , Poaceae/classificação , Poaceae/genética , Saccharum/classificação , Saccharum/genética , Sequência de Bases , Primers do DNA/metabolismo , Loci Gênicos , Fenótipo , Mapeamento Físico do Cromossomo , Especificidade da Espécie , Terminologia como Assunto
14.
Theor Appl Genet ; 132(4): 1235-1246, 2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-30607439

RESUMO

KEY MESSAGE: Identification of a novel pungency-controlling gene Pun3, which acts as a master regulator of capsaicinoid biosynthetic genes in Capsicum annuum. Capsaicinoid is a unique compound that gives hot peppers (Capsicum spp.) their spicy taste. The Pun1 and Pun2 loci are known to control pungency in Capsicum species. Whereas Pun1 encodes an acyltransferase, the identity of Pun2 is currently unknown. Here, we used recombinant inbred lines and F2 plants derived from a cross between the non-pungent C. annuum accession 'YCM334' and the pungent C. annuum cultivar 'Tean' to identify a novel non-pungency locus. Inheritance studies showed that non-pungency in C. annuum 'YCM334' is controlled by a single recessive gene, which we named Pun3. Using a high-density SNP map derived from genotyping-by-sequencing, Pun3 was mapped to chromosome 7. By comparing physical information about the Pun3 region in the C. annuum 'Zunla-1' and C. chinense 'PI159236' reference genomes, we identified candidate genes in this target region. One cDNA sequence from 'PI159236' was homologous to an unannotated gene in 'Zunla-1.' This sequence was also homologous to CaMYB31, which is expressed only in 'Tean' and harbors one stop codon in the non-pungent accession 'YCM334.' RNA-Seq analysis showed that major structural genes in the capsaicinoid biosynthetic pathway were significantly downregulated in 'YCM334' compared to pungent pepper. Therefore, CaMYB31 is a candidate gene for Pun3, which may act as a master regulator of capsaicinoid biosynthetic genes in pepper.


Assuntos
Capsicum/genética , Fatores de Transcrição/metabolismo , Alelos , Sequência de Aminoácidos , Vias Biossintéticas/genética , Segregação de Cromossomos , Cruzamentos Genéticos , Ecótipo , Genes de Plantas , Estudos de Associação Genética , Loci Gênicos , Genótipo , Endogamia , Padrões de Herança/genética , Filogenia , Mapeamento Físico do Cromossomo , Proteínas de Plantas/química , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo
15.
J Integr Plant Biol ; 61(3): 226-256, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30548413

RESUMO

In cereals, tillering and leaf development are key factors in the concept of crop ideotype, introduced in the 1960s to enhance crop yield, via manipulation of plant architecture. In the present review, we discuss advances in genetic analysis of barley shoot architecture, focusing on tillering, leaf size and angle. We also discuss novel phenotyping techniques, such as 2D and 3D imaging, that have been introduced in the era of phenomics, facilitating reliable trait measurement. We discuss the identification of genes and pathways that are involved in barley tillering and leaf development, highlighting key hormones involved in the control of plant architecture in barley and rice. Knowledge on genetic control of traits related to plant architecture provides useful resources for designing ideotypes for enhanced barley yield and performance.


Assuntos
Hordeum/anatomia & histologia , Hordeum/genética , Folhas de Planta/crescimento & desenvolvimento , Genes de Plantas , Fenótipo , Mapeamento Físico do Cromossomo , Folhas de Planta/anatomia & histologia , Brotos de Planta/anatomia & histologia , Brotos de Planta/genética , Brotos de Planta/crescimento & desenvolvimento
16.
Theor Appl Genet ; 132(4): 1049-1059, 2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-30535634

RESUMO

KEY MESSAGE: We lay the foundation for further research on maize resistance to Fusarium verticillioides cob rot by identifying a candidate resistance gene. Fusarium verticillioides ear rot is the most common type of maize ear rot in the Huanghuaihai Plain of China. Ear rot resistance includes cob and kernel resistance. Most of the current literature concentrates on kernel resistance, and genetic studies on cob resistance are scarce. We aimed on identifying the QTLs responsible for F. verticillioides cob rot (FCR) resistance. Twenty-eight genes associated with 48 single nucleotide polymorphisms (SNPs) were identified (P < 10-4) to correlate with FCR resistance using a whole-genome association study. The major quantitative trait locus, qRcfv2, for FCR resistance was identified on chromosome 2 through linkage mapping and was validated in near-isogenic line populations. Two candidate genes associated with two SNPs were detected in the qRcfv2 region with a lower threshold (P < 10-3). Through real-time fluorescence quantitative PCR, one candidate gene was found to have no expression in the cob but the other was expressed in response to F. verticillioides. These results lay a foundation for research on the resistance mechanisms of cob and provide resources for marker-assisted selection.


