scholarly journals Environmental and epigenetic regulation of Rider retrotransposons in tomato

2019 ◽  
Author(s):  
Matthias Benoit ◽  
Hajk-Georg Drost ◽  
Marco Catoni ◽  
Quentin Gouil ◽  
Sara Lopez-Gomollon ◽  
...  
Keyword(s):  
Residual Activity ◽  
Fruit Shape ◽  
Tomato Genome ◽  
Bioinformatics Pipeline ◽  
Breeding Programs ◽  
Long Terminal Repeat Retrotransposon ◽  
Potential Source ◽  
Methylation Pathway ◽  
Retrotransposon Family ◽  
Responsive Element

ABSTRACTTransposable elements in crop plants are the powerful drivers of phenotypic variation that has been selected during domestication and breeding programs. In tomato, transpositions of the LTR (long terminal repeat) retrotransposon family Rider have contributed to various phenotypes of agronomical interest, such as fruit shape and colour. However, the mechanisms regulating Rider activity are largely unknown. We have developed a bioinformatics pipeline for the functional annotation of retrotransposons containing LTRs and defined all full-length Rider elements in the tomato genome. Subsequently, we showed that accumulation of Rider transcripts and transposition intermediates in the form of extrachromosomal DNA is triggered by drought stress and relies on abscisic acid signalling. We provide evidence that residual activity of Rider is controlled by epigenetic mechanisms involving siRNAs and the RNA-dependent DNA methylation pathway. Finally, we demonstrate the broad distribution of Rider-like elements in other plant species, including crops. Thus our work identifies Rider as an environment-responsive element and a potential source of genetic and epigenetic variation in plants.

scholarly journals Adaptation assessment of drought tolerance in maize populations from the Sahara in both shores of the Mediterranean Sea

Euphytica ◽  
2021 ◽  
Vol 217 (8) ◽  
Author(s):  
Oula Maafi ◽  
Pedro Revilla ◽  
Lorena Álvarez-Iglesias ◽  
Rosa Ana Malvar ◽  
Abderahmane Djemel
Keyword(s):  
Drought Tolerance ◽  
Biomass Production ◽  
Genetic Regulation ◽  
Breeding Programs ◽  
Favorable Alleles ◽  
Maize Germplasm ◽  
Maize Populations ◽  
Potential Source ◽  
Main Stress ◽  
And Control

AbstractDrought is the main stress for agriculture, and maize (Zea mays L.) germplasm from the Sahara has been identified as potential source of drought tolerance; however, information about adaptation of semitropical maize germplasm from the Sahara to temperate areas has not been reported. Our objective was assessing the adaptation of maize germplasm from Saharan oases as sources of drought tolerance for improving yield and biomass production under drought conditions in temperate environments. A collection of maize populations from Saharan oases was evaluated under drought and control conditions in Spain and Algeria. Algerian populations were significantly different under drought for most traits, and the significant genotype × environment interactions indicated that drought tolerance is genotype-dependent, but tolerance differences among genotypes change across environments. Based on yield, the Algerian maize populations PI527474, PI527478, PI527472, PI527467, PI527470, and PI527473 would be appropriate sources of drought tolerance for temperate environments. Concerning biomass production, the most interesting populations were PI527467, PI542685, PI527478, and PI527472. These Saharan populations could provide favorable alleles for drought tolerance for temperate breeding programs, and could also be used for studying mechanisms and genetic regulation of drought tolerance.

scholarly journals Genetic Characterization of Apulian Olive Germplasm as Potential Source in New Breeding Programs

Plants ◽  
2019 ◽  
Vol 8 (8) ◽  
pp. 268 ◽  
Author(s):  
Sion ◽  
Taranto ◽  
Montemurro ◽  
Mangini ◽  
Camposeo ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Agronomic Traits ◽  
Rural Landscape ◽  
Sources Of Resistance ◽  
Breeding Programs ◽  
Potential Source ◽  
History Of ◽  
Olive Cultivation ◽  
Olive Quick Decline Syndrome

