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1.
Plant Cell Rep ; 43(8): 205, 2024 Aug 01.
Artículo en Inglés | MEDLINE | ID: mdl-39088074

RESUMEN

KEY MESSAGE: Transcriptomics and phenotypic data analysis identified 24 transcription factors (TFs) that play key roles in regulating the competitive accumulation of lignin and flavonoids. Tilia tuan Szyszyl. (T. tuan) is a timber tree species with important ecological and commercial value. However, its highly lignified pericarp results in a low seed germination rate and a long dormancy period. In addition, it is unknown whether there is an interaction between the biosynthesis of flavonoids and lignin as products of the phenylpropanoid pathway during seed development. To explore the molecular regulatory mechanism of lignin and flavonoid biosynthesis, T. tuan seeds were harvested at five stages (30, 60, 90, 120, and 150 days after pollination) for lignin and flavonoid analyses. The results showed that lignin accumulated rapidly in the early and middle stages (S1, S3, and S4), and rapid accumulation of flavonoids during the early and late stages (S1 and S5). High-throughput RNA sequencing analysis of developing seeds identified 50,553 transcripts, including 223 phenylpropanoid biosynthetic pathway genes involved in lignin accumulation grouped into 3 clusters, and 106 flavonoid biosynthetic pathway genes (FBPGs) grouped into 2 clusters. Subsequent WGCNA and time-ordered gene co-expression network (TO-GCN) analysis revealed that 24 TFs (e.g., TtARF2 and TtWRKY15) were involved in flavonoids and lignin biosynthesis regulation. The transcriptome data were validated by qRT-PCR to analyze the expression profiles of key enzyme-coding genes. This study revealed that there existed a competitive relationship between flavonoid and lignin biosynthesis pathway during the development of T. tuan seeds, that provide a foundation for the further exploration of molecular mechanisms underlying lignin and flavonoid accumulation in T. tuan seeds.


Asunto(s)
Flavonoides , Regulación de la Expresión Génica de las Plantas , Lignina , Semillas , Lignina/metabolismo , Lignina/biosíntesis , Flavonoides/metabolismo , Flavonoides/biosíntesis , Semillas/genética , Semillas/crecimiento & desarrollo , Semillas/metabolismo , Factores de Transcripción/metabolismo , Factores de Transcripción/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Perfilación de la Expresión Génica , Transcriptoma/genética , Redes Reguladoras de Genes , Genes de Plantas , Vías Biosintéticas/genética
2.
Science ; 385(6708): eado1663, 2024 Aug 02.
Artículo en Inglés | MEDLINE | ID: mdl-39088611

RESUMEN

An enduring question in evolutionary biology concerns the degree to which episodes of convergent trait evolution depend on the same genetic programs, particularly over long timescales. In this work, we genetically dissected repeated origins and losses of prickles-sharp epidermal projections-that convergently evolved in numerous plant lineages. Mutations in a cytokinin hormone biosynthetic gene caused at least 16 independent losses of prickles in eggplants and wild relatives in the genus Solanum. Homologs underlie prickle formation across angiosperms that collectively diverged more than 150 million years ago, including rice and roses. By developing new Solanum genetic systems, we leveraged this discovery to eliminate prickles in a wild species and an indigenously foraged berry. Our findings implicate a shared hormone activation genetic program underlying evolutionarily widespread and recurrent instances of plant morphological innovation.


Asunto(s)
Evolución Biológica , Citocininas , Genes de Plantas , Epidermis de la Planta , Solanum , Citocininas/biosíntesis , Citocininas/genética , Evolución Molecular , Mutación , Oryza/genética , Filogenia , Epidermis de la Planta/anatomía & histología , Epidermis de la Planta/genética , Solanum/anatomía & histología , Solanum/genética
3.
BMC Plant Biol ; 24(1): 739, 2024 Aug 02.
Artículo en Inglés | MEDLINE | ID: mdl-39095699

RESUMEN

BACKGROUND: The SET domain group (SDG) genes encode histone lysine methyltransferases, which regulate gene transcription by altering chromatin structure and play pivotal roles in plant flowering determination. However, few studies have investigated their role in the regulation of flowering in upland cotton. RESULTS: A total of 86 SDG genes were identified through genome-wide analysis in upland cotton (Gossypium hirsutum). These genes were unevenly distributed across 25 chromosomes. Cluster analysis revealed that the 86 GhSDGs were divided into seven main branches. RNA-seq data and qRT‒PCR analysis revealed that lysine methyltransferase 3 (KMT3) genes were expressed at high levels in stamens, pistils and other floral organs. Using virus-induced gene silencing (VIGS), functional characterization of GhKMT3;1a and GhKMT3;2a revealed that, compared with those of the controls, the GhKMT3;1a- and GhKMT3;2a-silenced plants exhibited later budding and flowering and lower plant heightwere shorter. In addition, the expression of flowering-related genes (GhAP1, GhSOC1 and GhFT) significantly decreased and the expression level of GhSVP significantly increased in the GhKMT3;1a- and GhKMT3;2a-silenced plants compared with the control plants. CONCLUSION: A total of 86 SDG genes were identified in upland cotton, among which GhKMT3;1a and GhKMT3;2a might regulate flowering by affecting the expression of GhAP1, GhSOC1, GhFT and GhSVP. These findings will provide genetic resources for advanced molecular breeding in the future.


