Polymorphisms and gene expression in the almond IGT family are not correlated to variability in growth habit in major commercial almond cultivars

Almond breeding programs aimed at selecting cultivars adapted to intensive orchards have recently focused on the optimization of tree architecture. This multifactorial trait is defined by numerous components controlled by processes such as hormonal responses, gravitropism and light perception. Gravitropism sensing is crucial to control the branch angle and therefore, the tree habit. A gene family, denominated IGT family after a shared conserved domain, has been described as involved in the regulation of branch angle in several species, including rice and Arabidopsis, and even in fruit trees like peach. Here we identified six members of this family in almond: LAZY1, LAZY2, TAC1, DRO1, DRO2, IGT-like. After analyzing their protein sequences in forty-one almond cultivars and wild species, little variability was found, pointing a high degree of conservation in this family. To our knowledge, this is the first effort to analyze the diversity of IGT family proteins in members of the same tree species. Gene expression was analyzed in fourteen cultivars of agronomical interest comprising diverse tree habit phenotypes. Only LAZY1, LAZY2 and TAC1 were expressed in almond shoot tips during the growing season. No relation could be established between the expression profile of these genes and the variability observed in the tree habit. However, some insight has been gained in how LAZY1 and LAZY2 are regulated, identifying the IPA1 almond homologues and other transcription factors involved in hormonal responses as regulators of their expression. Besides, we have found various polymorphisms that could not be discarded as involved in a potential polygenic origin of regulation of architectural phenotypes. Therefore, we have established that neither the expression nor the genetic polymorphism of IGT family genes are correlated to diversity of tree habit in currently commercialized almond cultivars, with other gene families contributing to the variability of these traits.

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Polymorphisms and gene expression in the almond IGT family are not correlated to variability in growth habit in major commercial almond cultivars

10.1101/2021.05.11.443553 ◽

2021 ◽

Author(s):

Álvaro Montesinos ◽

Chris Dardick ◽

María José Rubio-Cabetas ◽

Jérôme Grimplet

Keyword(s):

Gene Expression ◽

Critical Role ◽

Gene Families ◽

Fruit Trees ◽

Hormonal Responses ◽

Breeding Programs ◽

Branch Angle ◽

Conserved Domain ◽

Family Gene ◽

High Degree

Almond breeding programs aimed at selecting cultivars adapted to intensive orchards have recently focused on the optimization of tree architecture. This multifactorial trait is defined by numerous components controlled by processes such as hormonal responses, gravitropism and light perception. Gravitropism sensing is crucial to control the branch angle and therefore, the tree habit. A gene family, denominated IGT family after a share conserved domain, has been described as involved in the regulation of branch angle in several species, including rice and Arabidopsis, and even in fruit trees like peach. Here we identified six members of this family in almond: LAZY1 , LAZY2 , TAC1 , DRO1 , DRO2 , IGT-like . After analyzing their protein sequences in forty-one almond cultivars and wild species, little variability was found, pointing a high degree of conservation in this family. Gene expression was analyzed in fourteen cultivars of agronomical interest comprising diverse tree habit phenotypes. Only LAZY1 , LAZY2 and TAC1 were expressed in almond shoot tips during the growing season. No relation was established between the expression profile of these genes and the tree habit. However, some insight has been gained in how LAZY1 and LAZY2 are regulated, identifying the IPA1 almond homologues and other transcription factors involved in hormonal responses as regulators of their expression. Besides, we have found various polymorphisms that could not be discarded as involved in a potential polygenic origin of regulation of architectural phenotypes. Therefore, we have established that unlike many species, IGT family genes do not play a critical role in the control of tree habit in currently commercialized almond cultivars, with other gene families contributing to the variability of these traits.

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S-Genotype Profiles of Turkish Apricot Germplasm

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha44110350 ◽

2016 ◽

Vol 44 (1) ◽

pp. 67-71 ◽

Cited By ~ 4

Author(s):

Kadir Ugurtan YILMAZ ◽

Busra BASBUG ◽

Kahraman GURCAN ◽

Hasan PINAR ◽

Julia HALASZ ◽

...