The olive is a fruit tree species with a century-old history of cultivation in theMediterranean basin. In Apulia (Southern Italy), the olive is of main social, cultural and economicimportance, and represents a hallmark of the rural landscape. However, olive cultivation in thisregion is threatened by the recent spread of the olive quick decline syndrome (OQDS) disease, thusthere is an urgent need to explore biodiversity and search for genetic sources of resistance. Herein,a genetic variation in Apulian olive germplasm was explored, as a first step to identify genotypeswith enhanced bio-agronomic traits, including resistance to OQDS. A preselected set of nuclearmicrosatellite markers allowed the acquisition of genotypic profiles, and to define geneticrelationships between Apulian germplasm and widespread cultivars. The analysis highlighted thebroad genetic variation in Apulian accessions and the presence of different unique genetic profiles.The results of this study lay a foundation for the organization of new breeding programs for olivegenetic improvement.

scholarly journals Biomorphological Characterization of Brazilian Capsicum Chinense Jacq. Germplasm

Agronomy ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 447 ◽  
Author(s):  
Paola Alvares Bianchi ◽  
Lígia Renata Almeida da Silva ◽  
Antônio André da Silva Alencar ◽  
Pedro Henrique Araújo Diniz Santos ◽  
Samy Pimenta ◽  
...  
Keyword(s):  
Genetic Erosion ◽  
Fruit Shape ◽  
Joint Analysis ◽  
Capsicum Chinense ◽  
Breeding Programs ◽  
Mean Values ◽  
Relative Contribution ◽  
Inter Simple Sequence Repeats ◽  
Simple Sequence

Loss of biodiversity and ecosystem degradation become major concerns worldwide, making the conservation process an important strategy for maintaining biodiversity. Capsicum chinense Jacq. is the most Brazilian species of the genus, with representatives in different biomes. Anthropic pressure, such as burns, real estate speculation, and changing cultivation habit has led to risks of genetic erosion. Conservation and characterization of conserved accessions are paramount to ensure genetic diversity, useful for the bioeconomy and for genetic improvement. We report the characterization of 55 C. chinense accessions from four different regions of Brazil and one accession from Peru. The accessions were characterized based on 37 morpho-agronomic variables, Inter Simple Sequence Repeats—ISSR and Simple Sequence Repeat—SSR. Qualitative descriptors were analyzed using a descriptive statistical, while the quantitative descriptors were analyzed via F test and significant differences in mean values were separated using Scott-Knott test. The relative contribution of each quantitative trait was determined. A correlation between morphological and molecular distances was calculated. Color of ripe fruit and fruit shape had the largest number of observed classes. Six distinct groups and the joint analysis presented an entanglement rate of 0.58, evidencing the divergence of accessions between the groups of both dendrograms. Bayesian analysis allowed the distinction of two clusters for SSR. A significant variability was observed among accession with potential to integrate several breeding programs.

scholarly journals Overexpression of SlOFP20 affects floral organ and pollen development

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Shengen Zhou ◽  
Zongli Hu ◽  
Fenfen Li ◽  
Shibing Tian ◽  
Zhiguo Zhu ◽  
...  
Keyword(s):  
Pollen Development ◽  
Pollen Germination ◽  
Germination Rate ◽  
Floral Organ ◽  
Fruit Shape ◽  
Tomato Genome ◽  
Transcript Accumulation ◽  
Tomato Plants ◽  
Transgenic Lines ◽  
Negative Role