Asunto(s)
Flores , Regulación de la Expresión Génica de las Plantas , Gossypium , N-Metiltransferasa de Histona-Lisina , Proteínas de Plantas , Gossypium/genética , Gossypium/enzimología , Gossypium/fisiología , Flores/genética , Flores/crecimiento & desarrollo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , N-Metiltransferasa de Histona-Lisina/genética , N-Metiltransferasa de Histona-Lisina/metabolismo , Genes de Plantas , Silenciador del Gen
4.
BMC Plant Biol ; 24(1): 743, 2024 Aug 03.
Artículo en Inglés | MEDLINE | ID: mdl-39095733

RESUMEN

Soybean is a crucial crop for the Brazilian economy, but it faces challenges from the biotrophic fungus Phakopsora pachyrhizi, which causes Asian Soybean Rust (ASR). In this study, we aimed to identify SNPs associated with resistance within the Rpp1 locus, which is effective against Brazilian ASR populations. We employed GWAS and re-sequencing analyzes to pinpoint SNP markers capable of differentiating between soybean accessions harboring the Rpp1, Rpp1-b and other alternative alleles in the Rpp1 locus and from susceptible soybean cultivars. Seven SNP markers were found to be associated with ASR resistance through GWAS, with three of them defining haplotypes that efficiently distinguished the accessions based on their ASR resistance and source of the Rpp gene. These haplotypes were subsequently validated using a bi-parental population and a diverse set of Rpp sources, demonstrating that the GWAS markers co-segregate with ASR resistance. We then examined the presence of these haplotypes in a diverse set of soybean genomes worldwide, finding a few new potential sources of Rpp1/Rpp1-b. Further genomic sequence analysis revealed nucleotide differences within the genes present in the Rpp1 locus, including the ULP1-NBS-LRR genes, which are potential R gene candidates. These results provide valuable insights into ASR resistance in soybean, thus helping the development of resistant soybean varieties through genetic breeding programs.


Asunto(s)
Alelos , Resistencia a la Enfermedad , Estudio de Asociación del Genoma Completo , Glycine max , Phakopsora pachyrhizi , Enfermedades de las Plantas , Polimorfismo de Nucleótido Simple , Glycine max/genética , Glycine max/microbiología , Enfermedades de las Plantas/microbiología , Enfermedades de las Plantas/genética , Resistencia a la Enfermedad/genética , Phakopsora pachyrhizi/fisiología , Phakopsora pachyrhizi/genética , Haplotipos , Genes de Plantas , Basidiomycota/fisiología
5.
BMC Plant Biol ; 24(1): 737, 2024 Aug 02.
Artículo en Inglés | MEDLINE | ID: mdl-39095762

RESUMEN

BACKGROUND: BAK1 (Brassinosteroid insensitive 1-associated receptor kinase 1) plays an important role in disease resistance in plants. However, the function of BAK1 family in cucumber and the decisive genes for disease-resistance remain elusive. RESULTS: Here, we identified 27 CsBAK1s in cucumber, and classified them into five subgroups based on phylogenetic analysis and gene structure. CsBAK1s in the same subgroup shared the similar motifs, but different gene structures. Cis-elements analysis revealed that CsBAK1s might respond to various stress and growth regulation. Three segmentally duplicated pairwise genes were identified in cucumber. In addition, Ka/Ks analysis indicated that CsBAK1s were under positive selection during evolution. Tissue expression profile showed that most CsBAK1s in Subgroup II and IV showed constitutive expression, members in other subgroups showed tissue-specific expression. To further explore whether CsBAK1s were involved in the resistance to pathogens, the expression patterns of CsBAK1s to five pathogens (gummy stem blight, powdery mildew, downy mildew, grey mildew, and fusarium wilt) reveled that different CsBAK1s had specific roles in different pathogen infections. The expression of CsBAK1-14 was induced/repressed significantly by five pathogens, CsBAK1-14 might play an important role in disease resistance in cucumber. CONCLUSIONS: 27 BAK1 genes were identified in cucumber from a full perspective, which have important functions in pathogen infection. Our study provided a theoretical basis to further clarify the function of BAK1s to disease resistance in cucumber.


Asunto(s)
Cucumis sativus , Resistencia a la Enfermedad , Filogenia , Enfermedades de las Plantas , Proteínas de Plantas , Cucumis sativus/genética , Cucumis sativus/microbiología , Cucumis sativus/enzimología , Enfermedades de las Plantas/microbiología , Enfermedades de las Plantas/genética , Resistencia a la Enfermedad/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Regulación de la Expresión Génica de las Plantas , Proteínas Serina-Treonina Quinasas/genética , Proteínas Serina-Treonina Quinasas/metabolismo , Genes de Plantas , Genoma de Planta , Perfilación de la Expresión Génica
6.
Cell Mol Biol (Noisy-le-grand) ; 70(7): 243-251, 2024 Jul 28.
Artículo en Inglés | MEDLINE | ID: mdl-39097867

RESUMEN

Oil seeds now make up the world's second-largest food source after cereals. In recent years, the medicinal- oil plant Camelina sativa has attracted much attention for its high levels of unsaturated fatty acids and low levels of saturated fatty acids as well as its resistance to abiotic stresses. Improvement of oil quality is considered an important trait in this plant. Erucic acid is one of the fatty acids affecting the quality of camelina oil. Altering the fatty acid composition in camelina oil through genetic manipulation requires the identification, isolation, and cloning of genes involved in fatty acid biosynthesis. The Fatty Acid Elongase 1 (FAE1) gene encodes the enzyme ß-ketoacyl CoA synthase (KCS), a crucial enzyme in the biosynthesis of erucic acid. In this study, the isolation and cloning of the FAE1 gene from Camelina sativa were conducted to construct an antisense structure. The molecular homology modeling of DFAE1 proteins using the SWISS-MODEL server on ExPASy led to the generation of the 3D structures of FAE1 and DFAE1 proteins. The GMQE values of 0.44 for FAE1 and 0.08 for DFAE1 suggest high accuracy in the structural estimation of these genes. The fragments were isolated from the DNA source of the genomic Soheil cultivar with an erucic acid content of about 3% (in matured seeds) using PCR. After cloning the FAE1 gene into the Bluescript II SK+ vector and sequencing, the resulting fragments were utilized to construct the antisense structure in the pBI121 plant expression vector. The approved antisense structure was introduced into the Camelina plant using the Agrobacterium-mediated method, with optimization of tissue culture and gene transfer conditions. This approach holds potential to advance our knowledge of fat biosynthesis, leading to potential improvements in oil quality in Camelina sativa.