Keyword(s):

Fruit Trees ◽

Flowering Plants ◽

Single Locus ◽

Self Incompatibility ◽

Breeding Programs ◽

Allelic Variants ◽

Self Fertilization ◽

High Degree ◽

Research Institute

In flowering plants, gametophytic self-incompatibility, controlled by a single locus with several allelic variants, is one of the major problems preventing self-fertilization. Among fruit trees, apricots show to a high degree self-incompatibility, especially in Middle-Asian and Iranian-Caucasian eco-geographical groups. In the present study, self-(in)compatibility characteristics of a total of 236 apricot genotypes (218 Turkish and 18 foreign) found within the National Apricot Germplasms of Apricot Research Institute in Malatya, Turkey was studied. Analyses were carried out by using four primer pairs (SRc-F and SRc-R, EM-PC2consFD and EM-PC3consRD, AprSC8-R and PaConsI-F, AprFBC8-F and AprFBC8-R). A total of 11 S-RNase alleles (S2, S3, S6, S7, S8, S9, S11, S12, S13, S20 and Sc) were determined in the 236 apricot genotypes. As Turkish and foreign apricot genotypes are determined mostly self-incompatible, the data obtained hereby might be of good use for apricot breeding programs and more practically, for apricot new plantations; thus pollinator cultivars should be considered when self-incompatible apricot cultivars are being used.

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A Comprehensive Phylogenetic and Bioinformatics Survey of Lectins in the Fungal Kingdom

Journal of Fungi ◽

10.3390/jof7060453 ◽

2021 ◽

Vol 7 (6) ◽

pp. 453

Author(s):

Annie Lebreton ◽

François Bonnardel ◽

Yu-Cheng Dai ◽

Anne Imberty ◽

Francis M. Martin ◽

...

Keyword(s):

Evolutionary Relationship ◽

Large Family ◽

Gene Families ◽

Carbohydrate Binding ◽

Sequence Motifs ◽

Fungal Lectin ◽

Quaternary Structures ◽

High Degree ◽

Carbohydrate Ligand ◽

Fungal Kingdom

Fungal lectins are a large family of carbohydrate-binding proteins with no enzymatic activity. They play fundamental biological roles in the interactions of fungi with their environment and are found in many different species across the fungal kingdom. In particular, their contribution to defense against feeders has been emphasized, and when secreted, lectins may be involved in the recognition of bacteria, fungal competitors and specific host plants. Carbohydrate specificities and quaternary structures vary widely, but evidence for an evolutionary relationship within the different classes of fungal lectins is supported by a high degree of amino acid sequence identity. The UniLectin3D database contains 194 fungal lectin 3D structures, of which 129 are characterized with a carbohydrate ligand. Using the UniLectin3D lectin classification system, 109 lectin sequence motifs were defined to screen 1223 species deposited in the genomic portal MycoCosm of the Joint Genome Institute. The resulting 33,485 putative lectin sequences are organized in MycoLec, a publicly available and searchable database. These results shed light on the evolution of the lectin gene families in fungi.

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Integrating metabolomics and targeted gene expression to uncover potential biomarkers of fungal/oomycetes-associated disease susceptibility in grapevine

Scientific Reports ◽

10.1038/s41598-020-72781-2 ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 1

Author(s):

Marisa Maia ◽

António E. N. Ferreira ◽

Rui Nascimento ◽

Filipa Monteiro ◽

Francisco Traquete ◽

...