Assuntos
Resistência à Doença/genética , Fusarium/fisiologia , Doenças das Plantas/genética , Doenças das Plantas/microbiologia , Zea mays/genética , Zea mays/microbiologia , Mapeamento Cromossômico , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Estudo de Associação Genômica Ampla , Fenótipo , Mapeamento Físico do Cromossomo , Polimorfismo de Nucleotídeo Único/genética , Locos de Características Quantitativas/genética , Reprodutibilidade dos Testes
17.
Theor Appl Genet ; 132(3): 699-711, 2019 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-30341495

RESUMO

KEY MESSAGE: The large and complex genomes of many cereals hindered cloning efforts in the past. Advances in genomics now allow the rapid cloning of genes from humanity's most valuable crops. The past two decades were characterized by a genomics revolution that entailed profound changes to crop research, plant breeding, and agriculture. Today, high-quality reference sequences are available for all major cereal crop species. Large resequencing and pan-genome projects start to reveal a more comprehensive picture of the genetic makeup and the diversity among domesticated cereals and their wild relatives. These technological advancements will have a dramatic effect on dissecting genotype-phenotype associations and on gene cloning. In this review, we will highlight the status of the genomic resources available for various cereal crops and we will discuss their implications for gene cloning. A particular focus will be given to the cereal species barley and wheat, which are characterized by very large and complex genomes that have been inaccessible to rapid gene cloning until recently. With the advancements in genomics and the development of several rapid gene-cloning methods, it has now become feasible to tackle the cloning of most agriculturally important genes, even in wheat and barley.


Assuntos
Clonagem Molecular/métodos , Grão Comestível/genética , Genes de Plantas , Mutação/genética , Fenótipo , Mapeamento Físico do Cromossomo
18.
Theor Appl Genet ; 132(4): 883-893, 2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-30465063

RESUMO

KEY MESSAGE: A major grain length QTL on chromosome 5H was fine mapped from 180.5 to 1.7 Mb. Quantitative trait loci (QTLs) mapping has been used extensively in barley to detect QTLs that underlie complex traits such as grain size. In the present study, we utilised 312 double haploid lines derived from a cross between two Australian malting varieties, Vlamingh and Buloke, to dissect the genetic control of a number of grain size characteristics. Digital image analysis was used to measure grain size characteristics including length, width, thickness and plumpness which are important traits influencing barley yield and grain physical quality. Using data from four independent environments and molecular marker genotype data, we identified 23 significant QTLs for these four traits, ten of which were consensus QTLs and identified in two or more environments. A QTL region on chromosome 5H designated qGL5H that was associated with grain size was fine mapped to a 1.7 Mb interval. qGL5H was able to explain 21.6% of phenotypic variation for grain length within the population. This major QTL is an appropriate candidate for further genetic dissection.


Assuntos
Hordeum/anatomia & histologia , Hordeum/genética , Mapeamento Físico do Cromossomo/métodos , Locos de Características Quantitativas/genética , Sementes/anatomia & histologia , Cromossomos de Plantas/genética , Genes de Plantas , Genômica , Genótipo , Fenótipo , Análise de Componente Principal , Sementes/genética
19.
Theor Appl Genet ; 132(4): 871-882, 2019 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-30478615

RESUMO

KEY MESSAGE: The tomato gray leaf spot resistance gene Sm was fine-mapped in a 185-kb region through a map-based cloning strategy and genome-wide association study; a candidate gene was proved to be involved in Sm-mediated resistance through transient gene silencing. Gray leaf spot, caused by Stemphylium spp., is a warm weather foliar disease in tomato (Solanum lycopersicum L). Resistance against gray leaf spot is conferred by a single incompletely dominant gene (Sm) located on chromosome 11. This study aimed to map and identify molecular marker tightly linked to the Sm gene for the use of marker-assisted selection in breeding. Using an F2 population derived from a cross between the resistant line '9706' and the susceptible line 'Heinz 1706', the Sm gene was mapped to a 185-kb interval between two markers, InDel343 and InDel-FT-32 on chromosome 11, which was consistent with the result of a genome-wide association study using 289 diverse accessions. An ORF predicted in this region was proved to be involved in Sm-mediated resistance through transient gene silencing and seems to be a good candidate of the Sm locus. To clone the Sm gene, a bacterial artificial chromosome (BAC) library was screened and one BAC clone B80B15 containing the predicted ORF was identified. The analysis of sequence and structure characteristics demonstrated that the candidate gene was not a typical type resistance gene. Additionally, a co-dominant marker Sm-InDel, which produced a 122-bp or 140-bp fragment for resistant or susceptible alleles, respectively, was developed. This marker was validated in 289 germplasm and could be used in marker-assisted selection for gray leaf spot resistance.


Assuntos
Resistência à Doença/genética , Genes de Plantas , Lycopersicon esculentum/genética , Lycopersicon esculentum/microbiologia , Mapeamento Físico do Cromossomo/métodos , Doenças das Plantas/genética , Doenças das Plantas/microbiologia , Ascomicetos/fisiologia , Regulação da Expressão Gênica de Plantas , Ligação Genética , Loci Gênicos , Marcadores Genéticos , Estudo de Associação Genômica Ampla , Genótipo , Padrões de Herança/genética , Anotação de Sequência Molecular , Fenótipo , Recombinação Genética/genética
20.
Methods Mol Biol ; 1858: 177-194, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30414118

RESUMO

The development of genomic resources and tools is an important step in designing novel approaches to genetic control of mosquitoes. Physical genome maps enhance the quality of the genome assemblies, improve gene annotation, and provide a better framework for comparative and population genomics studies in mosquitoes. In this chapter, we describe protocols for an important procedure in physical genome mapping-fluorescence in situ hybridization (FISH). We provide details on (1) dissection of salivary glands, ovaries, and imaginal discs for obtaining high-quality polytene or mitotic chromosome preparations; (2) DNA-labeling procedures and extraction of repetitive DNA fractions; and (3) approaches to FISH on polytene and mitotic chromosomes.


Assuntos
Anopheles/genética , Cromossomos de Insetos , Genoma de Inseto , Hibridização in Situ Fluorescente/métodos , Mapeamento Físico do Cromossomo/métodos , Cromossomos Politênicos , Animais
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