Asunto(s)
Brassicaceae , Clonación Molecular , Ácidos Erucicos , Elongasas de Ácidos Grasos , Brassicaceae/genética , Brassicaceae/metabolismo , Clonación Molecular/métodos , Ácidos Erucicos/metabolismo , Elongasas de Ácidos Grasos/genética , Elongasas de Ácidos Grasos/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Plantas Modificadas Genéticamente/genética , Secuencia de Aminoácidos , Semillas/genética , Semillas/metabolismo , Modelos Moleculares , Regulación de la Expresión Génica de las Plantas , Acetiltransferasas/genética , Acetiltransferasas/metabolismo , Genes de Plantas
7.
Cell Mol Biol (Noisy-le-grand) ; 70(7): 66-72, 2024 Jul 28.
Artículo en Inglés | MEDLINE | ID: mdl-39097894

RESUMEN

Crocus sativus L. is known as an ornamental geophyte and a source of valuable spice and secondary metabolites. Network preservation module analysis is one of the best approaches to revealing special features of different conditions. It can determine patterns of divergence and conservation between transcriptome data. Herein, we explored the regulatory genes of the flowering process by RNA-Seq data containing flowering and non-flowering samples in gene expression profiles. Persevered module analysis revealed three significant non-persevered modules related to the flowering process, namely pink, green, and blue. Several hub genes associated with non-preserved modules such as PIA1, NAC90, ALY3, Sus3, MYB31, ARF5/MP, MYB31, HD-ZIP, SEP3d, OR_B, AGL6a, bZIP(TGA1) and GRAS were identified. These candidate genes can be considered key diagnostic biomarkers for the flowering process. Here, we also compared two approaches, WGCNA and NetRep for module preservation analysis. The results of these methods were consistent with non-preserved modules. NetRep was a faster (11 times) and more efficient (run more than 10000 permutations for each comparison) method than WGCNA module preservation. Differential expression genes (DEGs) screening showed that many hub genes were downregulated in non-flowering than flowering samples. Our finding revealed regulatory mechanisms of the flowering process in C. sativus as can be developed transcriptional biomarkers which could pave the way for promoting saffron yield via flowering induction.


Asunto(s)
Crocus , Flores , Regulación de la Expresión Génica de las Plantas , Redes Reguladoras de Genes , Flores/genética , Crocus/genética , Perfilación de la Expresión Génica/métodos , Biomarcadores/metabolismo , Transcriptoma/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Genes de Plantas
8.
Cell Mol Biol (Noisy-le-grand) ; 70(7): 1-7, 2024 Jul 28.
Artículo en Inglés | MEDLINE | ID: mdl-39097902

RESUMEN

Improving crop plants using biotechnological implications is a promising and modern approach compared to traditional methods. High-temperature exposure to the reproductive stage induces flower abortion and declines grain filling performance, leading to smaller grain production and low yield in lentil and other legumes. Thus, cloning effective candidate genes and their implication in temperature stress tolerance in lentil (Lens culinaris Medik.) using biotechnological tools is highly demandable. The 12-oxophytodienoic acid reductases (OPRs) are flavin mononucleotide-dependent oxidoreductases with vital roles in plants. They are members of the old yellow enzyme (OYE) family. These enzymes are involved in the octadecanoid pathway, which contributes to jasmonic acid biosynthesis and is essential in plant stress responses. Lentil is one of the vital legume crops affected by the temperature fluctuations caused by global warming. Therefore, in this study, the LcOPR1 gene was successfully cloned and isolated from lentils using RT-PCR to evaluate its functional responses in lentil under heat stress. The bioinformatics analysis revealed that the full-length cDNA of LcOPR1 was 1303 bp, containing an 1134 bp open reading frames (ORFs), encoding 377 amino acids with a predicted molecular weight of 41.63 and a theoretical isoelectric point of 5.61. Bioinformatics analyses revealed that the deduced LcOPR1 possesses considerable homology with other plant 12-oxophytodienoic acid reductases (OPRs). Phylogenetic tree analysis showed that LcOPR1 has an evolutionary relationship with other OPRs in different plant species of subgroup I, containing enzymes that are not required for jasmonic acid biosynthesis. The expression analysis of LcOPR1 indicated that this gene is upregulated in response to the heat-stress condition and during recovery in lentil. This study finding might be helpful to plant breeders and biotechnologists in LcOPR1 engineering and/or plant breeding programs in revealing the biological functions of LcOPR1 in lentils and the possibility of enhancing heat stress tolerance by overexpressing LcOPR1 in lentil and other legume plants under high temperature.