Keyword(s):

Gene Expression ◽

Plant Defence ◽

Breeding Programs ◽

Analysis Group ◽

Expression Of Genes ◽

Leucoanthocyanidin Reductase ◽

Defence Responses ◽

Targeted Gene Expression ◽

Plant Defence Responses ◽

First Time

Abstract Vitis vinifera, one of the most cultivated fruit crops, is susceptible to several diseases particularly caused by fungus and oomycete pathogens. In contrast, other Vitis species (American, Asian) display different degrees of tolerance/resistance to these pathogens, being widely used in breeding programs to introgress resistance traits in elite V. vinifera cultivars. Secondary metabolites are important players in plant defence responses. Therefore, the characterization of the metabolic profiles associated with disease resistance and susceptibility traits in grapevine is a promising approach to identify trait-related biomarkers. In this work, the leaf metabolic composition of eleven Vitis genotypes was analysed using an untargeted metabolomics approach. A total of 190 putative metabolites were found to discriminate resistant/partial resistant from susceptible genotypes. The biological relevance of discriminative compounds was assessed by pathway analysis. Several compounds were selected as promising biomarkers and the expression of genes coding for enzymes associated with their metabolic pathways was analysed. Reference genes for these grapevine genotypes were established for normalisation of candidate gene expression. The leucoanthocyanidin reductase 2 gene (LAR2) presented a significant increase of expression in susceptible genotypes, in accordance with catechin accumulation in this analysis group. Up to our knowledge this is the first time that metabolic constitutive biomarkers are proposed, opening new insights into plant selection on breeding programs.

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Analysis of Transcriptional Changes in Different Brassica napus Synthetic Allopolyploids

Genes ◽

10.3390/genes12010082 ◽

2021 ◽

Vol 12 (1) ◽

pp. 82

Author(s):

Yunxiao Wei ◽

Guoliang Li ◽

Shujiang Zhang ◽

Shifan Zhang ◽

Hui Zhang ◽

...

Keyword(s):

Gene Expression ◽

Brassica Napus ◽

Differentially Expressed Genes ◽

Expression Patterns ◽

Female Parent ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Transcriptional Changes ◽

Aa Genome ◽

High Degree

Allopolyploidy is an evolutionary and mechanistically intriguing process involving the reconciliation of two or more sets of diverged genomes and regulatory interactions, resulting in new phenotypes. In this study, we explored the gene expression patterns of eight F2 synthetic Brassica napus using RNA sequencing. We found that B. napus allopolyploid formation was accompanied by extensive changes in gene expression. A comparison between F2 and the parent shows a certain proportion of differentially expressed genes (DEG) and activation\silent gene, and the two genomes (female parent (AA)\male parent (CC) genomes) showed significant differences in response to whole-genome duplication (WGD); non-additively expressed genes represented a small portion, while Gene Ontology (GO) enrichment analysis showed that it played an important role in responding to WGD. Besides, genome-wide expression level dominance (ELD) was biased toward the AA genome, and the parental expression pattern of most genes showed a high degree of conservation. Moreover, gene expression showed differences among eight individuals and was consistent with the results of a cluster analysis of traits. Furthermore, the differential expression of waxy synthetic pathways and flowering pathway genes could explain the performance of traits. Collectively, gene expression of the newly formed allopolyploid changed dramatically, and this was different among the selfing offspring, which could be a prominent cause of the trait separation. Our data provide novel insights into the relationship between the expression of differentially expressed genes and trait segregation and provide clues into the evolution of allopolyploids.

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Gene networks underlying functional sex in Sparidae (Pisces, Teleostei)

10.12681/eadd/44179 ◽

2018 ◽

Author(s):

Αλέξανδρος Τσακογιάννης

Keyword(s):