AbstractThe OVATE gene was initially identified in tomato and serves as a key regulator of fruit shape. There are 31 OFP members in the tomato genome. However, their roles in tomato growth and reproductive development are largely unknown. Here, we cloned the OFP transcription factor SlOFP20. Tomato plants overexpressing SlOFP20 displayed several phenotypic defects, including an altered floral architecture and fruit shape and reduced male fertility. SlOFP20 overexpression altered the expression levels of some brassinosteroid (BR)-associated genes, implying that SlOFP20 may play a negative role in the BR response, similar to its ortholog OsOFP19 in rice. Moreover, the transcript accumulation of gibberellin (GA)-related genes was significantly affected in the transgenic lines. SlOFP20 may play an important role in the crosstalk between BR and GA. The pollen germination assay suggested that the pollen germination rate of SlOFP20-OE plants was distinctly lower than that of WT plants. In addition, the tomato pollen-associated genes SlCRK1, SlPMEI, LePRK3, SlPRALF, and LAT52 were all suppressed in the transgenic lines. Our data imply that SlOFP20 may affect floral organ and pollen development by modulating BR and GA signaling in tomato.

scholarly journals Genetic diversity and population structure of Luffa acutangula accessions in a Thailand collection using SNP markers

2020 ◽  
Author(s):  
Grimar Abdiel Perez ◽  
Pumipat Tongyoo ◽  
Julapark Chunwongse ◽  
Hans de Jong ◽  
Paweena Chuenwarin
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Phylogenetic Tree ◽  
Structure Analysis ◽  
Fruit Shape ◽  
Snp Markers ◽  
Distinguishing Characteristic ◽  
Breeding Programs ◽  
Unrooted Phylogenetic Tree ◽  
Luffa Acutangula

AbstractThis study explored a germplasm consisting of 112 Luffa acutangula (ridge gourd) accessions mainly from Thailand, and some accessions from Vietnam, China, Philippines, Indonesia, USA, Bangladesh and Laos for an analysis of the population structure and underlying genetic diversity using 2,834 SNPs. STRUCTURE analysis (ΔK at K=6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. The phylogenetic tree showed the diversity of L. acutangula in Thailand, and accessions from other countries apart from Thailand were grouped together in the same branches. In STRUCTURE, subpopulation 2 contained only accessions from Thailand while other subpopulations contained a combination of accessions from Thailand and from other countries. When plotted, the STRUCTURE bars to the area of collection, it revealed the geneflow from the surrounding places nearby as indicated by the admixed genetic in the STRUCTURE bars. AMOVA based on STRUCTURE clustering showed the variation between populations (12.83%) and confirmed the absence of population structure in subpopulations (−10.59%). There was a distinguishing characteristic fruit shape and length in each subpopulation. The ample genetic diversity found in the L. acutangula germplasm can be utilized in ridge gourd breeding programs to help meet the demands and needs of both consumers and farmers.

scholarly journals Morphological diversity of Zacatecas Guajillo chile landraces is broad and is given mainly by fruit traits

2019 ◽  
pp. 440
Author(s):  
Yolanda del Rocio Moreno-Ramírez, Amalio Santacruz-Varela ◽  
Pedro A. López, Higinio López-Sánchez ◽  
L. Córdova-Téllez, V. A. González-Hernández, T. Corona-Torres ◽  
Ricardo López- Ortega
Keyword(s):  
Phenotypic Diversity ◽  
Morphological Diversity ◽  
Fruit Shape ◽  
Local Economy ◽  
Fruit Traits ◽  
Breeding Programs ◽  
Morphological Heterogeneity ◽  
Selection Of Variables ◽  
Seed Characteristics ◽  
Selection Of

Guajillo (Capsicum annuum L.) is one of the five more important chile types used as food in Mexico and the most important to local economy in Zacatecas, whose production is supplied mainly by native populations. In spite of this, not much is known about the morphological diversity of Guajillo landraces of Zacatecas. Here, we describe and quantify their morphological variation in order to establish breeding programs and to preserve the phenotypic diversity. Thirty-two plant, flower, fruit, seed and phenological traits were assessed in 96 Guajillo chile landraces and four improved varities of Guajillo used as controls, grown during the 2015 agricultural cycle in Zacatecas, Mexico. The selection of variables was made based on the analysis of variance and multivariate analysis that were applied to the selected variables to estimate the morphological diversity. A wide variation of plant, fruit and seed characteristics was identified. This morphological heterogeneity is attributed mainly to fruit traits such as: size, weight, shape, color, transverse wrinkling of the fruit, shape of the peduncle and the number of fruits produced. This wide morphological diversity can potentially be utilized in the genetic improvement of Guajillo chile.