Asunto(s)
Clonación Molecular , Regulación de la Expresión Génica de las Plantas , Lens (Planta) , Filogenia , Lens (Planta)/genética , Lens (Planta)/enzimología , Clonación Molecular/métodos , Regulación de la Expresión Génica de las Plantas/genética , Oxidorreductasas/genética , Oxidorreductasas/metabolismo , Secuencia de Aminoácidos , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Calor , Genes de Plantas , Respuesta al Choque Térmico/genética , Oxilipinas/metabolismo , Oxidorreductasas actuantes sobre Donantes de Grupo CH-CH
9.
BMC Plant Biol ; 24(1): 735, 2024 Aug 02.
Artículo en Inglés | MEDLINE | ID: mdl-39090544

RESUMEN

The purple leaves of Brassica napus are abundant in anthocyanins, which are renowned for their role in conferring distinct colors, stress tolerance, and health benefits, however the genetic basis of this trait in B. napus remains largely unelucidated. Herein, the purple leaf B. napus (PL) exhibited purple pigments in the upper epidermis and a substantial increase in anthocyanin accumulation, particularly of cyanidin, compared to green leaf B. napus (GL). The genetic control of the purple leaf trait was attributed to a semi-dominant gene, pl, which was mapped to the end of chromosome A03. However, sequencing of the fragments amplified by the markers linked to pl indicated that they were all mapped to chromosome B05 from B. juncea. Within this B05 chromosomal segment, the BjMYB113 gene-specific marker showed perfect co-segregation with the purple leaf trait in the F2 population, suggesting that the BjMYB113 introgression from B. juncea was the candidate gene for the purple leaf trait in B. napus. To further verify the function of candidate gene, CRISPR/Cas9 was performed to knock out the BjMYB113 gene in PL. The three myb113 mutants exhibited evident green leaf phenotype, absence of purple pigments in the adaxial epidermis, and a significantly reduced accumulation of anthocyanin compared to PL. Additionally, the genes involved in positive regulatory (TT8), late anthocyanin biosynthesis (DFR, ANS, UFGT), as well as transport genes (TT19) were significantly suppressed in the myb113 mutants, further confirming that BjMYB113 was response for the anthocyanin accumulation in purple leaf B. napus. This study contributes to an advanced understanding of the regulation mechanism of anthocyanin accumulation in B. napus.


Asunto(s)
Antocianinas , Brassica napus , Planta de la Mostaza , Pigmentación , Hojas de la Planta , Brassica napus/genética , Brassica napus/metabolismo , Hojas de la Planta/genética , Hojas de la Planta/metabolismo , Antocianinas/metabolismo , Planta de la Mostaza/genética , Planta de la Mostaza/metabolismo , Pigmentación/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Fenotipo , Introgresión Genética , Genes de Plantas , Mapeo Cromosómico , Factores de Transcripción/genética , Factores de Transcripción/metabolismo
10.
BMC Genomics ; 25(1): 751, 2024 Aug 01.
Artículo en Inglés | MEDLINE | ID: mdl-39090588

RESUMEN

BACKGROUND: Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is an important disease of barley and wheat. A diverse sexual Pgt population from the Pacific Northwest (PNW) region of the US contains a high proportion of individuals with virulence on the barley stem rust resistance (R) gene, Rpg1. However, the evolutionary mechanisms of this virulence on Rpg1 are mysterious considering that Rpg1 had not been deployed in the region and the gene had remained remarkably durable in the Midwestern US and prairie provinces of Canada. METHODS AND RESULTS: To identify AvrRpg1 effectors, genome wide association studies (GWAS) were performed using 113 Pgt isolates collected from the PNW (n = 89 isolates) and Midwest (n = 24 isolates) regions of the US. Disease phenotype data were generated on two barley lines Morex and the Golden Promise transgenic (H228.2c) that carry the Rpg1 gene. Genotype data was generated by whole genome sequencing (WGS) of 96 isolates (PNW = 89 isolates and Midwest = 7 isolates) and RNA sequencing (RNAseq) data from 17 Midwestern isolates. Utilizing ~1.2 million SNPs generated from WGS and phenotype data (n = 96 isolates) on the transgenic line H228.2c, 53 marker trait associations (MTAs) were identified. Utilizing ~140 K common SNPs generated from combined analysis of WGS and RNAseq data, two significant MTAs were identified using the cv Morex phenotyping data. The 55 MTAs defined two distinct avirulence loci, on supercontig 2.30 and supercontig 2.11 of the Pgt reference genome of Pgt isolate CRL 75-36-700-3. The major avirulence locus designated AvrRpg1A was identified with the GWAS using both barley lines and was delimited to a 35 kb interval on supercontig 2.30 containing four candidate genes (PGTG_10878, PGTG_10884, PGTG_10885, and PGTG_10886). The minor avirulence locus designated AvrRpg1B identified with cv Morex contained a single candidate gene (PGTG_05433). AvrRpg1A haplotype analysis provided strong evidence that a dominant avirulence gene underlies the locus. CONCLUSIONS: The association analysis identified strong candidate AvrRpg1 genes. Further analysis to validate the AvrRpg1 genes will fill knowledge gaps in our understanding of rust effector biology and the evolution and mechanism/s of Pgt virulence on Rpg1.