Gene Expression ◽

Sex Determination ◽

Gene Networks ◽

Expression Patterns ◽

Gene Families ◽

Male And Female ◽

Dentex Dentex ◽

The Common ◽

Model Fish Species ◽

Model Fish

The differences between sexes and the concept of sex determination have always fascinated, yet troubled philosophers and scientists. Among the animals that reproduce sexually, teleost fishes show a very wide repertoire of reproductive modes. Except for the gonochoristic species, fish are the only vertebrates in which hermaphroditism appears naturally. Hermaphroditism refers to the capability of an organism to reproduce both as male and female in its life cycle and there are various forms of it. In sequential hermaphroditism, an individual begins as female first and then can change sex to become male (protogyny), or vice versa (protandry). The diverse sex-phenotypes of fish are regulated by a variety of sex determination mechanisms, along a continuum of environmental and heritable factors. The vast majority of sexually dimorphic traits result from the differential expression of genes that are present in both sexes. To date, studies regarding the sex-specific differences in gene expression have been conducted mainly in sex determination systems of model fish species that are well characterized at the genomic level, with distinguishable heteromorphic sex chromosomes, exhibiting genetic sex determination and gonochorism. Among teleosts, the Sparidae family is considered to be one of the most diversified families regarding its reproductive systems, and thus is a unique model for comparative studies to understand the molecular mechanisms underlying different sexual motifs. In this study, using RNA sequencing, we studied the transcriptome from gonads and brains of both sexes in five sparid species, representatives of four different reproductive styles. Specifically, we explored the sex-specific expression patterns of a gonochoristic species: the common dentex Dentex dentex, two protogynous hermaphrodites: the red porgy Pagrus pagrus and the common pandora Pagellus erythrinus, the rudimentary hermaphrodite sharpsnout seabream Diplodus puntazzo, and the protandrous gilthead seabream Sparus aurata. We found minor sex-related expression differences indicating a more homogeneous and sexually plastic brain, whereas there was a plethora of sex biased gene expression in the gonads. The functional divergence of the two gonadal types is reflected in their transcriptomic profiles, in terms of the number of genes differentially expressed, as well as the expression magnitude (i.e. fold-change differences). The observation of almost double the number of up-regulated genes in males compared to females indicates a male-biased expression tendency. Focusing on the pathways and genes implicated in sex determination/differentiation, we aimed to unveil the molecular pathways through which these non-model fish species develop a masculine or a feminine character. We observed the implicated pathways and major gene families (e.g. Wnt/b-catenin pathway and Retinoic-acid signaling pathway, Notch, TGFβ) behind sex-biased expression and the recruitment of known sex-related genes either to male or female type of gonads in these fish. (e.g Dmrt1, Sox9, Sox3, Cyp19a, Filgla, Ctnnb1, Gsdf9, Stra6 etc.). We also carefully investigated the presence of genes reported to be involved in sex determination/differentiation mechanisms in other vertebrates and fish and compared their expression patterns in the species under study. The expression profiling exposed known candidate molecular-players/genes establishing the common female (Cyp19a1, Sox3, Figla, Gdf9, Cyp26a, Ctnnb1, Dnmt1, Stra6) and male identity (Dmrt1, Sox9, Dnmt3aa, Rarb, Raraa, Hdac8, Tdrd7) of the gonad in these sparids. Additionally, we focused on those contributing to a species-specific manner either to female (Wnt4a, Dmrt2a, Foxl2 etc.) or to male (Amh, Dmrt3a, Cyp11b etc.) characters, and discussed the expression patterns of factors that belong to important pathways and/or gene families in the SD context, in our species gonadal transcriptomes. Taken together, most of the studied genes form part of the cascade of sex determination, differentiation, and reproduction across teleosts. In this study, we focused on genes that are active when sex is established (sex-maintainers), revealing the basic “gene-toolkit” & gene-networks underlying functional sex in these five sparids. Comparing related species with alternative reproductive styles, we saw different combinations of genes with conserved sex-linked roles and some “handy” molecular players, in a “partially- conserved” or “modulated” network formulating the male and female phenotype. The knowledge obtained in this study and tools developed during the process have set the groundwork for future experiments that can improve the sex control of this species and help the in-deep understanding the complex process of sex differentiation in the more flexible multi-component systems as these studied here.

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Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in Vitis vinifera Sheds Light on the Laccase and Dirigent Gene Families

Biomolecules ◽

10.3390/biom11121744 ◽

2021 ◽

Vol 11 (12) ◽

pp. 1744

Author(s):

Stefania Pilati ◽

Giulia Malacarne ◽

David Navarro-Payá ◽

Gabriele Tomè ◽

Laura Riscica ◽

...