scholarly journals Characterization of cis-elements in hormonal stress-responsive genes in Oryza sativa

2019 ◽  
pp. 95-102 ◽  
Author(s):  
Abbas Saidi ◽  
Zohreh Hajibarat
Keyword(s):  
Regulatory Elements ◽  
Environmental Stresses ◽  
Auxin Signaling ◽  
Cis Elements ◽  
Breeding Programs ◽  
Abiotic And Biotic Stresses ◽  
Biotic Stresses ◽  
Responsive Element ◽  
Dehydrin Gene

Phytohormones play a key role in plant growth and development. The process of plant’s perception and response to abiotic and biotic stresses is controlled mainly by the phytohormones which act as an endogenous messenger in the regulation of the plant’s status. They can be activated by different signaling pathways in response to environmental stresses. Plants respond to environmental stress through interaction of transcription factors with a handful of cis-regulatory elements (CREs). Some examples of cis elements include abscisic acid-responsive element (ABRE), G-box (CACGTG) element, and W-box. In order to investigate the effects of different hormonal stresses which have a key role in response to biotic and abiotic stresses in rice, microarray data was used. Of the available data, 931 genes revealed significant differences in response to different hormonal stresses such as auxin, cytokinin, abcisic acid, ethylene, salicylic acid, and jasmonic acid. The present results showed that 388 genes were up-regulated, and 543 genes were down-regulated. Most of the genes were up-regulated in response to Indole-3-acetic acid (IAA) hormone. Genes Ontology analysis revealed that they respond to various hormones involved in auxin- responsive genes, auxin-activated signaling pathway and cellular responses to environmental stimuli. G-box had the highest number of cis elements involved in hormonal stress and was regulated by auxin signaling and various stresses. Dehydrin was the only gene up-regulated in response to the six hormones. This gene can be activated in response to abiotic and biotic stresses. As such, dehydrin gene can be used in crop breeding programs to increase tolerance to different environmental stresses in various plant species.

scholarly journals Genomic diversity and novel genome-wide association with fruit morphology in Capsicum, from 746k polymorphic sites

2018 ◽  
Author(s):  
Vincenza Colonna ◽  
Nunzio D’Agostino ◽  
Erik Garrison ◽  
Jonas Meisner ◽  
Anders Albrechtsen ◽  
...  
Keyword(s):  
Genetic Association ◽  
Association Studies ◽  
Population Level ◽  
Fruit Shape ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Large Set ◽  
Vegetable Crops ◽  
Breeding Programs ◽  
Important Species

AbstractBackgroundCapsicum is one of the major vegetable crops grown world-wide. Current subdivision in clades and species is based on morphological traits and coarse sets of genetic markers. Fruits broad variability has been driven by breeding programs and has been mainly studied by linkage analysis.ResultsWe discovered 746k variable sites by sequencing 1.8% of the genome in a collection of 373 accessions belonging to 11 Capsicum species from 51 countries. We describe genomic variation at population-level, confirm major subdivision in clades and species, and show that the known subdivision of C. annuum in two groups separates large and bulky fruits form small ones. In C. annuum, we identify four novel loci associated with phenotypes determining the fruit shape, including a non-synonymous mutation in the gene Longifolia 1-like (CA03g16080).ConclusionsOur collection covers all the economically important species of Capsicum widely used in breeding programs, and represent the widest and largest study so far in terms of the number of species and genetic variants analyzed. We identified a large set of markers that can be used for population genetic studies and genetic association analyses. Our results foster fine genetic association studies and foresee genomic variability at population-level.

Sign in / Sign up

Export Citation Format

Share Document