Asunto(s)
Resistencia a la Enfermedad , Estudio de Asociación del Genoma Completo , Hordeum , Enfermedades de las Plantas , Puccinia , Hordeum/microbiología , Hordeum/genética , Enfermedades de las Plantas/microbiología , Enfermedades de las Plantas/genética , Resistencia a la Enfermedad/genética , Puccinia/patogenicidad , Puccinia/genética , Virulencia/genética , Mapeo Cromosómico , Polimorfismo de Nucleótido Simple , Sitios de Carácter Cuantitativo , Genes de Plantas , Fenotipo
11.
Int J Mol Sci ; 25(13)2024 Jun 27.
Artículo en Inglés | MEDLINE | ID: mdl-39000183

RESUMEN

Landraces are an important reservoir of genetic variation that can expand the narrow genetic base of cultivated cotton. In this study, quantitative trait loci (QTL) analysis was conducted using an F2 population developed from crosses between the landrace Hopi and inbred TM-1. A high-density genetic map spanning 2253.11 and 1932.21 cM for the A and D sub-genomes, respectively, with an average marker interval of 1.14 cM, was generated using the CottonSNP63K array. The linkage map showed a strong co-linearity with the physical map of cotton. A total of 21 QTLs were identified, controlling plant height (1), bract type (1), boll number (1), stem color (2), boll pitting (2), fuzz fiber development (2), boll shape (3), boll point (4), and boll glanding (5). In silico analysis of the novel QTLs for boll glanding identified a total of 13 candidate genes. Analysis of tissue-specific expression of the candidate genes suggests roles for the transcription factors bHLH1, MYB2, and ZF1 in gland formation. Comparative sequencing of open reading frames identified early stop codons in all three transcription factors in Hopi. Functional validation of these genes offers avenues to reduce glanding and, consequently, lower gossypol levels in cottonseeds without compromising the defense mechanisms of the plant against biotic stresses.


Asunto(s)
Mapeo Cromosómico , Gossypium , Sitios de Carácter Cuantitativo , Gossypium/genética , Gossypium/crecimiento & desarrollo , Proteínas de Plantas/genética , Ligamiento Genético , Cromosomas de las Plantas/genética , Fenotipo , Regulación de la Expresión Génica de las Plantas , Genes de Plantas
12.
Int J Mol Sci ; 25(13)2024 Jun 27.
Artículo en Inglés | MEDLINE | ID: mdl-39000188

RESUMEN

Premature leaf senescence significantly reduces rice yields. Despite identifying numerous factors influencing these processes, the intricate genetic regulatory networks governing leaf senescence demand further exploration. We report the characterization of a stably inherited, ethyl methanesulfonate(EMS)-induced rice mutant with wilted leaf tips from seedling till harvesting, designated lts2. This mutant exhibits dwarfism and early senescence at the leaf tips and margins from the seedling stage when compared to the wild type. Furthermore, lts2 displays a substantial decline in both photosynthetic activity and chlorophyll content. Transmission electron microscopy revealed the presence of numerous osmiophilic granules in chloroplast cells near the senescent leaf tips, indicative of advanced cellular senescence. There was also a significant accumulation of H2O2, alongside the up-regulation of senescence-associated genes within the leaf tissues. Genetic mapping situated lts2 between SSR markers Q1 and L12, covering a physical distance of approximately 212 kb in chr.1. No similar genes controlling a premature senescence leaf phenotype have been identified in the region, and subsequent DNA and bulk segregant analysis (BSA) sequencing analyses only identified a single nucleotide substitution (C-T) in the exon of LOC_Os01g35860. These findings position the lts2 mutant as a valuable genetic model for elucidating chlorophyll metabolism and for further functional analysis of the gene in rice.


Asunto(s)
Clorofila , Mutación , Oryza , Hojas de la Planta , Oryza/genética , Oryza/metabolismo , Oryza/crecimiento & desarrollo , Hojas de la Planta/genética , Hojas de la Planta/metabolismo , Clorofila/metabolismo , Senescencia de la Planta/genética , Mapeo Cromosómico , Fenotipo , Regulación de la Expresión Génica de las Plantas , Fotosíntesis/genética , Genes de Plantas , Peróxido de Hidrógeno/metabolismo
13.
Theor Appl Genet ; 137(8): 190, 2024 Jul 24.
Artículo en Inglés | MEDLINE | ID: mdl-39043952

RESUMEN

KEY MESSAGE: Extensive and comprehensive phenotypic data from a maize RIL population under both low- and normal-Pi treatments were used to conduct QTL mapping. Additionally, we integrated parental resequencing data from the RIL population, GWAS results, and transcriptome data to identify candidate genes associated with low-Pi stress in maize. Phosphorus (Pi) is one of the essential nutrients that greatly affect the maize yield. However, the genes underlying the QTL controlling maize low-Pi response remain largely unknown. In this study, a total of 38 traits at both seedling and maturity stages were evaluated under low- and normal-Pi conditions using a RIL population constructed from X178 (tolerant) and 9782 (sensitive), and most traits varied significantly between low- and normal-Pi treatments. Twenty-nine QTLs specific to low-Pi conditions were identified after excluding those with common intervals under both low- and normal-Pi conditions. Furthermore, 45 additional QTLs were identified based on the index value ((Trait_under_LowPi-Trait_under_NormalPi)/Trait_under_NormalPi) of each trait. These 74 QTLs collectively were classified as Pi-dependent QTLs. Additionally, 39 Pi-dependent QTLs were clustered in nine HotspotQTLs. The Pi-dependent QTL interval contained 19,613 unique genes, 6,999 of which exhibited sequence differences with non-synonymous mutation sites between X178 and 9782. Combined with in silico GWAS results, 277 consistent candidate genes were identified, with 124 genes located within the HotspotQTL intervals. The transcriptome analysis revealed that 21 genes, including the Pi transporter ZmPT7 and the strigolactones pathway-related gene ZmPDR1, exhibited consistent low-Pi stress response patterns across various maize inbred lines or tissues. It is noteworthy that ZmPDR1 in maize roots can be sharply up-regulated by low-Pi stress, suggesting its potential importance as a candidate gene for responding to low-Pi stress through the strigolactones pathway.