Keyword(s):

Gene Networks ◽

Functional Characterization ◽

Gene Families ◽

Stilbene Synthase ◽

Breeding Programs ◽

Transcriptomic Data ◽

Network Analyses ◽

Manual Curation ◽

Inference Methods

The abundance of transcriptomic data and the development of causal inference methods have paved the way for gene network analyses in grapevine. Vitis OneGenE is a transcriptomic data mining tool that finds direct correlations between genes, thus producing association networks. As a proof of concept, the stilbene synthase gene regulatory network obtained with OneGenE has been compared with published co-expression analysis and experimental data, including cistrome data for MYB stilbenoid regulators. As a case study, the two secondary metabolism pathways of stilbenoids and lignin synthesis were explored. Several isoforms of laccase, peroxidase, and dirigent protein genes, putatively involved in the final oxidative oligomerization steps, were identified as specifically belonging to either one of these pathways. Manual curation of the predicted sequences exploiting the last available genome assembly, and the integration of phylogenetic and OneGenE analyses, identified a group of laccases exclusively present in grapevine and related to stilbenoids. Here we show how network analysis by OneGenE can accelerate knowledge discovery by suggesting new candidates for functional characterization and application in breeding programs.

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The hem of the embryonic cerebral cortex is defined by the expression of multiple Wnt genes and is compromised in Gli3-deficient mice

Development ◽

10.1242/dev.125.12.2315 ◽

1998 ◽

Vol 125 (12) ◽

pp. 2315-2325 ◽

Cited By ~ 19

Author(s):

E.A. Grove ◽

S. Tole ◽

J. Limon ◽

L. Yip ◽

C.W. Ragsdale

Keyword(s):

Gene Expression ◽

Cerebral Cortex ◽

Choroid Plexus ◽

Gene Families ◽

Cubitus Interruptus ◽

Embryonic Mouse ◽

Developmental Relationship ◽

Cortical Hem ◽

Deficient Mice

In the developing vertebrate CNS, members of the Wnt gene family are characteristically expressed at signaling centers that pattern adjacent parts of the neural tube. To identify candidate signaling centers in the telencephalon, we isolated Wnt gene fragments from cDNA derived from embryonic mouse telencephalon. In situ hybridization experiments demonstrate that one of the isolated Wnt genes, Wnt7a, is broadly expressed in the embryonic telencephalon. By contrast, three others, Wnt3a, 5a and a novel mouse Wnt gene, Wnt2b, are expressed only at the medial edge of the telencephalon, defining the hem of the cerebral cortex. The Wnt-rich cortical hem is a transient, neuron-containing, neuroepithelial structure that forms a boundary between the hippocampus and the telencephalic choroid plexus epithelium (CPe) throughout their embryonic development. Indicating a close developmental relationship between the cortical hem and the CPe, Wnt gene expression is upregulated in the cortical hem both before and just as the CPe begins to form, and persists until birth. In addition, although the cortical hem does not show features of differentiated CPe, such as expression of transthyretin mRNA, the CPe and cortical hem are linked by shared expression of members of the Bmp and Msx gene families. In the extra-toesJ (XtJ) mouse mutant, telencephalic CPe fails to develop. We show that Wnt gene expression is deficient at the cortical hem in XtJ/XtJ mice, but that the expression of other telencephalic developmental control genes, including Wnt7a, is maintained. The XtJ mutant carries a deletion in Gli3, a vertebrate homolog of the Drosophila gene cubitus interruptus (ci), which encodes a transcriptional regulator of the Drosophila Wnt gene, wingless. Our observations indicate that Gli3 participates in Wnt gene regulation in the vertebrate telencephalon, and suggest that the loss of telencephalic choroid plexus in XtJ mice is due to defects in the cortical hem that include Wnt gene misregulation.