Asunto(s)
Mapeo Cromosómico , Fósforo , Sitios de Carácter Cuantitativo , Zea mays , Zea mays/genética , Zea mays/crecimiento & desarrollo , Mapeo Cromosómico/métodos , Fósforo/metabolismo , Fenotipo , Secuenciación de Nucleótidos de Alto Rendimiento , Genes de Plantas , Genoma de Planta , Regulación de la Expresión Génica de las Plantas , Simulación por Computador
14.
BMC Plant Biol ; 24(1): 699, 2024 Jul 24.
Artículo en Inglés | MEDLINE | ID: mdl-39044149

RESUMEN

BACKGROUND: Proteins harboring the SPX domain are crucial for the regulation of phosphate (Pi) homeostasis in plants. This study aimed to identify and analyze the entire SPX gene family within the cucumber genome. RESULTS: The cucumber genome encompassed 16 SPX domain-containing genes, which were distributed across six chromosomes and categorized into four distinct subfamilies: SPX, SPX-MFS, SPX-EXS and SPX-RING, based on their structure characteristics. Additionally, gene duplications and synteny analysis were conducted for CsSPXs, revealing that their promoter regions were enriched with a variety of hormone-responsive, biotic/abiotic stress and typical P1BS-related elements. Tissue expression profiling of CsSPX genes revealed that certain members were specifically expressed in particular organs, suggesting essential roles in cucumber growth and development. Under low Pi stress, CsSPX1 and CsSPX2 exhibited a particularly strong response to Pi starvation. It was observed that the cucumber cultivar Xintaimici displayed greater tolerance to low Pi compared to black-spined cucumber under low Pi stress conditions. Protein interaction networks for the 16 CsSPX proteins were predicted, and yeast two-hybrid assay revealed that CsPHR1 interacted with CsSPX2, CsSPX3, CsSPX4 and CsSPX5, implying their involvement in the Pi signaling pathway in conjunction with CsPHR1. CONCLUSION: This research lays the foundation for further exploration of the function of the CsSPX genes in response to low Pi stress and for elucidating the underlying mechanism.


Asunto(s)
Cucumis sativus , Familia de Multigenes , Fósforo , Proteínas de Plantas , Cucumis sativus/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Fósforo/metabolismo , Fósforo/deficiencia , Genoma de Planta , Genes de Plantas , Regulación de la Expresión Génica de las Plantas , Filogenia
15.
Theor Appl Genet ; 137(8): 192, 2024 Jul 25.
Artículo en Inglés | MEDLINE | ID: mdl-39052130

RESUMEN

Blackleg (also known as Phoma or stem canker) is a major, worldwide disease of Brassica crop species, notably B. napus (rapeseed, canola), caused by the ascomycete fungus Leptosphaeria maculans. The outbreak and severity of this disease depend on environmental conditions and management practices, as well as a complex interaction between the pathogen and its hosts. Genetic resistance is a major method to control the disease (and the only control method in some parts of the world, such as continental Europe), but efficient use of genetic resistance is faced with many difficulties: (i) the scarcity of germplasm/genetic resources available, (ii) the different history of use of resistance genes in different parts of the world and the different populations of the fungus the resistance genes are exposed to, (iii) the complexity of the interactions between the plant and the pathogen that expand beyond typical gene-for-gene interactions, (iv) the incredible evolutionary potential of the pathogen and the importance of knowing the molecular processes set up by the fungus to "breakdown' resistances, so that we may design high-throughput diagnostic tools for population surveys, and (v) the different strategies and options to build up the best resistances and to manage them so that they are durable. In this paper, we aim to provide a comprehensive overview of these different points, stressing the differences between the different continents and the current prospects to generate new and durable resistances to blackleg disease.


Asunto(s)
Resistencia a la Enfermedad , Leptosphaeria , Fitomejoramiento , Enfermedades de las Plantas , Enfermedades de las Plantas/microbiología , Enfermedades de las Plantas/genética , Resistencia a la Enfermedad/genética , Leptosphaeria/genética , Brassica napus/genética , Brassica napus/microbiología , Genes de Plantas , Productos Agrícolas/genética , Productos Agrícolas/microbiología , Brassica/genética , Brassica/microbiología
16.
BMC Plant Biol ; 24(1): 705, 2024 Jul 25.
Artículo en Inglés | MEDLINE | ID: mdl-39054416

RESUMEN

BACKGROUND: Drought stress limits significantly the crop productivity. However, plants have evolved various strategies to cope with the drought conditions by adopting complex molecular, biochemical, and physiological mechanisms. Members of the nuclear factor Y (NF-Y) transcription factor (TF) family constitute one of the largest TF classes and are involved in plant responses to abiotic stresses. RESULTS: TaNF-YB2, a NY-YB subfamily gene in T. aestivum, was characterized in this study focusing on its role in mediating plant adaptation to drought stress. Yeast two-hybrid (Y-2 H), biomolecular fluoresence complementation (BiFC), and Co-immunoprecipitation (Co-IP) assays indicated that TaNF-YB2 interacts with the NF-YA member TaNF-YA7 and NF-YC family member TaNF-YC7, which constitutes a heterotrimer TaNF-YB2/TaNF-YA7/TaNF-YC7. The TaNF-YB2 transcripts are induced in roots and aerial tissues upon drought signaling; GUS histochemical staining analysis demonstrated the roles of cis-regulatory elements ABRE and MYB situated in TaNF-YB2 promoter to contribute to target gene response to drought. Transgene analysis on TaNF-YB2 confirmed its functions in regulating drought adaptation via modulating stomata movement, osmolyte biosynthesis, and reactive oxygen species (ROS) homeostasis. TaNF-YB2 possessed the abilities in transcriptionally activating TaP5CS2, the P5CS family gene involving proline biosynthesis and TaSOD1, TaCAT5, and TaPOD5, the genes encoding antioxidant enzymes. Positive correlations were found between yield and the TaNF-YB2 transcripts in a core panel constituting 45 wheat cultivars under drought condition, in which two types of major haplotypes including TaNF-YB2-Hap1 and -Hap2 were included, with the former conferring more TaNF-YB2 transcripts and stronger plant drought tolerance. CONCLUSIONS: TaNF-YB2 is transcriptional response to drought stress. It is an essential regulator in mediating plant drought adaptation by modulating the physiological processes associated with stomatal movement, osmolyte biosynthesis, and reactive oxygen species (ROS) homeostasis, depending on its role in transcriptionally regulating stress response genes. Our research deepens the understanding of plant drought stress underlying NF-Y TF family and provides gene resource in efforts for molecular breeding the drought-tolerant cultivars in T. aestivum.


Asunto(s)
Sequías , Regulación de la Expresión Génica de las Plantas , Proteínas de Plantas , Factores de Transcripción , Triticum , Factores de Transcripción/metabolismo , Factores de Transcripción/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Triticum/genética , Triticum/fisiología , Triticum/metabolismo , Estrés Fisiológico/genética , Adaptación Fisiológica/genética , Genes de Plantas , Resistencia a la Sequía
17.
BMC Plant Biol ; 24(1): 709, 2024 Jul 25.
Artículo en Inglés | MEDLINE | ID: mdl-39054447

RESUMEN

BACKGROUND: Cicer arietinum is a significant legume crop cultivated mainly in short-season environments, where early-flowering is a desirable trait to overcome terminal constraints. Despite its agricultural significance, the genetic control of flowering time in chickpea is not fully understood. In this study, we developed, phenotyped, re-sequenced and genetically characterized a pair of near-isogenic lines (NILs) with contrasting days to flowering to identify candidate gene variants potentially associated with flowering time. RESULTS: In addition to days to flowering, noticeable differences in multiple shoot architecture traits were observed between the NILs. The resequencing data confirms that the NILs developed in this study serve as appropriate plant materials, effectively constraining genetic variation to specific regions and thereby establishing a valuable resource for future genetic and functional investigations in chickpea research. Leveraging bioinformatics tools and public genomic datasets, we identified homologs of flowering-related genes from Arabidopsis thaliana, including ELF3 and, for the first time in chickpea, MED16 and STO/BBX24, with variants among the NILs. Analysis of the allelic distribution of these genes revealed their preservation within chickpea diversity and their potential association with flowering time. Variants were also identified in members of the ERF and ARF gene families. Furthermore, in silico expression analysis was conducted elucidating their putative roles in flowering. CONCLUSIONS: While the gene CaELF3a is identified as a prominent candidate, this study also exposes new targets in chickpea, such as CaMED16b and LOC101499101 (BBX24-like), homologs of flowering-related genes in Arabidopsis, as well as ERF12 and ARF2. The in silico expression characterization and genetic variability analysis performed could contribute to their use as specific markers for chickpea breeding programs. This study lays the groundwork for future investigations utilizing this plant material, promising further insights into the complex mechanisms governing flowering time in chickpea.


Asunto(s)
Cicer , Flores , Fenotipo , Cicer/genética , Cicer/fisiología , Cicer/crecimiento & desarrollo , Flores/genética , Flores/fisiología , Flores/crecimiento & desarrollo , Genes de Plantas , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Variación Genética
18.
BMC Plant Biol ; 24(1): 696, 2024 Jul 23.
Artículo en Inglés | MEDLINE | ID: mdl-39044142

RESUMEN

BACKGROUND: Phosphorus (P) deficiency, a major nutrient stress, greatly hinders plant growth. Phosphate (Pi) uptake in plant roots relies on PHT1 family transporters. However, melon (Cucumis melo L.) lacks comprehensive identification and characterization of PHT1 genes, particularly their response patterns under diverse stresses. RESULTS: This study identified and analyzed seven putative CmPHT1 genes on chromosomes 3, 4, 5, 6, and 7 using the melon genome. Phylogenetic analysis revealed shared motifs, domain compositions, and evolutionary relationships among genes with close histories. Exon number varied from 1 to 3. Collinearity analysis suggested segmental and tandem duplications as the primary mechanisms for CmPHT1 gene family expansion. CmPHT1;4 and CmPHT1;5 emerged as a tandemly duplicated pair. Analysis of cis-elements in CmPHT1 promoters identified 14 functional categories, including putative PHR1-binding sites (P1BS) in CmPHT1;4, CmPHT1;6, and CmPHT1;7. We identified that three WRKY transcription factors regulated CmPHT1;5 expression by binding to its W-box element. Notably, CmPHT1 promoters harbored cis-elements responsive to hormones and abiotic factors. Different stresses regulated CmPHT1 expression differently, suggesting that the adjusted expression patterns might contribute to plant adaptation. CONCLUSIONS: This study unveils the characteristics, evolutionary diversity, and stress responsiveness of CmPHT1 genes in melon. These findings lay the foundation for in-depth investigations into their functional mechanisms in Cucurbitaceae crops.