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The Role of Plasticity and Adaptation in the Incipient Speciation of a Fire Salamander Population

Genes ◽

10.3390/genes10110875 ◽

2019 ◽

Vol 10 (11) ◽

pp. 875

Author(s):

Joana Sabino-Pinto ◽

Daniel J. Goedbloed ◽

Eugenia Sanchez ◽

Till Czypionka ◽

Arne W. Nolte ◽

...

Keyword(s):

Gene Expression ◽

Phenotypic Plasticity ◽

Local Adaptation ◽

Habitat Preferences ◽

Genetic Change ◽

Incipient Speciation ◽

Expression Of Genes ◽

Species Specific ◽

Reciprocal Transfer ◽

High Degree

Phenotypic plasticity and local adaptation via genetic change are two major mechanisms of response to dynamic environmental conditions. These mechanisms are not mutually exclusive, since genetic change can establish similar phenotypes to plasticity. This connection between both mechanisms raises the question of how much of the variation observed between species or populations is plastic and how much of it is genetic. In this study, we used a structured population of fire salamanders (Salamandra salamandra), in which two subpopulations differ in terms of physiology, genetics, mate-, and habitat preferences. Our goal was to identify candidate genes for differential habitat adaptation in this system, and to explore the degree of plasticity compared to local adaptation. We therefore performed a reciprocal transfer experiment of stream- and pond-originated salamander larvae and analyzed changes in morphology and transcriptomic profile (using species-specific microarrays). We observed that stream- and pond-originated individuals diverge in morphology and gene expression. For instance, pond-originated larvae have larger gills, likely to cope with oxygen-poor ponds. When transferred to streams, pond-originated larvae showed a high degree of plasticity, resembling the morphology and gene expression of stream-originated larvae (reversion); however the same was not found for stream-originated larvae when transferred to ponds, where the expression of genes related to reduction-oxidation processes was increased, possibly to cope with environmental stress. The lack of symmetrical responses between transplanted animals highlights the fact that the adaptations are not fully plastic and that some level of local adaptation has already occurred in this population. This study illuminates the process by which phenotypic plasticity allows local adaptation to new environments and its potential role in the pathway of incipient speciation.

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Transpiration effciency and its relationship with carbon isotope discrimination under well-watered and water-stressed conditions in Stylosanthes scabra

Australian Journal of Agricultural Research ◽

10.1071/a97169 ◽

1998 ◽

Vol 49 (7) ◽

pp. 1039 ◽

Cited By ~ 16

Author(s):

Bala R. Thumma ◽

Bodapati P. Naidu ◽

Don F. Cameron ◽

Len M. Bahnisch

Keyword(s):

Carbon Isotope ◽

Drought Resistance ◽

Carbon Isotope Discrimination ◽

Negative Relationship ◽

C3 Plants ◽

Breeding Programs ◽

Isotope Discrimination ◽

Matter Production ◽

Stylosanthes Scabra ◽

High Degree

Stylosanthes scabra cv. Seca is a widely sown tropical pasture legume in northern Australia and has a high degree of drought resistance. Identification of traits contributing to the drought resistance of Seca may be valuable for use in breeding programs. Transpiration efficiency (TE) has been suggested as one such trait contributing to drought resistance. Carbon isotope discrimination (Δ) has been proposed for estimating TE indirectly in C3 plants. A glasshouse experiment was conducted using 8 accessions of S. scabra to identify whether Seca differs in TE from other accessions of S. scabra and to determine the relationship between TE and Δ under both well-watered and water-stressed treatments. Seca maintained the highest TE (lowest Δ) under both control and stress treatments, and leaf Δ was significantly and negatively correlated with TE under both control and stress conditions. A significant and negative relationship was found between Δ and dry matter production under stress treatment. The interaction between accession and watering treatment was not significant for either TE or Δ. We also found a signirficant agreement between the performance in the field and in the laboratory for these 8 accessions. These results indicate that TE could be one of the significant factors contributing to drought resistance of Seca. Furthermore, Δ and/or specific leaf area may be useful as selection criteria in breeding programs to identify the lines with high TE.

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