Asunto(s)
Cucumis melo , Regulación de la Expresión Génica de las Plantas , Fosfatos , Filogenia , Proteínas de Plantas , Estrés Fisiológico , Cucumis melo/genética , Cucumis melo/metabolismo , Fosfatos/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Estrés Fisiológico/genética , Genes de Plantas , Proteínas de Transporte de Fosfato/genética , Proteínas de Transporte de Fosfato/metabolismo , Transporte Biológico/genética
19.
BMC Genomics ; 25(1): 671, 2024 Jul 05.
Artículo en Inglés | MEDLINE | ID: mdl-38970011

RESUMEN

BACKGROUND: The dirigent (DIR) genes encode proteins that act as crucial regulators of plant lignin biosynthesis. In Solanaceae species, members of the DIR gene family are intricately related to plant growth and development, playing a key role in responding to various biotic and abiotic stresses. It will be of great application significance to analyze the DIR gene family and expression profile under various pathogen stresses in Solanaceae species. RESULTS: A total of 57 tobacco NtDIRs and 33 potato StDIRs were identified based on their respective genome sequences. Phylogenetic analysis of DIR genes in tobacco, potato, eggplant and Arabidopsis thaliana revealed three distinct subgroups (DIR-a, DIR-b/d and DIR-e). Gene structure and conserved motif analysis showed that a high degree of conservation in both exon/intron organization and protein motifs among tobacco and potato DIR genes, especially within members of the same subfamily. Total 8 pairs of tandem duplication genes (3 pairs in tobacco, 5 pairs in potato) and 13 pairs of segmental duplication genes (6 pairs in tobacco, 7 pairs in potato) were identified based on the analysis of gene duplication events. Cis-regulatory elements of the DIR promoters participated in hormone response, stress responses, circadian control, endosperm expression, and meristem expression. Transcriptomic data analysis under biotic stress revealed diverse response patterns among DIR gene family members to pathogens, indicating their functional divergence. After 96 h post-inoculation with Ralstonia solanacearum L. (Ras), tobacco seedlings exhibited typical symptoms of tobacco bacterial wilt. The qRT-PCR analysis of 11 selected NtDIR genes displayed differential expression pattern in response to the bacterial pathogen Ras infection. Using line 392278 of potato as material, typical symptoms of potato late blight manifested on the seedling leaves under Phytophthora infestans infection. The qRT-PCR analysis of 5 selected StDIR genes showed up-regulation in response to pathogen infection. Notably, three clustered genes (NtDIR2, NtDIR4, StDIR3) exhibited a robust response to pathogen infection, highlighting their essential roles in disease resistance. CONCLUSION: The genome-wide identification, evolutionary analysis, and expression profiling of DIR genes in response to various pathogen infection in tobacco and potato have provided valuable insights into the roles of these genes under various stress conditions. Our results could provide a basis for further functional analysis of the DIR gene family under pathogen infection conditions.


Asunto(s)
Evolución Molecular , Familia de Multigenes , Nicotiana , Filogenia , Proteínas de Plantas , Solanum tuberosum , Solanum tuberosum/genética , Solanum tuberosum/microbiología , Nicotiana/genética , Nicotiana/microbiología , Proteínas de Plantas/genética , Regulación de la Expresión Génica de las Plantas , Enfermedades de las Plantas/microbiología , Enfermedades de las Plantas/genética , Estrés Fisiológico/genética , Regiones Promotoras Genéticas , Duplicación de Gen , Ralstonia solanacearum , Genes de Plantas
20.
Theor Appl Genet ; 137(8): 185, 2024 Jul 15.
Artículo en Inglés | MEDLINE | ID: mdl-39009774

RESUMEN

KEY MESSAGE: Phenotypical, physiological and genetic characterization was carried out on the hybrid necrosis gene from Haynaldia villosa, and the related gene Ne-V was mapped to chromosome arm 2VL. Introducing genetic variation from wild relatives into common wheat through wide crosses is a vital strategy for enriching genetic diversity and promoting wheat breeding. However, hybrid necrosis, a genetic autoimmunity syndrome, often occurs in the offspring of interspecific or intraspecific crosses, restricting both the selection of hybrid parents and the pyramiding of beneficial genes. To utilize the germplasms of Haynaldia villosa (2n = 2x = 14, VV), we conducted wide hybridization between durum wheat (2n = 4x = 28, AABB) and multiple H. villosa accessions to synthesize the amphiploids (2n = 6x = 42, AABBVV). This study revealed that 61.5% of amphiploids derived from the above crosses exhibited hybrid necrosis, with some amphiploids even dying before reaching maturity. However, the initiation time and severity of necrosis varied dramatically among the progenies, suggesting that there were multiple genetic loci or multiple alleles in the same genetic locus conferring to hybrid necrosis in H. villosa accessions. Genetic analysis was performed on the F2 and derived F2:3 populations, which were constructed between amphiploid STH59-1 with normal leaves and amphiploid STH59-2 with necrotic leaves. A semidominant hybrid necrosis-related gene, Ne-V, was mapped to an 11.8-cM genetic interval on the long arm of chromosome 2V, representing a novel genetic locus identified in Triticum-related species. In addition, the hybrid necrosis was correlated with enhanced H2O2 accumulation and cell death, and it was influenced by the temperature and light. Our findings provide a foundation for cloning the Ne-V gene and exploring its molecular mechanism.


Asunto(s)
Mapeo Cromosómico , Fenotipo , Triticum , Triticum/genética , Triticum/crecimiento & desarrollo , Hibridación Genética , Poaceae/genética , Cromosomas de las Plantas/genética , Genes de Plantas , Fitomejoramiento , Enfermedades de las Plantas/genética , Enfermedades de las Plantas/microbiología , Cruzamientos Genéticos , Necrosis
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